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GEOCHEMISTRY ARTICLES – November 2017?Analytical ChemistryAmiri, A., Ghaemi, F., 2017. Graphene grown on stainless steel mesh as a highly efficient sorbent for sorptive microextraction of polycyclic aromatic hydrocarbons from water samples. Analytica Chimica Acta 994, 29-37.Aramendia, J., Gomez-Nubla, L., Castro, K., Fdez-Ortiz de Vallejuelo, S., Arana, G., Maguregui, M., Baonza, V.G., Medina, J., Rull, F., Madariaga, J.M., 2018. Overview of the techniques used for the study of non-terrestrial bodies: Proposition of novel non-destructive methodology. TrAC Trends in Analytical Chemistry 98, 36-46.Ayoib, A., Hashim, U., Gopinath, S.C.B., Md Arshad, M.K., 2017. DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods. Applied Microbiology and Biotechnology 101, 8077-8088.Franzmann, M., Bosco, H., Walther, C., Wendt, K., 2017. A new resonant Laser-SNMS system for environmental ultra-trace analysis: Installation and optimization. International Journal of Mass Spectrometry 423, 27-32.Kikuchi, J., Yamada, S., 2017. NMR window of molecular complexity showing homeostasis in superorganisms. Analyst 142, 4161-4172.Mees, C., Souard, F., Delporte, C., Deconinck, E., Stoffelen, P., Stévigny, C., Kauffmann, J.-M., De Braekeleer, K., 2018. Identification of coffee leaves using FT-NIR spectroscopy and SIMCA. Talanta 177, 4-11.Nojavan, S., Yazdanpanah, M., 2017. Micro-solid phase extraction of benzene, toluene, ethylbenzene and xylenes from aqueous solutions using water-insoluble β-cyclodextrin polymer as sorbent. Journal of Chromatography A 1525, 51-59.Shahriman, M.S., Ramachandran, M.R., Zain, N.N.M., Mohamad, S., Manan, N.S.A., Yaman, S.M., 2018. Polyaniline-dicationic ionic liquid coated with magnetic nanoparticles composite for magnetic solid phase extraction of polycyclic aromatic hydrocarbons in environmental samples. Talanta 178, 211-221.Soriano, M.L., Zougagh, M., Valcárcel, M., Ríos, ?., 2018. Analytical nanoscience and nanotechnology: Where we are and where we are heading. Talanta 177, 104-121.van der Meer, F., 2018. Near-infrared laboratory spectroscopy of mineral chemistry: A review. International Journal of Applied Earth Observation and Geoinformation 65, 71-78.Wang, J., Zhu, J., Si, L., Du, Q., Li, H., Bi, W., Chen, D.D.Y., 2017. High throughput screening of phenoxy carboxylic acids with dispersive solid phase extraction followed by direct analysis in real time mass spectrometry. Analytica Chimica Acta 996, 20-28.Weston, C., Smuts, J., Mao, J.X., Schug, K.A., 2018. Investigation of gas phase absorption spectral similarity for stable-isotopically labeled compounds in the 125–240nm wavelength range. Talanta 177, 41-46.Zhang, P., Lu, S., Li, J., Chen, C., Xue, H., Zhang, J., 2018. Petrophysical characterization of oil-bearing shales by low-field nuclear magnetic resonance (NMR). Marine and Petroleum Geology 89, 775-785.Gas Chromatography/GC×GC/GC-MSBai, L., Smuts, J., Schenk, J., Cochran, J., Schug, K.A., 2018. Comparison of GC-VUV, GC-FID, and comprehensive two-dimensional GC–MS for the characterization of weathered and unweathered diesel fuels. Fuel 214, 521-527.Fanali, C., Micalizzi, G., Dugo, P., Mondello, L., 2017. Ionic liquids as stationary phases for fatty acid analysis by gas chromatography. Analyst 142, 4601-4612.Freye, C.E., Bahaghighat, H.D., Synovec, R.E., 2018. Comprehensive two-dimensional gas chromatography using partial modulation via a pulsed flow valve with a short modulation period. Talanta 177, 142-149.Heshka, N.E., Choy, J.M., Chen, J., 2017. Gas chromatographic sulphur speciation in heavy crude oil using a modified standard D5623 method and microfluidic Deans switching. Journal of Chromatography A 1530, 241-246.Hilaire, F., Basset, E., Bayard, R., Gallardo, M., Thiebaut, D., Vial, J., 2017. Comprehensive two-dimensional gas chromatography for biogas and biomethane analysis. Journal of Chromatography A 1524, 222-232.Jennerwein, M.K., Eschner, M.S., Wilharm, T., Zimmermann, R., Gr?ger, T.M., 2017. Proof of concept of high-temperature comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry for two-dimensional simulated distillation of crude oils. Energy & Fuels 31, 11651-11659.Kovalchik, K.A., MacLennan, M.S., Peru, K.M., Ajaero, C., McMartin, D.W., Headley, J.V., Chen, D.D.Y., 2017. Characterization of dicarboxylic naphthenic acid fraction compounds utilizing amide derivatization: Proof of concept. Rapid Communications in Mass Spectrometry 31, 2057-2065.Liu, H., Raffin, G., Trutt, G., Randon, J., 2017. Is vacuum ultraviolet detector a concentration or a mass dependent detector? Journal of Chromatography A 1530, 171-175.Magagna, F., Cordero, C., Cagliero, C., Liberto, E., Rubiolo, P., Sgorbini, B., Bicchi, C., 2017. Black tea volatiles fingerprinting by comprehensive two-dimensional gas chromatograph – mass spectrometry combined with high concentration capacity sample preparation techniques: Toward a fully automated sensomic assessment. Food chemistry 225, 276-287.Piotrowski, P.K., Weggler, B.A., Barth-Naftilan, E., Kelly, C.N., Zimmermann, R., Saiers, J.E., Dorman, F.L., 2018. Non-targeted chemical characterization of a Marcellus shale gas well through GC??×?GC with scripting algorithms and high-resolution time-of-flight mass spectrometry. Fuel 215, 363-369.Rodríguez-Maecker, R., Vyhmeister, E., Meisen, S., Rosales Martinez, A., Kuklya, A., Telgheder, U., 2017. Identification of terpenes and essential oils by means of static headspace gas chromatography-ion mobility spectrometry. Analytical and Bioanalytical Chemistry 409, 6595-6603.Savareear, B., Brokl, M., Wright, C., Focant, J.-F., 2017. Thermal desorption comprehensive two-dimensional gas chromatography coupled to time of flight mass spectrometry for vapour phase mainstream tobacco smoke analysis. Journal of Chromatography A 1525, 126-137.Schure, M.R., Davis, J.M., 2017. Orthogonality measurements for multidimensional chromatography in three and higher dimensional separations. Journal of Chromatography A 1523, 148-161.Tsizin, S., Bokka, R., Keshet, U., Alon, T., Fialkov, A.B., Tal, N., Amirav, A., 2017. Comparison of electrospray LC–MS, LC–MS with Cold EI and GC–MS with Cold EI for sample identification. International Journal of Mass Spectrometry 422, 119-125.Walters, C.C., Wang, F.C., Higgins, M.B., Madincea, M.E., 2018. Universal biomarker analysis using GC×GC with dual FID and ToF-MS (EI/FI) detection. Organic Geochemistry 115, 57-66.Yan, D., Tedone, L., Koutoulis, A., Whittock, S.P., Shellie, R.A., 2017. Parallel comprehensive two-dimensional gas chromatography. Journal of Chromatography A 1524, 202-209.Zarghani, M., Parastar, H., 2017. Joint approximate diagonalization of eigenmatrices as a high-throughput approach for analysis of hyphenated and comprehensive two-dimensional gas chromatographic data. Journal of Chromatography A 1524, 188-201.Imagine: SEM, TEM, HIM, AFM, nanoSIMSAchang, M., Pashin, J.C., Cui, X., 2017. The influence of particle size, microfractures, and pressure decay on measuring the permeability of crushed shale samples. International Journal of Coal Geology 183, 174-187.Amiri, A., Ghaemi, F., 2017. Graphene grown on stainless steel mesh as a highly efficient sorbent for sorptive microextraction of polycyclic aromatic hydrocarbons from water samples. Analytica Chimica Acta 994, 29-37.Baldwin, P.R., Tan, Y.Z., Eng, E.T., Rice, W.J., Noble, A.J., Negro, C.J., Cianfrocco, M.A., Potter, C.S., Carragher, B., 2018. Big data in cryoEM: automated collection, processing and accessibility of EM data. Current Opinion in Microbiology 43, 1-8.Bernard, S., Daval, D., Ackerer, P., Pont, S., Meibom, A., 2017. Burial-induced oxygen-isotope re-equilibration of fossil foraminifera explains ocean paleotemperature paradoxes. Nature Communications 8, Article1134.Chen, F., Lu, S., Ding, X., He, X., Xing, H., 2018. The splicing of backscattered scanning electron microscopy method used on evaluation of microscopic pore characteristics in shale sample and compared with results from other methods. Journal of Petroleum Science and Engineering 160, 207-218.Guo, Y., Song, Y., Fang, X., Pang, X., Li, T., 2018. Reservoir characterization of an organic-rich dolomitic tight-oil reservoir, the Lower Cretaceous Xiagou Formation in the Qingxi Sag, Jiuquan Basin, NW China. Marine and Petroleum Geology 89, 541-559.Hackley, P.C., Walters, C.C., Kelemen, S.R., Mastalerz, M., Lowers, H.A., 2017. Organic petrology and micro-spectroscopy of Tasmanites microfossils: Applications to kerogen transformations in the early oil window. Organic Geochemistry 114, 23-44.Jia, R., Yang, D., Xu, D., Gu, T., 2017. Anaerobic corrosion of 304 stainless steel caused by the Pseudomonas aeruginosa biofilm. Frontiers in Microbiology 8, 2335. doi: 2310.3389/fmicb.2017.02335.Liang, C., Cao, Y., Jiang, Z., Wu, J., Guoqi, S., Wang, Y., 2017. Shale oil potential of lacustrine black shale in the Eocene Dongying depression: Implications for geochemistry and reservoir characteristics. American Association of Petroleum Geologists Bulletin 101, 1835-1858.Liang, P., Yu, J., Zhang, Y., Jiao, T., Qin, X., 2017. Effects of natural dolomite catalysts on cracking anthracene oil. Energy & Fuels 31, 11765-11772.Liu, B., Schieber, J., Mastalerz, M., 2017. Combined SEM and reflected light petrography of organic matter in the New Albany Shale (Devonian-Mississippian) in the Illinois Basin: A perspective on organic pore development with thermal maturation. International Journal of Coal Geology 184, 57-72.Liu, W.E.I., Zhang, X., 2017. Possible biogenic structures from the Lower Cambrian strata in Yunnan Province, South China. Geological Magazine 154, 1285-1293.Luo, W., Hou, M., Liu, X., Huang, S., Chao, H., Zhang, R., Deng, X., 2018. Geological and geochemical characteristics of marine-continental transitional shale from the Upper Permian Longtan formation, Northwestern Guizhou, China. Marine and Petroleum Geology 89, Part 1, 58-67.Pierre, C., Blanc-Valleron, M.-M., Boudouma, O., Lofi, J., 2017. Carbonate and silicate cementation of siliciclastic sediments of the New Jersey shelf (IODP Expedition 313): relation with organic matter diagenesis and submarine groundwater discharge. Geo-Marine Letters 37, 537-547.Rivadeneyra, A., Gonzalez-Martinez, A., Portela, G.R., Martin-Ramos, D.J., Gonzalez-Lopez, J., Rivadeneyra, M.A., 2017. Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations. Extremophiles 21, 1049-1056.Rivas-Lamelo, S., Benzerara, K., Lefèvre, C.T., Jézéquel, D., Menguy, N., Viollier, E., Guyot, F., Férard, C., Poinsot, M., Skouri-Panet, F., Trcera, N., Miot, J., Duprat, E., 2017. Magnetotactic bacteria as a new model for P sequestration in the ferruginous Lake Pavin. Geochemical Perspectives Letters 5, 35-41.Schmatz, J., Klaver, J., Jiang, M., Urai, J.L., 2017. Nanoscale morphology of brine/oil/mineral contacts in connected pores of carbonate reservoirs: Insights on wettability from cryo-BIB-SEM. SPE Journal 22, 1374-1384.Shibata, M., Nishimasu, H., Kodera, N., Hirano, S., Ando, T., Uchihashi, T., Nureki, O., 2017. Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy. Nature Communications 8, Article 1430.Su, Y., Zha, M., Ding, X., Qu, J., Wang, X., Yang, C., Iglauer, S., 2018. Pore type and pore size distribution of tight reservoirs in the Permian Lucaogou Formation of the Jimsar Sag, Junggar Basin, NW China. Marine and Petroleum Geology 89, 761-774.Taheri-Shakib, J., Shekarifard, A., Naderi, H., 2017. The experimental investigation of effect of microwave and ultrasonic waves on the key characteristics of heavy crude oil. Journal of Analytical and Applied Pyrolysis 128, 92-101.Trembath-Reichert, E., Morono, Y., Ijiri, A., Hoshino, T., Dawson, K.S., Inagaki, F., Orphan, V.J., 2017. Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds. Proceedings of the National Academy of Sciences 114, E9206-E9215.Wang, H., Liang, J., Li, X., Ji, X., Zhang, Q., Huang, R., 2017. Analysis of the geological conditions for shale gas accumulation: Two different Carboniferous marine-continental transitional facies in the Bayanhot Basin, China. Energy & Fuels 31, 11515-11522.Wang, Q., Lu, H., Wang, T., Liu, D., Peng, P.a., Zhan, X., Li, X., 2018. Pore characterization of Lower Silurian shale gas reservoirs in the Middle Yangtze region, central China. Marine and Petroleum Geology 89, Part 1, 14-26.Wang, S., Pomerantz, A.E., Xu, W., Lukyanov, A., Kleinberg, R.L., Wu, Y.-S., 2017. The impact of kerogen properties on shale gas production: A reservoir simulation sensitivity analysis. Journal of Natural Gas Science and Engineering 48, 13-23.Wang, Y., Wang, L., Wang, J., Jiang, Z., Jin, C., Wang, Y., 2018. Characterization of organic matter pores in typical marine and terrestrial shales, China. Journal of Natural Gas Science and Engineering 49, 56-65.Wu, Z., Sun, X., Xu, H., Konishi, H., Wang, Y., Lu, Y., Cao, K., Wang, C., Zhou, H., 2018. Microstructural characterization and in-situ sulfur isotopic analysis of silver-bearing sphalerite from the Edmond hydrothermal field, Central Indian Ridge. Ore Geology Reviews 92, 318-347.Zhang, P., Lu, S., Li, J., Chen, C., Xue, H., Zhang, J., 2018. Petrophysical characterization of oil-bearing shales by low-field nuclear magnetic resonance (NMR). Marine and Petroleum Geology 89, 775-785.Zhang, S., Canter, L., Sonnenfeld, M., 2017. Capillary fluid dynamics within unconventional rocks investigated by scanning electron microscopy. American Association of Petroleum Geologists Bulletin 101, 1759-1765.Imagine: ?-Xray CTBackeberg, N.R., Iacoviello, F., Rittner, M., Mitchell, T.M., Jones, A.P., Day, R., Wheeler, J., Shearing, P.R., Vermeesch, P., Striolo, A., 2017. Quantifying the anisotropy and tortuosity of permeable pathways in clay-rich mudstones using models based on X-ray tomography. Scientific Reports 7, Article 14838.Chen, X., Yao, G., Cai, J., Huang, Y., Yuan, X., 2017. Fractal and multifractal analysis of different hydraulic flow units based on micro-CT images. Journal of Natural Gas Science and Engineering 48, 145-156.Hanna, R.D., Ketcham, R.A., 2017. X-ray computed tomography of planetary materials: A primer and review of recent studies. Chemie der Erde - Geochemistry 77, 547-572.Jing, Y., Armstrong, R.T., Mostaghimi, P., 2017. Impact of mineralization on digital coal properties. Energy & Fuels 31, 11558–11568.Luo, C.U.I., Pan, B., Reitner, J., 2017. Chambered structures from the Ediacaran Dengying Formation, Yunnan, China: comparison with the Cryogenian analogues and their microbial interpretation. Geological Magazine 154, 1269-1284.Müller, M., de Sena Oliveira, I., Allner, S., Ferstl, S., Bidola, P., Mechlem, K., Fehringer, A., Hehn, L., Dierolf, M., Achterhold, K., Gleich, B., Hammel, J.U., Jahn, H., Mayer, G., Pfeiffer, F., 2017. Myoanatomy of the velvet worm leg revealed by laboratory-based nanofocus X-ray source tomography. Proceedings of the National Academy of Sciences 114, 12378-12383.Nie, B., Fan, P., Li, X., 2018. Quantitative investigation of anisotropic characteristics of methane-induced strain in coal based on coal particle tracking method with X-ray computer tomography. Fuel 214, 272-284.Pang, X., Maxson, J.K., Cuello Jimenez, W., Singh, J.P., Morgan, R.G., 2017. Microscale characterization of field and laboratory foamed cement by use of X-ray microcomputed tomography. SPE Journal 22, 1690-1703.Saxena, N., Hofmann, R., Alpak, F.O., Berg, S., Dietderich, J., Agarwal, U., Tandon, K., Hunter, S., Freeman, J., Wilson, O.B., 2017. References and benchmarks for pore-scale flow simulated using micro-CT images of porous media and digital rocks. Advances in Water Resources 109, 211-235.Schmatz, J., Klaver, J., Jiang, M., Urai, J.L., 2017. Nanoscale morphology of brine/oil/mineral contacts in connected pores of carbonate reservoirs: Insights on wettability from cryo-BIB-SEM. SPE Journal 22, 1374-1384.Wang, X., Kellner, A.W.A., Jiang, S., Cheng, X., Wang, Q., Ma, Y., Paidoula, Y., Rodrigues, T., Chen, H., Say?o, J.M., Li, N., Zhang, J., Bantim, R.A.M., Meng, X., Zhang, X., Qiu, R., Zhou, Z., 2017. Egg accumulation with 3D embryos provides insight into the life history of a pterosaur. Science 358, 1197-1201.Xiong, Z., Lin, H., Liu, F., Xiao, P., Wu, Z., Li, T., Li, D., 2017. Flexible PVDF membranes with exceptional robust superwetting surface for continuous separation of oil/water emulsions. Scientific Reports 7, Article 14099.Yancy-Caballero, D., Ling, L.Y., Archilha, N.L., Ferreira, J.E., Driemeier, C., 2017. Mineral particles in sugar cane bagasse: Localization and morphometry using microtomography analysis. Energy & Fuels 31, 12288-12296.Zhao, J., 2017. Micro-CT scanning of gas hydrate decomposition in model porous media. Chemistry and Technology of Fuels and Oils 53, 600-609.Zhao, Y., Sun, Y., Liu, S., Chen, Z., Yuan, L., 2018. Pore structure characterization of coal by synchrotron radiation nano-CT. Fuel 215, 102-110.Li, A., Ding, W., Jiu, K., Wang, Z., Wang, R., He, J., 2018. Investigation of the pore structures and fractal characteristics of marine shale reservoirs using NMR experiments and image analyses: A case study of the Lower Cambrian Niutitang Formation in northern Guizhou Province, South China. Marine and Petroleum Geology 89, 530-540.Liquid Chromatography/LC-MS/SFCBataineh, M., Arabi, A.A., Iqbal, J., Howari, F.M., Brack, W., 2017. Method development for selective and nontargeted identification of nitro compounds in diesel particulate matter. Energy & Fuels 31, 11615-11626.Blanco-Zubiaguirre, L., Ribechini, E., Degano, I., La Nasa, J., Carrero, J.A., I?a?ez, J., Olivares, M., Castro, K., 2018. GC–MS and HPLC-ESI-QToF characterization of organic lipid residues from ceramic vessels used by Basque whalers from 16th to 17th centuries. Microchemical Journal 137, 190-203.Blue, L.E., Franklin, E.G., Godinho, J.M., Grinias, J.P., Grinias, K.M., Lunn, D.B., Moore, S.M., 2017. Recent advances in capillary ultrahigh pressure liquid chromatography. Journal of Chromatography A 1523, 17-39.Carabajal, M.D., Arancibia, J.A., Escandar, G.M., 2017. On-line generation of third-order liquid chromatography–excitation-emission fluorescence matrix data. Quantitation of heavy-polycyclic aromatic hydrocarbons. Journal of Chromatography A 1527, 61-69.Chiaia-Hernández, A.C., Günthardt, B.F., Frey, M.P., Hollender, J., 2017. Unravelling contaminants in the Anthropocene using statistical analysis of liquid chromatography–high-resolution mass spectrometry nontarget screening data recorded in lake sediments. Environmental Science & Technology 51, 12547-12556.Hutchings, J.A., Shields, M.R., Bianchi, T.S., Schuur, E.A.G., 2018. A rapid and precise method for the analysis of underivatized amino acids in natural samples using volatile-ion-pairing reverse-phase liquid chromatography–electrospray ionization tandem mass spectrometry. Organic Geochemistry 115, 46-56.Long, Z., Zhang, Y., Gamache, P., Guo, Z., Steiner, F., Du, N., Liu, X., Jin, Y., Liu, X., Liu, L., 2018. Determination of tropane alkaloids by heart cutting reversed phase – Strong cation exchange two dimensional liquid chromatography. Journal of Chromatography B 1072, 70-77.Lynch, K.B., Chen, A., Liu, S., 2018. Miniaturized high-performance liquid chromatography instrumentation. Talanta 177, 94-103.McCalley, D.V., 2017. Understanding and manipulating the separation in hydrophilic interaction liquid chromatography. Journal of Chromatography A 1523, 49-71.Naraoka, H., Yamashita, Y., Yamaguchi, M., Orthous-Daunay, F.-R., 2017. Molecular evolution of N-containing cyclic compounds in the parent body of the Murchison meteorite. ACS Earth and Space Chemistry 1, 540-550.Pirok, B.W.J., Molenaar, S.R.A., van Outersterp, R.E., Schoenmakers, P.J., 2017. Applicability of retention modelling in hydrophilic-interaction liquid chromatography for algorithmic optimization programs with gradient-scanning techniques. Journal of Chromatography A 1530, 104-111.Putman, J.C., Rowland, S.M., Podgorski, D.C., Robbins, W.K., Rodgers, R.P., 2017. Dual-column aromatic ring class separation with improved universal detection across mobile-phase gradients via eluate dilution. Energy & Fuels 31, 12064-12071.Richardson, A.E., Danielson, N.D., 2017. Hydrophilic interaction liquid chromatography of hydroxy aromatic carboxylic acid positional isomers. Analytica Chimica Acta 996, 98-105.Sandra, K., Steenbeke, M., Vandenheede, I., Vanhoenacker, G., Sandra, P., 2017. The versatility of heart-cutting and comprehensive two-dimensional liquid chromatography in monoclonal antibody clone selection. Journal of Chromatography A 1523, 283-292.Stoll, D.R., Sajulga, R.W., Voigt, B.N., Larson, E.J., Jeong, L.N., Rutan, S.C., 2017. Simulation of elution profiles in liquid chromatography ? II: Investigation of injection volume overload under gradient elution conditions applied to second dimension separations in two-dimensional liquid chromatography. Journal of Chromatography A 1523, 162-172.Tsizin, S., Bokka, R., Keshet, U., Alon, T., Fialkov, A.B., Tal, N., Amirav, A., 2017. Comparison of electrospray LC–MS, LC–MS with Cold EI and GC–MS with Cold EI for sample identification. International Journal of Mass Spectrometry 422, 119-125.Waggoner, D.C., Hatcher, P.G., 2017. Hydroxyl radical alteration of HPLC fractionated lignin: Formation of new compounds from terrestrial organic matter. Organic Geochemistry 113, 315-325.Wang, S., Wang, Z., Zhou, L., Shi, X., Xu, G., 2017. Comprehensive analysis of short-, medium-, and long-chain acyl-coenzyme A by online two-dimensional liquid chromatography/mass spectrometry. Analytical Chemistry 89, 12902-12908.Wang, X., Hayeck, N., Brüggemann, M., Yao, L., Chen, H., Zhang, C., Emmelin, C., Chen, J., George, C., Wang, L., 2017. Chemical characteristics of organic aerosols in Shanghai: A study by ultrahigh-performance liquid chromatography coupled with Orbitrap mass spectrometry. Journal of Geophysical Research: Atmospheres 122, 11,703-711,722.Wang, X., Wu, H., Luo, R., Xia, D., Jiang, Z., Han, H., 2017. Separation and detection of free D- and L-amino acids in tea by off-line two-dimensional liquid chromatography. Analytical Methods 9, 6131-6138.Wu, Z.-y., Zeng, Z., Xiao, Z., Kam-Wah Mok, D., Chan, H., 2017. Correlation and uncorrelation between hyphenated chromatographic data with chemometric tools. Chemometrics and Intelligent Laboratory Systems 171, 266-276.Xin, H., Fu, Q., Yuan, Y., Liu, Y., Ke, Y., Jin, Y., Liang, X., 2017. Construction of an off-line two dimensional reversed-phase liquid chromatography/ultra-high performance supercritical fluid chromatography method for rapid and comprehensive analysis of Piper kadsura. The Journal of Supercritical Fluids 127, 9-14.Yamamoto, K., Ueki, T., Higuchi, N., Takahashi, K., Kotani, A., Hakamata, H., 2017. A flow-through column electrolytic cell for supercritical fluid chromatography. Journal of Separation Science 40, 4085-4090.Zhang, H., Ma, S., Yao, Y., Li, Y., Li, Y., Ou, J., Ye, M., Wei, Y., 2017. Facile preparation of multi-functionalized hybrid monoliths via two-step photo-initiated reactions for two-dimensional liquid chromatography–mass spectrometry. Journal of Chromatography A 1524, 135-142.Zhang, J., Chen, Z., 2017. Metal-organic frameworks as stationary phase for application in chromatographic separation. Journal of Chromatography A 1530, 1-18.Zheng, N., Xiao, H., Zhang, Z., Gao, X., Zhao, J., 2017. Rapid and sensitive method for determining free amino acids in plant tissue by high-performance liquid chromatography with fluorescence detection. Acta Geochimica 36, 680-696.Mass Spectroscopy/ICR-FTMSAhad, J.M.E., Pakdel, H., Lavoie, D., Lefebvre, R., Peru, K.M., Headley, J.V., 2018. Naphthenic acids in groundwater overlying undeveloped shale gas and tight oil reservoirs. Chemosphere 191, 664-672.Bataineh, M., Arabi, A.A., Iqbal, J., Howari, F.M., Brack, W., 2017. Method development for selective and nontargeted identification of nitro compounds in diesel particulate matter. Energy & Fuels 31, 11615-11626.Ben-Nissan, G., Sharon, M., 2018. The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes. Current Opinion in Chemical Biology 42, 25-33.Chen, Z., Glover, M.S., Li, L., 2018. Recent advances in ion mobility–mass spectrometry for improved structural characterization of glycans and glycoconjugates. Current Opinion in Chemical Biology 42, 1-8.Cho, E., Witt, M., Hur, M., Jung, M.-J., Kim, S., 2017. Application of FT-ICR MS equipped with quadrupole detection for analysis of crude oil. Analytical Chemistry 89, 12101-12107.Costanzo, M.T., Boock, J.J., Kemperman, R.H.J., Wei, M.S., Beekman, C.R., Yost, R.A., 2017. Portable FAIMS: Applications and future perspectives. International Journal of Mass Spectrometry 422, 188-196.Crawford, E.A., Gerbig, S., Spengler, B., Volmer, D.A., 2017. Rapid fingerprinting of lignin by ambient ionization high resolution mass spectrometry and simplified data mining. Analytica Chimica Acta 994, 38-48.Dexter, A., Race, A.M., Steven, R.T., Barnes, J.R., Hulme, H., Goodwin, R.J.A., Styles, I.B., Bunch, J., 2017. Two-phase and graph-based clustering methods for accurate and efficient segmentation of large mass spectrometry images. 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Journal of Sedimentary Research 87, 1100-1120.Bechtel, A., Oberauer, K., Kosti?, A., Gratzer, R., Milisavljevi?, V., Aleksi?, N., Stojanovi?, K., Gro?, D., Sachsenhofer, R.F., 2018. Depositional environment and hydrocarbon source potential of the Lower Miocene oil shale deposit in the Aleksinac Basin (Serbia). Organic Geochemistry 115, 93-112.Bhaumik, A.K., Paikray, J., Dutta, J., Mitra, A., Tiwari, D., Patil, D.J., 2017. Biostratigraphy and depositional environment of the Miocene limestone bed of Baripada, Mayurbhanj district, Odisha: Foraminiferal, sedimentological and bulk organic geochemical evidences. Journal of the Geological Society of India 90, 437-446.dos Santos Rocha, Y., Pereira, R.C.L., Mendon?a Filho, J.G., 2018. Negative electrospray Fourier transform ion cyclotron resonance mass spectrometry determination of the effects on the distribution of acids and nitrogen-containing compounds in the simulated thermal evolution of a Type-I source rock. 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Early Triassic environmental dynamics and microbial development during the Smithian–Spathian transition (Lower Weber Canyon, Utah, USA). Sedimentary Geology 363, 136-151.Hackley, P.C., Walters, C.C., Kelemen, S.R., Mastalerz, M., Lowers, H.A., 2017. Organic petrology and micro-spectroscopy of Tasmanites microfossils: Applications to kerogen transformations in the early oil window. Organic Geochemistry 114, 23-44.Hou, H., Shao, L., Li, Y., Lu, J., Li, Z., Wang, S., Zhang, W., Wen, H., 2017. Geochemistry, reservoir characterization and hydrocarbon generation potential of lacustrine shales: A case of YQ-1 well in the Yuqia Coalfield, northern Qaidam Basin, NW China. Marine and Petroleum Geology 88, 458-471.Huang, X., Yang, X., Zhu, H., Kang, H., Jia, J., Wang, B., Ji, S., 2017. Lithofacies characteristics and sedimentary pattern of Madingo Formation marine hydrocarbon source rocks in Lower Congo Basin. Acta Petrolei Sinica 38, 1168-1182.Ji, L., Zhang, M., Ma, X., Xu, W., Zheng, G., 2018. 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Geological Journal 52, 1032-1048.Unconventional ResourcesAchang, M., Pashin, J.C., Cui, X., 2017. The influence of particle size, microfractures, and pressure decay on measuring the permeability of crushed shale samples. International Journal of Coal Geology 183, 174-187.Ahmed, H.R., Abduljauwad, S.N., 2017. A universal nanoscopic swell behavior model for gas shales. Journal of Natural Gas Science and Engineering 48, 85-99.Akkutlu, I.Y., Efendiev, Y., Vasilyeva, M., Wang, Y., 2017. Multiscale model reduction for shale gas transport in a coupled discrete fracture and dual-continuum porous media. Journal of Natural Gas Science and Engineering 48, 65-76.Aljamaan, H., Al Ismail, M., Kovscek, A.R., 2017. Experimental investigation and Grand Canonical Monte Carlo simulation of gas shale adsorption from the macro to the nano scale. Journal of Natural Gas Science and Engineering 48, 119-137.An, S., Yao, J., Yang, Y., Zhang, W., Zhao, J., Li, A., 2017. The microscale analysis of reverse displacement based on digital core. Journal of Natural Gas Science and Engineering 48, 138-144.Backeberg, N.R., Iacoviello, F., Rittner, M., Mitchell, T.M., Jones, A.P., Day, R., Wheeler, J., Shearing, P.R., Vermeesch, P., Striolo, A., 2017. Quantifying the anisotropy and tortuosity of permeable pathways in clay-rich mudstones using models based on X-ray tomography. Scientific Reports 7, Article 14838.Cao, C., Zhang, M., Tang, Q., Yang, Y., Lv, Z., Zhang, T., Chen, C., Yang, H., Li, L., 2018. Noble gas isotopic variations and geological implication of Longmaxi shale gas in Sichuan Basin, China. Marine and Petroleum Geology 89, Part 1, 38-46.Chen, F., Lu, S., Ding, X., He, X., Xing, H., 2017. Evaluation of the adsorbed gas amount in a shale reservoir using the three compositions adsorbing methane (TCAM) method: A case from the Longmaxi shale in southeast Chongqing, China. Energy & Fuels 31, 11523-11531.Chen, F., Lu, S., Ding, X., He, X., Xing, H., 2018. The splicing of backscattered scanning electron microscopy method used on evaluation of microscopic pore characteristics in shale sample and compared with results from other methods. Journal of Petroleum Science and Engineering 160, 207-218.Cui, G., Liu, J., Wei, M., Shi, R., Elsworth, D., 2018. Why shale permeability changes under variable effective stresses: New insights. Fuel 213, 55-71.Du, D., Zhang, N., Li, Y., Sun, R., Wang, C., 2017. Parametric studies on foam displacement behavior in a layered heterogeneous porous media based on the stochastic population balance model. Journal of Natural Gas Science and Engineering 48, 1-12.Duan, D., Zhang, D., Ma, X., Yang, Y., Ran, Y., Mao, J., 2018. Chemical and structural characterization of thermally simulated kerogen and its relationship with microporosity. Marine and Petroleum Geology 89, Part 1, 4-13.Feng, R., Pandey, R., 2017. Investigation of various pressure transient techniques on permeability measurement of unconventional gas reservoirs. Transport in Porous Media 120, 495-514.Gao, J., Wang, X., He, S., Guo, X., Zhang, B., Chen, X., 2017. Geochemical characteristics and source correlation of natural gas in Jurassic shales in the North Fuling area, Eastern Sichuan Basin, China. Journal of Petroleum Science and Engineering 158, 284-292.Guo, Y., Song, Y., Fang, X., Pang, X., Li, T., 2018. Reservoir characterization of an organic-rich dolomitic tight-oil reservoir, the Lower Cretaceous Xiagou Formation in the Qingxi Sag, Jiuquan Basin, NW China. Marine and Petroleum Geology 89, 541-559.Huang, L., Ning, Z., Wang, Q., Zhang, W., Cheng, Z., Wu, X., Qin, H., 2018. Effect of organic type and moisture on CO2/CH4 competitive adsorption in kerogen with implications for CO2 sequestration and enhanced CH4 recovery. Applied Energy 210, 28-43.Islam, A.W., Sun, A.Y., 2017. A theory-based simple extension of Peng–Robinson equation of state for nanopore confined fluids. Journal of Petroleum Exploration and Production Technology 7, 1197-1203.Jenkins, A., Fathi, E., Belyadi, F., 2017. Stress field behavior induced by hydraulic fracture in shale reservoirs: A practical view on cluster spacing. Journal of Natural Gas Science and Engineering 48, 186-196.Jiang, W., Lin, M., 2018. Molecular dynamics investigation of conversion methods for excess adsorption amount of shale gas. Journal of Natural Gas Science and Engineering 49, 241-249.Kudapa, V.K., Sharma, P., Kunal, V., Gupta, D.K., 2017. Modeling and simulation of gas flow behavior in shale reservoirs. Journal of Petroleum Exploration and Production Technology 7, 1095-1112.Li, A., Ding, W., Jiu, K., Wang, Z., Wang, R., He, J., 2018. Investigation of the pore structures and fractal characteristics of marine shale reservoirs using NMR experiments and image analyses: A case study of the Lower Cambrian Niutitang Formation in northern Guizhou Province, South China. Marine and Petroleum Geology 89, 530-540.Li, B., Su, Y., Wang, W., 2017. Temporal scale-based production analysis of fractured horizontal wells with stimulated reservoir volume. Journal of Natural Gas Science and Engineering 48, 46-64.Li, H., Misra, S., 2018. Assessment of miscible light-hydrocarbon-injection recovery efficiency in Bakken shale formation using wireline-log-derived indices. Marine and Petroleum Geology 89, 585-593.Li, J., Jiang, H., Wang, C., Zhao, Y., Gao, Y., Pei, Y., Wang, C., Dong, H., 2017. Pore-scale investigation of microscopic remaining oil variation characteristics in water-wet sandstone using CT scanning. 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Shale oil potential of lacustrine black shale in the Eocene Dongying depression: Implications for geochemistry and reservoir characteristics. American Association of Petroleum Geologists Bulletin 101, 1835-1858.Liu, B., Schieber, J., Mastalerz, M., 2017. Combined SEM and reflected light petrography of organic matter in the New Albany Shale (Devonian-Mississippian) in the Illinois Basin: A perspective on organic pore development with thermal maturation. International Journal of Coal Geology 184, 57-72.Liu, L., Yao, J., Zhang, L., An, S., Zhao, J., Sun, H., 2017. REV-scale simulation of micro-fractured unconventional gas reservoir. Journal of Natural Gas Science and Engineering 48, 100-110.Liu, P., Wang, X., Meng, Q., Wang, X., Zhang, L., Liu, C., Lei, Y., Jiang, C., Yin, J., 2018. Simulation of shale gas generation by using different experimental systems: A case study from Chang7 shale in the Ordos Basin. Journal of Natural Gas Science and Engineering 49, 169-178.Liu, Y., Li, H.A., Okuno, R., 2018. Phase behavior of N2/n-C4H10 in a partially confined space derived from shale sample. Journal of Petroleum Science and Engineering 160, 442-451.Lu, T., Li, Z., Li, J., Hou, D., Zhang, D., 2017. Flow behavior of N2 huff and puff process for enhanced oil recovery in tight oil reservoirs. Scientific Reports 7, Article 15695.Lv, Q., Chen, Z., Wang, M., 2017. An improved elastic-tubes model for the correlation of permeability and stress with correction for the Klinkenberg effect. Journal of Natural Gas Science and Engineering 48, 24-35.Moghaddam, R.N., Jamiolahmady, M., 2017. Study of slip flow in unconventional shale rocks using lattice Boltzmann method: Effects of boundary conditions and TMAC. Transport in Porous Media 120, 115-139.Ojha, S.P., Misra, S., Tinni, A., Sondergeld, C., Rai, C., 2017. Pore connectivity and pore size distribution estimates for Wolfcamp and Eagle Ford shale samples from oil, gas and condensate windows using adsorption-desorption measurements. Journal of Petroleum Science and Engineering 158, 454-468.Ortiz Cancino, O.P., Peredo Mancilla, D., Pozo, M., Pérez, E., Bessieres, D., 2017. Effect of organic matter and thermal maturity on methane adsorption capacity on shales from the Middle Magdalena Valley Basin in Colombia. Energy & Fuels 31, 11698-11709.Piotrowski, P.K., Weggler, B.A., Barth-Naftilan, E., Kelly, C.N., Zimmermann, R., Saiers, J.E., Dorman, F.L., 2018. Non-targeted chemical characterization of a Marcellus shale gas well through GC??×?GC with scripting algorithms and high-resolution time-of-flight mass spectrometry. Fuel 215, 363-369.Pranesh, V., 2018. Subsurface CO2 storage estimation in Bakken tight oil and Eagle Ford shale gas condensate reservoirs by retention mechanism. Fuel 215, 580-591.Ramirez-Corredores , M., 2017. 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Geological Journal 52, 1032-1048.AbstractsAanderud, Z.T., Smart, T.B., Wu, N., Taylor, A.S., Zhang, Y., Belnap, J., 2017. Fungal loop transfer of N depends on biocrust constituents and N form. Biogeosciences Discussions 2017, 1-32. performing multiple ecosystem services individually and collectively, biocrust constituents may also create biological networks connecting spatially and temporally distinct processes. In the fungal loop hypothesis, rainfall variability allows fungi to act as conduits and reservoirs, translocating resources between soils and host plants. To evaluate the extent biocrust species composition and N form influence loops, we created a minor, localized rainfall event containing 15NH4+ and 15NO3? and measured the resulting δ15N in surrounding cyanobacteria- and lichen-dominated crusts and grass, Achnatherum hymenoides, after twenty-four hours. We also estimated the biomass of fungal constituents using quantitative PCR and characterized fungal communities by sequencing the 18S rRNA gene. We only found evidence of fungal loops in cyanobacteria-dominated crusts where 15N, from 15NH4+, moved 40?mm?h?1 and the δ15N in crusts decreased as the radial distance from the water addition increased (linear regression analysis: R2?=?0.58, F?=?16, P?=?0.002, n?=?14). In cyanobacteria crusts, δ15N, from 15NH4+, was diluted as Ascomycota biomass increased (linear regression analysis: R2?=?0.50, F?=?8.8, P?=?0.02, n?=?14), Ascomycota accounted for 82?% (±2.8) of all fungal sequences, and one order, Pleosporales, comprised 66?% (±6.9) of Ascomycota. The lack of loops in moss-dominated crusts and substantial movement of 15NO3? may stem from mosses effectively sequestering newly fixed N and fungi preferring 15NH4+ for amino acid transformation and translocation. No label entered A. hymenoides. Our findings suggest that minor rainfall events allow dark septate Pleosporales to rapidly translocate N in the absence of a plant sink.Abolpour, B., 2018. Investigating effects of molecular structure on the behavior of saturated liquid hydrocarbons using a novel semi-empirical equation of state. Fluid Phase Equilibria 456, 184-192. this study, a novel equation of state has been developed to investigate the behavior of saturated liquid hydrocarbons. The developed equation was used to study the effects of molecular structure on this behavior. A set of logical rules was obtained to estimate the power of the presented equation of state. Finally, this equation and the obtained logics were validated using experimental data.Abubacker, J., Al-Attar, H., Zekri, A., Khalifi, M., Louiseh, E., 2017. Selecting a potential smart water for EOR implementation in Asab oil field. Journal of Petroleum Exploration and Production Technology 7, 1133-1147. IFT and contact angle are believed to have direct impact on wettability alteration of crude oil/water/rock systems. In this work, extensive laboratory work was conducted to investigate the effect of these two key parameters on wettability alteration at elevated temperature (90?°C) and ambient conditions. Twenty-six brines representing various scenarios of dilution and sulphate spiking were prepared and tested to identify the smart water most effective in the alteration of wettability. Sea water (SW) was used a base brine. Diluted and sulphate-spiked versions of SW were synthetically prepared following the standard brine preparation procedures. Also standard procedures were followed for the measurement of IFT and contact angle measurements using Teclis tracker. Pendant drop method was implemented to measure the IFT at ambient and 90?°C conditions using a special software package that adopts the axisymmetric drop shape analysis and fits the Laplace equation. The same software package was used to take snapshots of oil drops at 90?°C, and contact angle was measured manually. The effects of dilution and/or sulphate spiking on the observed IFT and contact angle measurements were investigated using a proposed brine categories-based plotting technique. Natural SW and its sulphate-spiked versions have shown the least oil/brine IFT at ambient and 90?°C conditions. The sulphate-spiked SW and its dilutions have resulted in the reduction in oil/brine IFT, whereas the diluted SW showed an increase in oil/brine IFT. Further reduction in IFT was observed at the elevated temperature. SW and SW/50 (50 times diluted sea water) were the only two brines that could yield a contact angle of 113° and 114°, respectively, indicating the change in wettability from oil-wet to the border line of intermediate-wettability conditions. The natural SW that contains 3944?mg/L of sulphate ion has been found to be the most effective in promoting wettability change and thus represents the selected smart water for EOR implementation in Asab oil field. The contact angle measurements were made from the drops formed by the natural drainage process. These measurements are believed to duplicate contact angles in the selected reservoir because of the continuous change in fluids saturation.Aceto, M., Agosta, E., Arrais, A., Calà, E., Mazzucco, E., Lomartire, S., Agostino, A., Fenoglio, G., 2017. Multi-technique characterization of adhesives used in Medieval jewellery. Archaeometry 59, 1105-1118. this work, a multi-technique analytical approach was used to characterize adhesive samples taken from medieval chef d'oeuvres jewellery, three manuscript bindings and a crucifix produced in northern Italy between the 8th and the 11th century ad, according to art-historical evaluation and 14C dating executed on adhesives. These materials being complex mixtures, mostly of organic/inorganic nature, various analytical techniques were utilized to thoroughly elucidate their composition. A preliminary survey with portable X-ray fluorescence spectrometry (XRF), applied in situ, suggested the presence of inorganic phases. X-ray diffraction analysis was used to identify crystalline phases. Fourier transform – infrared and Raman spectroscopies were used to identify the major components. Finally, gas chromatography coupled with mass spectrometry was used to identify, in the most accurate way possible, the organic compounds present in the mixtures. The combined approach of non-invasive measurements, applied for the first time to such precious objects, and of micro-invasive techniques allowed a complete characterization of the samples, widening the present view on such poorly studied materials.Achang, M., Pashin, J.C., Cui, X., 2017. The influence of particle size, microfractures, and pressure decay on measuring the permeability of crushed shale samples. International Journal of Coal Geology 183, 174-187. of matrix permeability is essential for predicting, evaluating, and modeling the performance of shale reservoirs. However, the repeatability and accuracy of these measurements can be questioned because procedures have not been standardized. As a result, permeability measurements from the same sample by different laboratories can vary by orders of magnitude. Microfracturing related to changes in stress during core retrieval and crushing during sample preparation is thought to be a significant source of error. Different interpretations of pressure decay curves could also account for inconsistent permeability values. The goals of this research were to analyze relationships among crushed particle size, microfractures, and matrix permeability, as well as to evaluate the ways in which pressure decay curves are interpreted and to determine the sample mass best suited for analysis.Crushed rock pressure-decay measurements of particles of different sizes were obtained using a shale matrix permeameter, and permeability was estimated by curve fitting using Core Laboratories software and by other methods that assess the geometry and evolution of pressure decay curves. Results indicate that the relationships between permeability and particle size vary considerably when determined by different methods.Analysis of pressure decay curves reveals three distinct segments. The early segment is characterized by hyperbolic decay, whereas the late segment is characterized by exponential decay. A third segment records a pseudo-steady state where pressure has declined to the extent that decay can no longer be characterized. Decay was measured for about 2000 s; most decay curves stabilize within 500 s, and data collected beyond 500 s are dominated by noise associated with the pseudo-steady state and are beyond the resolution of the apparatus used.Analysis of early hyperbolic curves yields permeability values one to two orders of magnitude greater than whole curve analysis. The hyperbolic pressure decay segment appears to be influenced by microfractures and other large pores near the surface of samples, whereas the late time segment and whole curve correlate more strongly with the microporous to nanoporous rock matrix. Also, permeability values derived from whole curve analysis are sensitive to measurement duration, and different values are obtained when permeability is determined from different time windows. SEM images of all particle sizes analyzed reveal microfractures with diameters ranging from 60 to 1020 nm, but no correlation was found between microfracture aperture and particle size. The optimal sample mass used in our shale permeameter is 50–100 g, which facilitates resolution of the major elements of the decay curve. Optimal particle sizes are between 1.0 and 1.4 mm.Adam, P.S., Borrel, G., Brochier-Armanet, C., Gribaldo, S., 2017. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. The Isme Journal 11, 2407-2425. Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages. This is revolutionizing our view of the diversity and metabolic potential of the Archaea in a wide variety of environments, an important step toward understanding their ecological role. The archaeal tree is being rapidly filled up with new branches constituting phyla, classes and orders, generating novel challenges for high-rank systematics, and providing key information for dissecting the origin of this domain, the evolutionary trajectories that have shaped its current diversity, and its relationships with Bacteria and Eukarya. The present picture is that of a huge diversity of the Archaea, which we are only starting to explore.Ahad, J.M.E., Pakdel, H., Lavoie, D., Lefebvre, R., Peru, K.M., Headley, J.V., 2018. Naphthenic acids in groundwater overlying undeveloped shale gas and tight oil reservoirs. Chemosphere 191, 664-672. acid extractable organics (AEOs) containing naphthenic acids (NAs) in groundwater overlying undeveloped shale gas (Saint-?douard region) and tight oil (Haldimand sector, Gaspé) reservoirs in Québec, Canada, were analysed using high resolution Orbitrap mass spectrometry and thermal conversion/elemental analysis – isotope ratio mass spectrometry. As classically defined by CnH2n+ZO2, the most abundant NAs detected in the majority of groundwater samples were straight-chain (Z = 0) or monounsaturated (Z = ?2) C16 and C18 fatty acids. Several groundwater samples from both study areas, however, contained significant proportions of presumably alicyclic bicyclic NAs (i.e., Z = ?4) in the C10-C18 range. These compounds may have originated from migrated waters containing a different distribution of NAs, or are the product of in situ microbial alteration of shale organic matter and petroleum. In most groundwater samples, intramolecular carbon isotope values generated by pyrolysis (δ13Cpyr) of AEOs were on average around 2–3‰ heavier than those generated by bulk combustion (δ13C) of AEOs, providing further support for microbial reworking of subsurface organic carbon. Although concentrations of AEOs were very low (<2.0 mg/L), the detection of potentially toxic bicyclic acids in groundwater overlying unconventional hydrocarbon reservoirs points to a natural background source of organic contaminants prior to any large-scale commercial hydrocarbon development.Ahmed, H.R., Abduljauwad, S.N., 2017. A universal nanoscopic swell behavior model for gas shales. Journal of Natural Gas Science and Engineering 48, 85-99. fracturing to tap unconventional shale gas reservoirs causes a volume change of the active clay minerals matrix in the gas shale structure, resulting in the clogging of the tiny nanopores and consequently undermining the production of the shale gas. Due to the complex natural structure and fabric of clay and non-clay minerals associated with high in-situ stresses at pre and post-fracking and the practical difficulties in the replication of the field stress conditions in the lab testing facilities, swell potential from the macro and micro investigations do not provide reliable and universally applicable results. None of the existing macro level and few molecular-level studies incorporate simulations cover natural structure of gas shales. In this study, we present comprehensive molecular level simulations based volume change constitutive model for clay minerals combining the effects of cation exchange capacity, density, water content, in-situ stress state, exchangeable-cations type and proportion, pore fluids, and the dissolved salts. Although in this paper, the developed protocol have been demonstrated for the gas shales, it can equally be used for several other fields involving the use of clay minerals such as agriculture, medicine, petroleum, environment, and geotechnical engineering.Ahn, S.Y., Zhu, M., 2017. Lowermost Cambrian acritarchs from the Yanjiahe Formation, South China: implication for defining the base of the Cambrian in the Yangtze Platform. Geological Magazine 154, 1217-1231. Asteridium–Heliosphaeridium–Comasphaeridium (AHC) acritarch assemblage is composed of common organic-walled microfossils in the basal Cambrian chert–phosphorite units in South China, indicating that the AHC assemblage can be a useful biostratigraphic tool for the Ediacaran–Cambrian boundary successions in the Yangtze Platform. To test the validity of the AHC acritarch assemblage as a biostratigraphic tool, the stratigraphic range of the AHC acritarch assemblage was confirmed, and its spatial and temporal relationships to other bio- and chemostratigraphic tools were analysed in the Yanjiahe Formation, Yangtze Gorges area, South China. The result shows that the AHC assemblage temporally correlates to the Anabarites trisulcatus–Protohertzina anabarica Assemblage Zone, and spatially correlates to the large negative carbon isotope anomaly of the lowermost Cambrian (BACE) in the Yanjiahe Formation. This implies that the radiation of phytoplankton occurred slightly before the radiation of the small shelly fossils, and the AHC acritarch assemblage can be another important chronological reference to the lowermost Cambrian successions in South China, and potentially to global correlations.Airapetian, V.S., Jackman, C.H., Mlynczak, M., Danchi, W., Hunt, L., 2017. Atmospheric beacons of life from exoplanets around G and K stars. Scientific Reports 7, Article 14141. current explosion in detection and characterization of thousands of extrasolar planets from the Kepler mission, the Hubble Space Telescope, and large ground-based telescopes opens a new era in searches for Earth-analog exoplanets with conditions suitable for sustaining life. As more Earth-sized exoplanets are detected in the near future, we will soon have an opportunity to identify habitale worlds. Which atmospheric biosignature gases from habitable planets can be detected with our current capabilities? The detection of the common biosignatures from nitrogen-oxygen rich terrestrial-type exoplanets including molecular oxygen (O2), ozone (O3), water vapor (H2O), carbon dioxide (CO2), nitrous oxide (N2O), and methane (CH4) requires days of integration time with largest space telescopes, and thus are very challenging for current instruments. In this paper we propose to use the powerful emission from rotational-vibrational bands of nitric oxide, hydroxyl and molecular oxygen as signatures of nitrogen, oxygen, and water rich atmospheres of terrestrial type exoplanets “highlighted” by the magnetic activity from young G and K main-sequence stars. The signals from these fundamental chemical prerequisites of life we call atmospheric “beacons of life” create a unique opportunity to perform direct imaging observations of Earth-sized exoplanets with high signal-to-noise and low spectral resolution with the upcoming NASA missions.Akinnifesi, J.O., Adebiyi, F.M., Olafisan, K.F., 2017. Structural characterization of asphaltenes derived from Nigerian bitumen using the x-ray diffraction technique. Petroleum Science and Technology 35, 1667-1672. asphaltenes consist of complex hydrocarbon molecules that pose a marked difficulty in the production of crude oils. They tend to flocculate and precipitate during oils refinery and this stimulates considerable interest in the elucidation of their molecular structure for improved processing. In this investigation, five bitumen samples obtained from oil sand outcrops at five localities in Nigeria were used. These were treated with n-pentane that necessitates the precipitation of asphaltene. The different asphaltene samples were analyzed by the x-ray diffraction technique to obtain their various structural parameters. The parameters were determined from the peaks of the gamma (?) band, graphene (c = c) or (002) band and the (10) or (11) band in the diffraction spectra of the respective samples. Slight variations in the distance between the aliphatic chains and the distance between the aromatic sheets were observed for three of the samples, while the remaining two presented significant variations in the structural parameters. Variations in the average number of carbon atoms per aromatic units correspond to the variation in the size and number of aromatic units and aliphatic chains. The variations consequently determined the level of processing necessary to improve the heavy oil (bitumen).Akkutlu, I.Y., Efendiev, Y., Vasilyeva, M., Wang, Y., 2017. Multiscale model reduction for shale gas transport in a coupled discrete fracture and dual-continuum porous media. Journal of Natural Gas Science and Engineering 48, 65-76. gas production from shale formations involves highly complex geological features consisting of fractures that are embedded spatially-distributed in a matrix made of organic and inorganic materials. In this paper, we develop a coupled multiscale and multi-continuum approach for simulating gas transport in the shale formation. The multiscale method allowed us to capture detailed interactions between the fractures and the background. For the fine-scale heterogeneities involving organic and inorganic materials distribution in the matrix, we use a dual-continuum approach. The matrix is coupled to the fractures by use of the Generalized Multiscale Finite Element Method (GMsFEM). In our previous work (Akkutlu et?al., 2016), we used a single-continuum background coupled to the fracture network. This paper presents a significant extension and considers dual-continuum media as a background. GMsFEM systematically identifies the fracture networks by constructing corresponding multiscale basis functions. GMsFEM also accurately represents the fractures interacting with the background media. Moreover, GMsFEM can handle any spatial fracture distributions and thus, it avoids the limitations of the multi-continuum approaches. Results show that the proposed numerical approach can accurately capture the interactions between the fractures and the multi-continuum model using a few multiscale basis functions.Al-Khdheeawi, E.A., Vialle, S., Barifcani, A., Sarmadivaleh, M., Iglauer, S., 2018. Effect of wettability heterogeneity and reservoir temperature on CO2 storage efficiency in deep saline aquifers. International Journal of Greenhouse Gas Control 68, 216-229. heterogeneity at various length scales is a well-established fact. This includes reservoir wettability ? a key factor influencing CO2 geo-storage efficiency and containment security ? which changes with depth, and is generally non-uniform due to different depositional environments and fluid flow paths over geological times. However, the effect of heterogeneous wettability distribution on CO2 storage efficiency is not understood. Moreover, there is a knowledge gap in terms of how temperature affects capillary and dissolution trapping, CO2 mobility and vertical CO2 migration distance, particularly when coupled with wettability heterogeneity effects. Thus, in this work we studied the effect of wettability heterogeneity and reservoir temperature on the vertical CO2 plume migration, and capillary and dissolution trapping capacities. Our results clearly show that both wettability heterogeneity and reservoir temperature have a significant effect on vertical CO2 migration, and the associated capillary and dissolution trapping mechanisms: both heterogeneously distributed wettability and higher temperature significantly accelerated the vertical CO2 migration, CO2 mobility and solubility trapping, while it reduced residual trapping. We thus conclude that wettability heterogeneity and reservoir temperature are important factors in the context of CO2 geo-storage, and that heterogeneous wettability and higher reservoir temperatures reduce storage capacity.Alcolea, M., Utrilla, P., Piqué, R., Laborda, R., Mazo, C., 2017. Fuel and acorns: Early Neolithic plant use from Cueva de Chaves (NE Spain). Quaternary International 457, 228-239. de Chaves is a particularly important archaeological site for the Early Neolithic of the northeast Iberian Peninsula. This study focuses on the archaeobotanical analysis of wood charcoals and charred fruits from two Neolithic levels dated from 5678 ± 50 to 5073 ± 107 cal BC. Charcoal analysis reveals the exploitation of firewood resources in different environments. A great variety of woody taxa and plant formations dominated by pines and oaks has been documented. The location of the archaeological site in a mid-mountain environment favors a mixed exploitation of resources in the valley and the mountains. Mesophytes indicate a relative humid environment where xerophytic and thermophilous trees and shrubs have an important presence. Taxonomic richness documented in the settlement provides an idea of long-term settling and development of diversified activities. The dramatic increase of colonizing secondary formations in the earliest level of occupation can only be explained by human intervention. According to pollen information human activity in the environment is well-documented since Early Neolithic that reveal the presence of several herbaceous plants (Plantago, Rumex, Chenopodiaceae, Asphodellus, etc). Among charred seeds we have only documented the presence of abundant and well-preserved acorns (Quercus sp.) but the presence of crops has not been attested just by indirect archaeological evidences.Alhuraishawy, A.K., Bai, B., Imqam, A., Wei, M., 2018. Experimental study of combining low salinity water flooding and preformed particle gel to enhance oil recovery for fractured carbonate reservoirs. Fuel 214, 342-350. recovery from carbonate reservoirs is usually low due to their extreme heterogeneity caused by natural fractures and the nature of the oil-wet matrix. Low salinity water flooding (LSWF) and preformed particle gels (PPG) control conformance are two novel technologies that have recently drawn great interest from the oil industry. Theoretically, LSWF can only increase displacement efficiency, and it has little or no effect on sweep efficiency; PPG can plug fractures, they can improve sweep efficiency, but they have little effect on displacement efficiency. We developed a cost-effective, novel, enhanced oil recovery (EOR) technology for carbonate reservoirs by coupling the two technologies into one process. The objective of this paper is to provide a comprehensive understanding of the combined technology and to demonstrate how the coupling method can improve oil recovery. The oil-wet carbonate cores provided a higher improved oil recovery than water-wet carbonate cores during LSWF. The decrease in fracture width resulted in a higher oil recovery factor. Compared to traditional bulk gel treatments, PPG forms stronger plugging but will not form an impermeable cake in the fracture surface; therefore, PPG allows low salinity water to penetrate into the matrix to modify its wettability, thereby producing more oil from the matrix. Results also show that oil recovery increased by 10% during LSWF after the second water flooding. Additionally, when PPGs were injected, another 4% of oil recovery was gained. As a result, the combined LSWF and PPG increased oil recovery by 18%. A full-factorial experimental design was performed to investigate the influence of the PPG-placed injection pressure (which refers to the maximum pressure used to inject PPG for each experiment), water salinity, and fracture width. Experimental results tell that PPG-placed injection pressure is the factor that strongly influences both oil recovery factor and residual resistance factor; fracture width is the least influential factor among the three. Experimental results prove that the coupled method bypasses the limitations of each method when used individually and improves both displacement and sweep efficiency.Ali, J., Cheang, U.K., Martindale, J.D., Jabbarzadeh, M., Fu, H.C., Jun Kim, M., 2017. Bacteria-inspired nanorobots with flagellar polymorphic transformations and bundling. Scientific Reports 7, Article 14098. controlled nanoscale robots have the potential to be used for both in vitro and in vivo biomedical applications. So far, the vast majority of reported micro- and nanoscale swimmers have taken the approach of mimicking the rotary motion of helical bacterial flagella for propulsion, and are often composed of monolithic inorganic materials or photoactive polymers. However, currently no man-made soft nanohelix has the ability to rapidly reconfigure its geometry in response to multiple forms of environmental stimuli, which has the potential to enhance motility in tortuous heterogeneous biological environments. Here, we report magnetic actuation of self-assembled bacterial flagellar nanorobotic swimmers. Bacterial flagella change their helical form in response to environmental stimuli, leading to a difference in propulsion before and after the change in flagellar form. We experimentally and numerically characterize this response by studying the swimming of three flagellar forms. Also, we demonstrate the ability to steer these devices and induce flagellar bundling in multi-flagellated nanoswimmers.Aljamaan, H., Al Ismail, M., Kovscek, A.R., 2017. Experimental investigation and Grand Canonical Monte Carlo simulation of gas shale adsorption from the macro to the nano scale. Journal of Natural Gas Science and Engineering 48, 119-137. paper sheds light on the potential of carbon storage and gas recovery from shale using pure and multicomponent sorption studies. A multi scale approach was adopted where experimental characterization at the core level was linked with a digital laboratory through molecular modeling to simulate and predict pure and multicomponent adsorption conditions that were hard to achieve in the lab. The sensitivity of shale physical properties to the gas mixture saturating the pore space was examined for possible carbon storage and enhanced gas shale recovery applications.A novel high precision volumetric gas adsorption apparatus was constructed in house to investigate multi-component gas sorption at the core level. The thermodynamically closed system allowed for simultaneous measurements of three fundamental rock properties at the core level including porosity, permeability and excess adsorption. Experiments were carried out to measure the preferential adsorption of different components in a gas mixture on intact core samples from the Haynesville and Barnett shale plays. Based on the pore size distribution (PSD) of the sample, the experimental observations were confirmed using a grand canonical Monte Carlo (GCMC) simulation employing a slit pore model composed of parallel planar graphitic surfaces.Experimental results revealed multi-layer adsorption coverage with CO2 in comparison to a mono-layer coverage with N2 and CH4. Mixed gas sorption measurements showed preferential adsorption of CO2 over CH4 as indicated by a selectivity coefficient greater than 1. GCMC simulations on pore sizes ranging from 1 nm to 50 nm were consistent with the core-scale experimental results and revealed an increasing selectivity for CO2 over CH4 in model shale pores. N2 injection, however, proved to be an unsuccessful enhanced gas recovery technique due to a preferential adsorption of CH4 over N2.Amador, E.S., Bandfield, J.L., Brazelton, W.J., Kelley, D., 2017. The Lost City hydrothermal field: A spectroscopic and astrobiological analogue for Nili Fossae, Mars. Astrobiology 17, 1138-1160. serpentinization is a critical process with respect to Earth's habitability and the Solar System. Exothermic serpentinization reactions commonly produce hydrogen as a direct by-product and typically produce short-chained organic compounds indirectly. Here, we present the spectral and mineralogical variability in rocks from the serpentine-driven Lost City Hydrothermal Field on Earth and the olivine-rich region of Nili Fossae on Mars. Near- and thermal-infrared spectral measurements were made from a suite of Lost City rocks at wavelengths similar to those for instruments collecting measurements of the martian surface. Results from Lost City show a spectrally distinguishable suite of Mg-rich serpentine, Ca carbonates, talc, and amphibole minerals. Aggregated detections of low-grade metamorphic minerals in rocks from Nili Fossae were mapped and yielded a previously undetected serpentine exposure in the region. Direct comparison of the two spectral suites indicates similar mineralogy at both Lost City and in the Noachian (4–3.7?Ga) bedrock of Nili Fossae, Mars. Based on mapping of these spectral phases, the implied mineralogical suite appears to be extensive across the region. These results suggest that serpentinization was once an active process, indicating that water and energy sources were available, as well as a means for prebiotic chemistry during a time period when life was first emerging on Earth. Although the mineralogical assemblages identified on Mars are unlikely to be directly analogous to rocks that underlie the Lost City Hydrothermal Field, related geochemical processes (and associated sources of biologically accessible energy) were once present in the subsurface, making Nili Fossae a compelling candidate for a once-habitable environment on Mars.Amiri, A., Ghaemi, F., 2017. Graphene grown on stainless steel mesh as a highly efficient sorbent for sorptive microextraction of polycyclic aromatic hydrocarbons from water samples. Analytica Chimica Acta 994, 29-37. this study, graphene grown on stainless steel mesh efficiently incorporates the advanced properties of graphene in the form of an ultra-thin coating with the open geometry of the substrate, resulting in a highly sensitive and fast sorptive device capable of extracting target analytes directly from sample matrices. The synthesis of graphene on the stainless steel mesh was confirmed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The advantages of the new microextraction device have been investigated for the determination of polycyclic aromatic hydrocarbons (PAHs) in environmental water samples in combination with gas chromatography–flame ionization detector (GC–FID). The factors affecting the extraction efficiency such as stirring speed, extraction time, ionic strength and desorption conditions, were investigated and the optimal extraction conditions were established. Under the optimal extraction condition, linearity was in the range of 0.003–100?ng?mL?1 with a correlation coefficient of 0.9923–0.9985. The limits of detection (LODs) of the developed method are obtained between 1 and 3?pg?mL?1. The repeatability was assessed at two concentration levels (0.01 and 10?ng?mL?1) and the relative standard deviations (RSDs) obtained were 4.9–8.7%. The preparation reproducibility of sorbent device, evaluated with the RSDs, was in the range of 7.3–10.2% (n?=?5) in one batch, and 8.3–11.0% (n?=?5) among different batches. Finally, the proposed method is applied for the determination of the target PAHs in the real water samples.Amon, D.J., Gobin, J., Van Dover, C.L., Levin, L.A., Marsh, L., Raineault, N.A., 2017. Characterization of methane-seep communities in a deep-sea area designated for oil and natural gas exploitation off Trinidad and Tobago. Frontiers in Marine Science 4, 342. doi: 10.3389/fmars.2017.00342. of the deep ocean (>200 m) is taking on added importance as human development encroaches. Despite increasing oil and natural gas exploration and exploitation, the deep ocean of Trinidad and Tobago is almost entirely unknown. The only scientific team to image the deep seafloor within the Trinidad and Tobago Exclusive Economic Zone was from IFREMER in the 1980s. That exploration led to the discovery of the El Pilar methane seeps and associated chemosynthetic communities on the accretionary prism to the east of Trinidad and Tobago. In 2014, the E/V Nautilus, in collaboration with local scientists, visited two previously sampled as well as two unexplored areas of the El Pilar site between 998 and 1629 m depth using remotely operated vehicles. Eighty-three megafaunal morphospecies from extensive chemosynthetic communities surrounding active methane seepage were observed at four sites. These communities were dominated by megafaunal invertebrates including mussels (Bathymodiolus childressi), shrimp (Alvinocaris cf. muricola), Lamellibrachia sp. 2 tubeworms, and Pachycara caribbaeum. Adjacent to areas of active seepage was an ecotone of suspension feeders including Haplosclerida sponges, stylasterids and Neovermilia serpulids on authigenic carbonates. Beyond this were large Bathymodiolus shell middens. Finally there was either a zone of sparse octocorals and other non-chemosynthetic species likely benefiting from the carbonate substratum and enriched production within the seep habitat, or sedimented inactive areas. This paper highlights these ecologically significant areas and increases the knowledge of the biodiversity of the Trinidad and Tobago deep ocean. Because methane seepage and chemosynthetic communities are related to the presence of extractable oil and gas resources, development of best practices for the conservation of biodiversity in Trinidad and Tobago waters within the context of energy extraction is critical. Potential impacts on benthic communities during oil and gas activities will likely be long lasting and include physical disturbance during drilling among others. Recommendations for the stewardship of these widespread habitats include: (1) seeking international cooperation; (2) holding wider stakeholder discussions; (3) adopting stringent environmental regulations; and (4) increasing deep-sea research to gather crucial baseline data in order to conduct appropriate marine spatial planning with the creation of marine protected areas.An, S., Yao, J., Yang, Y., Zhang, W., Zhao, J., Li, A., 2017. The microscale analysis of reverse displacement based on digital core. Journal of Natural Gas Science and Engineering 48, 138-144. recovery of the reservoir is always the center of development because of its renewable characteristic. There are many methods designed to enhance the development of residual hydrocarbon, such as water flooding, polymer flooding, and the adjustment of well pattern. But the microscale mechanisms of fluid flow in porous media is still ambiguous, especially for reverse flooding. So in-situ displacement experiment based on CT scanning was designed in this paper to analyze the trapped oil after various flooding. In pore scale level, the total number of residual oil and average volume were counted. For further observing distribution changes, we classified the shape of residual oil based on shape factor and Euler number, and calculated the corresponding proportion. These results show that the adjustment of flow streamline can effectively improve oil recovery after water forward flooding and polymer displacement.Anderson, R.P., Macdonald, F.A., Jones, D.S., McMahon, S., Briggs, D.E.G., 2017. Doushantuo-type microfossils from latest Ediacaran phosphorites of northern Mongolia. Geology 45, 1079-1082. of the latest Ediacaran upper Khesen Formation in the Khuvsgul Group of northern Mongolia preserve a newly discovered, three-dimensionally phosphatized Doushantuo-type microfossil assemblage. Eight genera include the second occurrence of the putative multicellular fossil animal embryo Megasphaera outside South China, the Doushantuo-Pertatataka–type acanthomorphic acritarchs h Cavaspina, and Variomargosphaeridium, and the possible alga Archaeophycus yunnanensis. The assemblage occurs in the lowermost phosphorite horizon in foreland basin deposits on the Khuvsgul terrane; lithostratigraphic and δ13C correlation with the Zavkhan terrane of southwestern Mongolia establishes a latest Ediacaran age for the fossiliferous phosphorites. Thus, this is the youngest Doushantuo-type assemblage yet reported. It extends the range of Megasphaera, and fills a gap in the record of phosphatized embryo-like forms between the ca. 600 Ma Doushantuo Weng’an biota and Cambrian examples. The Khesen fossil assemblage emphasizes the potential of Mongolian phosphorites to provide new paleontological data on the Ediacaran-Cambrian transition, and to resolve the phylogenetic debate surrounding Megasphaera embryo-like taxa.Angle, J.C., Morin, T.H., Solden, L.M., Narrowe, A.B., Smith, G.J., Borton, M.A., Rey-Sanchez, C., Daly, R.A., Mirfenderesgi, G., Hoyt, D.W., Riley, W.J., Miller, C.S., Bohrer, G., Wrighton, K.C., 2017. Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions. Nature Communications 8, Article 1567. current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur in anoxic habitats. In contrast, here we show clear geochemical and biological evidence for methane production in well-oxygenated soils of a freshwater wetland. A comparison of oxic to anoxic soils reveal up to ten times greater methane production and nine times more methanogenesis activity in oxygenated soils. Metagenomic and metatranscriptomic sequencing recover the first near-complete genomes for a novel methanogen species, and show acetoclastic production from this organism was the dominant methanogenesis pathway in oxygenated soils. This organism, Candidatus Methanothrix paradoxum, is prevalent across methane emitting ecosystems, suggesting a global significance. Moreover, in this wetland, we estimate that up to 80% of methane fluxes could be attributed to methanogenesis in oxygenated soils. Together, our findings challenge a widely held assumption about methanogenesis, with significant ramifications for global methane estimates and Earth system modeling.Aramendia, J., Gomez-Nubla, L., Castro, K., Fdez-Ortiz de Vallejuelo, S., Arana, G., Maguregui, M., Baonza, V.G., Medina, J., Rull, F., Madariaga, J.M., 2018. Overview of the techniques used for the study of non-terrestrial bodies: Proposition of novel non-destructive methodology. TrAC Trends in Analytical Chemistry 98, 36-46. and impact glasses have been largely analysed using different techniques, but most studies have been focused on their geological–mineralogical characterization and isotopic ratios, mainly of a destructive nature. However, much more information can be gained by applying novel non-destructive analytical procedures and techniques that have been scarcely used to analyse these materials. This overview presents some new methodologies to study these materials and compares these new approaches with the commonly used ones. Techniques such as X-Ray Fluorescence (XRF) and Laser Induced Breakdown Spectroscopy (LIBS), for elemental characterization, the hyphenated Raman spectroscopy-SEM/EDS and the combination of them, allow extracting simultaneous information from elemental, molecular and structural data of the studied sample; furthermore, the spectroscopic image capabilities of such techniques allow a better understanding of the mineralogical distribution.Arzhanov, M.M., Mokhov, I.I., 2017. Stability of continental relic methane hydrates for the Holocene climatic optimum and for contemporary conditions. Doklady Earth Sciences 476, 1163-1167. of the thermal regime of permafrost soils has made it possible to estimate the stability of methane hydrates in the continental permafrost in the Northern Eurasian and North American regions with the risk of gas emissions into the atmosphere as a result of possible dissociation of gas hydrates in the Holocene Optimum and under contemporary climatic conditions [1, 2]. Original Russian Text ? M.M. Arzhanov, I.I. Mokhov, 2017, published in Doklady Akademii Nauk, 2017, Vol. 476, No. 4, pp. 456–460.Asadi, F., Phan, C.M., Obanijesu, E.O., 2017. Biodegradation of diesel oil in marine environment by a floating water droplet. International Journal of Environmental Science and Technology 14, 2323-2330. oil is one of the derivatives of crude oil which resistance to biodegradation due to its complex structure and low solubility in water. A novel concept of enhancement of diesel degradation using floating water droplet is proposed and being investigated to address some key challenges encountered in diesel oil spillages in the aqueous area and wetlands. This study aims to increase the floatability of a floating water droplet on oil. A droplet containing a mixed consortium of 60 different hydrocarbon degrading bacteria and sodium dodecyl sulfate as a surfactant was deposited on the diesel oil surface. Contact angle and contact radius were monitored to observe the effect of bacterial activities on the droplet. The behavior of this droplet on diesel oil was different to a previous study with paraffin oil. In particular, the floatability, bacterial growth and biofilm formation demonstrate significant deviation due to the diesel interactions with biological processes. Nevertheless, the results show this method increase microbial activities within the droplet. The result verifies the applicability of the floating water droplet as an environmentally friendly method for diesel oil spillages.Assun??o, A.W.d.A., Souza, B.P.d., Silva, W.T.L.d., Cunha-Santino, M.B., Bianchini, I., 2017. Molecular changes of aquatic humic substances formed from four aquatic macrophytes decomposed under different oxygen conditions. Chemistry and Ecology 33, 918-931. macrophytes’ decomposition is a source of recalcitrant carbon in the long term contributing to humic substances (HS) formation. Understanding the influence of plant detritus quality and oxygen availability over molecular changes of these compounds provides ecological information related to their cycling. This study described the molecular variation of dissolved HS from Eichhornia azurea, Egeria najas, Oxycaryum cubense and Salvinia molesta decomposition under aerobic and anaerobic conditions. The aquatic HS formed from the four aquatic macrophytes showed similar features (e.g. molecular weight and aromaticity). This fact indicates little influence of the detritus quality or availability of oxygen on the fulvic acids (FA) and humic acid characteristics. Under aerobic condition a decrease in the polysaccharides content in FA occurred. HS from E. najas were related to less-recalcitrant features, while HS from S. molesta were related to recalcitrant.Asurmendi, E., Sánchez, M.L., Fennell, L., 2017. Neuquén Group (Upper Cretaceous): A case of underfilled-overfilled cycles in an Andean foreland basin, Neuquén basin, Argentina. Journal of South American Earth Sciences 80, 444-459. Nenquén Group was deposited during a period dominated by the Cretaceous Greenhouse and can be divided in three cycles correlated with large-scale changes in the evolution of the Andean foreland basin. The filling of the Neuquén Group is constituted by a complete cycle and two incomplete cycles of underfilled-overfilled, separated by first-order discontinuities assigned to the uplift of the Agrio fold-and-thrust belt during the Chasca/Catequil, Mid Ocean Ridge (CCMOR) collision, coinciding with first-order climatic changes within the Cretaceous greenhouse cycle. The Candeleros Formation in the base of this group was deposited in late underfilled conditions, showing prominent forebulge zones. It is demonstrated that during the Albian, with the cratonward migration of the uplifting forebulge zones, the axis of backbulge zones also migrated cratonwards and a wide uplifted forebulge zone was formed. On top, the Huincul Formation was deposited in an overfilled period without orogenic load, while the Cerro Lisandro Formation was deposited in early underfilled conditions with orogenic load. The Río Neuquén Subgroup started with a late underfilled period (Portezuelo Formation -second-order discontinuity), and after wards the Plottier Formation was deposited in an overfilled period without orogenic load. Finally, the Río Colorado Subgroup was deposited under late and early underfilled conditions (Bajo de la Carpa and Anacleto Formations respectively).Ayoib, A., Hashim, U., Gopinath, S.C.B., Md Arshad, M.K., 2017. DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods. Applied Microbiology and Biotechnology 101, 8077-8088. review covers a developmental progression on early to modern taxonomy at cellular level following the advent of electron microscopy and the advancement in deoxyribonucleic acid (DNA) extraction for expatiation of biological classification at DNA level. Here, we discuss the fundamental values of conventional chemical methods of DNA extraction using liquid/liquid extraction (LLE) followed by development of solid-phase extraction (SPE) methods, as well as recent advances in microfluidics device-based system for DNA extraction on-chip. We also discuss the importance of DNA extraction as well as the advantages over conventional chemical methods, and how Lab-on-a-Chip (LOC) system plays a crucial role for the future achievements.Babich, L.P., 2017. Radiocarbon production by thunderstorms. Geophysical Research Letters 44, 11,191-11,200. view of the neutron flux enhancements observed in thunderstorms, a contribution of thunderstorm neutrons to atmospheric radiocarbon (isotope 146C ) production is analyzed in connection with the archaeometry. Herein, estimates of neutron fluence per lightning electromagnetic pulse in regions with severe thunderstorm activity, at which a local rate of the 146C production is comparable to the observed rates, are shown to be consistent with the measured magnitudes of thunderstorm neutron fluence. At present, available observations of atmospheric neutron and parent gamma ray flashes correlated with thunderstorms do not allow making final conclusions about thunderstorm contributions to 146C production. For this, numerous studies of high-energy phenomena in thunderstorms are required, especially in the tropical belt where the thunderstorm activity is especially severe and where the 146C production by galactic cosmic rays is almost independent of the solar activity disturbing the Earth's magnetic field shielding the Earth from cosmic rays.Baciu, C., Ionescu, A., Etiope, G., 2018. Hydrocarbon seeps in Romania: Gas origin and release to the atmosphere. Marine and Petroleum Geology 89, Part 1, 130-143. is one of the countries with the largest number of surface hydrocarbon seeps in the world. Seeps may be an important tool for petroleum exploration as they can provide useful information regarding source rock maturity, reservoir quality, and secondary gas alterations. Seeps also represent an important source of methane, ethane, and propane to the atmosphere. To date, the genetic characterization of natural gas in Romania has only been based on molecular composition, without isotopic information. Here, we present an overview of investigations performed over the past 15 years for the main Romanian hydrocarbon seeps, and report the molecular and isotopic compositions of gas, and the fluxes of methane, ethane and propane to the atmosphere. We assessed gas origin and secondary alterations in 17 seeps from several Romanian petroleum systems, and potential source rock types and maturity have been evaluated. As previously inferred, gas within the Transylvanian Basin is largely microbial, but also displays indications of a minor thermogenic component that is likely related to a deep petroleum system. Carpathian Flysch and Foredeep petroleum systems contain thermogenic gas, with clear evidence of biodegradation in some cases. Thermogenic gas generation modelling and maturity plots suggest that most Romanian gases originate from mature type II and III kerogen (%Ro: 2–3). For cases of high flux seeps, gas has the same hydrocarbon molecular composition as the reservoir, while in weaker seeps and some mud volcanoes gas is altered by molecular fractionation (a loss of C2 and C3 during gas migration). Gas seep geochemistry, in general, reflects the different geological and maturity conditions of basins where seeps are located. A vertical sequence of petroleum systems has been suggested in some basins by seeps displaying different maturity and secondary alterations. Measurements of methane flux to the atmosphere from 94 seeps display a wide range of emissions (kilograms to hundreds of tons per year), with a total, conservative estimated methane emission of approximately 3000 t y?1. Microseepage may also release a similar quantity of methane. Consequently, seepage is a substantial contributor to natural emissions of methane on a national level.Backeberg, N.R., Iacoviello, F., Rittner, M., Mitchell, T.M., Jones, A.P., Day, R., Wheeler, J., Shearing, P.R., Vermeesch, P., Striolo, A., 2017. Quantifying the anisotropy and tortuosity of permeable pathways in clay-rich mudstones using models based on X-ray tomography. Scientific Reports 7, Article 14838. permeability of shales is important, because it controls where oil and gas resources can migrate to and where in the Earth hydrocarbons are ultimately stored. Shales have a well-known anisotropic directional permeability that is inherited from the depositional layering of sedimentary laminations, where the highest permeability is measured parallel to laminations and the lowest permeability is perpendicular to laminations. We combine state of the art laboratory permeability experiments with high-resolution X-ray computed tomography and for the first time can quantify the three-dimensional interconnected pathways through a rock that define the anisotropic behaviour of shales. Experiments record a physical anisotropy in permeability of one to two orders of magnitude. Two- and three-dimensional analyses of micro- and nano-scale X-ray computed tomography illuminate the interconnected pathways through the porous/permeable phases in shales. The tortuosity factor quantifies the apparent decrease in diffusive transport resulting from convolutions of the flow paths through porous media and predicts that the directional anisotropy is fundamentally controlled by the bulk rock mineral geometry. Understanding the mineral-scale control on permeability will allow for better estimations of the extent of recoverable reserves in shale gas plays globally.Baglai, A., Gargano, A.F.G., Jordens, J., Mengerink, Y., Honing, M., van der Wal, S., Schoenmakers, P.J., 2017. Comprehensive lipidomic analysis of human plasma using multidimensional liquid- and gas-phase separations: Two-dimensional liquid chromatography–mass spectrometry vs. liquid chromatography–trapped-ion-mobility–mass spectrometry. Journal of Chromatography A 1530, 90-103. advancements in separation science have resulted in the commercialization of multidimensional separation systems that provide higher peak capacities and, hence, enable a more-detailed characterization of complex mixtures. In particular, two powerful analytical tools are increasingly used by analytical scientists, namely online comprehensive two-dimensional liquid chromatography (LC × LC, having a second-dimension separation in the liquid phase) and liquid chromatography-ion mobility-spectrometry (LC-IMS, second dimension separation in the gas phase).The goal of the current study was a general assessment of the liquid-chromatography–trapped-ion-mobility–mass spectrometry (LC-TIMS–MS) and comprehensive two-dimensional liquid chromatography–mass spectrometry (LC × LC–MS) platforms for untargeted lipid mapping in human plasma.For the first time trapped-ion-mobility spectrometry (TIMS) was employed for the separation of the major lipid classes and ion-mobility-derived collision-cross-section values were determined for a number of lipid standards. The general effects of a number of influencing parameters have been inspected and possible directions for improvements are discussed.We aimed to provide a general indication and practical guidelines for the analyst to choose an efficient multidimensional separation platform according to the particular requirements of the application. Analysis time, orthogonality, peak capacity, and an indicative measure for the resolving power are discussed as main characteristics for multidimensional separation systems.Bahman, J., Sharifi, K., Nasiri, M., Haghighi Asl, M., 2018. Development of a Log-Log scaling law approach for prediction of asphaltene precipitation from crude oil by n-alkane titration. Journal of Petroleum Science and Engineering 160, 393-400. of the most significant problems that petroleum and gas industries tend to know much more is the behavior and the weight percent of Asphaltene precipitation in crude oils. A large number of researchers have been scrutinizing to develop new models for estimating Asphaltene precipitation. Of available approaches, scaling law which is not only relatively simple but also faster than other conventional mathematical methods is promising. In this study, the potential of Ashoori's scaling equation was firstly examined in detail. Afterwards, to solve its drawbacks, an alternative model was formulated exploiting the logarithm operator. Indeed, in this communication, the authors tried to drive a polynomial model that can estimate the amount of Asphaltene precipitation at all dilution ratio ranges with higher accuracy. To get proper outputs and to compare its results with Ashoori's and Rassamdana's outcomes, the polynomial function was fitted to experimental data points. The R2 (R-squared) of the present model, namely Log-Log scaling law, was about 0.999, and the results indicate that the Log-Log scaling law has better performance than that determined by others for prediction of Asphaltene precipitation from crude oil by n-alkane titration.Bai, L., Smuts, J., Schenk, J., Cochran, J., Schug, K.A., 2018. Comparison of GC-VUV, GC-FID, and comprehensive two-dimensional GC–MS for the characterization of weathered and unweathered diesel fuels. Fuel 214, 521-527. of diesel fuels and degraded diesel fuels in the environment is a common issue nowadays. Providing definitive information for litigation regarding determination and distinguishing the origins or sources of fuel spill contamination has been a significant need among the environmental forensics community. Diesel fuels contain more complex chemicals and isomers compared to gasoline. Here, we compare the use of gas chromatography – vacuum ultraviolet spectroscopy (GC-VUV), gas chromatography – flame ionization detection (GC-FID), and comprehensive two-dimensional gas chromatography – mass spectrometry (GC?×?GC–MS) for diesel fuel and weathered diesel fuel analysis in fingerprinting biomarkers. GC-VUV is a relatively new technique that can rapidly acquire full absorption spectra from 120 to 240?nm. Class information about individual components is readily obtained based on reference to a library of matched spectra. Direct comparison of GC-VUV, GC-FID, and GC?×?GC–MS was undertaken to identify different classes of compounds and biomarkers. Using GC-VUV, numerous peaks representing minor and major components were classified into different classes by applying spectral filters and, in some cases, spectral deconvolution. Isoprenoid biomarkers, such as pristane and phytane, and their ratios with n-alkanes, C17 and C18, respectively, were determined The biomarker ratio results from GC-VUV matched well with both GC-FID and GC?×?GC–MS. About 5%–20% difference in measured biomarker ratios were obtained for a series of commercial weathered diesel standard samples, which is good enough to allow the discrimination of different weathered diesel samples, according to prior literature.Bai, Y., Liu, Z., Sun, P., Liu, R., Hu, X., Zhou, R., Xu, Y., Zhao, H., Wang, J., 2017. Diverse sedimentary conditions during deposition of coal and oil shale from the Meihe Basin (Eocene, NE China). Journal of Sedimentary Research 87, 1100-1120. Meihe Basin in northeastern China is a normal-fault-controlled basin filled with Eocene nonmarine deposits, the sediments assigned to the Meihe Formation. Sediment grain-sizes, core study, well-log analysis and micropetrographic study combined with sedimentary facies analysis indicate that the main sedimentary facies of the Meihe Basin represent fan-delta, lake, and turbidite deposits. Thick coal seams that are mainly distributed in the eastern part of the studied area were deposited in the swamp facies of the Lower Coal-Bearing Member. Oil shale was mainly deposited in the deep lake represented by the Mudstone Member, and is mainly distributed in the southern part of the studied area. In the Lower Coal-Bearing Member, organic-rich sediments are characterized by TOC content between 0.6 wt.% and 43.1 wt.% and contain Type II and III kerogen. The thick coal seams are the result of high land-plant productivity and good preservation conditions. Thin coal seams in the fan-delta plain resulted from the migration and erosion of the fan-delta channel. In the shallow lake and fan-delta front, limited productivity coupled with dilution by inorganic matter resulted in lower organic-matter content in the Mudstone Member. Oil shale and mudstone rich in organic matter were deposited in a deep lake with an average TOC content of 3.4 wt.%. The origin of the organic matter was mainly algae and aquatic plants mixed with land plants. The improved preservation conditions and high bioproductivity in this environment resulted in three oil-shale layers in the lower part of this sedimentary succession.Three coal-bearing and oil-shale-bearing fault basins lie adjacent to the Dunhua–Mishan Fault zone, among which the Fushun Basin is located in the southwest, the Meihe Basin is in the middle, and the Huadian Basin is in the southeast. From the Fushun Basin to the Huadian Basin, the oil shale and coal seams have distinct sedimentation characters laterally. Vertically in each basin, the organic-matter sources all have the same variation trend from land plants to land plants mixed with algae to algae then to algae mixed with land plants, and the TOC content also shows a similar trend from high to medium-high then to low in each basin.Baia, L.V., Souza, W.C., de Souza, R.J.F., Veloso, C.O., Chiaro, S.S.X., Figueiredo, M.A.G., 2017. Removal of sulfur and nitrogen compounds from diesel oil by adsorption using clays as adsorbents. Energy & Fuels 31, 11731-11742. specifications for sulfur compounds content and the need to use oils with large amount of nitrogen compounds are challenges for fuel producers. Adsorption is an alternative process to remove sulfur and nitrogen compounds and clays are promising adsorbents for this removal. In this work, the adsorption performance of different commercial clays—Clay A (attapulgite), Clay B (bentonite), and Clay C (bentonite)—for the removal of sulfur and nitrogen compounds from a real diesel stream was studied through kinetic and isothermal experiments. The bentonite clays showed the best adsorptive capacity for the removal of sulfur and nitrogen compounds, probably due to the presence of Br?nsted acid sites. The highest adsorption capacity was observed for Clay B: 0.174 mol kg–1 for sulfur compounds and 0.127 mol kg–1 for nitrogen compounds. Clay A was more selective to the removal of nitrogen compounds. Equilibrium data showed that adsorbate–absorbate and adsorbate–surface interactions predominate for sulfur and nitrogen compounds, respectively, for Clay A and Clay B.Baldini, J.U.L., Brown, R.J., Mawdsley, N., 2017. Re-evaluating the link between the Laacher See volcanic eruption and the Younger Dryas. Climate of the Past Discussions 2017, 1-22. Younger Dryas is the most well-documented millennial-scale cooling event of the Quaternary, but the mechanisms responsible for its initiation remain elusive. Here we use a recently revised chronology for the GISP2 ice core ion dataset to identify a large volcanic sulphur spike coincident with both the sulphur-rich Laacher See volcanic eruption and the onset of Younger Dryas-related cooling (GS-1) in Greenland. Lake sediment and stalagmite records confirm that the eruption's timing was indistinguishable from the onset of cooling across the North Atlantic, but that it preceded westerly wind repositioning over central Europe by ~?200 years. We suggest that the initial short-lived volcanic sulphate aerosol cooling was amplified by oceanic circulation shifts or sea ice expansion, gradually cooling the North Atlantic region and incrementally shifting the mid-latitude westerlies to the south. The aerosol-related cooling probably only lasted 2–4 years, and the majority of Younger Dryas-related cooling was instead due to this positive feedback, which was particularly effective during the intermediate ice volume conditions characteristic of ~?13?ka?BP. We conclude that the large and sulphur-rich Laacher See eruption should be considered a viable trigger for the Younger Dryas.Baldwin, P.R., Tan, Y.Z., Eng, E.T., Rice, W.J., Noble, A.J., Negro, C.J., Cianfrocco, M.A., Potter, C.S., Carragher, B., 2018. Big data in cryoEM: automated collection, processing and accessibility of EM data. Current Opinion in Microbiology 43, 1-8. scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ～10–100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing.Basirat, F., Yang, Z., Niemi, A., 2017. Pore-scale modeling of wettability effects on CO2–brine displacement during geological storage. Advances in Water Resources 109, 181-195. properties of reservoir rocks and caprocks can vary significantly, and they strongly influence geological storage of carbon dioxide in deep saline aquifers, during which CO2 is supposed to displace the resident brine and to become permanently trapped. Fundamental understanding of the effect of wettability on CO2–brine displacement is thus important for improving storage efficiency and security. In this study, we investigate the influence of wetting properties on two-phase flow of CO2 and brine at the pore scale. A numerical model based on the phase field method is implemented to simulate the two-phase flow of CO2–brine in a realistic pore geometry. Our focus is to study the pore-scale fluid-fluid displacement mechanisms under different wetting conditions and to quantify the effect of wettability on macroscopic parameters such as residual brine saturation, capillary pressure, relative permeability, and specific interfacial area. Our simulation results confirm that both the trapped wetting phase saturation and the normalized interfacial area increase with decreasing contact angle. However, the wetting condition does not appear to influence the CO2 breakthrough time and saturation. We also show that the macroscopic capillary pressures based on the pressure difference between inlet and outlet can differ significantly from the phase averaging capillary pressures for all contact angles when the capillary number is high (log Ca?>??5). This indicates that the inlet–outlet pressure difference may not be a good measure of the continuum-scale capillary pressure. In addition, the results show that the relative permeability of CO2 can be significantly lower in strongly water-wet conditions than in the intermediate-wet conditions.Bassez, M.-P., 2017. Anoxic and oxic oxidation of rocks containing Fe(II)Mg-silicates and Fe(II)-monosulfides as source of Fe(III)-minerals and hydrogen. Geobiotropy. Origins of Life and Evolution of Biospheres 47, 453-480. this article, anoxic and oxic hydrolyses of rocks containing Fe (II) Mg-silicates and Fe (II)-monosulfides are analyzed at 25?°C and 250–350?°C. A table of the products is drawn. It is shown that magnetite and hydrogen can be produced during low-temperature (25?°C) anoxic hydrolysis/oxidation of ferrous silicates and during high-temperature (250?°C) anoxic hydrolysis/oxidation of ferrous monosulfides. The high-T (350?°C) anoxic hydrolysis of ferrous silicates leads mainly to ferric oxides/hydroxides such as the hydroxide ferric trihydroxide, the oxide hydroxide goethite/lepidocrocite and the oxide hematite, and to Fe(III)-phyllosilicates. Magnetite is not a primary product. While the low-T (25?°C) anoxic hydrolysis of ferrous monosulfides leads to pyrite. Thermodynamic functions are calculated for elementary reactions of hydrolysis and carbonation of olivine and pyroxene and E-pH diagrams are analyzed. It is shown that the hydrolysis of the iron endmember is endothermic and can proceed within the exothermic hydrolysis of the magnesium endmember and also within the exothermic reactions of carbonations. The distinction between three products of the iron hydrolysis, magnetite, goethite and hematite is determined with E-pH diagrams. The hydrolysis/oxidation of the sulfides mackinawite/troilite/pyrrhotite is highly endothermic but can proceed within the heat produced by the exothermic hydrolyses and carbonations of ferromagnesian silicates and also by other sources such as magma, hydrothermal sources, impacts. These theoretical results are confirmed by the products observed in several related laboratory experiments. The case of radiolyzed water is studied. It is shown that magnetite and ferric oxides/hydroxides such as ferric trihydroxide, goethite/lepidocrocite and hematite are formed in oxic hydrolysis of ferromagnesian silicates at 25?°C and 350?°C. Oxic oxidation of ferrous monosulfides at 25?°C leads mainly to pyrite and ferric oxides/hydroxides such as ferric trihydroxide, goethite/lepidocrocite and hematite and also to sulfates, and at 250?°C mainly to magnetite instead of pyrite, associated to the same ferric oxides/hydroxides and sulfates. Some examples of geological terrains, such as Mawrth Vallis on Mars, the Tagish Lake meteorite and hydrothermal venting fields, where hydrolysis/oxidation of ferromagnesian silicates and iron(II)-monosulfides may occur, are discussed. Considering the evolution of rocks during their interaction with water, in the absence of oxygen and in radiolyzed water, with hydrothermal release of H2 and the plausible associated formation of components of life, geobiotropic signatures are proposed. They are mainly Fe(III)-phyllosilicates, magnetite, ferric trihydroxide, goethite/lepidocrocite, hematite, but not pyrite.Basu, H., Dandele, P.S., Kumar, K.R., Achar, K.K., Umamaheswar, K., 2017. Geochemistry of black shales from the Mesoproterozoic Srisailam Formation, Cuddapah basin, India: Implications for provenance, palaeoweathering, tectonics, and timing of Columbia breakup. Chemie der Erde - Geochemistry 77, 596-613. Mesoproterozoic Srisailam Formation, exposed along the northern part of the Cuddapah basin, India, comprises mainly medium- to fine-grained siliciclastics, and is devoid of any carbonate sediment. Preliminary sedimentological studies helped in recognizing fifteen distinct facies (five facies associations) in Chitrial outlier of the Srisailam Formation deposited in continental half-graben basin(s). Black shales (sensu lato) are minor components of the Srisailam Formation, and inferred to have deposited in deep lacustrine and prodelta facies of the half-graben(s). The black shales show restricted thickness (up to 29.0 m), and are characterized by overall high ‘black shale' to ‘total shale' ratio (>0.51). Their geochemical characteristics were studied to constrain provenance, palaeoclimate, and tectonic setting of deposition of the Srisailam Formation. Further, an attempt has been made to use the Srisailam black shales as proxy for constraining the timing of breakup of the supercontinent Columbia.The Srisailam black shales are geochemically quite distinct. At similar SiO2 contents they are considerably different from PAAS. They are characterized by considerably lower ΣREE (Av. 136.0 ± 50.4 ppm) but a more conspicuous negative Eu-anomaly (Av. 0.34 ± 0.09) than PAAS. Al2O3/TiO2 and TiO2/Zr ratios coupled with Eu/Eu*, GdCN/YbCN, La/Sc, Th/Sc, and Th/Cr ratios suggest their derivation from granite and granodiorite. The CIA values (65–90, Av. 72 ± 9) as a whole indicate moderate chemical weathering under semiarid climate. Discriminating geochemical parameters indicate passive margin depositional setting. The combined sedimentological and geochemical characteristics reveal deposition of the Srisailam sediments in continental rift basin(s).Thick succession of black shales (with high CIA values) that deposited with shelf carbonates proxy for mantle superplume and supercontinent breakup events. The sedimentological characteristics and geochemical data of the Srisailam black shales plausibly exclude any large-scale breakup of Columbia during the interval (1400–1327 Ma) of deposition of the Srisailam Formation.Bataineh, M., Arabi, A.A., Iqbal, J., Howari, F.M., Brack, W., 2017. Method development for selective and nontargeted identification of nitro compounds in diesel particulate matter. Energy & Fuels 31, 11615-11626. compounds are associated with a host of adverse human health and ecological outcomes; however, current methods of detection are limited by the lack of accuracy for the nontargeted identification of nitro compounds. This paper describes the development of a novel, accurate, and selective method of identifying nitro compounds, especially nitro polycyclic aromatic hydrocarbons (PAHs), in complex soot mixtures. For the first time, high-performance liquid chromatography was used in combination with Orbitrap mass spectrometry for the nontargeted identification of nitro compounds. This method was validated on a mixture of 84 standard molecules containing 23 nitro compounds and then applied to a complex soot sample, the National Institute of Standards and Technology standard reference material (SRM) 1650a, to successfully identify 105 masses, 62% of which were monosubstituted nitro compounds. All nitro compounds reported in the latest certificate of analysis (COA) for SRM 1650b were successfully identified except for 1,3-dinitropyrene and 1,6-dinitropyrene. Compounds not reported in the COA of the SRM 1650b, including but not limited to 1,8-dinitropyrene, alkylated nitro-molecules of all masses in the COA of SRM 1650b, nitro-phenylnaphthalene isomers, dinitronaphthalene, nitro-phenols, nitro-keto-PAHs, nitro-carboxylic-PAHs, and other nitro partial polar compounds, were also tentatively identified. Future work will consider a larger set of classes, including isomers. This will help identify the chemical composition of mixtures in order to take proactive approaches to prevent health and environmental hazards.Baton, F., Nguyen Tu, T.T., Derenne, S., Delorme, A., Delarue, F., Dufraisse, A., 2017. Tree-ring δ13C of archeological charcoals as indicator of past climatic seasonality. A case study from the Neolithic settlements of Lake Chalain (Jura, France). Quaternary International 457, 50-59. fragments from the Neolithic settlements of Lake Chalain (Jura Mountains, France) were characterized by dendro-anthracology (charcoal-pith distance, tree-ring width, earlywood/latewood proportion) and ring-scale isotope geochemistry (13C) to assess the relevance of this combined approach for paleoclimate reconstructions. Two differing climatic periods were investigated: (i) a climatic deterioration period characterized by cool and moist conditions and (ii) a climatic improvement period characterized by slightly less precipitation and warmer temperature. Latewood proportion in charcoal tree-rings was similar for the two studied climatic periods. However, the charcoal tree-rings exhibited width and 13C-content significantly different between the two studied periods, in agreement with previously inferred climatic difference. Monitoring ring-to-ring 13C variation within each charcoal fragment revealed no noticeable climatic trend, for none of the studied periods. However, calculation of the difference in 13C-content between earlywood and latewood of a given tree-ring suggested that the cool and moist climatic period also corresponded to higher seasonal contrast than the dryer climatic period. Although this exploratory study needs further confirmation, it opens promising developments for paleoclimatic reconstructions based on the stable carbon isotope composition of archeological charcoals: the potential for recording subtle paleoclimatic variations and seasonal contrasts.Baum, D.A., Vetsigian, K., 2017. An experimental framework for generating evolvable chemical systems in the laboratory. Origins of Life and Evolution of Biospheres 47, 481-497. experimental work on the origin of life has focused on either characterizing the chemical synthesis of particular biochemicals and their precursors or on designing simple chemical systems that manifest life-like properties such as self-propagation or adaptive evolution. Here we propose a new class of experiments, analogous to artificial ecosystem selection, where we select for spontaneously forming self-propagating chemical assemblages in the lab and then seek evidence of a response to that selection as a key indicator that life-like chemical systems have arisen. Since surfaces and surface metabolism likely played an important role in the origin of life, a key experimental challenge is to find conditions that foster nucleation and spread of chemical consortia on surfaces. We propose high-throughput screening of a diverse set of conditions in order to identify combinations of “food,” energy sources, and mineral surfaces that foster the emergence of surface-associated chemical consortia that are capable of adaptive evolution. Identification of such systems would greatly advance our understanding of the emergence of self-propagating entities and the onset of adaptive evolution during the origin of life.Bechtel, A., Oberauer, K., Kosti?, A., Gratzer, R., Milisavljevi?, V., Aleksi?, N., Stojanovi?, K., Gro?, D., Sachsenhofer, R.F., 2018. Depositional environment and hydrocarbon source potential of the Lower Miocene oil shale deposit in the Aleksinac Basin (Serbia). Organic Geochemistry 115, 93-112. most prolific oil shale deposit in Serbia is located in the Aleksinac Basin and is assigned to the Lower Miocene. Depositional environments and hydrocarbon potential were assessed for the Aleksinac oil shale and coal layers through bulk geochemical, organic petrographical, biomarker, and carbon isotope data from core samples from a single well. Maturity parameters (vitrinite reflectance, Tmax, biomarker isomerisation ratios) prove that the organic matter (OM) is immature. A lower lacustrine oil shale sequence is comprised of alternating sandstone and clay-rich rocks and some thin coal beds, indicating strong variations in depositional environment. This stratum is covered with thick sandstone (50?m) terminated by the main 4?m thick coal seam that was deposited in a low-lying mire, as evidenced by high total sulfur and mineral matrix contents. The plant input was dominated by angiosperms. A relative rise in water level led to the drowning of the swamp and to the deposition of a 60?m thick upper oil shale in a lacustrine environment. The OM of the oil shale is dominated by kerogen Type I (lamalginite). Biomarker data suggest a stratified water column that likely formed due to differences in salinity. The stratified water column led to a strictly anoxic environment and photic zone euxinia in a mesosalinar, hydrologically closed lake, which enabled the accumulation of uncommonly high amounts of organic material (average TOC: 18.0?wt%) with excellent preservation (average HI: 743?mg HC/g TOC).Becraft, E.D., Dodsworth, J.A., Murugapiran, S.K., Thomas, S.C., Ohlsson, J.I., Stepanauskas, R., Hedlund, B.P., Swingley, W.D., 2017. Genomic comparison of two family-level groups of the uncultivated NAG1 archaeal lineage from chemically and geographically disparate hot springs. Frontiers in Microbiology 8, 2082. doi: 10.3389/fmicb.2017.02082. Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to construct a near-complete genome from a deeply branching uncultivated archaeal lineage sampled from Great Boiling Spring (GBS) in the U.S. Great Basin, Nevada. This taxon is distantly related (distinct families) to an archaeal genome, designated “Novel Archaeal Group 1” (NAG1), which was extracted from a metagenome recovered from an acidic iron spring in Yellowstone National Park (YNP). We compared the metabolic predictions of the NAG1 lineage to better understand how these archaea could inhabit such chemically distinct environments. Similar to the NAG1 population previously studied in YNP, the NAG1 population from GBS is predicted to utilize proteins as a primary carbon source, ferment simple carbon sources, and use oxygen as a terminal electron acceptor under oxic conditions. However, GBS NAG1 populations contained distinct genes involved in central carbon metabolism and electron transfer, including nitrite reductase, which could confer the ability to reduce nitrite under anaerobic conditions. Despite inhabiting chemically distinct environments with large variations in pH, GBS NAG1 populations shared many core genomic and metabolic features with the archaeon identified from YNP, yet were able to carve out a distinct niche at GBS.Beddow, H.M., Liebrand, D., Wilson, D.S., Hilgen, F.J., Sluijs, A., Wade, B.S., Lourens, L.J., 2017. A comparison of two astronomical tuning approaches for the Oligocene-Miocene Transition from Pacific Ocean Site U1334 and implications for the carbon cycle. Climate of the Past Discussions 2017, 1-35. tuning of sediment sequences requires both unambiguous cycle-pattern recognition in climate proxy records and astronomical solutions, and independent information about the phase relationship between these two. Here we present two astronomically tuned age models for the Oligocene-Miocene Transition (OMT) from Integrated Ocean Drilling Program Site U1334 (equatorial Pacific Ocean) to assess the effect tuning approaches have on astronomically calibrated ages and the geologic time scale. These age models are based on different phase-assumptions between climate proxy records and eccentricity: the first age model is based on an inverse and in-phase assumption of CaCO3 weight (wt?%) to Earth's orbital eccentricity, the second age model is based on an inverse and in-phase assumption of benthic foraminifer stable carbon isotope ratios (δ13C) to eccentricity. The phase-assumptions that underpin these age models represent two end-members on the range of possible tuning options. To independently test which tuned age model and tuning assumptions are correct, we assign their ages to magnetostratigraphic reversals identified in anomaly profiles. Subsequently we compute tectonic plate-pair spreading rates based on the tuned ages. These alternative spreading rate histories indicate that the CaCO3 tuned age model is most consistent with a conservative assumption of constant spreading rates. The CaCO3 tuned age model thus provides robust ages and durations for polarity chrons C6Bn.1n–C6Cn.1r, which are not based on astronomical tuning in the latest iteration of the Geologic Time Scale. Furthermore, it provides independent evidence that the relatively large (several 10,000 years) time lags documented in the benthic foraminiferal isotope records relative to orbital eccentricity, constitute a real feature of the Oligocene-Miocene climate system and carbon cycle. The age constraints from Site U1334 thus provide independent evidence that the delayed responses of the Oligocene-Miocene climate-cryosphere system and carbon cycle resulted from increased nonlinear feedbacks to astronomical forcing.Bélanger, ?., Lucotte, M., Moingt, M., Paquet, S., Oestreicher, J., Rozon, C., 2017. Altered nature of terrestrial organic matter transferred to aquatic systems following deforestation in the Amazon. Applied Geochemistry 87, 136-145. agriculture practiced by several thousand small-scale farmers in the Tapajós region of the Brazilian Amazon has contributed to accelerated deforestation over the past decades. The present study aims to quantify and qualify changes in the transfer of terrestrial organic matter (TOM) to aquatic environments following deforestation. Lignin biomarkers have been analyzed from sediment cores collected in three floodplain lakes and in suspended particulate matter sampled during both wet and dry seasons. These analyses are interpreted with regard to lignin biomarker signatures of surface and deeper horizons of common soils, and of dominant plant species from forested and deforested environments. Dating the sediment cores with 210Pb allows reconstructing the successive deforestation cycles since the onset of European colonization two centuries ago. Further, satellite images coupled to a GIS approach is used to correlate the evolution of sedimentary TOM and anthropogenic land-use from 1986 to 2009. Over this period, sedimentation rates have sharply increased, and the nature of the sedimentary TOM has been shifted from being linked to primeval forest soils to degraded soils following deforestation for subsistence cropping and/or pasture lands. The intensity of changes in the nature of sedimentary TOM appears inversely related to the connectivity of flood lakes to the river. In the least connected flood lake, weathering of pasture soils in the watershed dominates TOM inputs particularly during the dry season. Massive deforestation in the Amazon thus triggers major changes in the nature of TOM transferred and sedimented in aquatic systems.Ben-Nissan, G., Sharon, M., 2018. The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes. Current Opinion in Chemical Biology 42, 25-33. mass spectrometry (IM-MS) is an approach that can provide information on the stoichiometry, composition, protein contacts and topology of protein complexes. The power of this approach lies not only in its sensitivity and speed of analysis, but also in the fact that it is a technique that can capture the repertoire of conformational states adopted by protein assemblies. Here, we describe the array of available IM-MS based tools, and demonstrate their application to the structural characterization of various protein complexes, including challenging systems as amyloid aggregates and membrane proteins. We also discuss recent studies in which IM-MS was applied towards investigations of conformational transitions and stabilization effects induced by protein interactions.Bergstr?m, A., Tyler-Smith, C., 2017. Paleolithic networking. Science 358, 586-587. are connected by networks of many kinds, extending from immediate family to distant strangers. Two studies in this issue use ancient DNA (aDNA) to shed new light on the networks of Paleolithic Neandertals and modern humans, who lived before agriculture was invented about 10,000 years ago. On page 655 of this issue, Prüfer et al. (1) report the high-quality genome sequence of a Neandertal woman from Vindija Cave in Croatia who lived 50,000 to 65,000 years ago. The sequence provides insights into the genetic networks of Neandertals and their interactions with modern humans. On page 659 of this issue, Sikora et al. (2) present genome sequences of a small group of modern humans who lived 33,000 to 35,000 years ago at Sunghir in western Russia, showing that their local social network resembled those of present-day hunter-gatherer groups.These studies were made possible by advances in aDNA methodologies over the past few decades that have enabled tiny amounts of degraded, damaged, and sometimes contaminated DNA present in ancient remains to be analyzed. A key lesson emerging from this marriage of genetics and archaeology is that the human past was highly complex (3). Population movement, mixing, and local extinction have been ubiquitous throughout prehistory and history (4). Lifestyle and culture have also emerged as major factors in shaping the genetic—and, by extension, social—structure of human societies.Most of what we knew previously about the genetic history of Neandertals came from a single high-quality sequence from a Neandertal woman from the Altai Mountains in southern Siberia (5). With the sequencing of the Vindija individual, Prüfer et al. provide an important additional data point. The Altai Neandertal was highly inbred; her parents were related at the level of half-siblings. Furthermore, the background level of genetic diversity in her genome was also much lower than that of modern humans, suggesting a long history of small group sizes. The Vindija woman displays a similarly low level of genetic diversity, but no signs of recent inbreeding, suggesting that mating between close relatives was not a general feature of Neandertal groups, but small group sizes probably were. Prüfer et al. further show, by studying patterns of shared DNA, that the Vindija individual was more closely related than the Altai individual to the group of Neandertals who mixed with modern humans ～55,000 years ago.Whereas the genetic relationships between ancient individuals can be gauged from DNA, their social relationships, if any, are challenging to assess. Sikora et al. tackle this problem by sequencing the genomes of four Paleolithic modern humans at the well-preserved Sunghir site. Two of these shared a single grave, which also contained the femur of the third human, whereas the fourth was buried in a nearby grave; they were very likely part of the same social group. Yet, none of these individuals were related at the level we would typically call family, that is, at third degree or closer, and they also did not show evidence of recent inbreeding. If the Sunghir group is representative of Paleolithic modern-human hunter-gatherer groups, it suggests that such groups consisted mostly of distantly related people and were connected to other groups via networks of movement. These findings mirror the conclusions from anthropological studies of present-day hunter-gatherer groups (6). The study shows that this social structure was already in place 33,000 to 35,000 years ago and may be a general feature of the modern-human hunter-gatherer lifestyle.Neandertals went extinct soon after ～40,000 years ago, not long after modern humans had expanded into their Eurasian territory. The causes of their extinction (as well as that of the Denisovans, who vanished around the same time) are poorly understood, but competition with modern humans was probably a contributing factor. The current genetic studies (1, 2) raise the question of whether contrasting social structures played a role. This possibility is supported by previous archaeological analyses (7). Demographic modeling has suggested that whereas Neandertal groups might have been small and poorly connected, modern human groups had the sizes and network structures that allowed technology and culture to disseminate and persist over generations (8). Previous work has also shown that, as a genetic by-product of their long history of small group sizes, Neandertals suffered from a larger number of harmful mutations (9, 10).The studies of Prüfer et al. and Sikora et al. demonstrate the promise of aDNA as a tool for understanding the social as well as genetic networks of past humans. Further research should provide more details about the structures of ancient human networks and how they changed across time and space. This should include studies of Paleolithic humans in Africa, where most of human evolution took place, and of the transition to agriculture and the growth of population sizes that followed. Such work might even inform the social and cognitive sciences. For example, it has been hypothesized that the human mind has an upper limit on the number of social relationships it can maintain (11), shaped by the group sizes of our Paleolithic ancestors. But as always with aDNA, we should not expect a simple picture (3). Even Neandertals, who seem to have had less far-reaching social networks in general, mated with modern humans, probably representing the extreme edge of their networks.References1. K. Prüfer et al., Science 358, 655 (2017).2. M. Sikora et al., Science 358, 659 (2017).3. M. Haber et al., Genome Biol. 17, 1 (2016)4. Q. Fu et al., Nature 534, 200 (2016).5. K. Prüfer et al., Nature 505, 43 (2014).6. K. R. Hill et al., Science 331, 1286 (2011).7. P. Mellars, J. C. French, Science 333, 623 (2011).8. A. Powell et al., Science 324, 1298 (2009).9. K. Harris, R. Nielsen, Genetics 203, 881 (2016).10. I. Juric et al., PLOS Genet. 12, e1006340 (2016).11. R. I. M. Dunbar, J. Hum. Evol. 22, 469 (1992).Bernard, S., Daval, D., Ackerer, P., Pont, S., Meibom, A., 2017. Burial-induced oxygen-isotope re-equilibration of fossil foraminifera explains ocean paleotemperature paradoxes. Nature Communications 8, Article1134. compositions of fossilised planktonic and benthic foraminifera tests are used as proxies for surface- and deep-ocean paleotemperatures, providing a continuous benthic record for the past 115?Ma. However, visually imperceptible processes can alter these proxies during sediment burial. Here, we investigate the diffusion-controlled re-equilibration process with experiments exposing foraminifera tests to elevated pressures and temperatures in isotopically heavy artificial seawater (H218O), followed by scanning electron microscopy and quantitative NanoSIMS imaging: oxygen-isotope compositions changed heterogeneously at submicrometer length scales without any observable modifications of the test ultrastructures. In parallel, numerical modelling of diffusion during burial shows that oxygen-isotope re-equilibration of fossil foraminifera tests can cause significant overestimations of ocean paleotemperatures on a time scale of 107 years under natural conditions. Our results suggest that the late Cretaceous and Paleogene deep-ocean and high-latitude surface-ocean temperatures were significantly lower than is generally accepted, thereby explaining the paradox of the low equator-to-pole surface-ocean thermal gradient inferred for these periods.Bernstein, H.C., Brislawn, C.J., Dana, K., Flores-Wentz, T., Cory, A.B., Fansler, S.J., Fredrickson, J.K., Moran, J.J., 2017. Primary and heterotrophic productivity relate to multikingdom diversity in a hypersaline mat. FEMS Microbiology Ecology 93, Article fix121. microbial ecosystems are widespread yet knowledge gaps still remain on the relationships between the diversity of species across kingdoms and productivity. Here, we ask two fundamental questions: (i) How does species diversity relate to the rates of primary and heterotrophic productivity? (ii) How do diel variations in light-energy inputs influence productivity and microbiome diversity? To answer these questions, microbial mats from a magnesium sulfate hypersaline lake were used to establish microcosms. Both the number and relatedness between bacterial and eukaryotic taxa in the microbiome were assayed via amplicon-based sequencing of 16S and 18S rRNA genes over two diel cycles. These results correlated with biomass productivity obtained from substrate-specific 13C stable isotope tracers that enabled comparisons between primary and heterotrophic productivity. Both bacterial and eukaryotic species richness and evenness were related only to the rates of 13C-labeled glucose and acetate biomass incorporation. Interestingly, measures of these heterotrophic relationships changed from positive and negative correlations depending on carbon derived from glucose or acetate, respectively. The bacterial and eukaryotic diversity of this ecosystem is also controlled, in part, from energy constraints imposed by changing irradiance over a diel cycle.Bertaux, J.-L., Lallement, R., 2017. Diffuse interstellar bands carriers and cometary organic material. Monthly Notices of the Royal Astronomical Society 469, S646–S660. suggest that the large organic molecules found in the dust of comet 67P/CG originated from the interstellar medium (ISM), and that this material is the source of absorption features in stellar spectra known as Diffuse Interstellar Bands (DIBs). These large organic molecules were present in the ISM prior to the emergence of the pre-solar nebula and were conserved during comet formation in the solar nebula due to gentle, hierarchical accretion, a scenario based on many lines of evidences collected with Rosetta rendez-vous mission (Davidsson et al. 2016). This is in contrast with the sublimation of H2O ice, according to diverse comet D/H values. While the organic to mineral mass ratios RC for comet Halley and 67P/CG were measured in the range ～0.32–1.0, we estimate that the DIB carriers alone can provide RISM = 0.32, but that this ratio could be increased by other organic molecules in the ISM that do not show up in absorption. The decrease of DIB during line–of-sight crossings of the dense cores of interstellar clouds and the simultaneous steepening of the Far UV part of the reddening curve suggest that DIB carriers coagulate and are constituent of the very small grains eventually preserved in comets. This conclusion implies that a future sample-return mission of a comet nucleus would not only provide unique information on comets, but also on the exact nature of the interstellar species producing the hundreds of DIBs, an unanswered question since their discovery several decades ago.Bertoni, C., Kirkham, C., Cartwright, J., Hodgson, N., Rodriguez, K., 2017. Seismic indicators of focused fluid flow and cross-evaporitic seepage in the Eastern Mediterranean. Marine and Petroleum Geology 88, 472-488. present for the first time a synthesis of the evidence of focused fluid flow in the Eastern Mediterranean, providing an updated record that includes recent and past occurrences through the last ca. 6 My of evolution of the basin. We do this by adding the interpretation of a previously unpublished regional 2D seismic dataset to the existing occurrences of focused fluid flow reported in the literature. Our interpretation shows a high number (141) of focused fluid flow features, which span the stratigraphic interval from late Miocene to Recent. Of these features, (82) are at the seabed, and (59) are buried. The previous published record is more difficult to quantify, but in comparison shows an overwhelming majority of seabed features, with only rare examples of buried features.The spectrum of the buried and seabed features covers pockmarks, pipes, mud volcanoes, clastic intrusions and collapse structures. Clustering of the fluid flow features is observed at different times in specific areas, including the Nile Cone, and the Levant, Herodotus, Cyprus and Latakia basins. With the buried record, we are able to highlight the evolution of the leakage points through time. Focused fluid flow venting has been occurring since the onset of the Messinian Salinity Crisis and the start of basinwide deposition of evaporites. We focus in particular on seismic indicators of leakage through evaporites, and of sub-evaporitic source for fluids and remobilised sediments. We also discuss the role of the evaporites as a seal to ascending fluids, and in which circumstances they can be breached.Fluids (and associated remobilised sediments) are sourced from different intervals, from the sub- and supra-evaporitic section, and possibly within the evaporites. Only a minor proportion of the fluid flow features are certainly sourced from below the Messinian evaporites, and most of them are located in the Nile-Levant-Eratosthenes areas. The few examples of pathways that are able to cross thick, undeformed and well preserved evaporites are typically correlated to overpressure release and hydrofracturing. This confirms that the evaporites do act regionally as a very good seal as expected, while fluids are able to cross the evaporites only in their most extreme expression, i.e. in near-lithostathic overpressure conditions. This is confirmed by our observations made in the Eastern Mediterranean, where in the presence of relatively undisturbed evaporites, cross-evaporite vertical fluid pathways are only observed at the high end of the flux-pressure range, and involve sediment remobilisation. Maps combining these different elements can be used to detect areas potentially more prone to breaching.Bhattacharyya, A., Schmidt, M.P., Stavitski, E., Martínez, C.E., 2018. Iron speciation in peats: Chemical and spectroscopic evidence for the co-occurrence of ferric and ferrous iron in organic complexes and mineral precipitates. Organic Geochemistry 115, 124-137. speciation of iron (Fe) in organic matter (OM)-rich environments under in situ variable redox conditions is largely unresolved. Peatlands provide a natural setting to study Fe–OM interactions. Utilizing chemical, spectroscopic and theoretical modeling approaches, we report the chemical forms, oxidation states and local coordination environment of naturally occurring Fe in the vertically redox-stratified Manning peatlands of western New York. In addition, we report dominant carbon, sulfur and nitrogen species that can potentially stabilize the various Fe species present in these peatlands. Our results provide clear direct and indirect evidence for the co-occurrence of ferrous (Fe2+) and ferric (Fe3+) iron species in peats under both oxic and anoxic conditions. Iron is mostly present within the operationally defined organic and amorphous (i.e., short range ordered, SRO) fractions; ferric iron primarily as magnetically isolated paramagnetic Fe3+ in Fe(III)-organic complexes, but also in mineral forms such as ferrihydrite; ferrous iron in tetrahedral coordination in Fe(II)-organic complexes with minor contribution from pyrite. All of the Fe species identified stabilize Fe(III) and/or Fe(II) in anoxic and oxic peats. Fundamental differences are also observed in the relative proportion of C, S and N functionalities of OM in oxic and anoxic peats. Aromatic CC, ester, phenol and anomeric C (ROCOR), as well as thiol, sulfide and heterocyclic N functionalities are more prevalent in anoxic peats. Collectively, our experimental evidence suggests iron forms coordination complexes with O-, S- and N-containing functional groups of OM. We posit the co-occurrence of organic and mineral forms of Fe(II) and Fe(III) in both oxic and anoxic peat layers results from dynamic complexation and hydrolysis-precipitation reactions that occur under variable redox conditions. Our findings aid in understanding the crucial role OM plays in determining Fe species in soils and sediments.Bhaumik, A.K., Paikray, J., Dutta, J., Mitra, A., Tiwari, D., Patil, D.J., 2017. Biostratigraphy and depositional environment of the Miocene limestone bed of Baripada, Mayurbhanj district, Odisha: Foraminiferal, sedimentological and bulk organic geochemical evidences. Journal of the Geological Society of India 90, 437-446. Marine Beds (BMB) have been studied extensively in terms of its mega fossil content. However, not much has been discussed about the foraminiferal content and the organic matter assemblage in these beds. The fossiliferous sequence of BMB consists of sandstone, shale and limestone units. The present study is persued on the limestone unit of BMB. Foraminiferal, thin section and rock-eval pyrolysis studies were performed on the 33 surface samples collected from five sections of Jamdapal and Mukurmatia region along the Budhabalang river bank. Foraminifera are less abundant in the samples of Jamdapal, whereas Mukurmatia is comparatively rich. First appearance datum of Globorotalia menardii[ranges since middle Miocene (12.6 Ma); FAD at planktic foraminiferal zone N12] and last appearance datum of Neogloboquadrina continuosa [ranges between early Miocene (23.2 Ma) to late Miocene (8.3 Ma); FAD at planktic foraminiferal zone N4B and LAD at N16] together suggest that the limestone unit was deposited in between 12.6 to 8.3 Ma within the upper Miocene. Also, the association of shallow water benthic foraminifera (Species of Ammonia, Asterorotalia, Bolivina, Buliminella, Cibicides, Challengerella, Criboelphidium, Cribononion, Elphidium, Hanzawaia, Nonionella) and planktic foraminifera (Globigerina falcoensis, Globigerina woodi, Globorotalia menardii, Neogloboquadrina continuosa) together with oyster bank and shark teeth suggest deposition of limestone within well oxygenated, tropical, shallow water, open marine condition (within 40m water depth). Lithological and thin section studies together with global sea level fluctuation history advocate that upper Miocene marine transgression promoted the formation of this unit. Bulk organic geochemical data obtained by the rock-eval pyrolysis studies on selected samples indicate a low total organic carbon (TOC), with low hydrogen index (HI), high oxygen index (OI). The organic facies is characterised by type-IV kerogen with major contribution from near shore terrestrial plants. This also suggests deposition in shallow, oxygenated environments that did not promote significant accumulation and preservation of organic content in sediments.Black, J.R., Vu, H.P., Haese, R.R., 2017. Aqueous phase tracers for monitoring fluid mixing in geological reservoirs: Results from two field studies. International Journal of Greenhouse Gas Control 67, 103-110. species are widely used to determine the degree of fluid mixing and fluid-rock reactions in geological reservoirs where differences are observed in groundwater chemistry. Likewise these components can be added artificially to injection waters to act as aqueous phase tracers in field tests. Here we report results from two field studies where aqueous phase tracers were applied. The first field site was located in the Darling Basin of NSW where new exploration wells were drilled to determine if suitable CO2 storage reservoirs could be identified. In this field study fluorescein was continuously added to a drill mud used during the drilling of an exploration well. After drilling the well, a wireline tool was used to collect formation water from different depths in the well and the residual fluorescein concentration was used to determine contamination of formation waters by drill mud. The composition of dissolved solids in the in situ formation water samples were close to 100% of those found in the final drill mud composition, whereas, c. 70–83% of the drill mud fluorescein concentration was observed in the in situ water samples. This indicated significant drill mud contamination of samples collected by the wireline tool, and potential non-conservative behavior of the fluorescein. The second field site was located at the CO2CRC Otway field site near Nirranda South in Victoria, Australia. Here, a range of aqueous phase tracers (fluorescein, Na+, Cl?, Br?, Sr2+ and Li+) were added to a CO2-saturated injection water and analysed in the back-produced water of a push-pull experiment (Otway 2B Extension) in order to determine the degree of mixing between injection and formation water. Fluorescein behaved in a non-conservative manner under the mild acidic conditions (in situ pH = 4.5), most likely due to adsorption to mineral surfaces. Scatter in the Na+ and Cl? concentrations made their interpretation problematic, while some loss of Sr2+ is inferred possibly involving exchange with minerals in the reservoir. In contrast, Br? and Li+ showed conservative behavior and are recommended for future tracer studies in reservoirs where pH is variable.Blanco-Zubiaguirre, L., Ribechini, E., Degano, I., La Nasa, J., Carrero, J.A., I?a?ez, J., Olivares, M., Castro, K., 2018. GC–MS and HPLC-ESI-QToF characterization of organic lipid residues from ceramic vessels used by Basque whalers from 16th to 17th centuries. Microchemical Journal 137, 190-203. work is focused on the chemical characterization of the organic residues preserved in ceramic fragments that are suspected to have been used by the Basque whalers in the period from 16th to 17th Century to store whale oil. The lipid profiling along with the identification of biomolecular markers, makes possible to obtain information on the contents of the vessels and on the transformations undergone by the organic substances during the burial process. To achieve this goal, two complementary analytical techniques, High-Performance Liquid Chromatography - Electrospray Ionization - Quadrupole Time-of-Flight Mass Spectrometry (HPLC-ESI-QToF) and Gas Chromatography-Mass Spectrometry (GC–MS), were used not only to study the archaeological materials but also fresh whale oil products used as reference materials with the aim to detect potential diagnostic biomarkers. HPLC-ESI-QToF was used to identify triacylglycerols (TAGs) and study their distribution in the various samples, whereas GC–MS after suitable derivatization provided the fatty acid (FA) profile together with the detection of degradation compounds (dicarboxylic and dihydroxy fatty acids) and biomarkers related to marine commodities (isoprenoid acids). Samples of blubber from 5 different whale species belonging to the genus Balaenoptera (fin, sei and minke whale), Megaptera (Humpback whale) and Phocoena (harbour porpoise) were used as reference materials together with a sample of whale oil of unknown origin. The chemical results confirm the archaeological data regarding the vessels use as containers to store whale oil and indicate the whales from Balaenoptera genus as the most probable source of the oil.Blue, L.E., Franklin, E.G., Godinho, J.M., Grinias, J.P., Grinias, K.M., Lunn, D.B., Moore, S.M., 2017. Recent advances in capillary ultrahigh pressure liquid chromatography. Journal of Chromatography A 1523, 17-39. the twenty years since its initial demonstration, capillary ultrahigh pressure liquid chromatography (UHPLC) has proven to be one of most powerful separation techniques for the analysis of complex mixtures. This review focuses on the most recent advances made since 2010 towards increasing the performance of such separations. Improvements in capillary column preparation techniques that have led to columns with unprecedented performance are described. New stationary phases and phase supports that have been reported over the past decade are detailed, with a focus on their use in capillary formats. A discussion on the instrument developments that have been required to ensure that extra-column effects do not diminish the intrinsic efficiency of these columns during analysis is also included. Finally, the impact of these capillary UHPLC topics on the field of proteomics and ways in which capillary UHPLC may continue to be applied to the separation of complex samples are addressed.Bomble, Y.J., Lin, C.-Y., Amore, A., Wei, H., Holwerda, E.K., Ciesielski, P.N., Donohoe, B.S., Decker, S.R., Lynd, L.R., Himmel, M.E., 2017. Lignocellulose deconstruction in the biosphere. Current Opinion in Chemical Biology 41, 61-70. have evolved different and yet complementary mechanisms to degrade biomass in the biosphere. The chemical biology of lignocellulose deconstruction is a complex and intricate process that appears to vary in response to specific ecosystems. These microorganisms rely on simple to complex arrangements of glycoside hydrolases to conduct most of these polysaccharide depolymerization reactions and also, as discovered more recently, oxidative mechanisms via lytic polysaccharide monooxygenases or non-enzymatic Fenton reactions which are used to enhance deconstruction. It is now clear that these deconstruction mechanisms are often more efficient in the presence of the microorganisms. In general, a major fraction of the total plant biomass deconstruction in the biosphere results from the action of various microorganisms, primarily aerobic bacteria and fungi, as well as a variety of anaerobic bacteria. Beyond carbon recycling, specialized microorganisms interact with plants to manage nitrogen in the biosphere. Understanding the interplay between these organisms within or across ecosystems is crucial to further our grasp of chemical recycling in the biosphere and also enables optimization of the burgeoning plant-based bioeconomy.Bond, N.J., Koulman, A., Griffin, J.L., Hall, Z., 2017. massPix: an R package for annotation and interpretation of mass spectrometry imaging data for lipidomics. Metabolomics 13, 128.: Mass spectrometry imaging (MSI) experiments result in complex multi-dimensional datasets, which require specialist data analysis tools.Objectives: We have developed massPix—an R package for analysing and interpreting data from MSI of lipids in tissue.Methods: massPix produces single ion images, performs multivariate statistics and provides putative lipid annotations based on accurate mass matching against generated lipid libraries.Results: Classification of tissue regions with high spectral similarly can be carried out by principal components analysis (PCA) or k-means clustering.Conclusion: massPix is an open-source tool for the analysis and statistical interpretation of MSI data, and is particularly useful for lipidomics applications.Availability and implementation: The source code, R package, documentation and test data are freely available to download from . massPix is distributed under the GNU General Public Licence (version 3).Bostic, J.T., Aeppli, C., Swarthout, R.F., Reddy, C.M., Ziolkowski, L.A., 2018. Ongoing biodegradation of Deepwater Horizon oil in beach sands: Insights from tracing petroleum carbon into microbial biomass. Marine Pollution Bulletin 126, 130-136. weathered petroleum residues from the Deepwater Horizon (DwH) disaster continue to be found on beaches along the Gulf of Mexico as oiled-sand patties. Here, we demonstrate the ongoing biodegradation of weathered Macondo Well (MW) oil residues by tracing oil-derived carbon into active microbial biomass using natural abundance radiocarbon (14C). Oiled-sand patties and non-oiled sand were collected from previously studied beaches in Mississippi, Alabama, and Florida. Phospholipid fatty acid (PLFA) analyses illustrated that microbial communities present in oiled-sand patties were distinct from non-oiled sand. Depleted 14C measurements of PLFA revealed that microbes on oiled-sand patties were assimilating MW oil residues five years post-spill. In contrast, microbes in non-oiled sand assimilated recently photosynthesized carbon. These results demonstrate ongoing biodegradation of weathered oil in sand patties and the utility of 14C PLFA analysis to track the biodegradation of MW oil residues long after other indicators of biodegradation are no longer detectable.Bo?i?evi?, A., Dobrzyński, M., De Bie, H., Gafner, F., Garo, E., Hamburger, M., 2017. Automated comparative metabolite profiling of large LC-ESIMS data sets in an acd/ms workbook suite add-in, and data clustering on a new open-source web platform freeclust. Analytical Chemistry 89, 12682-12689. technological development of LC-MS instrumentation has led to significant improvements of performance and sensitivity, enabling high-throughput analysis of complex samples, such as plant extracts. Most software suites allow preprocessing of LC-MS chromatograms to obtain comprehensive information on single constituents. However, more advanced processing needs, such as the systematic and unbiased comparative metabolite profiling of large numbers of complex LC-MS chromatograms remains a challenge. Currently, users have to rely on different tools to perform such data analyses. We developed a two-step protocol comprising a comparative metabolite profiling tool integrated in ACD/MS Workbook Suite, and a web platform developed in R language designed for clustering and visualization of chromatographic data. Initially, all relevant chromatographic and spectroscopic data (retention time, molecular ions with the respective ion abundance, and sample names) are automatically extracted and assembled in an Excel spreadsheet. The file is then loaded into an online web application that includes various statistical algorithms and provides the user with tools to compare and visualize the results in intuitive 2D heatmaps. We applied this workflow to LC-ESIMS profiles obtained from 69 honey samples. Within few hours of calculation with a standard PC, honey samples were preprocessed and organized in clusters based on their metabolite profile similarities, thereby highlighting the common metabolite patterns and distributions among samples. Implementation in the ACD/Laboratories software package enables ulterior integration of other analytical data, and in silico prediction tools for modern drug discovery.Braadbaart, F., van Brussel, T., van Os, B., Eijskoot, Y., 2017. Fuel remains in archaeological contexts: Experimental and archaeological evidence for recognizing remains in hearths used by Iron Age farmers who lived in peatlands. The Holocene 27, 1682-1693. the archaeological record, ash and charred organic material are the only indications of the type of fuel used by ancient societies to feed their fires. This potential source of information may help further understanding of past human behaviour in relation to fuel selection, applied type of fire and function of fires lit in hearths. This study examined ash from reference samples and ash and char samples recovered from an Iron Age peatland site in Vlaardingen, the Netherlands. Local availability and abundance made it possible for the occupants of the site to choose from different fuel resources. Peat and cattle dung were readily available, while wood was less abundant. Reference samples from various locations were collected to investigate the properties of ash. Different types of wood, peat and cattle dung were accordingly ashed and analysed. In total, two techniques were used, that is, chemical analyses (x-ray fluorescence (XRF)) for the determination of the elemental composition and microscopic studies on field images of these ashes, mounted on glass slides, to investigate phytoliths quantitatively (Si and Ca types), siliceous aggregates and spherulites. The properties of the archaeological samples were compared with these results. The archaeological char samples were used for identification and analysed using reflective microscopy to study structure and temperature by reflectance (%Ro). It provided the necessary information to determine the type of fuel used by the Iron Age farmers and obtain more information on the function of the present fire structures. The results are strong indications that Iron Age farmers used all available fuels, that is, peat, cattle dung and wood, to feed their fires. The integrated application of phytolith, geochemical and char analyses has a high potential for the identification of the fuel selected by ancient societies.Bradac, C., Johnsson, M.T., Breugel, M.v., Baragiola, B.Q., Martin, R., Juan, M.L., Brennen, G.K., Volz, T., 2017. Room-temperature spontaneous superradiance from single diamond nanocrystals. Nature Communications 8, Article 1205. (SR) is a cooperative phenomenon which occurs when an ensemble of quantum emitters couples collectively to a mode of the electromagnetic field as a single, massive dipole that radiates photons at an enhanced rate. Previous studies on solid-state systems either reported SR from sizeable crystals with at least one spatial dimension much larger than the wavelength of the light and/or only close to liquid-helium temperatures. Here, we report the observation of room-temperature superradiance from single, highly luminescent diamond nanocrystals with spatial dimensions much smaller than the wavelength of light, and each containing a large number (~?103) of embedded nitrogen-vacancy (NV) centres. The results pave the way towards a systematic study of SR in a well-controlled, solid-state quantum system at room temperature.Braje, T.J., Dillehay, T.D., Erlandson, J.M., Klein, R.G., Rick, T.C., 2017. Finding the first Americans. Science 358, 592-594. much of the 20th century, most archaeologists believed humans first colonized the Americas ～13,500 years ago via an overland route that crossed Beringia and followed a long and narrow, mostly ice-free corridor to the vast plains of central North America. There, Clovis people and their descendants hunted large game and spread rapidly through the New World. Twentieth-century discoveries of distinctive Clovis artifacts throughout North America, some associated with mammoth or mastodon kill sites, supported this “Clovis-first” model. North America's coastlines and their rich marine, estuarine, riverine, and terrestrial ecosystems were peripheral to the story of how and when the Americas were first settled by humans. Recent work along the Pacific coastlines of North and South America has revealed that these environments were settled early and continuously provided a rich diversity of subsistence options and technological resources for New World hunter-gatherers.Confidence in the Clovis-first theory started to crumble in the late 1980s and 1990s, when archaeological evidence for late Pleistocene seafaring and maritime colonization of multiple islands off eastern Asia (such as the Ryukyu Islands and the Bismarck Archipelago) accumulated. By the early 2000s, the Clovis-first theory collapsed after widespread scholarly acceptance that the Monte Verde locality near central Chile's Pacific Coast was occupied at least ～14,500 years ago (and possibly 16,000 to 18,000 years ago), a millennium or more older than Clovis and the opening of a viable ice-free corridor no earlier than ～13,500 years ago (1, 2). Several more pre-Clovis sites in North America's interior dated between ～14,000 and 16,000 years ago have gained broad scholarly acceptance (3–6), along with possible evidence for human presence in eastern Beringia ～24,000 years ago (7).In a dramatic intellectual turnabout, most archaeologists and other scholars now believe that the earliest Americans followed Pacific Rim shorelines from northeast Asia to Beringia and the Americas (8). According to the kelp highway hypothesis, deglaciation of the outer coast of North America's Pacific Northwest ～17,000 years ago created a possible dispersal corridor rich in aquatic and terrestrial resources along the Pacific Coast, with productive kelp forest and estuarine ecosystems at sea level and no major geographic barriers (9, 10). Kelp resources extended as far south as Baja California, and then—after a gap in Central America, where productive mangrove and other aquatic habitats were available—picked up again in northern Peru, where the cold, nutrient-rich waters from the Humboldt Current supported kelp forests as far south as Tierra del Fuego.But finding proof for this dispersal route has remained elusive (8). Archaeological evidence for early maritime activity has been growing in several areas along the Pacific Coast of North America, including the ～13,000-year-old Arlington Man skeletal remains from California's Santa Rosa Island. But no definitively pre-Clovis coastal sites in North America have been well documented or widely accepted.Testing the kelp highway hypothesis is challenging because much of the archaeological evidence would have been submerged by rising seas since the last glacial maximum (LGM) ～26,500 years ago. The earlier such a dispersal took place, the further offshore (and at greater depth) the evidence may lie, enlarging already vast potential search areas on the submerged continental shelf. Although direct evidence of a maritime pre-Clovis dispersal has yet to emerge, recent discoveries confirm that late Pleistocene archaeological sites can be found underwater. Recent discoveries at the Page-Ladson site, for example, produced ～14,500-year-old butchered mastodon bones and chipped stone tools in the bottom of Florida's Aucilla River (3). Several multidisciplinary studies are currently mapping and exploring the submerged landscapes of North America's Pacific and Gulf of Mexico coasts, searching for submerged pre-Clovis sites (8).With Clovis-first's demise, debate has shifted to whether colonization occurred well before the last deglaciation (before 25,000 years ago) or after it. Currently, most archaeological and genomic data suggest that the Americas were colonized between ～25,000 and 15,000 years ago (11), probably in the latter half of that range, by anatomically modern humans (Homo sapiens) who followed a Pacific Rim coastal corridor from northeast Asia into the New World.The uncertainty left by the collapse of the Clovis-first paradigm, however, has opened a Pandora's box of alternative scenarios for the peopling of the Americas, with some scholars and members of the general public quick to accept implausible claims based on limited and equivocal evidence. For example, a recent report on the Cerutti Mastodon Locality (CML) in California would dramatically extend initial occupation of the Americas to ～130,000 years ago, possibly by a hominin other than Homo sapiens (12). The CML claim hinges on ambiguous artifacts associated with broken mastodon bones and provides minimal evidence for their geological and stratigraphic context (13). The CML claim—similar to a handful of previous assertions for human occupation of North and South America before the LGM—is at odds with most archaeological, paleoecological, and genomic evidence. And despite considerable effort, scientists have found no clear evidence that humans were even in far northeast Asia before ～50,000 years ago.Answers to the questions of how, when, and where humans first reached the Americas remain tentative. The small sample of pre-Clovis sites has yet to produce a coherent technological signature with the broad geographic patterning that characterizes Clovis. Distinctive fluted Clovis, other fluted Paleoindian, and fishtail points previously provided a roadmap that archaeologists used to trace the spread of Paleoindians throughout the Americas. Such a roadmap is lacking for pre-Clovis sites. Assemblages with distinctive stemmed (“tanged”) chipped-stone projectile points, crescents (lunate-shaped), and leaf-shaped bifaces found in Japan, northeast Asia, western North America, and South America (see the figure) have been proposed as potential markers of a pre-Clovis coastal dispersal (14) that seems generally consistent with genomic data, which suggest a northeast Asian origin for Native American ancestors some time in the past 20,000 years. But more data are needed to close substantial spatial and temporal gaps between these far-flung finds and trace a dispersal route from Asia to the Americas. Work on early coastal localities along the Pacific Coast from Alaska to Baja California (8), Peru (10), and Chile (1) is helping to fill these gaps.If the first Americans followed a coastal route from Asia to the Americas, finding evidence for their earliest settlements will require careful consideration of the effects of sea level rise and coastal landscape evolution on local and regional archaeological records (15). Around the globe, evidence for coastal occupations between ～50,000 and 15,000 years ago are rare because of postglacial sea level rise, marine erosion, and shorelines that have migrated tens or even hundreds of kilometers from their locations at the LGM. Overcoming these obstacles requires interdisciplinary research focused on coastal areas with relatively steep offshore bathymetry, formerly glaciated areas where ancient shorelines have not shifted so dramatically, or the submerged landscapes that are one of the last frontiers for archaeology in the Americas. Methodological and analytical advances are moving us closer than ever toward understanding when, how, and why people first colonized the Americas. Coastal regions are central to this debateReferences1. T. D. Dillehay et al., PLOS ONE 10, e0141923 (2015).2. M. W. Pedersen et al., Nature 537, 45 (2016).3. J. J. Halligan et al., Sci. Adv. 2, e1600375 (2016).4. D. L. Jenkins et al., Science 337, 223 (2012).5. M. R. Waters et al., Science 331, 1599 (2011).6. M. R. Waters et al., Science 334, 351 (2011).7. L. Bourgeon, A. Burke, T. Higham, PLOS ONE 12, e0169486 (2017).8. L. Wade, Science 357, 542 (2017).9. J. M. Erlandson et al., J. Isl. Coast. Arch. 2, 161 (2007)10. T. D. Dillehay et al., Sci. Adv. 3, e1602778 (2017).11. B. Llamas et al., Sci. Adv. 2, e1501385 (2016).12. S. R. Holen et al., Nature 544, 479 (2017).13. T. J. Braje et al., PaleoAmerica 3, 200 (2017)14. J. M. Erlandson, T. J. Braje, Quatern. Int. 239, 28 (2011)15. D. W. Fedje, H. Josenhans, Geology 28, 99 (2000).Brankovits, D., Pohlman, J.W., Niemann, H., Leigh, M.B., Leewis, M.C., Becker, K.W., Iliffe, T.M., Alvarez, F., Lehmann, M.F., Phillips, B., 2017. Methane- and dissolved organic carbon-fueled microbial loop supports a tropical subterranean estuary ecosystem. Nature Communications 8, Article 1835. estuaries extend inland into density-stratified coastal carbonate aquifers containing a surprising diversity of endemic animals (mostly crustaceans) within a highly oligotrophic habitat. How complex ecosystems (termed anchialine)?thrive in this globally distributed, cryptic environment is poorly understood. Here, we demonstrate that a microbial loop shuttles methane and dissolved organic carbon (DOC) to higher trophic levels of the anchialine food web in the Yucatan Peninsula (Mexico). Methane and DOC production and consumption within the coastal groundwater correspond with a microbial community capable of methanotrophy, heterotrophy, and chemoautotrophy, based on characterization by 16S rRNA gene?amplicon sequencing and respiratory quinone composition. Fatty acid and bulk stable carbon isotope values of cave-adapted shrimp suggest that carbon from methanotrophic bacteria comprises 21% of their diet, on average. These findings reveal a heretofore unrecognized subterranean methane sink and contribute to our understanding of the carbon cycle and ecosystem function of karst subterranean estuaries.Brown, E.A., Dickinson, P.J., Mansour, T., Sturges, B.K., Aguilar, M., Young, A.E., Korff, C., Lind, J., Ettinger, C.L., Varon, S., Pollard, R., Brown, C.T., Raudsepp, T., Bannasch, D.L., 2017. FGF4 retrogene on CFA12 is responsible for chondrodystrophy and intervertebral disc disease in dogs. Proceedings of the National Academy of Sciences 114, 11476-11481.: Chondrodystrophy, characterized by short limbs and intervertebral disc disease (IVDD), is a common phenotype in many of the most popular dog breeds, including the dachshund, beagle, and French bulldog. Here, we report the identification of a FGF4 retrogene insertion on chromosome 12, the second FGF4 retrogene reported in the dog, as responsible for chondrodystrophy and IVDD. Identification of the causative mutation for IVDD will impact an incredibly large proportion of the dog population and provides a model for IVDD in humans, as FGF-associated mutations are responsible for IVDD and short stature in human achondroplasia. This is a report of a second retrogene copy of the same parental gene, each causing complementary disease phenotypes in a mammalian species. Abstract: Chondrodystrophy in dogs is defined by dysplastic, shortened long bones and premature degeneration and calcification of intervertebral discs. Independent genome-wide association analyses for skeletal dysplasia (short limbs) within a single breed (PBonferroni = 0.01) and intervertebral disc disease (IVDD) across breeds (PBonferroni = 4.0 × 10?10) both identified a significant association to the same region on CFA12. Whole genome sequencing identified a highly expressed FGF4 retrogene within this shared region. The FGF4 retrogene segregated with limb length and had an odds ratio of 51.23 (95% CI = 46.69, 56.20) for IVDD. Long bone length in dogs is a unique example of multiple disease-causing retrocopies of the same parental gene in a mammalian species. FGF signaling abnormalities have been associated with skeletal dysplasia in humans, and our findings present opportunities for both selective elimination of a medically and financially devastating disease in dogs and further understanding of the ever-growing complexity of retrogene biology. Brune, S., Williams, S.E., Müller, R.D., 2017. Potential links between continental rifting, CO2 degassing and climate change through time. Nature Geoscience 10, 941-946. concentration of CO2 in the atmosphere is a key influence on Earth’s climate. Today, significant quantities of CO2 are emitted at continental rifts, suggesting that the spatial and temporal extent of rift systems may have influenced deep carbon fluxes and thus climate change throughout geological time. Here we test this hypothesis by conducting a worldwide census of continental rift lengths over the last 200 million years. We estimate tectonic CO2 release rates through time and show that along the extensive Mesozoic and Cenozoic rift systems, rift-related CO2 degassing rates reached more than 300% of present-day values. Using a numerical carbon cycle model, we find that two prominent periods of enhanced rifting 160 to 100 million years ago and after 55 million years ago coincided with greenhouse climate episodes, during which atmospheric CO2 concentrations were more than three times higher than today. We therefore propose that continental fragmentation and long-term climate change could plausibly be linked via massive CO2 degassing in rift systems.There are two carbon cycles on Earth: the short-term, surficial cycle that connects atmospheric CO2 to the biosphere, soils and oceans; and the long-term or deep carbon cycle, which links the carbon content of the crust and mantle to Earth’s surface. The mass of carbon stored within the crust and mantle exceeds that of the surface reservoirs by several orders of magnitude. Thus, solid Earth degassing rates exert a major control on long-term atmospheric CO2 variations and, via the greenhouse effect, on palaeo-temperatures. Despite being a key quantity in long-term carbon cycle modelling, CO2 degassing remains one of the least-constrained parameters.According to current knowledge, deep carbon is released to the surface by four major sources: volcanism at mid-oceanic ridges, subduction zones and hotspots, and metamorphism of carbonate rocks in regions of plate convergence. At the same time, silicate weathering and marine carbonate formation bind CO2 into the lithosphere that may be subducted back into the mantle. Despite general agreement that the length of plate boundaries exerts a first-order control on fluxes of the deep carbon cycle, reconstructing plate boundary length through deep time remains challenging. Moreover, plate boundaries can simultaneously act as CO2 sources and sinks: mid-ocean ridges release large amounts of CO2 via extensive volcanism, but hydrothermal activity in young ocean floor causes CO2 to be sequestered in carbonates1. This process may even outweigh the CO2 release at oceanic spreading centres so that mid-ocean ridges could in fact constitute net CO2 sinks.Much of our understanding of the global carbon budget is derived from analysing present-day Earth. However, our planet is currently in a state of continental dispersal that is not representative for other stages of the supercontinent cycle, such as the fragmentation of Pangaea and Gondwana, which occurred during the Jurassic and Early Cretaceous periods. Although it is clear that the extent of rift systems was much larger during supercontinental breakup than today, a quantitative analysis of continental rift length and its impact on atmospheric CO2 since Mesozoic times is lacking.Here we investigate the hypothesis that rift-related CO2 degassing affects the deep carbon cycle. We deduce the worldwide length of continental rift systems using plate tectonic reconstructions and the geological rift record. We illustrate that rift length history correlates with the long-term palaeo-atmospheric CO2 evolution, suggesting that rift-related CO2 degassing may plausibly constitute a missing key component of the deep carbon cycle.Bussmann, I., Hackbusch, S., Schaal, P., Wichels, A., 2017. Methane distribution and oxidation around the Lena Delta in summer 2013. Biogeosciences 14, 4985-5002. Lena River is one of the largest Russian rivers draining into the Laptev Sea. The predicted increases in global temperatures are expected to cause the permafrost areas surrounding the Lena Delta to melt at increasing rates. This melting will result in high amounts of methane reaching the waters of the Lena and the adjacent Laptev Sea. The only biological sink that can lower methane concentrations within this system is methane oxidation by methanotrophic bacteria. However, the polar estuary of the Lena River, due to its strong fluctuations in salinity and temperature, is a challenging environment for bacteria. We determined the activity and abundance of aerobic methanotrophic bacteria by a tracer method and by the quantitative polymerase chain reaction. We described the methanotrophic population with a molecular fingerprinting method (monooxygenase intergenic spacer analysis), as well as the methane distribution (via a headspace method) and other abiotic parameters, in the Lena Delta in September 2013. The median methane concentrations were 22?nmol?L?1 for riverine water (salinity (S)??<?5), 19?nmol?L?1 for mixed water (5?<?S?<?20) and 28?nmol?L?1 for polar water (S?>?20). The Lena River was not the source of methane in surface water, and the methane concentrations of the bottom water were mainly influenced by the methane concentration in surface sediments. However, the bacterial populations of the riverine and polar waters showed similar methane oxidation rates (0.419 and 0.400?nmol?L?1?d?1), despite a higher relative abundance of methanotrophs and a higher estimated diversity in the riverine water than in the polar water. The methane turnover times ranged from 167 days in mixed water and 91 days in riverine water to only 36 days in polar water. The environmental parameters influencing the methane oxidation rate and the methanotrophic population also differed between the water masses. We postulate the presence of a riverine methanotrophic population that is limited by sub-optimal temperatures and substrate concentrations and a polar methanotrophic population that is well adapted to the cold and methane-poor polar environment but limited by a lack of nitrogen. The diffusive methane flux into the atmosphere ranged from 4 to 163??mol?m2?d?1 (median 24). The diffusive methane flux accounted for a loss of 8?% of the total methane inventory of the investigated area, whereas the methanotrophic bacteria consumed only 1?% of this methane inventory. Our results underscore the importance of measuring the methane oxidation activities in polar estuaries, and they indicate a population-level differentiation between riverine and polar water methanotrophs.Butcher, M.G., Meyer, P.A., Hallen, R.T., Albrecht, K.O., Clayton, C.K., Polikarpov, E., Rappe, K.G., Jones, S.B., Magnuson, J.K., 2018. Fungal metabolites as precursors to renewable transportation fuels. Fuel 215, 123-141. are known to produce hundreds of different polyketide, terpene, and terpenoid compounds and based on their chemical structures, 33 of these were selected for further assessment to identify compounds with potential for liquid transportation fuels. Eight of the 33 compounds were identified as having potential as gasoline blend components. Based on predicted boiling points and octane numbers, 2-ethyl-5,5-dimethyl-1,3-cyclopentadiene, sabinene, isobutyric acid,1,8-cineole and linalool met the boiling point and octane number requirements used for the assessment, while 2-ethyl-5,5-dimethyl-1,3-cyclopentadiene and isobutyric acid would require some upgrading. Limonene, isoamyl acetate, and 2,2,5,5-tetramethyl-3-hexanone also have gasoline blend potential without upgrading. For diesel fuel, only 3,3,5-trimethyldecane met the boiling point, cetane number, and flashpoint requirements used for the assessment; however, with upgrading, 18 of the 33 compounds evaluated could potentially serve as blend components of diesel fuel. None of the 33 compounds without upgrading met the four ASTM D1655 specifications for Jet A and Jet A-1 fuel, but 3,3,5-trimethyldecane and limonene were very close. With chemical upgrading, 22 of the 33 compounds could have potential as jet fuel blend components. The monoterpene limonene and six sesquiterpenes were identified as fungal-derived compounds that with upgrading potentially could serve as components of high-energy jet, missile, or diesel fuels.The increasing availability of fungal genomes and transcriptomes enables the identification of important metabolic pathways for hydrocarbon production. The number of fungal-based compounds having potential for use in hydrocarbon fuels and products is increasing as new compound and pathway discoveries are made and advances in metabolic engineering and synthetic biology enable the production of these compounds. Several challenges remain including increasing carbon flux toward hydrocarbon fuel precursors in primary metabolism, increasing the low titers of hydrocarbons produced, and establishing robust host strains. Also, more fuel property testing of fungal-derived compounds individually or in fuel blendstocks is needed to determine the true potential of these compounds in liquid transportation fuels.Byerly, B.L., Kareem, K., Bao, H., Byerly, G.R., 2017. Early Earth mantle heterogeneity revealed by light oxygen isotopes of Archaean komatiites. Nature Geoscience 10, 871-875. processes on early Earth, especially the interaction between the crust and deep mantle, are poorly constrained and subject to much debate. The rarity of fresh igneous materials more than 3 billion years old accounts for much of this uncertainty. Here we examine 3.27-billion-year-old komatiite lavas from Weltevreden Formation in the Barberton greenstone belt, which is part of the Kaapvaal Craton in Southern Africa. We show that primary magmatic compositions of olivine are well preserved in these lavas based on major and trace element systematics. These komatiitic lavas represent products of deep mantle plumes. Oxygen isotope compositions (δ18O) of the fresh olivine measured by laser fluorination are consistently lighter (about 2‰) than those obtained from modern mantle-derived volcanic rocks. These results suggest a mantle source for the Weltevreden komatiites that is unlike the modern mantle and one that reflects mantle heterogeneity left over from a Hadean magma ocean. The anomalously light δ18O may have resulted from fractionation of deep magma ocean phases, as has been proposed to explain lithophile and siderophile isotope compositions of Archaean komatiites.Cai, T., Wang, X., Wen, W., Zhang, Z., Wang, T., 2017. Promotion effect of biosurfactant on heavy-oil biodegradation. Petroleum Science and Technology 35, 1692-1698. have received considerable attention in the field of heavy-oil remediation processes. Heavy oil was used to isolate biosurfactant-producing and oil-degrading bacteria. According to 16S rRNA, the isolated bacteria was identified as Bacillus amyloliquefaciens. The critical micelle concentration (CMC) of the produced biosurfactant was 100 mg/L. Biosurfactant could greatly improve the properties of heavy oil and significantly improve the biodegradation. The viscosity reduction rate was from 24 to 47% over the temperature range of 30–90°C. Biodegradation rates of saturated hydrocarbon (C13–C33) were from 21 to 85%. The biodegradation accelerating rate of biosurfactant for different aromatic hydrocarbon series was 9.89%, 9.60%, 29.71%, 16.75%, and 10.04%. These findings demonstrate that the produced biosurfactant could be useful in environmental remediation processes.Cajka, T., Smilowitz, J.T., Fiehn, O., 2017. Validating quantitative untargeted lipidomics across nine liquid chromatography–high-resolution mass spectrometry platforms. Analytical Chemistry 89, 12360-12368. chromatography–mass spectrometry (LC–MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted “best practice” documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC–MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.Cao, C., Zhang, M., Tang, Q., Yang, Y., Lv, Z., Zhang, T., Chen, C., Yang, H., Li, L., 2018. Noble gas isotopic variations and geological implication of Longmaxi shale gas in Sichuan Basin, China. Marine and Petroleum Geology 89, Part 1, 38-46. large difference in carbon isotopic compositions of shale gases from the Lower Silurian Longmaxi Formation marine organic-rich shales between Changning and Weiyuan areas in Sichuan Basin, China is a still debate issue. In this study, 30 produced shale gas samples were collected during 3 years production period and analyzed for noble gas (He, Ne and Ar) abundances and isotopic compositions to reveal the origin and variation causes of shale gases. The results show that the Longmaxi shale gases show low 3He/4He and 20Ne/22Ne, and varied but high 21Ne/22Ne and 40Ar/36Ar ratios. The Weiyuan shale gases are characterized by low 3He/4He, high 40Ar/36Ar ratios and varied 4He and 40Ar abundances, and a large increase in 40Ar contents and a slight decrease in 40Ar/36Ar ratios display during 3 years shale gas production period from Jan. 2014 to Jun. 2016. Whereas the Changning shale gases are characterized by low and varied 3He/4He ratios and high 4He and 40Ar abundances, and small fluctuations in 40Ar contents and 40Ar/36Ar ratios exhibit during 3 years production period. In addition, the shale gases produced from horizontal wells in the Weiyuan area possessed higher 40Ar and 40Ar/36Ar ratio than that those from vertical wells at same well site. The noble gas isotopic compositions and variation of Longmaxi shale gases suggested that they are originated mainly from crust, air saturated fluid (ASF) and radiogenic accumulation. The variation of 40Ar and 4He contents during shale gas production mainly reflects the degree of shale gas source supply from mineral matrix to fracture network, and the greater increases in 40Ar and 4He contents with production time show less abundant shale gas supply. Therefore, the increase trend of 40Ar contents with shale gas production time in the Weiyuan area during 3 years production period possibly suggests less adequate shale gas supply. In contrast, the uniform or nearly constant of 40Ar content through production time in the Changing area indicates abundant supply of shale gas sources from mineral matrix, resulting in less production decline. Variation in 4He and 40Ar contents through shale gas production time could be sensitive indicators of abundant or depleted shale gas source supply.Cao, F., Tzortziou, M., Hu, C., Mannino, A., Fichot, C.G., Del Vecchio, R., Najjar, R.G., Novak, M., 2018. Remote sensing retrievals of colored dissolved organic matter and dissolved organic carbon dynamics in North American estuaries and their margins. Remote Sensing of Environment 205, 151-165. organic carbon, DOC, and the colored component of dissolved organic matter, CDOM, are key indicators of coastal water quality and biogeochemical state. Yet applications of space-based remote sensing to monitoring of CDOM variability across estuarine ecosystems and assessment of DOC exchanges along highly dynamic terrestrial-aquatic interfaces have been scarce, in part due to the coarse spatial resolution of most existing ocean color sensors and the seasonal and regional dependence of most existing algorithms. Here, we used a rich dataset of field observations to develop and validate new CDOM and DOC algorithms that are broadly applicable to different estuarine and coastal regions, over different seasons and a wide range of in-water conditions. Algorithms were applied to satellite imagery from MERIS-Envisat at a spatial resolution (300 m) that can resolve much of the spatial variability that characterizes estuaries and their margins. Multi-spectral remote sensing reflectance (Rrs) was used to retrieve CDOM absorption at various wavelengths and CDOM absorption spectral slope in the 275–295 nm spectral range (S275–295). DOC concentrations were obtained from a tight relationship between the DOC-specific CDOM absorption and S275–295, two optical quantities that depend only on the quality of CDOM and strongly covary across spatial and temporal scales. Algorithm evaluation using MERIS satellite data across different estuarine and coastal environments (i.e., the northern Gulf of Mexico, the Delaware Bay, the Chesapeake Bay estuary, and the Middle Atlantic Bight coastal waters) and across different seasons over multiple years resulted in relative errors (mean absolute percent difference; MAPD) of 29% (N = 17), 9.5% (N = 14), and 18% (N = 32), for aCDOM(300), S275–295, and DOC, respectively. These relative errors are comparable to those previously reported for satellite retrievals of CDOM and DOC products in less optically complex offshore waters. Application of these algorithms to multi-year MERIS satellite imagery over the Chesapeake Bay estuary allowed, for the first time, to capture the impact of tidal exchanges on carbon dynamics along wetland-estuary interfaces, and resolved spatial gradients, seasonal variability, and year-to-year changes in estuarine carbon amount and quality associated with marsh carbon export, riverine inputs, and extreme precipitation events.Cao, W., Zahirovic, S., Flament, N., Williams, S., Golonka, J., Müller, R.D., 2017. Improving global paleogeography since the late Paleozoic using paleobiology. Biogeosciences 14, 5425-5439. reconstructions are important to understand Earth's tectonic evolution, past eustatic and regional sea level change, paleoclimate and ocean circulation, deep Earth resources and to constrain and interpret the dynamic topography predicted by mantle convection models. Global paleogeographic maps have been compiled and published, but they are generally presented as static maps with varying map projections, different time intervals represented by the maps and different plate motion models that underlie the paleogeographic reconstructions. This makes it difficult to convert the maps into a digital form and link them to alternative digital plate tectonic reconstructions. To address this limitation, we develop a workflow to restore global paleogeographic maps to their present-day coordinates and enable them to be linked to a different tectonic reconstruction. We use marine fossil collections from the Paleobiology Database to identify inconsistencies between their indicative paleoenvironments and published paleogeographic maps, and revise the locations of inferred paleo-coastlines that represent the estimated maximum transgression surfaces by resolving these inconsistencies. As a result, the consistency ratio between the paleogeography and the paleoenvironments indicated by the marine fossil collections is increased from an average of 75?% to nearly full consistency (100?%). The paleogeography in the main regions of North America, South America, Europe and Africa is significantly revised, especially in the Late Carboniferous, Middle Permian, Triassic, Jurassic, Late Cretaceous and most of the Cenozoic. The global flooded continental areas since the Early Devonian calculated from the revised paleogeography in this study are generally consistent with results derived from other paleoenvironment and paleo-lithofacies data and with the strontium isotope record in marine carbonates. We also estimate the terrestrial areal change over time associated with transferring reconstruction, filling gaps and modifying the paleogeographic geometries based on the paleobiology test. This indicates that the variation of the underlying plate reconstruction is the main factor that contributes to the terrestrial areal change, and the effect of revising paleogeographic geometries based on paleobiology is secondary.Capo, E., Domaizon, I., Maier, D., Debroas, D., Bigler, C., 2017. To what extent is the DNA of microbial eukaryotes modified during burying into lake sediments? A repeat-coring approach on annually laminated sediments. Journal of Paleolimnology 58, 479-495. provides a powerful framework to reconstruct the long-term temporal dynamics of various biological groups from aquatic sediments. However, validations are still required to ensure the authenticity of the molecular signal obtained from sedimentary DNA. Here, we investigated the effects of early diagenesis on the DNA signal from micro-eukaryotes preserved in sediments by comparing metabarcoding inventories obtained for two sediment cores sampled in 2007 and 2013 respectively. High-throughput sequencing (Illumina MiSeq) of sedimentary DNA was utilized to reconstruct the composition of microbial eukaryotic communities by targeting the V7 region of the 18S rDNA gene. No significant difference was detected between the molecular inventories obtained for the two cores both for total richness and diversity indices. Moreover, community structures obtained for the two cores were congruent as revealed by procrustean analysis. Though most of the eukaryotic groups showed no significant difference in terms of richness and relative proportion according to the core, the group of fungi was found to differ both in terms of richness and relative proportion (possibly due to their spatial heterogeneity and potential activity in sediments). Considering the OTUs level (i.e. Operational Taxonomic Units as a proxy of ecological species), our results showed that, for the older analyzed strata (age: 15–40?years), the composition and structure of communities were very similar for the two cores (except for fungi) and the DNA signal was considered stable. However, for the uppermost strata (age <?15?years), changes of moderate magnitude were detected in the relative abundance of few OTUs. Overall, this study points out that, in Nylandssj?n sediments, early diagenesis did not induce marked modifications in the micro-eukaryotic DNA signal, thus opening new perspectives based on the analysis of eukaryotic sedimentary DNA to address scientific issues both in the domains of paleolimnology and microbial ecology. Because this study site is ideal for DNA preservation in sediment (quick sedimentation processes, no sediment resuspension, anoxic conditions at sediment–water interface), the generalization of our conclusions, in particular for less favorable sites, must be considered cautiously.Carabajal, M.D., Arancibia, J.A., Escandar, G.M., 2017. On-line generation of third-order liquid chromatography–excitation-emission fluorescence matrix data. Quantitation of heavy-polycyclic aromatic hydrocarbons. Journal of Chromatography A 1527, 61-69. the first time, third-order liquid chromatography with excitation-emission fluorescence matrix detection (LC-EEFM) data were generated on-line and chemometrically processed for the simultaneous quantitation of the heavy-polycyclic aromatic hydrocarbons fluoranthene, pyrene, benz[a]anthracene, chrysene, benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[a]pyrene, and dibenz[a,h]anthracene. The applied experimental strategy is very simple, and is based on the reduction of the linear flow rate by fitting a larger diameter connecting-tube between the column outlet and the fluorimetric detector. In this way, EEFMs were successfully recorded on-line, without involving a large total analysis time. Because in the studied system quadrilinearity was fulfilled, four-way parallel factor (PARAFAC) analysis was applied for data processing. The second-order advantage, which is an intrinsic property of data of at least second-order, allowed the quantification of the analytes in interfering media. Moreover, resolution of the system with a high degree of collinearity was achieved thanks to the third-order advantage. In addition to a selectivity improvement, third-order/four-way calibration increased the sensitivity, with limits of detection in the range of 0.4 ? 2.9 ng mL?1. After a solid-phase extraction procedure with C18 membranes, considerably lower concentrations (between 0.033–2.70 ng mL?1) were determined in real waters, with most recoveries in the range 90–106%.Carere, C.R., Hards, K., Houghton, K.M., Power, J.F., McDonald, B., Collet, C., Gapes, D.J., Sparling, R., Boyd, E.S., Cook, G.M., Greening, C., Stott, M.B., 2017. Mixotrophy drives niche expansion of verrucomicrobial methanotrophs. The Isme Journal 11, 2599-2610. methanotrophic bacteria have evolved a specialist lifestyle dependent on consumption of methane and other short-chain carbon compounds. However, their apparent substrate specialism runs contrary to the high relative abundance of these microorganisms in dynamic environments, where the availability of methane and oxygen fluctuates. In this work, we provide in situ and ex situ evidence that verrucomicrobial methanotrophs are mixotrophs. Verrucomicrobia-dominated soil communities from an acidic geothermal field in Rotokawa, New Zealand rapidly oxidised methane and hydrogen simultaneously. We isolated and characterised a verrucomicrobial strain from these soils, Methylacidiphilum sp. RTK17.1, and showed that it constitutively oxidises molecular hydrogen. Genomic analysis confirmed that this strain encoded two [NiFe]-hydrogenases (group 1d and 3b), and biochemical assays revealed that it used hydrogen as an electron donor for aerobic respiration and carbon fixation. While the strain could grow heterotrophically on methane or autotrophically on hydrogen, it grew optimally by combining these metabolic strategies. Hydrogen oxidation was particularly important for adaptation to methane and oxygen limitation. Complementary to recent findings of hydrogenotrophic growth by Methylacidiphilum fumariolicum SolV, our findings illustrate that verrucomicrobial methanotrophs have evolved to simultaneously utilise hydrogen and methane from geothermal sources to meet energy and carbon demands where nutrient flux is dynamic. This mixotrophic lifestyle is likely to have facilitated expansion of the niche space occupied by these microorganisms, allowing them to become dominant in geothermally influenced surface soils. Genes encoding putative oxygen-tolerant uptake [NiFe]-hydrogenases were identified in all publicly available methanotroph genomes, suggesting hydrogen oxidation is a general metabolic strategy in this guild.Cesar, J., Grice, K., 2017. The significance of benzo[b]naphtho[d]furans in fluids and source rocks: New indicators of facies type in fluvial-deltaic systems. Organic Geochemistry 113, 175-183. distributions of benzo[b]naphtho[d]furans (BNFs) in source rocks and fluids (crude oil and condensate) are shown to be useful indicators of facies type in fluvial-deltaic systems from the Dampier sub-Basin, North West Shelf of Australia. The stratigraphy in the Dampier sub-Basin represents a challenging petroleum system where the organic matter is very similar in most of the Triassic-Jurassic sequences. These sections consist of a fluvial-deltaic system with increasing marine influence towards the end of the Jurassic period. Potential applications of BNFs for source rock characterisation as well as fluid – source rock correlations are reported for the first time. The formation of [1,2]BNF seems to be influenced by clay catalysis, and the ratio [2,1]/[1,2]BNF can be used to describe lithofacies. This ratio is much lower in sediments from fluvial-deltaic systems compared to clay-depleted sediments from marine environments (e.g. carbonate sequences). For this study, the Triassic source rocks show ratios of 0.9–1.5 with 25% w/w of clay content in the rock whereas the ratios for the Middle Jurassic source rocks are around 1.6–2.1 with 14% w/w of clay content. The BNF ratio is lowest in the Late Jurassic samples (0.8) with 28% w/w of clay minerals. The ternary plot of [2,1]-[1,2]-[2,3] BNFs could be applied to fluid–fluid and fluid-source rock correlations. However, further work needs to be done on the factors controlling the abundance of the [2,3]BNF which is more abundant in source rocks compared to the fluids generated and expelled from these.Chacón, F.J., Cayuela, M.L., Roig, A., Sánchez-Monedero, M.A., 2017. Understanding, measuring and tuning the electrochemical properties of biochar for environmental applications. Reviews in Environmental Science and Bio/Technology 16, 695-715., the solid carbon product from the pyrolysis of biomass, has been gaining attention due to its many possible applications such as soil amendment and water or air purification. Several effects have been observed when biochar is applied to soil, including reduced greenhouse gas emissions, contaminant degradation and increased microbial activity. Recently, it has been demonstrated that some of these effects are a direct consequence of its electrochemical properties. Understanding the mechanisms that allow biochar to store and transfer electrons is essential to obtain a complete view on its role in biogeochemical redox reactions. This paper reviews the current knowledge on the electrochemical properties of biochar as well as the different techniques available to measure and modify these properties. Specific conditions (different feedstocks, additives, pyrolysis conditions) and treatments that influence biochar’s electrochemical properties are also discussed, with the aim of developing biochars with enhanced electrochemical properties for specific environmental applications.Chang, Q., Gao, R., Li, H., Dai, Z., Yu, G., Liu, X., Wang, F., 2017. Effects of CO2 on coal rapid pyrolysis behavior and chemical structure evolution. Journal of Analytical and Applied Pyrolysis 128, 370-378. pyrolysis of Shenfu bituminous coal was conducted with a wall temperature 1073–1473 K and residence time 0–750 ms in both CO2 and N2 atmospheres to study the pyrolysis mechanism in CO2 atmosphere. The interest was focused on mass loss, gas yield, element content of chars and a series of chemical structure parameters (CH2/CH3, Har/H, fa and (R/C)u) obtained by FT-IR analyses. The results show that varied impacts dominated on pyrolysis at different temperatures in CO2 atmosphere. Mass loss decreased at 1073 K but increased at 1273 and 1473 K. Both heterogeneous reaction of CO2 with char and homogeneous reactions of CO2 with volatile occurred during pyrolysis in CO2 atmosphere. The combined effect of enhanced polycondensation of aromatic rings and C-CO2 reaction has been found to increase the mass loss of char. More H-containing free radicals generated during polycondensation, which consequenctly increase combination possibility with other radical fragments to inhibit the cross-linking reaction.Chaudhary, D.K., Lee, S.D., Kim, J., 2017. Lysobacter olei sp. nov., isolated from oil-contaminated soil. International Journal of Systematic and Evolutionary Microbiology 67, 4660-4666. D-14T, a brown-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, was isolated from oil-contaminated soil. It was able to grow at 20–40?°C, at pH 6.0–10.0 and at 0–1?% (w/v) NaCl concentration. Based on the 16S rRNA gene sequence analysis, strain D-14T belonged to the genus Lysobacter and was closely related to Lysobacter caeni BUT-8T (99.0?% sequence similarity), Lysobacter ruishenii CTN-1T (98.5?%), Lysobacter daejeonensis GH1-9T (98.2?%) and Lysobacter panacisoli CJ29T (97.2?%). The only respiratory quinone was ubiquinone-8. The polar lipid profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and phosphatidyl-N-methyl-ethanolamine. The predominant fatty acids of strain D-14T were iso-C15?:?0, iso-C16?:?0, summed feature 9 (iso-C17?:?1 ω9c and/or C16?:?0 10-methyl), summed feature 3 (C16?:?1 ω7c and/or C16?:?1 ω6c), iso-C14?:?0, C11?:?0iso 3-OH, C15?:?1iso F and C16?:?0. The genomic DNA G+C?content of this novel strain was 68.7?mol%. The DNA–DNA relatedness values between strain D-14T and L. caeni BUT-8T, L. ruishenii CTN-1T, L. daejeonensis GH1-9T and L. panacisoli CJ29T were 56.0, 46.3, 48.7 and 41.7?%, respectively, which fall below the threshold value of 70?% for the strain to be considered as novel. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus, strain D-14T represents a novel species of the genus Lysobacter , for which the name Lysobacter olei sp. nov. is proposed. The type strain is D-14T (=KEMB 9005-572T=KACC 19173T=JCM 31917T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain D-14T is KY313413.Chaves Torres, L., Melbourne, L.A., Hernandez-Sanchez, M.T., Inglis, G.N., Pancost, R.D., 2017. Insoluble prokaryotic membrane lipids in continental shelf sediments offshore Cape Town: Implications for organic matter preservation. Marine Chemistry 197, 38-51. largest organic carbon (OC) reservoir on Earth is in the geosphere, mainly comprising insoluble organic matter (IOM). IOM formation, therefore, plays an important role in the short and long-term carbon cycle, carbon bioavailability and formation of source rocks. To explore the mechanism of insolubilization of organic matter (OM), we have analysed soluble and IOM fractions of continental shelf marine sediments. We have applied sequential solvent-extractions followed by a selective chemical degradation of the post-extraction residue, specifically targeting prokaryotic membrane lipids (branched fatty acids – FAs, hopanoids, archaeol and glycerol dialkyl glycerol tetraethers – GDGTs). Up to 80% of prokaryotic membrane lipids are not solvent-extractable, and we observe compound-specific differences in partitioning between soluble and IOM fractions. Based on these observations, we propose a variety of mechanisms for the incorporation of prokaryotic lipids into IOM in marine sediments: First, OM association with authigenic carbonates; second, cross-linking via esterification reactions with time, which could be particularly relevant for FAs; third, competition between reactivity and loss of polar head groups, the latter rendering the OM less susceptible to incorporation; and finally, inherent solvent-insolubility of some lipids associated with prokaryotic cells.Chen, C.-C., Tew, K.S., Ho, P.-H., Ko, F.-C., Hsieh, H.-Y., Meng, P.-J., 2017. The impact of two oil spill events on the water quality along coastal area of Kenting National Park, southern Taiwan. Marine Pollution Bulletin 124, 974-983. 2009, the container ship Colombo Queen and the oil tanker W-O BUDMO grounded off Jialeshui and Houwan, respectively, in southern Taiwan. Water quality was monitored at each site to evaluate the environmental impact caused by the resulting oil spills. The results show that the PAHs, turbidity, and other nutrients increased shortly after oil spill, however levels of these parameters eventually returned to baseline levels. On the other hand, DO saturation, pH and chl. a decreased initially, reached maxima after 10 days, and returned to the baseline levels after 14 days. The chl. a concentration, pH and DO saturation fluctuated in a similar pattern at both sites during the oil spills, likely driven by algal blooms. In this study, we documented a full environmental recovery at coastal areas before, during and after the oil spills.Chen, D., Pang, X., Yan, Q., Liu, Y., Mou, J., Lv, C., 2017. Geochemical and stable carbon isotope composition variations of natural gases in tight sandstones from the West Sichuan Basin, China. Geological Journal 52, 1020-1031. exploration has revealed the great potential of gas resources, complicated gas distributions and geochemical characteristics of natural gases in tight sandstones of the West Sichuan Basin, China (WSBC). The chemical, stable carbon and light hydrocarbon compositions of natural gases from WSBC were investigated to assess the genesis, sources, and migration pattern leading to variations in the geochemical and stable carbon isotope compositions. The analysis shows that the natural gas in the Jurassic tight sandstones occurs as dry gas or wet gas in some places; however, most of the gas in the deep Triassic tight sandstones is apparently dry gas. Carbon isotope distributions increased in the order δ13C1?<?δ13C2?<?δ13C3?<?δ13C4. The light hydrocarbon content increased in the order of chain (i.e. non-cyclic) alkanes, cycloalkanes, and aromatic hydrocarbons. Relatively high ethane carbon isotope values and methylcyclohexane contents indicated the presence of lacustrine coal-formed gases. The Jurassic natural gas is in a lower thermally mature stage and possibly originated from a mixture of T3X3 and T3X5 black mudstones. The deep Triassic natural gas was possibly originated in the deep source rocks because the gas has a relatively higher thermal maturity. Positive correlations between burial depth and methane content, dryness coefficient, δ13C1, and δ13C1–δ13C2 for the deep Triassic gas suggest that the migration distance was short and the source was nearby or the gas accumulated in situ. The chemical compositions and geological studies revealed that the fractionation of the Jurassic natural gases in a tight reservoir was predominantly caused by vertical migration rather than the maturity of the local source rocks. Chen, F., Lu, S., Ding, X., He, X., Xing, H., 2017. Evaluation of the adsorbed gas amount in a shale reservoir using the three compositions adsorbing methane (TCAM) method: A case from the Longmaxi shale in southeast Chongqing, China. Energy & Fuels 31, 11523-11531. evaluate the amount of adsorbed methane in a shale reservoir under different conditions of temperature and pressure, the Longmaxi shale from the Py1 well of southeast Chongqing was selected as a case to establish the three compositions adsorbing methane (TCAM) method based on the results of total organic carbon, X-ray diffraction, and methane isothermal adsorption analyses. The amounts of methane adsorbed by organic matter (OM), clay, and other minerals were calculated under different conditions of temperature and pressure, followed by the evaluation of the occurrence characteristics of adsorbed gas in a shale reservoir. A comparison of data from experiments and the TCAM method with two shale samples revealed the uncertainty of TCAM. The results from the two samples range from 0.02 to 0.08 m3/t and from 0.01 to 0.09 m3/t, with average values of 0.05 and 0.04 m3/t, respectively. The methane adsorption capacities of OM, clay, and other minerals at temperatures ranging from 30 to 70 °C were 26.04–38.76, 1.83–2.76, and 0.43–0.53 m3/t, respectively, with average values of 32.86, 2.38, and 0.48 m3/t, respectively. These values are significantly reduced and are more likely to be affected by the temperature. The contributions of OM, clay, and other minerals to the total adsorbed gas are 34.83, 46.74, and 18.43%, respectively, on the basis of the limited data available. The efficient exploitation of adsorbed gas in a shale reservoir requires an increase in the reservoir temperature or a reduction in the reservoir pressure to lower than 10 MPa. The TCAM method requires the shale reservoir to be in a relatively stable sedimentary environment, to have the same diagenetic evolution, and to have the same type of OM. Once the TCAM model is established, it can be applied to the same marine shale reservoir with a similar diagenetic evolution in the same area.Chen, F., Lu, S., Ding, X., He, X., Xing, H., 2018. The splicing of backscattered scanning electron microscopy method used on evaluation of microscopic pore characteristics in shale sample and compared with results from other methods. Journal of Petroleum Science and Engineering 160, 207-218. splicing of backscattered scanning electron microscopy (SB-SEM) method was applied to evaluate the microscopic pore characteristics of the Lower Silurian Longmaxi Shale samples from Py1 well in Southeast Chongqing, China. The results from SB-SEM, including frequencies, volumes and specific surface areas of organic and inorganic pores with different sizes, were compared with those of low temperature nitrogen adsorption/desorption (LTNA) and mercury intrusion porosimetry (MIP). The results show that the changes in organic and inorganic surface porosity with increasing image area estimated from the SB-SEM method become almost stable when the SB-SEM image areas are larger than 0.4?mm2, which indicates that the heterogeneities of organic and inorganic pore volumes in shale samples can be largely overcome. This method is suitable for evaluating the microscopic pore characteristics of shale samples. Although the SB-SEM underestimates the frequencies, volumes and specific surface areas of pores smaller than its resolution, it can obtain these characteristics of pores larger than 100?nm in width, which are not effectively evaluated by the LTNA method and are underestimated by the MIP method.Chen, L., Miller, S.A., Ellis, B.R., 2017. Comparative human toxicity impact of electricity produced from shale gas and coal. Environmental Science & Technology 51, 13018-13027. human toxicity impact (HTI) of electricity produced from shale gas is lower than the HTI of electricity produced from coal, with 90% confidence using a Monte Carlo Analysis. Two different impact assessment methods estimate the HTI of shale gas electricity to be 1–2 orders of magnitude less than the HTI of coal electricity (0.016–0.024 DALY/GWh versus 0.69–1.7 DALY/GWh). Further, an implausible shale gas scenario where all fracturing fluid and untreated produced water is discharged directly to surface water throughout the lifetime of a well also has a lower HTI than coal electricity. Particulate matter dominates the HTI for both systems, representing a much larger contribution to the overall toxicity burden than VOCs or any aquatic emission. Aquatic emissions can become larger contributors to the HTI when waste products are inadequately disposed or there are significant infrastructure or equipment failures. Large uncertainty and lack of exposure data prevent a full risk assessment; however, the results of this analysis provide a comparison of relative toxicity, which can be used to identify target areas for improvement and assess potential trade-offs with other environmental impacts.Chen, X., Espinoza, D.N., 2018. Ostwald ripening changes the pore habit and spatial variability of clathrate hydrate. Fuel 214, 614-622. hydrate is a solid crystalline compound that consists of water cages with trapped gas molecules. Methane hydrate in permafrost and marine sediments is estimated to contain 2?×?103 to 4?×?106?Gt of carbon, which makes it both a potential energy source and a liability to global warming. The transport and mechanical properties of hydrate bearing sediments (HBS), and therefore hydrate dissociation through depressurization, thermal stimulation, or CO2 injection, depend on hydrate pore habit and spatial distribution in sediments. However, the evolution of hydrate pore habit and spatial distribution in HBS are not well understood yet. Here we show experimental evidence of Ostwald ripening of gas hydrate crystals in pores and porous media. We find that (1) hydrate growth rate (under nearly isothermal conditions) versus the degree of overpressurization fits an Arrhenius-type equation, and (2) Ostwald ripening gradually changes hydrate pore habit from grain-attaching to pore-filling and increases hydrate saturation heterogeneity at both pore and core scales. The latter ultimately creates significant spatial variations of permeability and sediment strength. Our results provide insights into kinetics and pore-scale physics that determine the geophysical signature from HBS at various scales. Based on our findings of hydrate occurrence in both gas and gas-water interface, we argue that hydrate growth in natural HBS is not limited to the water liquid phase. Our observation of hydrate pore habit alteration by Ostwald ripening explains patchy saturation and heterogeneous distribution of hydrate in natural HBS, which gives physical insight to improve geophysical hydrate models in porous media.Chen, X., Yao, G., Cai, J., Huang, Y., Yuan, X., 2017. Fractal and multifractal analysis of different hydraulic flow units based on micro-CT images. Journal of Natural Gas Science and Engineering 48, 145-156. structure is one of the key factors affecting the transport behavior in porous media, which is mainly determined by petrophysical facies. To accurately characterize the diversity of pore structure, hydraulic flow units (HFU) based on the modified flow zone indicator data are subdivided, and experiments of mercury injection and routine core analysis are conducted for 601 sandstone samples in this study. Five samples selected from different HFU (porosity is approximately equal, however permeability varies widely) are chosen to conduct micro-computerized tomography test. Then, fractal and multifractal methods are used to characterize complex pore space of chosen samples based on the number-area model, radius-volume model and number-radius model respectively, in which the effect of image scale on the fractal dimension is investigated. Each HFU has similar box dimension and generalized fractal dimension, but has significant difference in multifractal spectrum. Specially, the different values of singularity exponent in the multifractal spectrum have a good relationship with the experimentally measured permeability. There are clear inflections points on the fractal curves from mercury injection curve. Based on the value of maximum pore throat radius, only one segment (located in the middle) can be used to calculate the fractal dimension. Fractal dimension obtained by pore network model does not satisfy the traditional relationship. Correspondingly, fractal and multifractal characteristics pore structure of different hydraulic flow units are analyzed in detail.Chen, Z., Glover, M.S., Li, L., 2018. Recent advances in ion mobility–mass spectrometry for improved structural characterization of glycans and glycoconjugates. Current Opinion in Chemical Biology 42, 1-8. and glycoconjugates are involved in regulating a vast array of cellular and molecular processes. Despite the importance of glycans in biology and disease, characterization of glycans remains difficult due to their structural complexity and diversity. Mass spectrometry (MS)-based techniques have emerged as the premier analytical tools for characterizing glycans. However, traditional MS-based strategies struggle to distinguish the large number of coexisting isomeric glycans that are indistinguishable by mass alone. Because of this, ion mobility spectrometry coupled to MS (IM–MS) has received considerable attention as an analytical tool for improving glycan characterization due to the capability of IM to resolve isomeric glycans before MS measurements. In this review, we present recent improvements in IM–MS instrumentation and methods for the structural characterization of isomeric glycans. In addition, we highlight recent applications of IM–MS that illustrate the enormous potential of this technology in a variety of research areas, including glycomics, glycoproteomics, and glycobiology.Chen, Z., Lu, J., Gao, S.-H., Jin, M., Bond, P.L., Yang, P., Yuan, Z., Guo, J., 2018. Silver nanoparticles stimulate the proliferation of sulfate reducing bacterium Desulfovibrio vulgaris. Water Research 129, 163-171. intensive use of silver nanoparticles (AgNPs) in cosmetics and textiles causes their release into sewer networks of urban water systems. Although a few studies have investigated antimicrobial activities of nanoparticles against environmental bacteria, little is known about potential impacts of the released AgNPs on sulfate reducing bacteria in sewers. Here, we investigated the effect of AgNPs on Desulfovibrio vulgaris Hidenborough (D. vulgaris), a typical sulfate-reducing bacterium (SRB) in sewer systems. We found AgNPs stimulated the proliferation of D. vulgaris, rather than exerting inhibitory or biocidal effects. Based on flow cytometer detections, both the cell growth rate and the viable cell ratio of D. vulgaris increased during exposure to AgNPs at concentrations of up to 100 mg/L. The growth stimulation was dependent on the AgNP concentration. These results imply that the presence of AgNPs in sewage may affect SRB abundance in sewer networks. Our findings also shed new lights on the interactions of nanoparticles and bacteria.Cheng, B., Xu, J., Lu, Z., Li, Y., Wang, W., Yang, S., Liu, H., Wang, T., Liao, Z., 2018. Hydrocarbon source for oil and gas indication associated with gas hydrate and its significance in the Qilian Mountain permafrost, Qinghai, Northwest China. Marine and Petroleum Geology 89, Part 1, 202-215. gas hydrate was sampled by drilling in the Qilian Mountain permafrost in 2008, to investigate the source of the gas hydrate and the relationship between gas hydrate and the concomitant oil and gas indication (OGI) have become an important research focus. The rocks bearing gas hydrate and OGI from the Middle Jurassic strata in the Qilian Mountain permafrost, Qinghai, Northwest China were extracted by organic solvent and thermally treated (300 °C and 400 °C) in vacuum glass tubes. The hydrocarbons from the extracts and cracked products of the rocks and the stable carbon isotope of the gas hydrocarbons were studied. The results showed that the OGIs can be classified into two types according to different biomarker characteristics. The I-type of OGIs, which suffered from the process of early biodegradation and later-hydrocarbon input and featured high concentrations of 17α(H)-diahopane and αββ-regular steranes, mainly originated from the shallow source rocks of the Middle Jurassic strata, while the II-type one with a series of long-chain alkylnaphthalene may originate from the lower portion of Middle Jurassic or deeper source rocks than the Middle Jurassic strata. The adsorbed gas (300 °C) of the Middle Jurassic rocks was very wet, had a normal carbon isotope sequence, and can be regarded as an organic thermogenic gas derived from Middle Jurassic source rocks. Comparing the adsorbed (300 °C) and cracked (400 °C) gases from the rocks with gases from the gas hydrate and drilling core, we found they had similar stable carbon isotope distributions but different relative contents of methane (C1), ethane (C2), and propane (C3). The Middle Jurassic source rocks are mainly deposited in a freshwater paleo-environment, similar to the parent biomass of the gas hydrate and drilling core gas. The difference of the relative concentrations of C1-C3 may result from different formation processes between the adsorbed and cracked gases and the gas hydrate and drilling core gas. The II-type OGI, which possibly originated from deeper strata than the Middle Jurassic, were closely associated with the gas hydrate under the drilling well and had a similar parent biomass and depositional environment as the gas hydrate, showing they have a closely correlated hydrocarbon origin.Cheng, Z., Xiao, L., Wang, H., Yang, H., Li, J., Huang, T., Xu, Y., Ma, N., 2017. Bacterial and archaeal lipids recovered from subsurface evaporites of Dalangtan Playa on the Tibetan Plateau and their astrobiological implications. Astrobiology 17, 1112-1122. Basin (Tibetan Plateau) is considered an applicable analogue to Mars with regard to sustained extreme aridity and abundant evaporites. To investigate the possibility of the preservation of microbial lipids under these Mars analog conditions, we conducted a mineralogical and organic geochemistry study on samples collected from two Quaternary sections in Dalangtan Playa, northwestern Qaidam Basin, which will enhance our understanding of the potential preservation of molecular biomarkers on Mars. Two sedimentary units were identified along two profiles: one salt unit characterized by a predominance of gypsum and halite, and one detrital unit with a decrease of gypsum and halite and enrichment in siliciclastic minerals. Bacterial fatty acids and archaeal acyclic diether and tetraether membrane lipids were detected, and they varied throughout the sections in concentration and abundance. Bacterial and archaeal biomolecules indicate a dominance of Gram-positive bacteria and halophilic archaea in this hypersaline ecosystem that is similar to those in other hypersaline environments. Furthermore, the abundance of bacterial lipids decreases with the increase of salinity, whereas archaeal lipids showed a reverse trend. The detection of microbial lipids in hypersaline environments would indicate, for example on Mars, a high potential for the detection of microbial biomarkers in evaporites over geological timescales.Cheptsov, V.S., Vorobyova, E.A., Manucharova, N.A., Gorlenko, M.V., Pavlov, A.K., Vdovina, M.A., Lomasov, V.N., Bulat, S.A., 2017. 100?kGy gamma-affected microbial communities within the ancient Arctic permafrost under simulated Martian conditions. Extremophiles 21, 1057-1067. research aimed to investigate the viability and biodiversity of microbial communities within ancient Arctic permafrost after exposure to a gamma-radiation dose of 100?kGy at low temperature (??50?°C), low pressure (1?Torr) and dehydration conditions. The main objective was to assess the possibility for long-term survival of Earth-bound microorganisms in the subsurface of Martian regolith or inside small space bodies at constant absorption and accumulation of the gamma radiation dose. Investigated microbial communities had shown high resistance to a simulated Martian environment. After irradiation the total count of prokaryotic cells and number of metabolically active bacterial cells remained at the control level, while the number of bacterial CFUs decreased by 2 orders of magnitude, and the number of metabolically active cells of archaea decreased threefold. Besides, the abundance of culturable bacteria after irradiation was kept at a high level: not less than 3.7?×?105?cells/g. Potential metabolic activity of irradiated microbial communities in general were higher than in the control sample. A fairly high biodiversity of bacteria was detected in the exposed sample of permafrost, although the microbial community structure underwent significant changes after irradiation. In particular, actinobacteria populations of the genus Arthrobacter, which was not revealed in the control samples, became predominant in bacterial communities following the exposure. The results of the study testify that long-term preservation of microbial life inside Martian permafrost is possible. The data obtained can also be evaluated from the perspective of the potential for discovering viable Earth-bound microorganisms on other objects in the Solar system and inside of small bodies in outer space.Cheung, M.-C., Zong, Y., Zheng, Z., Liu, Z., Aitchison, J.C., 2017. Holocene temperature and precipitation variability on the central Tibetan Plateau revealed by multiple palaeo-climatic proxy records from an alpine wetland sequence. The Holocene 27, 1669-1681. study has reconstructed the Holocene environmental history of central Tibetan Plateau, a transitional area between monsoon-dominated Asia and Westerlies-dominated Asia, to examine the interplay between the two circulation systems and effects of other potential mechanisms on the temporal variability of Holocene climatic conditions in the study area. Specifically, this study has produced a twin record of palaeo-hydrology and palaeo-temperature from an alpine wetland sediment sequence using two sets of lipid-based biomarker indices: n-alkanes and branched glycerol dialkyl glycerol tetraethers (bGDGTs). The results show that (1) the Asian summer monsoon has supplied moisture that helped initiate the wetland habitat around 8000 cal. yr BP, about 2000 years later than locations along the southeastern edge of the plateau; (2) a significant decline in moisture supply is evident since the Medieval Warm period; (3) the Westerlies have transmitted variability of the North Atlantic climate to the study area, resulting in periodic increases in evaporation and causing short-term expansion or contraction of the wetland and (4) the palaeo-air temperature change follows closely that of global sea level and sea surface temperature, implying a link to global ice volume change throughout the Holocene. This study concludes that the Holocene climate history of central Tibetan Plateau is a result of monsoonal moisture supply interacted with the Westerlies variability, while the palaeo-temperature has followed changes in global ice volume during the present warm interglacial.Chiaia-Hernández, A.C., Günthardt, B.F., Frey, M.P., Hollender, J., 2017. Unravelling contaminants in the Anthropocene using statistical analysis of liquid chromatography–high-resolution mass spectrometry nontarget screening data recorded in lake sediments. Environmental Science & Technology 51, 12547-12556. significant increase in traces of human activity in the environment worldwide provides evidence of the beginning of a new geological era, informally named the Anthropocene. The rate and variability of these human modifications at the local and global scale remain largely unknown, but new analytical methods such as high-resolution mass spectrometry (HRMS) can help to characterize chemical contamination. We therefore applied HRMS to investigate the contamination history of two lakes in Central Europe over the preceding 100 years. A hierarchical clustering analysis (HCA) of the collected time series data revealed more than 13?000 profiles of anthropogenic origin in both lakes, defining the beginning of large-scale human impacts during the 1950s. Our results show that the analysis of temporal patterns of nontarget contaminants is an effective method for characterizing the contamination pattern in the Anthropocene and an important step in prioritizing the identification of organic contaminants not yet successfully targeted by environmental regulation and pollution reduction initiatives. As proof of the concept, the success of the method was demonstrated with the identification of the pesticide imazalil, which probably originated from imported fruits. This new approach applicable to palaeoarchives can effectively be used to document the time and rate of change in contamination over time and provide additional information on the onset of the Anthropocene.Cho, E., Witt, M., Hur, M., Jung, M.-J., Kim, S., 2017. Application of FT-ICR MS equipped with quadrupole detection for analysis of crude oil. Analytical Chemistry 89, 12101-12107. power is a critical factor determining the quality of ultrahigh-resolving power mass spectra of crude oil. In this study, 7T Fourier-transform ion cyclotron mass spectrometry (FT-ICR MS), equipped with quadrupole detection, was applied and evaluated for crude oil analysis for the first time. Four spectra were obtained from two oil samples using two ionization methods. Resolving power of 1500000 was observed at m/z 400 with 4 s transient signal. Comparison with literature reports revealed that the achieved resolving power was comparable with or superior to those obtained from instruments using higher magnetic fields but without quadrupole detection. A total of 6000–10000 peaks with an S/N ratio of 3 or higher were observed from the obtained spectra and over 97% of the peaks could be assigned to appropriate chemical formulas with an error within 1 ppm. Double bond equivalents vs carbon number plots generated from the obtained data agreed well with those previously reported without quadrupole detection. Mass accuracy values of the assigned elemental formulas were examined and the average root-mean-square error was calculated to be only 160 ppb. Low unassignment rate of the observed peaks and strong agreement with previously reported results suggests that unwanted harmonics of reduced frequency are not significant for the data obtained with quadrupole detection. Overall, the data presented in this study show that FT-ICR MS equipped with quadrupole detection can be a powerful tool to examine complex mixtures like crude oil. To the best of our knowledge, this is the first paper reporting application of FT-ICR MS equipped with quadrupole detection for the oil analysis.Chowdhury, R., Dhar, K., Ahamed, F., Alam, S., Uddin, M., 2017. Biodegradation of anthracene and phenanthrene by bacteria isolated from oil-contaminated soil of Bangladesh. Chemistry and Ecology 33, 843-855. aromatic hydrocarbons (PAHs) are ubiquitous environmental pollutants entering into the environment through natural and anthropogenic activities. Owing to their toxicity to various life forms including humans, detoxification of PAHs is crucial to reduce their effects on cells. In this study, we have isolated two bacteria capable of degrading two common PAHs, anthracene and phenanthrene, from contaminated soil samples by using selective enrichment culture supplemented with test PAHs as the sole source of carbon and energy. The isolated bacteria were identified and affiliated as Pseudomonas aeruginosa strain KD and Stenotrophomonas maltophilia strain RC based on their 16s rRNA gene sequences. The degradation of anthracene and phenanthrene was estimated indirectly by measuring the decolourisation extent of a redox indicator, 2, 6-dichlorophenolindophenol, incorporated into PAH-supplemented mineral salt media. In the case of anthracene, ≥90% decolourisation was recorded at 20 and 48 days for P. aeruginosa and S. Maltophilia, respectively. On the other hand, ≥94% decolourisation was recorded at 56 and 52 days for P. aeruginosa and S. maltophilia, respectively during the utilisation of phenanthrene.Christiansen, T., Cotte, M., Loredo-Portales, R., Lindelof, P.E., Mortensen, K., Ryholt, K., Larsen, S., 2017. The nature of ancient Egyptian copper-containing carbon inks is revealed by synchrotron radiation based X-ray microscopy. Scientific Reports 7, Article 15346. the first time it is shown that carbon black inks on ancient Egyptian papyri from different time periods and geographical regions contain copper. The inks have been investigated using synchrotron-based micro X-ray fluorescence (XRF) and micro X-ray absorption near-edge structure spectroscopy (XANES) at the European Synchrotron Radiation Facility (ESRF). The composition of the copper-containing carbon inks showed no significant differences that could be related to time periods or the geographical locations. This renders it probable that the same technology for ink production was used throughout Egypt for a period spanning at least 300 years. It is argued that the black pigment material (soot) for these inks was obtained as by-products of technical metallurgy. The copper (Cu) can be correlated with the following three main components: cuprite (Cu2O), azurite (Cu3[CO3]2[OH]2) and malachite (Cu2CO3[OH]2).Clark, J.B., Long, W., Hood, R.R., 2017. Estuarine sediment dissolved organic matter dynamics in an enhanced sediment flux model. Journal of Geophysical Research: Biogeosciences 122, 2669-2682. derived dissolved organic matter (DOM) can comprise a substantial portion of the organic carbon budget in coastal bottom waters, yet it is often neglected in coastal carbon cycle models. In most modern sediment-water column flux models, biologically mediated reactions that remineralize particulate organic matter (POM) into inorganic compounds are simplified. In reality, organic matter remineralization is a complex suite of reactions that include DOM intermediate compounds. To better represent the sequential breakdown of POM and remineralization of DOM, a DOM state variable was built into a widely used sediment flux model. In the model, DOM is created in the sediment by hydrolysis of POM, and all organic matter passes through the DOM pool before remineralization. The model was run for 11?years and tuned to reproduce observed sediment flux data collected in Chesapeake Bay and then used to assess the role of DOM in sediment organic matter dynamics. Sediment-water column fluxes of DOM are highly variable both on seasonal and interannual scales, with substantial variability among stations in both magnitude and flux direction. Across all stations, semilabile and inert DOM is lost and labile DOM is taken up into the reactive first layer of the modeled sediment, with the net flux a balance of the two processes. The improved sediment flux model can be utilized to better understand the role of sediment biogeochemistry in the estuarine and coastal carbon cycle and shed light on difficult to measure processes involving DOM intermediate compounds.Clery, D., 2017. Signs of life. Science 358, 578-581. have found Earth-sized exoplanets. Now, they're figuring out how to detect life on them.Stephen Kane spends a lot of time staring at bad pictures of a planet. The images are just a few pixels across and nearly featureless. Yet Kane, an astronomer at the University of California, Riverside, has tracked subtle changes in the pixels over time. They are enough for him and his colleagues to conclude that the planet has oceans, continents, and clouds. That it has seasons. And that it rotates once every 24 hours.He knows his findings are correct because the planet in question is Earth. Kane took images from the Deep Space Climate Observatory satellite, which has a camera pointing constantly at Earth from a vantage partway to the sun, and intentionally degraded them from 4 million pixels to just a handful. The images are a glimpse into a future when telescopes will be able to just make out rocky, Earth-sized planets around other stars. Kane says he and his colleagues are trying to figure out “what we can expect to see when we can finally directly image an exoplanet.” Their exercise shows that even a precious few pixels can help scientists make the ultimate diagnosis: Does a planet harbor life?Finding conclusive evidence of life, or biosignatures, on a planet light-years away might seem impossible, given that space agencies have spent billions of dollars sending robot probes to much closer bodies that might be habitable, such as Mars and the moons of Saturn, without detecting even a whiff of life. But astronomers hope that a true Earth twin, bursting with flora and fauna, would reveal its secrets to even a distant observer.Detecting them won't be easy, considering the meager harvest of photons astronomers are likely to get from such a tiny, distant world, its signal almost swamped by its much brighter nearby star. The new generation of space telescopes heading toward the launch pad, including NASA's mammoth James Webb Space Telescope (JWST), have only an outside chance of probing an Earth twin in sufficient detail. But they will be able to sample light from a range of other planets, and astronomers are already dreaming of a space telescope that might produce an image of an Earth-like planet as good as Kane's pixelated views of Earth. To prepare for the coming flood of exoplanet data, and help telescope designers know what to look for, researchers are now compiling lists of possible biosignatures, from spectral hints of gases that might emanate from living things to pigments that could reside in alien plants or microbes.There is unlikely to be a single smoking gun. Instead, context and multiple lines of evidence will be key to a detection of alien life. Finding a specific gas—oxygen, say—in an alien atmosphere isn't enough without figuring out how the gas could have gotten there. Knowing that the planet's average temperature supports liquid water is a start, but the length of the planet's day and seasons and its temperature extremes count, too. Even an understanding of the planet's star is imperative, to know whether it provides steady, nourishing light or unpredictable blasts of harmful radiation.“Each [observation] will provide crucial evidence to piece together to say if there is life,” says Mary Voytek, head of NASA's astrobiology program in Washington, D.C.In the heady early days following the discovery of the first exoplanet around a normal star in 1995, space agencies drew up plans for extremely ambitious—and expensive—missions to study Earth twins that could harbor life. Some concepts for NASA's Terrestrial Planet Finder and the European Space Agency's Darwin mission envisaged multiple giant telescopes flying in precise formation and combining their light to increase resolution. But neither mission got off the drawing board. “It was too soon,” Voytek says. “We didn't have the data to plan it or build it.”Instead, efforts focused on exploring the diversity of exoplanets, using both ground-based telescopes and missions such as NASA's Kepler spacecraft. Altogether they have identified more than 3500 confirmed exoplanets, including about 30 roughly Earth-sized worlds capable of retaining liquid water. But such surveys give researchers only the most basic physical information about the planets: their orbits, size, and mass. In order to find out what the planets are like, researchers need spectra: light that has passed through the planet's atmosphere or been reflected from its surface, broken into its component wavelengths.Most telescopes don't have the resolution to separate a tiny, dim planet from its star, which is at least a billion times brighter. But even if astronomers can't see a planet directly, they can still get a spectrum if the planet transits, or passes in front of the star, in the course of its orbit. As the planet transits, starlight shines through its atmosphere; gases there absorb particular wavelengths and leave characteristic dips in the star's spectrum.Astronomers can also study a transiting planet by observing the star's light as the planet's orbit carries it behind the star. Before the planet is eclipsed, the spectrum will include both starlight and light reflected from the planet; afterward, the planet's contribution will disappear. Subtracting the two spectra should reveal traces of the planet.Teasing a recognizable signal from the data is far from easy. Because only a tiny fraction of the star's light probes the atmosphere, the spectral signal is minuscule, and hard to distinguish from irregularities in the starlight itself and from absorption by Earth's own atmosphere. Most scientists would be “surprised at how horrible the data is,” says exoplanet researcher Sara Seager of the Massachusetts Institute of Technology in Cambridge.In spite of those hurdles, the Hubble and Spitzer space telescopes, plus a few others, have used these methods to detect atmospheric gases, including sodium, water, carbon monoxide and dioxide, and methane, from a handful of the easiest targets. Most are “hot Jupiters”—big planets in close-in orbits, their atmospheres puffed up by the heat of their star.The approach will pay much greater dividends after the launch of the JWST in 2019. Its 6.5-meter mirror will collect far more light from candidate stars than existing telescopes can, allowing it to tease out fainter exoplanet signatures, and its spectrographs will produce much better data. And it will be sensitive to the infrared wavelengths where the absorption lines of molecules such as water, methane, and carbon monoxide and dioxide are most prominent.Once astronomers have such spectra, one of the main gases that they hope to find is oxygen. Not only does it have strong and distinctive absorption lines, but many believe its presence is the strongest sign that life exists on a planet.Oxygen-producing photosynthesis made Earth what it is today. First cyanobacteria in the oceans and then other microbes and plants have pumped out oxygen for billions of years, so that it now makes up 21% of the atmosphere—an abundance that would be easily detectable from afar. Photosynthesis is evolution's “killer app,” says Victoria Meadows, head of the NASA-sponsored Virtual Planet Laboratory (VPL) at the University of Washington in Seattle. It uses a prolific source of energy, sunlight, to transform two molecules thought to be common on most terrestrial planets—water and carbon dioxide—into sugary fuel for multicellular life. Meadows reckons it is a safe bet that something similar has evolved elsewhere. “Oxygen is still the first thing to go after,” she says.Fifteen years ago, when exoplanets were new and researchers started thinking about how to scan them for life, “Champagne would have flowed” if oxygen had been detected, Meadows recalls. But since then, researchers have realized that things are not that simple: Lifeless planets can have atmospheres full of oxygen, and life can proliferate without ever producing the gas. That was the case on Earth, where, for 2 billion years, microbes practiced a form of photosynthesis that did not produce oxygen or many other gases. “We've had to make ourselves more aware of how we could be fooled,” Meadows says.To learn what a genuine biosignature might look like, and what might be a false alarm, Meadows and her colleagues at the VPL explore computer models of exoplanet atmospheres, based on data from exoplanets as well as observations of more familiar planets, including Earth. They also do physical experiments in vacuum chambers. They recreate the gaseous cocktails that may surround exoplanets, illuminate them with simulated starlight of various kinds, and see what can be measured.Over the past few years, VPL researchers have used such models to identify nonbiological processes that could make oxygen and produce a “false positive” signal. For example, a planet with abundant surface water might form around a star that, in its early years, surges in brightness, perhaps heating the young planet enough to boil off its oceans. Intense ultraviolet light from the star would bombard the resulting water vapor, perhaps splitting it into hydrogen and oxygen. The lighter hydrogen could escape into space, leaving an atmosphere rich in oxygen around a planet devoid of life. “Know thy star, know thy planet,” recites Siddharth Hegde of Cornell University's Carl Sagan Institute.Discovering methane in the same place as oxygen, however, would strengthen the case for life. Although geological processes can produce methane, without any need for life, most methane on Earth comes from microbes that live in landfill sites and in the guts of ruminants. Methane and oxygen together make a redox pair: two molecules that will readily react by exchanging electrons. If they both existed in the same atmosphere, they would quickly combine to produce carbon dioxide and water. But if they persist at levels high enough to be detectable, something must be replenishing them. “It's largely accepted that if you have redox molecules in large abundance they must be produced by life,” Hegde says.Some argue that by focusing on oxygen and methane—typical of life on Earth—researchers are ignoring other possibilities. If there is one thing astronomers have learned about exoplanets so far, it is that familiar planets are a poor guide to exoplanets' huge diversity of size and nature. And studies of extremophiles, microbes that thrive in inhospitable environments on Earth, suggest life can spring up in unlikely places. Exobiology may be entirely unlike its counterpart on Earth, and so its gaseous byproducts might be radically different, too.But what gases to look for? Seager and her colleagues compiled a list of 14,000 compounds that might exist as a gas at “habitable” temperatures, between the freezing and boiling points of water; to keep the list manageable they restricted it to small molecules, with no more than six nonhydrogen atoms. About 2500 are made of the biogenic atoms carbon, nitrogen, oxygen, phosphorus, sulfur, and hydrogen, and about 600 are actually produced by life on Earth. Detecting high levels of any of these gases, if they can't be explained by nonbiological processes, could be a sign of alien biology, Seager and her colleagues argue.Light shining through the atmospheres of transiting exoplanets is likely to be the mainstay of biosignature searches for years to come. But the technique tends to sample the thin upper reaches of a planet's atmosphere; far less starlight may penetrate the thick gases that hug the surface, where most biological activity is likely to occur. The transit technique also works best for hot Jupiters, which by nature are less likely to host life than small rocky planets with thinner atmospheres. The JWST may be able to tease out atmospheric spectra from small planets if they orbit small, dim stars like red dwarfs, which won't swamp the planet's spectrum. But these red dwarfs have a habit of spewing out flares that would make it hard for life to establish itself on a nearby planet.To look for signs of life on a terrestrial planet around a sunlike star, astronomers will probably have to capture its light directly, to form a spectrum or even an actual image. That requires blocking the overwhelming glare of the star. Ground-based telescopes equipped with “coronagraphs,” which precisely mask a star so nearby objects can be seen, can now capture only the biggest exoplanets in the widest orbits. To see terrestrial planets will require a similarly equipped telescope in space, above the distorting effect of the atmosphere. NASA's Wide Field Infrared Survey Telescope (WFIRST), expected to launch in the mid-2020s, is meant to fill that need.Even better, WFIRST could be used in concert with a “starshade”—a separate spacecraft stationed 50,000 kilometers from the telescope that unfurls a circular mask tens of meters across to block out starlight. A starshade is more effective than a coronagraph at limiting the amount of light going into the telescope. It not only blocks the star directly, but also suppresses diffraction with an elaborate petaled edge. That reduces the stray scattered light that can make it hard to spot faint planets. A starshade is a much more expensive prospect than a coronagraph, however, and aligning telescope and starshade over huge distances will be a challenge.Direct imaging will provide much better spectra than transit observations because light will pass through the full depth of the planet's atmosphere twice, rather than skimming through its outer edges. But it also opens up the possibility of detecting life directly, instead of through its waste gases in the atmosphere. If organisms, whether they are plants, algae, or other microbes, cover a large proportion of a planet's surface, their pigments may leave a spectral imprint in the reflected light. Earthlight contains an obvious imprint of this sort. Known as the “red edge,” it is the dramatic change in the reflectance of green plants at a wavelength of about 720 nanometers. Below that wavelength, plants absorb as much light as possible for photosynthesis, reflecting only a few percent. At longer wavelengths, the reflectance jumps to almost 50%, and the brightness of the spectrum rises abruptly, like a cliff. “An alien observer could easily tell if there is life on Earth,” Hegde says.There's no reason to assume that alien life will take the form of green plants. So Hegde and his colleagues are compiling a database of reflectance spectra for different types of microbes. Among the hundreds the team has logged are many extremophiles, which fill marginal niches on Earth but may be a dominant life form on an exoplanet. Many of the microbes on the list have not had their reflectance spectra measured, so the Cornell team is filling in those gaps. Detecting pigments on an exoplanet surface would be extremely challenging. But a tell-tale color in the faint light of a distant world could join other clues—spectral absorption lines from atmospheric gases, for example—to form “a jigsaw puzzle which overall gives us a picture of the planet,” Hegde says.None of the telescopes available now or in the next decade is designed specifically to directly image exoplanets, so biosignature searches must compete with other branches of astronomy for scarce observing time. What researchers really hanker after is a large space telescope purpose-built to image Earth-like alien worlds—a new incarnation of the idea behind NASA's ill-fated Terrestrial Planet Finder.The Habitable Exoplanet Imaging Mission, or HabEx, a mission concept now being studied by NASA, could be the answer. Its telescope would have a mirror up to 6.5 meters across—as big as the JWST's—but would be armed with instruments sensitive to a broader wavelength range, from the ultraviolet to the near-infrared, to capture the widest range of spectral biosignatures. The telescope would be designed to reduce scattered light and have a coronagraph and starshade to allow direct imaging of Earth-sized exoplanets.Such a mission would reveal Earth-like planets at a level of detail researchers can now only dream about—probing atmospheres, revealing any surface pigments, and even delivering the sort of blocky surface images that Kane has been simulating. But will that be enough to conclude we are not alone in the universe? “There's a lot of uncertainty about what would be required to put the last nail in the coffin,” Kane says. “But if HabEx is built according to its current design, it should provide a pretty convincing case.”Cleveland, D., Brumbaugh, W.G., MacDonald, D.D., 2017. A comparison of four porewater sampling methods for metal mixtures and dissolved organic carbon and the implications for sediment toxicity evaluations. Environmental Toxicology and Chemistry 36, 2906-2915. of sediment quality conditions are commonly conducted using whole-sediment chemistry analyses but can be enhanced by evaluating multiple lines of evidence, including measures of the bioavailable forms of contaminants. In particular, porewater chemistry data provide information that is directly relevant for interpreting sediment toxicity data. Various methods for sampling porewater for trace metals and dissolved organic carbon (DOC), which is an important moderator of metal bioavailability, have been employed. The present study compares the peeper, push point, centrifugation, and diffusive gradients in thin films (DGT) methods for the quantification of 6 metals and DOC. The methods were evaluated at low and high concentrations of metals in 3 sediments having different concentrations of total organic carbon and acid volatile sulfide and different particle-size distributions. At low metal concentrations, centrifugation and push point sampling resulted in up to 100 times higher concentrations of metals and DOC in porewater compared with peepers and DGTs. At elevated metal levels, the measured concentrations were in better agreement among the 4 sampling techniques. The results indicate that there can be marked differences among operationally different porewater sampling methods, and it is unclear if there is a definitive best method for sampling metals and DOC in porewater. Environ Toxicol Chem 2017;36:2906–2915. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.Coles, V.J., Stukel, M.R., Brooks, M.T., Burd, A., Crump, B.C., Moran, M.A., Paul, J.H., Satinsky, B.M., Yager, P.L., Zielinski, B.L., Hood, R.R., 2017. Ocean biogeochemistry modeled with emergent trait-based genomics. Science 358, 1149-1154.: Marine ecosystem models have advanced to incorporate metabolic pathways discovered with genomic sequencing, but direct comparisons between models and “omics” data are lacking. We developed a model that directly simulates metagenomes and metatranscriptomes for comparison with observations. Model microbes were randomly assigned genes for specialized functions, and communities of 68 species were simulated in the Atlantic Ocean. Unfit organisms were replaced, and the model self-organized to develop community genomes and transcriptomes. Emergent communities from simulations that were initialized with different cohorts of randomly generated microbes all produced realistic vertical and horizontal ocean nutrient, genome, and transcriptome gradients. Thus, the library of gene functions available to the community, rather than the distribution of functions among specific organisms, drove community assembly and biogeochemical gradients in the model ocean.Editor's summary. Functional ocean biogeography: Marine ecosystems are well represented in metagenomic and transcriptomic data. These data are not routinely used to test ecosystem models that explore ocean biogeography or biogeochemistry. Coles et al. built a model in which genes for a range of functions were assigned to different suites of simulated microbes (see the Perspective by Rynearson). Communities emerged from the model with realistic biogeographical and biogeochemical profiles when compared to microbial data collected from the Amazon River plume. However, functional composition trumped the details of taxonomy, and different, coevolving community compositions emerged that provided similar biogeochemical outcomes.Collins, J.A., Prange, M., Caley, T., Gimeno, L., Beckmann, B., Mulitza, S., Skonieczny, C., Roche, D., Schefu?, E., 2017. Rapid termination of the African Humid Period triggered by northern high-latitude cooling. Nature Communications 8, Article 1372. rapidity and synchrony of the African Humid Period (AHP) termination at around 5.5?ka are debated, and it is unclear what caused a rapid hydroclimate response. Here we analysed the hydrogen isotopic composition of sedimentary leaf-waxes (δDwax) from the Gulf of Guinea, a proxy for regional precipitation in Cameroon and the central Sahel-Sahara. Our record indicates high precipitation during the AHP followed by a rapid decrease at 5.8–4.8?ka. The similarity with a δDwax record from northern East Africa suggests a large-scale atmospheric mechanism. We show that northern high- and mid-latitude cooling weakened the Tropical Easterly Jet and, through feedbacks, strengthened the African Easterly Jet. The associated decrease in precipitation triggered the AHP termination and combined with biogeophysical feedbacks to result in aridification. Our findings suggest that extratropical temperature changes, albeit smaller than during the glacial and deglacial, were important in triggering rapid African aridification during the Holocene.Connan, J., Kavak, O., Sa?lamtimur, H., Engel, M., Zumberge, A., Zumberge, J., 2018. A geochemical study of bitumen residues on ceramics excavated from Early Bronze age graves (3000–2900 BCE) at Ba?ur H?yük in SE Turkey. Organic Geochemistry 115, 1-11. black residues, scraped from outer surfaces of painted ceramics, unearthed from graves 1–3 at Ba?ur H?yük (SE Turkey), were analysed by geochemical techniques in order to characterize bitumens and to try to identify their source. Ceramics are dated from the Early Bronze period (3100–2900 BCE). The black organic matter was indeed identified as bitumen, but its source has not been discovered despite its comparison with several oil seeps from the area. The bitumen at Ba?ur H?yük does not match the bitumens analyzed at Kavu?an H?yük, Salat H?yük, Hakemi Use and Kuriki H?yük which are Cretaceous in origin and likely imported from the Eruh tars deposit. The stable carbon isotope values of their asphaltene fraction suggest a Silurian origin, however the occurrence of the 18α(H)-oleanane emphasized a younger source, i.e. Tertiary or Cretaceous. Our interpretation favours the mixture of two oils, a Silurian age and a Tertiary-Cretaceous age. This mixture may occur geologically, due to the uptake of a Tertiary signal by a Silurian oil along its migration route to the surface. It may also be a consequence of human activity carried out by the inhabitants at the mortuary ceremony where the bituminous mixture has been applied to ceramics, prior to their deposit in the graves. The oil seep character of the archaeological bitumen at Ba?ur H?yük and the lack of obvious oxidation suggest the following explanation: freshly collected oil seeps were splashed on ceramics as ritual practices and the tarry potteries were then buried and therefore sealed. The fast burial prevented the bitumen from any oxidative alteration.Cooper, R.E., Eusterhues, K., Wegner, C.E., Totsche, K.U., Küsel, K., 2017. Ferrihydrite-associated organic matter (OM) stimulates reduction by Shewanella oneidensis MR-1 and a complex microbial consortia. Biogeosciences 14, 5171-5188. formation of Fe(III) oxides in natural environments occurs in the presence of natural organic matter (OM), resulting in the formation of OM–mineral complexes that form through adsorption or coprecipitation processes. Thus, microbial Fe(III) reduction in natural environments most often occurs in the presence of OM–mineral complexes rather than pure Fe(III) minerals. This study investigated to what extent does the content of adsorbed or coprecipitated OM on ferrihydrite influence the rate of Fe(III) reduction by Shewanella oneidensis MR-1, a model Fe(III)-reducing microorganism, in comparison to a microbial consortium extracted from the acidic, Fe-rich Schl?ppnerbrunnen fen. We found that increased OM content led to increased rates of microbial Fe(III) reduction by S. oneidensis MR-1 in contrast to earlier findings with the model organism Geobacter bremensis. Ferrihydrite–OM coprecipitates were reduced slightly faster than ferrihydrites with adsorbed OM. Surprisingly, the complex microbial consortia stimulated by a mixture of electrons donors (lactate, acetate, and glucose) mimics S. oneidensis under the same experimental Fe(III)-reducing conditions suggesting similar mechanisms of electron transfer whether or not the OM is adsorbed or coprecipitated to the mineral surfaces. We also followed potential shifts of the microbial community during the incubation via 16S rRNA gene sequence analyses to determine variations due to the presence of adsorbed or coprecipitated OM–ferrihydrite complexes in contrast to pure ferrihydrite. Community profile analyses showed no enrichment of typical model Fe(III)-reducing bacteria, such as Shewanella or Geobacter sp., but an enrichment of fermenters (e.g., Enterobacteria) during pure ferrihydrite incubations which are known to use Fe(III) as an electron sink. Instead, OM–mineral complexes favored the enrichment of microbes including Desulfobacteria and Pelosinus sp., both of which can utilize lactate and acetate as an electron donor under Fe(III)-reducing conditions. In summary, this study shows that increasing concentrations of OM in OM–mineral complexes determines microbial Fe(III) reduction rates and shapes the microbial community structure involved in the reductive dissolution of ferrihydrite. Similarities observed between the complex Fe(III)-reducing microbial consortia and the model Fe(III)-reducer S. oneidensis MR-1 suggest electron-shuttling mechanisms dominate in OM-rich environments, including soils, sediments, and fens, where natural OM interacts with Fe(III) oxides during mineral formation.Correia, V.F., Riding, J.B., Duarte, L.V., Fernandes, P., Pereira, Z., 2017. The palynological response to the Toarcian Oceanic Anoxic Event (Early Jurassic) at Peniche, Lusitanian Basin, western Portugal. Marine Micropaleontology 137, 46-63. uppermost Pliensbachian and lower Toarcian (Lower Jurassic) succession exposed at Peniche in the central part of the Lusitanian Basin, western Portugal, was examined for palynomorphs. The 45 samples span the Emaciaticeras emaciatum, Dactylioceras polymorphum and Hildaites levisoni ammonite biozones (ABs), and the succession includes the Global boundary Stratotype Section and Point (GSSP) for the Toarcian Stage and the Toarcian Oceanic Anoxic Event (T-OAE). A low diversity dinoflagellate cyst flora, typical of the Sub-Boreal Realm, was recovered from the Emaciaticeras emaciatum and Dactylioceras polymorphum ABs. The dominant element is the cold water species Luehndea spinosa, which is an index for the Pliensbachian to earliest Toarcian, and is thought to have migrated from the more northerly Boreal Realm. Prior to the T-OAE, dinoflagellates thrived in the Lusitanian Basin, except during a brief warm period in the earliest Toarcian. Despite the latter, the recovery from this event was relatively rapid and was characterised by a return to relatively cool temperatures. The Hildaites levisoni AB at Peniche represents the T-OAE and the overlying strata, and is characterised by a profound reduction in dinoflagellate cyst relative abundances. This dinoflagellate cyst ‘blackout’, and the associated rise of prasinophytes, reflects significant environmental stress, such as marine anoxia, elevated temperatures and reduced salinity, with the former two probably being most important. The low proportions of dinoflagellate cysts following the T-OAE indicates a protracted recovery phase from the bottom and water column anoxia developed throughout the Lusitanian Basin.Costanzo, M.T., Boock, J.J., Kemperman, R.H.J., Wei, M.S., Beekman, C.R., Yost, R.A., 2017. Portable FAIMS: Applications and future perspectives. International Journal of Mass Spectrometry 422, 188-196. mass spectrometry (MMS) is optimal for a wide variety of applications that benefit from field-portable instrumentation. Like MMS, field asymmetric ion mobility spectrometry (FAIMS) has proven capable of providing in situ analysis, allowing researchers to bring the lab to the sample. FAIMS compliments MMS very well, but has the added benefit of operating at atmospheric pressure, unlike MS. This distinct advantage makes FAIMS uniquely suited for portability. Since its inception, FAIMS has been envisioned as a field-portable device, as it affords less expense and greater simplicity than many similar methods Ideally, these are simple, robust devices that may be operated by non-professional personnel, yet still provide adequate data when in the field. While reducing the size and complexity tends to bring with it a loss of performance and accuracy, this is made up for by the incredibly high throughput and overall convenience of the instrument. Moreover, the FAIMS device used in the field can be brought back to the lab, and coupled to a conventional mass spectrometer to provide any necessary method development and compound validation. This work discusses the various considerations, uses, and applications for portable FAIMS instrumentation, and how the future of each applicable field may benefit from the development and acceptance of such a device.Crawford, E.A., Gerbig, S., Spengler, B., Volmer, D.A., 2017. Rapid fingerprinting of lignin by ambient ionization high resolution mass spectrometry and simplified data mining. Analytica Chimica Acta 994, 38-48. ionization techniques are typically used to analyze samples in their native states with minimal or no sample pretreatment prior to mass spectrometric (MS) analysis. Desorption electrospray ionization (DESI) and direct analysis in real time (DART) were systematically investigated in this work for direct solid analysis of depolymerized lignin samples, with the goal of rapidly fingerprinting these samples, to efficiently characterize the subunits of this renewable energy source. High resolution MS was required for enhanced selectivity in this study due to the inherent structural complexity of lignin. DESI provided results across a broader mass range (up to m/z 700) than DART and also ionized saturated compounds of low oxygen-to-carbon (O/C) ratios and low double bond equivalents (DBE). While DART detected the same core lignin monomeric and dimeric compounds as seen with DESI and electrospray ionization (ESI), results were restricted to a narrower mass range to m/z 500, due to thermal degradation and losses of methoxy groups. In contrast to DESI and ESI, the DART spectra were nearly void of saturated components. On a structural level, the core lignin compounds were visually fingerprinted and ionization method performances critically assessed by employing simplified Kendrick-based data mining approaches. A novel simplified data visualization approach was developed in this work based on modified Kendrick mass defect (KMD) filtering for lignin subunits and plotting the mass defect values against the degree of unsaturation. Direct visualization of monomeric, dimeric and trimeric lignin species was simplified by the KMD separation plots, easily allowing the core lignin compounds to be visually identified and compared. Modified KMD bases, namely methoxy and phenol bases, which represent monomer-specific lignin constituents, were successfully used to classify and group the complex mixture of lignin species. Further separation of methoxy-related lignin species was successfully achieved by employing the more specific phenolic KMD base.Creydt, M., Fischer, M., 2017. Plant metabolomics: Maximizing metabolome coverage by optimizing mobile phase additives for nontargeted mass spectrometry in positive and negative electrospray ionization mode. Analytical Chemistry 89, 11083-11090. screening methods with ultrahigh-performance liquid chromatography-electrospray ionization/quadrupole-time-of-flight mass spectrometry have been extensively applied to plant metabolomics to very diverse scientific issues in plant metabolomics. In this study, different mobile phase additives were tested in order to improve the electrospray ionization process and to detect as many metabolites as possible with high peak intensities in positive and negative ionization mode. Influences of modifiers were examined for nonpolar and polar compounds, as optimal conditions are not always the same. By combining different additives, metabolite coverage could be significantly increased. The best results for polar metabolites in positive ionization mode were achieved by using 0.1% acetic acid and 0.1% formic acid in negative ionization mode. For measurements of nonpolar metabolites in positive ionization mode, the application of 10 mmol/L ammonium formate led to the best findings, while the use of 0.02% acetic acid was more appropriate in negative ionization mode.Crognale, S., Amalfitano, S., Casentini, B., Fazi, S., Petruccioli, M., Rossetti, S., 2017. Arsenic-related microorganisms in groundwater: a review on distribution, metabolic activities and potential use in arsenic removal processes. Reviews in Environmental Science and Bio/Technology 16, 647-665. plays a central role in the hydrological cycle and represents the utmost natural resource for human consumption and activities on a global scale. Therefore, any source of contamination of either geogenic or anthropogenic origin may provide a serious environmental health threat. Within the long list of organic and inorganic groundwater contaminants, arsenic, a toxic element retrieved in air, soils, rocks, waters and organisms, can occur at high concentrations in aquifers representing an issue of worldwide concern. Over the past years, research efforts aimed to elucidate the microorganisms and mechanisms involved in the biogeochemical cycling of this element. An emerging challenge is to identify and exploit microbial metabolic potentialities for arsenic-contaminated water treatment. The objective of this review is to outline the existing knowledge about ecology, biochemistry and genomics of arsenic-related microorganisms, with particular reference to their distribution and their capabilities to oxidize As(III) in groundwater. Moreover, a broad evaluation of the application potentialities of microbiological processes suitable for treatment strategies of arsenic-contaminated groundwater is provided.Crognale, S., D'Annibale, A., Pesciaroli, L., Stazi, S.R., Petruccioli, M., 2017. Fungal community structure and As-resistant fungi in a decommissioned gold mine site. Frontiers in Microbiology 8, 2202. doi: 10.3389/fmicb.2017.02202. large quantities of heavy metal laden wastes are released in an uncontrolled manner by gold mining activities with ensuing contamination of the surrounding areas, there is scant information on the mycobiota of gold-mine sites. Thus, the present study was aimed to describe the fungal community structure in three differently As- and Hg-polluted soils collected from the Pestarena decommissioned site by using Illumina? metabarcoding. Fungal richness was found to increase as the contamination level increased while biodiversity was not related to the concentrations of inorganic toxicants. Within the phylum Zygomigota which, irrespective of the contamination level, was predominant in all the soils under study, the most abundant genera were Mucor and Mortierella. The relative abundances of Basidiomycota, instead, tended to raise as the contamination increased; within this phylum the most abundant genera were Cryptococcus and Pseudotomentella. The abundance of Ascomycota, ranging from about 8 to 21%, was not related to the contamination level. The relative abundances of those genera (i.e., Penicillium, Trichoderma, and Chaetomium), the cultivable isolates of which exhibited significant As-resistance, were lower than the set threshold (0.5%). Mass balances obtained from As-exposure experiments with these isolates showed that the main mechanisms involved in counteracting the toxicant were accumulation and, above all, volatilization, the respective extents of which ranged from 0.6 to 5.9% and from 6.4 to 31.2% in dependence of the isolate.Cronin, T.M., Dwyer, G.S., Caverly, E.K., Farmer, J., DeNinno, L.H., Rodriguez-Lazaro, J., Gemery, L., 2017. Enhanced Arctic amplification began at the Mid-Brunhes Event ~400,000 years ago. Scientific Reports 7, Article 14475. Ocean temperatures influence ecosystems, sea ice, species diversity, biogeochemical cycling, seafloor methane stability, deep-sea circulation, and CO2 cycling. Today’s Arctic Ocean and surrounding regions are undergoing climatic changes often attributed to “Arctic amplification” – that is, amplified warming in Arctic regions due to sea-ice loss and other processes, relative to global mean temperature. However, the long-term evolution of Arctic amplification is poorly constrained due to lack of continuous sediment proxy records of Arctic Ocean temperature, sea ice cover and circulation. Here we present reconstructions of Arctic Ocean intermediate depth water (AIW) temperatures and sea-ice cover spanning the last ~ 1.5 million years (Ma) of orbitally-paced glacial/interglacial cycles (GIC). Using Mg/Ca paleothermometry of the ostracode Krithe and sea-ice planktic and benthic indicator species, we suggest that the Mid-Brunhes Event (MBE), a major climate transition ~ 400–350 ka, involved fundamental changes in AIW temperature and sea-ice variability. Enhanced Arctic amplification at the MBE suggests a major climate threshold was reached at ~ 400 ka involving Atlantic Meridional Overturning Circulation (AMOC), inflowing warm Atlantic Layer water, ice sheet, sea-ice and ice-shelf feedbacks, and sensitivity to higher post-MBE interglacial CO2 concentrations.Cui, G., Li, X., Li, Q., Huang, J., Tao, Y., Li, S., Zhang, J., 2017. Damming effects on dissolved inorganic carbon in different kinds of reservoirs in Jialing River, Southwest China. Acta Geochimica 36, 581-597. assess the effects of river damming on dissolved inorganic carbon in the Jialing River, a total of 40 water samples, including inflow, outflow, and stratified water in four cascade reservoirs (Tingzikou, Xinzheng, Dongxiguan, Caojie) were collected in January and July, 2016. The major cations, anions, and δ13CDIC values were analyzed. It was found that the dissolved compositions are dominated by carbonate weathering, while sulfuric acids may play a relatively important role during carbonate weathering and increasing DIC concentration. Different reservoirs had variable characteristics of water physiochemical stratification. The DIC concentrations of reservoir water were lower in summer than those in winter due to the dilute effects and intensive aquatic photosynthesis, as well as imported tributaries. The δ13CDIC values in Tingzikou Reservoir were higher during summer than those in winter, which indicated that intensive photosynthesis increased the δ13CDIC values in residual water, but a similar trend was not obvious in other reservoirs. Except for in Xinzheng Reservoir, the δ13CDIC values in inflow and outflow reservoir water were lower than those in the surface water of stratified sampling in summer. For stratified sampling, it could be found that, in summer, the Tingzikou Reservoir δ13CDIC values significantly decreased with water depth due to the anaerobic breakdown of organic matter. The significant correlation (p < 0.01 or 0.05) between the DIC concentrations, the δ13CDIC values and anthropogenic species (Na++K+, Cl–, SO 2? 4 SO42?and NO ? 3 NO3?) showed that the isotope composition of DIC can be a useful tracer of contaminants. In total, Tingzikou Reservoir showed lacustrine features, Xinzheng Reservoir and Dongxiguan Reservoir had “transitional” features, and Caojie Reservoir had a total of “fluvial” features. Generally, cascade reservoirs in the Jialing River exhibited natural river features rather than typical lake features due to characteristics of reservoir water in physiochemical stratification, spatiotemporal variations of DIC concentrations and isotopic compositions. It is evident that the dissolved inorganic carbon dynamics of natural rivers had been partly remolded by dam building.Cui, G., Liu, J., Wei, M., Shi, R., Elsworth, D., 2018. Why shale permeability changes under variable effective stresses: New insights. Fuel 213, 55-71. measurements of shale permeability are normally conducted under conditions of constant effective stresses. Based on the theory of poroelasticity, shale permeability in non-sorbing media is determined by the effective stress alone and remains unchanged if the effective stress does not change. This theoretical conclusion contradicts some experimental observations in sorbing media. These enigmatic phenomena are analyzed through a model accommodating gas slippage. This approach can explain why shale permeability is significant at low gas pressure but does not explain the contradiction with poromechanics. In this work, we develop and apply an alternative approach to resolve this dilemma. The model comprises flow within a nanotube capillary embedded within the shale matrix (discrete approach) and allows the evolution of shale permeability to be followed during the processes of shale gas flow. In the formulation, we define four strains: global strain of the shale, fracture-local strain, matrix-global strain, and pore-local strain. Shale permeability is defined as a function of these strains that are, in turn, a consequence of effective stress transfer between the matrix and the fracture systems. This behavior is regulated by the differential compliance of the various components and by gas diffusion from the fracture system to the matrix. We use the strain evolution to define how shale permeability changes with time or gas pressure in the matrix system. We apply the new model to generate a series of shale permeability profiles. These profiles are consistent with experimental observations reported in the literature. Through this study, we demonstrate that the experimental observations can indeed be explained through the inclusion of explicit interactions between shale microstructures and gas transport processes.Culp-Hill, R., Reisz, J.A., Hansen, K.C., D'Alessandro, A., 2017. Investigation of the effects of storage and freezing on mixes of heavy-labeled metabolite and amino acid standards. Rapid Communications in Mass Spectrometry 31, 2030-2034.: High-throughput metabolomics has now made it possible for small/medium-sized laboratories to analyze thousands of samples/year from the most diverse biological matrices including biofluids, cell and tissue extracts. In large-scale metabolomics studies, stable-isotope-labeled standards are increasingly used to normalize for matrix effects and control for technical reproducibility (e.g. extraction efficiency, chromatographic retention times and mass spectrometry signal stability). However, it is currently unknown how stable mixes of commercially available standards are following repeated freeze/thaw cycles or prolonged storage of aliquots.Methods: Standard mixes for 13C, 15N or deuterated isotopologues of amino acids and key metabolites from the central carbon and nitrogen pathways (e.g. glycolysis, Krebs cycle, redox homeostasis, purines) were either repeatedly frozen/thawed for up to 10 cycles or diluted into aliquots prior to frozen storage for up to 42 days. Samples were characterized by ultra-high-pressure liquid chromatography/mass spectrometry to determine the stability of the aliquoted standards upon freezing/thawing or prolonged storage.Results: Metabolite standards were stable over up to 10 freeze/thaw cycles, with the exception of adenosine and glutathione, showing technical variability across aliquots in a freeze/thaw-cycle-independent fashion. Storage for up to 42 days of mixes of commercially available standards did not significantly affect the stability of amino acid or metabolite standards for the first 2 weeks, while progressive degradation (statistically significant for fumarate) was observed after 3 weeks.Conclusions: Refrigerated or frozen preservation for at least 2 weeks of aliquoted heavy-labeled standard mixes for metabolomics analysis is a feasible and time-/resource-saving strategy for standard metabolomics laboratories.D'Alessandro, W., Daskalopoulou, K., Calabrese, S., Bellomo, S., 2018. Water chemistry and abiogenic methane content of a hyperalkaline spring related to serpentinization in the Argolida ophiolite (Ermioni, Greece). Marine and Petroleum Geology 89, Part 1, 185-193. mineral springs related to active continental serpentinization are a theme of growing interest since they may contain significant amounts of abiotic gas and have important implications for energy resource exploration, subsurface microbiology and astrobiology. We report the discovery of a new hyperalkaline (pH～12) spring issuing in the Agioi Anargyroi monastery at Ermioni (Greece), connected to serpentinization of peridotites of the Argolis ophiolite. Two water samples have been collected from separated springs and analysed for the chemical composition of major, minor and trace elements, and isotopic composition (2H and 18O) of water by IC, ICP-OES, ICP-MS and IRMS, and for the chemical (H2, O2, N2, CH4, CO2 and C2H6) and isotopic (He, δ2H-CH4 and δ13C-CH4) composition of dissolved gases. The Iliokastron Mélange Unit, comprising abundant serpentinized harzburgite, represent the aquifer feeding the hyperalkaline springs. The isotopic composition of water indicates a recent meteoric recharge probably through the close by and stratigraphically higher limestones of the Faniskos Unit. The Ca-OH water composition resulted to be similar to other hyperalkaline waters of Greece and worldwide. Although the concentrations of dissolved H2 are very low (tens of nmol/L) compared to other gases collected in similar manifestations, the concentrations of CH4 are considerable (38–314 μmol/L) and display isotopic compositions indicating a substantial if not exclusive abiogenic origin. Methane oxidation is also hypothesized in one of the two springs.D'Alessandro, W., Yüce, G., Italiano, F., Bellomo, S., Gülbay, A.H., Yasin, D.U., Gagliano, A.L., 2018. Large compositional differences in the gases released from the Kizildag ophiolitic body (Turkey): Evidences of prevailingly abiogenic origin. Marine and Petroleum Geology 89, Part 1, 174-184. investigated the geochemical features of the gases released from the Kizildag ophiolitic complex (Hatay, Turkey). Twenty-three samples both dissolved in hyperalkaline waters and free gases (bubbling gases and dry seeps) were collected. Samples were analysed for their chemical (He, H2, O2, N2, CH4 and CO2) and isotopic (He, δ13C-CH4, δ2H-CH4, δ2H-H2) composition including the content and C-isotopic composition of C2 to C5 alkanes in free gases. Analytical results evidence H2 production through low-temperature (<80 °C) serpentinization processes and subsequent abiogenic CH4 production through Fischer-Tropsch-type reactions. In some sample small additions of methane either of microbial or of thermogenic origin can be hypothesized. At one of the sites (Kisecik) a clear fractionation pattern due to microbial methane oxidation leading to strongly enriched isotopic values (δ13C +15‰ and δ2H ?68‰) and depletion in methane concentrations has been evidenced. At the dry gas seep of Kurtbagi methane flux measurements have been made and a preliminary output estimation of about 1000 kg per year has been obtained.Dai, K., Yu, Q., Zhang, Z., Wang, Y., Wang, X., 2018. Non-methane hydrocarbons in a controlled ecological life support system. Chemosphere 193, 207-212. hydrocarbons (NMHCs) are vital to people's health and plants' growth, especially inside a controlled ecological life support system (CELSS) built for long-term space explorations. In this study, we measured 54 kinds of NMHCs to study their changing trends in concentration levels during a 4-person-180-day integrated experiment inside a CELSS with four cabins for plants growing and other two cabins for human daily activities and resources management. During the experiment, the total mixing ratio of measured NMHCs was 423 ± 283 ppbv at the first day and it approached 2961 ± 323 ppbv ultimately. Ethane and propane were the most abundant alkanes and their mixing ratios kept growing from 27.5 ± 19.4 and 31.0 ± 33.6 ppbv to 2423 ± 449 ppbv and 290 ± 10 ppbv in the end. For alkenes, ethylene and isoprene presented continuously fluctuating states during the experimental period with average mixing ratios of 30.4 ± 19.3 ppbv, 7.4 ± 5.8 ppbv. For aromatic hydrocarbons, the total mixing ratios of benzene, toluene, ethylbenzene and xylenes declined from 48.0 ± 44 ppbv initially to 3.8 ± 1.1 ppbv ultimately. Biomass burning, sewage treatment, construction materials and plants all contributed to NMHCs inside CELSS. In conclusion, the results demonstrate the changing trends of NMHCs in a long-term closed ecological environment's atmosphere which provides valuable information for both the atmosphere management of CELSS and the exploration of interactions between humans and the total environment.Dalai, P., Pleyer, H.L., Strasdeit, H., Fox, S., 2017. The influence of mineral matrices on the thermal behavior of glycine. Origins of Life and Evolution of Biospheres 47, 427-452. the Hadean–Early Archean Earth, the first islands must have provided hot and dry environments for abiotically formed organic molecules. The heat sources, mainly volcanism and meteorite impacts, were also available on Mars during the Noachian period. In recent work simulating this scenario, we have shown that neat glycine forms a black, sparingly water-soluble polymer (“thermomelanoid”) when dry-heated at 200?°C under pure nitrogen. The present study explores whether relevant minerals and mineral mixtures can change this thermal behavior. Most experiments were conducted at 200 or 250?°C for 2 or 7?days. The mineral matrices used were phyllosilicates (Ca-montmorillonites SAz-1 and STx-1, Na-montmorillonite SAz-1-Na, nontronite NAu-1, kaolinite KGa-1), salts (NaCl, NaCl-KCl, CaCl2, artificial sea salt, gypsum, magnesite), picritic basalt, and three Martian regolith simulants (P-MRS, S-MRS, JSC Mars-1A). The main analytical method employed was high-performance liquid chromatography (HPLC). Glycine intercalated in SAz-1 and SAz-1-Na was well protected against thermomelanoid formation and sublimation at 200?°C: after 2?days, 95 and 79?%, respectively, had either survived unaltered or been transformed into the cyclic dipeptide (DKP) and linear peptides up to Gly6. The glycine survival rate followed the order SAz-1?>?SAz-1-Na?>?STx-1?≈?NAu-1?>?KGa-1. Very good protection was also provided by artificial sea salt (84?% unaltered glycine after 200?°C for 7?days). P-MRS promoted the condensation up to Gly6, consistent with its high phyllosilicate content. The remaining matrices were less effective in preserving glycine as such or as peptides.Daura, J., Sanz, M., Allué, E., Vaquero, M., López-García, J.M., Sánchez-Marco, A., Domènech, R., Martinell, J., Carrión, J.S., Ortiz, J.E., Torres, T., Arnold, L.J., Benson, A., Hoffmann, D.L., Skinner, A.R., Julià, R., 2017. Palaeoenvironments of the last Neanderthals in SW Europe (MIS 3): Cova del Coll Verdaguer (Barcelona, NE of Iberian Peninsula). Quaternary Science Reviews 177, 34-56. isotope stage 3 (MIS 3) was characterised by marked oscillations of extreme cold episodes with very short warm events during the stadial, and several regional differences have been recorded in the ice cores and marine deposits. The aim of this study is to reconstruct this period by evaluating both terrestrial and regional responses. Cova del Coll Verdaguer, a site located on the Iberian Peninsula, preserves a sedimentary deposit dated to between 34 and 56 ka BP and provides an opportunity for evaluating the impact of climate changes on the regional landmass during a period that coincided with the last Neanderthal population on the Iberian Peninsula. Several dating methods, including U-series, electron spin resonance, amino acid racemization and radiocarbon (14C), were applied to the site and the ages obtained show good agreement. The biotic evidence obtained is substantial, comprising floristic data from palynology and charcoal analysis, and faunal data from large and small mammals, birds and gastropods. Environmental reconstruction points to an initially open meadow landscape at the base of the sequence (～56 ka) that progressively changes to a woodland environment dominated by conifers (～34 ka). The presence of few thermophilous taxa, in contrast with lower latitudes of the Iberian Peninsula, is also detected. The environmental conditions of mid-altitude, Mediterranean, limestone mountains for the last Neanderthal populations appear to have been dominated by a forested landscape comprising boreal or mixed coniferous forest, characterised by a low usable biomass with poor comestible plant resources and dispersed herbivore populations.Davies, R.J., Maqueda, M.?.M., Li, A., Ganopolski, A., 2017. Millennial-scale shifts in the methane hydrate stability zone due to Quaternary climate change. Geology 45, 1027-1030. Establishing whether past millennial-scale climate change affected the stability of marine methane hydrate is important for our understanding of climatic change and determining the fate of marine hydrates in a future warmer world. We show, using three-dimensional seismic data offshore of Mauritania, that episodic, millennial-scale shifts of the base of the hydrate stability zone can be imaged below the ocean floor. Process modeling suggests that the base of the hydrate stability zone should have shallowed and deepened in response to climate change over the past ～150,000 yr. Specifically, there is seismic evidence for millennial-scale shifts during the Holocene (～11,700 yr ago to present) at a temporal resolution that has previously been unrealized. This is the first evidence that millennial-scale climatic cycles caused hydrate formation and dissociation and that hydrate instability should be expected in a warming world.Davis, K.J., Gerlach, R., 2018. Transition of biogenic coal-to-methane conversion from the laboratory to the field: A review of important parameters and studies. International Journal of Coal Geology 185, 33-43. methane (CBM) is an important unconventional natural gas resource in the U.S. and around the world. Many of the CBM containing coal formations are home to microbial communities producing the gas by converting coal to methane. Biogenically produced CBM provides an opportunity for developing technologies to enhance the microbial processes and increase the recoverable gas. To transfer strategies for biogenic CBM enhancement from small-scale laboratory studies to large-scale commercial applications in subsurface coal beds, there are several factors that should be considered to facilitate this transfer. Coal rank, chemistry and structure, formation water chemistry, as well as microbial communities can vary widely among coal formations, and matching these components in laboratory studies to each other and the coal bed of interest should be considered. More work is required to understand the effects of gas sorption, pressure, and water movement through coal formations on biogenic gas production. Additionally, methods for applying methane enhancement strategies in situ must be further investigated to develop commercial applications of enhanced microbial coalbed methane production.de Azevedo, S., González, M.F., Cintas, C., Ramallo, V., Quinto-Sánchez, M., Márquez, F., Hünemeier, T., Paschetta, C., Ruderman, A., Navarro, P., Pazos, B.A., Silva de Cerqueira, C.C., Velan, O., Ramírez-Rozzi, F., Calvo, N., Castro, H.G., Paz, R.R., González-José, R., 2017. Nasal airflow simulations suggest convergent adaptation in Neanderthals and modern humans. Proceedings of the National Academy of Sciences 114, 12442–12447.: Due to its role in humidifying and warming the air before it reaches the lungs, adaptations in the internal nasal anatomy are suspected to have been essential for modern humans and Neanderthals during the settlement of Eurasian harsh landscapes. Unfortunately, the lack of soft-tissue evidence in the fossil record precludes any study of Neanderthal respiratory performance. Here, we use warping techniques to reconstruct a generic Neanderthal nose, computational fluid dynamics simulations to compare the respiratory performance on both species, and evolutionary analyses to detect signals of selection. We report striking differences on fluid residence times under cold/dry climatic conditions. Different from previously suggested, our results indicate that both species would have achieved an advantageous species-specific respiratory performance in cold climates. Abstract: Both modern humans (MHs) and Neanderthals successfully settled across western Eurasian cold-climate landscapes. Among the many adaptations considered as essential to survival in such landscapes, changes in the nasal morphology and/or function aimed to humidify and warm the air before it reaches the lungs are of key importance. Unfortunately, the lack of soft-tissue evidence in the fossil record turns difficult any comparative study of respiratory performance. Here, we reconstruct the internal nasal cavity of a Neanderthal plus two representatives of climatically divergent MH populations (southwestern Europeans and northeastern Asians). The reconstruction includes mucosa distribution enabling a realistic simulation of the breathing cycle in different climatic conditions via computational fluid dynamics. Striking across-specimens differences in fluid residence times affecting humidification and warming performance at the anterior tract were found under cold/dry climate simulations. Specifically, the Asian model achieves a rapid air conditioning, followed by the Neanderthals, whereas the European model attains a proper conditioning only around the medium-posterior tract. In addition, quantitative-genetic evolutionary analyses of nasal morphology provided signals of stabilizing selection for MH populations, with the removal of Arctic populations turning covariation patterns compatible with evolution by genetic drift. Both results indicate that, departing from important craniofacial differences existing among Neanderthals and MHs, an advantageous species-specific respiratory performance in cold climates may have occurred in both species. Fluid dynamics and evolutionary biology independently provided evidence of nasal evolution, suggesting that adaptive explanations regarding complex functional phenotypes require interdisciplinary approaches aimed to quantify both performance and evolutionary signals on covariation patterns. Debiagi, P.E.A., Trinchera, M., Frassoldati, A., Faravelli, T., Vinu, R., Ranzi, E., 2017. Algae characterization and multistep pyrolysis mechanism. Journal of Analytical and Applied Pyrolysis 128, 423-436. paper presents a new characterization method and a multistep kinetic mechanism for describing the pyrolysis process of algae fuels. Since third generation biomasses are still largely unexplored, we first organized a database by collecting literature information on the nature and main features of algal biomass. The algal species, both macro- and micro-algae, are constituted by proteins, carbohydrates and lipids, present in various amounts depending on the taxonomy and growing conditions. Noteworthy, algae contain higher levels of proteins, lipids, nitrogen and ashes compared to vegetal biomasses. Starting from the ultimate analysis and ash content, the biochemical composition of each algal species is defined in terms of proteins, carbohydrates, and lipids. To this aim, a limited number of representative reference species is first defined, based on atomic mass balances. The predicted biochemical compositions fairly agree with experimental information. Then, a multi-step semi-detailed kinetic mechanism of algae pyrolysis has been developed for the different reference components, following the same approach successfully applied for lignocellulosic biomasses. Moreover, a further release of ammonium, nitrates, and carbonates groups is estimated and related to the ash content. Despite the reduced number of reference species and the rough assumptions to reduce the complexity of the overall problem, the model is already able to satisfactorily predict the pyrolysis behavior of micro- and macro-algae. To our knowledge, and despite all the strong simplifications, this is the first method to characterize algae species, as well as the first kinetic model able to predict the algae pyrolysis process.Dejam, M., Hassanzadeh, H., 2018. Diffusive leakage of brine from aquifers during CO2 geological storage. Advances in Water Resources 111, 36-57. area of investigation in this study is designed around an improved understanding of fundamentals of the diffusive leakage of brine from a storage aquifer into overlying and underlying low permeability layers during geosequestration of carbon dioxide (CO2) through development of a theoretical model. Here, we consider a two-dimensional domain in cylindrical coordinates, comprised of an aquifer and an overburden, where the interaction between the two media is handled by imposing the continuities of pressures and fluid fluxes at the aquifer-overburden interface. This coupled problem is solved by successive implementation of the Laplace and finite Hankel transforms. The developed solutions can be used to analyze diffusive leakage of brine from the aquifer into overburden and generate type curves for average pressures in the aquifer and overburden during injection and post injection periods. The results show that the leakage rate at early times is scaled with t1/2 while it remains constant at late times. It is also shown that the average pressure in the aquifer is scaled with t for short and long times. Moreover, the average pressure in the overburden is scaled with t at late times while it is scaled with t3/2 at early times. In addition, the results reveal that factors affecting diffusive leakage rate through intact overburden during CO2 storage are, in decreasing order of significance, thickness of overburden, thickness of aquifer, aquifer to overburden permeability ratio, and aquifer to overburden porosity ratio. However, thickness of aquifer has minimal effect on diffusive leakage of brine within post injection period. To evaluate the theoretical model, case studies for two potential sites in United Kingdom, one in Lincolnshire and the other one in the Firth of Forth, are conducted. The field studies show that the diffusive leakage from the aquifer into the overburden diminishes ～40 years after the injection has ceased for Lincolnshire while it stops after ～12 years for Firth of Forth. The average amount of the brine leaked from the aquifers per standard cubic meter (Sm3) of the injected CO2 through diffusive leakage was found to be 6.28?×?10?4 m3 of brine (or 0.330?kg of brine/kg of CO2) over ～70 years for Lincolnshire and 4.59?×?10?4 m3 of brine (or 0.242?kg of brine/kg of CO2) over ～42 years for Firth of Forth.Deng, Y., Yang, F., Deng, C., Yang, J., Jia, J., Yuan, H., 2017. Biodegradation of BTEX aromatics by a haloduric microbial consortium enriched from a sediment of Bohai Sea, China. Applied Biochemistry and Biotechnology 183, 893-905. study focused on a haloduric BTEX-degrading microbial consortium EC20 enriched from Bohai Sea sediment. EC20 degraded 87% of BTEX at 435?mg L?1 initial concentration (benzene, toluene, ethylbenzene, and xylenes in equal proportions) in the presence of 3.4% NaCl. 16S rRNA gene-based PCR-DGGE profiles revealed that the dominant bacteria in EC20 were Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes at the phylum level, and Pseudomonas, Mesorhizobium, Achromobacter, Stenotrophomonas, and Halomonas at the genus level. PCR detection of genes coding the key enzymes which participated in BTEX degradation pathways showed that the enriched consortium EC20 contained TOL pathway and TOD pathway to initiate biodegradation of BTEX.Denis, M., Jeanneau, L., Petitjean, P., Murzeau, A., Liotaud, M., Yonnet, L., Gruau, G., 2017. New molecular evidence for surface and sub-surface soil erosion controls on the composition of stream DOM during storm events. Biogeosciences 14, 5039-5051. events are responsible for more than 60?% of the export of dissolved organic matter (DOM) from headwater catchments due to an increase in both the discharge and concentration. The latter was attributed to changing water pathways inducing the mobilization of DOM from the surface soil horizons. Recent molecular investigations have challenged this view and hypothesized (i) a contribution of an in-stream partition of organic matter (OM) between eroded particles and the dissolved fraction and (ii) the modification of the composition of soil DOM during storm events. To investigate these assumptions, soil solutions in the macropores, surface runoff and stream outlet were sampled at high frequency during three storm events in the Kervidy–Naizin catchment, part of the French critical zone observatory AgrHyS. The molecular composition of the DOM was analysed by thermally assisted hydrolysis and methylation (THM) with tetramethylammonium hydroxide (TMAH) coupled to a gas chromatograph and a quadrupole mass spectrometer. These analyses highlighted a modification of the DOM composition in soil solution controlled by the water-table dynamic and pre-event hydrological conditions. These findings fit with the mechanism of colloidal and particulate destabilization in the soil macroporosity. The different behaviour observed for lignins, carbohydrates and fatty acids highlights a potential chemical segregation based on their hydrophobicity. The composition of surface runoff DOM is similar to the DOM composition in soil solution and could be generated by the same mechanism. The DOM composition in both soil solution and surface runoff corresponds to the stream DOM composition observed during storm events. On the basis of these results, modifications of the stream DOM composition during storm events seem to be due to surface and sub-surface soil erosion rather than in-stream production.Deniz, C.U., Yasar, M., Klein, M.T., 2017. Stochastic reconstruction of complex heavy oil molecules using an artificial neural network. Energy & Fuels 31, 11932-11938. approach for the stochastic reconstruction of petroleum fractions based on the joint use of artificial neural networks and genetic algorithms was developed. This hybrid approach reduced the time required for optimization of the composition of the petroleum fraction without sacrificing accuracy. A reasonable initial structural parameter set in the optimization space was determined using an artificial neural network. Then, the initial parameter set was optimized using a genetic algorithm. The simulations show that the time savings were between 62 and 74% for the samples used. This development is critical, considering that the characteristic time required for the optimization procedure is hours or even days for stochastic reconstruction. In addition, the standalone use of the artificial neural network step that produces instantaneous results may help where it is necessary to make quick decisions.Dewers, T., Eichhubl, P., Ganis, B., Gomez, S., Heath, J., Jammoul, M., Kobos, P., Liu, R., Major, J., Matteo, E., Newell, P., Rinehart, A., Sobolik, S., Stormont, J., Reda Taha, M., Wheeler, M., White, D., 2018. Heterogeneity, pore pressure, and injectate chemistry: Control measures for geologic carbon storage. International Journal of Greenhouse Gas Control 68, 203-215. outcomes for geologic carbon storage include maximizing storage efficiency, preserving injectivity, and avoiding unwanted consequences such as caprock or wellbore leakage or induced seismicity during and post injection. To achieve these outcomes, three control measures are evident including pore pressure, injectate chemistry, and knowledge and prudent use of geologic heterogeneity. Field, experimental, and modeling examples are presented that demonstrate controllable GCS via these three measures. Observed changes in reservoir response accompanying CO2 injection at the Cranfield (Mississippi, USA) site, along with lab testing, show potential for use of injectate chemistry as a means to alter fracture permeability (with concomitant improvements for sweep and storage efficiency). Further control of reservoir sweep attends brine extraction from reservoirs, with benefit for pressure control, mitigation of reservoir and wellbore damage, and water use. State-of-the-art validated models predict the extent of damage and deformation associated with pore pressure hazards in reservoirs, timing and location of networks of fractures, and development of localized leakage pathways. Experimentally validated geomechanics models show where wellbore failure is likely to occur during injection, and efficiency of repair methods. Use of heterogeneity as a control measure includes where best to inject, and where to avoid attempts at storage. An example is use of waste zones or leaky seals to both reduce pore pressure hazards and enhance residual CO2 trapping.Dexter, A., Race, A.M., Steven, R.T., Barnes, J.R., Hulme, H., Goodwin, R.J.A., Styles, I.B., Bunch, J., 2017. Two-phase and graph-based clustering methods for accurate and efficient segmentation of large mass spectrometry images. Analytical Chemistry 89, 11293-11300. is widely used in MSI to segment anatomical features and differentiate tissue types, but existing approaches are both CPU and memory-intensive, limiting their application to small, single data sets. We propose a new approach that uses a graph-based algorithm with a two-phase sampling method that overcomes this limitation. We demonstrate the algorithm on a range of sample types and show that it can segment anatomical features that are not identified using commonly employed algorithms in MSI, and we validate our results on synthetic MSI data. We show that the algorithm is robust to fluctuations in data quality by successfully clustering data with a designed-in variance using data acquired with varying laser fluence. Finally, we show that this method is capable of generating accurate segmentations of large MSI data sets acquired on the newest generation of MSI instruments and evaluate these results by comparison with histopathology.Ding, D., Liu, G., Sun, X., Sun, R., 2018. Response of carbon isotopic compositions of Early-Middle Permian coals in North China to palaeo-climate change. Journal of Asian Earth Sciences 151, 190-196. investigate the magnitude to which the carbon isotopic ratio (δ13C) varies in coals in response to their contemporary terrestrial environment, the Early-Middle Permian Huainan coals (including coals from the Shanxi Formation, Lower Shihezi Formation and Upper Shihezi Formation) in North China were systematically sampled. A 2.5‰ variation range of δ13C values (?25.15‰ to ?22.65‰) was observed in Huainan coals, with an average value of ?24.06‰. As coal diagenesis exerts little influence on carbon isotope fractionation, δ13C values in coals were mainly imparted by those of coal-forming flora assemblages which were linked to the contemporary climate. The δ13C values in coals from the Shanxi and Lower Shihezi Formations are variable, reflecting unstable climatic oscillations. Heavy carbon isotope is enriched in coals of the Capitanian Upper Shihezi Formation, implying a shift to high positive δ13C values of coeval atmospheric CO2. Notably, our study provides evidence of the Kamura event in the terrestrial environment for the first time.Ding, H., Zhu, C., Zhang, K., Xiao, S., Cui, X., Sun, Y., 2017. Source and composition of sedimentary organic matter in the head of Three Gorges Reservoir: a multiproxy approach using δ13C, lignin phenols, and lipid biomarker analyses. Acta Geochimica 36, 452-455. multiproxy approach including bulk organic carbon, δ13C, lignin phenols, and lipid biomarker analyses were applied to characterize the source and composition of sedimentary organic matter in the head part of Three Gorges Reservoir. OM consisted of both natural (autochthonous and allochthonous) and anthropogenic inputs. The natural OM included input from vascular plants, especially non-woody angiosperms. The allochthonous input included plankton and microbial production, likely due to localized eutrophication. Anthropogenic inputs likely derived from petroleum input and/or urban activities. Other anthropogenic inputs were untreated sewage waste. These influences were concluded to be regionally specific point sources of pollution based on relative distributions and on the fact that molecular characteristics of sedimentary OM were not distributed smoothly along a gradient.Dirri, F., Palomba, E., Longobardo, A., Zampetti, E., 2017. Measuring enthalpy of sublimation of volatiles by means of piezoelectric crystal microbalances. Origins of Life and Evolution of Biospheres 47, 533-544. Crystal Microbalances (PCM’s) are widely used to study the chemical processes involving volatile compounds in any environment, such as condensation process. Since PCM’s are miniaturized sensor, they are very suitable for planetary in situ missions, where can be used to detect and to measure the mass amount of astrobiologically significant compounds, such as water and organics. This work focuses on the realization and testing of a new experimental setup, able to characterize volatiles which can be found in a planetary environment. In particular the enthalpy of sublimation of some dicarboxylic acids has been measured. The importance of dicarboxylic acids in planetology and astrobiology is due to the fact that they have been detected in carbonaceous chondritic material (e.g. Murchinson), among the most pristine material present in our Solar System. In this work, a sample of acid was heated in an effusion cell up to its sublimation. For a set of temperatures (from 30?°C to 75?°C), the deposition rate on the PCM surface has been measured. From these measurements, it has been possible to infer the enthalpy of sublimation of Adipic acid, i.e. ΔH?=?141.6?±?0.8?kJ/mol and Succinic acid, i.e. ΔH?=?113.3?±?1.3?kJ/mol. This technique has so demonstrated to be a good choice to recognise a single compound or a mixture (with an analysis upstream) even if some improvements concerning the thermal stabilization of the system will be implemented in order to enhance the results’ accuracy. The experiment has been performed in support of the VISTA (Volatile In Situ Thermogravimetry Analyzer) project, which is included in the scientific payload of the ESA MarcoPolo-R mission study.dos Santos Rocha, Y., Pereira, R.C.L., Mendon?a Filho, J.G., 2018. Negative electrospray Fourier transform ion cyclotron resonance mass spectrometry determination of the effects on the distribution of acids and nitrogen-containing compounds in the simulated thermal evolution of a Type-I source rock. Organic Geochemistry 115, 32-45. thermal maturity level impact on polar compounds was analyzed for a suite of hydrous pyrolysis (HP) products using a 7.2 Tesla LTQ FTICR-MS instrument. The sample suite was analyzed via electrospray ionization in the negative ion mode focusing on the polar compounds, i.e., nitrogen-, sulfur-, and oxygen-containing (NSO) compounds. The HP experiments were performed under isothermal conditions for 2 h at eleven different temperatures (300, 310, 320, 325, 330, 340, 345, 350, 355, 360 and 365 °C) to simulate the full range of thermal levels starting at early bitumen generation to maximum oil generation. The maturity suite samples consist of one immature bitumen (original sample), eleven expelled oil samples and eight residual bitumen samples. In general, Ox compounds are destroyed by decarboxylation and dehydration with increasing maturity; sulfur compounds decrease; the aromaticity and degree of condensation increase; and steranoic and hopanoic acids decrease. Additionally, we investigated fluid retention properties comparing the carbon number distribution between the expelled oil and residual bitumen samples from each experiment. The maturity related changes of the acidic O2 compounds in the expelled oil samples led us to create several regressions that we propose as new maturity parameters covering the full range of oil generation.Dosko?il, L., Burdíková-Szewieczková, J., Enev, V., Kalina, L., Wasserbauer, J., 2018. Spectral characterization and comparison of humic acids isolated from some European lignites. Fuel 213, 123-132. acids isolated from seven lignite samples from six European coal basins were characterized using spectral methods and elemental analysis and compared with each other. X-ray photoelectron spectroscopy and fluorescence spectrometry are not commonly used for the investigation of lignite humic acids, although they may provide relevant information. Comparison of the examined lignite humic acids shows that they are very similar to each other in chemical nature regarding the at least degree of aromaticity, molecular weight, and the distribution of functional groups. Fluorophores of lignite humic acids lie within the A region with typical maxima centred in the range 255–265/460–510?nm. EEM spectra have the character of fingerprints for humic acids, and lignites (as the starting material). In this work, the capacity of lignite as a parent source of humic acids for agricultural applications is appreciated mainly on the base of extractability and ash content.Dou, J., Qin, W., Ding, A., Liu, X., Zhu, Y., 2017. iTRAQ-based proteomic profiling of a Microbacterium sp. strain during benzo(a)pyrene removal under anaerobic conditions. Applied Microbiology and Biotechnology 101, 8365-8377. study focused on the protein expression of a Microbacterium sp. strain that utilized various concentrations of benzo(a)pyrene (BaP) as the sole source of carbon and energy under anaerobic conditions. A total of 1539 protein species were quantified by isobaric tags for relative and absolute quantitation (iTRAQ) coupled with LC-MS/MS. GO, COG, and pathway enrichment analysis showed that most proteins demonstrated catalytic and binding functions and were mainly involved in metabolic processes, cellular processes, and single-organism processes. Sixty-two proteins were found in their abundances in BaP-stress conditions different from normal conditions. These proteins function in the metabolic pathways; the biosynthesis of secondary metabolites, the biosynthesis of antibiotics, microbial metabolism in diverse environments, carbon metabolism, and the biosynthesis of amino acids were markedly altered. Furthermore, enoyl-CoA hydratase was proposed to be a key protein during BaP removal of the Microbacterium sp. strain. This study provides a powerful platform for the further exploration of BaP removal, and the differentially expressed proteins provide insight into the mechanism of the BaP removal pathway.Douglas, P.M.J., Stolper, D.A., Eiler, J.M., Sessions, A.L., Lawson, M., Shuai, Y., Bishop, A., Podlaha, O.G., Ferreira, A.A., Santos Neto, E.V., Niemann, M., Steen, A.S., Huang, L., Chimiak, L., Valentine, D.L., Fiebig, J., Luhmann, A.J., Seyfried, W.E., Etiope, G., Schoell, M., Inskeep, W.P., Moran, J.J., Kitchen, N., 2017. Methane clumped isotopes: Progress and potential for a new isotopic tracer. Organic Geochemistry 113, 262-282. isotopic composition of methane is of longstanding geochemical interest, with important implications for understanding petroleum systems, atmospheric greenhouse gas concentrations, the global carbon cycle, and life in extreme environments. Recent analytical developments focusing on multiply substituted isotopologues (‘clumped isotopes’) are opening a valuable new window into methane geochemistry. When methane forms in internal isotopic equilibrium, clumped isotopes can provide a direct record of formation temperature, making this property particularly valuable for identifying different methane origins. However, it has also become clear that in certain settings methane clumped isotope measurements record kinetic rather than equilibrium isotope effects. Here we present a substantially expanded dataset of methane clumped isotope analyses, and provide a synthesis of the current interpretive framework for this parameter. In general, clumped isotope measurements indicate plausible formation temperatures for abiotic, thermogenic, and microbial methane in many geological environments, which is encouraging for the further development of this measurement as a geothermometer, and as a tracer for the source of natural gas reservoirs and emissions. We also highlight, however, instances where clumped isotope derived temperatures are higher than expected, and discuss possible factors that could distort equilibrium formation temperature signals. In microbial methane from freshwater ecosystems, in particular, clumped isotope values appear to be controlled by kinetic effects, and may ultimately be useful to study methanogen metabolism.Douglas, R.K., Nawar, S., Alamar, M.C., Mouazen, A.M., Coulon, F., 2018. Rapid prediction of total petroleum hydrocarbons concentration in contaminated soil using vis-NIR spectroscopy and regression techniques. Science of The Total Environment 616–617, 147-155. and near infrared spectrometry (vis-NIRS) coupled with data mining techniques can offer fast and cost-effective quantitative measurement of total petroleum hydrocarbons (TPH) in contaminated soils. Literature showed however significant differences in the performance on the vis-NIRS between linear and non-linear calibration methods. This study compared the performance of linear partial least squares regression (PLSR) with a nonlinear random forest (RF) regression for the calibration of vis-NIRS when analysing TPH in soils. 88 soil samples (3 uncontaminated and 85 contaminated) collected from three sites located in the Niger Delta were scanned using an analytical spectral device (ASD) spectrophotometer (350–2500 nm) in diffuse reflectance mode. Sequential ultrasonic solvent extraction-gas chromatography (SUSE-GC) was used as reference quantification method for TPH which equal to the sum of aliphatic and aromatic fractions ranging between C10 and C35. Prior to model development, spectra were subjected to pre-processing including noise cut, maximum normalization, first derivative and smoothing. Then 65 samples were selected as calibration set and the remaining 20 samples as validation set. Both vis-NIR spectrometry and gas chromatography profiles of the 85 soil samples were subjected to RF and PLSR with leave-one-out cross-validation (LOOCV) for the calibration models. Results showed that RF calibration model with a coefficient of determination (R2) of 0.85, a root means square error of prediction (RMSEP) 68.43 mg kg? 1, and a residual prediction deviation (RPD) of 2.61 outperformed PLSR (R2 = 0.63, RMSEP = 107.54 mg kg? 1 and RDP = 2.55) in cross-validation. These results indicate that RF modelling approach is accounting for the nonlinearity of the soil spectral responses hence, providing significantly higher prediction accuracy compared to the linear PLSR. It is recommended to adopt the vis-NIRS coupled with RF modelling approach as a portable and cost effective method for the rapid quantification of TPH in soils.Driskill, A.K., Alvey, J., Dotson, A.D., Tomco, P.L., 2018. Monitoring polycyclic aromatic hydrocarbon (PAH) attenuation in Arctic waters using fluorescence spectroscopy. Cold Regions Science and Technology 145, 76-85. oil exploration in the Arctic grows, the risk of crude oil exposure to the environment through spills and leakage increases. Polycyclic aromatic hydrocarbons (PAHs) are a toxic component of crude oil that are highly insoluble and persist in the environment. Much is known about PAH degradation through abiotic and biotic factors and remediation strategies in temperate climates; however, little is known about the degradation of these compounds in the Arctic where cold temperatures and sea ice predominate and remediation strategies differ greatly. In this study, excitation-emission matrix (EEM) fluorescence spectroscopy was used along with parallel factor analysis (PARAFAC) to analyze concentrations of PAHs, associated hydroxylated metabolites, and microbial biomass (as based on the protein-like indicators: tryptophan and tyrosine) in surrogate solutions to develop a correlation between PAH biodegradation and native microbial growth. EEMs generated from solutions of 16 EPA-listed priority pollutant PAHs, metabolites, tryptophan, and tyrosine were characterized. Based on maximum emission wavelength peak intensity (EMλmax), PAHs were found to best categorically group, in an effort to determine which PAHs would serve as effective indicators in comparison to bioindicators (microbial fluorescence-absorbing proteins, smaller labile PAHs, and hydroxyl-PAHs), when EEMs were divided into two regions at EM = 400 nm for all excitation wavelengths, establishing a line of division within the matrix to minimize spectral overlap between indicator groups. Five high molecular weight PAHs (benzo(b)fluoranthene, benzo(k)fluoranthene, fluoranthene, benzo(ghi)perylene, and indeno(1,2,3-cd)pyrene) exhibited peak fluorescence intensities above EM = 400 nm allowing them to serve as PAH indicators while bioindicators presented near or below the line of division. A microcosm batch-incubation experiment, consisting of two PAH treatment groups and a control, demonstrated degradation/dissipation of the high molecular weight PAHs (p < 0.05). A half-life of 128 d was derived for the PAH group treated with a solution of the five high molecular weight PAHs (C0 = 512 μg/L) and 31 d for a treatment of only fluoranthene (C0 = 96 μg/L). A three component PARAFAC model containing incubation samples and aqueous standards accounted for 98.8% variance. The combination of EEM fluorescence spectroscopy and multivariate analysis provides a valuable method for modeling degradation studies and monitoring PAH concentrations and microbial growth under Arctic conditions.Du, D., Zhang, N., Li, Y., Sun, R., Wang, C., 2017. Parametric studies on foam displacement behavior in a layered heterogeneous porous media based on the stochastic population balance model. Journal of Natural Gas Science and Engineering 48, 1-12. numerical analysis employing the stochastic population balance (SPB) model is presented on foam displacement behavior in a water saturated heterogeneous porous media consisted of two parallel layers of medium with different permeabilities. Detailed parameter studies of the two key parameters of the SPB model, bubble generate rate Kg and maximum bubble density n∞, are carried out to understand foam flow behavior and mechanisms in the heterogeneous porous media. Numerical results indicate variation of Kg and n∞ values could significantly affect the ongoing foam flooding process and lead to obviously different pressure drops and sweep efficiencies. The parameter of Kg stands for the formation rate of foam, therefore determines the distance and time for foam fluid reaching equilibrium in the displacement process. Higher Kg values result in higher pressure drop and lower water saturation after foam sweeping through the heterogeneous porous media. The parameter of n∞, on the other hand, determines directly the magnitude of foam apparent viscosity through defining the maximum bubble density of the flooding foam fluid. Larger n∞ values lead to higher pressure drops and higher foam sweep efficiencies of the heterogeneous porous media. Reasonable numerical results indicate the SPB model could adequately describe foam displacement process in the heterogeneous media, therefore supplies an important alternative for foam mechanistic studies to promote essentially the foam field applications.Duan, D., Zhang, D., Ma, X., Yang, Y., Ran, Y., Mao, J., 2018. Chemical and structural characterization of thermally simulated kerogen and its relationship with microporosity. Marine and Petroleum Geology 89, Part 1, 4-13. was isolated from the Maoming shale at different temperatures to understand changes in chemical, structural and porosity characteristics during artificial maturation. Advanced solid-state 13C nuclear magnetic resonance (NMR) techniques were employed along with Fourier transform infrared (FT-IR), Raman spectroscopy (RS), stable carbon isotopes, and Rock-Eval pyrolysis to characterize the organic matter (OM), whereas the microporosity and surface properties were elucidated using N2 and CO2 adsorption techniques. As the temperature increased, the aliphatic and carbonyl carbons of the kerogen samples showed remarkable decreases in abundance together with an increase of non-protonated and protonated aromatic carbons. Moreover, the kerogen became more enriched in 13C and had a higher degree of crystallization with increasing Ro and Tmax. The aromaticity ranged from 46.9% to 94.7% and the minimum aromatic cluster size varied from 10 carbons at 350 °C to 38 carbons at 500 °C, which was significantly related to the microporosity (Vo, d-co2) of the kerogen samples and their nonlinear sorption of phenanthrene and benzene. The microporosity was extensively affected by the loss of aliphatic carbon and the increase of aromatic fused carbon. When the temperature reached 500 °C, the collapse of aromatic interlayer remarkably reduced the micropore volume in the kerogen, and then resulted in the decreasing adsorption of hydrophobic organic chemicals (HOCs). The above observation confirms the molecular sieve effect in the kerogen samples. In addition, the micro-filling adsorption for HOCs is dominant on the thermally simulated kerogen samples.Duffin, L., Wang, X., Stoesz, J., 2017. Detection of volatile organic compounds in froth multiphase systems from oil sands operations using a headspace GC–MS method. Energy & Fuels 31, 11925-11931. of air quality due to oil sands operations is one of the largest concerns for stakeholders and regulators. Volatile organic compounds (VOCs) released from tailings ponds are an important contributor to poor air quality. Current government regulations impose a limit on hydrocarbon losses to the froth treatment tailings at 4 barrels per 1000 barrels of dry bitumen produced. However, considering the scale of bitumen production, atmospheric pollution from allowable VOC emissions is still problematic. One source of solvent loss to tailings ponds is solvent trapped in rag layers formed during froth treatment (a multiphase system that sometimes develops at the interface between the diluted bitumen and water). It would be useful to have a method for directly determining solvent loss in rag layers as support to efforts to optimize solvent recovery from froth treatment tailings. In this paper, analytical methods for the direct determination of solvent content in multiphase waste streams from oil sand froth treatment have been developed using headspace sampling combined with gas chromatographic separation and mass spectroscopic detection. The respective detection limits for heptane, toluene, octane, and p-xylene in the water layer are 0.1, 0.4, 0.03, and 0.4 ppm. The detection limits for heptane, toluene, octane, and p-xylene in the rag layer and oil are all approximately 1 wt %. The respective detection limits for naphtha in water, rag layer, and oil are 0.5 ppm, 6 wt %, and 6 wt %.Dundas, C.M., McEwen, A.S., Chojnacki, M., Milazzo, M.P., Byrne, S., McElwaine, J.N., Urso, A., 2017. Granular flows at recurring slope lineae on Mars indicate a limited role for liquid water. Nature Geoscience 10, 903-907. liquid water flow on Mars has been proposed based on geomorphological features, such as gullies. Recurring slope lineae — seasonal flows that are darker than their surroundings — are candidate locations for seeping liquid water on Mars today, but their formation mechanism remains unclear. Topographical analysis shows that the terminal slopes of recurring slope lineae match the stopping angle for granular flows of cohesionless sand in active Martian aeolian dunes. In Eos Chasma, linea lengths vary widely and are longer where there are more extensive angle-of-repose slopes, inconsistent with models for water sources. These observations suggest that recurring slope lineae are granular flows. The preference for warm seasons and the detection of hydrated salts are consistent with some role for water in their initiation. However, liquid water volumes may be small or zero, alleviating planetary protection concerns about habitable environments.Dunkley Jones, T., Manners, H.R., Hoggett, M., Kirtland Turner, S., Westerhold, T., Leng, M.J., Pancost, R.D., Ridgwell, A., Alegret, L., Duller, R., Grimes, S.T., 2017. Orbital forcing of terrestrial hydrology, weathering and carbon sequestration during the Palaeocene-Eocene Thermal Maximum. Climate of the Past Discussions 2017, 1-22. response of the Earth System to greenhouse-gas driven warming is of critical importance for the future trajectory of our planetary environment. Hypethermal events – past climate transients with significant global-scale warming – can provide insights into the nature and magnitude of these responses. The largest hyperthermal of the Cenozoic was the Palaeocene-Eocene Thermal Maximum (PETM ~?56?Ma). Here we present a new high-resolution cyclostratigraphy for the classic PETM section at Zumaia, Spain. With this new age model we are able to demonstrate that detrital sediment accumulation rates within this continental margin section increased more than four-fold during the PETM, representing a radical change in regional hydrology that drove dramatic increases in terrestrial to marine sediment flux. During the body of the PETM, orbital-scale variations in bulk sediment Si/Fe ratios are evidence for the continued orbital pacing of sediment erosion and transport processes, most likely linked to precession controls on sub-tropical hydroclimates. Most remarkable is that detrital accumulation rates remain high throughout the body of the PETM, and even reach peak values during the recovery phase of the characteristic PETM carbon isotope excursion (CIE). Using a series of Earth System Model inversions, we demonstrate that the silicate weathering feedback alone is insufficient to recover the PETM CIE, and that active organic carbon burial is required to match the observed dynamics of the CIE. Further, that the period of maximum organic carbon sequestration coincides with the peak in detrital accumulation rates observed at Zumaia. Based on these results, we hypothesize that precession controls on tropical and sub-tropical hydroclimates, and the sediment dynamics associated with this variation, play a significant role in the timing of the rapid climate and CIE recovery from peak-PETM conditions.Dunn, C.D., 2017. Some liked it hot: A hypothesis regarding establishment of the proto-mitochondrial endosymbiont during eukaryogenesis. Journal of Molecular Evolution 85, 99-106. cells are characterized by a considerable increase in subcellular compartmentalization when compared to prokaryotes. Most evidence suggests that the earliest eukaryotes consisted of mitochondria derived from an α-proteobacterial ancestor enclosed within an archaeal host cell. However, what benefits the archaeal host and the proto-mitochondrial endosymbiont might have obtained at the beginning of this endosymbiotic relationship remains unclear. In this work, I argue that heat generated by the proto-mitochondrion initially permitted an archaeon living at high temperatures to colonize a cooler environment, thereby removing apparent limitations on cellular complexity. Furthermore, heat generation by the endosymbiont would have provided phenotypic flexibility not available through fixed alleles selected for fitness at specific temperatures. Finally, a role for heat production by the proto-mitochondrion bridges a conceptual gap between initial endosymbiont entry to the archaeal host and a later role for mitochondrial ATP production in permitting increased cellular complexity.Dunn, C.W., 2017. Ctenophore trees. Nature Ecology & Evolution 1, 1600-1601. jellies are remarkably different from other animals. Phylogenetic analyses of broadly sampled ctenophore transcriptome data provide additional evidence that they are the sister group to all other animals and reveal details of their evolutionary relationships to each other.Dykstra, C.M., Pavlostathis, S.G., 2017. Zero-valent iron enhances biocathodic carbon dioxide reduction to methane. Environmental Science & Technology 51, 12956-12964. bioelectrochemical systems (BESs), which convert carbon dioxide (CO2) directly to methane (CH4), promise to be an innovative technology for anaerobic digester biogas upgrading. Zero-valent iron (ZVI), which has previously been used to improve CH4 production in anaerobic digesters, has not been explored in methanogenic biocathodes. Thus, the objective of this study was to assess the effect of biocathode ZVI on BES performance at 1 and 2 g/L initial ZVI concentrations and at various cathode potentials (?0.65 to ?0.80 V versus SHE). The total CH4 produced during a 7-day feeding cycle with 1 and 2 g/L initial ZVI was 2.8- and 2.9-fold higher, respectively, than the mean CH4 production in the four prior cycles without ZVI addition. Furthermore, CH4 production by the ZVI-amended biocathodes remained elevated throughout three subsequent feeding cycles, despite catholyte replacement and no new ZVI addition. The fourth cycle following a single ZVI addition of 1 g/L and 2 g/L yielded 123% and 231% more total CH4 than in the non-ZVI cycles, respectively. The higher CH4 production could not be fully explained by complete anaerobic oxidation of the ZVI and utilization of produced H2 by hydrogenotrophic methanogens. Microbial community analysis showed that the same phylotype, most closely related to Methanobrevibacter arboriphilus, dominated the archaeal community in the ZVI-free and ZVI-amended biocathodes. However, the bacterial community experienced substantial changes following ZVI exposure, with more Proteobacteria and fewer Bacteroidetes in the ZVI-amended biocathode. Furthermore, it is likely that a redox-active precipitate formed in the ZVI-amended biocathode, which sorbed to the electrode and/or biofilm, acted as a redox mediator, and enhanced electron transfer and CH4 production. Thus, ZVI may be used to increase biocathode CH4 production, assist in the start-up of an electromethanogenic biocathode, and/or maintain microbial activity during voltage interruptions.Eastoe, C., Toolin, L., 2018. A multi-century δ13C record of the C4 grass Setaria macrostachya in the US Southwest: Identifying environmental causes of variability. Palaeogeography, Palaeoclimatology, Palaeoecology 489, 129-136. and 5-year averages of δ13C measured on florets of the C4 grass Setaria macrostachya decreased from 10 to 13‰ between 1849 and 2016. Atmosphere-plant δ13C discrimination (Δ) changed from 3 to 4 early in this interval, to 4–5 since 1970. These century-scale changes result from decrease in atmospheric δ13C and, prior to 1970, from changes in Δ related to increase in the partial pressure of CO2 in the atmosphere, both largely caused by the burning of fossil fuels. Short-term fluctuations (interannual to decadal) in slope of the time series of averaged δ13C do not result from natural causes, but in certain cases appear to coincide with human economic activities. Annual δ13C ranges in years with sufficient measurements are consistently about 2‰. It is unlikely that useful information on past atmospheric δ13C will be obtained from S. macrostachya seeds preserved in packrat middens or other archives.Eckard, R.S., Pellerin, B.A., Bergamaschi, B.A., Bachand, P.A.M., Bachand, S.M., Spencer, R.G.M., Hernes, P.J., 2017. Dissolved organic matter compositional change and biolability during two storm runoff events in a small agricultural watershed. Journal of Geophysical Research: Biogeosciences 122, 2634-2650.: Agricultural watersheds are globally pervasive, supporting fundamentally different organic matter source, composition, and concentration profiles in comparison to natural systems. Similar to natural systems, agricultural storm runoff exports large amounts of organic carbon from agricultural land into waterways. But intense management of upper soil layers, waterway channelization, wetland and riparian habitat removal, and postharvest vegetation removal promise to uniquely drive organic matter release to waterways. During a winter first flush and a subsequent storm event, this study investigated the influence of a small agricultural watershed on dissolved organic matter (DOM) source, composition, and biolability. Storm water discharge released strongly terrestrial yet biolabile (23 to 32%) dissolved organic carbon (DOC). Following a 21 day bioassay, a parallel factor analysis identified an 80% reduction in a protein-like (phenylpropyl) component (C2) that was previously correlated to lignin phenol concentration, and a 10% reduction in a humic-like, terrestrially sourced component (C4). Storm-driven releases tripled DOC concentration (from 2.8 to 8.7 mg L?1) during the first flush event in comparison to base flow and were terrestrially sourced, with an eightfold increase in vascular plant derived lignin phenols (23.0 to 185 μg L?1). As inferred from system hydrology, lignin composition, and nitrate as a groundwater tracer, an initial pulse of dilute water from the upstream watershed caused a counterclockwise DOC hysteresis loop. DOC concentrations peaked after 3.5 days, with the delay between peak discharge and peak DOC attributed to storm water hydrology and a period of initial water repellency of agricultural soils, which delayed DOM leaching.Plain Language Summary: Human activities have transformed vast areas of Earth's surface to agricultural use. Contemporary agricultural practices have vastly increased crop yield but have also greatly intensified agricultural land management practices, which deviate strongly from many of the basic processes that affect natural habitats. It follows, then, that agricultural land use could affect carbon cycling and water quality in agricultural watersheds very differently from how natural systems affect those same parameters. This study seeks to deepen scientific knowledge surrounding how storms drive carbon release from land to waterways, specific to an agricultural watershed. Results indicate that over a quarter of the carbon released from the subject agricultural watershed during storms has the potential to be used as energy by downstream ecosystems. This could support future management actions seeking to benefit downstream ecosystems or may pose a threat to ecosystem health. The study also suggests that the timing, amount, and quality of carbon released from the watershed depend on rainfall patterns and watershed plumbing, and on whether or not soil wetting has occurred recently, prior to the event in question.Edwards, C.T., Fike, D.A., Saltzman, M.R., Lu, W., Lu, Z., 2018. Evidence for local and global redox conditions at an Early Ordovician (Tremadocian) mass extinction. Earth and Planetary Science Letters 481, 125-135. changes in environmental conditions, particularly atmospheric oxygen levels, are thought to be important drivers of several major biotic events (e.g. mass extinctions and diversifications). The early Paleozoic represents a key interval in the oxygenation of the ocean–atmosphere system and evolution of the biosphere. Global proxies (e.g. carbon (δ13C) and sulfur (δ34S) isotopes) are used to diagnose potential changes in oxygenation and infer causes of environmental change and biotic turnover. The Cambrian–Ordovician contains several trilobite extinctions (some are apparently local, but others are globally correlative) that are attributed to anoxia based on coeval positive δ13C and δ34S excursions. These extinction and excursion events have yet to be coupled with more recently developed proxies thought to be more reflective of local redox conditions in the water column (e.g. I/Ca) to confirm whether these extinctions were associated with oxygen crises over a regional or global scale.Here we examine an Early Ordovician (Tremadocian Stage) extinction event previously interpreted to reflect a continuation of recurrent early Paleozoic anoxic events that expanded into nearshore environments. δ13C, δ34S, and I/Ca trends were measured from three sections in the Great Basin region to test whether I/Ca trends support the notion that anoxia was locally present in the water column along the Laurentian margin. Evidence for anoxia is based on coincident, but not always synchronous, positive δ13C and δ34S excursions (mainly from carbonate-associated sulfate and less so from pyrite data), a 30% extinction of standing generic diversity, and near-zero I/Ca values. Although evidence for local water column anoxia from the I/Ca proxy broadly agrees with intervals of global anoxia inferred from δ13C and δ34S trends, a more complex picture is evident where spatially and temporally variable local trends are superimposed on time-averaged global trends. Stratigraphic sections from the distal and deeper part of the basin (Shingle Pass and Meiklejohn Peak) preserve synchronous global (δ13C and δ34S) and water column (I/Ca) evidence for anoxia, but not at the more proximal section (Ibex, UT). Although geochemical and paleontological evidence point toward anoxia as the driver of this Early Ordovician extinction event, differences between I/Ca and δ13C–δ34S signals suggest regional variation in the timing, extent, and persistence of anoxia.Edwards, C.T., Saltzman, M.R., Royer, D.L., Fike, D.A., 2017. Oxygenation as a driver of the Great Ordovician Biodiversification Event. Nature Geoscience 10, 925-929. largest radiation of Phanerozoic marine animal life quadrupled genus-level diversity towards the end of the Ordovician Period about 450 million years ago. A leading hypothesis for this Great Ordovician Biodiversification Event is that cooling of the Ordovician climate lowered sea surface temperatures into the thermal tolerance window of many animal groups, such as corals. A complementary role for oxygenation of subsurface environments has been inferred based on the increasing abundance of skeletal carbonate, but direct constraints on atmospheric O2 levels remain elusive. Here, we use high-resolution paired bulk carbonate and organic carbon isotope records to determine the changes in isotopic fractionation between these phases throughout the Ordovician radiation. These results can be used to reconstruct atmospheric O2 levels based on the O2-dependent fractionation of carbon isotopes by photosynthesis. We find a strong temporal link between the Great Ordovician Biodiversification Event and rising O2 concentrations, a pattern that is corroborated by O2 models that use traditional carbon–sulfur mass balance. We conclude that that oxygen levels probably played an important role in regulating early Palaeozoic biodiversity levels, even after the Cambrian Explosion.During the Ordovician period one of the greatest biological radiations of the Phanerozoic took place, when genus-level diversity quadrupled and ecospace utilization increased. During this Great Ordovician Biodiversification Event (GOBE), marine communities expanded into new niches such as epifaunal suspension feeding and deep burrowing. This new niche space was largely exploited by members of the Palaeozoic Evolutionary Fauna (EF), which includes articulated brachiopods, crinoids, ostracodes, cephalopods, corals, and bryozoans. Both the Cambrian EF (trilobites and inarticulate brachiopods) and Modern EF (bivalves, gastropods, fish, and so on) also diversified, but it was the expansion of the Paleozoic EF that drove the GOBE.The causes of the GOBE remain poorly understood and may include both intrinsic biological factors and external environmental drivers (such as global cooling, nutrient delivery from erosion, higher sea levels that expanded habitable platform area, and oxygenation). Oxygen isotopes from well-preserved conodont apatite provide proxy evidence for high sea surface temperatures (~40?°C) at the onset of the Ordovician that may have inhibited diversification, but global cooling throughout the Early–Middle Ordovician brought temperatures closer to modern conditions and possibly into the tolerance window (27–32?°C) for members of the Palaeozoic EF. Cooling oceans could also store more dissolved oxygen and more effectively ventilate subsurface environments, which would in turn create a stronger vertical gradient in carbonate saturation that lowered the metabolic costs of skeletal carbonate biomineralization in surface waters. A global increase in atmospheric oxygen and oxygenation of shallow marine environments may have also eased stressful conditions for benthic animal life and expanded the range of habitable ecospace for infaunal burrowers deeper into the sediment. A more oxygenated ocean could also have supported more predators in the food chain (fish and cephalopods), setting into motion an evolutionary ‘arms race. Ordovician global cooling is generally thought to have been caused by decreasing atmospheric CO2 (the cause of this drop is itself not well understood, but hypotheses include increased silicate weathering and the advent of land plants), but a role for increased atmospheric O2 is possible via an increase in total atmospheric pressure and the associated inhibition of solar optical depth, scattering incident solar radiation that would have otherwise contributed to the surface latent heat flux. These arguments for linking oxygenation to cooling and biodiversification, while compelling, are hindered by poorly constrained ocean–atmosphere oxygen records. Existing isotope mass balance models are hampered by coarse time resolution (typically 10?Myr bins) that are not capable of resolving changes in atmospheric O2 as a cause of the main pulses of biodiversification across the GOBE (Supplementary Fig.) The absence of charcoal is interpreted to reflect atmospheric O2 levels below 13–15% until the Late Silurian, but primitive non-vascular land plants only expanded into terrestrial environments by the Middle–Late Ordovician, thus the charcoal record is not well suited to constrain Early Ordovician O2 levels. Land plant expansion is thought to have increased organic burial rates and oxygenated the atmosphere to near modern levels, but the timing and magnitude of this oxygenation is also poorly resolved. Similarly, although iron-based redox proxies suggest that O2 levels were between 2% and 21% throughout the Ordovician, their resolution is not yet sufficient to resolve finer temporal trends. Here we apply a new approach to reconstruct the changes in atmospheric oxygen with high age-resolution based on the O2-dependence of carbon isotope fractionation during photosynthesis.Eiler, J., Cesar, J., Chimiak, L., Dallas, B., Grice, K., Griep-Raming, J., Juchelka, D., Kitchen, N., Lloyd, M., Makarov, A., Robins, R., Schwieters, J., 2017. Analysis of molecular isotopic structures at high precision and accuracy by Orbitrap mass spectrometry. International Journal of Mass Spectrometry 422, 126-142. technologies are being developed to examine the intramolecular isotopic structures of molecules (i.e., site-specific and multiple substitution), but limitations in sample size and type or (for mass spectrometry) resolution have so far prevented the creation of a general technique. We have now demonstrated the capacity for precise and accurate study of molecular isotopic contents and structures by Fourier transform mass spectrometry, using instruments containing a Thermo Scientific? Orbitrap? mass analyzer, here the Thermo Scientific Q Exactive GC? and Q Exactive HF? instruments. Orbitrap mass analyzers achieve mass resolutions in the range ～250,000–1 M (FWHM) in the mass range of greatest interest to studies of molecular isotopic structure, 50–200 amu. This allows for resolution of many nearly isobaric interferences for compounds containing H, C, N, O and/or S. In this paper we show that internal and external experimental reproducibilities of isotope ratio analyses using the Orbitrap analysis can conform to shot-noise limits down to levels of tenths of per mil (1SE), with similar accuracy when standardized to reference materials. Precision reaches ±0.015‰ for exceptionally long integrations. Such measurements do not call for modifications to the ion optics of the Q Exactive instruments, but do require specially designed sample introduction devices to permit sample/standard comparison and long integration times. The sensitivity of the Q Exactive instruments permit analysis of sub-nanomolar samples and quantification of multiply-substituted species. Site-specific capabilities arise from the fact that mass spectra of molecular analytes commonly contain diverse fragment ion species, each of which samples a specific sub-set of molecular sites.Ekpo, B.O., Essien, N., Neji, P.A., Etsenake, R.O., 2018. Geochemical fingerprinting of western offshore Niger Delta oils. Journal of Petroleum Science and Engineering 160, 452-464. study reports the findings based on analyses of saturated (normal alkanes and aliphatic isoprenoid) hydrocarbons and biomarkers in twenty four (24) crude oil samples from western offshore Niger Delta of Nigeria using gas chromatography (GC), gas chromatography-mass spectrometry (GC-MS) and carbon isotopy. The major objectives were to apply reservoir geochemistry and oil fingerprinting to characterize the oils in order to determine their origin and to identify the existence of reservoir continuity and/or compartmentalization. Results from this study using the distributions of normal alkanes, tricyclic and tetracyclic terpanes as well as source specific maturity and facies controlled biomarker ratios of the oils including pristane/phytane (Pr/Ph), Pr/n-C17, Ph/n-Cl8, C31:22S/(22S + 22R) homohopane, C29:αα(20S/(20S + 20R)) steranes, moretane/C30-Hopane and Ts/(Ts + Tm), showed that the entire crude oil samples from three reservoir units are the same, the differences are small. The oils originated from same source rocks which were deposited under oxidizing condition with mixed marine/terrigeneous organic source inputs and thermal maturity. This genetic classification is supported by stable carbon isotopic compositions (δ13C) of the hydrocarbon fractions and multivariate statistical (Principal Component and Cluster) analyses. Geochemical, fingerprinting and multivariate statistical data provided corroborative evidence of a single compartment with vertical and lateral reservoir continuity across the fault complex within the studied fields. This information can be utilized by geologists and petroleum engineers in solving production related problems such as optimising hydrocarbon production via drilling horizontal wells to arrest the reservoir communication that occurs with existing vertical wells.Eme, L., Spang, A., Lombard, J., Stairs, C.W., Ettema, T.J.G., 2017. Archaea and the origin of eukaryotes. Nature Reviews Microbiology 15, 711–723. and Fox's 1977 paper on the discovery of the Archaea triggered a revolution in the field of evolutionary biology by showing that life was divided into not only prokaryotes and eukaryotes. Rather, they revealed that prokaryotes comprise two distinct types of organisms, the Bacteria and the Archaea. In subsequent years, molecular phylogenetic analyses indicated that eukaryotes and the Archaea represent sister groups in the tree of life. During the genomic era, it became evident that eukaryotic cells possess a mixture of archaeal and bacterial features in addition to eukaryotic-specific features. Although it has been generally accepted for some time that mitochondria descend from endosymbiotic alphaproteobacteria, the precise evolutionary relationship between eukaryotes and archaea has continued to be a subject of debate. In this Review, we outline a brief history of the changing shape of the tree of life and examine how the recent discovery of a myriad of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of eukaryotes. Furthermore, we revisit central questions regarding the process of eukaryogenesis and discuss what can currently be inferred about the evolutionary transition from the first to the last eukaryotic common ancestor.Key points·The Archaea was recognized as a third domain of life 40 years ago. Molecular evidence soon suggested that the Eukarya represented a sister group to the Archaea or that eukaryotes descended from archaea.·Culture-independent genomics has revealed the vast diversity existing among the Archaea, including the recently described Asgard superphylum. Phylogenomic analyses have placed the Asgard archaea as the closest prokaryotic relatives of eukaryotes.·Comparative genomic analyses have reconstructed a complex last eukaryotic common ancestor. However, how and in which order these complex eukaryotic features evolved in an Asgard archaea-related ancestor remains largely unclear.·Genomic investigation of Asgard archaea showed that they carry several genes formerly believed to be eukaryotic specific, illuminating early events during eukaryogenesis.·Fully understanding the process of eukaryogenesis requires finding answers to several challenging and intertwined questions. Although we have seemingly answered some of these questions, others remain fiercely debated, and new questions continue to arise.Enoto, T., Wada, Y., Furuta, Y., Nakazawa, K., Yuasa, T., Okuda, K., Makishima, K., Sato, M., Sato, Y., Nakano, T., Umemoto, D., Tsuchiya, H., 2017. Photonuclear reactions triggered by lightning discharge. Nature 551, 481-484. and thunderclouds are natural particle accelerators. Avalanches of relativistic runaway electrons, which develop in electric fields within thunderclouds, emit bremsstrahlung γ-rays. These γ-rays have been detected by ground-based observatories, by airborne detectors and as terrestrial γ-ray flashes from space. The energy of the γ-rays is sufficiently high that they can trigger atmospheric photonuclear reactions that produce neutrons and eventually positrons via β+ decay of the unstable radioactive isotopes, most notably 13N, which is generated via 14N?+?γ?→?13N?+?n, where γ denotes a photon and n a neutron. However, this reaction has hitherto not been observed conclusively, despite increasing observational evidence of neutrons and positrons that are presumably derived from such reactions. Here we report ground-based observations of neutron and positron signals after lightning. During a thunderstorm on 6 February 2017 in Japan, a γ-ray flash with a duration of less than one millisecond was detected at our monitoring sites 0.5–1.7 kilometres away from the lightning. The subsequent γ-ray afterglow subsided quickly, with an exponential decay constant of 40–60?milliseconds, and was followed by prolonged line emission at about 0.511 megaelectronvolts, which lasted for a minute. The observed decay timescale and spectral cutoff at about 10 megaelectronvolts of the γ-ray afterglow are well explained by de-excitation γ-rays from nuclei excited by neutron capture. The centre energy of the prolonged line emission corresponds to electron–positron annihilation, providing conclusive evidence of positrons being produced after the lightning.Estrada, C.F., Adcock, A.K., Sverjensky, D.A., Hazen, R.M., 2017. Cooperative and inhibited adsorption of D-ribose onto brucite [Mg(OH)2] with divalent cations. ACS Earth and Space Chemistry 1, 591-600. adsorption and concentration of sugars onto mineral surfaces in geochemical environments, such as hydrothermal systems, may have influenced the evolution of early life on Earth. We conducted batch adsorption experiments between d-Ribose and brucite [Mg(OH)2], a mineral produced from serpentinite-hosted hydrothermal systems, over variable initial ribose concentrations at four ionic strengths resulting from different Mg2+ and Ca2+ ion concentrations in the aqueous phase. Ribose adsorption generally increased with greater initial concentration and up to 0.3 μmol·m–2 ribose attached onto brucite with 0.6 mM Mg2+ present. Ribose adsorption decreased over 6-fold (4.9 × 10–2 μmol·m–2) when the total Mg2+ ion concentration increased to 5.8 mM. Ribose adsorption increased to 0.4 μmol·m–2 when 4.2 mM CaCl2 was added to the system. Substantial amounts (over 21 μmol·m–2) of dissolved Ca also attached to the brucite surface independent of ribose concentration. We characterized the interactions between ribose, Ca, and the brucite surface by fitting a surface complexation model to adsorption data. We propose three types of surface reactions that were consistent with the experimental data and involve (1) a bidentate outer sphere or a “standing” ribose surface species, (2) a monodentate Ca-ribose outer-sphere species, and (3) a monodentate Ca outer-sphere species. Our model predicts brucite particle surface charge is negative at low Mg2+ concentrations and further decreases upon the addition of MgCl2, which may hinder our proposed surface complexation of the ribose species, Rib–. We predict that brucite becomes positively charged with CaCl2 addition, which may be a consequence of the significant extent of Ca adsorption. The increase in ribose adsorption with CaCl2 is likely driven by Ca attachment and the formation of a positively charged, cooperative Ca–ribose species that our model predicts will predominate over the “standing” ribose species on brucite. Our model of the ribose–brucite system, established by a combination of batch adsorption experiments and surface complexation modeling, has enabled predictions of ribose adsorption over a wide range of pH and complex environmental conditions.Etiope, G., Doezema, L.A., Pacheco, C., 2017. Emission of methane and heavier alkanes from the La Brea Tar Pits seepage area, Los Angeles. Journal of Geophysical Research: Atmospheres 122, 12,008-12,019. hydrocarbon (oil and gas) seeps are widespread in Los Angeles, California, due to gas migration, along faults, from numerous subsurface petroleum fields. These seeps may represent important natural contributors of methane (CH4) and heavier alkanes (C2-C4) to the atmosphere, in addition to anthropogenic fossil fuel and biogenic sources. We measured the CH4 flux by closed-chamber method from the La Brea Tar Pits park (0.1 km2), one of the largest seepage sites in Los Angeles. The gas seepage occurs throughout the park, not only from visible oil-asphalt seeps but also diffusely from the soil, affecting grass physiology. About 500 kg CH4 d?1 is emitted from the park, especially along a belt of enhanced degassing that corresponds to the 6th Street Fault. Additional emissions are from bubble plumes in the lake within the park (order of 102–103 kg d?1) and at the intersection of Wilshire Boulevard and Curson Avenue (>130 kg d?1), along the same fault. The investigated area has the highest natural gas flux measured thus far for any onshore seepage zone in the USA. Gas migration, oil biodegradation, and secondary methanogenesis altered the molecular composition of the original gas accumulated in the Salt Lake Oil Field (>300 m deep), leading to high C1/C2+ and i-butane/n-butane ratios. These molecular alterations can be important tracers of natural seepage and should be considered in the atmospheric modeling of the relative contribution of fossil fuel (anthropogenic fugitive emission and natural geologic sources) versus biogenic sources of methane, on local and global scales.Evans, C.D., Futter, M.N., Moldan, F., Valinia, S., Frogbrook, Z., Kothawala, D.N., 2017. Variability in organic carbon reactivity across lake residence time and trophic gradients. Nature Geoscience 10, 832-835. transport of dissolved organic carbon from land to ocean is a large dynamic component of the global carbon cycle. Inland waters are hotspots for organic matter turnover, via both biological and photochemical processes, and mediate carbon transfer between land, oceans and atmosphere. However, predicting dissolved organic carbon reactivity remains problematic. Here we present in situ dissolved organic carbon budget data from 82 predominantly European and North American water bodies with varying nutrient concentrations and water residence times ranging from one week to 700 years. We find that trophic status strongly regulates whether water bodies act as net dissolved organic carbon sources or sinks, and that rates of both dissolved organic carbon production and consumption can be predicted from water residence time. Our results suggest a dominant role of rapid light-driven removal in water bodies with a short water residence time, whereas in water bodies with longer residence times, slower biotic production and consumption processes are dominant and counterbalance one another. Eutrophication caused lakes to transition from sinks to sources of dissolved organic carbon. We conclude that rates and locations of dissolved organic carbon processing and associated CO2 emissions in inland waters may be misrepresented in global carbon budgets if temporal and spatial reactivity gradients are not accounted for.Fabiańska, M.J., Misz-Kennan, M., Ciesielczuk, J., Pierwo?a, J., Nitecka, N., Brzoznowski, J., 2017. Thermal history of coal wastes reflected in their organic geochemistry and petrography; the case study: The Katowice-We?nowiec dump, Poland. International Journal of Coal Geology 184, 11-26. thermal history of the We?nowiec dump significantly affected the coal waste used for the dump reclamation. Their geochemical- and petrographic characteristics reflect the duration and intensity of fires there. Examples of geochemical features are single Gaussian n-alkane distributions reflecting one self-heating event, overlapping Gaussian n-alkane distributions reflecting two separate heating events, phenolic-compound occurrence and values of aromatic-hydrocarbon parameters that increase in areas where self-heating and/or open fire was particularly intense. Elevated values of geochemical parameters of thermal maturity, particularly those based on alkyl aromatic hydrocarbons, can be also used to work out dump thermal history. PAHs diagnostic ratios applied in environmental studies are of variable use, though most reflect heating events well. Among petrographic features which can be applied to help delineate the thermal history of the dump are modes of strongly- and moderately-altered organic matter occurrence, solid bitumen expelled during heating, and chars from power-plant ash often used to prevent fire on coal-waste dumps. However, vitrinite reflectance seems not to register short temperature increases well.The persistence of fire incidents in the We?nowiec dump indicates that the use of coal-waste as reclamation material on landfills should be considered environmentally questionable. Even in a relatively thin (3-7 m) coal-waste covering, self-heating can start and wastes may burn for many years despite all efforts to extinguish the fires. Obviously, this material is not inert and organic products of heating such as phenols and polycyclic aromatic hydrocarbons are a serious hazard to the environment and to the health of any living nearby.Fadul Abul Gebbayin, O.I.M., Zhong, N., Ali Ibrahim, G., Ali Alzain, M., 2018. Origin of a Tertiary oil from El Mahafir wildcat & geochemical correlation to some Muglad source rocks, Muglad Basin, Sudan. Journal of African Earth Sciences 137, 133-148. rock screening analysis was performed on four stratigraphic units from the Muglad basin namely; Abu Gabra, Zarqa, Ghazal, and Baraka formations using pyrolysis and Vitrinite Reflectance (Ro). Results, integrated with the chromatographic and isotopic data from these rocks extracts and a Tertiary oil from El Mahafir-1 wild cat, were used to determine the origin of the oil.A good organic source within the Middle Abu Gabra Formation is observed in wells El Toor-6 and Neem Deep-1 (TOC, 1.0–2.0% & S2 5.0–10.0 mg C/g rock), with mixed kerogens I, II, & III, and thermally mature (% Ro = 0.74–0.94). The Campanian-Early Maastrichtian sequence, i.e. Zarqa and Ghazal formations are generally poor (TOC, <0.5% & S2 <2.5 mg C/g rock), dominated by type III kerogens, and immature at the studied locations. The Baraka shale nevertheless, is good at El Mahafir-1 well (avg. TOC 1.8% & S2 5.0–10.0 mg C/g rock) and fair at Timsah-1 well (Avg. TOC 0.69% & S2 2.5–5.0 mg C/g rock) with a Kerogen that is predominantly Sapropellic at the former, and an exclusively Humic at the later. The formation is mature at Timsah (% Ro = 0.77–1.16) and early mature at El Mahafir-1 (% Ro = 0.64–0.81).Consistent with the pyrolysis, chromatographic data of the rock extracts confirms the mixed source nature of the Abu Gabra Formation which consists of both algal [prominent LMW n-alkanes & elevated C27 steranes (36–47%)], as well as terrigenous material [higher diasterane/regular sterane ratios (0.50–0.56), abundant rearranged hopanes, & relatively high CPIs (1.22–1.9)], accumulated in an oxic to sub-oxic environment (Pr/Ph, 1.3–3.0). Abu Gabra further shows low C29/C30 hopanes (0.45–0.54), low C28 steranes (21–26%) with high Gammacerane index (20.3). In contrast, the environment during the Late Cretaceous was strongly reducing (Pr/Ph, 0.37–1.0), associated with a wide organic diversity, both in space and time and is characterized by dominant algal input at some areas and or stratigraphic intervals [Elevated tricyclics, higher C29/C30 hopanes (0.5–1.14), and relatively low Gammacerane indices (4.6–14.4)], while mixed with abundant terrigenous material at others.A direct correlation between El Mahafir oil and the Abu Gabra extracts is thus inferred based on: its mixed organic source nature, oxic to sub-oxic depositional environment (Pr/Ph 1.22), relatively low C29/C30 hopanes (0.54), low C28 steranes (29%), and a high gammacerane index (20.5). This is largely supported by the maturity modeling results which suggest generation is only from the Abu Gabra at this location.Fagliarone, C., Mosca, C., Ubaldi, I., Verseux, C., Baqué, M., Wilmotte, A., Billi, D., 2017. Avoidance of protein oxidation correlates with the desiccation and radiation resistance of hot and cold desert strains of the cyanobacterium Chroococcidiopsis. Extremophiles 21, 981-991. investigate the relationship between desiccation and the extent of protein oxidation in desert strains of Chroococcidiopsis a selection of 10 isolates from hot and cold deserts and the terrestrial cyanobacterium Chroococcidiopsis thermalis sp. PCC 7203 were exposed to desiccation (air-drying) and analyzed for survival. Strain CCMEE 029 from the Negev desert and the aquatic cyanobacterium Synechocystis sp. PCC 6803 were further investigated for protein oxidation after desiccation (drying over silica gel), treatment with H2O2 up to 1?M and exposure to γ-rays up to 25?kGy. Then a selection of desert strains of Chroococcidiopsis with different survival rates after prolonged desiccation, as well as Synechocystis sp. PCC 6803 and Chroococcidiopsis thermalis sp. PCC 7203, were analyzed for protein oxidation after treatment with 10 and 100?mM of H2O2. Results suggest that in the investigated strains a tight correlation occurs between desiccation and radiation tolerance and avoidance of protein oxidation.Fan, F., Zhang, B., Morrill, P.L., Husain, T., 2017. Profiling of sulfate-reducing bacteria in an offshore oil reservoir using phospholipid fatty acid (PLFA) biomarkers. Water, Air, & Soil Pollution 228, 410. analysis was conducted to profile microorganisms and trace sulfate-reducing bacteria (SRB) in water samples from an offshore oil reservoir. From the results of spiked phospholipid standards, more than 90% of the phospholipids were recovered before the treatment of fatty acid methyl ester (FAME) derivatization while the relative standard deviations (RSD) were below 8.0%. The water samples from the injection well and four producing wells exhibited various reducing conditions and were further subjected to PLFA analysis. Fourteen kinds of phospholipid fatty acids were detected in the five wellbores and the concentrations of total fatty acids ranged from 368.4 to 3468.9?ng/L. Possible SRB biomarkers and significant phospholipid fatty acids associated with SRB including C14:0, i-C15:0, a-C15:0, C15:0, C16:1 (cis-9), C17:0, C18:1 (cis-9), C18:1 (cis-11) and C18:0 were selected for determining the presence of SRB species and evaluating the sulfate-related microbial biomass. The possible existence of SRB genera Desulfobacter, Desulfotomaculum, Desulfovibrio, and sulfur-oxidizing bacteria (SOB) in the reservoir were proposed based on PLFA profiles. The highest biomass was found in the most reducing well where very limited SOB biomarkers were found. Results indicated that the presence of SRB and SOB species was closely associated with the redox environment of the reservoir wellbores. The species distribution patterns were interpreted to elucidate the biological souring process.Fanali, C., Micalizzi, G., Dugo, P., Mondello, L., 2017. Ionic liquids as stationary phases for fatty acid analysis by gas chromatography. Analyst 142, 4601-4612. present paper provides an overview of the application of ionic liquid (IL) columns for GC analysis of fatty acid methyl esters (FAMEs). Although their separation can be carried out utilizing GC columns containing polar stationary phases, some ILs have been employed as stationary phases, either commercial or laboratory made, in GC analysis. Monodimensional and bidimensional GC methods have been optimized in order to achieve the best separation especially considering the geometric and positional isomers of unsaturated fatty acids. Several methods for the analysis of trans-fatty acids have also been reported. The use of GC-GC, using either the same IL columns or different columns in the first and second dimensions, allowed the separation of a large number of FAMEs. The application of the IL columns for GC analysis of FAMEs in different types of real samples is described, e.g., oil of different nature (fish, flaxseed, and olive), margarine and butter, biodiesel, milk, bacteria etc.Fang, R.-H., Li, M.-J., Lü, H.-T., Wang, T.-G., Yuan, Y., Liu, Y.-L., Ni, Z.-Y., 2017. Oil charging history and pathways of the Ordovician carbonate reservoir in the Tuoputai region, Tarim Basin, NW China. Petroleum Science 14, 662-675. analysis of 64 oils sampled from an Ordovician carbonate reservoir in the Tuoputai region was undertaken to study the composition of molecular markers. All the oils have similar geochemical characteristics and belong to a single oil family. They are presumed to derive from the same source kitchen and have similar oil charging history. A histogram of homogenization temperatures (Th) of aqueous inclusions in reservoir rocks shows a bimodal distribution pattern, indicating that the Ordovician reservoir has been charged twice. Coupling the measured Th (°C) with the burial and geothermal histories reconstructed using 1D basin modeling, we relate the homogenization temperature to the relevant geological ages: i.e., 425–412 and 9–4?Ma, corresponding to the Middle to Late Silurian and the Miocene to Pliocene, respectively. The oil filling orientation and pathways are traced using molecular indicators related to alkyldibenzothiophenes and benzo[b]naphthothiophenes. The oil charging orientation is from south to north generally. It can be predicted that the Ordovician reservoirs were sourced from a kitchen located to the south of the Tuoputai region, most probably between the Awati and Manjiaer Depressions. Traps located in the southern side of the Tuoputai region, along the oil charging pathways, should therefore be preferred oil exploration targets.Faulk, S.P., Mitchell, J.L., Moon, S., Lora, J.M., 2017. Regional patterns of extreme precipitation on Titan consistent with observed alluvial fan?distribution. Nature Geoscience 10, 827-831. features typically associated with extreme rainfall events in terrestrial settings, including extensive fluvial features and alluvial fans, have been detected on Titan’s surface. Methane flow from precipitation on Titan can transport sediments and potentially erode the icy bedrock, but averaged precipitation rates from prior global-scale modelling are too low by at least an order of magnitude to initiate sediment transport of observed grain sizes at low latitudes. Here, we quantify the regional magnitude, frequency and variability of extreme rainfall events from simulations of present-day Titan, with a general circulation model coupled to a land model partially covered by wetlands reservoirs that can capture Titan’s regionally varying hydroclimate. We find that the most extreme storms tend to occur in the mid-latitudes, where observed alluvial fans are most concentrated. Storms capable of sediment transport and erosion occur at all latitudes in our simulations, consistent with the observed global coverage of fluvial features. Our results demonstrate the influential role of extreme precipitation in shaping Titan’s surface. We therefore suggest that, similarly to Earth but differently from Mars, active geomorphic work may be ongoing in the present climate on Titan.Fei, Y., Johnson Jr, R.L., Gonzalez, M., Haghighi, M., Pokalai, K., 2018. Experimental and numerical investigation into nano-stabilized foams in low permeability reservoir hydraulic fracturing applications. Fuel 213, 133-143. fracturing is one of the most effective and efficient methods to enhance oil and gas recovery from reservoirs. Well productivity is mainly determined by the propped dimensions of the fracture. However, the propped dimensions are controlled by proppant transport and proppant placement, of which settling and convection are the controlling mechanisms. In this paper, a new concept is described to overcome the problem of proppant settling during a foam fracturing treatment and prior to fracture closure. This new concept consists of introducing nanoparticles into the base fracturing fluid system to stabilize the foam structure and reduce proppant settling. The results show that foam stability directly influences proppant placement and final fracture conductivity. When foam fracturing fluids experience long closure times, most often as a result of low leakoff, foam breakage occurs. This breakage results in proppant settling and accumulation at the bottom of the fracture, reducing propped dimensions. Whilst, high pumping rates and foam quality provide greater initial propped area, foam stability is major factor controlling the final propped area and productivity. Experimental results show that foam stability increases 2–3-fold in presence of 0.8-wt% silica nanoparticles under 90?°C. The enhancement of foam stability using nanoparticles, particularly foam life-time, allows better proppant suspension, maintains post-fracture conductivity, and minimizes productivity losses. This work is intended to guide the practitioner in the use of nano-stabilized foam to improve unconventional reservoir stimulation.Feldbusch, E., Wiersberg, T., Zimmer, M., Regenspurg, S., 2018. Origin of gases from the geothermal reservoir Gro? Sch?nebeck (North German Basin). Geothermics 71, 357-368. operation of a geothermal facility is largely affected by the content and composition of gases dissolved in the formation fluids. Typically, the geothermal gas mixtures consists of different types of gases of different origin. In this study, the origin of various gas components from the Rotliegend – Permocarboniferous geothermal reservoir Gro? Sch?nebeck (North German Basin) was investigated. Three formation fluid samples were collected from the depth of the production well Gt GrSk 04/05 (between 4120 and 4240 m) at conditions of the Rotliegend/Permocarboniferus reservoir (about 140–150 °C and 430–450 bar). Identified and further investigated gases are N2, CH4, CO2, H2, higher gaseous alkanes, and noble gases. The stable isotope ratio of individual gas components range from 0.2 to 1.5‰ (δ15NAir) for N2, from ?16.5 to ?21.2‰ for CH4, from ?18 to ?26‰ for C2H6, from ?24 to ?30‰ for C3H8, and from ?13.1 to ?20.2‰ for CO2 (δ13CV-PDB for all hydrocarbons and carbon dioxide). Isotopic ratios measured for the noble gases He, Ne, and Ar indicated that 20Ne/22Ne and 38Ar/36Ar are indistinguishable from air, while all other isotope ratios show excess of radiogenic or nucleogenic isotopes.Results of δ15NAir suggest that the source of N2 are the highly matured Westphalian coals (Upper Carboniferous)l. Isotopic ratios of CH4 and CO2 confirmed thermogenic decomposition of terrestrial plants from a similar source as the most likely precursor for these gases. The inverse carbon isotope trend might be linked to heavy metal catalysed cracking of long-chain hydrocarbons and/or evolution of precipitates during fluid evaporation in the basin.The observed 3He/4He ratios of ≤0.0642 ± 0.0026 Ra demonstrate a crustal origin of He. The N2/40Ar ratio (1648 ± 480) indicates a crustal origin and practically without any influence of the air. 21Ne/22Ne is distinguished from the air and more enriched in nucleogenic 21Ne, relative to 22Ne, when compared to the average crustal Ne composition. The calculated residence time of fluids by means of in situ produced nuclides varies for 40Ar from 72 to 80 Ma and for 4He from 365 to 401 Ma. The apparent age discrepancy gives a hint for He migration from older stratigraphic layers or stratas enriched in parent nuclides (U, Th).Fenaille, F., Saint-Hilaire, P.B., Rousseau, K., Junot, C., 2017. Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: where do we stand? Journal of Chromatography A 1526, 1-12. mass spectrometry (MS) based untargeted metabolomics protocols are tedious as well as time- and sample-consuming. In particular, they often rely on “full-scan-only” analyses using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) from which metabolites of interest are first highlighted, and then tentatively identified by using targeted MS/MS experiments. However, this situation is evolving with the emergence of integrated HRMS based-data acquisition protocols able to perform multi-event acquisitions. Most of these protocols, referring to as data dependent and data independent acquisition (DDA and DIA, respectively), have been initially developed for proteomic applications and have recently demonstrated their applicability to biomedical studies. In this context, the aim of this article is to take stock of the progress made in the field of DDA- and DIA-based protocols, and evaluate their ability to change conventional metabolomic and lipidomic data acquisition workflows, through a review of HRMS instrumentation, DDA and DIA workflows, and also associated informatics tools.Feng, L., Huang, J., Lu, D., Zhang, Q., 2017. Major and trace element geochemistry of the Neoproterozoic syn-glacial Fulu iron formation, South China. Geological Magazine 154, 1371-1380. Fulu iron formation (IF) is an iron-rich unit in the Neoproterozoic glacial successions, South China. The major element data suggest that the iron sources of the Fulu IF are derived from binary mixing from hydrothermal and detrital loads. The Fulu IF is characterized by slightly positive Eu anomalies similar to other Neoproterozoic IFs, indicating that a high-temperature hydrothermal input may contribute little to Neoproterozoic IFs. A shift from non-existent to slightly negative Ce anomalies of the Fulu IF indicates that the IF precipitated across an iron chemocline separating a weakly oxic surface ocean from an oxygen-depleted deep ocean.Feng, R., Pandey, R., 2017. Investigation of various pressure transient techniques on permeability measurement of unconventional gas reservoirs. Transport in Porous Media 120, 495-514. evaluation of fluid flow behavior in porous media is necessary considering its widespread applications in geo-engineering projects, such as reservoir productivity and hydraulic fracturing. In order to improve the understanding of gas flow characteristics in porous media, particularly permeability estimation of unconventional gas reservoirs, various pressure transient measurement techniques were numerically evaluated in this study based on the established mathematical models, closely representing each experimental design of these transient techniques. Given that both compressive storage and sorption capacity of unconventional reservoirs vary at different pressures, the practicability of the conventional pulse decay method (PDM), initially adopted by Brace et al. (J Geophys Res 73(6):2225–2236, 1968), was examined. The results showed that compressive storage and sorption effect are the limiting factors in the application of the conventional PDM for permeability measurement of sorptive rocks. Meanwhile, the degree to which these factors affect the accuracy of pressure response and permeability were investigated quantitatively. It was found that pulse size, rock porosity, gas compressibility and reservoir volumes are the main parameters influencing compressive storage and sorption effect, and thus the application of the conventional PDM. A comprehensive numerical investigation was also conducted on Metwally and Sondergeld’s technique, a modified PDM, initially proposed for measuring low permeabilities of gas sands and shales. Considering limitations in the derived permeabilities of sorptive rocks when using the conventional PDM techniques and Metwally and Sondergeld’s technique, an optimized PDM was then proposed by creating dual-pressure pulses to avoid the pressure disturbance due to compressive storage, and ad-/de- sorption during the course of measurement. To verify the feasibility of the optimized PDM, a suite of numerical investigation was carried out for various PDM techniques, and the pressure responses were also compared with calculated data obtained from the mathematical model and experimental results. Both numerically calculated and experimental results exhibit the practicality of the optimized PDM, providing a fast, accurate and reliable approach for permeability measurement of sorptive rocks.Feng, Y., Zhao, Y., Guo, Y., Liu, S., 2018. Microbial transcript and metabolome analysis uncover discrepant metabolic pathways in autotrophic and mixotrophic anammox consortia. Water Research 128, 402-411. ability of anammox bacteria to utilize organic matter has drawn extensive attention. However, the metabolic discrepancies between autotrophic and mixotrophic anammox consortia need to be further explored. Here, microbial transcript and metabolomic analysis were conducted for the samples harvested in the reactors and batch assays to investigate the phenotype discrepancies and intrinsic causes in autotrophic and mixotrophic anammox consortia. Results showed that metabolically active community structures did not show significant difference between autotrophic and mixotrophic anammox consortia (C/N = 0.3). Changes in the metabolic state were the main cause for those discrepancies in virtue of the added acetate oxidized via the acetyl-CoA pathway by mixotrophic anammox bacteria. At C/N ratio of 0.3, anammox activity was obviously promoted compared to that in the autotrophic condition, due to higher levels of NADH and NAD+, as well as ATP consumption. Mixotrophic anammox consortia were found to yield more biomass, resulting from enhanced purine, pyrimidine, and putrescine synthetic pathways for regulating bacterial growth. Up-regulated amino sugar and nucleotide sugar metabolism pathways participating in regulating more extracellular polysaccharides secreted by mixotrophic anammox consortia. In adverse environment with higher COD concentration, more extracellular proteins were produced by anammox consortia to protect themselves and amino acids also accumulated in the cell. This study provides useful information to catch the optimal metabolism way of anammox consortia and accelerate anammox bacterial cultivation or reactor startup for wastewater treatment.Fike, D.A., Houghton, J.L., Moore, S.E., Gilhooly, W.P., Dawson, K.S., Druschel, G.K., Amend, J.P., Orphan, V.J., 2017. Spatially resolved capture of hydrogen sulfide from the water column and sedimentary pore waters for abundance and stable isotopic analysis. Marine Chemistry 197, 26-37. cycling is ubiquitous in sedimentary environments, where it plays a major role in mediating carbon remineralization and impacts both local and global redox budgets. Microbial sulfur cycling is dominated by metabolic activity that either produces (e.g., sulfate reduction, disproportionation) or consumes (sulfide oxidation) hydrogen sulfide (H2S). As such, improved constraints on the production, distribution, and consumption of H2S in the natural environment will increase our understanding of microbial sulfur cycling. These different microbial sulfur metabolisms are additionally associated with particular stable isotopic fractionations. Coupling measurements of the isotopic composition of the sulfide with its distribution can provide additional information about environmental conditions and microbial ecology. Here we investigate the kinetics of sulfide capture on photographic films as a way to document the spatial distribution of sulfide in complex natural environments as well as for in situ capture of H2S for subsequent stable isotopic analysis. Laboratory experiments and timed field deployments demonstrate the ability to infer ambient sulfide abundances from the yield of sulfide on the films. This captured sulfide preserves the isotopic composition of the ambient sulfide, offset to slightly lower δ34S values by ~ 1.2 ± 0.5‰ associated with the diffusion of sulfide into the film and subsequent reaction with silver to form Ag2S precipitates. The resulting data enable the exploration of cm-scale lateral heterogeneity that complement most geochemical profiles using traditional techniques in natural environments. Because these films can easily be deployed over a large spatial area, they are also ideal for real-time assessment of the spatial and temporal dynamics of a site during initial reconnaissance and for integration over long timescales to capture ephemeral processes.Fiorentini, M., 2017. Primordial light oxygen pockets. Nature Geoscience 10, 803-804. lavas reveal the presence of deep mantle reservoirs with anomalously light oxygen signatures. These lavas fingerprint heterogeneous mantle domains in early Earth that may have since been mixed away.Komatiites are remarkable rocks. These crystallized products of the hottest lava flows ever erupted on the surface of the planet provide a snapshot of early Earth and a glimpse of the planet's origin. Writing in Nature Geoscience, Byerly et al.1 show that the three-billion-year-old Weltevreden komatiites (Fig. 1) from the Barberton greenstone belt of South Africa were derived from a mantle source with much lighter oxygen isotope composition than the modern mantle. This discovery is puzzling because there was previously no indication that the Archaean mantle may have had a different oxygen make-up to its modern counterpart.Most of the preserved komatiites are Archaean and Proterozoic in age, although a few rare but notable examples formed in the Phanerozoic, such as the ones outcropping on Gorgona Island off the coast of Colombia2. Komatiites are thought to be associated with mantle plumes sourced from deep mantle reservoirs, possibly at the core–mantle boundary. Thus, these lavas provide invaluable insights into the composition of the deep mantle, the nature of core–mantle differentiation processes and the chemical, physical and thermal state of early Earth3.The modern mantle has an inferred bulk oxygen isotope composition (δ18O) of about 5.5‰ (ref. 4). Hadean and Archaean magmatic zircons derived from sources in the upper mantle have δ18O compositions in a similar range, implying that the oxygen isotopic composition of the upper mantle has remained relatively constant, and comparable to the modern mantle throughout Earth's history5.Conversely, Byerly and colleagues1 suggest that the composition of the deep mantle, as inferred from δ18O measurements on olivine crystals from komatiites, has changed through time. Specifically, they find that the source of the Weltevreden komatiites has a δ18O signature of about 3 to 4‰ — significantly lighter than present-day mantle values and much lighter, too, than the Phanerozoic Gorgona lavas that are derived from a source with δ18O signatures between 4.4 and 5.5‰ (ref. 2).To reconcile the heterogeneous oxygen isotope signature of the deep mantle with the seemingly constant composition of the upper mantle through time5, it is necessary to unravel the nature of the deep mantle reservoirs that were tapped by the mantle plumes sourcing the komatiites. On the basis of the discordance between hafnium and neodymium isotope systems, some have proposed that deep-sea sediments were present in the source of the Barberton greenstone belt komatiites6. If true, the presence of a surface component in an ancient deep mantle source could explain its lighter oxygen isotope nature.However, Byerly et al.1 make a convincing case that the light oxygen isotope signature of the Weltevreden komatiites does not reflect the presence of subducted crustal material in their source or the effects of crustal assimilation upon eruption of the lavas. Instead, the authors argue that the anomalous δ18O signature may represent a residue of a magma ocean on early Earth. They suggest that an in-gassing process could have introduced large-scale oxygen isotope heterogeneities in the deep primordial mantle. However, it is unclear why a remnant of the early magma ocean would exhibit such extreme oxygen isotope fractionation.Further work is required to understand whether the observed light oxygen isotope signature is an isolated phenomenon, related only to the three-billion-year-old komatiite magmatic event preserved in the Barberton greenstone belt, or whether any secular evolution in the oxygen isotope composition of Archaean komatiites globally can be ascertained. A question also remains as to why that anomalous portion of the mantle is apparently no longer sampled in modern magmas. It is either inaccessible to modern-day mantle plumes or it no longer exists because it has since been wiped out by homogenization.Analysis of the secular evolution of the platinum content of komatiites globally could provide a hint to solving this conundrum. Komatiites erupted more than about 2.9 billion years ago display anomalously low platinum contents7, which reflect derivation from a platinum-depleted source. Conversely, the composition of younger komatiites is consistent with derivation from a source that contains similar platinum levels to the modern mantle. The platinum-depleted signature of the mantle source supplying the older komatiites could have been caused by segregation of the proto-core about 4.4 billion years ago7. Then, as the platinum content of the Archaean mantle steadily increased following the Late Heavy Bombardment event7, this anomalous signature was effectively homogenized away. This implies that the reservoir that fed the three-billion-year-old Weltevreden lavas may now be extinct8.Data from the Weltevreden komatiites could provide precious insights into the thermal evolution of the planet. Komatiites are thought to form from lavas erupted at very high temperatures of up to 1,600 °C, which implies even higher temperatures in their mantle source. However, these inferred temperatures only hold true if the komatiites were essentially dry and originated in mantle plumes9. If the magmas contained several per cent water, their eruption temperature would be drastically reduced10. It has recently been argued that a hydrous reservoir may have even existed in the deep mantle of early Earth11, and that hydrous and CO2-rich komatiites could have formed from carbonated wet spots in Archaean mantle plumes12. A fascinating question to ask then is whether the anomalously light oxygen composition of the Weltevreden komatiites may in fact reflect the presence in their mantle source of a non-terrestrial component derived from the proto-solar nebula13.Byerly and colleagues1 show that the oxygen isotopic signature of lavas erupted above a mantle plume more than three-billion-years ago is anomalously light compared to the present-day mantle. This implies that Earth's early mantle was heterogeneous, made up of reservoirs with different compositions and has since been homogenized by millions of years of mantle convection. The source of the anomalously light oxygen has yet to be unravelled.References1. Byerly, B. L. et al. Nat. Geosci. 10, 871–875 (2017).2. Gurenko, A. A. et al. Earth Planet. Sci. Lett. 454, 154–165 (2016).3. Arndt, N. T. Komatiite (Cambridge Univ. Press, 2008).4. Mattey, D., Lowry, D. & Macpherson, C. Earth Planet. Sci. Lett. 128, 231–241 (1994).5. Valley, J. W. et al. Contrib. Mineral. Petrol. 150, 561–580 (2005).6. Blichert-Toft, J. & Puchtel, I. S. Earth Planet. Sci. Lett. 297, 598–606 (2010).7. Maier, W. D. et al. Nature 460, 620–623 (2009).8. Fiorentini, M. L. et al. J. Petrol. 52, 83–112 (2011).9. Arndt, N. et al. Geology 26, 739–742 (1998).10. Grove, T. L. & Parman, S. W. Earth Planet. Sci. Lett. 219, 173–187 (2004).11. Sobolev, A. V. et al. Nature 531, 628–632 (2016).12. Herzberg, C. J. Petrol. 57, 2271–2288 (2016).13. Hashizume, K. & Chaussidon, M. Nature 434, 619–622 (2005).Fohlmeister, J., Plessen, B., Dudashvili, A.S., Tjallingii, R., Wolff, C., Gafurov, A., Cheng, H., 2017. Winter precipitation changes during the Medieval Climate Anomaly and the Little Ice Age in arid Central Asia. Quaternary Science Reviews 178, 24-36. strength of the North Atlantic Oscillation (NAO) is considered to be the main driver of climate changes over the European and western Asian continents throughout the last millennium. For example, the predominantly warm Medieval Climate Anomaly (MCA) and the following cold period of the Little Ice Age (LIA) over Europe have been associated with long-lasting phases with a positive and negative NAO index. Its climatic imprint is especially pronounced in European winter seasons. However, little is known about the influence of NAO with respect to its eastern extent over the Eurasian continent.Here we present speleothem records (δ13C, δ18O and Sr/Ca) from the southern rim of Fergana Basin (Central Asia) revealing annually resolved past climate variations during the last millennium. The age control of the stalagmite relies on radiocarbon dating as large amounts of detrital material inhibit accurate 230Th dating. Present-day calcification of the stalagmite is most effective during spring when the cave atmosphere and elevated water supply by snow melting and high amount of spring precipitation provide optimal conditions. Seasonal precipitation variations cause changes of the stable isotope and Sr/Ca compositions. The simultaneous changes in these geochemical proxies, however, give also evidence for fractionation processes in the cave. By disentangling both processes, we demonstrate that the amount of winter precipitation during the MCA was generally higher than during the LIA, which is in line with climatic changes linked to the NAO index but opposite to the higher mountain records of Central Asia. Several events of strongly reduced winter precipitation are observed during the LIA in Central Asia. These dry winter events can be related to phases of a strong negative NAO index and all results reveal that winter precipitation over the central Eurasian continent is tightly linked to atmospheric NAO modes by the westerly wind systems.Foley, S.F., Fischer, T.P., 2017. An essential role for continental rifts and lithosphere in the deep carbon cycle. Nature Geoscience 10, 897-902. continental lithosphere is a vast store for carbon. The carbon has been added and reactivated by episodic freezing and re-melting throughout geological history. Carbon remobilization can lead to significant variations in CO2 outgassing and release in the form of magmas from the continental lithosphere over geological timescales. Here we use calculations of continental lithospheric carbon storage, enrichment and remobilization to demonstrate that the role for continental lithosphere and rifts in Earth’s deep carbon budget has been severely underestimated. We estimate that cratonic lithosphere, which formed 2 to 3 billion years ago, originally contained about 0.25 Mt C km–3. A further 14 to 28 Mt C km–3 is added over time from the convecting mantle and about 43 Mt C km–3 is added by plume activity. Re-melting focuses carbon beneath rifts, creating zones with about 150 to 240 Mt C km–3, explaining the well-known association of carbonate-rich magmatic rocks with rifts. Reactivation of these zones can release 28 to 34 Mt of carbon per year for the 40 million year lifetime of a continental rift. During past episodes of supercontinent breakup, the greater abundance of continental rifts could have led to short-term carbon release of at least 142 to 170 Mt of carbon per year, and may have contributed to the high atmospheric CO2 at several times in Earth's history.Fox, P.M., Nico, P.S., Tfaily, M.M., Heckman, K., Davis, J.A., 2017. Characterization of natural organic matter in low-carbon sediments: Extraction and analytical approaches. Organic Geochemistry 114, 12-22. carbon (OC) concentrations in subsurface sediments are typically 10 to 200 times lower than in surface soils, posing a distinct challenge for characterization. In this study, a range of chemical extractions were evaluated for extraction of natural organic matter (NOM) from two low-carbon (< 0.2%) alluvial sediments. The OC extraction efficiency followed the order pyrophosphate (PP) > NaOH > HCl, hydroxylamine hydrochloride > dithionite, water. A NOM extraction and purification scheme was developed using sequential extraction with water (MQ) and sodium pyrophosphate at pH 10 (PP), combined with purification by dialysis and solid phase extraction in order to isolate different fractions of sediment-associated NOM. Characterization of these pools of NOM for metal content and by Fourier transform infrared spectroscopy (FITR) showed that the water soluble fraction (MQ-SPE) had a higher fraction of aliphatic and carboxylic groups, while the PP-extractable NOM (PP-SPE and PP > 1kD) had higher fractions of CC groups and higher residual metals. This trend from aliphatic to more aromatic is also supported by the specific UV absorbance at 254 nm (SUVA254) (3.5 vs 5.4 for MQ-SPE and PP-SPE, respectively) and electrospray ionization Fourier transform ion cyclotron resonance spectrometry (ESI-FTICR-MS) data which showed a greater abundance of peaks in the low O/C and high H/C region (0–0.4 O/C, 0.8–2.0 H/C) for the MQ-SPE fraction of NOM. Radiocarbon measurements yielded standard radiocarbon ages of 1020, 3095, and 9360 years BP for PP-SPE, PP > 1kD, and residual (non-extractable) OC fractions, indicating an increase in NOM stability correlated with greater metal complexation, apparent molecular weight, and aromaticity.Franzmann, M., Bosco, H., Walther, C., Wendt, K., 2017. A new resonant Laser-SNMS system for environmental ultra-trace analysis: Installation and optimization. International Journal of Mass Spectrometry 423, 27-32., analysis and mobility of radioactive contaminated particles is of major concern for assessment of contamination threads and nuclear forensics. For this purpose, a new resonant Laser-SNMS system was developed and set up at the Institute for Radioecology and Radiation Protection for spatially resolved ultra-trace analysis of low concentrated radionuclides directly on environmental samples. This paper describes the adaption and combination of a dedicated Ti:sapphire laser system with a commercial TOF-SIMS instrument for resonant Laser-SNMS. The project includes computer simulations for optimization of the TOF analyzer. Results on synthetic uranium and technetium samples verify the expected excellent suppression of interfering isobaric contaminations.Freedman, A.H., Wayne, R.K., 2017. Deciphering the origin of dogs: From fossils to genomes. Annual Review of Animal Biosciences 5, 281-307. the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic history. An initial severe bottleneck was associated with domestication followed by postdivergence gene flow between dogs and wolves, as well as population expansions, contractions, and replacements. In addition, because the domestication of dogs occurred in the relatively recent past, much of the observed polymorphism may be shared between dogs and wolves, limiting the power to distinguish between alternative models of dog history. Greater insight into the domestication process will require explicit tests of alternative models of domestication through the joint analysis of whole genomes from modern lineages and ancient wolves and dogs from across Eurasia.Freye, C.E., Bahaghighat, H.D., Synovec, R.E., 2018. Comprehensive two-dimensional gas chromatography using partial modulation via a pulsed flow valve with a short modulation period. Talanta 177, 142-149. modulation via a pulsed flow valve for comprehensive two-dimensional (2D) gas chromatography (GC × GC) is demonstrated, producing narrow peak widths, 2Wb, on the secondary separation dimension, 2D, coupled with short modulation periods, PM, thus producing a high peak capacity on the 2D dimension, 2nc. The GC × GC modulator is a pulse flow valve that injects a pulse of carrier gas at the specified PM, at the connection between the primary, 1D, column and the 2D column. Using a commercially available pulse flow valve, this injection technique performs a combination of vacancy chromatography and frontal analysis, whereby each pulse disturbance in the analyte concentration profile as it exits the 1D column results in data that is readily converted into a 2D separation. A three-step process converts the raw data into a format analogous to a GC × GC separation, incorporating signal differentiation, baseline correction and conversion to a GC × GC chromatogram representation. A 115-component test mixture with a wide range of boiling points (36–372 °C) of nine compound classes is demonstrated using modulation periods of PM = 50, 100, 250, and 500 ms, respectively. For the test mixture with a PM of 250 ms, peak shapes on 2D are symmetric with apparent 2Wb ranging from 12 to 45 ms producing a 2nc of ~ 10. Based on the average peak width of 0.93 s on the 1D separation for a time window of 400 s, the 1D peak capacity is 1nc ～ 430. Thus, the ideal 2D peak capacity nc,2D is 4300 or a peak capacity production of 650 peaks/min using the PM of 250 ms. Additionally, for a PM of 50, 100 and 500 ms, the 2nc are 4, 7, and 12, respectively. Retention times on 2D, 2tR, are reproducible having standard deviations less than 1 ms. Finally, the processed data is shown to be quantitative, with an average RSD of 4.7% for test analytes.Fry, C.R., Ray, D.C., Wheeley, J.R., Boomer, I., Jarochowska, E., Loydell, D.K., 2017. The Homerian carbon isotope excursion (Silurian) within graptolitic successions on the Midland Platform (Avalonia), UK: implications for regional and global comparisons and correlations. GFF 139, 301-313. δ13Ccarb data from the most stratigraphically extensive graptolitic sections of Homerian age in the study area are reported from Wenlock Edge and the Ludlow Anticline (UK). These sections, situated upon the Midland Platform (Avalonia), were key in establishing the Homerian graptolite biozonation used within the type Wenlock Series, and are consequently of international importance. Based upon 162 δ13Ccarb samples from four outcrops (Eaton Track, Longville–Stanway Road Cutting, Burrington Section and Mortimer Forest Stop 1), new graptolite collections and a re-evaluation of the original graptolite collections, the onset of both lower (older) and upper (younger) peaks of the Homerian Carbon Isotope Excursion have been calibrated to a revised graptolite biozonation (lundgreni – nassa – praedeubeli-deubeli – ludensis biozones). In addition, high-resolution correlation between the Ludlow Anticline and Wenlock Edge has been achieved by bio-, chemo- and sequence stratigraphic techniques. These correlations suggest a uniformity of depositional rates across the study area and indicate minor diachroneity at the base of the Much Wenlock Limestone Formation. Finally, correlations of the Midland Platform Homerian Carbon Isotope Excursion have allowed for better comparisons with other sections from which high-resolution graptolite and carbon isotope data are available. Such comparisons highlight the pan-regional synchronicity of the Homerian Carbon Isotope Excursion.Fu, C.-C., Yang, T.F., Chen, C.-H., Lee, L.-C., Wu, Y.-M., Liu, T.-K., Walia, V., Kumar, A., Lai, T.-H., 2017. Spatial and temporal anomalies of soil gas in northern Taiwan and its tectonic and seismic implications. Journal of Asian Earth Sciences 149, 64-77. this paper, we study (1) the spatial anomalies and (2) the temporal anomalies of soil gas in northern Taiwan. The spatial anomalies of soil gas are related to tectonic faults, while the temporal anomalies of soil gas are associated with pre-earthquake activities. Detailed soil gas sampling was systematically performed, and the analysis of the collected gas species shows that high helium and nitrogen concentrations appear in samples from specific sites, which coincide with the structural setting of the area studied. This analysis indicates the possibility of using these soil gases to determine fault zones in the studied area. Based on the soil gas data, a station (Tapingti) for automatic soil gas monitoring was constructed on an appropriate site at the fault zone. Some anomalous high radon concentrations at certain times can be identified from the dataset, which was generated by the continuous monitoring of soil gas for over a year. Notably, many of these anomalies were observed several hours to a few days before the earthquakes (ML > 3) that occurred in northern Taiwan. By combining the information of epicenters and fault plane solutions of these earthquakes, we find that the shallow earthquakes (<15 km) were mainly strike-slip and normal-type earthquakes, and concentrated within a distance of 30 km to the monitoring site (Group A). The deep earthquakes (>20 km) were mainly thrust-type earthquakes and distributed in greater distances (>45 km) east of the monitoring site (Group B). Such focal mechanisms of earthquakes suggest an extensional and compressional structural domain in the continental crust for Group A and Group B earthquakes, respectively. It is suggested that the pre-earthquake activities associated with the seismicity of Group B may be transmitted along the major decollement in the region below the Tapingti station, leading to the observed soil gas enhancements.Fujii, T., Imasaka, T., Imasaka, T., 2017. Use of chemical conversion for determination of nitrated aromatic hydrocarbons using femtosecond ionization mass spectrometry. Analytica Chimica Acta 996, 48-53. sample containing nitrated aromatic hydrocarbons (NPAHs) was injected into the sample inlet port of a gas chromatograph (GC), along with hydrazine, a reducing reagent. The analytes that eluted from the GC column were measured by mass spectrometry (MS) using an ultraviolet femtosecond laser as the ionization source. When no reducing reagent was used, large numbers of polycyclic aromatic hydrocarbons (PAHs) including NPAHs were observed in the two-dimensional GC/MS display. In contrast, when hydrazine was present, reduced forms of NPAHs, which included amino PAHs, were detected. When a palladium or platinum catalyst was placed in the GC inlet port, the compounds were further reduced to non-aromatic hydrocarbons. The present approach would be useful for studies to evaluate the chemical reaction that converts the constituents contained in exhaust emitted from a diesel engine.Fulton, J.M., Fredricks, H.F., Van Mooy, B.A.S., 2017. Intact polar lipid export in the temperate western North Atlantic and Sargasso Sea. Organic Geochemistry 114, 45-56. polar diacylglycerolipids (IP-DAGs), abundant membrane components in phytoplankton and bacterioplankton, comprised 5.9 ± 0.5% of suspended particulate organic carbon (POC) in the euphotic zone at two stations in the western North Atlantic Ocean. The IP-DAG assemblage included 9 phospholipid, glycolipid and betaine lipid classes that are routinely found in marine samples. We also report the pelagic occurrence of two recently discovered IP-DAGs, phosphatidyl-S,S-dimethylpropanethiol (PDPT) and a betaine-like lipid, both originally identified in Emiliania huxleyi. At the mesotrophic station north of the Gulf Stream, IP-DAGs comprised 0.62 ± 0.38% of sinking POC collected in sediment traps, and at the oligotrophic station in the Sargasso Sea they comprised 0.31 ± 0.05% of sinking POC.Phospholipids and glycolipids with polyunsaturated fatty acid (PUFA) moieties were relatively abundant in sinking particles at 150 m compared with suspended particles in the euphotic zone at the mesotrophic station north of the Gulf Stream. The sinking particles were probably associated with the demise of a dinoflagellate or diatom bloom that resulted in a maximum total IP-DAG export flux of 1.8 μmol/m2/day. At the oligotrophic station in the Sargasso Sea, sinking particles included microalgal glycolipids, phospholipids and betaine lipids with PUFAs; picocyanobacterial glycolipids with saturated and monounsaturated FAs; and bacterial phospholipids with saturated and monounsaturated FAs. The microalgal and bacterial IP-DAGs were relatively abundant in sinking particles compared with suspended particles. The IP-DAG export flux at the station in the Sargasso Sea was similar in three sediment traps deployed on consecutive days, with an average of 0.46 ± 0.08 μmol/m2/day.A diel cycle was observed in the IP-DAG euphotic zone inventory in the Sargasso Sea, with higher concentration in samples taken at dusk than at dawn, and we propose a model using this dynamic to calculate IP-DAG residence time. Export efficiency was calculated from the residence time and the ratio of IP-DAG export flux to euphotic zone inventory, with values ranging from 0.02% for PDPT to 6.9% for monogalactosyldiacylglycerol (MGDG) with PUFAs. The greater export flux and export efficiency of IP-DAGs with PUFAs contrasts with previous results for total FAs in sinking particles, which showed preferential export of saturated and monounsaturated FAs. The difference likely resulted from IP-DAGs with PUFAs being membrane components of rapidly sinking organic matter from microalgae. Alternatively, PUFA moieties cause steric hindrance of microbial lipase activity, potentially decreasing their hydrolysis rate and increasing the relative concentration of IP-DAGs with PUFAs in sinking particles.Furutani, Y., Kudo, S., Hayashi, J.-i., Norinaga, K., 2018. Predicting molecular composition of primary product derived from fast pyrolysis of lignin with semi-detailed kinetic model. Fuel 212, 515-522. numerical approach is presented for predicting the yields of char and volatile components obtained from fast pyrolysis of three types of lignin (enzymatic hydrolysis lignin, EHL; organic extracted lignin, OEL; and Klason lignin, KL) in a two-stage tubular reactor (TS-TR) at 773–1223?K. The heating rate of lignin particle in the TS-TR was estimated at 102–104?K/s by solving the heat transfer equation. The pyrolytic behavior of lignin and the formation of products in the temperature rising process were predicted using a semi-detailed kinetic model consisting of 93 species and 406 reactions, and the predicted yields of 8 primary products (i.e., char, tar, CO, CO2, H2O, CH3OH, C2H6, and C3H6) were compared with experimental data for the critical evaluation. For EHL, the predicted yields of char and H2O were in good agreement with the experimental results at all temperatures. However, the numerical simulation overestimated tar yield and underestimated CO yield at high temperature probably due to a lack of the kinetic model of the tar cracking reaction. The predicted yields of CH3OH, C2H6, and C3H6 were close to the experimental values at high temperature by adding the detailed chemical kinetic model of the secondary vapor-phase reaction. Moreover, the model reproduced the experimental observation that among the three types of lignin the char yield increased in the order of EHL?<?OEL?<?KL, whereas the tar yield decreased.Gabelica, V., Marklund, E., 2018. Fundamentals of ion mobility spectrometry. Current Opinion in Chemical Biology 42, 51-59. questions in ion mobility spectrometry have practical implications for analytical applications in general, and omics in particular, in three respects. (1) Understanding how ion mobility and collision cross section values depend on the collision gas, on the electric field and on temperature is crucial to ascertain their transferability across instrumental platforms. (2) Predicting collision cross section values for new analytes is necessary to exploit the full potential of ion mobility in discovery workflows. (3) Finally, understanding the fate of ion structures in the gas phase is essential to infer meaningful information on solution structures based on gas-phase ion mobility measurements. We review here the most recent advances in ion mobility fundamentals, relevant to these three aspects.Gainey, S.R., Hausrath, E.M., Adcock, C.T., Tschauner, O., Hurowitz, J.A., Ehlmann, B.L., Xiao, Y., Bartlett, C.L., 2017. Clay mineral formation under oxidized conditions and implications for paleoenvironments and organic preservation on Mars. Nature Communications 8, Article 1230. mineral-bearing locations have been targeted for martian exploration as potentially habitable environments and as possible repositories for the preservation of organic matter. Although organic matter has been detected at Gale Crater, Mars, its concentrations are lower than expected from meteoritic and indigenous igneous and hydrothermal reduced carbon. We conducted synthesis experiments motivated by the hypothesis that some clay mineral formation may have occurred under oxidized conditions conducive to the destruction of organics. Previous work has suggested that anoxic and/or reducing conditions are needed to synthesize the Fe-rich clay mineral nontronite at low temperatures. In contrast, our experiments demonstrated the rapid formation of Fe-rich clay minerals of variable crystallinity from aqueous Fe3+ with small amounts of aqueous Mg2+. Our results suggest that Fe-rich clay minerals such as nontronite can form rapidly under oxidized conditions, which could help explain low concentrations of organics within some smectite-containing rocks or sediments on Mars.Gao, G., Yang, S., Zhang, W., Wang, Y., Gang, W., Lou, G., 2018. Organic geochemistry of the lacustrine shales from the Cretaceous Taizhou Formation in the Gaoyou Sag, Northern Jiangsu Basin. Marine and Petroleum Geology 89, 594-603. shale from the Cretaceous Taizhou Formation is an important source rock in the Gaoyou Sag, Northern Jiangsu Basin. Fifty-three shale core samples analyzed for total organic carbon (TOC) and Rock-Eval pyrolysis analyses were used to evaluate the geochemistry of this shale. Twenty-one samples of them were analyzed using solvent extraction, extract fractionation, Gas Chromatography-Mass Spectrometer (GC-MS) of the saturated fraction, and organic petrology analyses. Based on the test results, the shale of the Taizhou Formation contains mainly Type II-III organic matter and is chiefly oil-prone and oil-gas-prone, as a fair to good oil-source rock with a small quantity of gas-source rock. Vitrinite reflectance, Rock-Eval pyrolysis, and biomarker suggest that in this sag, the shale of the Taizhou Formation is mainly in the early mature stage and within the oil window, so the shale generates chiefly liquid oil. The Gaoyou Sag is an oil-generating sag. The saturated fraction and biomarker composition of the shale provide evidence that the Taizhou Formation shale was formed mainly in a reductive sedimentary environment with anoxic fresh to low salinity water. The organic matter came chiefly from plankton and partly from land plants and bacterial organisms.Gao, J., Wang, X., He, S., Guo, X., Zhang, B., Chen, X., 2017. Geochemical characteristics and source correlation of natural gas in Jurassic shales in the North Fuling area, Eastern Sichuan Basin, China. Journal of Petroleum Science and Engineering 158, 284-292. North Fuling area is located in the Eastern Sichuan Basin, China. Natural gas and condensates are commonly found in the Jurassic shales (including Lianggaoshan, Da'anzhai, and Dongyuemiao shales.) in this area. Multiple geochemical approaches and tests including methane concentration, C2+ concentration, and stable isotopes were employed to determine the geochemical characteristics and the origin of the gas samples from the Jurassic shales. The analyses reveal that: (1) natural gas in the Jurassic shales is predominantly wet gas with the methane concentration of 36.89% ～ 94.27%; (2) δ13C values range between ?49.4 ～ ?44.2‰/VPDB in methane, ?33.0 ～ ?30.0‰/VPDB in ethane, and ?28.7 ～ ?26.5‰/VPDB in propane; the crossplot of isotope data indicates the gas samples are oil-associated gas which probably originated from the cracking of crude oil; (3) thermal maturity in terms of vitrinite reflectance equivalence of the gas samples ranges from 0.8% to 1.2%; and (4) gas-source correlation suggests the gas in Jurassic shales is generated from Da'anzhai shale, of which organic matter is primarily Type II1 and Ro ranges from 1.06% to 1.28%.Garcias-Bonet, N., Duarte, C.M., 2017. Methane production by seagrass ecosystems in the Red Sea. Frontiers in Marine Science 4, 340. doi: 10.3389/fmars.2017.00340. methane (CH4) is the second strongest greenhouse gas and it is emitted to the atmosphere naturally by different sources. It is crucial to define the dimension of these natural emissions in order to forecast changes in atmospheric CH4 mixing ratio in future scenarios. However, CH4 emissions by seagrass ecosystems in shallow marine coastal systems have been neglected although their global extension. Here we quantify the CH4 production rates of seagrass ecosystems in the Red Sea. We measured changes in CH4 concentration and its isotopic signature by cavity ring-down spectroscopy on chambers containing sediment and plants. We detected CH4 production in all the seagrass stations with an average rate of 85.09 ± 27.80 μmol CH4 m?2 d?1. Our results show that there is no seasonal or daily pattern in the CH4 production rates by seagrass ecosystems in the Red Sea. Taking in account the range of global estimates for seagrass coverage and the average seagrass CH4 production, the global CH4 production and emission by seagrass ecosystems could range from 0.09 to 2.7 Tg yr?1. Because CH4 emission by seagrass ecosystems had not been included in previous global CH4 budgets, our estimate would increase the contribution of marine global emissions, hitherto estimated at 9.1 Tg yr?1, by about 30%. Thus, the potential contribution of seagrass ecosystems to marine CH4 emissions provides sufficient evidence of the relevance of these fluxes as to include seagrass ecosystems in future assessments of the global CH4 budgets.Gautam, R., Varma, A.K., Vinu, R., 2017. Apparent kinetics of fast pyrolysis of four different microalgae and product analyses using pyrolysis-FTIR and pyrolysis-GC/MS. Energy & Fuels 31, 12339-12349. study reports an experimental technique to obtain the isothermal mass loss profiles of four different microalgae (Chlorella vulgaris, Nannochlorpsis oculata, Schizochytrium limacinum, and Arthrospira platensis) under fast pyrolysis conditions in the temperature range of 400–700 °C at short residence times of 2–60 s using an analytical pyrolyzer. The microalgae investigated in this study vary significantly, based on elemental and biochemical composition. The apparent kinetic parameters of fast pyrolysis of the algae were evaluated using first-order and multidimensional diffusion models. The apparent activation energy and pre-exponential factor evaluated under fast heating rate conditions were lower compared to those reported under slow pyrolysis conditions, which is attributed to the diffusion effects. The rate parameters were validated by constructing a kinetic compensation plot, which showed that ln(A) = 0.19Ea + 0.43. The product time evolution at short time scales was studied using in situ Fourier transform infrared spectroscopy, and a majority of the functional groups evolved in the range of 5–12 s. The evolution of C═O and aliphatic C–H stretching vibrations for lipid-rich algae was slow, compared to that for protein-rich algae. The pyrolysates were characterized using gas chromatography/mass spectrometry, and the yield of nitrogen-containing organics followed a linear trend with the elemental nitrogen content in the algae.Gavard, R., Rossell, D., Spencer, S.E.F., Barrow, M.P., 2017. Themis: Batch preprocessing for ultrahigh-resolution mass spectra of complex mixtures. Analytical Chemistry 89, 11383-11390. transform ion cyclotron resonance mass spectrometry affords the resolving power to determine an unprecedented number of components in complex mixtures, such as petroleum. The software tools required to also analyze these data struggle to keep pace with advancing instrument capabilities and increasing quantities of data, particularly in terms of combining information efficiently across multiple replicates. Improved confidence in data and the use of replicates is particularly important where strategic decisions will be based upon the analysis. We present a new algorithm named Themis, developed using R, to jointly preprocess replicate measurements of a sample with the aim of improving consistency as a preliminary step to assigning peaks to chemical compositions. The main features of the algorithm are quality control criteria to detect failed runs, ensuring comparable magnitudes across replicates, peak alignment, and the use of an adaptive mixture model-based strategy to help distinguish true peaks from noise. The algorithm outputs a list of peaks reliably observed across replicates and facilitates data handling by preprocessing all replicates in a single step. The processed data produced by our algorithm can subsequently be analyzed by use of relevant specialized software. While Themis has been demonstrated with petroleum as an example of a complex mixture, its basic framework will be useful for complex samples arising from a variety of other applications.Ge, J.W., Zhu, X.M., Zhang, X.T., Jones, B.G., Yu, F.S., Niu, Z.C., Li, M., 2017. Tectono-stratigraphic evolution and hydrocarbon exploration in the Eocene Southern Lufeng Depression, Pearl River Mouth Basin, South China Sea. Australian Journal of Earth Sciences 64, 931-956. structural evolution and stratigraphic architecture of the Southern Lufeng Depression in the Pearl River Mouth Basin, South China Sea show two second-order sequences (SSQ1 and SSQ2) and nine third-order sequences (WSQ1-5 and ESQ1-4) within the Eocene rift-related successions. Based on integrated interpretations of seismic reflections, well logs and core data, five distinct tectono-stratigraphic patterns are identified: (1) the initial synrift-I sequence (WSQ1) of low tectonic subsidence, overfilled by alluvial fan or fan-delta deposits and volcanic deposits, with no clear systems tracts; (2) the climax synrift-I sequences (WSQ2?4) developed in response to rapid tectonic subsidence, generally consisting of a low-stand systems tract (LST), transgressive systems tract (TST) and high-stand systems tract (HST); (3) the late synrift-I sequence (WSQ5) characterised by a decreased tectonic subsidence rate, dominated by braided delta, deep and shallow lacustrine sediments, mainly constructed by TST and HST; (4) the early synrift-II sequences (ESQ1?2) rapidly filled by braided deltaic sandstone and mainly composed of TST and HST with less common LST units; and (5) the late synrift-II sequences (ESQ3?4), which are totally filled by braided deltaic system in a shallow-water lake setting, presenting typical imbricate clinoforms or sub-parallel seismic configurations, consisting of only TST and HST components. During the climax stage of synrift-I development, the depositional setting changed from a prominent shallow lake (WSQ2) to a deep-lucustrine with turbiditic deposits (WSQ3) and finally dominated by mostly braided deltaic-shallow lacustrine deposits (WSQ4); the HST occupies an increasing proportion from early to late. Furthermore, the stratigraphic patterns, especially LST units of the climax synrift-I stage, are significantly influenced by topographic variations and slope-break belt types in the hanging dip-slope. This study reveals that the spatial and temporal evolution of lacustrine depositional and stratigraphic patterns were significantly controlled by the interplay of tectonic subsidence and sediment supply, and provides a fundamental basis for predicting the favourable reservoirs and geometry of source rocks related to the general variability of Eocene rift-related tectonic subsidence in the Southern Lufeng Depression of the Pearl River Mouth Basin. Furthermore, the topographic responses of differential active fault-stepped patterns associated with magma intrusions, highlight the variability of relevant sequence architectures in the hanging dip-slope in lacustrine rift basins.Gess, R.W., Prestianni, C., 2018. Kowieria alveoformis gen. nov. sp. nov., a new heterosporous lycophyte from the Latest Devonian of Southern Africa. Review of Palaeobotany and Palynology 249, 1-8. new lycopsid, Kowieria alveoformis gen. et sp. nov., is described from the Famennian Witpoort Formation, Grahamstown, South Africa. It possesses spirally arranged elongated falcate vegetative leaves. Terminal bisporangiate strobili are present and show loosely grouped micro- and megasporophylls. Sporophylls are similar in shape to the vegetative leaves though somewhat wider with a marked expansion to house the sporangium. One sporangium is attached directly to the adaxial surface of the lamina. Each megasporangium contains up to four heavily ornamented hologulate megaspores of the Lagenicula type. The combination of both basal and derived characters within this plant places it at an interesting position at the base of the phylogenetic tree of rhizomorphic lycopsids.Ghasemi, M., Astutik, W., Alavian, S., Whitson, C.H., Sigalas, L., Olsen, D., Suicmez, V.S., 2018. Tertiary-CO2 flooding in a composite fractured-chalk reservoir. Journal of Petroleum Science and Engineering 160, 327-340. paper presents the oil recovery mechanism by tertiary-CO2 flooding in a composite fractured chalk core. We perform two different core flooding experiments at reservoir conditions. We evaluate the efficiency of tertiary-CO2 flooding in different conditions, taking into account the effect of capillary continuity, water composition, and the heterogeneity.The composite core consists of six core plugs placed vertically in-line in the core holder with total length of 45 cm and average diameter of 3.74 cm. We use qualitative filter paper between each core plug to reserve the capillary continuity at reservoir conditions (258 bara and 110 °C). The “fracture” is represented by a centralized axial hole with a diameter of 0.6 cm. In all experiments, the composite fractured core is initially saturated with North Sea Chalk Field (NSCF) stock tank oil (STO) and synthetic connate water. Once the reservoir conditions are established, brine is injected from the bottom of the fracture and the oil is produced from the top. We stop water flooding (WF) after no more oil is being produced. CO2 is then injected from the top of the fracture and the oil is produced from the bottom.Experiments Exp-1C and Exp-2C utilize Sigerslev outcrop chalk cores. To account for the effect of initial water composition during WF, system is initially saturated with synthetic sea water with considerable amount of sulfate instead of formation water in Exp-1C. Whereas, we employ synthetic formation water with zero sulfate content in Exp-2C.The results of experimental work are reproduced via validated compositional reservoir simulator with a tuned equation of state (EOS). We develop an automated history matching algorithm to match the experimental data of WF and CO2 flooding (CF) periods.We observe a major impact of the initial water composition that results in strong- to moderate-spontaneous imbibition during WF period. Moreover, both experiments and simulations show that the tertiary CO2 recovery is significantly affected by the water saturation in the core after the secondary WF. We conduct a sensitivity analysis to study different CO2 injection scenarios such as in a single block, in a composite core with capillary continuity, and in a composite core with horizontal fractures in between. The results show the oil recovery during tertiary-CO2 flooding is barely affected by the degree of the capillary contacts between the chalk matrixes. Moreover, it is found that the mass transport during CF is mainly covered by diffusion rather than the convective flux or viscous forces.We build a modeling framework that accounts for proper modeling of imbibition and diffusion dominated processes in a composite chalk system at reservoir conditions.Ghiasikhou, S., da Silva, M.F., Zhu, Y., Zenobi, R., 2017. The capillary gap sampler, a new microfluidic platform for direct coupling of automated solid-phase microextraction with ESI-MS. Analytical and Bioanalytical Chemistry 409, 6873-6883. new technology for rapid, automated coupling of solid-phase microextraction and mass spectrometry is introduced. Use of a so-called capillary gap sampler for automated solid-phase microextraction and direct delivery of the extracted analytes to a mass spectrometer provides certain advantages over existing technologies: coupling of the capillary gap sampler to a mass spectrometer offers quick, automated, and site-specific extraction from very low volume samples. High stability, reusability, and repeatability were achieved through systematic optimization. Diazepam, oxazepam, and nordiazepam were used as test compounds in all experiments. The ability of the sampler to extract benzodiazepines from human plasma (limit of detection 0.3 μg/mL) in the therapeutic range was confirmed. A linear dynamic range from 1 to 1000 ng/mL for all three analytes was found. The relative standard deviation of 20 extractions was between 11% and 17%, for oxazepam, nordiazepam, and diazepam, indicating acceptable repeatability of the method.Ghosh, S., Sengupta, A., Chandra, K., 2017. SOFAST-HMQC—an efficient tool for metabolomics. Analytical and Bioanalytical Chemistry 409, 6731-6738. magnetic resonance (NMR)-based metabolomics relies mostly on 1D NMR; however, the technique is limited by overlap of the signals from the metabolites. In order to circumvent this problem, 2D 1H-13C correlation spectroscopy techniques are often used. However owing to poorer natural abundance and gyromagnetic ratio of 13C, the acquisition time for 2D 1H-13C heteronuclear single quantum coherence spectroscopy (HSQC) is long. This makes it almost impossible to be used in high throughput study. We have reported the application of selective optimized flip angle short transient (SOFAST) technique coupled to heteronuclear multiple quantum correlation (HMQC) along with nonlinear sampling (NUS) in urine and serum samples. This technique takes sevenfold less experimental time than the conventional 1H-13C HSQC experiment with retention of almost all molecular information. Hence, this can be used for high throughput study.Glikson, A., 2018. Structure and origin of Australian ring and dome features with reference to the search for asteroid impact events. Tectonophysics 722, 175-196., dome and crater features on the Australian continent and shelf include (A) 38 structures of confirmed or probable asteroid and meteorite impact origin and (B) numerous buried and exposed ring, dome and crater features of undefined origin. A large number of the latter include structural and geophysical elements consistent with impact structures, pending test by field investigations and/or drilling. This paper documents and briefly describes 43 ring and dome features with the aim of appraising their similarities and differences from those of impact structures. Discrimination between impact structures and igneous plugs, volcanic caldera and salt domes require field work and/or drilling. Where crater-like morphological patterns intersect pre-existing linear structural features and contain central morphological highs and unique thrust and fault patterns an impact connection needs to tested in the field. Hints of potential buried impact structures may be furnished by single or multi-ring TMI patterns, circular TMI quiet zones, corresponding gravity patterns, low velocity and non-reflective seismic zones. A. Examples of crater-form and dome-form features containing elements consistent with an impact origin, though unproven, include Auvergne, Delamere, Fiery Creek, Monte Christo, Mount Moffatt, Tanami East, Youngerina, and Tingha.B. Examples of buried multi-ring features of possible to probable impact origin include Augathella, Balfour Downs, Calvert Hills, Camooweal, Green Swamp Well, Herbert, Ikybon River, Ilkurka, Lennis, McLarty Hills, Mount Davies, Mulkara; Neale; Sheridan Creek, Oodjuongari and Renehan.C. Examples of igneous plugs unrelated to impacts include the Monto gabbro and numerous circular granitoid plugs such as Windinie Hills granite and Yataga granodiorite.D. Large circular structures such as Mount Ashmore and Gnargoo are considered to have convincing structural deformation features warranting classification as probable impact structures.The origin of very large circular TMI and gravity patterns such as of the Diamantina River drainage feature, Coonamona anomaly and the multiple TMI ring pattern of the Deniliquin-Booligal remain unresolved. The advent of ~ 40 m TMI grid coverage promises to further uncover ring and dome features, such as the McLarty Hills multi-ring feature, potentially increasing the inventory of ring structures on the Australian continent. Compared with frequency distribution patterns of extra-terrestrial impact structures worldwide, the Australian record displays a relatively common occurrence of large impact structures and relative depletion in small impact structures and craters. This is explained by the better preservation of large structures at deep crustal zones as compared to the erosion of small craters.Goldstein, R.A., Pollock, D.D., 2017. Sequence entropy of folding and the absolute rate of amino acid substitutions. Nature Ecology & Evolution 1, 1923-1930. representations of protein evolution should consider how the acceptance of mutations depends on the sequence context in which they arise. However, epistatic interactions among sites in a protein result in hererogeneities in the substitution rate, both temporal and spatial, that are beyond the capabilities of current models. Here we use parallels between amino acid substitutions and chemical reaction kinetics to develop an improved theory of protein evolution. We constructed a mechanistic framework for modelling amino acid substitution rates that uses the formalisms of statistical mechanics, with principles of population genetics underlying the analysis. Theoretical analyses and computer simulations of proteins under purifying selection for thermodynamic stability show that substitution rates and the stabilization of resident amino acids (the ‘evolutionary Stokes shift’) can be predicted from biophysics and the effect of sequence entropy alone. Furthermore, we demonstrate that substitutions predominantly occur when epistatic interactions result in near neutrality; substitution rates are determined by how often epistasis results in such nearly neutral conditions. This theory provides a general framework for modelling protein sequence change under purifying selection, potentially explains patterns of convergence and mutation rates in real proteins that are incompatible with previous models, and provides a better null model for the detection of adaptive changes.Gon?alves, V.N., Vitoreli, G.A., de Menezes, G.C.A., Mendes, C.R.B., Secchi, E.R., Rosa, C.A., Rosa, L.H., 2017. Taxonomy, phylogeny and ecology of cultivable fungi present in seawater gradients across the Northern Antarctica Peninsula. Extremophiles 21, 1005-1015. seawater samples collected at different depths of the Gerlache and Bransfield Straits in the Northern Antarctic Peninsula were analyzed, and the average of the total fungal counts ranged from 0.3 to >300 colony forming units per liter (CFU/L) in density. The fungal were purified and identified as 15 taxa belonged to the genera Acremonium, Aspergillus, Cladosporium, Cystobasidium, Exophiala, Glaciozyma, Graphium, Lecanicillium, Metschnikowia, Penicillium,?Purpureocillium and Simplicillium. Penicillium chrysogenum, Cladosporium sphaerospermum, and Graphium rubrum were found at high densities in at least two different sites and depths. Our results show at the first time that in the seawater of Antarctic Ocean occur diverse fungal assemblages despite extreme conditions, which suggests the presence of a complex aquatic fungi food web, including species reported as barophiles, symbionts, weak and strong saprobes, parasites and pathogens, as well as those found in the polluted environments of the world. Additionally, some taxa were found in different sites, suggesting that the underwater current might contribute to fungal (and microbial) dispersal across the Antarctic Ocean, and nearby areas such as South America and Australia.Gong, D., Wang, Y., Yuan, M., Liu, C., Mi, J., Lu, S., Zhao, L., 2017. Genetic types and origins of natural gases from eastern Fukang Sub-depression of the Junggar Basin, NW China: Implication for low-mature coal-derived gases. Journal of Natural Gas Geoscience 2, 179-189. the Fukang Sub-depression is the largest hydrocarbon generation depression in the Junggar Basin and promises favorable potential for oil and gas exploration, only several small–medium oil/gas accumulations have been discovered so far. After analyzing the molecular and stable carbon isotopic compositions of natural gases and its associated low molecular weight hydrocarbons (LMWHs) from eastern Fukang Sub-depression, their genetic types and origins are discussed in this study. Natural gases are wet gases with an average dryness coefficient of 0.84. Stable carbon isotopes of methane and ethane are well correlated with the thermal evolution trend of coal-derived gases. The C5–7 LMWHs are enriched in methyl cyclohexane but they lack n-alkanes, indicating a predominance of higher plant input. Gases have maturities ranging 0.76%–0.93%Ro and are well consistent with their low n-heptane (H) and iso-heptane (I) contents. The geochemical characteristics of natural gases from eastern Fukang Sub-depression are quite similar with those from the Turpan–Hami Basin. Their gases are considered to be low-mature gases derived from the Lower–Middle Jurassic coal measures. In contrast, they show remarkable differences with those from the Wucaiwan gas field; they are considered to have high-mature gases derived from the Carboniferous coal measures.González-Ruiz, V., Pezzatti, J., Roux, A., Stoppini, L., Boccard, J., Rudaz, S., 2017. Unravelling the effects of multiple experimental factors in metabolomics, analysis of human neural cells with hydrophilic interaction liquid chromatography hyphenated to high resolution mass spectrometry. Journal of Chromatography A 1527, 53-60. work introduces a strategy for decomposing variable contributions within the data obtained from structured metabolomic studies. This approach was applied in the context of an in vitro human neural model to investigate biochemical changes related to neuroinflammation. Neural cells were exposed to the neuroinflammatory toxicant trimethyltin at different doses and exposure times. In the frame of an untargeted approach, cell contents were analysed using HILIC hyphenated with HRMS. Detected features were annotated at level 1 by comparison against a library of standards, and the 126 identified metabolites were analysed using a recently proposed chemometric tool dedicated to multifactorial Omics datasets, namely, ANOVA multiblock OPLS (AMOPLS). First, the total observed variability was decomposed to highlight the contribution of each effect related to the experimental factors. Both the dose of trimethyltin and the exposure time were found to have a statistically significant impact on the observed metabolic alterations. Cells that were exposed for a longer time exhibited a more mature and differentiated metabolome, whereas the dose of trimethyltin was linked to altered lipid pathways, which are known to participate in neurodegeneration. Then, these specific metabolic patterns were further characterised by analysing the individual variable contributions to each effect. AMOPLS was highlighted as a useful tool for analysing complex metabolomic data. The proposed strategy allowed the separation, quantitation and characterisation of the specific contribution of the different factors and the relative importance of every metabolite to each effect with respect to the total observed variability of the system.Górniak, A., 2017. Spatial and temporal patterns of total organic carbon along the Vistula River course (Central Europe). Applied Geochemistry 87, 93-101. recent trends of river organic matter concentrations and flux have been presented for Northern Hemisphere. The catchment of the Vistula River has been a place of intensive economic transformation since the 1980s, which has been accompanied by increase of extreme weather and hydrological events. The patterns of total organic carbon (TOC) has not yet been studied on Vistula River, the largest Polish river, with a basin area of 194000 km2 and a mean annual flow exceeding 1000 m3s-1. Annual TOC concentrations in the river mouth decreased from 10.7 mgC dm?3 to 7 mgC dm?3 between years 2000–2014; however, during a 55-year period, the TOC decrease was estimated to be 45% as a result of a large scale reduction of waste supply to Polish rivers. The Vistula River annual mean TOC export (flow normalized) was 1.54 gC m?2 and significantly decreased, with a high inter-annual variations depending on hydrology. Gradual decreases of TOC flux were observed along the river continuum from headwaters to downstream. TOC export in wet years was 5 times higher than in dry years, indicating the important role of river flooding and droughts on TOC load to the southern Baltic Sea. Dam reservoir located on the lower part of the Vistula River course have had a large impact on the retention of terrestrial TOC load, reducing annual flux by approximately 20%.Gratia, J.-P., 2017. Genetic recombinational events in prokaryotes and their viruses: insight into the study of evolution and biodiversity. Antonie van Leeuwenhoek 110, 1493-1514. exact meaning of sexual reproduction and the precise evolutionary period at which recombination first took place remains the subject of intense debates. Despite some unity in biochemical organisation of genetic recombination, a plethora of mechanisms are found to exist in microbes and their viruses. Some routes used by viruses bypass barriers to genetic heterology and provide bacteria with genes conferring a selective advantage, and some contribute to genome enlargement. The present review aims at highlighting the diversity of such mechanisms with a particular focus on spontaneous zygogenesis (or Z-mating). The latter mode of genetic recombination, which was recently discovered in Escherichia coli, resembles gamete fusion in eukaryotes in that it involves complete genetic mixing. Vertical and horizontal evolution through mutations and homo- or heterospecific Z-mating can be monitored to some extent, providing a mean to interrogate the mechanisms of evolution in a way similar to introgression and symbiogenesis. The question arises as to whether Z-mating might represent a remainder of what happened in the very first organisms appearing on earth, as well as recombination events among viruses.Grosjean, A.-S., Vennin, E., Olivier, N., Caravaca, G., Thomazo, C., Fara, E., Escarguel, G., Bylund, K.G., Jenks, J.F., Stephen, D.A., Brayard, A., 2018. Early Triassic environmental dynamics and microbial development during the Smithian–Spathian transition (Lower Weber Canyon, Utah, USA). Sedimentary Geology 363, 136-151. Early Triassic biotic recovery following the end-Permian mass extinction is well documented in the Smithian–Spathian Thaynes Group of the western USA basin. This sedimentary succession is commonly interpreted as recording harsh conditions of various shallow marine environments where microbial structures flourished. However, recent studies questioned the relevance of the classical view of long-lasting deleterious post-crisis conditions and suggested a rapid diversification of some marine ecosystems during the Early Triassic. Using field and microfacies analyses, we investigate a well-preserved Early Triassic marine sedimentary succession in Lower Weber Canyon (Utah, USA). The identification of microbial structures and their depositional settings provide insights on factors controlling their morphologies and distribution. The Lower Weber Canyon sediments record the vertical evolution of depositional environments from a middle Smithian microbial and dolosiliciclastic peritidal system to a late Smithian-early Spathian bioclastic, muddy mid ramp. The microbial deposits are interpreted as Microbially Induced Sedimentary Structures (MISS) that developed either (1) in a subtidal mid ramp where microbial wrinkles and chips are associated with megaripples characterizing hydrodynamic conditions of lower flow regime, or (2) in protected areas of inter- to subtidal inner ramp where they formed laminae and domal structures. Integrated with other published data, our investigations highlight that the distribution of these microbial structures was influenced by the combined effects of bathymetry, hydrodynamic conditions, lithology of the substrat physico-chemical characteristics of the depositional environment and by the regional relative sea-level fluctuations. Thus, we suggest that local environmental factors and basin dynamics primarily controlled the modalities of microbial development and preservation during the Early Triassic in the western USA basin.Guido, A., Rosso, A., Sanfilippo, R., Russo, F., Mastandrea, A., 2017. Microbial biomineralization in biotic crusts from a Pleistocene marine cave (NW Sicily, Italy). Geomicrobiology Journal 34, 864-872. crusts occurring in the Early Pleistocene Rumena Cave, in NW Sicily, have been analyzed from a geomicrobiological point of view. The crusts consist largely of scleractinians and of subordinate bryozoans and serpuloideans, all typical of submarine cave biota. Encrustations document a blind cave in a shadowed setting, or possibly below the fair weather swell zone. Autochthonous and, subordinately, detrital fractions were observed within the skeletal framework of biotic crusts. The syndepositional lithified fraction occurs mainly as very fine-grained laminations. Clotted peloidal and aphanitic (structureless) textures occur in the micrites as well. Autochthonous micrite is always associated with a significant amount of organic matter remains. In caves from the Plemmirio area in SE Sicily, the autochthonous microbial micrite, occurring in the bioconstructions, contains bacterial lipid biomarkers, including abundant compounds derived from sulfate-reducing bacteria. It is likely that a similar microbial mediation was involved in the formation of the autochthonous micrite present in the biotic crusts of the Rumena Cave.Guo, Q., Deng, Y., Hu, J., Wang, L., 2017. Carbonate carbon isotope evolution of seawater across the Ediacaran–Cambrian transition: evidence from the Keping area, Tarim Basin, NW China. Geological Magazine 154, 1244-1256. rocks from the Ediacaran–Cambrian boundary record important biological, climatic and geotectonic changes during this time. To date, only few geochemical investigations on the upper Ediacaran – upper Cambrian rocks in the Tarim Basin have been carried out. Here, we report high-resolution δ13Ccarb records from the Penglaiba, the Wushi phosphorite and the Dongergou sections from Ediacaran–Cambrian Series 3 in the Keping area of the Tarim Basin. The sections display several obvious δ13Ccarb shifts; δ13Ccarb values increased from 3‰ to 6.7‰ across the Qigebulage Formation. Moreover, a negative δ13Ccarb shift across the Ediacaran–Cambrian boundary is apparent; δ13Ccarb values decreased to a minimum of ?9.8‰ in the Wushi phosphorite section (?7.7‰ in Dongergou section and ?5.4‰ in Penglaiba section), followed by a positive carbonate carbon isotopic excursion across the Yuertusi Formation into the middle of the overlying Xiaoerbulak Formation. Furthermore, more or less invariable positive δ13Ccarb values characterize the middle and upper Xiaoerbulak Formation. The most negative δ13Ccarb value (?14.3‰) occurred near the base of the Shayilik Formation, which is the absolute minimum value among the studied sections of the Cambrian Series 2 to Cambrian Series 3 transition in the world. The δ13C data from Keping, Tarim Basin are in good agreement with carbon isotope profiles recorded in South China, and these events may reflect the perturbation of the carbon cycle in the Tarim Basin during the Ediacaran–Cambrian and the Cambrian Series 2 – Cambrian Series 3 transitions.Guo, Y., Song, Y., Fang, X., Pang, X., Li, T., 2018. Reservoir characterization of an organic-rich dolomitic tight-oil reservoir, the Lower Cretaceous Xiagou Formation in the Qingxi Sag, Jiuquan Basin, NW China. Marine and Petroleum Geology 89, 541-559. study presents the reservoir characterization of the unconventional, organic-rich dolomitic tight-oil reservoir of the Lower Cretaceous Xiagou Formation in the Qingxi Sag, Jiuquan Basin. To better describe pore characteristics and understand contributors to pore development of the mixed siliciclastic-carbonate reservoirs, samples were examined by thin section, X-ray diffraction (XRD) analysis, total organic carbon (TOC) and Rock-Eval pyrolysis, porosity and permeability measurement, field emission scanning electron microscopy (FESEM), and nuclear magnetic resonance (NMR). Four types of laminations, including carbonate lamination, siliceous lamination, argillaceous lamination and organic matter lamination, are developed. The average TOC of 1.67% and calculated Ro of 0.72%–0.96% indicate that the Xiagou source rocks are qualifed oil-source. Various types of pores with different sizes and micro-fractures are observed in such tight, mixed siliciclastic–carbonate reservoirs. Compared to mudstone/shale and tight sandstone, the tight and mixed siliciclastic–carbonate reservoirs are characterized by: (1) widely developed and multiple types of lamina structure, (2) various pore types without secondary OM pores generated by organic matter conversion, (3) wide pore size distributions, and (4) abundant and multiple genetic types of micro-fractures. The difference in mineral composition is the primary cause of different pore structure characteristics. Dolomitic mudstone is dominated by interlayer pore of clay mineral, while argillaceous dolomite is characterized by interparticle fractures, interparticle pores, and micro-fractures (including shrinked micro-fracture). In dolomitic siltstone, the residual intergranular pore and intergranular dissolved pore are the most common pores. The nanopore occurs widely in all lithologies, but the proportion of micrometers-scale pores and macro-scale nanopore increases from dolomitic mudstone to argillaceous dolomite and dolomitic siltstone. The positive correlation between porosity/permeability and TOC indicate the existence of pores or micro-fractures within or along the edge of organic matters. The similar thermal maturity level (Ro 0.72%–0.96%) eliminates maturation as a variable in porosity development in the studying area. The lithofacies associations with high-quality source rocks and reservoirs (relatively high porosity and permeability or rich in brittle minerals) are the favorable targets.Guseva, E., Zuckermann, R.N., Dill, K.A., 2017. Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers. Proceedings of the National Academy of Sciences 114, E7460-E7468.: Today’s lifeforms are based on informational polymers, namely proteins and nucleic acids. It is thought that simple chemical processes on the early earth could have polymerized monomer units into short random sequences. It is not clear, however, what physical process could have led to the next level—to longer chains having particular sequences that could increase their own concentrations. We study polymers of hydrophobic and polar monomers, such as today’s proteins. We find that even some random sequence short chains can collapse into compact structures in water, with hydrophobic surfaces that can act as primitive catalysts, and that these could elongate other chains. This mechanism explains how random chemical polymerizations could have given rise to longer sequence-dependent protein-like catalytic polymers. Abstract: It is not known how life originated. It is thought that prebiotic processes were able to synthesize short random polymers. However, then, how do short-chain molecules spontaneously grow longer? Also, how would random chains grow more informational and become autocatalytic (i.e., increasing their own concentrations)? We study the folding and binding of random sequences of hydrophobic (H H) and polar (P P) monomers in a computational model. We find that even short hydrophobic polar (HP) chains can collapse into relatively compact structures, exposing hydrophobic surfaces. In this way, they act as primitive versions of today’s protein catalysts, elongating other such HP polymers as ribosomes would now do. Such foldamer catalysts are shown to form an autocatalytic set, through which short chains grow into longer chains that have particular sequences. An attractive feature of this model is that it does not overconverge to a single solution; it gives ensembles that could further evolve under selection. This mechanism describes how specific sequences and conformations could contribute to the chemistry-to-biology (CTB) transition. Hackley, P.C., Walters, C.C., Kelemen, S.R., Mastalerz, M., Lowers, H.A., 2017. Organic petrology and micro-spectroscopy of Tasmanites microfossils: Applications to kerogen transformations in the early oil window. Organic Geochemistry 114, 23-44. transformation of kerogen to hydrocarbons in the early stages of oil generation is critical for understanding the resource potential of liquid-rich shale plays. Organic petrology commonly is used for visual evaluation of type, quality, and thermal maturity of organic matter, but the relationship of visual petrographic changes to chemical transformations is not well characterized. To improve understanding of these processes, organic-walled microfossils of the unicellular green alga Tasmanites (composed of algaenan) in Upper Devonian Ohio Shale (Huron Member, Appalachian Basin) were analyzed by micro-spectroscopy techniques including micro-Fourier transform infrared (micro-FTIR), X-ray photoelectron (XPS), electron probe microanalysis (EPMA), and fluorescence. Immature to mid-oil window maturation sequences of core and outcrop samples with solid bitumen reflectance (BR) and vitrinite reflectance (VR) values ranging from 0.45 to 0.80%Ro were used. Hydrous pyrolysis was applied to low-maturity (BR: 0.25–0.39%Ro) Huron and time-correlative New Albany shale samples to create similar artificial maturation sequences for comparison. Micro-FTIR spectroscopy revealed a decrease in the CH2/CH3 ratio with increasing maturity, indicating Tasmanites aliphatic chains become shorter and more branched. Oxygenated functional groups decreased relative to aliphatic stretching bands and increased aromaticity was noted at the highest maturities. In samples that were pyrolyzed for 72 h at temperatures of 300 °C to 320 °C (BR: 0.56–0.68%Ro), Tasmanites showed similar trends, whereas at pyrolysis temperatures of 340 °C and higher (BR > 1.0%Ro), Tasmanites was pseudomorphed by accumulations of solid bitumen, carbonate and sulfide. Replacement of Tasmanites by these phases in hydrous pyrolysis experiments ≥ 340 °C and its absence at higher maturities (peak oil, VR and BR ≥ 0.9%Ro) in naturally matured samples, as documented in a previous study, implies that a large fraction of the algaenan component of original organic carbon is converted to petroleum during thermal maturation. XPS analysis indicated the molar proportion of aliphatic carbon increases with increasing thermal maturity, accompanied by decreases in oxygenated functional groups and olefinic carbon. EPMA of Tasmanites showed highest concentrations of S, with concentrations of redox-sensitive trace elements U, Mo, Ni and V generally at or below detection limits. Decrease in organic S with increasing thermal maturity may be related to cleavage of Tasmanites at C–S linkages; however, this relationship was inconsistent and presence of adjacent or entrained nanoscale silicate or sulfide phases may impact measured trace element concentrations. Fluorescence microscopy and spectroscopy showed a red shift in spectral maxima and decreased emission intensities with increasing maturity, interpreted as due to non-radiative energy loss possibly because of increased aromaticity. Collectively, these results provide new insights into the in situ chemical transformations that accompany petrographic changes as oil-prone kerogen converts to petroleum with thermal advance from immature conditions into the mid-oil window.Hall, M.A., Wallace, J., Lucas, A., Kim, D., Basile, A.O., Verma, S.S., McCarty, C.A., Brilliant, M.H., Peissig, P.L., Kitchner, T.E., Verma, A., Pendergrass, S.A., Dudek, S.M., Moore, J.H., Ritchie, M.D., 2017. PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies. Nature Communications 8, Article 1167., imputed, sequence, and structural data are now available for exceedingly large sample sizes. The needs for data management, handling population structure and related samples, and performing associations have largely been met. However, the infrastructure to support analyses involving complexity beyond genome-wide association studies is not standardized or centralized. We provide the PLatform for the Analysis, Translation, and Organization of large-scale data (PLATO), a software tool equipped to handle multi-omic data for hundreds of thousands of samples to explore complexity using genetic interactions, environment-wide association studies and gene–environment interactions, phenome-wide association studies, as well as copy number and rare variant analyses. Using the data from the Marshfield Personalized Medicine Research Project, a site in the electronic Medical Records and Genomics Network, we apply each feature of PLATO to type 2 diabetes and demonstrate how PLATO can be used to uncover the complex etiology of common traits.Ham, B., Choi, B.-Y., Chae, G.-T., Kirk, M.F., Kwon, M.J., 2017. Geochemical influence on microbial communities at CO2-leakage analog sites. Frontiers in Microbiology 8, 2203. doi: 10.3389/fmicb.2017.02203. influence the chemical and physical properties of subsurface environments and thus represent an important control on the fate and environmental impact of CO2 that leaks into aquifers from deep storage reservoirs. How leakage will influence microbial populations over long time scales is largely unknown. This study uses natural analog sites to investigate the long-term impact of CO2 leakage from underground storage sites on subsurface biogeochemistry. We considered two sites with elevated CO2 levels (sample groups I and II) and one control site with low CO2 content (group III). Samples from sites with elevated CO2 had pH ranging from 6.2 to 4.5 and samples from the low-CO2 control group had pH ranging from 7.3 to 6.2. Solute concentrations were relatively low for samples from the control group and group I but high for samples from group II, reflecting varying degrees of water-rock interaction. Microbial communities were analyzed through clone library and MiSeq sequencing. Each 16S rRNA analysis identified various bacteria, methane-producing archaea, and ammonia-oxidizing archaea. Both bacterial and archaeal diversities were low in groundwater with high CO2 content and community compositions between the groups were also clearly different. In group II samples, sequences classified in groups capable of methanogenesis, metal reduction, and nitrate reduction had higher relative abundance in samples with relative high methane, iron, and manganese concentrations and low nitrate levels. Sequences close to Comamonadaceae were abundant in group I, while the taxa related to methanogens, Nitrospirae, and Anaerolineaceae were predominant in group II. Our findings provide insight into subsurface biogeochemical reactions that influence the carbon budget of the system including carbon fixation, carbon trapping, and CO2 conversion to methane. The results also suggest that monitoring groundwater microbial community can be a potential tool for tracking CO2 leakage from geologic storage sites.Han, J.-C., Chen, G.-J., Qin, L.-P., Mu, Y., 2017. Metal respiratory pathway-independent Cr isotope fractionation during Cr(VI) reduction Shewanella oneidensis MR-1. Environmental Science & Technology Letters 4, 500-504. isotope fractionation during microbial reduction processes is commonly recognized as a promising tool in biogeochemistry and bioremediation. However, the mechanism of Cr isotope fractionation during microbial reduction is poorly understood. In this work, the relationship between the bacterial respiratory pathway and Cr isotope fractionation was investigated in Shewanella oneidensis MR-1. For comparison with the wild type, a mutant strain (ΔomcA/ΔmtrC) with a deficiency in extracellular Cr(VI) reduction was constructed by deleting the omcA and mtrC genes, which encode the terminal reductase during extracellular reduction. The magnitudes of Cr isotope fractionation (ε) for Cr(VI) reduction by the wild type and ΔomcA/ΔmtrC were ?2.42 ± 0.68‰ and ?2.70 ± 0.22‰, respectively. Surprisingly, the ε values were not significantly different between the two strains. This suggests that isotope fractionation is independent of the metal respiratory pathway during Cr(VI) reduction by S. oneidensis MR-1. Moreover, a three-step Cr isotope fractionation model that includes uptake, reduction, and efflux was proposed to exist during intracellular Cr(VI) reduction by S. oneidensis MR-1. The developed model provides a better understanding of Cr isotope fractionation during microbial reduction.Han, J., Cai, Y., Schiffbauer, J.D., Hua, H., Wang, X., Yang, X., Uesugi, K., Komiya, T., Sun, J.I.E., 2017. A Cloudina-like fossil with evidence of asexual reproduction from the lowest Cambrian, South China. Geological Magazine 154, 1294-1305. earliest fossil record of animal biomineralization occurs in the latest Ediacaran Period (c. 550 Ma). Cloudina and Sinotubulites are two important tubular taxa among these earliest skeletal fossils. The evolutionary fate of Cloudina-type fossils across the Ediacaran–Cambrian transition, however, remains poorly understood. Here we report a multi-layered tubular microfossil Feiyanella manica gen. et sp. nov. from a phosphorite interval of the lowest Cambrian Kuanchuanpu Formation, southern Shaanxi Province, South China. This newly discovered fossil is a conical tube with a ‘funnel-in-funnel’ construction, showing profound morphological similarities to Cloudina and Conotubus. On the other hand, the outer few layers, and particularly the outermost layer, of Feiyanella tubes are regularly to irregularly corrugated, a feature strikingly similar to the variably folded/wrinkled tube walls of Sinotubulites. The Feiyanella tubes additionally exhibit two orders of dichotomous branching, similar to branching structures reported occasionally in Cloudina and possibly indicative of asexual reproduction. Owing to broad similarities in tube morphology, tube wall construction and features presumably indicative of asexual reproduction, Cloudina, Conotubus, Sinotubulites and the here described Feiyanella may thus constitute a monophyletic group traversing the Ediacaran–Cambrian boundary. The tube construction and palaeoecological strategy of Feiyanella putatively indicate evolutionary continuity in morphology and palaeoecology of benthic metazoan communities across the Ediacaran–Cambrian transition.Handley, K.M., Piceno, Y.M., Hu, P., Tom, L.M., Mason, O.U., Andersen, G.L., Jansson, J.K., Gilbert, J.A., 2017. Metabolic and spatio-taxonomic response of uncultivated seafloor bacteria following the Deepwater Horizon oil spill. The Isme Journal 11, 2569-2583. release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60?km away. Many of these genomes exhibited phylogenetic clustering indicative of common trait selection by the environment, and within half we identified 264 genes associated with hydrocarbon degradation. Alkane degradation ability was near ubiquitous among candidate hydrocarbon degraders, whereas just three harbored elaborate gene inventories for the degradation of alkanes and aromatic and polycyclic aromatic hydrocarbons (PAHs). Differential gene expression profiles revealed a spill-promoted microbial sulfur cycle alongside gene upregulation associated with PAH degradation. Gene expression associated with alkane degradation was widespread, although active alkane degrader identities changed along the pollution gradient. Analyses suggest that a broad metabolic capacity to respond to oil inputs exists across a large array of usually rare indigenous deep-sea bacteria.Hanke, U.M., Reddy, C.M., Braun, A.L.L., Coppola, A.I., Haghipour, N., McIntyre, C.P., Wacker, L., Xu, L., McNichol, A.P., Abiven, S., Schmidt, M.W.I., Eglinton, T.I., 2017. What on Earth have we been burning? Deciphering sedimentary records of pyrogenic carbon. Environmental Science & Technology 51, 12972-2980. have interacted with fire for thousands of years, yet the utilization of fossil fuels marked the beginning of a new era. Ubiquitous in the environment, pyrogenic carbon (PyC) arises from incomplete combustion of biomass and fossil fuels, forming a continuum of condensed aromatic structures. Here, we develop and evaluate 14C records for two complementary PyC molecular markers, benzene polycarboxylic acids (BPCAs) and polycyclic aromatic hydrocarbons (PAHs), preserved in aquatic sediments from a suburban and a remote catchment in the United States (U.S.) from the mid-1700s to 1998. Results show that the majority of PyC stems from local sources and is transferred to aquatic sedimentary archives on subdecadal to millennial time scales. Whereas a small portion stems from near-contemporaneous production and sedimentation, the majority of PyC (～90%) experiences delayed transmission due to “preaging” on millennial time scales in catchment soils prior to its ultimate deposition. BPCAs (soot) and PAHs (precursors of soot) trace fossil fuel-derived PyC. Both markers parallel historical records of the consumption of fossil fuels in the U.S., yet never account for more than 19% total PyC. This study demonstrates that isotopic characterization of multiple tracers is necessary to constrain histories and inventories of PyC and that sequestration of PyC can markedly lag its production.Hanna, R.D., Ketcham, R.A., 2017. X-ray computed tomography of planetary materials: A primer and review of recent studies. Chemie der Erde - Geochemistry 77, 547-572. computed tomography (XCT) is a powerful 3D imaging technique that has been used to investigate meteorites, mission-returned samples, and other planetary materials of all scales from dust particles to large rocks. With this technique, a 3D volume representing the X-ray attenuation (which is sensitive to composition and density) of the materials within an object is produced, allowing various components and textures to be observed and quantified. As with any analytical technique, a thorough understanding of the underlying physical principles, system components, and data acquisition parameters provides a strong foundation for the optimal acquisition and interpretation of the data. Here we present a technical overview of the physics of XCT, describe the major components of a typical laboratory-based XCT instrument, and provide a guide for how to optimize data collection for planetary materials using such systems. We also discuss data processing, visualization and analysis, including a discussion of common data artifacts and how to minimize them. We review a variety of recent studies in which XCT has been used to study extraterrestrial materials and/or to address fundamental problems in planetary science. We conclude with a short discussion of anticipated future directions of XCT technology and application.Hanson, J.R., 2017. Diterpenoids of terrestrial origin. Natural Product Reports 34, 1233-1243.: January to December, 2016 previous review Nat. Prod. Rep., 2016, 33, 1227-1238 This review covers the isolation and chemistry of diterpenoids from terrestrial as opposed to marine sources and includes labdanes, clerodanes, abietanes, pimaranes, kauranes, cembrenes and their cyclization products. There are 205 references.Haq, S.R., Tamamura, S., Igarashi, T., Kaneko, K., 2018. Characterization of organic substances in lignite before and after hydrogen peroxide treatment: Implications for microbially enhanced coalbed methane. International Journal of Coal Geology 185, 1-11. reaction of coal with hydrogen peroxide (H2O2) has been reported to accelerate the microbial transformation of coal into biogenic methane. To understand the mechanism of the increased bioavailability of coal as a result of H2O2 treatment, we investigated the effects of H2O2 reaction on humic substances of lignite by characterizing their structure and relative abundance. The H2O2-treated lignite, referred to as lignite-H2O2, was also examined in column experiments to confirm the increases in lignite solubilization and organic acids as indicators of enhanced bioavailability. The results showed that the alkali-soluble carbon content of lignite increased by 4.9 times (from 0.4 to 2.1 g C) after H2O2 treatment, and the humic acid (HA) content of this fraction increased by 7.7 times (from 0.2 to 1.5 g C). Previously, the enhanced solubility of lignite after H2O2 treatment was attributed to increased hydrophilicity of the lignite. However, we propose that this phenomenon is actually caused by chemical fragmentation (i.e., β-fragmentation) involving a radical reaction. In the column experiments, lignite treated with H2O2 showed higher dissolved organic carbon (up to 84.8 mg/L) and organic acid (up to 18.9 mg/L for acetic acid, and up to 19.9 mg/L for formic acid) concentrations than lignite without treatment. These results indicate the potential to optimize CH4 production from microbially enhanced coalbed methane operations using H2O2.Harries, D., Langenhorst, F., 2018. Carbide-metal assemblages in a sample returned from asteroid 25143 Itokawa: Evidence for methane-rich fluids during metamorphism. Geochimica et Cosmochimica Acta 222, 53-73. found that the particle RA-QD02-0115 returned by the Hayabusa spacecraft from near-Earth asteroid 25143 Itokawa contains the iron carbide haxonite (Fe21.9-22.7Co0.2-0.3Ni0.2-0.8)C6 and several Fe,Ni alloys, including multi-domain tetrataenite and spinodally decomposed taenite. Ellipsoidal to nearly spherical voids occur throughout the particle and suggest the presence of a fluid phase during textural and chemical equilibration of the host rock within the parent asteroid of 25143 Itokawa. The calculated solubility of carbon in Fe,Ni metal indicates that the carbide formed at temperatures larger than 600?°C during thermal metamorphism of the LL-chondritic mineral assemblage. Haxonite formed metastably with respect to graphite and cohenite, probably due to its high degree of lattice match with neighboring taenite, a low cooling rate at peak metamorphic temperatures, and the hindered nucleation of graphite. Thermodynamic equilibrium calculations indicate that the fluid present was dry (H2O-poor) and dominated by methane. The reactive fluid most plausibly had an atomic H/C ratio of 4–5 and was derived from the reduction of macromolecular, insoluble organic matter (IOM) that initially co-accreted with water ice. The initial presence of water is a necessary assumption to provide sufficient hydrogen for the formation of methane from hydrolyzed IOM. Metallic iron was in turn partially oxidized and incorporated into the ferromagnesian silicates during the high-temperature stage of metamorphism. An exemplary bulk reaction from unequilibrated material on the left to an equilibrated assemblage on the right may be written as:330 CH0.8O0.2(IOM)?+?500 H2O(ice/g)?+?681 Fe(in alloy)?+?566 FeSiO3(in Opx)?→?300 CH4(g)?+?32 H2(g)?+?5 Fe23C6(in Hx)?+?566 Fe2SiO4(in Ol)(Opx?=?orthopyroxene, Hx?=?haxonite, Ol?=?olivine, g?=?fluid species).The best estimate of the fluid/rock ratio in the region of the LL parent body where RA-QD02-0115 formed is about 3?×?10?3 and corresponds to an initial ice/rock ratio of about 7?×?10?3 (both by mass).Hassan, H.M., Castillo, A.B., Yigiterhan, O., Elobaid, E.A., Al-Obaidly, A., Al-Ansari, E., Obbard, J.P., 2018. Baseline concentrations and distributions of Polycyclic Aromatic Hydrocarbons in surface sediments from the Qatar marine environment. Marine Pollution Bulletin 126, 58-62. sediments in marine waters of Qatar have the potential of being contaminated by Polycyclic Aromatic Hydrocarbons (PAHs) due to extensive petroleum exploration and transportation activities within Qatar's Marine Exclusive Economic Zone. In this study, the concentration and distribution of sixteen PAHs classed as USEPA priority pollutants were measured in sediments from the eastern Qatari coast. PAHs were recovered from sediments via accelerated solvent extraction and then analyzed using Gas Chromatography–Mass Spectrometry. Total concentrations of the PAHs were in the range of 3.15–14.35μg/kg, and the spatial distribution of PAHs is evaluated in the context of sediment total organic content, depth and the grain size together with and the proximity of petroleum exploration and transportation activities. The data show that the concentrations of PAHs within the study area were in the low-range, suggesting a low risk to marine organisms and limited transfer of PAHs into the food web.Hatcher, P.G., Obeid, W., Wozniak, A.S., Xu, C., Zhang, S., Santschi, P.H., Quigg, A., 2018. Identifying oil/marine snow associations in mesocosm simulations of the Deepwater Horizon oil spill event using solid-state 13C NMR spectroscopy. Marine Pollution Bulletin 126, 159-165. Deepwater Horizon oil spill stimulated the release of marine snow made up of dead/living plankton/bacteria and their exopolymeric polysaccharide substances (EPS), termed marine oil snow (MOS), promoting rapid removal of oil from the water column into sediments near the well site. Mesocosm simulations showed that Macondo surrogate oil readily associates with the marine snow. Quantitative solid-state 13C NMR readily distinguishes this oil from naturally formed marine snow and reveals that adding the dispersant Corexit enhances the amount of oil associated with the MOS, thus contributing to rapid removal from the water column. Solvent extraction of MOS removes the oil-derived compounds for analysis by one and two-dimensional GC/MS and evaluation of potential transformations they undergo when associated with the EPS. The results reveal that the oil associated with EPS is subjected to rapid transformation, in a matter of days, presumably by bacteria and fungi associated with EPS.Hayek, M., 2017. A model for subsurface oil pollutant migration. Transport in Porous Media 120, 373-393. subsurface spill of hydrocarbon fluids (from an underground leaking tank or from pipelines) is a widespread problem in the oil industry and hydrology. Under the assumption of low oil saturation, the migration of oil pollutant may be modeled by a nonlinear convection–diffusion equation with power law nonlinearities. The saturation-dependent diffusion coefficient is proportional to a power of saturation for which the exponent may be negative or positive depending on the porous medium and the pollutant characteristics. This paper presents general analytical solutions for the one-dimensional transient saturation distribution in immiscible zone. The solutions describe the longtime behavior of a contaminant oil pollutant caused by a continuous source of contaminant (e.g., leakage from pipelines, disposal dumps or storage tanks). Two general forms corresponding to positive and negative power exponents of the diffusion coefficient are presented. The general forms express implicitly the position as function of oil saturation and time. An alternative explicit closed-form solution near the front position is also proposed. An exact explicit solution is obtained for the particular case of constant diffusion coefficient. The proposed solutions are fully analytical in the sense that they do not require any numerical implementation. The solutions may be used to study the porous medium and pollutant parameters. They can be applied to aquifer contamination problems, and they are also important for the verification of numerical solutions.Hemingway, J.D., Rothman, D.H., Rosengard, S.Z., Galy, V.V., 2017. Technical note: An inverse method to relate organic carbon reactivity to isotope composition from serial oxidation. Biogeosciences 14, 5099-5114. oxidation coupled with stable carbon and radiocarbon analysis of sequentially evolved CO2 is a promising method to characterize the relationship between organic carbon (OC) chemical composition, source, and residence time in the environment. However, observed decay profiles depend on experimental conditions and oxidation pathway. It is therefore necessary to properly assess serial oxidation kinetics before utilizing decay profiles as a measure of OC reactivity. We present a regularized inverse method to estimate the distribution of OC activation energy (E), a proxy for bond strength, using serial oxidation. Here, we apply this method to ramped temperature pyrolysis or oxidation (RPO) analysis but note that this approach is broadly applicable to any serial oxidation technique. RPO analysis directly compares thermal reactivity to isotope composition by determining the E range for OC decaying within each temperature interval over which CO2 is collected. By analyzing a decarbonated test sample at multiple masses and oven ramp rates, we show that OC decay during RPO analysis follows a superposition of parallel first-order kinetics and that resulting E distributions are independent of experimental conditions. We therefore propose the E distribution as a novel proxy to describe OC thermal reactivity and suggest that E vs. isotope relationships can provide new insight into the compositional controls on OC source and residence time.Hemme, C., van Berk, W., 2017. Potential risk of H2S generation and release in salt cavern gas storage. Journal of Natural Gas Science and Engineering 47, 114-123. storage of natural gas in salt caverns can entail the risk of H2S generation, which in turn leads to gas pollution. H2S is generated by bacterial sulfate reduction. The bacteria use aqueous sulfate(aq) as an electron acceptor to oxidize the dissolved hydrocarbons and generate sulfide. Anhydrite is available in the rock salt surrounding the cavern and acts as a sulfate(aq) source. The stored natural gas, with its main component, methane, is in solubility equilibrium with the brine and is additionally delivered by diffusion into the brine. The generated H2S reaches the stored gas by outgassing from the brine. In this study, these processes are simulated by one- and three-dimensional hydrogeochemical diffusive mass transport models, which are based on equilibrium reactions for gas-water-rock interactions and kinetic reactions for sulfate reduction. Modelling results show that the greatest amount of H2S is generated in the brine. The amount of generated H2S(g) is mainly controlled by the amount of available sulfate(aq) as well as the rate of diffusion, which is coupled with the maximum operating live time of salt caverns. Additionally, the amount of generated and released H2S(g) is sensitive to the chosen kinetic rate constant.To ensure constant gas quality over time, the gas and the brine must be analyzed continuously and technical methods must be applied when the H2S(g) concentration increases. According to the modelling results, H2S(g) generation is inhibited by addition of dissolved ferrous iron to the brine. Dissolved ferrous iron reacts with sulfide-sulfur to form mackinawite (FeS(s)) so that aqueous sulfide is no longer available for H2S(g) generation. Another method is the addition of NaOH to increase the pH of the brine. Then, higher fractions of generated sulfide-sulfur are transformed to free S2?(aq) instead of H2S(g) and H2S(aq).Hendra, A., Pracoyo, P.A., 2017. Geochemistry of natural gas seepages in Boto Area, Bancak, Semarang, Central Java. Indonesian Journal on Geoscience 4, 61-70. seepage gas samples collected from Boto Area, Bancak, Semarang, Central Java, were studied to determine their chemical characteristics using GC and GC-IRMS methods. They are composed 53 - 85% of methane predominantly. However, gas seep Site 3 sample has the highest N2 compound and the lesser extent to the samples Site 2 and Site 1 respectively. The two hydrocarbon gas seeps (Site 1, 2, and Site 3 samples) that are characterized by δ13C methane of -35.61‰ and -27.97‰, and values of δD methane of -112‰ and -109‰ respectively, are each isotopically distinct from all others suggesting, at least, they are derived from different maturity level. The Site 3 gas sample is suggested to be more mature than the others.Herren, C.M., McMahon, K.D., 2017. Cohesion: a method for quantifying the connectivity of microbial communities. The Isme Journal 11, 2426-2438. ability to predict microbial community dynamics lags behind the quantity of data available in these systems. Most predictive models use only environmental parameters, although a long history of ecological literature suggests that community complexity should also be an informative parameter. Thus, we hypothesize that incorporating information about a community’s complexity might improve predictive power in microbial models. Here, we present a new metric, called community ‘cohesion,’ that quantifies the degree of connectivity of a microbial community. We analyze six long-term (10+ years) microbial data sets using the cohesion metrics and validate our approach using data sets where absolute abundances of taxa are available. As a case study of our metrics’ utility, we show that community cohesion is a strong predictor of Bray–Curtis dissimilarity (R2=0.47) between phytoplankton communities in Lake Mendota, WI, USA. Our cohesion metrics outperform a model built using all available environmental data collected during a long-term sampling program. The result that cohesion corresponds strongly to Bray–Curtis dissimilarity is consistent across the six long-term time series, including five phytoplankton data sets and one bacterial 16S rRNA gene sequencing data set. We explain here the calculation of our cohesion metrics and their potential uses in microbial ecology.Heshka, N.E., Choy, J.M., Chen, J., 2017. Gas chromatographic sulphur speciation in heavy crude oil using a modified standard D5623 method and microfluidic Deans switching. Journal of Chromatography A 1530, 241-246. modification to American Society for Testing and Materials (ASTM) method D5623 is proposed to enable successful and repeatable analysis of heavy crude oil samples. A two-dimensional gas chromatography configuration was implemented, with separation of sulphur compounds occurring on two columns. A Deans switch is used to enable heart-cutting of volatile sulphur compounds onto a DB-Sulfur stationary phase, and separation occurs concurrently with the backflushing of the primary column. The use of a sulphur-selective detector increases selectivity, and 22 volatile sulphur species are quantified in less than 15min, which is almost half the time of the original ASTM method. Samples ranging from light distillation cuts to whole crudes (boiling from 100°C to >750°C) were analyzed with minimal sample preparation. The calculated limit of detection was 0.7mg/kg, repeatability was 3% relative standard deviation (RSD), and a linear range of 1–250mg/kg was obtained, with an R2 value of 0.994 or better, depending on the compound.Hilaire, F., Basset, E., Bayard, R., Gallardo, M., Thiebaut, D., Vial, J., 2017. Comprehensive two-dimensional gas chromatography for biogas and biomethane analysis. Journal of Chromatography A 1524, 222-232. gas industry is going to be revolutionized by being able to generate bioenergy from biomass. The production of biomethane – a green substitute of natural gas – is growing in Europe and the United-States of America. Biomethane can be injected into the gas grid or used as fuel for vehicles after compression. Due to various biomass inputs (e.g. agricultural wastes, sludges from sewage treatment plants, etc.), production processes (e.g. anaerobic digestion, municipal solid waste (MSW) landfills), seasonal effects and purification processes (e.g. gas scrubbers, pressure swing adsorption, membranes for biogas upgrading), the composition and quality of biogas and biomethane produced is difficult to assess. All previous publications dealing with biogas analysis reported that hundreds of chemicals from ten chemical families do exist in trace amounts in biogas. However, to the best of our knowledge, no study reported a detailed analysis or the implementation of comprehensive two-dimensional gas chromatography (GC × GC) for biogas matrices. This is the reason why the benefit of implementing two-dimensional gas chromatography for the characterization of biogas and biomethane samples was evaluated. In a first step, a standard mixture of 89 compounds belonging to 10 chemical families, representative of those likely to be found, was used to optimize the analytical method. A set consisting of a non-polar and a polar columns, respectively in the first and the second dimension, was used with a modulation period of six seconds. Applied to ten samples of raw biogas, treated biogas and biomethane collected on 4 industrial sites (two MSW landfills, one anaerobic digester on a wastewater treatment plant and one agricultural biogas plant), this analytical method provided a “fingerprint” of the gases composition at the molecular level in all biogas and biomethane samples. Estimated limits of detection (far below the μg Nm?3) coupled with the resolution of GC × GC allowed the comparison of the real samples considered. This first implementation of GC × GC for the analysis of biogas and biomethane demonstrated unambiguously that it is a promising tool to provide a “fingerprint” of samples, and to monitor trace compounds by families.Hiruta, A., Yang, T.F., Lin, S., Su, C.-C., Chen, N.-C., Chen, Y.-J., Chen, H.-W., Yang, T.-H., Huang, Y.-C., Wei, K.-Y., Huang, J.-J., Chen, S.-C., Song, S.-R., 2017. Activation of gas bubble emissions indicated by the upward decreasing Lead-210 activity at a submarine mud volcano (TY1) offshore southwestern Taiwan. Journal of Asian Earth Sciences 149, 160-171. submarine mud volcano (MV) known as TY1 is one of the largest conical structures found offshore southwestern Taiwan. Active gas bubble emissions at the flat crest of the mud volcano disperse sediment particles into the water column. Changes in the mud volcanism of TY1 were revealed by radiograph and grain size analysis of the sediment cores. 210Pb geochronology was applied to the near-seafloor sediments to reveal the detailed mud volcanism from the deposition rate. In a 58-cm long sediment core taken from the northern margin of the crest, known as TY1-N.170, the size and frequency of the mud clasts decrease upward. The clasts are smaller than 8 mm above a sediment depth of 34 cm below the sea floor (cmbsf). Sediments between 0 and 19 cmbsf are massive, and particles larger than 2 mm are absent. An enrichment of coarse, silt-sized particles in the massive sediment unit and the restricted distribution of the unit suggest that the massive unit was generated by re-deposition of sediment particles that were dispersed into the water column by gas bubble emission. These characteristics suggest that during the last mud volcanism of TY1, there was a decrease in mud eruption energy, and gas bubble emission became the main activity. In core TY1-S.440, taken from the southern slope, a massive sediment unit enriched with coarse, silt-sized particles, is intercalated between mud breccia structures. This suggests repeated mud breccia flows caused by TY1. The excess 210Pb activity present in the massive sediment unit of TY1-N.170 suggests activation of gas bubble emission. In the massive unit, a decrease in excess 210Pb activity appears upward toward the seafloor. The highest value is 3.1 dpm/g at 19.8 cmbsf (26.4 g/cm2 in cumulative mass); values lower than 1.0 dpm/g are distributed 2.8–6.8 cmbsf (3.6–8.8 g/cm2). The upwardly decreasing trend is opposite that of the reference core from which a reasonable areal sedimentation rate was obtained using a constant-flux constant-sedimentation model. The anomalous depth profile at the massive unit indicates an increasing rate of sediment deposition, which originated from the activation of gas bubble emission.Hochuli, P.A., Schneebeli-Hermann, E., Mangerud, G., Bucher, H., 2017. Evidence for atmospheric pollution across the Permian-Triassic transition. Geology 45, 1123-1126. for a cause-and-effect relationship between the emplacement of the Siberian Traps large igneous province and the Permian-Triassic marine mass extinction has been growing over the past decades. However, how the Siberian Traps volcanism affected the terrestrial vegetation is still a matter of controversy. Here, we demonstrate that a substantial part of plants’ life cycle, namely their reproductive organs, was adversely affected by environmental conditions. Effects include malformed spores and pollen grains, unseparated tetrads, and darkened walls of spores and pollen (sporoderm) from Permian-Triassic sediments from the Finnmark Platform offshore Norway. The co-occurrence of these morphological changes with the main carbon isotope excursion and the marine mass extinction may suggest that they were caused by atmospheric pollution linked to Siberian Traps emissions.Hodgskiss, M.S.W., Kunzmann, M., Poirier, A., Halverson, G.P., 2018. The role of microbial iron reduction in the formation of Proterozoic molar tooth structures. Earth and Planetary Science Letters 482, 1-11. tooth structures are poorly understood early diagenetic, microspar-filled voids in clay-rich carbonate sediments. They are a common structure in sedimentary successions dating from 2600–720 Ma, but do not occur in rocks older or younger, with the exception of two isolated Ediacaran occurrences. Despite being locally volumetrically significant in carbonate rocks of this age, their formation and disappearance in the geological record remain enigmatic. Here we present iron isotope data, supported by carbon and oxygen isotopes, major and minor element concentrations, and total organic carbon and sulphur contents for 87 samples from units in ten different basins spanning ca. 1900–635 Ma. The iron isotope composition of molar tooth structures is almost always lighter (modal depletion of 2‰) than the carbonate or residue components in the host sediment. We interpret the isotopically light iron in molar tooth structures to have been produced by dissimilatory iron reduction utilising Fe-rich smectites and Fe-oxyhydroxides in the upper sediment column. The microbial conversion of smectite to illite results in a volume reduction of clay minerals (～30%) while simultaneously increasing pore water alkalinity. When coupled with wave loading, this biogeochemical process is a viable mechanism to produce voids and subsequently precipitate carbonate minerals. The disappearance of molar tooth structures in the mid-Neoproterozoic is likely linked to a combination of a decrease in smectite abundance, a decline in the marine DIC reservoir, and an increase in the concentration of O2 in shallow seawater.Hoffman, P.F., Abbot, D.S., Ashkenazy, Y., Benn, D.I., Brocks, J.J., Cohen, P.A., Cox, G.M., Creveling, J.R., Donnadieu, Y., Erwin, D.H., Fairchild, I.J., Ferreira, D., Goodman, J.C., Halverson, G.P., Jansen, M.F., Le Hir, G., Love, G.D., Macdonald, F.A., Maloof, A.C., Partin, C.A., Ramstein, G., Rose, B.E.J., Rose, C.V., Sadler, P.M., Tziperman, E., Voigt, A., Warren, S.G., 2017. Snowball Earth climate dynamics and Cryogenian geology-geobiology. Science Advances 3, Article e1600983. evidence indicates that grounded ice sheets reached sea level at all latitudes during two long-lived Cryogenian (58 and ≥5 My) glaciations. Combined uranium-lead and rhenium-osmium dating suggests that the older (Sturtian) glacial onset and both terminations were globally synchronous. Geochemical data imply that CO2 was 102 PAL (present atmospheric level) at the younger termination, consistent with a global ice cover. Sturtian glaciation followed breakup of a tropical supercontinent, and its onset coincided with the equatorial emplacement of a large igneous province. Modeling shows that the small thermal inertia of a globally frozen surface reverses the annual mean tropical atmospheric circulation, producing an equatorial desert and net snow and frost accumulation elsewhere. Oceanic ice thickens, forming a sea glacier that flows gravitationally toward the equator, sustained by the hydrologic cycle and by basal freezing and melting. Tropical ice sheets flow faster as CO2 rises but lose mass and become sensitive to orbital changes. Equatorial dust accumulation engenders supraglacial oligotrophic meltwater ecosystems, favorable for cyanobacteria and certain eukaryotes. Meltwater flushing through cracks enables organic burial and submarine deposition of airborne volcanic ash. The subglacial ocean is turbulent and well mixed, in response to geothermal heating and heat loss through the ice cover, increasing with latitude. Terminal carbonate deposits, unique to Cryogenian glaciations, are products of intense weathering and ocean stratification. Whole-ocean warming and collapsing peripheral bulges allow marine coastal flooding to continue long after ice-sheet disappearance. The evolutionary legacy of Snowball Earth is perceptible in fossils and living organisms.Hofgartner, J.D., Buratti, B.J., Devins, S.L., Beyer, R.A., Schenk, P., Stern, S.A., Weaver, H.A., Olkin, C.B., Cheng, A., Ennico, K., Lauer, T.R., McKinnon, W.B., Spencer, J., Young, L.A., 2018. A search for temporal changes on Pluto and Charon. Icarus 302, 273-284. search for temporal changes on Pluto and Charon was motivated by (1) the discovery of young surfaces in the Pluto system that imply ongoing or recent geologic activity, (2) the detection of active plumes on Triton during the Voyager 2 flyby, and (3) the abundant and detailed information that observing geologic processes in action provides about the processes. A thorough search for temporal changes using New Horizons images was completed. Images that covered the same region were blinked and manually inspected for any differences in appearance. The search included full-disk images such that all illuminated regions of both bodies were investigated and higher resolution images such that parts of the encounter hemispheres were investigated at finer spatial scales. Changes of appearance between different images were observed but in all cases were attributed to variability of the imaging parameters (especially geometry) or artifacts. No differences of appearance that are strongly indicative of a temporal change were found on the surface or in the atmosphere of either Pluto or Charon. Limits on temporal changes as a function of spatial scale and temporal interval during the New Horizons encounter are determined. The longest time interval constraint is one Pluto/Charon rotation period (～6.4 Earth days). Contrast reversal and high-phase bright features that change in appearance with solar phase angle are identified. The change of appearance of these features is most likely due to the change in phase angle rather than a temporal change. Had active plumes analogous to the plumes discovered on Triton been present on the encounter hemispheres of either Pluto or Charon, they would have been detected. The absence of active plumes may be due to temporal variability (i.e., plumes do occur but none were active on the encounter hemispheres during the epoch of the New Horizons encounter) or because plumes do not occur. Several dark streak features that may be deposits from past plumes are identified.H?rst, S.M., Yoon, Y.H., Ugelow, M.S., Parker, A.H., Li, R., de Gouw, J.A., Tolbert, M.A., 2018. Laboratory investigations of Titan haze formation: In situ measurement of gas and particle composition. Icarus 301, 136-151. to the arrival of the Cassini-Huygens spacecraft, aerosol production in Titan’s atmosphere was believed to begin in the stratosphere where chemical processes are predominantly initiated by far ultraviolet (FUV) radiation. However, measurements taken by the Cassini Ultraviolet Imaging Spectrograph (UVIS) and Cassini Plasma Spectrometer (CAPS) indicate that haze formation initiates in the thermosphere where there is a greater flux of extreme ultraviolet (EUV) photons and energetic particles available to initiate chemical reactions, including the destruction of N2. The discovery of previously unpredicted nitrogen species in measurements of Titan’s atmosphere by the Cassini Ion and Neutral Mass Spectrometer (INMS) indicates that nitrogen participates in the chemistry to a much greater extent than was appreciated before Cassini. The degree of nitrogen incorporation in the haze particles is important for understanding the diversity of molecules that may be present in Titan’s atmosphere and on its surface. We have conducted a series of Titan atmosphere simulation experiments using either spark discharge (Tesla coil) or FUV photons (deuterium lamp) to initiate chemistry in CH4/N2 gas mixtures ranging from 0.01% CH4/99.99% N2 to 10% CH4/90% N2. We obtained in situ real-time measurements using a high-resolution time-of-flight aerosol mass spectrometer (HR-ToF-AMS) to measure the particle composition as a function of particle size and a proton-transfer ion-trap mass spectrometer (PIT-MS) to measure the composition of gas phase products. These two techniques allow us to investigate the effect of energy source and initial CH4 concentration on the degree of nitrogen incorporation in both the gas and solid phase products. The results presented here confirm that FUV photons produce not only solid phase nitrogen bearing products but also gas phase nitrogen species. We find that in both the gas and solid phase, nitrogen is found in nitriles rather than amines and that both the gas phase and solid phase products are composed primarily of molecules with a low degree of aromaticity. The UV experiments reproduce the absolute abundances measured in Titan’s stratosphere for a number of gas phase species including C4H2, C6H6, HCN, CH3CN, HC3N, and C2H5CN.Horváthová, H., Lászlová, K., Dercová, K., 2018. Bioremediation of PCB-contaminated shallow river sediments: The efficacy of biodegradation using individual bacterial strains and their consortia. Chemosphere 193, 270-277. of dangerous toxic and hydrophobic chlorinated aromatic compounds, mainly PCBs from the environment, is one of the most important aims of the environmental biotechnologies. In this work, biodegradation of an industrial mixture of PCBs (Delor 103, equivalent to Aroclor 1242) was performed using bacterial consortia composed of four bacterial strains isolated from the historically PCB-contaminated sediments and characterized as Achromobacter xylosoxidans, Stenotrophomonas maltophilia, Ochrobactrum anthropi and Rhodococcus ruber. The objective of this research was to determine the biodegradation ability of the individual strains and artificially prepared consortia composed of two or three bacterial strains mentioned above. Based on the growth parameters, six consortia were constructed and inoculated into the historically contaminated sediment samples collected in the efflux canal of Chemko Strá?ske plant – the former producer of the industrial mixtures of PCBs. The efficacy of the biotreatment, namely bioaugmentation, was evaluated by determination of ecotoxicity of treated and non-treated sediments. The most effective consortia were those containing the strain R. ruber. In the combination with A. xylosoxidans, the biodegradation of the sum of the indicator congeners was 85% and in the combination with S. maltophilia nearly 80%, with inocula applied in the ratio 1:1 in both cases. Consortium containing the strain R. ruber and S. maltophilia showed pronounced degradation of the highly chlorinated PCB congeners. Among the consortia composed of three bacterial strains, only that consisting of O. anthropi, R. ruber and A. xylosoxidans showed higher biodegradation (73%). All created consortia significally reduced the toxicity of the contaminated sediment.Hou, H., Shao, L., Li, Y., Lu, J., Li, Z., Wang, S., Zhang, W., Wen, H., 2017. Geochemistry, reservoir characterization and hydrocarbon generation potential of lacustrine shales: A case of YQ-1 well in the Yuqia Coalfield, northern Qaidam Basin, NW China. Marine and Petroleum Geology 88, 458-471. since a breakthrough of marine shales in China, lacustrine shales have been attracting by the policy makers and scientists. Organic-rich shales of the Middle Jurassic strata are widely distributed in the Yuqia Coalfield of northern Qaidam Basin. In this paper, a total of 42 shale samples with a burial depth ranging from 475.5 m to 658.5 m were collected from the Shimengou Formation in the YQ-1 shale gas borehole of the study area, including 16 samples from the Lower Member and 26 samples from the Upper Member. Geochemistry, reservoir characteristics and hydrocarbon generation potential of the lacustrine shales in YQ-1 well were preliminarily investigated using the experiments of vitrinite reflectance measurement, maceral identification, mineralogical composition, carbon stable isotope, low-temperature nitrogen adsorption, methane isothermal adsorption and rock eval pyrolysis. The results show that the Shimengou shales have rich organic carbon (averaged 3.83%), which belong to a low thermal maturity stage with a mean vitrinite reflectance (Ro) of 0.49% and an average pyrolytic temperature of the generated maximum remaining hydrocarbon (Tmax) of 432.8 °C. Relative to marine shales, the lacustrine shales show low brittleness index (averaged 34.9) but high clay contents (averaged 55.1%), high total porosities (averaged 13.71%) and great Langmuir volumes (averaged 4.73 cm?3 g). Unlike the marine and marine-transitional shales, the quartz contents and brittleness index (BI) values of the lacustrine shales first decrease then increase with the rising TOC contents. The kerogens from the Upper Member shales are dominant by the oil-prone types, whereas the kerogens from the Lower Member shales by the gas-prone types. The sedimentary environment of the shales influences the TOC contents, thus has a close connection with the hydrocarbon potential, mineralogical composition, kerogen types and pore structure. Additionally, in terms of the hydrocarbon generation potential, the Upper Member shales are regarded as very good and excellent rocks whereas the Lower Member shales mainly as poor and fair rocks. In overall, the shales in the top of the Upper Member can be explored for shale oil due to the higher free hydrocarbon amount (S1), whereas the shales in the Lower Member and the Upper Member, with the depths greater than 1000 m, can be suggested to explore shale gas.Hou, Q., Jin, Q., Li, P., Jiang, W., Zhang, F., Tian, F., 2017. A computational method for determining oil expulsion efficiency based on the ideal effective oil expulsion mode. Journal of Petroleum Exploration and Production Technology 7, 925-931. oil expulsion efficiency of hydrocarbon source rocks is a key parameter for predicting conventional oil and gas resources and is closely related to the source rock thickness. Pyrolysis experiments and oil expulsion models were used to establish an oil expulsion efficiency calculation formula and to then analyze the trend of the oil expulsion efficiency. We determine the theoretical maximum oil expulsion efficiency via pyrolysis experiments to investigate hydrocarbon generation and expulsion. Then, we establish three ideal and effective oil expulsion models based on the single-layer source rock thickness: full type, full and transition type, and full and transition and retention type. Finally, we derive a corresponding correction formula for the oil expulsion efficiency. Using a type II1 hydrocarbon source rock from the Dongying Sag as an example, we calculate the oil expulsion efficiencies. The oil expulsion efficiencies of single-layer source rocks of different thicknesses exhibit only small differences at a low-maturity stage but exhibit obvious differences at a high-maturity stage. The oil expulsion of thin hydrocarbon source rocks is high, even exceeding 70%, but the oil expulsion of super-thick hydrocarbon source rocks is only approximately 30%. Therefore, the thickness of a single-layer hydrocarbon source rock exerts an important influence on oil expulsion, particularly during the raw oil generation and peak discharge stages.Hsu, H.-H., Liu, C.-S., Chang, Y.-T., Chang, J.-H., Ko, C.-C., Chiu, S.-D., Chen, S.-C., 2017. Diapiric activities and intraslope basin development offshore of SW Taiwan: A case study of the Lower Fangliao Basin gas hydrate prospect. Journal of Asian Earth Sciences 149, 145-159. architecture and distribution of mud diapirs are shaped by tectonic activity, sediment filling and unbalanced loading characteristics. Mud diapir development also controls spatial variations of intraslope basins in slope areas and can spur upward fluid migration with diapiric intrusion. The offshore area of southwestern Taiwan is an incipient collision zone in which thick sequences of deep marine sediments filled a rapidly subsided foredeep basin during the Pliocene. Large volumes of deposited sediment serve as source materials of diapiric ridges that extend NNE-SSW, and some mud diapirs even extend to on land SW Taiwan with subsurface signatures of gas. This study examines relationships between mud diapir and intraslope basin development in convergent tectonics through seismic and bathymetry data analyses. Four types of mud diapirs are identified: (1) buried symmetrical diapirs; (2) symmetrical diapirs extruded above the seafloor; (3) asymmetric and irregular diapirs; and (4) small individual diapirs manifested as mud intrusions found in local areas. A 3-stage model is proposed as a tool for describing the development and distribution of these types of diapirs. We further examine the relationship between mud diapirs and intraslope basin development patterns by analyzing 2D and 3D seismic images to reveal structural and sedimentary processes occurring in the Lower Fangliao Basin. This basin is characterized by BSR and amplitude anomalies of seismic profiles and is a prospect of the Taiwanese gas hydrate investigation project. An 8-stage development model with six depositional units is proposed as a means to explain the evolution of diapirs, submarine canyons, and fold and fault activities in the Lower Fangliao Basin, in turn revealing the relationship between mud diapir formation and intraslope basin development offshore of southwestern Taiwan.Hu, B., Wang, P., Wang, C., Qian, J., Hou, J., Cui, X., Zhang, N., 2017. The effect of anthropogenic impoundment on dissolved organic matter characteristics and copper binding affinity: Insights from fluorescence spectroscopy. Chemosphere 188, 424-433. matrix fluorescence spectroscopy combined with parallel factor analysis (EEM-PARAFAC) and two-dimensional correlation spectroscopy (2D-COS) were applied to evaluate the effects of anthropogenic impoundment on the characteristics of dissolved organic matter (DOM) and its heavy metal binding affinity. Three field-sampling cruises conducted in Hongze Lake from 2015 to 2016 were classified as early impoundment and late impoundment cruises according to the hydrological conditions. Five fluorescence components were derived from EEM-PARAFAC, including three humic-like components (C1C3) and two protein-like components (C4 and C5). The results show a higher dissolved organic carbon concentration, humification degree, molecular size, and level of terrestrial humic-like substances (C1C3) for early impoundment DOM compared with late impoundment DOM, which were derived from the relatively high inflow discharges present before impoundment. Meanwhile, the relatively high autochthonous contribution and level of protein-like substances found in late impoundment DOM suggested that anthropogenic impoundment can influence the DOM composition in Hongze Lake. Increases in the binding affinities (log Km) of humic-like substances (C1 and C3) and decreases in the log Km of tryptophan-like substances (C4) were observed during the impoundment period. Additionally, 2D-COS results suggested that the preferential Cu(II) binding ligands in early and late impoundment DOM were tryptophan- (C4) and humic-like (C1) substances, respectively. These results indicated that impoundment-derived DOM composition alteration can decrease the bioavailability and toxicity of Cu in Hongze Lake. The results reported here will improve the understanding of DOM and heavy metal cycling in impoundment lakes.Hu, C.-Y., Frank Yang, T., Burr, G.S., Chuang, P.-C., Chen, H.-W., Walia, M., Chen, N.-C., Huang, Y.-C., Lin, S., Wang, Y., Chung, S.-H., Huang, C.-D., Chen, C.-H., 2017. Biogeochemical cycles at the sulfate-methane transition zone (SMTZ) and geochemical characteristics of the pore fluids offshore southwestern Taiwan. Journal of Asian Earth Sciences 149, 172-183. this study, we used pore water dissolved inorganic carbon (DIC), SO42?, Ca2+ and Mg2+ gradients at the sulfate-methane transition zone (SMTZ) to estimate biogeochemical fluxes for cored sediments collected offshore SW Taiwan. Net DIC flux changes (ΔDIC-Prod) were applied to determine the proportion of sulfate consumption by organic matter oxidation (heterotrophic sulfate reduction) and anaerobic oxidation of methane (AOM), and to determine reliable CH4 fluxes at the SMTZ. Our results show that SO42? profiles are mainly controlled by AOM rather than heterotrophic sulfate reduction. Refinement of CH4 flux estimates enhance our understanding of methane abundance from deep carbon reservoirs to the SMTZ. Concentrations of chloride (Cl?), bromide (Br?) and iodide (I?) dissolved in pore water were used to identify potential sources that control fluid compositions and the behavior of dissolved ions. Constant Cl? concentrations throughout ～30 m sediment suggest no influence of gas hydrates for the compositions within the core. Bromide (Br?) and Iodine (I?) concentrations increase with sediment depth. The I?/Br? ratio appears to reflect organic matter degradation. SO42? concentrations decrease with sediment depth at a constant rate, and sediment depth profiles of Br? and I? concentrations suggests diffusion as the main transport mechanism. Therefore diffusive flux calculations are reasonable. Coring sites with high CH4 fluxes are more common in the accretionary wedge, amongst thrust faults and fractures, than in the passive continental margin offshore southwestern Taiwan. AOM reactions are a major sink for CH4 passing upward through the SMTZ and prevent high methane fluxes in the water column and to the atmosphere.Hu, G., Peng, W., Yu, C., 2017. Insight into the C8 light hydrocarbon compositional differences between coal-derived and oil-associated gases. Journal of Natural Gas Geoscience 2, 157-163. analyze the C8 light hydrocarbon of absorbed gas in the source rock and natural gas, both the PY-GC and GC were applied. This is done in order to develop the discrimination parameters of different genetic gases. Eight samples, including six mudstones with type II1 and type I organic matter and two coals, were analyzed by PY-GC. On the other hand, the sixteen typical coal-derived gases and sixteen oil-associated gases were analyzed by GC. The results show that there exists a great difference in the ratio of 2-methylheptane and 1-cis-3-dimethylcyclohexane in coal-derived gases, oil-associated gases, and source rock absorbed gases. The ratio in coal-derived gases is less than 0.5, whereas it is higher than 0.5 in oil-associated gases. In addition, there are also differences in the relative composition of C8 normal alkanes, isoparaffin, and cycloparaffin in coal-derived and oil-associated gases. Coal-derived gas is characterized by high cycloparaffin content that is generally higher than 40%, while the oil-associated gas exhibits low cycloparaffin content that generally less than 40%, as well as high isoparaffin content. Therefore, these parameters can be used to identify a coal-derived gas from an oil-associated gas.Hu, S.-X., Zhu, M.-Y., Zhao, F.-C., Steiner, M., 2017. A crown group priapulid from the early Cambrian Guanshan Lagerst?tte. Geological Magazine 154, 1329-1333. well-preserved fossil priapulid worm, Xiaoheiqingella sp., is reported from the early Cambrian Guanshan Lagerst?tte (Cambrian Series II, Stage 4) near Kunming City, Yunnan Province, SW China. The body of the animal consists of four sections: a swollen introvert, a constricted neck, a finely annulated trunk and a caudal appendage. The body configuration exhibits a close resemblance to that of the crown group priapulid Xiaoheiqingella peculiaris from the early Cambrian Chengjiang Lagerst?tte. The new discovery provides another striking example of crown group priapulids, representing the third occurrence of crown group fossil priapulids after the Chengjiang Lagerst?tte (Cambrian Series II, Stage 3) and the Mazon Creek Lagerst?tte (late Moscovian Stage, Pennsylvanian). The discovery also sheds new light on the early diversity and evolution of priapulid worms.Hua, Y., Mirnaghi, F.S., Yang, Z., Hollebone, B.P., Brown, C.E., 2018. Effect of evaporative weathering and oil-sediment interactions on the fate and behavior of diluted bitumen in marine environments. Part 1. Spill-related properties, oil buoyancy, and oil-particulate aggregates characterization. Chemosphere 191, 1038-1047. fate and behavior of diluted bitumen spilled in marine conditions has recently become a topic of much interest, yet, only limited knowledge is available. One of the major issues of a diluted bitumen spill on water is whether the product will sink, especially when suspended sediment is present in the water column. This study demonstrated how weathering processes influenced the key spill-related properties of a diluted bitumen product (Cold Lake Blend-Winter), and how interaction of diluted bitumen with sediment affected its tendency to float or sink in water. This study showed that the weathering states of the oils as well as the size of sediment are important factors influencing oil-sediment interactions and the tendency of the formed oil-particulate aggregates for buoyancy. When mixing with fine- and medium-sized sediments, the fresh to moderately weathered oils formed oil-particulate aggregates and sank in saltwater, while the very heavily-weathered oil formed discrete free-floating tarballs.Huang, L., Ning, Z., Wang, Q., Zhang, W., Cheng, Z., Wu, X., Qin, H., 2018. Effect of organic type and moisture on CO2/CH4 competitive adsorption in kerogen with implications for CO2 sequestration and enhanced CH4 recovery. Applied Energy 210, 28-43. research attentions for CO2 injection in gas-bearing reservoirs have been drawn to CO2 sequestration with enhanced gas recovery (CS-EGR), the microscopic competitive adsorption mechanism of methane (CH4) and carbon dioxide (CO2) considering the effect of organic type and moisture remains to be determined. In this work, we focus on the competitive adsorption behaviors of CH4 and CO2 on dry and moist realistic kerogen models of different organic types by performing combined molecular dynamics (MD) and grand canonical Monte Carlo (GCMC) simulations. The effects of organic type and moisture content on kerogen pore structures, moisture distribution and interaction between CH4/CO2 and kerogen surfaces are discussed in details. Simulation results show that CO2/CH4 adsorption capacity and adsorption selectivity are in the order of kerogen IA?<?IIA?<?IIIA, consistent with the sequence of enterable pore volume fraction (IA, 9.38%; IIA, 13.59%; IIIA, 28.88%). H2O molecules are preferentially adsorbed on the sulfur- and oxygen-containing groups at low moisture, and then migrate and aggregate into clusters in the middle of enterable pores at high moisture. The CO2/CH4 adsorption capacity decreases with increasing moisture content, while the CO2/CH4 adsorption selectivity, specific adsorption energy and CO2 isosteric heat decrease at the beginning, and then increase with the moisture content. Moisture has a bigger effect on the adsorption of CO2 than that of CH4. This study indicates that kerogen IIIA is the optimized organic type for CS-EGS due to its large and stable CO2 storage capacity. Despite its negative effect on gas adsorption capacity, moisture can potentially boost the displacement of CH4 by CO2 at certain moisture conditions. Results of this study lay the foundation for future optimization design of CS-EGR projects with application to coal and shale systems.Huang, R., Chen, Y., Meshref, M.N.A., Chelme-Ayala, P., Dong, S., Ibrahim, M.D., Wang, C., Klamerth, N., Hughes, S.A., Headley, J.V., Peru, K.M., Brown, C., Mahaffey, A., El-Din, M.G., 2018. Characterization and determination of naphthenic acids species in oil sands process-affected water and groundwater from oil sands development area of Alberta, Canada. Water Research 128, 129-137. work reports the monitoring and assessment of naphthenic acids (NAs) in oil sands process-affected water (OSPW), Pleistocene channel aquifer groundwater (PLCA), and oil sands basal aquifer groundwater (OSBA) from an active oil sands development in Alberta, Canada, using ultra performance liquid chromatography time-of-flight mass spectrometry analysis with internal standard (ISTD) and external standard (ESTD) calibration methods and Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) for compositional analysis. PLCA was collected at 45–51 m depth and OSBA was collected at 67–144 m depth. Results of Ox?NA concentrations follow an order as OSPW > OSBA > PLCA, indicating that occurrences of NAs in OSBA were likely related to natural bitumen deposits instead of OSPW. Liquid-liquid extraction (LLE) was applied to avoid the matrix effect for the ESTD method. Reduced LLE efficiency accounted for the divergence of the ISTD and ESTD calibrated results for oxidized NAs. Principle component analysis results of O2 and O4 species could be employed for differentiation of water types, while classical NAs with C13?15 and Z (-4)?(-6) and aromatic O2?NAs with C16?18 and Z (-14)?(-16) could be measured as marker compounds to characterize water sources and potential temporal variations of samples, respectively. FTICR-MS results revealed that compositions of NA species varied greatly among OSPW, PLCA, and OSBA, because of NA transfer and transformation processes. This work contributed to the understanding of the concentration and composition of NAs in various types of water, and provided a useful combination of analytical and statistical tools for monitoring studies, in support of future safe discharge of treated OSPW.Huang, S., Fang, C., Peng, W., Jiang, Q., Feng, Z., 2017. Stable carbon isotopic composition of light hydrocarbons and n-alkanes of condensates in the Tarim Basin, NW China. Journal of Natural Gas Geoscience 2, 165-177. carbon isotope ratios of individual light hydrocarbons and the n-alkanes of twenty-one condensates from the Tarim Basin, as well as 47 condensates and oils from other petroliferous basins (Ordos Basin, Sichuan Basin, Turpan-Harmi Basin, Qiongdongnan Basin, Beibu Gulf Basin and Bohai Bay Basin) in China, were analyzed. We investigated the oil–oil correlation, the effects of gas washing and maturity, as well as the distinguishing parameters of humic and sapropelic condensates, and have come to the following conclusion. The carbon isotopic patterns of condensates and oils in the Ordovician strata of Tarim Basin are very similar, indicating they originate from the same type of source rocks. The condensates from Dawanqi oil field and Yinan 2, as well as Ti'ergen and Yitikelike gas fields, have similar carbon isotopic patterns. Thus, they probably have originated from the same terrestrial Jurassic source rock. The carbon isotopic patterns of the condensates from the Dabei, Kela 2, and Keshen gas fields are also similar, indicating they are of the same oil family and sourced from the Triassic and Jurassic terrestrial source rock. The carbon isotopic ratios of 2-MP, 3-MP, 3-MH, and nC5-8 are much more susceptible to maturity level than other light hydrocarbons. Gas washing has minor effects on the δ13C compositions of individual light hydrocarbons and n-alkanes, although it causes <2‰ shifts. The δ13C compositions of MCP, CH, MCH, benzene, and toluene can be used as identification parameters for humic and sapropelic condensates. Humic condensates generally have δ13CMCP > ?25‰, δ13CCH > ?24‰, δ13CMCH > ?24‰, δ13Cbenzene > ?25‰, and δ13Ctoluene > ?24‰, whereas sapropelic condensates mainly have δ13CMCP < ?26‰, δ13CCH < ?26‰, δ13CMCH < ?24‰, δ13Cbenzene < ?25‰ and δ13Ctoluene < ?24‰. Moreover, the mixing humic and sapropelic condensates usually show intermediate values.Huang, X., Yang, X., Zhu, H., Kang, H., Jia, J., Wang, B., Ji, S., 2017. Lithofacies characteristics and sedimentary pattern of Madingo Formation marine hydrocarbon source rocks in Lower Congo Basin. Acta Petrolei Sinica 38, 1168-1182. on analyzing thin section by microscopic observation, scanning electron microscopy, X-ray diffraction as well as constant and trace element measurement, and considering the mineral composition of fine-grained sediment, lithologic fabric, micro-palaeontological characteristics and typical minerals, 6 types of hydrocarbon source rock lithofacies have been identified in marine source rocks of Madingo Formation:the silt fine-grained lithofacies, radiolarian enriched fine-grained lithofacies, phosphatic fine-grained lithofacies, foraminiferan enriched fine-grained lithofacies, cinereal fine-grained lithofacies (lime mud)and clayey fine-grained lithofacies. As demonstrated by the comprehensive analysis of fine-grained sediment lithofacies, micro-palaeontological fossils, constant and trace elements as well as seismic data, the biogenic deposit containing biosilicon, upwelling sediment containing phosphate rock, suspension sediment enriched with silicious clastic particles and bottom current sediment with graded bedding were developed in marine source rocks from Madingo Formation. As a whole, marine source rocks in Madingo Formation of the Lower Congo Basin were deposited under a reducing environment with low-energy water medium in post-rift continental shelf, and in the early deposition stage the semi-closed-closed restricted sea environment was developed in the continental shelf and the high-quality source rocks enriched with radiolarian were accumulated; and following the Campanian period, the regional geological background was converted to a wide continental shelf where high-quality source rocks enriched with phosphate and foraminiferan were developed due to upwelling on the continental shelf.Hughes, S.A., Mahaffey, A., Shore, B., Baker, J., Kilgour, B., Brown, C., Peru, K.M., Headley, J.V., Bailey, H.C., 2017. Using ultrahigh-resolution mass spectrometry and toxicity identification techniques to characterize the toxicity of oil sands process-affected water: The case for classical naphthenic acids. Environmental Toxicology and Chemistry 36, 3148-3157. assessments of oil sands process-affected water (OSPW) toxicity were hampered by lack of high-resolution analytical analysis, use of nonstandard toxicity methods, and variability between OSPW samples. We integrated ultrahigh-resolution mass spectrometry with a toxicity identification evaluation (TIE) approach to quantitatively identify the primary cause of acute toxicity of OSPW to rainbow trout (Oncorhynchus mykiss). The initial characterization of OSPW toxicity indicated that toxicity was associated with nonpolar organic compounds, and toxicant(s) were further isolated within a range of discrete methanol fractions that were then subjected to Orbitrap mass spectrometry to evaluate the contribution of naphthenic acid fraction compounds to toxicity. The results showed that toxicity was attributable to classical naphthenic acids, with the potency of individual compounds increasing as a function of carbon number. Notably, the mass of classical naphthenic acids present in OSPW was dominated by carbon numbers ≤16; however, toxicity was largely a function of classical naphthenic acids with ≥17 carbons. Additional experiments found that acute toxicity of the organic fraction was similar when tested at conductivities of 400 and 1800?μmhos/cm and that rainbow trout fry were more sensitive to the organic fraction than larval fathead minnows (Pimephales promelas). Collectively, the results will aid in developing treatment goals and targets for removal of OSPW toxicity in water return scenarios both during operations and on mine closure. Hutchings, J.A., Shields, M.R., Bianchi, T.S., Schuur, E.A.G., 2018. A rapid and precise method for the analysis of underivatized amino acids in natural samples using volatile-ion-pairing reverse-phase liquid chromatography–electrospray ionization tandem mass spectrometry. Organic Geochemistry 115, 46-56. acids are effective tracers of organic carbon and nitrogen cycling in natural substrates. However, total analytical time can be long due to extraction, derivatization, and chromatography. Here, we present a liquid chromatographic separation of 19 naturally occurring amino acids requiring no derivatization using triple-quadrupole mass spectrometry. This method builds on recent advances in volatile ion pairing and was applied to natural soil samples collected from two distinct systems with highly variable organic C contents. Separation and quantification of amino acids were achieved with an 18 min sample-to-sample run time employing a one-point standard addition to account for variable matrix effects during ionization. Detection limits ranged from 5.9 to 187.5 fmol (mean 30.0 fmol) while instrumental precision averaged 5.8% and 12.0% for intra- and inter-day error, respectively. The highest yields (mean > 100 ?mol/g C) in our natural substrates were observed for glycine, aspartic acid, alanine, and glutamic acid while low yields (mean < 20 ?mol/g C) were observed for all non-proteinogenic amino acids as well as histidine and tyrosine. A typical hot acid hydrolysis in 6N HCl was used and hydrolyzates were diluted and filtered rather than being subjected to solid-phase extraction or similar techniques, which require significant investment of time during sample preparation. This method enables high throughput and reliable analysis of hydrolyzable amino acids, while also reducing user workload and instrument time compared to previous techniques. The Alaskan tundra system had significantly higher absolute yields of amino acids (mean 88.4 vs 25.6 ?mol/g dry sediment), in part driven by higher organic C concentrations, while the Louisiana delta system had significantly higher organic C normalized yields of amino acids (mean 1492.5 vs 541.6 ?mol/g C). Despite these differences, both systems exhibited broadly similar mole-percent amino acid compositions.Ibrahim, H., Jurcic, K., Wang, J.S.H., Whitehead, S.N., Yeung, K.K.C., 2017. 1,6-Diphenyl-1,3,5-hexatriene (DPH) as a novel matrix for MALDI MS imaging of fatty acids, phospholipids, and sulfatides in brain tissues. Analytical Chemistry 89, 12828-12836. (DPH) is a commonly used fluorescence probe for studying cell membrane-lipids due to its affinity toward the acyl chains in the phospholipid bilayers. In this work, we investigated its use in matrix-assisted laser desorption/ionization (MALDI) as a new matrix for mass spectrometry imaging (MSI) of mouse and rat brain tissue. DPH exhibits very minimal matrix-induced background signals for the analysis of small molecules (below m/z of 1000). In the negative ion mode, DPH permits the highly sensitive detection of small fatty acids (m/z 200–350) as well as a variety of large lipids up to m/z of 1000, including lyso-phospholipid, phosphatidic acid (PA), phosphoethanolamine (PE), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), and sulfatides (ST). The analytes were mostly detected as the deprotonated ion [M – H]?. Our results also demonstrate that sublimated DPH is stable for at least 24 h under the vacuum of our MALDI mass spectrometer. The ability to apply DPH via sublimation coupled with its low volatility allows us to perform tissue imaging of the above analytes at high spatial resolution. The degree of lipid fragmentation was determined experimentally at varying laser intensities. The results illustrated that the use of relatively low laser energy is important to minimize the artificially generated fatty acid signals. On the other hand, the lipid fragmentation obtained at higher laser energies provided tandem MS information useful for lipid structure elucidation.Indrupskiy, I.M., Lobanova, O.A., Zubov, V.R., 2017. Non-equilibrium phase behavior of hydrocarbons in compositional simulations and upscaling. Computational Geosciences 21, 1173-1188. models widely used for hydrocarbon phase behavior and compositional flow simulations are based on assumption of thermodynamic equilibrium. However, it is not uncommon for oil and gas-condensate reservoirs to exhibit essentially non-equilibrium phase behavior, e.g., in the processes of secondary recovery after pressure depletion below saturation pressure, or during gas injection, or for condensate evaporation at low pressures. In many cases, the ability to match field data with equilibrium model depends on simulation scale. The only method to account for non-equilibrium phase behavior adopted by the majority of flow simulators is the option of limited rate of gas dissolution (condensate evaporation) in black oil models. For compositional simulations, no practical yet thermodynamically consistent method has been presented so far except for some upscaling techniques in gas injection problems. Previously reported academic non-equilibrium formulations have a common drawback of doubling the number of flow equations and unknowns compared with the equilibrium formulation. In the paper, a unified thermodynamically consistent formulation for compositional flow simulations with non-equilibrium phase behavior model is presented. Same formulation and a special scale-up technique can be used for upscaling of an equilibrium or non-equilibrium model to a coarse-scale non-equilibrium model. A number of test cases for real oil and gas-condensate mixtures are given. Model implementation specifics in a flow simulator are discussed and illustrated with test simulations. A non-equilibrium constant volume depletion algorithm is presented to simulate condensate recovery at low pressures in gas-condensate reservoirs. Results of satisfactory model matching to field data are reported and discussed.Isaacman-VanWertz, G., Sueper, D.T., Aikin, K.C., Lerner, B.M., Gilman, J.B., de Gouw, J.A., Worsnop, D.R., Goldstein, A.H., 2017. Automated single-ion peak fitting as an efficient approach for analyzing complex chromatographic data. Journal of Chromatography A 1529, 81-92. provides important detail on the composition of environmental samples and their chemical processing. However, the complexity of these samples and their tendency to contain many structurally and chemically similar compounds frequently results in convoluted or poorly resolved data. Data reduction from raw chromatograms of complex environmental data into integrated peak areas consequently often requires substantial operator interaction. This difficulty has led to a bottleneck in analysis that increases analysis time, decreases data quality, and will worsen as advances in field-based instrumentation multiply the quantity and informational density of data produced. In this work, we develop and validate an automated approach to fitting chromatographic data within a target retention time window with a combination of multiple idealized peaks (Gaussian peaks either with or without an exponential decay component). We compare this single-ion peak fitting approach to drawn baseline integration methods of more than 70,000 peaks collected by field-based chromatographs spanning across a wide range of volatilities and functionalities. Accuracy of peak fitting under real-world conditions is found to be within 10%. The quantitative parameters describing the fit (e.g. coefficients, fit residuals, etc.) are found to provide valuable information to increase the efficiency of quality control and provide constraints to accurately integrate peaks that are significantly convoluted with neighboring peaks. Implementation of the peak fitting method is shown to yield accurate integration of peaks otherwise too poorly resolved to separate into individual compounds and improved quantitative metrics to determine the fidelity of the data reduction process, while substantially decreasing the time spent by operators on data reduction.Islam, A.W., Sun, A.Y., 2017. A theory-based simple extension of Peng–Robinson equation of state for nanopore confined fluids. Journal of Petroleum Exploration and Production Technology 7, 1197-1203. a recent publication (Islam et al. in J Nat Gas Sci Eng 25:134–139, 2015), the van der Waals equation of state (EOS) was modified to assess phase behavior of nanopore confined fluids. Although the changes of critical properties were well captured, it was limited to only subcritical conditions. Peng–Robinson EOS showed inconsistent critical shifts. Here, we develop a simple extension of Peng–Robinson (PR) derived similarly from the Helmholtz free energy function by applying the same energy and volume parameter relations. This modified PR reproduces experimental and molecular simulation results satisfactorily. It shows that there is pore proximity effect also in supercritical condition which, however, diminishes as temperature increases. The proposed model can show heterogeneous density or layered distribution of molecules inside nanopore. We have tested common shale (natural) gas molecules and the condition of Haynesville plays where temperature and pressure can be very high. This simple model can offer alternatives to more computationally expensive molecular simulations to study the pore proximity phenomenon.Iuculano, F., Duarte, C.M., Marbà, N., Agustí, S., 2017. Seagrass as major source of transparent exopolymer particles in the oligotrophic Mediterranean coast. Biogeosciences 14, 5069-5075. role of seagrass, Posidonia oceanica, meadows as a source of transparent exopolymer particles (TEPs) to Mediterranean coastal waters was tested by comparing the TEP dynamics in two adjacent coastal waters in the oligotrophic NW Mediterranean Sea, one characterized by oligotrophic open-sea waters and the other accumulating seagrass leaf litter, together with an experimental examination of TEP release by seagrass litter. TEP concentrations ranged from 4.6 to 90.6??g?XG (xanthan gum)?Eq?L?1, with mean (±SE) values of 38.7?(±?2.02)??g?XG?Eq?L?1 in the site devoid of seagrass litter, whereas the coastal beach site accumulating leaf litter had >?10-fold mean TEP concentrations of 487.02?(±?72.8)??g?XG?Eq?L?1. Experimental evaluation confirmed high rates of TEP production by P. oceanica litter, allowing calculations of the associated TEP yield. We demonstrated that P. oceanica is an important source of TEPs to the Mediterranean Sea, contributing an estimated 76?Gg?C as TEPs annually. TEP release by P. oceanica seagrass explains the elevated TEP concentration relative to the low chlorophyll a concentration in the Mediterranean Sea.Ivonin, D.V., Ivanov, A.Y., 2017. On classification of sea surface oil films using TerraSAR-X satellite polarization data. Oceanology 57, 738-750. paper presents the results of applying a new polarization method proposed in [28] to identify the type of surface pollution and differentiate between mineral oil films (crude oil and its emulsion and petroleum products) and films of other origin in sea surface radar images. The method is based on calculation of the quantitative characteristics for the ratios of suppression or intensification of scattered radio signals of different physical nature, viz., caused by capillary ripples several centimeters long, or wave breaking. TerraSAR-X satellite coaxial-polarized (VV/HH) SAR images are used. The data for analysis have been collected in areas where spots and slicks of known origin regularly occur, such as oil spills and natural oil seeps in the Gulf of Mexico and the Caspian Sea, and biogenic films in the Caspian Sea. The results of analyzing radar images from the TerraSAR-X satellite with controlled experimental oil emulsion spills in the North Sea are used for comparison. Based on the analysis of ten TerraSAR-X radar polarization images with surface sensing angles greater than 30°, it is shown that this method makes it possible to distinguish between oil spills and slicks formed by natural oil seeps and biogenic films with an accuracy higher than 80% regardless of the observation area. Original Russian Text ? D.V. Ivonin, A.Yu. Ivanov, 2017, published in Okeanologiya, 2017, Vol. 57, No. 5, pp. 815–829.Izumi, K., Kemp, D.B., Itamiya, S., Inui, M., 2018. Sedimentary evidence for enhanced hydrological cycling in response to rapid carbon release during the early Toarcian oceanic anoxic event. Earth and Planetary Science Letters 481, 162-170. pronounced excursion in the carbon-isotope composition of biospheric carbon and coeval seawater warming during the early Toarcian (～183 Ma) has been linked to the large-scale transfer of 12C-enriched carbon to the oceans and atmosphere. A European bias in the distribution of available data means that the precise pattern, tempo and global expression of this carbon cycle perturbation, and the associated environmental responses, remain uncertain. Here, we present a new cm-scale terrestrial-dominated carbon-isotope record through an expanded lower Toarcian section from Japan that displays a negative excursion pattern similar to marine and terrestrial carbon-isotope records documented from Europe. These new data suggest that 12C-enriched carbon was added to the biosphere in at least one rapid, millennial-scale pulse. Sedimentological analysis indicates a close association between the carbon-isotope excursion and high-energy sediment transport and enhanced fluvial discharge. Together, these data support the hypothesis that a sudden strengthening of the global hydrological cycle occurred in direct and immediate response to rapid carbon release and atmospheric warming.Jacobel, A.W., McManus, J.F., Anderson, R.F., Winckler, G., 2017. Repeated storage of respired carbon in the equatorial Pacific Ocean over the last three glacial cycles. Nature Communications 8, Article 1727. the largest reservoir of carbon exchanging with the atmosphere on glacial–interglacial timescales, the deep ocean has been implicated as the likely location of carbon sequestration during Pleistocene glaciations. Despite strong theoretical underpinning for this expectation, radiocarbon data on watermass ventilation ages conflict, and proxy interpretations disagree about the depth, origin and even existence of the respired carbon pool. Because any change in the storage of respiratory carbon is accompanied by corresponding changes in dissolved oxygen concentrations, proxy data reflecting oxygenation are valuable in addressing these apparent inconsistencies. Here, we present a record of redox-sensitive uranium from the central equatorial Pacific Ocean to identify intervals associated with respiratory carbon storage over the past 350?kyr, providing evidence for repeated carbon storage over the last three glacial cycles. We also synthesise our data with previous work and propose an internally consistent picture of glacial carbon storage and equatorial Pacific Ocean watermass structure.Jaisi, D.P., Hou, Y., Stout, L.M., Massoudieh, A., 2017. Modeling of biotic and abiotic processes affecting phosphate oxygen isotope ratios in a mineral-water-biota system. Water Research 126, 262-273. and biotic reactions operate side by side in the cycling of phosphorus (P) in the environment, but the relative roles of these two reactions vary both spatially and temporally. In biotic reactions, the uptake and release of P are catalyzed by enzymes and thus change phosphate oxygen isotope ratios, while in abiotic reactions, the absence of hydrolysis-condensation reactions results in no apparent changes in isotope composition, except short-term kinetic isotope effect due solely to preferential ion exchange. Therefore, isotope method could be a promising tool to differentiate relative roles of these two reactions in the environment but the relationship of the dynamic concentration and isotope exchange at the biota-water interface is largely unknown. In this study, we aimed to develop a process-based isotope model underpinning the competition of abiotic (sorption, desorption, and ion exchange) and biotic (uptake, metabolism, and release) reactions during uptake and recycling of ferrihydrite-bound P by E. coli. Our model comprises equations describing the partitioning relationship among different P pools and their corresponding oxygen isotope compositions and is based exclusively on oxygen isotope exchange at multiple sites including mineral surface, aqueous phase, and bacterial cells. The process-based model adequately reproduced the measured concentration and isotope compositions over time. Furthermore, parametric and sensitivity analyses using the model indicated that the rate of biological uptake of P was the major factor controlling the changes of phosphate isotope composition. In conclusion, our model provides new insights into a mechanistic aspect of isotope exchange and could be potentially useful for future efforts to understand the interplay of biotic and abiotic factors on phosphorus cycling in natural environments.Jakob, K.A., Pross, J., Scholz, C., Fiebig, J., Friedrich, O., 2017. Thermocline state change in the Eastern Equatorial Pacific during the late Pliocene/early Pleistocene intensification of Northern Hemisphere Glaciation. Climate of the Past Discussions 2017, 1-22. late Pliocene/early Pleistocene intensification of Northern Hemisphere Glaciation (iNHG) ~?2.5 million years ago (Marine Isotope Stages [MIS] 100–96) stands out as the most recent major tipping point in Earth's climate history. It strongly influenced oceanographic and climatic patterns including trade-wind and upwelling strength in the Eastern Equatorial Pacific (EEP). The thermocline depth in the EEP, in turn, plays a pivotal role in the evolution of short-term climate phenomena such the El Ni?o-Southern Oscillation, and thus bears important consequences for the Earth's climate system. However, thermocline dynamics in the EEP during to the iNHG have yet remained unclear. While numerous studies have suggested a link between a thermocline shoaling in the EEP and Northern Hemisphere ice growth, other studies have indicated a stable thermocline depth during iNHG, thereby excluding a causal relationship between thermocline dynamics and ice-sheet growth. In light of these contradictory views, we have generated geochemical (planktic foraminiferal δ18O, δ13C and Mg/Ca), sedimentological (sand-accumulation rates) and faunal (abundance data of thermocline-dwelling foraminifera) records for Ocean Drilling Program Site 849 located in the central part of the EEP. Our records span the interval from ~?2.75 to 2.4?Ma (MIS G7–95), which is critical for understanding thermocline dynamics during the final phase of the iNHG. They document a thermocline shoaling from ~?2.64 to 2.55?Ma (MIS G2–101) and a relatively shallow thermocline from ~?2.55?Ma onwards (MIS 101–95). This indicates a state change in EEP thermocline depth shortly before the final phase of iNHG. Ultimately, our data support the hypothesis that (sub-)tropical thermocline shoaling may have contributed to the development of large Northern Hemisphere ice sheets.Jambon, A., 2017. Bronze Age iron: Meteoritic or not? A chemical strategy. Journal of Archaeological Science 88, 47-53. Age iron artifacts could be derived from either meteoritic (extraterrestrial) or smelted (terrestrial) iron. This unresolved question is the subject of a controversy: are some, all or none made of smelted iron? In the present paper we propose a geochemical approach, which permits us to differentiate terrestrial from extraterrestrial irons. Instead of evaluating the Ni abundance alone (or the Ni to Fe ratio) we consider the relationship between Fe, Co and Ni abundances and their ratios. The study of meteoritic irons, Bronze Age iron artifacts and ancient terrestrial irons permit us to validate this chemical approach. The major interest is that non-invasive p-XRF analyses provide reliable Fe:Co:Ni abundances, without the need to remove a sample; they can be performed in situ, in the museums where the artifacts are preserved. The few iron objects from the Bronze Age sensu stricto that could be analyzed are definitely made of meteoritic iron, suggesting that speculations about precocious smelting during the Bronze Age should be revised. In a Fe:Co:Ni array the trend exhibited by meteoritic irons departs unambiguously from modern irons and iron ores. The trend of Ni/Fe vs Ni/Co in different analysis points of a single object corroded to variable extents provides a robust criterion for identifying the presence of meteoritic iron. It opens the possibility of tracking when and where the first smelting operations happened, the threshold of a new era. It emphasizes the importance of analytical methods for properly studying the evolution of the use of metals and metal working technologies in our past cultures.Jammet, M., Dengel, S., Kettner, E., Parmentier, F.J.W., Wik, M., Crill, P., Friborg, T., 2017. Year-round CH4 and CO2 flux dynamics in two contrasting freshwater ecosystems of the subarctic. Biogeosciences 14, 5189-5216. and wetlands, common ecosystems of the high northern latitudes, exchange large amounts of the climate-forcing gases methane (CH4) and carbon dioxide (CO2) with the atmosphere. The magnitudes of these fluxes and the processes driving them are still uncertain, particularly for subarctic and Arctic lakes where direct measurements of CH4 and CO2 emissions are often of low temporal resolution and are rarely sustained throughout the entire year. Using the eddy covariance method, we measured surface–atmosphere exchange of CH4 and CO2 during 2.5 years in a thawed fen and a shallow lake of a subarctic peatland complex. Gas exchange at the fen exhibited the expected seasonality of a subarctic wetland with maximum CH4 emissions and CO2 uptake in summer, as well as low but continuous emissions of CH4 and CO2 throughout the snow-covered winter. The seasonality of lake fluxes differed, with maximum CO2 and CH4 flux rates recorded at spring thaw. During the ice-free seasons, we could identify surface CH4 emissions as mostly ebullition events with a seasonal trend in the magnitude of the release, while a net CO2 flux indicated photosynthetic activity. We found correlations between surface CH4 emissions and surface sediment temperature, as well as between diel CO2 uptake and diel solar input. During spring, the breakdown of thermal stratification following ice thaw triggered the degassing of both CH4 and CO2. This spring burst was observed in 2 consecutive years for both gases, with a large inter-annual variability in the magnitude of the CH4 degassing. On the annual scale, spring emissions converted the lake from a small CO2 sink to a CO2 source: 80?% of total annual carbon emissions from the lake were emitted as CO2. The annual total carbon exchange per unit area was highest at the fen, which was an annual sink of carbon with respect to the atmosphere. Continuous respiration during the winter partly counteracted the fen summer sink by accounting for, as both CH4 and CO2, 33?% of annual carbon exchange. Our study shows (1) the importance of overturn periods (spring or fall) for the annual CH4 and CO2 emissions of northern lakes, (2) the significance of lakes as atmospheric carbon sources in subarctic landscapes while fens can be a strong carbon sink, and (3) the potential for ecosystem-scale eddy covariance measurements to improve the understanding of short-term processes driving lake–atmosphere exchange of CH4 and CO2.Jamshidi, M.P., MacDonald, M.J., Beauchemin, A.M., 2017. On the ability of formaldehyde to act as a tethering catalyst in water. Origins of Life and Evolution of Biospheres 47, 405-412. low concentration issue is a fundamental challenge when it comes to prebiotic chemistry, as macromolecular systems need to be assembled via intermolecular reactions, and this is inherently difficult in dilute solutions. This is especially true when the reactions are challenging, and reactions that proceeded more rapidly could have dictated chemical evolution. Herein we establish that formaldehyde is capable of catalyzing, via temporary intramolecularity, a challenging reaction in water at low concentrations, thus providing an alternative to other approaches that can either lead to higher concentrations or higher effective molarities.Janusz, G., Pawlik, A., Sulej, J., ?widerska-Burek, U., Jarosz-Wilko?azka, A., Paszczyński, A., 2017. Lignin degradation: microorganisms, enzymes involved, genomes analysis and evolution. FEMS Microbiology Reviews 41, 941-962. research efforts have been dedicated to describing degradation of wood, which is a complex process; hence, microorganisms have evolved different enzymatic and non-enzymatic strategies to utilize this plentiful plant material. This review describes a number of fungal and bacterial organisms which have developed both competitive and mutualistic strategies for the decomposition of wood and to thrive in different ecological niches. Through the analysis of the enzymatic machinery engaged in wood degradation, it was possible to elucidate different strategies of wood decomposition which often depend on ecological niches inhabited by given organism. Moreover, a detailed description of low molecular weight compounds is presented, which gives these organisms not only an advantage in wood degradation processes, but seems rather to be a new evolutionatory alternative to enzymatic combustion. Through analysis of genomics and secretomic data, it was possible to underline the probable importance of certain wood-degrading enzymes produced by different fungal organisms, potentially giving them advantage in their ecological niches. The paper highlights different fungal strategies of wood degradation, which possibly correlates to the number of genes coding for secretory enzymes. Furthermore, investigation of the evolution of wood-degrading organisms has been described.Jasper, A., Agnihotri, D., Tewari, R., Spiekermann, R., Pires, E.F., Da Rosa, ?.A.S., Uhl, D., 2017. Fires in the mire: repeated fire events in Early Permian ‘peat forming’ vegetation of India. Geological Journal 52, 955-969., as direct evidence of palaeo-wildfires, is a common constituent throughout an Early Permian (Cisuralian) inertinite-rich coal seam from the Dhanpuri Coal Mine (Barakar Formation, Sohagpur Coalfield, Madhya Pradesh, India). The continuous presence of macro-charcoal within this particular seam demonstrates that fires occurred repeatedly in the source vegetation of the seam. Based on these macro-charcoal remains, an anatomical assessment of the diversity and taxonomic composition of the vegetation, which experienced wildfires and contributed to the formation of peat/coal, is provided. The vegetation that experienced regular fires was dominated by gymnosperms, with a minor component of pteridophytes. The results also support previous studies, which suggest a pyrogenic origin for the high inertinite contents of many Permian coals within Gondwana. Copyright ? 2016 John Wiley & Sons, Ltd.Jeanne, P., Rutqvist, J., Foxall, W., Rinaldi, A.P., Wainwright, H.M., Zhou, Q., Birkholzer, J., Layland-Bachmann, C., 2017. Effects of the distribution and evolution of the coefficient of friction along a fault on the assessment of the seismic activity associated with a hypothetical industrial-scale geologic CO2 sequestration operation. International Journal of Greenhouse Gas Control 66, 254-263. capture and storage (CCS) in geological formations is considered as a promising option that could limit CO2 emissions from human activities into the atmosphere. However, there is a risk that pressure buildup inside the storage formation can induce slip along preexisting faults and create seismic event felt by the population. To prevent this to happen a geomechanical fault stability analysis should be performed, considering uncertainties of input parameters. In this paper, we investigate how the distribution of the coefficient of friction and the applied frictional law could influence the assessment of fault stability and the characteristics of potential injection-induced seismic events. Our modelling study is based on a hypothetical industrial-scale carbon sequestration project located in the Southern San Joaquin Basin in California, USA, where the stability on a major (25 km long) fault that bounds the sequestration site is assessed during 50 years of CO2 injection. We conduct nine simulations in which the distributions of the coefficients of static and dynamic friction are changed to simulate a hardening and softening phase before and during rupture. Our main findings are: (i) variations in friction along the fault have an important effect on the predicted seismic activity, with maximum magnitude ranging from 1.88 to 5.88 and number of seismic events ranging from 338 to 3272; (ii) the extreme values of the coefficient of friction (lowest and highest) present along the rupture area control how much stress is accumulated before rupture; and (iii) an argillaceous caprock can prevent the development of large magnitude seismic events but favor the occurrence of a large number of smaller events.Jenkins, A., Fathi, E., Belyadi, F., 2017. Stress field behavior induced by hydraulic fracture in shale reservoirs: A practical view on cluster spacing. Journal of Natural Gas Science and Engineering 48, 186-196. fracturing is a complicated hydro-mechanical process, which is used to stimulate reservoir volume, where a pressurized fluid drives fracture propagation in a solid, or porous medium. This process changes the initial state of stress in the reservoir as the applied hydraulic pressure develops discontinuity throughout the media. As the fracture network propagates, it achieves a greater surface contact area with the producing formation and the wellbore, allowing for a greater rate of oil and gas migration in ultra-low permeability reservoirs (e.g. shale reservoirs). This process greatly enhances production, but may lead to instability within surrounding discontinuities or changes to the local stress distribution, which may cause unfavorable events such as hydraulic fracture cluster merging. Hydraulic fracture design is not recommended when only complicated numerical simulation and modeling techniques are used without verification through accompanying field data. Often times, comparing with field data, complicated mathematical simulation models are altered to better correlate the simulation results to real-time or post-treatment field data. This raises uncertainty in whether the physics of the hydraulic fracturing are being captured correctly or not using commercial numerical simulators. Many times this leads to a trial and error based approach for fracture treatment operations, which are backed by physical results, such as microseismic, or production data. Unfortunately, in initial field or well completion design scenarios, there is significant uncertainty associated with stimulation treatment designs. Observations of treated wells are required to corroborate the simulated data using scientific evidence. The Theory of Critical Distance (TCD) was developed as a quick analysis method to determining material failure; most often to notched type cases of non-propagating crack fatigue (Taylor, 2007). This theory demonstrates the ability to predict failure based upon the stress concentrations surrounding the notch (Yin, 2014; Louks, 2014). In a similar fashion this methodology is derived and applied to a dynamic pressurized fluid front within a fracture in order to predict stress concentrations surrounding the fracture (Lajtai, 1971; Ito, 1991). The premise of modifying TCD theory is nothing new as this has been done for various cases, however it has yet to be used in this type of application concerning dynamic loading and hydraulic driven fracture propagation. The application of a modified TCD theory displays the possibility of using a simple technique to predict hydraulic fracture cluster spacing by precisely defining the dynamics of the failure envelope around the fracture tip and surrounding fracture geometry and also to optimize injection pressure required for propagation but eliminate interference between clusters. In this paper Von Mises stress has been calculated and used to analyze the multi-fracture interactions. This behavior can be idealized such that the maximum Von Mises stress emanates from the fracture tip creating a critical angle with the fracture plane or fracture tip. The angle and magnitude of stress can be used to justify the stability of the reservoir or to interpret stress reorientations that are seen surrounding propagating fractures. These reorientations can affect the geometry and relative stress distributions surrounding adjacent fracture propagation by either easing or impeding the ability of the fracture to propagate. As a result of this study, the modified TCD theory provides a tool for the determination of these stress interactions in order to make quick decisions in the field to modify stimulation treatment plans during injection, which would typically require complicated modeling and simulation results.Jennerwein, M.K., Eschner, M.S., Wilharm, T., Zimmermann, R., Gr?ger, T.M., 2017. Proof of concept of high-temperature comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry for two-dimensional simulated distillation of crude oils. Energy & Fuels 31, 11651-11659. this work, a reversed-phase high-temperature comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC–TOFMS) approach for the qualitative and quantitative analyses of crude oils will be presented. The proposed setup provides the best utilization of the two-dimensional separation space for carbon numbers between C10 and C60. Visual Basic Script (VBS) was successfully applied for data processing to achieve comprehensive classification of the main compound classes. On this basis, crude oils from different origins could be compared by their composition. Real distillation cuts following ASTM D2892 and ASTM D5236 were applied for the development of area-based templates representing virtual boiling point cuts. By this approach, a quantification of an artificial crude oil sample with a defined initial boiling point was evaluated versus the quantitative result according to ASTM D7169 (one-dimensional simulated distillation for high boiling samples, hereinafter 1D-SimDist), and by this, a two-dimensional simulated distillation (2D-SimDist) was successfully developed.Jeong, E.S., Cha, E., Cha, S., Kim, S., Oh, H.B., Kwon, O.-S., Lee, J., 2017. Online simultaneous hydrogen/deuterium exchange of multitarget gas-phase molecules by electrospray ionization mass spectrometry coupled with gas chromatography. Analytical Chemistry 89, 12284-12292. this study, a hydrogen/deuterium (H/D) exchange method using gas chromatography–electrospray ionization/mass spectrometry (GC–ESI/MS) was first investigated as a novel tool for online H/D exchange of multitarget analytes. The GC and ESI source were combined with a homemade heated column transfer line. GC–ESI/MS-based H/D exchange occurs in an atmospheric pressure ion source as a result of reacting the gas-phase analyte eluted from GC with charged droplets of deuterium oxide infused as the ESI spray solvent. The consumption of the deuterated solvent at a flow rate of 2 μL min–1 was more economical than that in online H/D exchange methods reported to date. In-ESI-source H/D exchange by GC–ESI/MS was applied to 11 stimulants with secondary amino or hydroxyl groups. After H/D exchange, the spectra of the stimulants showed unexchanged, partially exchanged, and fully exchanged ions showing various degrees of exchange. The relative abundances corrected for naturally occurring isotopes of the fully exchanged ions of stimulants, except for etamivan, were in the range 24.3–85.5%. Methylephedrine and cyclazodone showed low H/D exchange efficiency under acidic, neutral, and basic spray solvent conditions and nonexchange for etamivan with an acidic phenolic OH group. The in-ESI-source H/D exchange efficiency by GC–ESI/MS was sufficient to determine the number of hydrogen by elucidation of fragmentation from the spectrum. Therefore, this online H/D exchange technique using GC–ESI/MS has potential as an alternative method for simultaneous H/D exchange of multitarget analytes.Ji, L., Zhang, M., Ma, X., Xu, W., Zheng, G., 2018. Characteristics of mixed sporopollen assemblage from sediments of Dushanzi mud volcano in southern Junggar Basin and indication to the source of mud and debris ejecta. Marine and Petroleum Geology 89, Part 1, 194-201. order to search for the source of muddy eruption debris, a series of erupted mud samples were collected from a corn of the Dushanzi mud volcanoes in southern Junggar Basin, NW China and analyzed for palynological records. Two palynomorph groups were revealed in the mixed sporopollen assemblage from the erupted sediments according to their colors. The light color group, accounting for about 95% of the total, was dominated by the Chenopodiaceae and Artemisia and in a color of faint yellow, indicating an immature stage of organic matter evolution. The dark color group was composed of Cyathidites, Classopollis, Schizaeoisporites, Lygodiumsporites and Rugubivesiculites, in a color of brown yellow, indicating a low maturity to maturity stage of organic matter evolution. The palynomorph records suggested that most of the muddy debris ejecta of the Dushanzi mud volcano might be sourced from the Cenozoic deposits, mainly the Middle-Late Miocene Taxihe and Dushanzi Formations, and a small portion likely from the Lower Cretaceous Tugulu Group. In addition, there is also a possibility that a little part of eruption debris is from the Upper Jurassic Qigu Formation. The Dushanzi anticline occurred strong extrusion and thrust faults in the late Himalayan period, and the oil and gas reservoirs were destroyed and resulted in eruption of the mud volcano in the Dushanzi area.Ji, X., Xu, J., Ning, S., Li, N., Tan, L., Shi, S., 2017. Cometabolic degradation of dibenzofuran and dibenzothiophene by a naphthalene-degrading Comamonas sp. JB. Current Microbiology 74, 1411-1416. sp. JB was used to investigate the cometabolic degradation of dibenzofuran (DBF) and dibenzothiophene (DBT) with naphthalene as the primary substrate. Dehydrogenase and ATPase activity of the growing system with the presence of DBF and DBT were decreased when compared to only naphthalene in the growing system, indicating that the presence of DBF and DBT inhibited the metabolic activity of strain JB. The pathways and enzymes involved in the cometabolic degradation were tested. Examination of metabolites elucidated that strain JB cometabolically degraded DBF to 1,2-dihydroxydibenzofuran, subsequently to 2-hydroxy-4-(3′-oxo-3′H-benzofuran-2′-yliden)but-2-enoic acid, and finally to catechol. Meanwhile, strain JB cometabolically degraded DBT to 1,2-dihydroxydibenzothiophene and subsequently to the ring cleavage product. A series of naphthalene-degrading enzymes including naphthalene dioxygenase, 1,2-dihydroxynaphthalene dioxygenase, salicylaldehyde dehydrogenase, salicylate hydroxylase, and catechol 2,3-oxygenase have been detected, confirming that naphthalene was the real inducer of expression the degradation enzymes and metabolic pathways were controlled by naphthalene-degrading enzymes.Jia, R., Yang, D., Xu, D., Gu, T., 2017. Anaerobic corrosion of 304 stainless steel caused by the Pseudomonas aeruginosa biofilm. Frontiers in Microbiology 8, 2335. doi: 10.3389/fmicb.2017.02335. aeruginosa is a ubiquitous bacterium capable of forming problematic biofilms in many environments. They cause biocorrosion of medical implants and industrial equipment and infrastructure. Aerobic corrosion of P. aeruginosa against stainless steels has been reported by some researchers while there is a lack of reports on anaerobic P. aeruginosa corrosion in the literature. In this work, the corrosion by a wild-type P. aeruginosa (strain PAO1) biofilm against 304 stainless steel (304 SS) was investigated under strictly anaerobic condition for up to 14 days. The anaerobic corrosion of 304 SS by P. aeruginosa was reported for the first time. Results showed that the average sessile cell counts on 304 SS coupons after 7- and 14-day incubations were 4.8 × 107 and 6.2 × 107 cells/cm2, respectively. Scanning electron microscopy and confocal laser scanning microscopy corroborated the sessile cell counts. The X-ray diffraction analysis identified the corrosion product as iron nitride, confirming that the corrosion was caused by the nitrate reducing biofilm. The largest pit depths on 304 SS surfaces after the 7- and 14-day incubations with P. aeruginosa were 3.9 and 7.4 μm, respectively. Electrochemical tests corroborated the pitting data.Jiang, R., Jiao, Y., Zhang, P., Liu, Y., Wang, X., Huang, Y., Zhang, Z., Xu, F., 2017. Twin derivatization strategy for high-coverage quantification of free fatty acids by liquid chromatography–tandem mass spectrometry. Analytical Chemistry 89, 12223–12230. fatty acids (FFAs) are vitally important components of lipids that modulate biological metabolism in various ways. Although the molecular structures are simple, the analysis of FFAs is still challenging due to their unique properties and wide concentration range. In the present study, a high-coverage liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was established for the quantification of FFAs in serum samples using two structural analogues 5-(dimethylamino)naphthalene-1-sulfonyl piperazine (Dns-PP) and (diethylamino)naphthalene-1-sulfonyl piperazine (Dens-PP) as twin derivatization reagents. The Dns labeling of FFAs could significantly enhance their MS response via the introduction of the easily ionizable moiety of a tertiary amine-containing part and aid fragmentation in the multiple reaction monitoring (MRM) mode. Our results demonstrated that the detection sensitivities of FFAs were increased by 50–1500 fold compared with the nonderivatization method. At the same time, Dens-labeled standards were used as one-to-one internal standards to ensure accurate quantifications. Thirty-eight FFAs, covering short-, medium-, and long-chain, could be quantified in wide dynamic range with the lower limit of quantification (LLOQ) varied from 2 to 20 nM. Using this method, we analyzed serum FFAs in rat models of cisplatin-induced nephrotoxicity and irinotecan-induced gastrointestinal toxicity, respectively. The findings were further compared with those revealed by previous untargeted metabolomics. The results indicate that twin derivatization-based LC-MS provides a more accurate view of global FFA alternation and has great application potential in the fields of targeted metabolomics.Jiang, W., Li, Y., Xiong, Y., 2018. The effect of organic matter type on formation and evolution of diamondoids. Marine and Petroleum Geology 89, 714-720. series of anhydrous pyrolysis experiments, using sealed gold tubes, were performed on three types of kerogen to investigate the effect organic matter type has on the generation and evolution of thermogenic diamondoids. Based on the compositional variation of pyrolysis products, the cracking of kerogens can be divided into three stages: oil generation (0.6%–1.5% EasyRo), wet-gas generation (1.5%–2.1% EasyRo) and dry-gas generation (>2.1% EasyRo). The experimental results indicate that diamondoids were mainly generated in the oil and wet-gas generation stages and decomposed in the dry-gas generation stage. In addition to thermal maturity, the formation of diamondoids is also influenced by the type of organic matter. Type I and IIA kerogens produced more diamondoids than Type III kerogen, and diamondoids generated from Type III kerogen were dominantly adamantanes. Therefore, the concentration and concentration ratios of diamondoids can be used to assess the maturity of source rocks (1.0%–1.5% EasyRo) and determine the type of organic matter (1.0%–2.0% EasyRo). Isomerization ratios of diamondoids depend mainly on thermal maturity and the type of organic matter has little effect. The use of isomerization ratios to determine thermal maturity is best for source rocks at higher maturity levels (1.5%–3.0% EasyRo). Therefore, bivariate diagrams of concentration versus isomerization indices of diamondoids (e.g., DMAs/MDs vs. DMAI-1 and DMAs/MDs vs. TMAI-1) can be used to evaluate the source rock maturity over a wider EasyRo range (1.0%–3.0% EasyRo) than single diamondoid parameters. As there are differences in the concentration and distribution of diamondoids in the extracts of three source rocks, the possibility exists to use diamondoid indices of immature rocks to determine the type of source rock.Jiang, W., Lin, M., 2018. Molecular dynamics investigation of conversion methods for excess adsorption amount of shale gas. Journal of Natural Gas Science and Engineering 49, 241-249. investigations of shale gas found within shale formations, the conversion of the experimentally determined excess adsorption amount to the absolute amount is crucial to the interpretation of experimental adsorption data. In our study, the excess isotherms of a shale sample from the Longmaxi Formation in China are converted to absolute ones using existing methods. Keeping in mind that the results differ widely across methods and that the accuracies of these methods are poorly understood, we take a first step towards revealing and evaluating the possible discrepancies. We construct a molecular dynamics (MD) model considering methane adsorption in nanometer channels of different widths, and the model is able to calculate the excess and absolute adsorption amounts. Our simplified MD model is proved to be able to reproduce the excess adsorption isotherms of the shale sample through comparison with experimental data. We also evaluate existing conversion methods for calculation of the excess adsorption amount based on MD results. The methods that use predetermined adsorbed-phase density values usually underestimate the absolute amount. Further, the modified Langmuir and T?th equation methods underestimate results under most conditions. The relative error is large at higher pressure, higher temperature, and in smaller channels, and it can be as large as45%. Our study will serve to remind researchers about uncertainty of the results these methods, which can be useful in application.Jin, C., Li, C., Algeo, T.J., Cheng, M., Lei, L., Zhang, Z., Shi, W.E.I., 2017. Evidence for marine redox control on spatial colonization of early animals during Cambrian Age 3 (c. 521–514 Ma) in South China. Geological Magazine 154, 1360-1370. early Cambrian Period was a key interval in Earth history with regard to changes in both ocean chemistry and animal evolution. Although increasing ocean ventilation has been widely assumed to have played a key role in the rapid appearance, diversification and spatial colonization of early animals, this relationship is in fact not firmly established. Here, we report a high-resolution Fe-C-S-Al-Ti geochemical study of the lower Cambrian Wangjiaping section from an outer-shelf setting of the Yangtze Sea of South China. Iron speciation data document a redox transition from dominantly euxinic to ferruginous conditions during Cambrian Age 3 (c. 521–514 Ma). Interpretation of coexisting pyrite sulphur isotope (δ34Spy) records from Wangjiaping reveals relatively high marine sulphate availability at Wangjiaping. Furthermore, Wangjiaping section shows lower δ34Spy (?2.1±5.3‰) and lower TOC (2.4±1.1%) values but higher positive correlation (R 2 = 0.66, p < 0.01) between TOC and Fepy/FeHR relative to deeper sections reported previously, suggesting that euxinia developed at Wangjiaping in response to increasing marine productivity and organic matter-sinking fluxes. Our reconstructed redox conditions and fossils at Wangjiaping in comparison with previously well-studied strata in the inner-shelf Xiaotan and Shatan sections suggest that planktonic and benthic planktonic trilobites with bioturbation appeared in the oxic water columns, whereas only planktonic trilobites without bioturbation occurred within the anoxic (even euxinic) water columns during Cambrian Age 3. This finding indicates that spatial heterogeneity of redox conditions in the shelves had an important effect on early animal distribution in the Yangtze Block.Jin, L., Hawthorne, S., Sorensen, J., Pekot, L., Kurz, B., Smith, S., Heebink, L., Herdegen, V., Bosshart, N., Torres, J., Dalkhaa, C., Peterson, K., Gorecki, C., Steadman, E., Harju, J., 2017. Advancing CO2 enhanced oil recovery and storage in unconventional oil play—Experimental studies on Bakken shales. Applied Energy 208, 171-183. well logs and core data show that there is significant oil content in Bakken shales, the oil transport behavior in these source rocks is still not well understood. This lack of understanding impedes the drilling and production operations in the shale members. A series of experiments were conducted to investigate the rock properties of the Bakken shales and how to extract oil from the shales using supercritical CO2. High-pressure mercury injection tests showed that pore throat radii are less than 10 nm for most pores in both the upper and lower Bakken samples. Such small pore sizes yield high capillary pressure in the rock and make fluid flow difficult. Total organic carbon content was measured using 180 shale samples, and kerogen was characterized by Rock-Eval pyrolysis, which indicated considerable organic carbon present (10–15 wt%) in the shales. However, oil and gas are difficult to mobilize from organic matter using conventional methods. A systematic experimental procedure was carried out to reveal the potential for extracting hydrocarbons from the shale samples using supercritical CO2 under typical Bakken reservoir conditions (e.g., 34.5 MPa and 110 °C). Results showed that supercritical CO2 enables extraction of a considerable portion (15–65%) of hydrocarbons from the Bakken shales within 24 h. Measurement of CO2 adsorption isotherm showed that Bakken shale has a considerable capability to trap CO2 (up to 17 mg/g) under a wide range of pressures. The experimental results suggest the possibility of using supercritical CO2 injection to increase the ultimate oil recovery and store a considerable quantity of CO2 in the Bakken Formation.Jin, Y.-S., Cate, J.H.D., 2017. Metabolic engineering of yeast for lignocellulosic biofuel production. Current Opinion in Chemical Biology 41, 99-106. of biofuels from lignocellulosic biomass remains an unsolved challenge in industrial biotechnology. Efforts to use yeast for conversion face the question of which host organism to use, counterbalancing the ease of genetic manipulation with the promise of robust industrial phenotypes. Saccharomyces cerevisiae remains the premier host for metabolic engineering of biofuel pathways, due to its many genetic, systems and synthetic biology tools. Numerous engineering strategies for expanding substrate ranges and diversifying products of S. cerevisiae have been developed. Other yeasts generally lack these tools, yet harbor superior phenotypes that could be exploited in the harsh processes required for lignocellulosic biofuel production. These include thermotolerance, resistance to toxic compounds generated during plant biomass deconstruction, and wider carbon consumption capabilities. Although promising, these yeasts have yet to be widely exploited. By contrast, oleaginous yeasts such as Yarrowia lipolytica capable of producing high titers of lipids are rapidly advancing in terms of the tools available for their metabolic manipulation.Jing, Y., Armstrong, R.T., Mostaghimi, P., 2017. Impact of mineralization on digital coal properties. Energy & Fuels 31, 11558–11568. seam gas (CSG) is an unconventional energy resource, whereby production is mainly controlled by the underlying fracture networks, known as “cleats”. The natural cleats are generally mineralized during diagenesis, which significantly reduces fracture conductivity because of the more tortuous flow pathways and smaller cross-sectional area perpendicular to the flow. This work aims at characterizing the mineral fillings of the coal cleat network by utilizing X-ray microcomputed tomography (micro-CT) imaging to investigate the effect of minerals on the petrophysical properties of coal. We apply a high-resolution micro-CT to obtain a 3D digital representation of a mineralized coal sample collected from Moura mine of Bowen Basin. The main components of the coal sample, including coal matrix, cleats, and minerals, are individually analyzed to give the statistics of cleat orientation, length, and thickness using quantitative image analysis. According to the measured statistical data, digital coal models with mineralization are stochastically constructed and then used for simulation to obtain petrophysical properties. Our results show that minerals in cleats can significantly reduce the conductivity of the cleat network by reducing the permeability by up to 75% and increasing the tortuosity by 21%. In addition, by studying the deformed sample under external stresses, we find that porosity reduction due to compression of the cleat network with minerals is significantly less than models without minerals. In addition, mineralization has a detrimental effect on the matrix–fracture contact area, which is reduced by 17% with the addition of minerals. Lastly, by comparing digital coal models to the original micro-CT images, the mineralized digital coal models are found to be more representative in terms of permeability estimation, with an error of only 4.4%.Jochum, L.M., Chen, X., Lever, M.A., Loy, A., J?rgensen, B.B., Schramm, A., Kjeldsen, K.U., 2017. Depth distribution and assembly of sulfate-reducing microbial communities in marine sediments of Aarhus Bay. Applied and Environmental Microbiology 83, 15 e01547-17.: Most sulfate-reducing microorganisms (SRMs) present in subsurface marine sediments belong to uncultured groups only distantly related to known SRMs, and it remains unclear how changing geochemical zones and sediment depth influence their community structure. We mapped the community composition and abundance of SRMs by amplicon sequencing and quantifying the dsrB gene, which encodes dissimilatory sulfite reductase subunit beta, in sediment samples covering different vertical geochemical zones ranging from the surface sediment to the deep sulfate-depleted subsurface at four locations in Aarhus Bay, Denmark. SRMs were present in all geochemical zones, including sulfate-depleted methanogenic sediment. The biggest shift in SRM community composition and abundance occurred across the transition from bioturbated surface sediments to nonbioturbated sediments below, where redox fluctuations and the input of fresh organic matter due to macrofaunal activity are absent. SRM abundance correlated with sulfate reduction rates determined for the same sediments. Sulfate availability showed a weaker correlation with SRM abundances and no significant correlation with the composition of the SRM community. The overall SRM species diversity decreased with depth, yet we identified a subset of highly abundant community members that persists across all vertical geochemical zones of all stations. We conclude that subsurface SRM communities assemble by the persistence of members of the surface community and that the transition from the bioturbated surface sediment to the unmixed sediment below is a main site of assembly of the subsurface SRM community. Importance :Sulfate-reducing microorganisms (SRMs) are key players in the marine carbon and sulfur cycles, especially in coastal sediments, yet little is understood about the environmental factors controlling their depth distribution. Our results suggest that macrofaunal activity is a key driver of SRM abundance and community structure in marine sediments and that a small subset of SRM species of high relative abundance in the subsurface SRM community persists from the sulfate-rich surface sediment to sulfate-depleted methanogenic subsurface sediment. More generally, we conclude that SRM communities inhabiting the subsurface seabed assemble by the selective survival of members of the surface community. Johns, C.W., Lee, A.B., Springer, T.I., Rosskopf, E.N., Hong, J.C., Turechek, W., Kokalis-Burelle, N., Finley, N.L., 2017. Using NMR-based metabolomics to monitor the biochemical composition of agricultural soils: A pilot study. European Journal of Soil Biology 83, 98-105. metabolomics plays a major role in the study of complex living systems. While there is a known connection between soil microbial metabolism and productivity in agricultural systems, very few researchers describe the application of NMR to the evaluation of agricultural soil metabolomes. Here, we introduce a simple protocol for the NMR metabolic analysis of biochemical compounds from agricultural soils where microbial communities are influenced by the application of anaerobic soil disinfestation (ASD). Following ASD treatment, aqueous metabolites were extracted from soil samples and the compound identities of the resulting mixtures were determined using 1D and 2D NMR in combination with metabolome database searches. It was found that the ASD treatments altered the metabolite composition of soil as evidenced by the detection of natural biochemical products such as organic acids. Principle component analysis revealed distinct biochemical differences between non-treated and ASD-treated soils. Our findings support that this protocol is efficacious in the rapid and reliable determination of metabolite profiles even within complex mixtures obtained from ASD-treated agricultural soils. Thus, NMR spectroscopy has the potential to impact soil science by investigating the adaptable biochemical fingerprint of soil metabolomes in agricultural fields, knowledge of which may be used to improve crop production.Johnson, B.W., Poulton, S.W., Goldblatt, C., 2017. Marine oxygen production and open water supported an active nitrogen cycle during the Marinoan Snowball Earth. Nature Communications 8, Article 1316. Neoproterozoic Earth was punctuated by two low-latitude Snowball Earth glaciations. Models permit oceans with either total ice cover or substantial areas of open water. Total ice cover would make an anoxic ocean likely, and would be a formidable barrier to biologic survival. However, there are no direct data constraining either the redox state of the ocean or marine biological productivity during the glacials. Here we present iron-speciation, redox-sensitive trace element, and nitrogen isotope data from a Neoproterozoic (Marinoan) glacial episode. Iron-speciation indicates deeper waters were anoxic and Fe-rich, while trace element concentrations indicate surface waters were in contact with an oxygenated atmosphere. Furthermore, synglacial sedimentary nitrogen is isotopically heavier than the modern atmosphere, requiring a biologic cycle with nitrogen fixation, nitrification and denitrification. Our results indicate significant regions of open marine water and active biologic productivity throughout one of the harshest glaciations in Earth history.Johnson, M.R., Tyner, D.R., Conley, S., Schwietzke, S., Zavala-Araiza, D., 2017. Comparisons of airborne measurements and inventory estimates of methane emissions in the Alberta upstream oil and gas sector. Environmental Science & Technology 51, 13008-13017. measurements of methane emissions from oil and gas infrastructure were completed over two regions of Alberta, Canada. These top-down measurements were directly compared with region-specific bottom-up inventories that utilized current industry-reported flaring and venting volumes (reported data) and quantitative estimates of unreported venting and fugitive sources. For the 50 × 50 km measurement region near Red Deer, characterized by natural gas and light oil production, measured methane fluxes were more than 17 times greater than that derived from directly reported data but consistent with our region-specific bottom-up inventory-based estimate. For the 60 × 60 km measurement region near Lloydminster, characterized by significant cold heavy oil production with sand (CHOPS), airborne measured methane fluxes were five times greater than directly reported emissions from venting and flaring and four times greater than our region-specific bottom up inventory-based estimate. Extended across Alberta, our results suggest that reported venting emissions in Alberta should be 2.5 ± 0.5 times higher, and total methane emissions from the upstream oil and gas sector (excluding mined oil sands) are likely at least 25–50% greater than current government estimates. Successful mitigation efforts in the Red Deer region will need to focus on the >90% of methane emissions currently unmeasured or unreported.Jolley, D.W., Daly, R.J., Ebinghaus, A., Kemp, D.B., Gilmour, I., Mac Niocaill, C., Kelley, S.P., 2017. Centennial to decadal vegetation community changes linked to orbital and solar forcing during the Dan-C2 hyperthermal event. Journal of the Geological Society 174, 1019-1030. close to the K–Pg boundary, the Boltysh meteorite crater, Ukraine, preserves >400?m of lacustrine sedimentary rocks that include a record of the early Danian Dan-C2 hyperthermal event. Abundant pollen, spores and algae recovered from these sediments have yielded a cyclic record of plant ecology change paced by c. 21?kyr orbital precession cycles. New, higher resolution sampling across the inception of the Dan-C2 hyperthermal event has identified oscillations in vegetation community ecology at sub-orbital periods of c. 2?kyr, c. 200?years and c. 11?years. These are consistent with possible Hallstatt, DeVreis–Suess and Schwabe solar cycles, respectively. Rapid regime shift from savanna to a mesic forest ecosystem was paced by c. 21?kyr precession, with the shift probably occurring in <200?years. Prior to regime shift, c. 2?kyr (i.e. possible Hallstatt) oscillations between mesic- and winterwet-dominated plant communities increased in intensity, suggestive of ecological flickering. Supplementary material: Detrended correspondence and changepoint analysis, palynological frequency data for DCA groups and core photographs are available at , B.B., 2017. Microbial life in deep subseafloor coal beds. Proceedings of the National Academy of Sciences 114, 11568-11570. beneath the seafloor, microbial communities thrive on the leftovers of organic material that in the past settled down from the surface layers of the ocean to the sediment. As the organic matter was buried deeper and deeper over geological time it became increasingly recalcitrant to microbial degradation. Microbial cells that still persist in these ancient deposits appear to survive at the limit of starvation. However, it is estimated that half of all bacteria and most of all archaea in the ocean live under such nutrient-poor conditions in the deep seabed (1). This deep biosphere extends around the globe and, on a long geological time scale, interacts with the chemistry of the sea water. Thus, the nutrients in the ocean and the oxygen in the atmosphere are affected by the efficiency with which subseafloor microorganisms degrade and remineralize the buried organic matter. Microbiologists who study this deep biosphere have been searching for the limits to life in the subsurface and have set new records in finding even deeper and older microbial communities. Trembath-Reichert et al. now report in PNAS (2) that microorganisms live in 20 million-y-old coal beds buried 2 km beneath the seafloor and that the organisms are able to take up nutrients and grow when kept for years under seminatural conditions in the laboratory. Trembath-Reichert et al. (2) studied deep lignite coal beds that had been discovered by seismic profiling at 1,200-m water depth off the east coast of Japan. A forearc basin is here formed by the subduction of the Pacific Ocean plate, which has gradually also pulled down the continental plate. During the early Miocene, organic remains of rich coastal forests were buried in warm backswamps that later subsided into the cold ocean and formed lignite seams, which were subsequently overlaid by 2-km-thick marine shales. Expedition ...Junium, C.K., Meyers, S.R., Arthur, M.A., 2018. Nitrogen cycle dynamics in the Late Cretaceous Greenhouse. Earth and Planetary Science Letters 481, 404-411. attention has been paid to the origin of anomalously low nitrogen isotope values during the Late Cretaceous. Nitrogen isotope values are often as low as ?3‰?3‰ and are typically less than +2‰+2‰, even in relatively organic matter-lean sediments. Here we evaluate nitrogen isotope variability during a relatively quiescent phase of the Late Cretaceous Greenhouse, between Oceanic Anoxic Events 2 and 3, using the black shales of Demerara Rise (DR). Selection of this site allows us to isolate some of the factors that control nitrogen cycle dynamics and contribute to low nitrogen isotope values. New N-isotope measurements from ODP Site 1259 reveal δ15δ15N values that range from +0.2‰+0.2‰ to ?3.5‰ and oscillate by 1.5‰ to 3‰ over 1.6 million years (Ma). Temporal calibration of our data using a new astronomical time scale reveals a strong ～100 thousand year (ka) eccentricity cyclicity in δ15δ15N. We attribute this cyclicity to oscillations in the position of the intertropical convergence zone (ITCZ) over DR that modulate upwelling intensity, chemocline depth and the degree of 15N-depletion. We also recognize a statistically significant correlation (p=0.0022)(p=0.0022) between the TEX86 indices and δ15δ15N, with the lowest δ15δ15N corresponding to the highest TEX86 indices. This relationship suggests that the activity and ecology of ammonia oxidizing Thaumarchaeota and the δ15δ15N of dissolved inorganic nitrogen utilized by primary producers are linked. We therefore interpret the observed variability in the δ15δ15N data and TEX86 indices as primarily reflecting fluctuation of upwelling intensity and chemocline depth, and the significant inverse relationship between these data sets suggests that caution should be exercised when interpreting the TEX86 in terms of temperature in similar paleoenvironmental settings.Kadnikov, V.V., Frank, Y.A., Mardanov, A.V., Beletsky, A.V., Ivasenko, D.A., Pimenov, N.V., Karnachuk, O.V., Ravin, N.V., 2017. Variability of the composition of the microbial community of the deep subsurface thermal aquifer in Western Siberia. Microbiology 86, 765-772. deep subsurface biosphere is one of the least studied ecosystems on Earth, containing communities of extremophilic microorganisms. The present work was aimed at molecular genetic characterization of microbial communities of underground thermal waters in Western Siberia, lying at depths of 2–3 km. Water samples were collected from the 5P oil-exploration well, drilled to a depth of 2.8 km near the village Chazhemto (Tomsk region). The water had a temperature of about 20°C, a neutral pH and a low redox potential (–304 mV). Underground aquifers have a complex structure and may contain both planktonic microorganisms and those immobilized on the surface of rocks in the form of biofilms, which may be washed out and detected in the water flowing out of the well. Community composition was analyzed by amplification and pyrosequencing of the 16S rRNA gene fragments in seven water samples taken at different times during 26 hours. Bacteria, which constituted about half of the community, were represented mainly by uncultured lineages of the phyla Firmicutes, Ignavibacteria, Chloroflexi, Bacteroidetes, and Proteobacteria. Archaea belonged mainly to known methanogens of the genera Methanothermobacter, Methanosaeta, and Methanomassiliicoccus. Analysis of the samples taken at different times revealed large variations in the content of most groups of bacteria, with a decrease in Firmicutes abundance accompanied by an increase in the shares of Ignavibacteria and Chloroflexi. The share of archaea of the genus Methanothermobacter varied slightly during the day, while significant variations were observed for the phylotypes assigned to Methanosaeta and Methanomassiliicoccus. Hydrogenotrophic archaea of the genus Methanothermobacter are probably a permanent component of the microbial community occurring in the planktonic state, while most of the identified groups of bacteria are present in biofilms or spatially localized parts of the underground water reservoir, the material of which accidentally enters the well. Original Russian Text ? V.V. Kadnikov, Yu.A. Frank, A.V. Mardanov, A.V. Beletsky, D.A. Ivasenko, N.V. Pimenov, O.V. Karnachuk, N.V. Ravin, 2017, published in Mikrobiologiya, 2017, Vol. 86, No. 6, pp. 739–747.Kaiho, K., Oshima, N., 2017. Site of asteroid impact changed the history of life on Earth: the low probability of mass extinction. Scientific Reports 7, Article 14855. million years ago, an asteroid approximately 9?km in diameter hit the hydrocarbon- and sulfur-rich sedimentary rocks in what is now Mexico. Recent studies have shown that this impact at the Yucatan Peninsula heated the hydrocarbon and sulfur in these rocks, forming stratospheric soot and sulfate aerosols and causing extreme global cooling and drought. These events triggered a mass extinction, including dinosaurs, and led to the subsequent macroevolution of mammals. The amount of hydrocarbon and sulfur in rocks varies widely, depending on location, which suggests that cooling and extinction levels were dependent on impact site. Here we show that the probability of significant global cooling, mass extinction, and the subsequent appearance of mammals was quite low after an asteroid impact on the Earth’s surface. This significant event could have occurred if the asteroid hit the hydrocarbon-rich areas occupying approximately 13% of the Earth’s surface. The site of asteroid impact, therefore, changed the history of life on Earth.Kaiser, D., Konovalov, S., Schulz-Bull, D.E., Waniek, J.J., 2017. Organic matter along longitudinal and vertical gradients in the Black Sea. Deep Sea Research Part I: Oceanographic Research Papers 129, 22-31. studied organic matter in the central Black Sea and its northeastern and northwestern shelf break within three weeks in November 2013 to test the hypothesis that in situ production could explain lateral and vertical variability in its composition and distribution. The wide spatial coverage over a short period of time achieved during this study revealed longitudinal variability in organic matter characteristics reflecting productivity at the Black Sea surface. Particulate organic matter was dominantly autochthonous in the central Black Sea. Allochthonous influence of river discharge was only traced on the northwestern shelf by high concentrations but low freshness of particulate organic matter. Compared to the NW shelf break and central Black Sea, primary production was high near the NE shelf break, likely fueled by input from the Azov Sea. Vertical patterns were similar throughout the deep Black Sea and appeared to also be governed by in situ processes rather than reflect variability in the surface water. As concentrations of organic matter decreased with depth, its elemental and isotopic composition indicated chemoautotrophic production at the oxic-anoxic interface and organic matter degradation in the benthic boundary layer. Though profiles of dissolved organic carbon indicated a minor source in anoxic deep water, likely linked to chemosynthesis and reflux from sediments, a negative deviation of concentrations from a conservative mixing line between two endmembers suggested net removal of labile dissolved organic carbon.Kallistova, A.Y., Merkel, A.Y., Tarnovetskii, I.Y., Pimenov, N.V., 2017. Methane formation and oxidation by prokaryotes. Microbiology 86, 671-691. review deals with systematization and generalization of new information concerning the phylogenetic and functional diversity of prokaryotes involved in the methane cycle. Methane is mostly produced by methanogenic archaea, which are responsible for the terminal stage of organic matter decomposition in a number of anoxic ecotopes. Although phylogeny, physiology, and biochemistry of methanogens have been extensively studied, important discoveries were made recently. Thus, members of deep phylogenetic lineages within the Euryarchaeota phylum (Methanomassiliicoccales, “Candidatus Methanofastidiosa,” “Methanonatronarchaeia”) and even outside it (“Ca. Verstraetearchaeota” and “Ca. Bathyarchaeota”) were reported to carry out methyl-reducing methanogenesis. Moreover, evidence was obtained on aerobic methane production by marine heterotrophic bacteria, which demethylate polysaccharide esters of methylphosphonic acid. Methanotrophic microorganisms oxidize methane both aerobically and anaerobically, decreasing significantly the release of this greenhouse gas into the atmosphere. In the presence of oxygen methane is oxidized by methanotrophic members of Alpha- and Gammaproteobacteria, as well as by Verrucomicrobia. Methanotrophic gammaproteobacteria have been recently revealed in hypoxic and even anoxic environments, where they probably oxidize methane either in a trophic consortium with oxygenic phototrophs and/or methylotrophs or using electron acceptors other than oxygen. Anaerobic methane oxidation has been known for a long time. Sulfat- and nitrate-dependent anaerobic methane oxidation carried out by the ANME archaea via reverse methanogenesis are the best studied processes. While metal-dependent anaerobic methane oxidation is considered possible, the mechanisms and agents responsible for this process have not been reliably identified. Intracellular oxygen production during nitrite-dependent anaerobic methane oxidation was shown for bacteria “Ca. Methylomirabilis oxyfera.” These findings stimulate interest in the processes and microorganisms of the methane cycle. Original Russian Text ? A.Yu. Kallistova, A.Yu. Merkel, I.Yu. Tarnovetskii, N.V. Pimenov, 2017, published in Mikrobiologiya, 2017, Vol. 86, No. 6, pp. 661–683.Kallus, Y., Miller, J.H., Libby, E., 2017. Paradoxes in leaky microbial trade. Nature Communications 8, Article 1361. produce metabolic resources that are important for cell growth yet leak into the environment. Other microbes can use these resources, adjust their own metabolic production accordingly, and alter the resources available for others. We analyze a model in which metabolite concentrations, production regulation, and population frequencies coevolve in the simple case of two cell types producing two metabolites. We identify three paradoxes where changes that should intuitively benefit a cell type actually harm it. For example, a cell type can become more efficient at producing a metabolite and its relative frequency can decrease—or alternatively the total population growth rate can decrease. Another paradox occurs when a cell type manipulates its counterpart’s production so as to maximize its own instantaneous growth rate, only to achieve a lower final growth rate than had it not manipulated. These paradoxes highlight the complex and counterintuitive dynamics that emerge in simple microbial economies.Kamel, A.H., 2017. A technical review of radial jet drilling. Journal of Petroleum and Gas Engineering 8, 79-89. jet drilling (RJD) is an unconventional drilling technique that uses the jet energy of high velocity fluids to drill laterals with different geometries in both conventional and unconventional reservoirs. Many case studies available worldwide have proven RJD as a viable alternative to traditional stimulation techniques, especially in marginal fields. RJD has a lot of application in the oil and gas industry. It is a cost effective completion technique to reach the untapped sweet spots, by-pass damaged zones near wellbore, re-complete old wells, and many other applications. The present paper outlines the basics of newly developed radial jet drilling technology. Advances in technologies, developments, forces imposed, jet fluid hydraulics, procedures, applications, and challenges of RJD are reviewed in this paper. Simulation studies and several worldwide case studies are discussed to evaluate the RJD technology.Kang, S., Shin, K.-H., Kim, J.-H., 2017. Occurrence and distribution of hydroxylated isoprenoid glycerol dialkyl glycerol tetraethers (OH-GDGTs) in the Han River system, South Korea. Acta Geochimica 36, 367-369. investigated the occurrence and distribution of terrestrial-derived hydroxylated isoprenoid glycerol dialkyl glycerol tetraethers (OH-GDGTs) in the Han River system and their potential impact on the application of the ring index of OH-GDGTs (RI-OH) as a sea surface temperature (SST) proxy in the eastern Yellow Sea. Thereby, we analyzed various samples collected along the Han River and from its surrounding areas (South Korea, n = 34). The OH-GDGTs were found in all samples investigated. OH-GDGT-0 was the dominant OH-GDGT component in the estuary and marine samples while OH-GDGT-2 was generally dominant in the soils, the lake sediments and the river suspended particulate matter (SPM). Our results thus suggests a possible warm bias of the RI-OH-derived summer SSTs in the coastal zone to which a large amount of terrestrial organic matter is being supplied. Further studies are necessary to better assess the applicability of the RI-OH proxy in the eastern Yellow Sea.Karayi?it, A.?., Mastalerz, M., Oskay, R.G., Querol, X., Lieberman, N.R., 2017. Meso- and microporosity of the subbituminous kM2 coal seam (Soma, Turkey) and its relationship with coal characteristics. International Journal of Coal Geology 184, 73-87. study focuses on meso- and microporosity of the subbituminous kM2 coal seam and its relation to coal characteristics. The coal seam is being mined in an underground coal mine at the Eynez sector in the Soma Basin (Western Turkey). The analysed coal samples are characterized by low moisture (avg. 8.2%, on air-dry basis) and total S content (avg. 1.5%, on dry basis), and moderate ash yield (avg. 26.1%, on dry basis). The predominant maceral group is huminite, in which telohuminite is the dominant maceral subgroup (up to 57.1 vol.%, on whole-coal basis), whereas liptinite and inertinite maceral groups occur in low but variable proportions. Mineralogically, the samples are composed of quartz, clay minerals (kaolinite and illite), carbonates, pyrite, and rarely feldspars and gypsum. Statistical and SEM-EDX analyses indicate that the majority of elements have inorganic affinity, particularly the aluminosilicate minerals. The specific surface area and volume of mesopores, and average mesopore size determined by low pressure N2 adsorption, range widely throughout the studied seam section. Micropore characteristics, analysed by low-pressure CO2 adsorption, demonstrate that micropores are abundant, and specific surface area and volume of micropores vary widely. Surface area and volume of mesopores are slightly higher in the lower part of the seam, whereas the opposite was observed for surface area and volume of microspores. These trends may imply that hydrostatic pressure has little impact upon mesopore characteristics, although increased ash yields in the lower part of the seam suggest that minerals are the major contributor of coal mesopores. Furthermore, total C contents and huminite macerals, particularly telohuminite, display positive correlations with micropore characteristics. Thus, the variations in the microporosity are mainly correlated with the proportion of organic matter (macerals) in the analysed samples. The contents of aluminosilicate-affiliated elements display moderate to strong positive correlations with surface area and volume of mesopores, and total S and B contents display weak positive correlations with surface area and volume of micropores. The element B likely precipitated from porewater or intra-seam solutions during coalification and was absorbed by macerals having abundant microporosity. The abundance of micropores along with frequent disseminated pyrite crystals within the reactive macerals (telohuminite group) and higher total S contents in the upper parts of the seam could increase the risk of self-heating. Therefore, care should be taken to use caution when mining the upper part of the seam.Kaya, E., Zarrouk, S.J., 2017. Reinjection of greenhouse gases into geothermal reservoirs. International Journal of Greenhouse Gas Control 67, 111-129. work addresses the feasibility of reinjecting H2S and CO2, captured and dissolved in effluents from the geothermal field, back into the geothermal reservoir. A series of numerical modelling scenarios was used to assess the effect of NCG (non-condensable gases) reinjection on energy recovery, understand permanent trapping, and forecast potential NCG breakthrough into production wells.Although the gas species from geothermal systems typically have moderate solubility in water, formation of gas phases at lower pressures and/or the shallow subsurface requires careful consideration of the injection rate and composition of NCG. Possible fluid paths and distribution of gas components were investigated to estimate the NCG storage capability of a reservoir, and evaluate the potential risk of the reinjected NCG growing into fingers that may lead to an early breakthrough or potential leakage to the ground surface.Modified versions of benchmark geothermal reinjection models were constructed with initial conditions of a liquid-dominated geothermal system. The results obtained show that the effects of injection depend on the reinjection and production wells arrangement and the recharge conditions. The risk of leakage to the surface is very limited since the injected NCG remain in the liquid phase.Keelor, J.D., Zambrzycki, S., Li, A., Clowers, B.H., Fernández, F.M., 2017. Atmospheric pressure drift tube ion mobility–Orbitrap mass spectrometry: Initial performance characterization. Analytical Chemistry 89, 11301-11309. pressure drift tube ion mobility spectrometry (AP-DTIMS) was coupled with Fourier transform Orbitrap mass spectrometry. The performance capabilities of this versatile new arrangement were demonstrated for different DTIMS ion gating operation modes and Orbitrap mass spectrometer parameters with regard to sensitivity and resolving power. Showcasing the optimized AP-DTIMS-Orbitrap MS system, isobaric peptide and sugar isomers were successfully resolved and the identities of separated species validated by high-energy collision dissociation experiments.Keiluweit, M., Wanzek, T., Kleber, M., Nico, P., Fendorf, S., 2017. Anaerobic microsites have an unaccounted role in soil carbon stabilization. Nature Communications 8, Article 1771. represent the largest carbon reservoir within terrestrial ecosystems. The mechanisms controlling the amount of carbon stored and its feedback to the climate system, however, remain poorly resolved. Global carbon models assume that carbon cycling in upland soils is entirely driven by aerobic respiration; the impact of anaerobic microsites prevalent even within well-drained soils is missed within this conception. Here, we show that anaerobic microsites are important regulators of soil carbon persistence, shifting microbial metabolism to less efficient anaerobic respiration, and selectively protecting otherwise bioavailable, reduced organic compounds such as lipids and waxes from decomposition. Further, shifting from anaerobic to aerobic conditions leads to a 10-fold increase in volume-specific mineralization rate, illustrating the sensitivity of anaerobically protected carbon to disturbance. The vulnerability of anaerobically protected carbon to future climate or land use change thus constitutes a yet unrecognized soil carbon–climate feedback that should be incorporated into terrestrial ecosystem models.Keller, B., Schoene, B., 2018. Plate tectonics and continental basaltic geochemistry throughout Earth history. Earth and Planetary Science Letters 481, 290-304. magmas constitute the primary mass flux from Earth's mantle to its crust, carrying information about the conditions of mantle melting through which they were generated. As such, changes in the average basaltic geochemistry through time reflect changes in underlying parameters such as mantle potential temperature and the geodynamic setting of mantle melting. However, sampling bias, preservation bias, and geological heterogeneity complicate the calculation of representative average compositions. Here we use weighted bootstrap resampling to minimize sampling bias over the heterogeneous rock record and obtain maximally representative average basaltic compositions through time. Over the approximately 4 Ga of the continental rock record, the average composition of preserved continental basalts has evolved along a generally continuous trajectory, with decreasing compatible element concentrations and increasing incompatible element concentrations, punctuated by a comparatively rapid transition in some variables such as La/Yb ratios and Zr, Nb, and Ti abundances approximately 2.5 Ga ago. Geochemical modeling of mantle melting systematics and trace element partitioning suggests that these observations can be explained by discontinuous changes in the mineralogy of mantle partial melting driven by a gradual decrease in mantle potential temperature, without appealing to any change in tectonic process. This interpretation is supported by the geochemical record of slab fluid input to continental basalts, which indicates no long-term change in the global proportion of arc versus non-arc basaltic magmatism at any time in the preserved rock record.Khan, M.K., Kwek, W., Kim, J., 2017. Upgrading heavy crude oils and extra heavy fractions in supercritical methanol. Energy & Fuels 31, 12054-12063., we report a method of upgrading unconventional crude oils and extra heavy fractions using supercritical methanol (scMeOH) and compare it to supercritical water (scH2O)-based and pyrolytic upgrading. The yields and properties of upgraded oil are explored as functions of operating parameters (temperature, pressure, and concentration) and feedstocks for high-acid crude oils (Laguna and Bachaquero-13), a heavy crude oil (Rubiales), and a vacuum tower bottom (VTB). As a result, scMeOH upgrading of unconventional crude oils at 400 °C and 30 MPa effectively reduced their asphaltene content to ～0 wt % and increased that of naphtha–diesel fractions to 30–40 wt %. Conversely, a considerable amount of asphaltenes (8.8–10.0 wt %) was present in oil upgraded using scH2O and pyrolysis. Additionally, scMeOH upgrading resulted in a more effective reduction of the total acid number (TAN) of high-acid crude oils (<0.5 mg of KOH/g of oil) compared to values achieved by scH2O and pyrolysis methods. Finally, scMeOH treatment significantly reduced the metal (Ni, V, and Fe) content of the upgraded oil. The effective asphaltene content and TAN reduction realized in scMeOH was attributed to its hydrogen donation and esterification ability, with plausible mechanisms of scMeOH, scH2O, and pyrolytic upgrading presented and discussed in detail.Khatibi, S., Ostadhassan, M., Tuschel, D., Gentzis, T., Bubach, B., Carvajal-Ortiz, H., 2018. Raman spectroscopy to study thermal maturity and elastic modulus of kerogen. International Journal of Coal Geology 185, 103-118. organic-rich oil-producing mudrocks have been studied extensively during the last decade, kerogen, as one the main constituents, is not thoroughly understood. The unknowns about kerogen elevate when it comes to its modulus of elasticity. Since kerogen is not as stiff as inorganic minerals, its presence can have a significant impact on the initiation and propagation of fractures in kerogen-rich formations that should undergo stimulation.This study proposes an approach to estimate modulus of elasticity of kerogen with different thermal maturities using Raman spectroscopy. Various shale samples from the upper and lower members of the Bakken Formation were picked from several wells within the Williston Basin in North Dakota, USA. These samples were analyzed using Rock-Eval (RE) pyrolysis and vitrinite reflectance (%Ro) for thermal maturity. In addition, Raman spectroscopic measurements were made on samples and followed by PeakForce AFM for Young's modulus estimation of the organic matter. First, the Raman responses were correlated with the thermal maturity and then, a correlation was established to show the potential relationship between elastic modulus of organic matter and its Raman response based on the maturity levels.Kiko, R., Biastoch, A., Brandt, P., Cravatte, S., Hauss, H., Hummels, R., Kriest, I., Marin, F., McDonnell, A.M.P., Oschlies, A., Picheral, M., Schwarzkopf, F.U., Thurnherr, A.M., Stemmann, L., 2017. Biological and physical influences on marine snowfall at the equator. Nature Geoscience 10, 852-858. primary productivity in the equatorial Atlantic and Pacific oceans is one of the key features of tropical ocean biogeochemistry and fuels a substantial flux of particulate matter towards the abyssal ocean. How biological processes and equatorial current dynamics shape the particle size distribution and flux, however, is poorly understood. Here we use high-resolution size-resolved particle imaging and Acoustic Doppler Current Profiler data to assess these influences in equatorial oceans. We find an increase in particle abundance and flux at depths of 300 to 600?m at the Atlantic and Pacific equator, a depth range to which zooplankton and nekton migrate vertically in a daily cycle. We attribute this particle maximum to faecal pellet production by these organisms. At depths of 1,000 to 4,000?m, we find that the particulate organic carbon flux is up to three times greater in the equatorial belt (1°?S–1°?N) than in off-equatorial regions. At 3,000?m, the flux is dominated by small particles less than 0.53?mm in diameter. The dominance of small particles seems to be caused by enhanced active and passive particle export in this region, as well as by the focusing of particles by deep eastward jets found at 2°?N and 2°?S. We thus suggest that zooplankton movements and ocean currents modulate the transfer of particulate carbon from the surface to the deep ocean.Kikuchi, J., Yamada, S., 2017. NMR window of molecular complexity showing homeostasis in superorganisms. Analyst 142, 4161-4172. offers tremendous advantages in the analyses of molecular complexity, such as crude bio-fluids, bio-extracts, and intact cells and tissues. Here we introduce recent applications of NMR approaches, as well as next generation sequencing (NGS), for the evaluation of human and environmental health (i.e., maintenance of a homeostatic state) based on metabolic and microbial profiling and data science. We describe useful databases and web tools that are used to support these studies by facilitating the characterization of metabolites from complex NMR spectra. Because the NMR spectra of metabolic mixtures can produce numerical matrix data (e.g., chemical shift versus intensity) with high reproducibility and inter-institution convertibility, advanced data science approaches, such as multivariate analysis and machine learning, are desirable; therefore, we also introduce informatics techniques derived from heterogeneously measured data, such as environmental microbiota, for the extraction of submerged information using data science approaches. We summarize recent studies of microbiomes that are based on these techniques and show that, particularly in human studies, NMR-based metabolic characterization of non-invasive samples, such as feces, can provide a large quantity of beneficial information regarding human health and disease.Kim, A.-R., Kim, H.-S., Cho, G.-C., Lee, J.Y., 2017. Estimation of model parameters and properties for numerical simulation on geomechanical stability of gas hydrate production in the Ulleung Basin, East Sea, Korea. Quaternary International 459, 55-68. process of hydrate dissociation and production induced by depressurization incorporates intricate hydraulic, thermal, and mechanical phenomena. Thus, coupled thermal-hydraulic-mechanical (T-H-M) simulation is critically necessary to evaluate the geomechanical stability of hydrate production in hydrate-bearing sediments (HBS). However, methods of estimating the input model parameters and properties of the target reservoir, in particular in unconsolidated marine sediments, have received limited attention compared to studies on production simulators. The T-H-M properties of the marine sediments change considerably with depth, geological strata, and soil type of each layer. Therefore, it is important that representative layers and their corresponding T-H-M properties should be properly estimated to analyze the stability and productivity of methane gas recovery in the field. This study provides a comprehensive estimation for the model parameters and properties of unconsolidated marine sediments, based on vast data from field seismic surveys and laboratory experimental results with core samples, investigates empirical correlations between model parameters and methane hydrate saturation, and finally summarizes the estimated model parameters and properties, which can possibly be applied to on-going numerical research into stability assessment of the pilot gas hydrate (GH) production test, which is soon to be performed in the Ulleung basin.Kim, J., Kim, J., Hong, S., 2018. Recovery of water and minerals from shale gas produced water by membrane distillation crystallization. Water Research 129, 447-459. gas produced water (SGPW) treatment imposes greater technical challenges because of its high concentration of various contaminants. Membrane distillation crystallization (MDC) has a great potential to manage SGPW since it is capable of recovering both water and minerals at high rates, up to near a zero liquid discharge (ZLD) condition. To evaluate the feasibility of MDC for SGPW treatment, MDC performance indicators, such as water recovery rate, solid production rate (SPR) and specific energy consumption (SEC), were systematically investigated, to our knowledge for the first time, by using actual SGPW from Eagle Ford Shale (USA). The main operating parameters including feed cross-flow velocity (CFV) and crystallization temperature (TCr) were optimized by performing a series of MDC experiments. The results reported that water and minerals were effectively recovered with 84% of recovery rate and 2.72 kg/m2day of SPR under respective optimal operating conditions. Furthermore, the scale mechanism was firstly identified as limiting factor for MDC performance degradation. Lastly, SEC of MDC was estimated to be as low as 28.2 kWh/m3 under ideal optimal operating conditions. Our experimental observations demonstrated that MDC could sustainably and effectively recover water and mineral with low energy consumption from SGPW by optimizing operating condition.Kim, S., Khim, B.-K., Ikehara, M., Takahashi, K., 2017. Relationship between δ15N values of bulk sediments and total organic carbon concentration in response to orbital-scale biogenic opal production in the Bering slope area over the last 600 kyrs. Quaternary International 459, 144-152. opal production in the surface water of the Bering Sea shows clear orbital-scale variations such as interglacial highs and glacial lows. In this study, we examined the variation patterns in δ15N of bulk sediment (δ15Nbulk) reflecting nitrate utilization, and total organic carbon (TOC) concentration in terms of organic carbon (OC) production, in response to the orbital-scale biogenic opal production during the last 600 kyrs at Site U1343 (IODP Exp. 323) in the Bering slope area. At Site U1343, δ15Nbulk value and TOC concentration do not show the distinct glacial-interglacial change. Moreover, contrary to the weak correlation between TOC and biogenic opal concentrations, TOC concentration is positively correlated with δ15Nbulk value, indicating the strong control of OC production on nitrate utilization. It should be noted that glacial terminations are characterized by high δ15Nbulk value, high TOC and low biogenic opal concentration whereas the following full interglacials are characterized by low δ15Nbulk value, low TOC and high biogenic opal concentration during the last 600 kyrs. In other words, glacial terminations are characterized by complete nitrate utilization associated with high OC production under low biogenic opal production, whereas the following full interglacial periods are characterized by decreased nitrate utilization associated with low OC production under high biogenic opal production. Such different glacial-interglacial variation patterns of OC production and nitrate utilization in response to biogenic opal production can best be explained by variable Si/C (or Si/N) uptake ratio by diatoms possibly owing to Fe availability. The glacial Fe input increase at Site U1343 is thought to be ascribed to more dust input or large discharge from the glacial Yukon River. These findings imply that Fe transport and contribution may play a significant role in governing the nutrient cycles in the Bering slope region of the Northern Hemisphere.Kinnari, K.J., M. Askvik, K., Li, X., Austvik, T., Zhang, X., Sa, J.-H., Lee, B.R., Sum, A.K., 2017. Hydrate management of deadlegs in oil and gas production systems – background and development of experimental systems. Energy & Fuels 31, 11783-11792. the oil and gas industry, deadlegs—pipe sections without through-flow—often pose hydrate control challenges to gas and oil production systems. The hydrate challenges, if not properly managed, can cause severe consequences in terms of safety and cost for oil/gas production. This paper provides an overview of deadlegs in oil and gas production systems with some examples of typical challenges faced in the oil industry. Two different types of vertical deadleg experimental systems have been developed to acquire a better understanding of hydrate risks in gas-dominated deadlegs. These systems offer valuable quantitative information on hydrate deposit, such as thickness, porosity, morphology, growth rate, distribution, temperature profile, and amount of water and/or gas consumed as a factor of time in the deadleg system.Kipp, M.A., Stüeken, E.E., 2017. Biomass recycling and Earth’s early phosphorus cycle. Science Advances 3, Article eaao4795. sets the pace of marine biological productivity on geological time scales. Recent estimates of Precambrian phosphorus levels suggest a severe deficit of this macronutrient, with the depletion attributed to scavenging by iron minerals. We propose that the size of the marine phosphorus reservoir was instead constrained by muted liberation of phosphorus during the remineralization of biomass. In the modern ocean, most biomass-bound phosphorus gets aerobically recycled; but a dearth of oxidizing power in Earth’s early oceans would have limited the stoichiometric capacity for remineralization, particularly during the Archean. The resulting low phosphorus concentrations would have substantially hampered primary productivity, contributing to the delayed rise of atmospheric oxygen.Kloppmann, W., Leroux, L., Bromblet, P., Le Pogam, P.-Y., Cooper, A.H., Worley, N., Guerrot, C., Montech, A.T., Gallas, A.M., Aillaud, R., 2017. Competing English, Spanish, and French alabaster trade in Europe over five centuries as evidenced by isotope fingerprinting. Proceedings of the National Academy of Sciences 114, 11856-11860.: Gypsum alabaster in medieval artwork equaled or even surpassed the importance of marble for religious sculptures and effigies. Based on isotope fingerprints, a large corpus of European alabaster sculptures are linked to historical quarries and trade in the Middle Ages and Renaissance period. We demonstrate that English alabaster export was competed on the continent by the Spanish and by a particularly long-lived (>500 y) French Alpine trade. Our study reveals historical trade routes and transport, the diversity of supply of medieval artists and workshops, as well as the presence and provenance of restoration materials. Abstract: A lack of written sources is a serious obstacle in the reconstruction of the medieval trade of art and art materials, and in the identification of artists, workshop locations, and trade routes. We use the isotopes of sulfur, oxygen, and strontium (S, O, Sr) present in gypsum alabaster to unambiguously link ancient European source quarries and areas to alabaster artworks produced over five centuries (12th–17th) held by the Louvre museum in Paris and other European and American collections. Three principal alabaster production areas are identified, in central England, northern Spain, and a major, long-lived but little-documented alabaster trade radiating from the French Alps. The related trade routes are mostly fluvial, although terrestrial transport crossing the major river basin borders is also confirmed by historical sources. Our study also identifies recent artwork restoration using Italian alabaster and provides a robust geochemical framework for provenancing, including recognition of restoration and forgeries. Kobraei, M., Rabbani, A.R., Taati, F., 2017. Source rock characteristics of the Early Cretaceous Garau and Gadvan formations in the western Zagros Basin–southwest Iran. Journal of Petroleum Exploration and Production Technology 7, 1051-1070. source succession in the Zagros Basin comprises the Garau, Gadvan, and Kazhdumi formations, which have probably generated most of the oil and associated gas in the region. In the following study, the generation potential as well as maturity, molecular, and isotopic characteristics of the Early Cretaceous source rocks (Garau and Gadvan formations) in southwest Iran were investigated. One hundred and forty core and cutting samples of Early Cretaceous sediments were obtained from 24 wells in 12 oil fields from the northern Dezful Embayment and Abadan plain. Geochemical measurements such as Rock–Eval pyrolysis, vitrinite reflectance, GC, GC–MS, and isotopic studies were conducted on selected samples. The results have shown that the Gadvan Formation, with an average TOC of 0.65?wt% and HI values of 122?mgHC/g TOC, can be classified as poor source rock, while the Garau Formation, with TOC and HI values of up to 5.72?wt% and 413?mgHC/g TOC, respectively, can be considered as having good to excellent source potential. Kerogen in the Gadvan Formation belongs to Type III/II, while kerogen in the Garau Formation belongs to Type II. Samples from the Gadvan Formation are at the beginning of oil generation, while the current maturity of the Garau samples is already in the peak oil generation stage. Maturity in the studied samples increases eastward toward the Dezful Embayment. GC, GC–MS and isotopic values for the Gadvan Formation indicate high land plant contribution, low maturity, and oxic to sub-oxic depositional environment of the organic matter. In contrast, the Garau Formation shows an advanced level of maturity and marine depositional environment. Considering the results of this study, the Garau Formation, with excellent production potential and a high level of maturity, can be regarded as a source of a huge amount of oil and gas in the region.Kolesnikov, A.Y., Saul, J.M., Kutcherov, V.G., 2017. Chemistry of hydrocarbons under extreme thermobaric conditions. ChemistrySelect 2, 1336-1352. will happen when methane is at a temperature of 1500?K? On the first glance the answer seems to be obvious - methane will decompose into hydrogen and one of the forms of carbon. Yes. However is does not do so at very high pressure, when novel reaction pathways become possible. The latest experimental results and theoretical calculations show that methane and heavier hydrocarbons are, remarkably enough, stable under extreme pressures and temperatures. Even more, experiments confirm the possibility of abiogenic synthesis of natural gas at 5.0 GPa and 1500?K. The review summarizes published results of theoretical and experimental investigations of possible pathways under the conditions of pressure and temperature that prevail in the Earth's upper mantle for the formation of (1) particular species of hydrocarbon molecules, and of (2) complex hydrocarbon systems. The results raise fundamental questions on the genesis of hydrocarbons.Kolodny, O., Feldman, M.W., 2017. A parsimonious neutral model suggests Neanderthal replacement was determined by migration and random species drift. Nature Communications 8, Article 1040. hypotheses in the heated debate about the Neanderthals’ replacement by modern humans highlight the role of environmental pressures or attribute the Neanderthals’ demise to competition with modern humans, who occupied the same ecological niche. The latter assume that modern humans benefited from some selective advantage over Neanderthals, which led to the their extinction. Here we show that a scenario of migration and selectively neutral species drift predicts the Neanderthals’ replacement. Our model offers a parsimonious alternative to those that invoke external factors or selective advantage, and represents a null hypothesis for assessing such alternatives. For a wide range of parameters, this hypothesis cannot be rejected. Moreover, we suggest that although selection and environmental factors may or may not have played a role in the inter-species dynamics of Neanderthals and modern humans, the eventual replacement of the Neanderthals was determined by the repeated migration of modern humans from Africa into Eurasia.Kolster, C., Agada, S., Mac Dowell, N., Krevor, S., 2018. The impact of time-varying CO2 injection rate on large scale storage in the UK Bunter Sandstone. International Journal of Greenhouse Gas Control 68, 77-85. capture and storage (CCS) is expected to play a key role in meeting targets set by the Paris Agreement and for meeting legally binding greenhouse gas emissions targets set within the UK (Energy and Climate Change Committee, 2016). Energy systems models have been essential in identifying the importance of CCS but they neglect to impose constraints on the availability and use of geologic CO2 storage reservoirs. In this work we analyse reservoir performance sensitivities to varying CO2 storage demand for three sets of injection scenarios designed to encompass the UK's future low carbon energy market. We use the ECLIPSE reservoir simulator and a model of part of the Southern North Sea Bunter Sandstone saline aquifer. From a first set of injection scenarios we find that varying amplitude and frequency of injection on a multi-year basis has little effect on reservoir pressure response and plume migration. Injectivity varies with site location due to variations in depth and regional permeability. In a second set of injection scenarios, we show that with envisioned UK storage demand levels for a large coal fired power plant, it makes no difference to reservoir response whether all injection sites are deployed upfront or gradually as demand increases. Meanwhile, there may be an advantage to deploying infrastructure in deep sites first in order to meet higher demand later. However, deep-site deployment will incur higher upfront cost than shallow-site deployment. In a third set of injection scenarios, we show that starting injection at a high rate with ramping down, a low rate with ramping up or at a constant rate makes little difference to the overall injectivity of the reservoir. Therefore, such variability is not essential to represent CO2 storage in energy systems models resolving plume and pressure evolution over decadal timescales.Korrensalo, A., M?nnist?, E., Alekseychik, P., Mammarella, I., Rinne, J., Vesala, T., Tuittila, E.S., 2017. Small spatial but large sporadic variability in methane emission measured from a patterned boreal bog. Biogeosciences Discussions 2017, 1-35. measured methane fluxes of a patterned bog from six different plant community types in three growing seasons 2012–2014 using the static chamber method. A mixed effects model was applied for quantifying the effect of the controlling factors on the methane flux. The plant community types differed from each other in their water level, total leaf area (LAITOT) and leaf area of aerenchymatous plant species (LAIAER). Excluding the highest 2.5?% of all fluxes, methane emissions ranged from ?309 to 556?mg?m?2?d?1. Although methane fluxes increased with increasing peat temperature, LAITOT and LAIAER, they had no correlation with water table or with plant community type. The only exception were higher fluxes from hummocks than from other plant community types in 2013. Chamber fluxes upscaled to ecosystem level for the peak season were of the same magnitude as the fluxes measured with the eddy covariance (EC) technique. In 2012 and in August 2014 there was a good agreement between the two methods, in 2013 and in July 2014, the chamber fluxes were higher than the EC fluxes. Net fluxes to soil, indicating higher methane oxidation than production, were detected every year and on all community types. Exceptionally high methane emissions up to 17?000?mg?m?2?d?1 were measured sporadically in 2013 and 2014. These extreme emissions not detected in EC measurements we were not able to exclude as measurement errors and they did not correlate with any measured variables. Our results underline the importance of both LAIAER and LAITOT in controlling methane fluxes and indicate need for automatized chambers to reliably capture localized events to support more robust EC method.Kovalchik, K.A., MacLennan, M.S., Peru, K.M., Ajaero, C., McMartin, D.W., Headley, J.V., Chen, D.D.Y., 2017. Characterization of dicarboxylic naphthenic acid fraction compounds utilizing amide derivatization: Proof of concept. Rapid Communications in Mass Spectrometry 31, 2057-2065.: The characterization of naphthenic acid fraction compounds (NAFCs) in oil sands process affected water (OSPW) is of interest for both toxicology studies and regulatory reasons. Previous studies utilizing authentic standards have identified dicarboxylic naphthenic acids using two-dimensional gas chromatography hyphenated to time-of-flight mass spectrometry (GC × GC/TOFMS). The selective derivatization of hydroxyl groups has also recently aided in the characterization of oxy-NAFCs, and indirectly the characterization of dicarboxylic NAFCs. However, there has been no previous report of derivatization being used to directly aid in the standard-free characterization of NAFCs with multiple carboxylic acid functional groups. Herein we present proof-of-concept for the characterization of dicarboxylic NAFCs utilizing amide derivatization.Methods: Carboxylic acid groups in OSPW extract and in a dicarboxylic acidstandard were derivatized to amides using a previously described method. The derivatized extract and derivatized standard were analyzed by direct-injection positive-mode electrospray ionization ((+)ESI) high-resolution mass spectrometry (HRMS), and the underivatized extract was analyzed by (?)ESI MS. Tandem mass spectrometry (MS/MS) was carried out on selected ions of the derivatized standard and derivatized OSPW. Data analysis was carried out using the Python programming language.Results: The distribution of monocarboxylic NAFCs observed in the amide-derivatized OSPW sample by (+)ESI-MS was generally similar to that seen in underivatized OSPW by (?)ESI-MS. The dicarboxylic acid standard shows evidence of being doubly derivatized, although the second derivatization appears to be inefficient. Furthermore, a spectrum of potential diacid NAFCs is presented, identified by both charge state and derivatization mass. Interference due to the presence of multiple derivatization products is noted, but can be eliminated using on-line separation or an isotopically labelled derivatization reagent.Conclusions: Proof of concept for the characterization of dicarboxylic NAFCs utilizing amide derivatization is demonstrated. Furthermore, (+)ESI-HRMS of the derivatized monocarboxylic NAFCS yields similar information to (?)ESI-MS analysis of underivatized NAFCs, with the benefit of added selectivity for carboxylic acid species and the characterization of diacids.Krajewski, L.C., Rodgers, R.P., Marshall, A.G., 2017. 126?264 Assigned chemical formulas from an atmospheric pressure photoionization 9.4 T Fourier transform positive ion cyclotron resonance mass spectrum. Analytical Chemistry 89, 11318-11324., we present atmospheric pressure photoionization (APPI) Fourier transform ion cyclotron resonance (FTICR) mass analysis of a volcanic asphalt sample by acquiring data for 20 Da wide mass segments across a 1000 Da range, stitched into a single composite mass spectrum, and compare to a broad-band mass spectrum for the same sample. The segmented spectrum contained 170?000 peaks with magnitude greater than 6σ of the root-mean-square (rms) baseline noise, for which 126?264 unique elemental compositions could be assigned. Approximately two-thirds of those compositions represent monoisotopic (i.e., chemically different) species. That complexity is higher than that for any previously reported mass spectrum and almost 3 times greater than that obtained from the corresponding broad-band spectrum (59?015). For the segmented mass spectrum, the signal-to-noise ratio (S/N) was significantly higher throughout the spectrum, but especially at the lower and upper ends of mass distribution relative to that of the near-Gaussian broad-band mass distribution. Despite this S/N improvement, mass measurement accuracy was noticeably improved only at lower masses. The increased S/N did, however, yield a higher number of peaks and higher dynamic range throughout the entire segmented spectrum relative to the conventional broad-band spectrum. The additional assigned peaks include higher heteroatom species, as well as additional radicals and isotopologues. Segmenting can require a significant investment in data acquisition and analysis time over broad-band spectroscopy (～1775% in this case) making it best suited for targeted analysis and/or when complete compositional coverage is important. Finally, the present segmented spectrum contains, to our knowledge, more assigned peaks than any spectrum of any kind (e.g., UV–vis, infrared, microwave, magnetic resonance, etc.).Kramer, M.G., Lajtha, K., Aufdenkampe, A.K., 2017. Depth trends of soil organic matter C:N and 15N natural abundance controlled by association with minerals. Biogeochemistry 136, 237-248. residues show carbon:nitrogen (C:N) decreases, 15N isotopic enrichment and preferential loss of labile substrates during microbial decay. In soil profiles, strikingly similar patterns of decreasing C:N and 15N isotopic enrichment with increasing depth are well documented. The parallel trend in organic matter composition with soil depth and during plant residue decay has been used as evidence to suggest that organic products accumulate or develop in the subsoil due to increasing intensity of microbially-driven processing, although no studies to date have verified this. Here, by applying sequential density fractionation, specific surface area, oxalate extractable Fe and Al, C:N and δ15N measures with depth to soils with relatively uniform soil mineralogy (Oxisols), climates and vegetation we show that changes in organo-mineral associations drive subsoil C:N and δ15N and C:N depth patterns more than in situ organic matter decay. Our results provide the first direct evidence that soil depth trends could be driven by mineral association instead of in situ processing.Kudapa, V.K., Sharma, P., Kunal, V., Gupta, D.K., 2017. Modeling and simulation of gas flow behavior in shale reservoirs. Journal of Petroleum Exploration and Production Technology 7, 1095-1112. is a growing prospect in this world with decreasing conventional sources of fossil fuel. With the growth in demand for natural gas, there is impending need for the development of the robust model for the flow of shale gas (Behar and Vandenbroucke in Org Geochem, 11:15–24, 1987). So the major driving force behind the working on this major project is the unavailability of desired models that could lead to enhanced production of these wells and that too efficiently. This model mainly includes the movement of shale gas from tight reservoir through the conductive fractures to wellbore and production model of the decline in pressure inside the reservoir with respect to time. This result has been further compared with the help of MATLAB so as to obtain a complete pressure-derived model. The result shows the applicability of this in the real-life projects where it is difficult to model the fractures and obtain the flow rate with them in fractures and how to set the production facilities becomes a question.Kukla, P.A., Strozyk, F., Mohriak, W.U., 2018. South Atlantic salt basins – Witnesses of complex passive margin evolution. Gondwana Research 53, 41-57. aged salt and salt-free basins along the continental margins of Brazil and Angola/Namibia exhibit a rather heterogeneous geometry and basin fill which implies a complex tectonic-sedimentary evolution. As a consequence, the origin of the South Atlantic Aptian salt province has been widely discussed with rather contrasting concepts presented for the distribution of the salt depocentres relative to the protracted evolution of both continental margins. The work presented here aims on integrating conjugated basins transects with kinematic reconstruction models to evaluate the evolution and the geodynamic role of salt basins since the early opening of the South Atlantic. Comparing basin pairs along both margins reveals pronounced symmetry changes attributed to a shift in the spreading centre location from the South American to the African side, which at the same time explains changes in salt basin sizes, the continent/ocean crustal locations and seaward dipping reflector distributions. Furthermore, the arrangement of presalt sag sediments on subsiding, rifted continental crust in the proximal basins and newly formed proto-oceanic crust in the distal basins controlled the distribution and thickness of Aptian salt deposits. The subsequent structural and sedimentary record and the response of the salt systems in the South Atlantic indicate a prolonged history of spatial and temporal tectonic impacts that were rather unique for the individual margin segments. In particular phases of postrift margin uplift and tilting with associated salt tectonics and sediment deposition amplified structural differences in conjugated and neighboring salt basins. These also reflect the combined effects of plate tectonic and vertical motions with associated dynamic topography components along both South Atlantic margins.Kumar, A., Schimmelmann, A., Sauer, P.E., Brassell, S.C., 2017. Distribution and sources of polycyclic aromatic hydrocarbons (PAHs) in laminated Santa Barbara Basin sediments. Organic Geochemistry 113, 303-314. Santa Barbara Basin (SBB) preserves a high-resolution sediment record that is varved down to ca. 1700 CE and laminated for at least 2500 years. The distributions of 25 polycyclic aromatic hydrocarbons (PAHs) were investigated in a suite of samples from sediment cores representing different depositional scenarios – varves/laminae, terrigenous flood layers, and marine turbidites. The concentrations of these PAHs were determined using gas chromatography–mass spectrometry in selected ion mode and evaluated in terms of their distributions, diagnostic ratios, and loadings recognized by principal component analysis (PCA). Two biogenic PAHs, perylene and retene, provided the greatest variation in their downcore concentration values. Perylene concentrations increased downcore exhibiting markedly higher abundance in sediments older than 300 CE, consistent with the interpretation that perylene is formed diagenetically in reducing sediments. A modest increase in perylene concentrations in sediments from the late 1960s may be associated with flood-derived transport of higher amounts of degraded terrestrial organic matter from fire-denudated landscapes into the coastal environment. The markedly higher concentrations of retene in flood layers and turbidites relative to varves/laminae suggest that these lithologies are more effective in transporting pyrogenic PAHs and can be interpreted as a proxy for wildfires in SBB. Changes in key diagnostic ratios reveal the shift from a dominance of petrogenic PAHs in older sediments to a strong pyrogenic signal beginning in the latter half of the 20th century. Statistical analysis using PCA of the PAH distributions in the samples revealed that modern sediments showed a strong, positive relationship with PC1, which represents the greatest variation among the samples, whereas flood layers showed a strong relationship with the second major variable (PC2). Thus, statistical approaches provide the capability to elucidate modern, anthropogenic signatures within the complex PAH distributions of SBB and also establish a PAH profile that characterizes the lithological signature of flood layers.Kwek, W., Khan, M.K., Sarkar, B., Insyani, R., Yi, M., Kim, J., 2017. A non-catalytic, supercritical methanol route for producing high-yield saturated and aromatic compounds from de-oiled asphaltenes. The Journal of Supercritical Fluids 120, 140-150. of de-oiled asphaltenes (DOAs), i.e., the heavy fraction obtained after solvent deasphalting of vacuum residue, was investigated in supercritical methanol (scMeOH) without using external catalysts and molecular hydrogen. Process parameters, including temperature (350–400 °C), reaction time (30–120 min), and additive (formic acid), were explored to optimize the yield of light oil with few impurities. As a result of the beneficial in-situ hydrogen-donation ability and reactivity of scMeOH, its use resulted in higher DOA conversion, increased light-fraction yield, and fewer impurities as compared to those obtained in supercritical water (scH2O). Higher reaction temperatures and residence times increased the DOA conversion to low-molecular-weight saturates and aromatics. With the addition of formic acid as a secondary source of H2 in scMeOH at 400 °C, a 16.7 wt% DOA concentration, and a 90 min residence time, a remarkably high liquid oil yield of 83.9 wt% was obtained. The produced light fraction oil contains a low asphaltene content (0.53 wt%) and few impurities (S, 2.74 wt%; Fe, 19.6 ppm; Ni, non-detectable; V, 18 ppm). In addition, the maltenes content (i.e., saturates + aromatics) was 78.3% and the naphtha-to-diesel fraction was 18 wt% in the light-fraction oil; these results indicate effective cracking, desulfurization, and demetallization in the scMeOH medium with formic acid. A plausible reaction mechanism for scMeOH-based upgrading is discussed.Lai, Y.-H., Zhou, Z., Basheer, C., Zare, R.N., 2017. Upgrading asphaltenes by oil droplets striking a charged TiO2-immobilized paper surface. Energy & Fuels 31, 12685-12690. conversion of heavy oil fractions into lighter oil fractions is highly essential for meeting the growing demand for fuels in continuous depletion of oil reserves and for environmental remediation. We demonstrate an oil degradation approach where oil microdroplets are sprayed in air at room temperature onto untreated TiO2 nanoparticles-coated filter paper to which we apply an electrical potential. Two model polycyclic aromatic hydrocarbons as well as a crude oil sample show degradation on the microsecond time scale. Heterogeneous catalysis of a biphasic (organic/aqueous) reaction occurs at the interface of microdroplets and the charged TiO2 surface. The fragmentation yield is increased by cycling the process. The relative fragmentation yield of a model compound (rubrene) increased from 16.9% in the first cycle to 32.6% in the third cycle. This convenient and efficient method suggests possible future industrial applications.Lammers, J.M., Schubert, C.J., Middelburg, J.J., Reichart, G.J., 2017. Microbial carbon processing in oligotrophic Lake Lucerne (Switzerland): results of in situ 13C-labelling studies. Biogeochemistry 136, 131-149. lakes play a major role in the storage of organic carbon, processes involved are not yet very well characterized, especially for oligotrophic lakes. Whether a lake functions as a net source or sink for carbon depends on relative rates of primary production, inputs of terrestrial organic matter and respiration. The microbial community will affect the efficiency of carbon cycling and thereby potential carbon storage. Because the organic matter fluxes are smaller in oligotrophic lakes they have been studied less intensively with respect to their carbon cycling compared to eutrophic lakes. Whether they play an appreciable role in freshwater carbon cycling relies on unraveling primary and secondary production. Here we present the results from such a study in oligotrophic Lake Lucerne, Switzerland. Based on in situ carbon isotopic labelling experiments using dark, glucose-labelled and transparent, DIC-labelled bottles positioned at different depths in the water column, we conclude that even though the photic zone was very deep, integrated primary productivity was consistently low. The carbon processing efficiency of the heterotrophic producers was such that photosynthesized organic matter was fully consumed, even during times of maximum productivity. This implies that the heterotrophic producers were well adapted to rapidly respond to a temporary increase in primary productivity, which is in line with calculated bacterial growth efficiencies in the surface water layer. Highest glucose-based productivity, as a measure of the heterotrophic potential, was observed in the deepest parts of the water column. Chemoautotrophy was shown at 60?m water depth and is of relatively minor importance for overall fluxes. Mixotrophy was recognized as a strategy to keep up production when light conditions become less favorable for autotrophic growth. A mesocosm experiment earlier in the year indicated lower primary production, which agrees well with the timing of this experiment preceding the annual spring bloom. During the low-productivity season the coupling between phytoplankton and bacterial production was much weaker and potentially more organic matter could escape recycling at that time, although quantitatively fluxes remained very low.Landa-Marbán, D., Radu, F.A., Nordbotten, J.M., 2017. Modeling and simulation of microbial enhanced oil recovery including interfacial area. Transport in Porous Media 120, 395-413. focus of this paper is the derivation of a nonstandard model for microbial enhanced oil recovery (MEOR) that includes the interfacial area (IFA) between oil and water. We consider the continuity equations for water and oil, a balance equation for the oil–water interfacial area, and advective–dispersive transport equations for bacteria, nutrients, and biosurfactants. Surfactants lower the interfacial tension (IFT), which improves oil recovery. Therefore, the parametrizations of the IFT reduction and residual oil saturation are included as a function of the surfactant concentration in the model. We consider for the first time in context of MEOR, the role of IFA in enhanced oil recovery. The motivation to include the IFA is to model the hysteresis in the capillary pressure–saturation relationship in a physically based manner, to include the effects of observed bacteria migration toward the oil–water interface and the production of biosurfactants at the oil–water interface. A comprehensive 2D implementation based on two-point flux approximation and backward Euler is proposed. An efficient and robust linearization scheme is used to solve the nonlinear systems at each time step. Illustrative numerical simulations are presented. The differences in the oil recovery profiles obtained with and without IFA are discussed. The presented model can also be used to design new experiments toward a better understanding and eventually optimization of MEOR.Lantz, C.A., Schulz, K.G., Stoltenberg, L., Eyre, B.D., 2017. The short-term combined effects of temperature and organic matter enrichment on permeable coral reef carbonate sediment metabolism and dissolution. Biogeosciences 14, 5377-5391. of gross primary production (GPP), respiration (R), and net calcification (Gnet) in coral reef sediments are expected to change in response to global warming (and the consequent increase in sea surface temperature) and coastal eutrophication (and the subsequent increase in the concentration of organic matter, OM, being filtered by permeable coral reef carbonate sediments). To date, no studies have examined the combined effect of seawater warming and OM enrichment on coral reef carbonate sediment metabolism and dissolution. This study used 22?h in situ benthic chamber incubations to examine the combined effect of temperature (T) and OM, in the form of coral mucus and phytodetritus, on GPP, R, and Gnet in the permeable coral reef carbonate sediments of Heron Island lagoon, Australia. Compared to control incubations, both warming (+2.4?°C) and OM increased R and GPP. Under warmed conditions, R (Q10?=??10.7) was enhanced to a greater extent than GPP (Q10?=??7.3), resulting in a shift to net heterotrophy and net dissolution. Under both phytodetritus and coral mucus treatments, GPP was enhanced to a greater extent than R, resulting in a net increase in GPP?/?R and Gnet. The combined effect of warming and OM enhanced R and GPP, but the net effect on GPP?/?R and Gnet was not significantly different from control incubations. These findings show that a shift to net heterotrophy and dissolution due to short-term increases in seawater warming may be countered by a net increase GPP?/?R and Gnet due to short-term increases in nutrient release from OM.Lasich, M., 2018. An improved description of clathrate hydrates using classical density functional theory coupled with a simple lattice gas and van der Waals-Platteeuw theory. Fluid Phase Equilibria 456, 131-139. present study refines a recently published model which described clathrate hydrate phase equilibria by coupling the statistical mechanical van der Waals-Platteeuw approach with a mean-field lattice gas in the framework of classical density functional theory. This model yielded analytical expressions for the cavity occupancy, and requires, in principle, knowledge of only two parameters: The potential energy well depth, and a hard-sphere radius for the gas-water interaction. The present contribution expands on this model by examining the utility of several modifications in order to improve its accuracy in describing the dissociation pressure curves of a dozen clathrate hydrates: Argon, carbon dioxide, carbon monoxide, ethane, ethene, hydrogen sulphide, krypton, methane, nitrogen, propane, sulphur dioxide, and 1,1,1,2-tetrafluoroethane. A modified model is demonstrated which produced a good fit to experimental data for the 12 gas hydrate systems considered in this study, with an absolute average temperature deviation of less than 0.7% in all cases.Lechleitner, F.A., Dittmar, T., Baldini, J.U.L., Prufer, K.M., Eglinton, T.I., 2017. Molecular signatures of dissolved organic matter in a tropical karst system. Organic Geochemistry 113, 141-149. areas are widespread landforms present on all continents, formed by the dissolution of carbonate or evaporite host rock. Little is known about the composition and nature of dissolved organic matter (DOM) as it moves through karst systems, although karst DOM has been recognized as important for a range of natural processes. Microbial communities living in karst systems are some of the most diverse and intriguing on the planet, and their metabolism and life cycle can give clues related to the development of a host of different life forms. Karst areas are also of interest due to their mostly subterranean hydrology, and the repercussions of these processes on local carbon cycles.We illustrate some of the processes acting on DOM in karst waters through the analysis of soil, drip and cave pool waters at the tropical site of Yok Balum Cave, in southern Belize. Water samples were analyzed using ultra-high resolution electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FT-ICR-MS), a technique that enables the resolution of single molecular formulae within a DOM spectrum. We perform multivariate statistics to detect trends in the data and identify provenance of detected molecular components. In addition to karst waters, four aliquots of a powdered stalagmite sample from the same cave system are analyzed. Our results show a clear gradient between the soil and the cave system. We hypothesize that both sorption on mineral surfaces and microbial reworking are responsible for the observed trend in DOM composition. The stalagmite extracts show an anomalous DOM pattern, which may be due to a variety of factors, including microbial activity on the stalagmite surface and different affinities of compounds to incorporation in the carbonate. The goal of this study was to follow the molecular transformations of DOM on its journey from the surface to the cave, and to provide a molecular basis for the establishment of stalagmite DOM proxies in karst systems.Lee, K.J., Dempsey, J.L., 2017. When electrochemistry met methane: Rapid catalyst oxidation fuels hydrocarbon functionalization. ACS Central Science 3, 1137-1139. energy challenges have motivated the development of electrochemical transformations of abundant feedstocks into valuable fuels and commodity chemicals.(1) Now, reporting in ACS Central Science, Surendranath and co-workers introduce an electrochemical strategy that enables an organic transformation long-considered a grand challenge: selective methane activation.(2)Methane, the primary component of natural gas, is globally abundant and inexpensive, making it an increasingly important part of the global energy portfolio. However, the dearth of efficient methods for converting this gaseous carbon feedstock into liquid fuels and commodity chemicals has limited our ability to take full advantage of this hydrocarbon, fueling decades of research into ways to overcome methane’s chemical inertness. This endeavor is made even more challenging by methane’s propensity for overoxidation and low selectivity.(3)While the majority of industrial processes in the petrochemical industry utilize reactor beds with metal oxide or supported metal catalysts, the heterogeneous approach commercialized for the conversion of methane to methanol entails an indirect two-step route that operates at high temperatures, rendering it cost-prohibitive for more widespread use.(3) Molecular catalysts are an attractive alternative to heterogeneous systems for the selective C–H functionalization of methane because they promise to operate at low temperatures and with high selectivity.(3) To get past the chemical inertness of methane, these catalysts must be electrophilic, and most exploit high-valent transition metals, such as Pt(IV).(4) C–H bond activation and functionalization by these electrophilic intermediates reduce the catalyst to a low-valent species that must be reoxidized in a two-electron process to regenerate the reactive, high-valent complex and turn over the catalyst. Building on the seminal work of Shilov, who demonstrated in the early 1970s that K2PtCl4 catalyzes the oxidation of methane to methanol and chloromethane with stoichiometric K2PtCl6, molecular catalysts have been developed for methane oxidation using stoichiometric oxidants.(5) These include the system reported by Periana and co-workers in which (2,2′-bipyrimidyl)platinum(II) dichloride catalyzes the selective oxidation of methane to methyl bisulfate in concentrated sulfuric acid—with sulfuric acid acting as both solvent and oxidizing reagent.(6) While this system boasts high conversion and selectivity, it still crawls along at rates of around 10 h–1. Recent work by Schüth and co-workers demonstrated that both (2,2′-bipyrimidyl)platinum(II) dichloride and K2PtCl4 can carry out similar chemistry in 20% oleum (a H2SO4/SO3 mixture) with turnover frequencies that are orders of magnitude higher than the original Periana system.(7)The ideal terminal oxidant for a large scale commercial processes is O2, but the sluggish kinetics associated with direct oxidation by O2 renders it too impractical to be used directly. Many reported systems thus attempt to exploit intermediate chemical oxidants that can be directly regenerated by O2, such as the SO3/SO2 couple.(3) However, even with catalyst turnover mediated by these O2-regenerable oxidants, catalyst reoxidation is often still rate-limiting and continues to almost universally hinder the practicality of reported systems. Indeed, despite decades of research devoted to the discovery of catalytic systems for methane functionalization, the kinetics of catalyst reoxidation with O2-regenerable stoichiometric oxidants has stymied molecular catalysts, preventing them from meeting the performance metrics necessary for industrial applicationsRecognizing the limitations imposed by chemical oxidants, Surendranath and co-workers sought to employ an alternative approach to catalyst reoxidation. They posited they could generate and maintain the electrophilic high-valent catalytic intermediates necessary to activate C–H bonds with electrical polarization. Hypothetically, this method would effectively decouple catalyst oxidation from the O2 reduction half reaction, thus circumventing the kinetic limitations imposed by stoichiometric chemical oxidants. This strategy had been previously employed to electrocatalytically functionalization alkane C–H bonds using Pt-based molecular catalysts; however the slow interfacial electron transfer kinetics typical of Pt ions made these systems ill-suited for methane functionalization.(8) In this current report, the authors turned to Pd ions as a way to overcome the kinetic challenges that had hampered previous work.Through the electrochemical generation of a high-valent Pd species, Surendranath and co-workers now demonstrate the rapid and selective catalytic functionalization of methane to the methanol precursors methyl bisulfate and methanesulfonic acid (Figure 1).(2) This simple system, based on PdSO4 in concentrated sulfuric acid, catalyzes methane functionalization at high rates without necessitating high reaction temperatures—reaching turnover frequencies of 2300 h–1 at only 140 °C. Comparatively, the current state-of-the-art non-electrochemical catalysts functionalize methane at rates that are over 20-fold slower under these conditions. The rate enhancement illustrates the power of the electrochemical approach to develop efficient catalytic systems while still maintaining mild reaction temperatures. Further, the work highlights a key advantage of electrochemical methods, namely, the ability to extract kinetic and mechanistic information with relative ease; information much more difficult to obtain for conventional stoichiometric systems. The authors applied these electroanalytical techniques to establish that an electrophilic high-valent binuclear PdIII–PdIII species is the intermediate responsible for methane functionalization. The mechanistic aspects of this discovery have far-reaching parallels in chemical oxidant-based C–H functionalization, where the groups of Ritter and Sanford have led a wave of interest in binuclear Pd catalysts for activation of aryl compounds with chelating nitrogen donors.(9, 10) This sort of chemical oxidant-based reactivity was subsequently translated to an electrocatalytic system for chlorination of benzo[h]quinoline by Gray and co-workers, who demonstrated that the two-electron oxidation of a binuclear PdII–PdII species can be driven electrochemically.(11) The similarity between this reactive, electrochemically accessed PdIII–PdIII intermediate and the motif identified by Surendranth is intriguing. As research moves forward, electrochemical methods could prove essential to identifying and characterizing important structural motifs of catalysts for C–H functionalization.Prior to this work, the use of electrochemical methods to enable rapid and selective methane functionalization had proved an elusive goal despite success in developing electrocatalysts for a variety of other reactions. This newly reported electrochemical approach has potentially powerful implications. The authors’ general approach of using electrochemical methods to generate and maintain highly reactive high-valent metal species could prove invaluable for accessing catalytic intermediates for the functionalization of other chemically inert substrates, thus providing a strategy to accelerate a variety of kinetically challenging reactions. Moving away from chemical oxidants for these transformations could ultimately lead to the development of electrochemical cells where electrons extracted to maintain reactive populations of catalytic intermediates drive O2 reduction at a separate electrode, allowing for continuous generation of a variety of C–H bond functionalization products. More extensive application of this methodology may thus prove central in advancing catalysis research for a wide range of important chemical reactions.References1. Bertozzi, C. R.; Chang, C. J.; Davis, B. G.; Olvera de la Cruz, M.; Tirrell, D. A.; Zhao, D. ACS Cent. Sci. 2016, 2 (1) 1– 3 2. O’Reilly, M. E.; Kim, R. S.; Oh, S.; Surendranath, Y. ACS Cent. Sci. 2017, DOI: 10.1021/acscentsci.7b00342 3. Gunsalus, N. J.; Koppaka, A.; Park, S. H.; Bischof, S. M.; Hashiguchi, B. G.; Periana, R. A. Chem. Rev. 2017, 117 (13) 8521– 8573 4. Labinger, J. A.; Bercaw, J. E. Nature 2002, 417 (6888) 507– 514 5. Shilov, A. E.; Shul’pin, G. B. Chem. Rev. 1997, 97 (8) 2879– 2932 6. Periana, R. A.; Taube, D. J.; Gamble, S.; Taube, H.; Satoh, T.; Fuji, H. Science 1998, 280 (5363) 560– 564 7. Zimmermann, T.; Soorholtz, M.; Bilke, M.; Schüth, F. J. Am. Chem. Soc. 2016, 138 (38) 12395– 12400 8. Freund, M. S.; Labinger, J. A.; Lewis, N. S.; Bercaw, J. E. J. Mol. Catal. 1994, 87 (1) L11– L15 9. Powers, D. C.; Geibel, M. A. L.; Klein, J. E. M. N.; Ritter, T. J. Am. Chem. Soc. 2009, 131 (47) 17050– 17051 10. Deprez, N. R.; Sanford, M. S. J. Am. Chem. Soc. 2009, 131 (31) 11234– 1124111. Durrell, A. C.; Jackson, M. N.; Hazari, N.; Gray, H. B. Eur. J. Inorg. Chem. 2013, 2013 (7) 1134– 1137Lemetre, C., Maniko, J., Charlop-Powers, Z., Sparrow, B., Lowe, A.J., Brady, S.F., 2017. Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale. Proceedings of the National Academy of Sciences 114, 11615-11620.: Secondary metabolites encoded by soil bacteria have proved to be a rich source of lead structures for the development of small-molecule therapeutics. Environmental factors that contribute to differences in the composition of natural product biosynthetic gene clusters found in geographically distant soil microbiomes have remained elusive. In this study, we sought to address this key outstanding question. Of the factors we assessed, changes in latitude were found to correlate most consistently with changes in biosynthetic domain composition on a continent-wide scale. Although further studies are needed to better understand the underlying causes driving this relationship, these findings provide insights into how best to direct future natural product drug discovery efforts. Abstract: Although bacterial bioactive metabolites have been one of the most prolific sources of lead structures for the development of small-molecule therapeutics, very little is known about the environmental factors associated with changes in secondary metabolism across natural environments. Large-scale sequencing of environmental microbiomes has the potential to shed light on the richness of bacterial biosynthetic diversity hidden in the environment, how it varies from one environment to the next, and what environmental factors correlate with changes in biosynthetic diversity. In this study, the sequencing of PCR amplicons generated using primers targeting either ketosynthase domains from polyketide biosynthesis or adenylation domains from nonribosomal peptide biosynthesis was used to assess biosynthetic domain composition and richness in soils collected across the Australian continent. Using environmental variables collected at each soil site, we looked for environmental factors that correlated with either high overall domain richness or changes in the domain composition. Among the environmental variables we measured, changes in biosynthetic domain composition correlate most closely with changes in latitude and to a lesser extent changes in pH. Although it is unclear at this time the exact mix of factors that may drive the relationship between biosynthetic domain composition and latitude, from a practical perspective the identification of a latitudinal basis for differences in soil metagenome biosynthetic domain compositions should help guide future natural product discovery efforts.Lennox, S.J., Bamford, M.K., 2017. Identifying Asteraceae, particularly Tarchonanthus parvicapitulatus, in archaeological charcoal from the Middle Stone Age. Quaternary International 457, 155-171. rockshelter, an archaeological site in KwaZulu-Natal, has evidence of the local vegetation, environment and wood use during the Middle Stone Age, from well-preserved seeds and charcoal, approximately 77–38 000 years ago. In order to confidently identify some charcoal taxa, closely related species were studied in detail. Modern wood was charred and examined under the light microscope and a combination of anatomical features was used to distinguish the various taxa. Tarchonanthus parvicapitulatus P.P.J. Herman (syn. in part Tarchonanthus camphoratus L.) is an evergreen, woodland shrub or tree, which is tolerant of hot, dry, salty or icy conditions. Essential oils from the leaves have antimicrobial and insecticidal properties. The camphor smoke is used in traditional African medicine, the aromatic leaves are used in organic camp bedding and the hard, heavy wood is insect resistant. Since the wood anatomy of this shrub is very similar to Brachylaena discolor DC, another woody member of the Asteraceae, the modern reference charcoal has been studied, to distinguish between these and other species. The confirmed presence of aromatic T. parvicapitulatus in hearths probably implies deliberate burning for insect repellent smoke.Levchuk, I., Rueda Márquez, J.J., Sillanp??, M., 2018. Removal of natural organic matter (NOM) from water by ion exchange – A review. Chemosphere 192, 90-104. organic matter (NOM) is present in underground and surface waters. The main constituents of NOM are humic substances, with a major fraction of refractory anionic macromolecules of various molecular weights. The NOM concentration in drinking water is typically 2–10?ppm. Both aromatic and aliphatic components with carboxylic and phenolic functional groups can be found in NOM, leading to negatively charged humic substances at the pH of natural water. The presence of NOM in drinking water causes difficulties in conventional water treatment processes such as coagulation. Problems also arise when applying alternative treatment techniques for NOM removal. For example, the most significant challenge in nanofiltration (NF) is membrane fouling. The ion exchange process for NOM removal is an efficient technology that is recommended for the beginning of the treatment process. This approach allows for a significant decrease in the concentration of NOM and prevents the formation of disinfection byproducts (DBPs) such as trihalomethanes (THMs). This article provides a state-of-the-art review of NOM removal from water by ion exchange.Li, A., Davies, R.J., Mathias, S.A., Yang, J., Hobbs, R., Wilson, M., 2017. Gas venting that bypasses the feather edge of marine hydrate, offshore Mauritania. Marine and Petroleum Geology 88, 402-409. can be released from the vast marine hydrate reservoirs that surround continents into oceans and perhaps the atmosphere. But how these pathways work within the global carbon cycle now and during a warmer world is only partially understood. Here we use 3-D seismic data to identify what we interpret to be a gas venting system that bypasses the hydrate stability zone (HSZ) offshore of Mauritania. This venting is manifested by the presence of the acoustic wipe-out (AWO) across a densely faulted succession above a salt diapir and a set of morphological features including a substantial, ～260 m wide and ～32 m deep, pockmark at the seabed. The base of the HSZ is marked by a bottom simulating reflector (BSR) which deflects upwards above the diapir, rather than mimicking the seabed. We use a numerical modelling to show that this deflection is caused by the underlying salt diapir. It creates a trapping geometry for gas sealed by hydrate-clogged sediment. After entering the HSZ, some methane accumulated as hydrate in the levees of a buried canyon. Venting in this locality probably reduces the flux of gas to the landward limit of feather edge of hydrate, reducing the volume of gas that would be susceptible for release during a warmer world.Li, A., Ding, W., Jiu, K., Wang, Z., Wang, R., He, J., 2018. Investigation of the pore structures and fractal characteristics of marine shale reservoirs using NMR experiments and image analyses: A case study of the Lower Cambrian Niutitang Formation in northern Guizhou Province, South China. Marine and Petroleum Geology 89, 530-540. pore structures and fractal characteristics of the organic-rich marine shales of the Lower Cambrian Niutitang Formation in northern Guizhou Province were investigated using nuclear magnetic resonance (NMR) and field emission scanning electron microscopy (FE-SEM). In this paper, the NMR fractal dimensions and pore morphology fractal dimensions were calculated based on NMR T2 spectra and SEM image analyses. The relationships among the total organic carbon (TOC) contents, mineral compositions, porosities, permeabilities, CH4 adsorptions and NMR fractal dimensions (DN1 and DN2) of the shales are discussed, and the properties of the different pores are quantitatively analyzed using pore extraction based on SEM images. Moreover, the geological significances of fractal dimensions are discussed. The results reveal that DN1 is positively correlated with TOC contents, whereas DN2 does not have an apparent relationship with TOC contents. The quartz content presents a positive linear correlation with DN1 and DN2, whereas the clay content is positively correlated with DN1 but is not correlated with DN2. DN1 increases with decreases in porosity and permeability, and DN2 increases with increases in porosity but is not correlated with permeability. The organic matter (OM) pores are smaller in size and have a larger number than the interparticle pores and intraparticle pores. The interparticle pores have the smallest average roundness values, implying that their roundness is the worst. Moreover, the fractal dimension of the OM pores is the largest, whereas the fractal dimension of the intraparticle pores is the smallest. The pore morphology fractal dimension has no apparent relationship with the roundness but shows a negative correlation with pore size. Shale samples with larger surface fractal dimensions have higher methane adsorption capacities.Li, B., Su, Y., Wang, W., 2017. Temporal scale-based production analysis of fractured horizontal wells with stimulated reservoir volume. Journal of Natural Gas Science and Engineering 48, 46-64. volume fracture, the permeability field is found to be varying with space. This is not only a commonly-occurring production effect, but has also become a hot research topic in the field of tight gas reservoirs. However, different flow velocities and temporal scales controlled by varying permeability field are often neglected. In this study, the temporal scale analysis for two-dimensional (2D) inhomogeneous permeability field is introduced to explain the inhomogeneity and different flow velocities in the stimulated-reservoir-volume (SRV). Firstly, a new mathematical approach for temporal scale analysis to the well response has been provided. According to the proposed approach, the solution is obtained by using finite element method in the Laplace domain. The well performance is then speared into the temporal scales, which are derived from the analytical Laplace inversion of the solution. Based on this, the temporal scale diagrams are provided for production performance analysis and comparison. Secondly, the significant differences in the well response and its temporal scale analysis from one-dimensional (1D) field have been highlighted. The results showed that the varying permeability is observed to be properly represented by two-dimensional field. In general, the shape of the temporal scale distribution stripe is different with varying pattern of the permeability, and its width and density are enhanced by the rapid variation of the permeability. The temporal scales are enhanced at higher permeability area, while their contributions are reduced by the permeability, though these are enhanced by the initial energy of their corresponding area. By analyzing the initial energy, the propagation of the pressure and the exploited area are presented in a better way. Furthermore, the exponential and power fields explain the permeability inhomogeneity better than the linear field. In spite of this, the linear field is described better by the temporal scale analysis, while multiple temporal scale is the result of permeability inhomogeneity. Last but not the least, the effect of the less permeable outer boundary is eliminated by decelerating the decline in permeability in the whole SRV. The temporal scales fail to couple in terms of both mass and energy, and their corresponding processes fail to influence each other. Finally, practical guidelines for the volume fracture techniques are derived based upon the proposed model.Li, C., Zhong, S., Zhang, F., Wang, Z., Jiang, F., Wan, Y., 2017. Response of microbial communities to supercritical CO2 and biogeochemical influences on microbially mediated CO2-saline-sandstone interactions. Chemical Geology 473, 1-9. this study, laboratory experiments were conducted to investigate the influences of supercritical CO2 (scCO2) on the indigenous microbial communities. Results revealed that the abundance of gene copies (mL? 1) in samples and the shifts in the microbial community were strongly affected by scCO2 injection. Furthermore, Proteobacteria showed better ability of tolerance to the scCO2 injection than Firmicutes in initial period and both of them were the predominant phyla after 180 days' experiments. In addition, the acidogenic mineral-attached biofilms formed by Pseudomonas stutzeri, Acinetobacter soli etc. surrounding the feldspars and clays could lower the pH in solution and accelerate the dissolution of silicate minerals. As the secondary carbon sink minerals, amount of CaCO3 and FeCO2 were observed in the microbially mediated CO2-saline-sandstone interactions, demonstrated the Fe(III)-reducing microbes (Shewanella putrefaciens, Citrobacter sp. LAR-1 and Pseudomonas fluorescens) could reduce the Fe(III) released from clays to Fe(II) and induce siderite biomineralization through metabolic processes.Li, D., Zhang, X., Chen, K., Zhang, G., Chen, X., Huang, W.E.I., Peng, S., Shen, Y., 2017. High-resolution C-isotope chemostratigraphy of the uppermost Cambrian stage (Stage 10) in South China: implications for defining the base of Stage 10 and palaeoenvironmental change. Geological Magazine 154, 1232-1243. Wa'ergang section in South China has been proposed as a potential Global Stratotype Section and Point (GSSP) for the base of Stage 10, the uppermost stage of the Cambrian System. In this study, high-resolution C-isotopic compositions are reported and we identified three large negative δ13C excursions, namely N1, N2 and N3, at Wa'ergang. The N1 is located just above the First Appearance Datum (FAD) of Lotagnostus americanus, corresponding to the possible base of the Proconodontus posterocostatus conodont Zone. The N2 was identified within the Micragnostus chuishuensis trilobite Zone and the Proconodontus muelleri conodont Zone. The N3 is located in the lowermost part of the Leiagnostus cf. bexelli – Archaeuloma taoyuanense trilobite Zone or Eoconodontus conodont Zone. The N1 and N2 can be correlated with the negative δ13C excursions preceding the Top of Cambrian Carbon Isotope Excursion (TOCE) observed globally. The N3 can be correlated with the TOCE or the HEllnmaria–Red Tops Boundary (HERB) Event. The inter-basinal correlation of N1 and L. americanus strongly supports that the base of Stage 10 may be best defined by the FAD of L. americanus. We also used a box model to quantitatively explore the genesis of the negative δ13C excursions from South China. Our numerical simulations suggest that weathering of the organic-rich sediments on the platform, probably driven by intermittent sea level fall and/or the oxygenation of the Dissolved Organic Carbon (DOC) reservoir in seawater, may have contributed to the generation of the negative δ13C excursions observed in the Stage 10 at Wa'ergang in South China.Li, G., Li, L., Tarozo, R., Longo, W.M., Wang, K.J., Dong, H., Huang, Y., 2018. Microbial production of long-chain n-alkanes: Implication for interpreting sedimentary leaf wax signals. Organic Geochemistry 115, 24-31. distributions as well as compound-specific carbon and hydrogen isotope ratios of long-chain C25 to C33 n-alkanes in sediments provide important paleoclimate and paleoenvironmental information. These compounds in aquatic sediments are generally attributed to leaf waxes produced by higher plants. However, whether microbes, such as fungi and bacteria, can make a significant contribution to sedimentary long-chain n-alkanes is uncertain, with only scattered reports in the early 1960s to 1970s that microbes can produce long-chain n-alkanes. Given the rapidly expanding importance of leaf waxes in paleoclimate and paleoenvironmental studies, the impact of microbial contribution to long-chain n-alkanes in sediments must be fully addressed. In this study, we performed laboratory incubation of peatland soils under both anaerobic and aerobic conditions in the absence of light with deuterium-enriched water over 1.5?years and analyzed compound-specific hydrogen isotopic ratios of n-alkanes. Under aerobic conditions, we find n-alkanes of different chain length display variable degrees of hydrogen isotopic enrichments, with short-chain (C18–C21) n-alkanes showing the greatest enrichment, followed by long-chain “leaf wax” (C27–C31) n-alkanes, and minimal or no enrichment for mid-chain (C22–C25) n-alkanes. In contrast, only the shorter chain (C18 and C19) n-alkanes display appreciable isotopic enrichment under anaerobic conditions. The degrees of isotopic enrichment for individual n-alkanes allow for a quantitative assessment of microbial contributions to n-alkanes. Overall our results show the microbial contribution to long-chain n-alkanes can reach up to 0.1% per year in aerobic conditions. For shorter chain n-alkanes, up to 2.5% per year could be produced by microbes in aerobic and anaerobic conditions respectively. Our results indicate that prolonged exposure to aerobic conditions can lead to substantial accumulation of microbially derived long-chain n-alkanes in sediments while original n-alkanes of leaf wax origin are degraded; hence caution must be exercised when interpreting sedimentary records of long-chain n-alkanes, including chain length distributions and isotopic ratios.Li, H., Misra, S., 2018. Assessment of miscible light-hydrocarbon-injection recovery efficiency in Bakken shale formation using wireline-log-derived indices. Marine and Petroleum Geology 89, 585-593. original oil-in-place estimates accompanied by low primary recovery potential of organic-rich shale formations make them suitable candidates for enhanced oil recovery (EOR) projects. The organic-rich shale formation under investigation in this paper is the Bakken shale formation that exhibits significant variations in lithology, rock texture, clay content, porosity, and total organic carbon (TOC). Three wireline-log-derived EOR-efficiency indices are generated across the 200-feet-thick Upper, Middle, and Lower Bakken formations to identify flow units suitable for EOR using light, miscible hydrocarbon injection.R-index is one of the three EOR-efficiency indices. R-index is calculated using kerogen content, water saturation, permeability, principal pore throat diameter, and porosity. Microscopic Displacement (MD) Index computes the microscopic displacement efficiency for the miscible gas injection. An important step in computing MD-index is to decompose NMR T2 distribution at each depth using factor analysis to compute the free oil, movable water, and bound fluid volumes. Moreover, the MD-index accounts for the effect of pore confinement on miscible oil volume and the effect kerogen content on the displacement efficiency. MD-index relies on a novel method to calculate the miscible free-oil volume from subsurface NMR T2-distribution logs. Lastly, k-means clustering method was used to generate the third index, referred as the KC-index, which is in the form of a step-wise curve. KC-index partitions the entire formation into four groups, representing miscible-gas-injection recovery potentials at discrete levels. The method uses water saturation, porosity, permeability, bound fluid volume, and principal pore throat diameter derived from various logs.The proposed log-derived EOR-efficiency indices generate consistent predictions of miscible light-hydrocarbon injection performance in the Bakken shale formation at various resolutions. Indices indicate that several formation zones in the middle section of the formation will have much higher recovery potential in comparison to the upper and lower sections of the formation. At a resolution of 1-foot depth interval, several flow units were successfully identified in the middle section that exhibit high miscible-gas-injection recovery potential.Li, J., Jiang, H., Wang, C., Zhao, Y., Gao, Y., Pei, Y., Wang, C., Dong, H., 2017. Pore-scale investigation of microscopic remaining oil variation characteristics in water-wet sandstone using CT scanning. Journal of Natural Gas Science and Engineering 48, 36-45. the aid of CT scanning and image processing techniques, water displacing oil experiments were performed to analyze six natural water-wet sandstone cores of different permeability and porosity visually and quantitatively. Microscopic remaining oil was categorized on the basis of quantitative characterization parameters, such as shape factor, contact ratio, Euler number etc. The remaining oil characteristics with different flow types were presented in different water displacement stages. Experimental results show that the remaining oil can be divided into five categories. They are, respectively membranous flow, droplet flow, columnar flow, multi-porous flow and clustered flow from hard-to-produce to easy-to-produce. The relative permeability of oil phase is represented by the macro-average relative permeability of all the above five flow regimes. Among them, clustered flow possesses strong producing capacity and high relative permeability, and the other four flow regimes have weaker producing capacity and lower relative permeability. Variation of number and average volume of five types remaining oil and several measurements of the ganglion size distribution have been performed in the literature. The nonlinear knee point on the relative permeability ratio curve is intrinsically caused by the decreasing of volume and quantity fraction of clustered flow when water saturation increases. This paper has studied the flowing law of microscopic remaining oil, explained the intrinsic mechanism for the appearance of an inflection point on the relative permeability ratio curve and microscopic sweep phenomena, and also presented a new effective way of upscaling to a certain extent.Li, J., Li, J., Li, Z., Zhang, C., Cui, H., Zhu, Z., 2018. Characteristics and genetic types of the Lower Paleozoic natural gas, Ordos Basin. Marine and Petroleum Geology 89, Part 1, 106-119. source of the Lower Paleozoic natural gas in the Ordos Basin has been a highly controversial issue. Using data obtained from newly drilled wells, we present the geochemical characteristics of Lower Paleozoic natural gas in various regions of the Ordos Basin. The Lower Paleozoic natural gas is dominated by hydrocarbons, of which methane accounts for 40.17%–97.24%, and the heavier gaseous hydrocarbon (C2+) ranges from 0.01% to 9.72%. Non-hydrocarbon gases in the Lower Paleozoic gas reservoir are mainly CO2 and N2, 2%–10% for CO2 and 0.04%–48.56% for N2, higher than those in the Upper Paleozoic gas reservoir. This observation showed that the high CO2 and N2 content was related to the Ordovician marine carbonate rock deposits. The carbon and hydrogen isotopes of the methane, ethane, and propane in the Lower Paleozoic natural gas of the Ordos Basin showed various degrees of reversal, indicating the mixing origin of natural gas. In the central–eastern Ordos Basin, coal-derived gas from the Carboniferous–Permian (C-P) coal measure and oil-associated from the Lower Ordovician Majiagou Formation marine source rocks gas coexist, as well as mixtures of these two gases. For the Lower Paleozoic natural gas from the western margin of the basin, coal-derived gas coexist with oil-associated gas, but no mixing gas, in which coal-derived gas originated mainly from the C–P source rocks and oil-associated gas from the Lower Ordovician Kelimoli Formation and Middle Ordovician Wulalike Formation source rocks in the western margin of the basin. The Lower Paleozoic natural gas in the southern part of the Ordos Basin was mixing gas, and the oil-associated gas is the dominant one. The natural gas was originated from the Lower Ordovician Majiagou Formation source rocks in the central–eastern Ordos Basin and the Pingliang Formation mudstone and argillaceous limestone at the southern margin of the basin.Li, J., Ma, Y., Huang, K., Zhang, Y., Wang, W., Liu, J., Li, Z., Lu, S., 2018. Quantitative characterization of organic acid generation, decarboxylation, and dissolution in a shale reservoir and the corresponding applications—A case study of the Bohai Bay Basin. Fuel 214, 538-545. order to study the generation of organic acids and their dissolution effects on reservoirs, the type, yield and stability of common organic acids in the stratum were analyzed by laboratory simulations of the organic acid generation from kerogen and the decarboxylation of these organic acids. A kinetic model for the generation of organic acids and thermodynamic models of the decarboxylation of organic acids and the dissolution reaction were established. Acetic acid was used as an example to characterize the integration of the organic acid generation, decarboxylation, and dissolution under geological conditions. In addition, the process of dissolution pore development in shale reservoirs of various ages was reproduced. The results show that among the organic acids produced in the kerogen thermal simulation, the most stable is acetic acid with a decarboxylation temperature higher than 250?°C, followed by formic acid, and oxalic acid is the least stable. A large amount of organic acids can be produced in the middle thermal maturation stage (Ro?=?0.89%–1.25%) of organic matter (OM). The modeling method combining kinetics and thermodynamics can achieve the quantitative characterization of the process of dissolution pore development. According to the calculation results, if the organic acids dissolve the reservoir as a whole, the porosity increment produced by the dissolution of the reservoir’s minerals is not significant. In other words, the dissolution of the reservoir by organic acids does not have an overall significance. However, if the organic acids only move along the predominant pathway (such as fractures) after their generation and dissolved the surrounding minerals of this channel, obvious dissolution can be produced. Comparison of the mineral composition and crack development of shale reservoirs indicates that organic acids could preferentially dissolve the reservoir cracks, so as to improve the porosity and permeability of the reservoir.Li, J., Sultan, A.S., 2017. Klinkenberg slippage effect in the permeability computations of shale gas by the pore-scale simulations. Journal of Natural Gas Science and Engineering 48, 197-202. prediction of permeability (i.e., apparent permeability) for the shale gas is challenging due to the Klinkenberg slippage effect that depends on the pore size and gas pressure. A recent Monte Carlo molecular simulation method (i.e., DSBGK method) is employed to accurately compute the permeability by the pore-scale simulations at different pressures. The computed results of a benchmark problem proposed here are used to verify the accuracy of the simple Klinkenberg correlation model, which relates the permeability to the intrinsic permeability (i.e., liquid permeability) and pressure. The verification shows that the Klinkenberg correlation model as a data fitting formula is appropriate for the industry applications since the relative error is small in the whole range of the flow regime as long as it has been calibrated for each particular rock sample at the two ends with low and high pressures, respectively, by determining the model parameters using accurate permeability data that can be obtained by the scheme presented herein. This conclusion is consistent with the experimental observations of real rock samples by Klinkenberg as shown in Appendix.Li, J., Zhang, D., Song, M., Jiang, L., Wang, Y., Luo, C., Zhang, G., 2017. Novel bacteria capable of degrading phenanthrene in activated sludge revealed by stable-isotope probing coupled with high-throughput sequencing. Biodegradation 28, 423-436. indigenous microorganisms responsible for degrading phenanthrene (PHE) in activated biosludge were identified using DNA-based stable isotope probing. Besides the well-known PHE degraders Burkholderia, Ralstonia, Sinobacteraceae and Arthrobacter, we for the first time linked the taxa Paraburkholderia and Kaistobacter with in situ PHE biodegradation. Analysis of PAH-RHDα gene detected in the heavy DNA fraction of 13C-PHE treatment suggested the mechanisms of horizontal gene transfer or inter-species hybridisation in PAH-RHD gene spread within the microbial community. Additionally, three cultivable PHE degraders, Microbacterium sp. PHE-1, Rhodanobacter sp. PHE-2 and Rhodococcus sp. PHE-3, were isolated from the same activated biosludge. Among them, Rhodanobacter sp. PHE-2 is the first identified strain in its genus with PHE-degrading ability. However, the involvement of these strains in PHE degradation in situ was questionable, due to their limited enrichment in the heavy DNA fraction of 13C-PHE treatment and lack of PAH-RHDα gene found in these isolates. Collectively, our findings provide a deeper understanding of the diversity and functions of indigenous microbes in PHE degradation.Li, L., Voskov, D., Yao, J., Li, Y., 2018. Multiphase transient analysis for monitoring of CO2 flooding. Journal of Petroleum Science and Engineering 160, 537-554. potential of well test technology is discussed in this paper to estimate the miscible condition and displacement fronts position during CO2 flooding. To interpret the multiphase well test curve of CO2 flooding process, an accurate compositional numerical model is developed in this study. The model includes fully EoS-based compositional nonlinear formulation, unstructured gridding and multi-segmented well. A systematic well test analysis of CO2 flooding at different regimes, including immiscible, multi-contact miscible and first-contact miscible gas injection, was performed for hydrocarbon systems with different number of components. Based on the interpretation root cause analysis, proposed in this work, the specific characteristics of the well test curve of CO2 flooding have been identified and described. These characteristics provide the guidance for the distinction among the different regime of CO2 displacement. It was demonstrated that the most important characteristics stay invariant from the number of components involved into numerical study. Finally, a tangent line method has been proposed to detect the key point on the pressure derivative curve corresponding to a CO2 front. This method allows to predict the displacement front position for problems of practical interest.Li, L., Zhu, B., Yan, X., Zhou, Q., Wang, Y., Jiang, G., 2018. Effect of silver sulfide nanoparticles on photochemical degradation of dissolved organic matter in surface water. Chemosphere 193, 1113-1119. sulfide nanoparticles (Ag2SNPs) have shown photocatalytic activity, yet little is known about the effect of Ag2SNPs on the photochemical degradation of dissolved organic matter (DOM) in surface water, which seriously impairs understanding of Ag2SNPs' environmental risks. Herein, this study on the basis of electrospray ionization coupled with Fourier-transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) showed for the first time that photodegradation of natural organic matter (NOM, 2R101 N) could be accelerated by both bared and polyvinylpyrrolidone (PVP)-coated Ag2SNPs; the NOM with Ag2SNPs (e.g., 500 μg/L) exposed to light irradiation for 96 h showed molecular formulas with lower O/C ratios as compared to the NOM alone. Also, added number of points (ranging from 1 to 2 carboxyl groups) having the same Kendrick mass defect (KMD) (COO) values and higher intensity in smaller Kendrick mass (KM) (COO) values were observed in NOM with Ag2SNPs compared to NOM alone. However, negligible effects of Ag2SNPs on photodegradation of humic acid (HA, 2S101H) were observed, even when the concentration of Ag2SNPs was as high as 5 mg/L. Besides molecular characteristics, a great reduction in organic carbon content of NOM within 96 h was only observed in the presence of Ag2SNPs under light condition. More importantly, the enhanced photodegradation of DOM by Ag2SNPs even at a concentration of 100 μg/L was also validated in surface water. These findings suggest that Ag2SNPs have the potential to accelerate the photochemical degradation of DOM in surface water.Li, M., Sun, M., Lu, Y., Zhang, J., 2017. Experimental study on the strength of original samples of wax deposits from pipelines in the field. Energy & Fuels 31, 11977-11986. yield stress of the wax deposit, characterizing its mechanical strength, provides critical design basis for pigging. The deposits naturally formed in a pipeline (hereafter, “natural wax deposits”) and those artificially generated from model wax–oil mixtures (hereafter, “model wax deposits”) usually present different yield stress due to structural variations. Investigations on the distinctive yielding characteristics between natural and model deposits are limited in the literature. In this research, we present a comprehensive comparative mechanical and structural analysis of natural and model wax deposits, based on which representative laboratory tests can be designed to guide pigging operations. A rheometer with the vane geometry was enhanced to preserve the microstructure of the deposit sample collected from the field prior to the yielding test. Field wax deposits from different radial positions of the pipe were analyzed. It was discovered that the yield stress of the natural wax deposits increases exponentially with solid paraffin content. Moreover, the deposit layer closer to the center has lower solid paraffin content and lower resulting yield stress than the layer in the vicinity of the inner pipe wall. The original sample of natural wax deposits (called “original sample” for short following) was heated until completely melted and cooled again for the reformed solid sample similar to the model wax deposits in common use. The tested yield stress for the newly formed deposits can be 5–13 times that of the original sample at the same temperature due to the compact microstructure. Consequently, the required pressure to remove the wax deposits in the pipeline could be relatively high estimated based on the yield stress of model wax deposits. On the other hand, the natural wax deposits and model wax deposits formed on the coldfinger or in the flow loop are more alike in structure. So model deposits obtained in these ways should be used in the studies relative to pig motion, rather than the wax–oil gel which is currently very popular.Li, N., Yi, F., Liao, P., Chen, W., Fu, M., Zheng, J., Du, L., Liu, J.-l., Li, C.-y., 2017. Imaging the pore structure of geological materials with bifunctional nanoparticles. Analytical Chemistry 89, 12550-12555. of complex pore structure of geomaterials is a fundamental issue in geoscience. Here bifunctional nanoparticles with magnetic and fluorescent properties are introduced as novel markers for optical imaging of pore structure in geomaterials. Using the paramagnetic property, powder of the nanoparticle is driven into pores under an external magnetic field, avoiding a tedious sample preparation and eliminating artificial damage of sample preparation in conventional methods. Meanwhile, the fluorescent nanoparticle marker offers a sharp contrast imaging between the rock matrix (black) and pores (bright) under microscopy. Furthermore, fluorescent nanoparticles with different sizes and colors are designed to demonstrate the potential of the method for describing pore throat sizes. Combining the merits of the paramagnetic and fluorescent properties of nanoparticles, a convenient and practical sample preparation is proposed to promote optical imaging analysis of the pore structure in geomaterials.Li, Q., Pang, X., Li, B., Zhao, Z., Shao, X., Zhang, X., Wang, Y., Li, W., 2018. Discrimination of effective source rocks and evaluation of the hydrocarbon resource potential in Marsel, Kazakhstan. Journal of Petroleum Science and Engineering 160, 194-206. rounds of exploration in Marsel, Kazakhstan show that the area has good petroleum geological conditions; however, the exploration degree is low and the resource potential is unclear. The total organic carbon (TOC) content is the criteria for effective source rocks and is also the key parameter to calculate the amount of resources; while previous evaluations of the effective source rocks and calculated amounts of resources were based on residual TOC, which gradually decreases with mass hydrocarbon expulsion; therefore, this will inevitably produce errors. For greater accuracy, the TOC recovery coefficient formula was used to recover the residual TOC in Marsel; then, the criteria of the effective source rocks were revised to calculate the Carboniferous and Devonian resources in Marsel. The results are as follows: for the source rocks in Marsel, the TOC recovery coefficient of the Carboniferous source rocks is approximately 1.6, while that for the Devonian is approximately 2.0; the revised lower limit of TOC for the effective source rocks is 0.3% and 0.25% for the Carboniferous and Devonian, respectively; after TOC recovery, the total amount of hydrocarbon expulsion is 26.7 × 1012 m3, the total amount of recoverable resources is 2.62–5.10 × 1012 m3, and the mean is 3.79 × 1012 m3 for the main source rocks. The effective source rocks evaluated based on the recovered TOC and the latter resources could reflect the quantity of source rocks and actual resource potential of Marsel more accurately. This has certain significance for the exploration of areas that have low levels of exploration with an unclear understanding of the resource potential as well as a high degree of thermal evolution and a low quantity of residual TOC.Li, Q., You, X., Jiang, Z., Zhao, X., Zhang, R., 2017. A type of continuous petroleum accumulation system in the Shulu sag, Bohai Bay basin, eastern China. American Association of Petroleum Geologists Bulletin 101, 1791-1811. study analyzed crude oils from the lower part of the third member of the Eocene Shahejie Formation (Es3L) and three prospective source rocks from the Shulu sag, Bohai Bay basin, eastern China, using a variety of organic geochemical methods. Biomarker characteristics were used to interpret source rock organic matter input and depositional environment, and oil–source rock correlation. The biomarker data indicate that the crude oils originated from the Es3L source rock, which contains a mixture of plankton and land plant organic matters deposited in brackish–fresh water under reducing conditions. The oil in the Es3L is self-sourced instead of migrated from the overlying source rocks. The petroleum generation potential of the Es3L source rock was evaluated using organic geochemistry. Total organic carbon (TOC) values for approximately 100 samples are between 1.02 and 4.92 wt. %, and hydrogen indices range from 285 to 810 mg hydrocarbons/g TOC. The Es3L source rock contains mainly type II and III kerogen, and most of the samples are thermally mature. The data show that the Es3L source rock has good potential for liquid hydrocarbon generation. The Es3L rock also acts as the oil reservoir, having very low bulk porosity and permeability. Various types of storage space in the marlstone and carbonate rudstone in the Es3L of the Shulu sag include (1) fractures, (2) intergranular pores, (3) dissolution pores, (4) organic matter pores, (5) intragranular pores, and (6) seams around gravels. Pore size ranges from nanometers to millimeters. Because the oil was generated and stored in Es3L strata, which lack any obvious trap and seal and have low permeability, the unit represents a continuous petroleum accumulation.Li, S.-S., Keerthy, S., Santosh, M., Singh, S.P., Deering, C.D., Satyanarayanan, M., Praveen, M.N., Aneeshkumar, V., Indu, G.K., Anilkumar, Y., Sajinkumar, K.S., 2018. Anatomy of impactites and shocked zircon grains from Dhala reveals Paleoproterozoic meteorite impact in the Archean basement rocks of Central India. Gondwana Research 54, 81-101. Dhala structure in Central India has been a topic of global interest ever since the report of an ancient meteorite impact event there. Here we present an integrated study of the petrology, geochemistry, and zircon U-Pb zircon geochronology and rare earth element geochemistry from the structure along with and an analysis of the grain morphology and textural features. Our results provide new insight into the nature and timing of the impact event. The zircon grains from the impactites show textures typical of shock deformation which we correlate with the impact event. We also identified the presence of reidite based on Raman spectroscopy and characteristics such as a persistent planar fracture, bright backscattered electron images, and a lack of zoning, which are all diagnostic features of this mineral formed during an impact event. Our zircon U-Pb data from the various rock types in the basement show magma emplacement at ca. 2.5–2.47 Ga, and the Pb loss features suggest that the impact might have occurred between ca. 2.44 Ga and ca. 2.24 Ga. Another minor group of late Paleoproterozoic zircons with concordant ages of 1826 and 1767 Ma in the brecciated quartz reefs along the margins of the impact crater from unfractured grains represent an younger thermal event after the impact. The rare-earth element patterns of the Neoarchean to early Paleoproterozoic zircon population reflect the effects of hydrothermal alteration on a peralkaline host rock. The abnormally high concentration of K2O in the impactite (up to 15.91 wt%), is also consistent with metasomatic alteration associated with the impact event.Li, S., Jin, S., Song, C., Jia, S., Zhang, Y., Feng, Y., Du, Z., Jiang, H., 2017. The strategy for establishment of the multiple reaction monitoring based characteristic chemical profile of triterpenes in Alismatis rhizoma using two combined tandem mass spectrometers. Journal of Chromatography A 1524, 121-134. was reported that triterpenes compounds in Alismatis rhizoma (AR) contributed to the lipid lowering effect on high fat diet (HFD)-induced hyperlipidemia. To date only 24 triterpenes (including the isomers) were characterized by LC-QTOF-MS/MS due to the lack of strategies for systematic discovery, classification and identification of triterpenes in AR. In this study, an integrated strategy combining various QTOF-MS/MS and QTRAP-MS/MS scan functions was developed for systematic identification and specific characterization of triterpenes in AR and processed AR. First, MS/MS fragmentation behaviors of different types of triterpenes were investigated and their diagnostic product ions were systematically summarized for discovery and classification of triterpenes. Second, diagnostic product ions were used to filter the data acquired by UHPLC-QTOF MS/MS for efficient identification of targeted triterpenes. Third, MRM-based characteristic chemical profile (CCP) of triterpenes was established using 30 MRM transitions by UHPLC-QTRAP-MS/MS. Fourth, MRM-based CCP was applied for comparative analyses of triterpenes in AR from different regions and from two other processed AR (salt processed AR and bran processed AR). Consequently, a total of 80 triterpenes including 14 novel compounds were identified in the AR, and 7 more triterpenes compounds were discovered using MRM-based CCP in the processed AR. This work is the most comprehensive characterization of triterpenes compounds in AR to date. The established MRM-based CCP of triterpenes compounds can be instructive for qualitative analyses and relative quantitative analyses of triterpenes in AR and its related medicinal products for potential applications including quality control and classification of different AR materials.Li, W., Liu, H., Song, X., 2017. Influence of fluid exposure on surface chemistry and pore-fracture morphology of various rank coals: Implications for methane recovery and CO2 storage. Energy & Fuels 31, 12552-12569. surface chemistry and pore-fracture morphology of coals are critical to the process of CO2 sequestration in coal seams with enhanced coalbed methane (CH4) recovery (CO2-ECBM). To assess the influence of deionized water–CO2 mixture (DH2O–CO2) exposure on these properties, the interaction of DH2O–CO2 with three rank coals, i.e., sub-bituminous coal (SBC), high volatile bituminous coal (HVBC), and anthracite, was conducted on a dynamic supercritical fluid extraction system with a temperature of 45 °C and an equilibrium pressure of 12 MPa. Characterization methods including proximate analysis (PA), Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), probe molecule (N2/CO2) adsorption, and low-field nuclear magnetic resonance (NMR) were adopted to fully address the changes in surface functional groups and pore-fracture characteristics. The results indicate that the geochemical interaction occurs between the mineral matters and DH2O–CO2 as demonstrated by the change in the content of clays, carbonates, and sulfates in the coal matrix. DH2O–CO2 exposure also causes a decrease in the content of organic oxygen and carbon–oxygen functional groups, especially for COOH groups, but an increase in C–C/C-H species, and the impact is strengthened with the decreasing coal rank. The aforementioned aspects illustrate the reconfiguration of surface geometry and the chemical interaction between DH2O–CO2 and the oxygen-containing functional groups. In combination with the reduced volatile matter and organic sulfur groups, the results imply that the extraction effect and chemical interaction may contribute to the change in coal surface chemistry. DH2O–CO2 interaction degrades the accessibility of micropores of all the coals, whereas the reverse trend is found for macropores and fractures. DH2O–CO2 interaction facilitates the development of macropores and fractures and thus improves the permeability of coal seams, which can be attributed to the dissolution and mobilization of mineral matters by the acid water and the shrinkage of coal induced by the water loss. The variation of mesopores due to DH2O–CO2 exposure is strongly related to coal rank and surface chemistry. Specifically, the decreasing mesoporosity is found for SBC, whereas this trend is opposite for HVBC and anthracite. The relationship between adsorption pores (<100 nm) and macropores and fractures of SBC decreases, while the opposite trend is recorded in HVBC and anthracite after fluid exposure. The results obtained from this work indicate that the net effect of the surface chemistry and the accessibility of porosity in various rank coals after fluid exposure is crucial for the potential of CH4 recovery and CO2 storage during the implementation of the CO2-ECBM process.Li, X., Danell, R.M., Pinnick, V.T., Grubisic, A., van Amerom, F., Arevalo Jr, R.D., Getty, S.A., Brinckerhoff, W.B., Southard, A.E., Gonnsen, Z.D., Adachi, T., 2017. Mars Organic Molecule Analyzer (MOMA) laser desorption/ionization source design and performance characterization. International Journal of Mass Spectrometry 422, 177-187. Mars Organic Molecule Analyzer (MOMA), a dual-source, ion trap-based instrument capable of both pyrolysis-gas chromatography mass spectrometry (pyr/GC-MS) and laser desorption/ionization mass spectrometry (LDI-MS), is the core astrobiology investigation on the ExoMars rover. The MOMA instrument will be the first spaceflight mass analyzer to exploit the LDI technique to detect refractory organic compounds and characterize host mineralogy; this mode of analysis will be conducted at Mars ambient conditions. In order to achieve high performance in the Martian environment while keeping the instrument compact and low power, a number of innovative designs and components have been implemented for MOMA. These include a miniaturized linear ion trap (LIT), a fast actuating aperture valve with ion inlet tube, and a Microelectromechanical System (MEMS) Pirani sensor. Advanced analytical capabilities like Stored Waveform Inverse Fourier Transform (SWIFT) for selected ion ejection and tandem mass spectrometry (MS/MS) are realized in LDI-MS mode, and enable the isolation and enhancement of specific mass ranges and structural analysis, respectively. We report here the technical details of these instrument components as well as system-level analytical capabilities, and we review the applications of this technology to Mars and other high-priority targets of planetary exploration.Li, X., Krooss, B.M., 2017. Influence of grain size and moisture content on the high-pressure methane sorption capacity of Kimmeridge Clay. Energy & Fuels 31, 11548-11557. study investigates the effect of grain size and water content on the methane (CH4) excess sorption capacity of Jurassic Kimmeridge clay from the U.K. Methane sorption isotherms were measured at 45 °C and pressures up to 25 MPa on dry and moist samples with particle sizes of <0.1, 0.177–0.3, 0.5–1, 1.4–2, and 2.36–4 mm. The finest particle-size fraction had a lower TOC content than the other fractions. Water contents determined at different relative humidity (RH) levels decreased with increasing grain size, indicating a significant effect of grain size on the water uptake of shales. The decrease in water uptake capacity from the smallest to the largest fraction ranges between 10 and 16%, depending on the RH level. The maximum methane excess sorption capacity in the smallest grain-size (<0.1 mm) fraction decreases by 46% at 97% RH as compared to the dry state. For the largest fraction (2.36–4 mm) with 16% less water uptake, the reduction of methane sorption capacity upon moisture equilibration is only 24%. Methane sorption isotherms show only a small grain-size dependence for dry samples, while this effect is significant in moist samples and controlled by the grain-size dependence of water sorption capacity. This investigation contributes to a better assessment of the gas storage capacity of gas shale systems.Li, X., Krooss, B.M., Ostertag-Henning, C., Weniger, P., Littke, R., 2018. Liberation of hydrogen-containing gases during closed system pyrolysis of immature organic matter-rich shales. International Journal of Coal Geology 185, 23-32. liberation of hydrogen sulfide (H2S), molecular hydrogen (H2) and hydrocarbon gases as well as CO2 from three immature carbonaceous rocks has been studied by Micro-Scale Sealed Vessel (MSSV) pyrolysis in the temperature range from 350 to 600 °C at a heating rate of 1 °C/min. The samples analyzed were the lacustrine Miocene Condor Shale from Australia (CON-1) and two marine marlstones (HBY-1 and HBY-2) from Southern Lebanon, with different contents of total sulfur (TS; 0.38–1.6%), total organic carbon (TOC; 3.7–11.6%) and total inorganic carbon (TIC; 2.8–9.3%). The Condor Shale has a high siderite (FeCO3) content (20.3%) and 0.2% pyrite (FeS2). The total iron (Fe) content is 10.5% and the kerogen is sulfur-lean. The iron (Fe) contents of the HBY samples are below 1% (0.9% and 0.3%, respectively) and insignificant amounts of pyrite are present, indicating a predominance of organic sulfur (sulfur-rich kerogen) with Sorg values of > 1%. The low Rock-Eval Tmax values support the presence of sulfur-rich, labile kerogen.CO2 was the major pyrolysis gas released from the CON-1 over the entire pyrolysis temperature range while no H2S was detected at any temperature level. The molar H2 yields tend to exceed the CH4 yields up to 475 °C while at higher pyrolysis temperatures CH4 is the predominant hydrogen-containing product gas. For the HBY-1 and HBY-2 samples H2S and CO2 are the major product gases up to 450 °C. Up to this temperature H2S is also the predominant hydrogen-bearing gas component. Subsequently methane and ethane yields exceed the molar H2S yields. At higher temperatures an increasing proportion of hydrogen is released as H2. Ultimately the molar H2 yields approach or even exceed the H2S yields from the sulfur-rich HBY samples.At pyrolysis temperatures < 450 °C the sulfur-rich kerogens liberate more hydrogen as H2S than as CH4 and H2. At high temperatures hydrogen release as H2 and H2S is less significant. These results indicate that, besides the amounts of molecular hydrogen released, the liberation of H2S should be taken into account for a comprehensive H mass balance of organic sulfur-rich source rocks. Approximately 50% of the hydrogen in sulfur-rich kerogen is released as CH4 during cracking at high temperatures (600 °C).Li, X., Tang, Z., Pang, X., Zhang, M., Liu, Y., 2017. Mesosomes associated with hydrogen peroxide in bacteria. Microbiology 86, 692-697. are unique membranous structures in bacteria. It is recognized that the mesosomes should be involved in several fundamental processes. The structure and behaviour of mesosomes have been studied and largely identified, while new evidences of mesosome function have been strikingly obtained. Our previous studies confirmed that hydrogen peroxide is involved in mesosomes formation during cell injury and cell division processes. Mesosome formation is always accompanied by excessive H2O2 accumulation. Furthermore, our recent data showed that mesosomes could not only enrich the excess H2O2, but also bring the H2O2 outside of the cells injured by antibiotics. It is a possibility that the enrichment of H2O2 in mesosomes might be a mechanism of drug resistance of bacteria. This article describes the bacterial mesosome and its functions as well as the involvement of hydrogen peroxide in mediating these functions.Li, X., Xu, R., Wei, X., Hu, H., Zhao, S., Liu, Y.-M., 2017. Direct analysis of biofluids by mass spectrometry with microfluidic voltage-assisted liquid desorption electrospray ionization. Analytical Chemistry 89, 12014-12022. suppression by sample matrix in direct electrospray ionization–mass spectrometric (ESI-MS) analysis hampers its clinical and biomedical applications. We report herein the development of a microfluidic voltage-assisted liquid desorption electrospray ionization (VAL-DESI) source to overcome this limitation. Liquid DESI is achieved for the first time in a microfluidic format. Direct analysis of urine, serum, and cell lysate samples by using the proposed microfluidic VAL-DESI-MS/MS method to detect chemical compounds of biomedical interest, including nucleosides, monoamines, amino acids, and peptides is demonstrated. Analyzing a set of urine samples spiked with dihydroxyphenylalanine (DOPA) showed that the assay had a linear calibration curve with r2 value of 0.997 and a limit of detection of 0.055 μM DOPA. The method was applied to simultaneous quantification of nucleosides, that is, cytidine, adenosine, uridine, thymidine, and guanosine in cell lysates using 8-bromoadenosine as internal standard. Adenosine was found most abundant at 26.5 ± 0.57 nmol/106 cells, while thymidine was least at 3.1 ± 0.31 nmol/106 cells. Interestingly, the ratio of adenosine to deoxyadenosine varied significantly from human red blood cells (1.07 ± 0.06) to cancerous cells, including lymphoblast TK6 (0.52 ± 0.02), skin melanoma C32 (0.82 ± 0.04), and promyelocytic leukemia NB4 cells (0.38 ± 0.06). These results suggest that the VAL-DESI-MS/MS technique has a good potential in direct analysis of biofluids. Further, because of the simplicity in its design and operation, the proposed microfluidic liquid DESI source can be fabricated as a disposable device for point-of-care measurements.Li, Y., Jiang, S., Jiang, Z., Liu, H., Li, B., 2017. Reconstruction of the Cenozoic history of hydrocarbon fluids from rifting stage to passive continental margin stage in the Huizhou Sag, the Pearl River Mouth Basin. Geofluids 2017, Article 4358985, 32 pp. Eocene lacustrine sediments are the primary source rocks in the Huizhou Sag of the Pear River Mouth Basin. This study employs basin modeling for four representative wells and two profiles in the Huizhou Sag to reconstruct the process of generation, expulsion, migration, and accumulation of hydrocarbon fluids. The Eocene source rocks started to generate hydrocarbon at 33.9?Ma and are currently in a mid-mature and postmature stage. Hydrocarbons are mainly expelled from the Eocene Wenchang Fm, and the contribution of the Eocene Enping formation is minor. Under the driving forces of buoyancy and excess pressure, major hydrocarbons sourced from the Eocene source rocks firstly migrated laterally to the adjacent Eocene reservoirs during the postrift stage, then vertically via faults to Oligo-Miocene carrier beds, and finally laterally to the structural highs over a long distance during the Pliocene-Quaternary Neotectonic stage, which is controlled by both structural morphology and heterogeneity of carrier beds. Fault is the most important conduit for hydrocarbon fluid migration during the Neotectonic stage. Reactivation of previous faults and new-formed faults caused by the Dongsha Movement (9.8–4.4?Ma) served as vertical migration pathways after 10.0?Ma, which significantly influenced the timing of hydrocarbon accumulation in the postrift traps.Li, Y., Song, Z.-G., Zhou, Q.-Z., Xu, X.-M., Cao, X.-X., 2017. The source and paleoclimatic implication of hydrogen isotopic composition of n-alkanes in sediments from the Yixian Formation, western Liaoning Province, NE China. Gondwana Research 52, 142-152. isotopic composition of n-alkanes was measured in sediments from an excavated profile of the Early Cretaceous Yixian Formation in Liaoning Province, NE China, aiming to assess the significance of the δD value of n-alkanes in ancient lacustrine sediments as the indicator for determining the source inputs of organic matters and paleoclimatic conditions. The δD values of n-alkanes are in the range of ? 250‰ to ? 85‰ and display an obvious three-stage variation pattern through the profile, which is consistent with the distribution of the dominated n-alkanes and the profile of their δ13C values. The δD and δ13C values of n-alkanes suggest that short-chain n-alkanes are primarily derived from photosynthetic bacteria and algae; n-C29 and n-C31 are mainly originated from terrestrial higher plants; n-C28 and n-C30 may be derived from the same precursor but via the different biological mechanism of hydrogen isotopic fractionation; while the source inputs of medium-chain n-alkanes are more complicated, with n-C23 being derived from some specific algae or biosynthesized by various aquatic organisms. The paleoclimatic conditions are reconstructed via two approaches. The reconstructed hydrogen isotopic values of lake water and meteoric water (expressed as δDLW and δDMW, respectively) were at the intervals of ? 51.8‰ to 17.0‰ and ? 118.1‰ to ? 43.5‰, respectively, indicating a general climate transition from semi-arid to arid. The calculated ΔδDLW-MW values vary from 37.0‰ to 89.1‰ and display a similar but a significant large-scale variation trend with the ΔδDC23 ‐ long (? 28.8‰ to 85.0‰; long represents long-chain n-alkanes) and ΔδDmid-long (? 15.4‰ to 43.4‰; mid represents medium-chain n-alkanes) values. The discrepancy may be attributed to the source input overlap for n-alkanes and the uncertainties of εwater/lipid values. The coupling of ΔδDC23 ‐ long, ΔδDmid-long and ΔδDLW-MW values with the paleoclimatic evidence indicates that the δD values of n-alkanes could be more sensitive to the change of paleoclimatic conditions.Li, Z., Cassar, N., 2017. A mechanistic model of an upper bound on oceanic carbon export as a function of mixed layer depth and temperature. Biogeosciences 14, 5015-5027. production reflects the amount of organic matter transferred from the ocean surface to depth through biological processes. This export is in large part controlled by nutrient and light availability, which are conditioned by mixed layer depth (MLD). In this study, building on Sverdrup's critical depth hypothesis, we derive a mechanistic model of an upper bound on carbon export based on the metabolic balance between photosynthesis and respiration as a function of MLD and temperature. We find that the upper bound is a positively skewed bell-shaped function of MLD. Specifically, the upper bound increases with deepening mixed layers down to a critical depth, beyond which a long tail of decreasing carbon export is associated with increasing heterotrophic activity and decreasing light availability. We also show that in cold regions the upper bound on carbon export decreases with increasing temperature when mixed layers are deep, but increases with temperature when mixed layers are shallow. A meta-analysis shows that our model envelopes field estimates of carbon export from the mixed layer. When compared to satellite export production estimates, our model indicates that export production in some regions of the Southern Ocean, particularly the subantarctic zone, is likely limited by light for a significant portion of the growing season.Li, Z., Li, L., Xing, L., Liu, Y., Zhang, M., Wang, X., Cao, C., Wang, Z., 2018. Development of new method for D/H ratio measurements for volatile hydrocarbons of crude oils using solid phase micro-extraction (SPME) coupled to gas chromatography isotope ratio mass spectrometry (GC-IRMS). Marine and Petroleum Geology 89, Part 1, 232-241. compound-specific isotope analysis (CSIA), one major challenge is the effective sample treatment and the isolation of sufficient amount of analytes for accurate measurements for isotope ratios. The hydrogen isotope ratio (D/H) of normal level hydrocarbons in crude oils has been successfully used as an isotopic tracer in oil-oil and oil-gas correlations, but little progress so far has been made for small size hydrocarbons (C6C15). In this paper, we presented a novel method for sample treatment and achieved the D/H ratio analysis for these particular compounds. The method can be characterized as an efficient approach featured by SPME (solid phase micro-extraction) coupled to GC-IRMS (gas chromatography-isotope ratio mass spectrometry). In this investigation, the CAR/DVB/PDMS fiber was evaluated and used as the absorptive material, and the operating conditions, including the extraction time (0.1 min–150 min) and the extraction temperature (?30 °C–140 °C), which may affect the adsorption amount, were carefully evaluated, and it was found that the adsorption yields varied considerably not only with the operating conditions but also with the molecular size. In addition, the possible hydrogen isotopic fractionation, which may exert strong influence on D/H ratios, were also discussed, it was found that the hydrogen isotopic fractionation were not observed in the extraction process, and the D/H ratios obtained via SPME-GC/IRMS were in good agreement with the EA-IRMS. Notably, the difference between the two approaches was generally within the expected uncertainties from 0.8‰ to 4.2‰, indicating the method is high efficient for volatile hydrocarbon enrichments and the D/H measurements. To assess the validity of the established method, one typical crude oil sample was analyzed, and the D/H ratio results displayed considerable large variation, enough to distinguished between different compounds, showing the established method is well suited for trace hydrocarbon enrichment, and provides so far the most efficient and reliable means for D/H analysis.Liang, C., Cao, Y., Jiang, Z., Wu, J., Guoqi, S., Wang, Y., 2017. Shale oil potential of lacustrine black shale in the Eocene Dongying depression: Implications for geochemistry and reservoir characteristics. American Association of Petroleum Geologists Bulletin 101, 1835-1858. geochemistry and reservoir characteristics of the lacustrine shale in the Eocene Dongying depression are described in detail based on thin-section and field-emission–scanning electron microscope observations of well cores combined with x-ray diffraction, physical property testing, and geochemical indicators. The Eocene Shahejie (Es) Formation Es4s–Es3x shale member is predominantly carbonate, clay minerals, and quartz. Six lithofacies were identified: (1) laminated limestone (organic-rich laminated limestone and organic-poor laminated limestone), (2) laminated marl, (3) laminated calcareous mudstone, (4) laminated dolomite mudstone, (5) laminated gypsum mudstone, and (6) massive mudstone. The Es4s–Es3x shale samples from three cored wells had total organic carbon (TOC) contents in the range of 0.58 to 11.4 wt. %, with an average of 3.17 wt. %. The hydrocarbon generation potential (free hydrocarbons [S1] + the hydrocarbons cracked from kerogen [S2]) values range from 2.53 to 87.68 mg/g, with an average of 24.19 mg/g. The Es4s–Es3x shale of the Dongying depression has a high organic-matter content with very good or excellent hydrocarbon generation potential. The organic maceral composition is predominantly sapropelinite (up to 95%). The hydrogen index (being S2/TOC) versus the maximum yield temperature of pyrolysate (Tmax) indicates that the organic matter is predominantly type I kerogen, which contains a high proportion of convertible organic carbon. The Es4s–Es3x shale is thermally mature and within the oil window, with the vitrinite reflectance values ranging from 0.46% to 0.74% and the Tmax value ranging from 413°C to 450°C, with the average being 442°C. The shale contains interparticle pores, organic-matter pores, dissolution pores, intracrystalline pores, interlaminar fractures, tectonic fractures, and abnormal-pressure fractures. The primary matrix pore storage is secondary recrystallized intercrystal pores and dissolution pores that formed during thermal maturation of organic matter. The TOC content and effective thickness of the organic-rich shales are the primary factors for hydrocarbon generation. The reservoir capacity is related to the scale, abundance, and connectivity of pore spaces, which are controlled by the characteristics of the lithofacies, mineral composition, TOC content, and microfractures.Liang, L., Liu, C., Jiang, F., Chen, Q., Zhang, L., Xue, H., Jiang, H.-L., Qian, J., Yuan, D., Hong, M., 2017. Carbon dioxide capture and conversion by an acid-base resistant metal-organic framework. Nature Communications 8, Article 1233. the rapid increase of CO2 emission, especially from power plants, there is a constant need for materials which can effectively eliminate post-combustion CO2 (the main component: CO2/N2?=?15/85). Here, we show the design and synthesis of a Cu(II) metal-organic framework (FJI-H14) with a high density of active sites, which displays unusual acid and base stability and high volumetric uptake (171?cm3?cm?3) of CO2 under ambient conditions (298?K, 1?atm), making it a potential adsorbing agent for post-combustion CO2. Moreover, CO2 from simulated post-combustion flue gas can be smoothly converted into corresponding cyclic carbonates by the FJI-H14 catalyst. Such high CO2 adsorption capacity and moderate catalytic activity may result from the synergistic effect of multiple active sites.Liang, L., Zhang, Z.-m., 2017. Structure-aware enhancement of imaging mass spectrometry data for semantic segmentation. Chemometrics and Intelligent Laboratory Systems 171, 259-265. Spectrometry Imaging data contains structural information, where similar mass spectra represent the same object. However, due to data contaminations during the measurement, the structural information in the image is in-apparent. We develop a new approach to enhance these structures and then semantically segmenting the given Mass Spectrometry Imaging data by following the enhanced structures. After the pipelined steps of image enhancement, raw segmentation and semantic clustering, meaningful color-coded image segmentation is produced, which greatly captures the main structure of the image and also suppress pixel-wise variations introduced during the measurement. Comparisons show the effectiveness of our pipeline. A biological application based on our enhancement and segmentation shows that our method can be used to identify regions of tissue sections.Liang, P., Yu, J., Zhang, Y., Jiao, T., Qin, X., 2017. Effects of natural dolomite catalysts on cracking anthracene oil. Energy & Fuels 31, 11765-11772. dolomite catalysts, representing a cheap and environmentally friendly alternative to nickel-based compounds, can be used for the cracking of anthracene oil to form more valuable products. The impact of operating conditions (temperature, water/oil mass ratio, and space velocity) on the distribution and yield of pyrolysis products was investigated in a fixed-bed reactor, providing insights into the mechanism of cracking. The gaseous products were analyzed by gas chromatography; the catalysts were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), and transmission electron microscopy; and the pyrolysis oil was analyzed by gas chromatography–mass spectrometry. The obtained results revealed that the gaseous products comprised H2, CO, CO2, CH4, and C2+. In comparison to anthracene oil, the pyrolysis oil contained significantly decreased amounts of alkyl aromatic hydrocarbons and indene compounds as well as an increased content of polycyclic aromatic hydrocarbons, such as naphthalene and phenanthrene. XRD and SEM analyses revealed granular coke deposition on the catalyst surface at a high temperature accompanied by partial conversion of the catalyst to CaCO3, which could be mitigated using high water/oil ratios. Thus, this study demonstrated the influence of reaction conditions on natural-dolomite-catalyzed cracking of anthracene oil, which is important for optimizing industrial production processes.Liao, L., Wang, Y., Chen, C., Shi, S., Deng, R., 2018. Kinetic study of marine and lacustrine shale grains using Rock-Eval pyrolysis: Implications to hydrocarbon generation, retention and expulsion. Marine and Petroleum Geology 89, Part 1, 164-173. kinetic parameters of marine and lacustrine shale grains (4 mm) were retrieved by using Rock-Eval pyrolysis in comparison with finely ground powder (<0.178 mm) and kerogen of same samples. Results of grains show remarkable differences from powder and kerogen. Grains of Pingliang marine shale exhibit a relatively broader distribution of activation energies than powder and kerogen while grains of Yanchang lacustrine shale show higher dominant activation energies than powder and kerogen. At laboratory heating rates (5–25 °C/min), the corresponding temperatures to the maximum hydrocarbon generating rate of grains are 3–8 °C higher than powder and kerogen for marine shale and 6–8 °C higher for lacustrine shale, respectively. Extrapolated to geological heating rate (3 °C/my), the corresponding maturity and geological temperature to the maximum hydrocarbon expulsion rate of grains lags powder 0.02 Ro% and 3 °C, as well as 0.05 Ro% and 6 °C for marine shale and lacustrine shale, respectively. After the peak of hydrocarbon generation (Ro = 1%), the retention percentage for grain and powder of marine shale reach 7.33% and 0.09% while those for lacustrine shale reach 16.50% and 10.85%, respectively. These results suggest grains enjoy higher expulsion threshold and higher retention ability. The results suggest that Yanchang lacustrine shale exhibits stronger retention ability and weaker expulsion ability than Pingliang marine shale. The results presented in this study show that grain-based pyrolysis provides a novel method for evaluating the residual oil and gases for shale, which can study the hydrocarbon generation, expulsion and retention comprehensively.Liaudat, J., Martínez, A., López, C.M., Carol, I., 2018. Modelling acid attack of oilwell cement exposed to carbonated brine. International Journal of Greenhouse Gas Control 68, 191-202. diffusion-reaction model for the carbonation process of oilwell cement exposed to carbonated brine under CO2 geological storage conditions is presented. The formulation consists of two main diffusion/reaction field equations for the concentrations of aqueous calcium and carbon species in the pore solution of the hardened cement paste, complemented by two diffusion-only field equations for chloride and alkalis concentrations, and by a number of chemical kinetics and chemical equilibrium equations. The volume fraction distribution of the solid constituents of the hardened cement paste and the reaction products evolve with the progress of the reaction, determining the diffusivity properties of the material. The model is used to simulate experimental tests performed by Duguid and Scherer (2010), leading to promising results indicating that the fundamental aspects of the phenomenon are captured.Lima, F.C.D.A., Alvim, R.d.S., Miranda, C.R., 2017. From single asphaltenes and resins to nanoaggregates: A computational study. Energy & Fuels 31, 11743-11754. understanding of intermolecular interactions on asphaltene nanoaggregates has important implications over the petroleum industry. Here, we investigated the aggregation of asphaltene and resin using a hierarchical approach that combines Density Functional Theory (DFT) with dispersion corrections and molecular mechanics (MM) calculations. From molecular models already established in the literature for specific types of asphaltene (A) and resin (R) molecules, we employed MM simulations to calculate the potential energy surface to obtain the best conformations for the possible dimers A-A, A-R, and R-R, as well as the relevant combinations of trimers A-R-A, A-A-R, and A-A-A, which have been further relaxed by the DFT calculations. Indeed, the formation of the dimer A-A is energetically more favored with respect to A-R and R-R mainly due to the enhanced effect on the intermolecular interaction of the aromatic region of A. In this context, the trimers have shown to be almost 3 times more stable than the dimers. Our result suggests that the nanoaggregates have a charge density well distributed but centralized between the aromatic ring π-orbitals, whereas A molecules are added, creating a tightly packed structure. In this case, the contribution from the aliphatic chains is just steric to stabilize the aggregate and shield the aromatic center for new interactions. Although the π–π stacking can guide the nanoaggregate formation, the presence of the R molecule leads to a possible disaggregation. When R molecules are inserted, the growth of the nanoaggregate seems to be yet continued due to a dipole moment and radius of gyration increasing. However, we observed charge rearrangement from the aromatic center of π–π interaction to aliphatic chains with heteroatoms that displaces into the structure. The HOMO-1 and HOMO degeneracy is broken in this time, being more significant in trimers derived from particular dimer conformation. The formation energy in some asphaltene and resin conformations is decreased compared to the asphaltene nanoaggregates with larger aromatic islands. Therefore, R rich in heteroatoms may be seen like an inner destabilizer naturally present in oil. These findings can guide new methods to control the stability of asphaltene aggregates by external chemical agents through the degradation mechanism directly upon the aliphatic chains.Lin, D.-C., Chen, M.-T., Yamamoto, M., Yokoyama, Y., 2017. Hydrographic variability in the northern South China Sea over the past 45,000 years: New insights based on temperature reconstructions by U37k' and TEX86H proxies from a marine sediment core (MD972146). Quaternary International 459, 1-16. climate variability was persistent feature for Greenland ice core and North Atlantic marine records during the Marine Isotope Stage (MIS) 3. Studying high quality climatic archives outside of the Greenland and North Atlantic with precise constraint of absolute dating and high resolution sampling is a prerequisite to understand how the millennial-scale changes well expressed in North Hemisphere (NH) high latitudes had been propagated out to the other regions. Here, we generated the surface and subsurface hydrography (U37k' and TEX86H temperatures) and terrestrial material input (n-alkanes) records with precise AMS 14C dated control for the 45 ka from a core (MD972146) retrieved from the northern South China Sea (SCS). Then, we compared our records to the oxygen isotope record from a Greenland NGRIP ice core, and the mean grain size record from a loess sequence at Gulang, China. We found that the millennial-scale oscillations of hydrolography and terrestrial material inputs records during the time since the last deglaciation and of ～33–45 ka share similar patterns in timing and amplitude of the NH high latitude climate. However, we found that a non-NH pattern of millennial-scale oscillations for the late MIS 3, ～20–33 ka of our hydrography and terrestrial material inputs records. Our studies imply that the changes of obliquity also may be important in determining the timing and amplitude of millennial-scale East Asian Monsoon (EAM) variability expressed in the northern SCS hydrography and terrestrial material inputs.Lin, Y.-J., He, P., Tavakkoli, M., Mathew, N.T., Fatt, Y.Y., Chai, J.C., Goharzadeh, A., Vargas, F.M., Biswal, S.L., 2017. Characterizing asphaltene deposition in the presence of chemical dispersants in porous media micromodels. Energy & Fuels 31, 11660-11668. are components in crude oil known to deposit and interrupt flows in critical regions during oil production, such as the wellbore and transportation pipelines. Chemical dispersants are commonly used to disperse asphaltenes into smaller agglomerates or increase asphaltene stability in solution with the goal of preventing deposition. However, in many cases, these chemical dispersants fail in the field or even worsen the deposition problems in the wellbores. Further understanding of the mechanisms by which dispersants alter asphaltene deposition under dynamic flowing conditions is needed to better understand flow assurance problems. Here, we describe the use of porous media microfluidic devices to evaluate how chemical dispersants change asphaltene deposition. Four commercially used alkylphenol model chemical dispersants are tested with model oils flowing through porous media, and the resulting deposition kinetics are visualized at both the matrix scale and pore scale. Interestingly, initial asphaltene deposition worsens in the presence of the tested dispersants, but the mechanism by which plugging and permeability reduction in the porous media varies. The velocity profiles near the deposit are analyzed to further investigate how shear forces affect asphaltene deposition. The deposition tendency is also related to the intermolecular interactions governing the asphaltene–dispersant systems. Furthermore, the model system is extended to a real case. The use of porous media microfluidic devices offers a unique platform to develop and design effective chemical dispersants for flow assurance problems.Lipson, M., Szécsényi-Nagy, A., Mallick, S., Pósa, A., Stégmár, B., Keerl, V., Rohland, N., Stewardson, K., Ferry, M., Michel, M., Oppenheimer, J., Broomandkhoshbacht, N., Harney, E., Nordenfelt, S., Llamas, B., Gusztáv Mende, B., K?hler, K., Oross, K., Bondár, M., Marton, T., Osztás, A., Jakucs, J., Paluch, T., Horváth, F., Csengeri, P., Koós, J., Seb?k, K., Anders, A., Raczky, P., Regenye, J., Barna, J.P., Fábián, S., Serlegi, G., Toldi, Z., Gy?ngyvér Nagy, E., Dani, J., Molnár, E., Pálfi, G., Márk, L., Melegh, B., Bánfai, Z., Domboróczki, L., Fernández-Eraso, J., Antonio Mujika-Alustiza, J., Alonso Fernández, C., Jiménez Echevarría, J., Bollongino, R., Orschiedt, J., Schierhold, K., Meller, H., Cooper, A., Burger, J., Bánffy, E., Alt, K.W., Lalueza-Fox, C., Haak, W., Reich, D., 2017. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368-372. DNA studies have established that Neolithic European populations were descended from Anatolian migrants who received a limited amount of admixture from resident hunter-gatherers. Many open questions remain, however, about the spatial and temporal dynamics of population interactions and admixture during the Neolithic period. Here we investigate the population dynamics of Neolithization across Europe using a high-resolution genome-wide ancient DNA dataset with a total of 180 samples, of which 130 are newly reported here, from the Neolithic and Chalcolithic periods of Hungary (6000–2900 bc, n?=?100), Germany (5500–3000 bc, n?=?42) and Spain (5500–2200 bc, n?=?38). We find that genetic diversity was shaped predominantly by local processes, with varied sources and proportions of hunter-gatherer ancestry among the three regions and through time. Admixture between groups with different ancestry profiles was pervasive and resulted in observable population transformation across almost all cultural transitions. Our results shed new light on the ways in which gene flow reshaped European populations throughout the Neolithic period and demonstrate the potential of time-series-based sampling and modelling approaches to elucidate multiple dimensions of historical population interactions.Lísa, M., Cífková, E., Khalikova, M., Ov?a?íková, M., Hol?apek, M., 2017. Lipidomic analysis of biological samples: Comparison of liquid chromatography, supercritical fluid chromatography and direct infusion mass spectrometry methods. Journal of Chromatography A 1525, 96-108. analysis of biological samples in a clinical research represents challenging task for analytical methods given by the large number of samples and their extreme complexity. In this work, we compare direct infusion (DI) and chromatography – mass spectrometry (MS) lipidomic approaches represented by three analytical methods in terms of comprehensiveness, sample throughput, and validation results for the lipidomic analysis of biological samples represented by tumor tissue, surrounding normal tissue, plasma, and erythrocytes of kidney cancer patients. Methods are compared in one laboratory using the identical analytical protocol to ensure comparable conditions. Ultrahigh-performance liquid chromatography/MS (UHPLC/MS) method in hydrophilic interaction liquid chromatography mode and DI-MS method are used for this comparison as the most widely used methods for the lipidomic analysis together with ultrahigh-performance supercritical fluid chromatography/MS (UHPSFC/MS) method showing promising results in metabolomics analyses. The nontargeted analysis of pooled samples is performed using all tested methods and 610 lipid species within 23 lipid classes are identified. DI method provides the most comprehensive results due to identification of some polar lipid classes, which are not identified by UHPLC and UHPSFC methods. On the other hand, UHPSFC method provides an excellent sensitivity for less polar lipid classes and the highest sample throughput within 10 min method time. The sample consumption of DI method is 125 times higher than for other methods, while only 40 μL of organic solvent is used for one sample analysis compared to 3.5 mL and 4.9 mL in case of UHPLC and UHPSFC methods, respectively. Methods are validated for the quantitative lipidomic analysis of plasma samples with one internal standard for each lipid class. Results show applicability of all tested methods for the lipidomic analysis of biological samples depending on the analysis requirements.Liu, B., Bechtel, A., Gross, D., Fu, X., Li, X., Sachsenhofer, R.F., 2018. Middle Permian environmental changes and shale oil potential evidenced by high-resolution organic petrology, geochemistry and mineral composition of the sediments in the Santanghu Basin, Northwest China. International Journal of Coal Geology 185, 119-137. in the Middle Permian Lucaogou Formation have been considered as one of the most important unconventional reservoirs in NW China, due to their excellent shale oil and tight oil potential. Based on the data of previous organic geochemical studies, the overall evolution of the ecosystem in the lake, water conditions and organic matter sources have been outlined. Here we present the results of the mineralogical and organic-petrological examinations and the Rock-Eval pyrolysis, on samples of a fine-grained, mixed carbonate-clastic sedimentary succession from the Santanghu Basin, providing new detailed insights into paleoenvironmental evolution and lake level changes. In addition, shale oil potential was further evaluated on this oil-prone shale.Analytical results from a total of 196 shale samples from the second member of the Lucaogou Formation, collected from one newly drilled core, indicate algal/microbial sources of organic matter, classified by Rock-Eval pyrolysis as type I kerogen. Samples characterized by lower hydrogen index (HI) values (type II kerogen) contain increased contributions of terrigenous organic matter, evidenced by enhanced inertinite and vitrinite contents. Vertical variations in mineralogical and bulk geochemical composition reflect an evolution from a saline, anoxic to a deep, freshwater lake. Two environmental changes subdivided the sequence into three units. The boundary between the lower Unit I and the middle Unit II is characterized by the drastic decrease of smectite and K-feldspar contents and a sharp increase in total organic carbon (TOC) content. The upper Unit III is distinguished by high TOC/S ratios. Based on variations in petrography and carbon isotopes of hopanes, the middle Unit II can be further subdivided into two parts reflecting changes in water level of the lake. All the periods of high-water level are characterized by higher lamalginite contents (> 40 vol%) and higher HI values than those obtained from sediments deposited during periods of shallower water levels. Deposition in a shallow lake is evidenced by increased dolomite and decreased lamaginite contents. Lake level fluctuations, indicated by mineralogical and geochemical parameters, are associated with changes in organic matter sources, leading to the great variability in mineral content, organic petrography and hydrocarbon generation potential. High TOC and brittle minerals contents, micro-nanopores system and large thickness of the shale show that the Lucaogou Formation holds a significant shale oil potential in areas where oil window maturity is reached.Liu, B., Schieber, J., Mastalerz, M., 2017. Combined SEM and reflected light petrography of organic matter in the New Albany Shale (Devonian-Mississippian) in the Illinois Basin: A perspective on organic pore development with thermal maturation. International Journal of Coal Geology 184, 57-72. pores are an important aspect of pore systems in unconventional gas shale reservoirs. Along with thermal maturity, organic maceral type critically controls the development of secondary organic-matter-hosted pores. Three New Albany Shale samples (Devonian-Mississippian, kerogen type II sequence) having thermal maturities ranging from a vitrinite reflectance (Ro) of 0.55% to 1.42% were analyzed using a reflected light microscope and a field emission scanning electron microscope. Organic pores were examined in specific organic macerals and solid bitumen at different thermal maturities. Vitrinite and inertinite, derived from terrestrial woody materials, occur as discrete particles in this black shale. Within the resolution limits of the scanning electron microscope, these two macerals do not appear to display enhanced secondary pores associated with increases in thermal maturity. Cellular pores (0.2–10 μm) in inertinite were observed throughout the entire maturity range and were typically filled with authigenic quartz or solid bitumen. Because of thermal degradation, amorphous organic matter was not observed at maturities greater than Ro 0.80%. Alginite derived from Tasmanites cysts matures later than amorphous organic matter and is still present at Ro 0.80%; however, it is in the process of transforming to pre-oil bitumen and shows weak orange yellow fluorescence compared to strong greenish-yellow fluorescence in lower-maturity samples. At a maturity of Ro 1.42%, alginite could no longer be observed as a distinct phase because of its complete transformation to hydrocarbons and bitumen. Alginite began to develop secondary pores when it was in the process of transforming to pre-oil bitumen, which indicates that some liquid and gaseous hydrocarbons left the alginite during this part of the maturation process. Solid bitumen developed along the original amorphous organic matter networks and now occupies interparticle space between quartz, dolomite, K-feldspar, clay, and mica grains, as well as the cellular pores in inertinite particles. Solid bitumen becomes smaller and more porous with thermal maturation and, thus, becomes increasingly unidentifiable with the optical microscope. Solid bitumen-hosted pores (20–1000 nm) are the main organic pore type documented in the studied samples, and they are more common in shales within the gas window than those in the oil window. Secondary nanopores in the solid bitumen network play a significant role in hydrocarbon storage and migration.Liu, B., Zhang, G., Mao, F., Liu, J., Cheng, D., Lü, M., 2017. The petroleum system of the Tenere Basin: oil geochemistry from the SH-1 wildcat well in eastern Niger. Petroleum Geoscience 23, 427-439. SH-1 wildcat well, firstly encountering oil, proved the existence of a working petroleum system in the Tenere Basin, but the origin of oil and its generation history is not fully understood. In this regard, one crude oil and nine Upper Cretaceous source rock samples from the SH-1 wildcat well in the Tenere Basin were characterized by a variety of biomarker parameters and stable carbon isotopic composition. The oil from the Tenere Basin displays a low pristine/phytane (Pr/Ph) ratio, low C29/C30 and C35/C34 hopane ratios, low C22/C21 and high C24/C23 tricyclic terpane ratios, and high gammacerane index (gammacerane/C30 hopane), suggesting shale source rocks deposited under an anoxic and relatively high-salinity environment. Relatively high C29 sterane concentrations, a low value of the regular steranes/17α(H)-hopanes ratio and a canonical variable from stable carbon isotopic composition larger than 0.47 indicate that the oil is mainly derived from terrestrial higher plants. Both aromatic maturity parameters and sterane isomerization parameters suggest that the oil was generated from an early mature source rock. Correlation between oils from the Tenere Basin and those from the Termit Basin confirms that these oils belong to the same genetic family. The oil–source rock correlation suggests that the oil from the Tenere Basin originated from the Upper Cretaceous marine source rocks, and the Yogou Formation can be considered as effective source potential.Liu, H., Raffin, G., Trutt, G., Randon, J., 2017. Is vacuum ultraviolet detector a concentration or a mass dependent detector? Journal of Chromatography A 1530, 171-175. vacuum ultraviolet detector (VUV) is a very effective tool for chromatogram deconvolution and peak identification, and can also be used for quantification. To avoid quantitative issues in relation to time drift, such as variation of peak area or peak height, the detector response type has to be well defined. Due to the make-up flow and pressure regulation of make-up, the detector response (height of the peak) and peak area appeared to be dependent on experimental conditions such as inlet pressure and make-up pressure. Even if for some experimental conditions, VUV looks like mass-flow sensitive detector, it has been demonstrated that VUV is a concentration sensitive detector.Liu, H., Zhang, B., Yuan, H., Cheng, Y., Wang, S., He, Z., 2017. Microbial reduction of vanadium (V) in groundwater: Interactions with coexisting common electron acceptors and analysis of microbial community. Environmental Pollution 231, 1362-1369. (V) pollution in groundwater has posed serious risks to the environment and public health. Anaerobic microbial reduction can achieve efficient and cost-effective remediation of V(V) pollution, but its interactions with coexisting common electron acceptors such as NO3?, Fe3+, SO42? and CO2 in groundwater remain unknown. In this study, the interactions between V(V) reduction and reduction of common electron acceptors were examined with revealing relevant microbial community and identifying dominant species. The results showed that the presence of NO3? slowed down the removal of V(V) in the early stage of the reaction but eventually led to a similar reduction efficiency (90.0% ± 0.4% in 72-h operation) to that in the reactor without NO3?. The addition of Fe3+, SO42?, or CO2 decreased the efficiency of V(V) reduction. Furthermore, the microbial reduction of these coexisting electron acceptors was also adversely affected by the presence of V(V). The addition of V(V) as well as the extra dose of Fe3+, SO42? and CO2 decreased microbial diversity and evenness, whereas the reactor supplied with NO3? showed the increased diversity. High-throughput 16S rRNA gene pyrosequencing analysis indicated the accumulation of Geobacter, Longilinea, Syntrophobacter, Spirochaeta and Anaerolinea, which might be responsible for the reduction of multiple electron acceptors. The findings of this study have demonstrated the feasibility of anaerobic bioremediation of V(V) and the possible influence of coexisting electron acceptors commonly found in groundwater.Liu, J., Hou, J., Liu, H., Liu, M., Xu, J., Chen, G., Zhang, J., 2018. Molecular mechanism of formation of the face-sharing double cages in structure-I methane hydrate. Chemical Physics Letters 691, 155-162. the potential applications and ubiquity of clathrate hydrates, the molecular mechanism of formation of these compounds is not yet well-understood. In this work, the formation mechanism of the face-sharing double cages in structure-I hydrate was studied by density functional theory calculations, which is responsible to the hydrate nucleation and growth. The results show that the clathrate cages favor to form one after another, and the 512 cages are thermodynamically feasible in the beginning. The water-water and water-methane interactions mostly dominate the formation of the clathrate cages, while the methane-methane interactions have little effect on the formation process.Liu, J., Hu, Q., Young Kim, D., Wu, Z., Wang, W., Xiao, Y., Chow, P., Meng, Y., Prakapenka, V.B., Mao, H.-K., Mao, W.L., 2017. Hydrogen-bearing iron peroxide and the origin of ultralow-velocity zones. Nature 551, 494-497. zones (ULVZs) at Earth’s core–mantle boundary region have important implications for the chemical composition and thermal structure of our planet, but their origin has long been debated. Hydrogen-bearing iron peroxide (FeO2Hx) in the pyrite-type crystal structure was recently found to be stable under the conditions of the lowermost mantle. Using high-pressure experiments and theoretical calculations, we find that iron peroxide with a varying amount of hydrogen has a high density and high Poisson ratio as well as extremely low sound velocities consistent with ULVZs. Here we also report a reaction between iron and water at 86 gigapascals and 2,200 kelvin that produces FeO2Hx. This would provide a mechanism for generating the observed volume occupied by ULVZs through the reaction of about one-tenth the mass of Earth’s ocean water in subducted hydrous minerals with the effectively unlimited reservoir of iron in Earth’s core. Unlike other candidates for the composition of ULVZs, FeO2Hx synthesized from the superoxidation of iron by water would not require an extra transportation mechanism to migrate to the core–mantle boundary. These dense FeO2Hx-rich domains would be expected to form directly in the core–mantle boundary region and their properties would provide an explanation for the many enigmatic seismic features that are observed in ULVZs.Liu, L., Yao, J., Zhang, L., An, S., Zhao, J., Sun, H., 2017. REV-scale simulation of micro-fractured unconventional gas reservoir. Journal of Natural Gas Science and Engineering 48, 100-110. fractures such as hydraulic fractures and natural micro-fractures coexist in unconventional gas reservoir among which micro-fractures have great effect on the effective matrix permeability at representative elementary volume (REV) scale. In addition, in the development of unconventional gas, matrix properties and fracture aperture are influenced by gas transport mechanisms including Klinkenberg effect, stress sensitivity and gas adsorption. To investigate the influence of micro-fractures and gas transport mechanisms, a new model for REV-scale unconventional gas flow simulation has been presented based on REV-scale Lattice Boltzmann Method model and gas transport mechanisms. And the effects of different fracture features were analyzed and the most important feature was filtered. In addition, the effects of gas transport mechanisms on matrix permeability and effective permeability were investigated. The results indicate that fracture density has the greatest effect on the effective permeability that the increase multiple can reach to 1 order of magnitude when matrix permeability is at 10?4?μm2 level while fracture aperture has little effect. Moreover, gas transport mechanisms have significant effects on matrix properties and effective permeability. With the decline of gas pressure, matrix permeability increases and fracture aperture decreases which lead to the decrease of the effective permeability. But the decrease of the effective permeability is not great which is approximately 50% under the gas pressure decline of 20?MPa.Liu, M., Mostaghimi, P., 2017. Pore-scale modelling of CO2 storage in fractured coal. International Journal of Greenhouse Gas Control 66, 246-253. disposal of CO2 is a key issue for greenhouse gas control. We apply a reactive transport model based on lattice Boltzmann and finite volume methods to simulate the injection of CO2-saturated brine into a fractured coal. Fluid flow, transport of solute and dissolution are modelled at the pore scale. Fracture closure under overburden pressure is considered in the numerical model by performing mineral detachment identification and aperture adjustment. Variations of permeability and porosity are investigated. Mechanical properties are calculated to study the effect of mineral dissolution on formation stability. The results show that injection of CO2 causes fracture demineralisation. However, the removal of minerals may result in closure of existing fractures increasing resistance to fluid flow. This paper helps improve understanding of CO2 injection into coal seams and discusses its potential effect on coal properties.Liu, P., Qin, Y., Liu, S., Hao, Y., 2018. Non-linear gas desorption and transport behavior in coal matrix: Experiments and numerical modeling. Fuel 214, 1-13. desorption and transport in coal matrix plays pivot roles to estimate in situ gas content, forecast gas production from coalbed methane (CBM) wellbores, classify the gas/coal outburst proneness of coal seams and estimate gas emission rate for active mine ventilation planning. Only using Fick’s law to depict methane transport in coal matrix may result in an erroneous prediction because it uses only adsorbed phase gas to calculate methane concentration gradient. In this study, a series of coal-methane ad/desorption experiments were carried out under different pressure boundary conditions. Following this, an effort is made to propose a semi-empirical desorption model describing the entire methane diffusion process and discuss its superiority and applicability by comparing to various commonly used models. The proposed approach includes two different theoretical models (Fick diffusion model, assuming concentration-difference transports gas; and Density model, assuming density-difference transports gas), to model methane diffusion corresponding to the experimental sections conducted in this study. Afterward a series of comparisons between the experimental desorption data and two sets of simulated desorption data obtained by numerically calculating the two theoretical models were conducted, and it shows that Density model exhibited a higher accuracy over Fick model. The proposed Density model is more effective in describing the non-linear gas diffusion behavior in coal matrix for the experimentally studied coals. Essentially, the Density model covers and promotes the Fick diffusion model, and is competent in mathematically modeling both adsorbing gas and non-adsorbing gas transport behavior in porous media. Moreover, the Density model can be directly incorporated to the existing dual-porosity model to model methane migration in coal matrix in coal seam.Liu, P., Wang, X., Meng, Q., Wang, X., Zhang, L., Liu, C., Lei, Y., Jiang, C., Yin, J., 2018. Simulation of shale gas generation by using different experimental systems: A case study from Chang7 shale in the Ordos Basin. Journal of Natural Gas Science and Engineering 49, 169-178. this study, open system and closed system laboratory pyrolysis are conducted on a low maturity shale sample from Yanchang Formation of the Ordos Basin. The kinetics parameters in different experimental systems were calculated and extrapolated to geological conditions to predict the yield of hydrocarbon gases and the hydrocarbon generation history. In addition, the amount of hydrocarbon gases expelled during generation was estimated by using hydrocarbon gas generation kinetics extrapolation and the residual gas measurement of the shale. Moreover, the desorbed gas in 98 shale core samples from 4 drilling wells were measured and the ratio of desorbed hydrocarbon gases to generated hydrocarbon gases was calculated. The yield and transformation ratio of methane (C1) in the study area ranged from 22.80 to 36.52 ml/g·TOC and 0.07 to 0.31, respectively. The yield and transformation ratio of hydrocarbon gases (C1-C5) in the study area ranged from 36.13 to 59.28 ml/g·TOC and 0.12 to 0.34, respectively. During the generation process, shale gas was expelled in quantities ranging from 4.68 to 27.83 ml/g·TOC. The average ratios of desorbed hydrocarbon gases to generated hydrocarbon gases in 98 shale samples ranged from 33.78% to 55.79%; however, the ratios of samples for 4 different drilling wells were different, suggesting different adsorption capacities in shales from different parts of the southeastern Ordos Basin.Liu, Q., Jin, Z., Li, H., Wu, X., Tao, X., Zhu, D., Meng, Q., 2018. Geochemistry characteristics and genetic types of natural gas in central part of the Tarim Basin, NW China. Marine and Petroleum Geology 89, Part 1, 91-105. to the chemical, carbon isotopic, and hydrogen isotopic compositions and 3He/4He ratios of 127 natural gas samples, the natural gas in the Tarim Basin is mainly composed of gaseous alkanes dominated by methane. The contents of the gaseous alkanes decrease with the increase of their carbon numbers. The δ13C values of CH4, C2H6 and C3H8 in the platform area of the Tarim Basin vary in the range of ?54.4‰～-24.4‰ (an average value of ?39.2‰), ?43.1‰～-26.7‰ (an average value of ?36.1‰) and ?37.9‰～-21.6‰ (an average value of ?31.8‰), respectively. The overall carbon isotopic composition of the alkanes follows the trend of δ13C1< δ13C2< δ13C3< δ13C4 and in some cases varies with δ13C1>δ13C2 or δ13C3> δ13C4. The lower carbon isotope values of methane (δ13C1< δ13C2) may be attributed to thermal sulfate reduction (TSR), and the higher propane value (δ13C3> δ13C4) was caused by the mixing of the natural gases of the same genetic type formed at different stages. The methane hydrogen isotopes (δ2H-C1) of the natural gases in the Tarim Basin are in the range of ?195‰～-122‰ with an average value of ?156‰. The 3He/4He ratios of the natural gases are in the range of 2.3 × 10?8～66.8 × 10?8, suggesting that there is no deep mantle-derived gas in the platform area of the Tarim Basin. The carbon isotope fractionation of alkane gases (δ13C2<?28‰ and δ13C3<?25‰) indicates that the natural gas in the platform area of the Tarim Basin is oil-type. The modified plots of lnC1/C2 vs. lnC2/C3 and C2/C3 vs. δ13C2-δ13C3 of the natural gases indicate that the oil-type gas in the Tarim Basin has different predominant formation processes, including kerogen-cracking, oil-cracking, oil- and gas-cracking, secondary gas-cracking and mixing of the kerogen-cracking and oil-cracking gases. The gas evolved from gas-cracking gas, to oil- and gas-cracking gas and oil-cracking gas along the direction from the west side of the Manjar Sag to the central Tarim Basin. The natural gases in some areas of Tazhong are the mixtures of the kerogen-cracking and oil-cracking gases.Liu, S., Li, L., Guo, L., Jin, H., Kou, J., Li, G., 2017. Sulfur transformation characteristics and mechanisms during hydrogen production by coal gasification in supercritical water. Energy & Fuels 31, 12046-12053. supercritical water gasification (SCWG) is famous for generating clean gas without SOx pollutant. Study of sulfur transformation characteristics can provide the basis of sulfur removal during hydrogen production by coal gasification in supercritical water (SCW) at the source. In this work, two coals produced from Linfen and Zhangjiamao in China (hereinafter to be referred as L-coal and Z-coal), were chosen as experimental feedstocks to investigate sulfur transformation characteristics during hydrogen production by coal gasification in SCW (550–750 °C, 20 min, 25 MPa). Sulfur transformation pathway and sulfur forms in the products were complex but detected comprehensively. H2S was the only gaseous product instead of SOx, whereas SO42– was the main liquid–sulfur product. Inorganic and organic sulfur compounds were used to investigate sulfur transformation mechanisms. H2S had three sources as follows. First, among inorganic sulfur of raw coal, FeS2 (Pyrite) was chemically stable in SCW lacking of hydrogen. When FeS2 was in hydrogen atmosphere, H2S was generated and FeS2 was converted to Fe1–xS and Fe3O4 under SCW. Second, H2S came from unstable sulfate minerals such as FeSO4 which may decompose and be converted to Fe3O4. Third, organic sulfur, especially thiophene sulfur transformed to H2S. The two sulfur products H2S and SO42– depend on H or OH free radical in SCW. More H free radical provided a reducing environment of SCW to generate H2S at higher temperatures, whereas more OH radical provided an oxidizing environment of SCW to generate SO42– at lower temperatures, but the final trend was generating H2S when coal gasified completely at a higher temperature. The results of this study may provide an experimental basis of solving the SOx emission from coal at the source and demonstrate a promising clean utilization way of coal.Liu, W.E.I., Zhang, X., 2017. Possible biogenic structures from the Lower Cambrian strata in Yunnan Province, South China. Geological Magazine 154, 1285-1293. induced sedimentary structures (MISS) are microbial traces in sandy deposits. They have been formed by various modes of microbial behaviour in response to the prevailing physical dynamics in shallow-marine environments since early Archaean time. An association of fossils, phosphatic structures and grains, stromatolites and microbial laminated levelling structures is documented from the Zhongyicun Member of Lower Cambrian strata in the Baideng section dated close to 535 Ma. SEM examination demonstrates that microbial laminated levelling structures are the result of the development of microbial mats composed of filamentous structures. We propose that there was a short hiatus after the dolomite layer deposited when the dolomite layer was weathered to form centimetre-scale valleys firstly, and then microbes accumulated in these valleys and formed the microbial laminated levelling structures.Liu, X.-L., Lipp, J.S., Birgel, D., Summons, R.E., Hinrichs, K.-U., 2018. Predominance of parallel glycerol arrangement in archaeal tetraethers from marine sediments: Structural features revealed from degradation products. Organic Geochemistry 115, 12-23. monobiphytanyl glycerol diethers (GMGDs) have recently been identified as degradation products of glycerol dibiphytanyl glycerol tetraethers (GDGTs) and occur as regioisomers. The distribution patterns of GMGD regioisomers are diagnostic for the glycerol configuration of their precursor GDGTs. We systematically examined the distributions of GMGDs and other regioisomer-specific degradation products in a suite of marine sediments and methane seep carbonates. The distinctly different patterns of GMGD compounds in these contrasting environments affords a new way of examining and elucidating the structures of the GDGT precursors. In contrast to the prevalent assumption of a predominant antiparallel GDGT glycerol arrangement in marine sediments, we show that the pool of GDGT-typical marine sediments, which harbor the remains of predominantly planktonic Thaumarchaeota, is composed largely of parallel regioisomers. In the contrasting environments of methane seep carbonates and Cascadia Margin subsurface sediment impacted by anaerobic methane oxidation, the patterns of the GMGD regioisomers indicate a substantial antiparallel GDGT fraction, implying that this may be a feature of methane-metabolizing Euryarchaeota. Crenarchaeol, presently considered specific to planktonic Thaumarchaeota, has an exclusively parallel glycerol arrangement with its tricyclic biphytane moiety bound to the sn3 carbon of glycerol on both sides. We provide data to show that the compound widely known as the ‘crenarchaeol regioisomer’, a compound factored into the widely used TEX86 paleotemperature proxy, rather than having an antiparallel glycerol arrangement, actually possesses a different ring configuration on its tricyclic biphytane moiety.Liu, Y., Chen, D., Qiu, N., Fu, J., Jia, J., 2018. Geochemistry and origin of continental natural gas in the western Sichuan basin, China. Journal of Natural Gas Science and Engineering 49, 123-131. molecular compositions and stable carbon and hydrogen isotopes of natural gases of Jurassic and Upper Triassic strata in western Sichuan Basin were investigated to assess the origin, maturity, sources. Then the results were compared with those of central Sichuan Basin. Results show that the natural gas in Western Sichuan basin is wet gas and the dry coefficient is higher than that of central Sichuan basin. The stable carbon and hydrogen isotopes represent a positive carbon isotopic series of alkanes (i.e. δ13C1<δ13C2<δ13C3). Continental natural gases in Sichuan Basin mainly belong to coal-derived gases, and only the gases from Jurassic strata in central Sichuan basin are oil-derived gases. Carbon dioxide is mainly abiogenic, with some biogenic. The abiogenic carbon dioxide is a result of the thermal metamorphism of carbonates. The natural gas in the Sichuan Basin mainly come from mature and high mature stage, while only the gases of Jurassic strata in central Sichuan Basin were generated in the mature stage. The Jurassic natural gas in western Sichuan basin possibly originated from a mixture of T3X3 and T3X5 black mudstones with low thermal maturity. However, the oil-derived gases of Jurassic strata in central Sichuan basin were found to come from Ziliujing-baitianba source rock. The deep Triassic natural gases in Western and Central Sichuan basin originated from the nearby or in situ source rocks of Xujiahe formation.Liu, Y., Li, H.A., Okuno, R., 2018. Phase behavior of N2/n-C4H10 in a partially confined space derived from shale sample. Journal of Petroleum Science and Engineering 160, 442-451. behavior of shale fluids in small pores is not well understood. One complexity comes from the fact that sorption of components by organic-rich shale can be significant and selective. In an attempt to elucidate the effect of sorption on phase behavior of shale fluids, we present a new experimental method that can be used to measure the bubble-point pressures of N2/n-C4H10 mixtures in the presence of an actual shale sample. Pressure/volume (P/V) isotherms for a given mixture were firstly measured in a PVT cell. Then, the measurements of the P/V isotherms for the same mixture were repeated in a partially confined space by opening a valve between the PVT cell and a shale container. The so-called partially confined space consists of the pore space inside the shale sample, the bulk space in the PVT cell and in the connecting tubing, and the non-cementing pore spaces among the shale particles. Results show that, the measured bubble-point pressure of the N2/n-C4H10 mixture in the partially confined space was higher than the corresponding bubble-point pressure in the bulk space. A detailed analysis indicates that, when loaded in the partially confined space, n-C4H10 exhibits a higher level of sorption capacity on the shale sample than N2, resulting in a higher concentration of N2 left in the free fluid than that in the initial mixture, which is the so-called selective sorption. The higher concentration of N2 led to the higher bubble-point pressure as observed in the measurements. The increase of the bubble-point pressure due to the selective sorption was observed to be greater at a lower temperature. This is because the sorption of n-C4H10 relative to that of N2 is more significant at a lower temperature. A higher temperature did not lead to a higher increment in the bubble-point pressure likely because bubble-point is more sensitive to composition than to temperature for these mixtures at the conditions tested. This emphasizes the importance of considering sorption in phase behavior for small pores.Liu, Y., Liu, G., Qu, Q., Qi, C., Sun, R., Liu, H., 2017. Geochemistry of vanadium (V) in Chinese coals. Environmental Geochemistry and Health 39, 967-986. in coals may have potential environmental and economic impacts. However, comprehensive knowledge of the geochemistry of V in coals is lacking. In this study, abundances, distribution and modes of occurrence of V are reviewed by compiling >2900 reported Chinese coal samples. With coal reserves in individual provinces as the weighting factors, V in Chinese coals is estimated to have an average abundance of 35.81?μg/g. Large variation of V concentration is observed in Chinese coals of different regions, coal-forming periods, and maturation ranks. According to the concentration coefficient of V in coals from individual provinces, three regions are divided across Chinese coal deposits. Vanadium in Chinese coals is probably influenced by sediment source and sedimentary environment, supplemented by late-stage hydrothermal fluids. Specifically, hydrothermal fluids have relatively more significant effect on the enrichment of V in local coal seams. Vanadium in coals is commonly associated with aluminosilicate minerals and organic matter, and the modes of V occurrence in coal depend on coal-forming environment and coal rank. The Chinese V emission inventory during coal combustion is estimated to be 4906?mt in 2014, accounting for 50.55?% of global emission. Vanadium emissions by electric power plants are the largest contributor.Long, Z., Zhang, Y., Gamache, P., Guo, Z., Steiner, F., Du, N., Liu, X., Jin, Y., Liu, X., Liu, L., 2018. Determination of tropane alkaloids by heart cutting reversed phase – Strong cation exchange two dimensional liquid chromatography. Journal of Chromatography B 1072, 70-77. Chinese Pharmacopoeia (ChP) standards apply liquid extraction combined with one dimensional liquid chromatography (1DLC) method for determining alkaloids in herbal medicines. The complex pretreatments lead to a low analytical efficiency and possible component loss. In this study, a heart cutting reversed phase – strong cation exchange two dimensional liquid chromatography (RP – SCX 2DLC) approach was optimized for simultaneously quantifying tropane alkaloids (anisodine, scopolamine and hyoscyamine) in herbal medicines and herbal medicine tablets without further treatment of the filtered extract. The chromatographic conditions were systematically optimized in terms of column type, mobile phase composition and flow rate. To improve peak capacity and obtain symmetric peak shape of alkaloids, a polar group embedded C18 column combined with chaotropic salts was used in the first dimension. To remove the disturbance of non-alkaloids, achieve unique selectivity and acquire symmetric peak shape of alkaloids, an SCX column combined with phosphate buffer was used in the second dimension. Method validation was performed in terms of linearity, precision (0.54–0.82%), recovery (94.1–105.2%), limit of detection (LOD) and limit of quantification (LOQ) of the three analytes varied between 0.067–0.115 mg L?1 and 0.195–0.268 mg L?1, respectively. The method demonstrated superiority over 1DLC method in respect of resolution (less alkaloid co-eluted), sample preparation (no pretreatment procedure) and transfer rate (minimum component loss). The optimized RP – SCX 2DLC approach was subsequently applied to quantify target alkaloids in five herbal medicines and herbal medicine tablets from three different manufactures. The results demonstrated that the developed heart cutting RP – SCX 2DLC approach represented a new, strategically significant methodology for the quality evaluation of tropane alkaloid in related herbal medicines that involve complex chemical matrix.Lopes, N.P., da Silva, R.R., 2018. Mass Spectrometry in Chemical Biology: Evolving Applications Royal Society of Chemistry, p. 298. spectrometry is one of the most widespread technologies in chemistry and has been increasingly used in biology with the rise of omics sciences. This book summarizes some important methodological approaches in mass spectrometry and applications in the field of chemical biology. The core chapters build on basic concepts introduced in the opening chapter and explore established fields such as high throughput screening, proteomics and metabolomics. Emerging applications of mass spectrometry in elucidating biosynthetic pathways, enzyme mechanisms and protein-protein interactions are then presented. Connections between these diverse research fields are highlighted throughout. The book concludes with a discussion of databases and future perspectives. This book will be a useful tool to early chemical biology researchers wishing to incorporate mass spectrometry as a tool in their research.Chapter 1 : Introduction: V. Zagoriy, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 1 DOI:10.1039/9781788010399-00001Chapter 2 : Introduction to Mass Spectrometry Instrumentation and Methods Used in Chemical Biology: P. Herrero, A. Delpino-Rius, M. R. Ras-Mallorquí, L. Arola and N. Canela, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 17 DOI:10.1039/9781788010399-00017Chapter 3 : Metabolomics: Ricardo R. da Silva, Norberto Peporine Lopes and Denise Brentan Silva, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 57 DOI:10.1039/9781788010399-00057Chapter 4 : Proteomics: Swati Varshney, Trayambak Basak, Mainak Dutta and Shantanu Sengupta, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 82 DOI:10.1039/9781788010399-00082Chapter 5 : Mass Spectrometry for Discovering Natural Products: Paulo C. Vieira, Ana Carolina A. Santos and Taynara L. Silva, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 144 DOI:10.1039/9781788010399-00144Chapter 6 : Applications of Mass Spectrometry in Synthetic Biology: Zaira Bruna Hoffmam, Viviane Cristina Heinzen da Silva, Marina C. M. Martins and Camila Caldana, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 159 DOI:10.1039/9781788010399-00159Chapter 7 : Studying Enzyme Mechanisms Using Mass Spectrometry, Part 1: Introduction: Cristina Lento, Peter Liuni and Derek J. Wilson, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 173 DOI:10.1039/9781788010399-00173Chapter 8 : Studying Enzyme Mechanisms Using Mass Spectrometry, Part 2: Applications: Peter Liuni, Cristina Lento and Derek J. Wilson, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 197 DOI:10.1039/9781788010399-00197Chapter 9 : Chemical Biology Databases: Alan C. Pilon, Ana Paez-Garcia, Daniel Petinatti Pavarini and Marcus Tullius Scotti, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 221 DOI:10.1039/9781788010399-00221Chapter 10 : Perspectives for the Future: Anelize Bauermeister, Larissa A. Rolim, Ricardo Silva, Paul J. Gates and Norberto Peporine Lopes, Mass Spectrometry in Chemical Biology: Evolving Applications, 2017, 264 DOI:10.1039/9781788010399-00264López-Bascón, M.A., Calderón-Santiago, M., Sánchez-Ceinos, J., Fernández-Vega, A., Guzmán-Ruiz, R., López-Miranda, J., Malagon, M.M., Priego-Capote, F., 2018. Influence of sample preparation on lipidomics analysis of polar lipids in adipose tissue. Talanta 177, 86-93. main limitations of lipidomics analysis are the chemical complexity of the lipids, the range of concentrations at which they exist, and the variety of samples usually analyzed. These limitations particularly affect the characterization of polar lipids owing to the interference of neutral lipids, essentially acylglycerides, which are at high concentration and suppress ionization of low concentrated lipids in mass spectrometry detection. The influence of sample preparation on lipidomics analysis of polar lipids in adipose tissue by LC–MS/MS was the aim of this research. Two common extractants used for lipids isolation, methanol:chloroform (MeOH:CHCl3) and methyl tert-butyl ether (MTBE), were qualitatively and quantitatively compared for the extraction of the main families of lipids. The obtained results showed that each family of lipids is influenced differently by the extractant used. However, as a general trend, the use of MTBE as extractant led to higher extraction efficiency for unsaturated fatty acids, glycerophospholipids and ceramides, while MeOH:CHCl3 favored the isolation of saturated fatty acids and plasmalogens. The implementation of a solid-phase extraction (SPE) step for selective isolation of glycerophospholipids prior to LC–MS/MS analysis was assayed to evaluate its influence on lipids detection coverage as compared to direct analysis. This step was critical to enhance the detection coverage of glycerophospholipids by removal of ionization suppression effects caused by acylglycerides.Lord, N.S., Crucifix, M., Lunt, D.J., Thorne, M.C., Bounceur, N., Dowsett, H., O'Brien, C.L., Ridgwell, A., 2017. Emulation of long-term changes in global climate: application to the late Pliocene and future. Climate of the Past 13, 1539-1571. transient simulations of climate changes have a range of important applications, such as for investigating key geologic events and transitions for which high-resolution palaeoenvironmental proxy data are available, or for projecting the long-term impacts of future climate evolution on the performance of geological repositories for the disposal of radioactive wastes. However, due to the high computational requirements of current fully coupled general circulation models (GCMs), long-term simulations can generally only be performed with less complex models and/or at lower spatial resolution. In this study, we present novel long-term continuous projections of climate evolution based on the output from GCMs, via the use of a statistical emulator. The emulator is calibrated using ensembles of GCM simulations, which have varying orbital configurations and atmospheric CO2 concentrations and enables a variety of investigations of long-term climate change to be conducted, which would not be possible with other modelling techniques on the same temporal and spatial scales. To illustrate the potential applications, we apply the emulator to the late Pliocene (by modelling surface air temperature – SAT), comparing its results with palaeo-proxy data for a number of global sites, and to the next 200?kyr (thousand years) (by modelling SAT and precipitation). A range of CO2 scenarios are prescribed for each period. During the late Pliocene, we find that emulated SAT varies on an approximately precessional timescale, with evidence of increased obliquity response at times. A comparison of atmospheric CO2 concentration for this period, estimated using the proxy sea surface temperature (SST) data from different sites and emulator results, finds that relatively similar CO2 concentrations are estimated based on sites at lower latitudes, whereas higher-latitude sites show larger discrepancies. In our second illustrative application, spanning the next 200?kyr into the future, we find that SAT oscillations appear to be primarily influenced by obliquity for the first ～?120?kyr, whilst eccentricity is relatively low, after which precession plays a more dominant role. Conversely, variations in precipitation over the entire period demonstrate a strong precessional signal. Overall, we find that the emulator provides a useful and powerful tool for rapidly simulating the long-term evolution of climate, both past and future, due to its relatively high spatial resolution and relatively low computational cost. However, there are uncertainties associated with the approach used, including the inability of the emulator to capture deviations from a quasi-stationary response to the forcing, such as transient adjustments of the deep-ocean temperature and circulation, in addition to its limited range of fixed ice sheet configurations and its requirement for prescribed atmospheric CO2 concentrations.Lu, L., Williams, N.B., Turner, J.A., Maness, P.-C., Gu, J., Ren, Z.J., 2017. Microbial photoelectrosynthesis for self-sustaining hydrogen generation. Environmental Science & Technology 51, 13494-13501. artificial photosynthesis (APS) systems are promising for the storage of solar energy via transportable and storable fuels, but the anodic half-reaction of water oxidation is an energy intensive process which in many cases poorly couples with the cathodic half-reaction. Here we demonstrate a self-sustaining microbial photoelectrosynthesis (MPES) system that pairs microbial electrochemical oxidation with photoelectrochemical water reduction for energy efficient H2 generation. MPES reduces the overall energy requirements thereby greatly expanding the range of semiconductors that can be utilized in APS. Due to the recovery of chemical energy from waste organics by the mild microbial process and utilization of cost-effective and stable catalyst/electrode materials, our MPES system produced a stable current of 0.4 mA/cm2 for 24 h without any external bias and ～10 mA/cm2 with a modest bias under one sun illumination. This system also showed other merits, such as creating benefits of wastewater treatment and facile preparation and scalability.Lu, T., Li, Z., Li, J., Hou, D., Zhang, D., 2017. Flow behavior of N2 huff and puff process for enhanced oil recovery in tight oil reservoirs. Scientific Reports 7, Article 15695. the present work, the potential of N2 huff and puff process to enhance the recovery of tight oil reservoir was evaluated. N2 huff and puff experiments were performed in micromodels and cores to investigate the flow behaviors of different cycles. The results showed that, in the first cycle, N2 was dispersed in the oil, forming the foamy oil flow. In the second cycle, the dispersed gas bubbles gradually coalesced into the continuous gas phase. In the third cycle, N2 was produced in the form of continuous gas phase. The results from the coreflood tests showed that, the primary recovery was only 5.32%, while the recoveries for the three N2 huff and puff cycles were 15.1%, 8.53% and 3.22%, respectively.The recovery and the pressure gradient in the first cycle were high. With the increase of huff and puff cycles, and the oil recovery and the pressure gradient rapidly decreased. The oil recovery of N2 huff and puff has been found to increase as the N2 injection pressure and the soaking time increased. These results showed that, the properly designed and controlled N2 huff and puff process can lead to enhanced recovery of tight oil reservoirs.Lu, Y.-C., Song, S.-R., Wang, P.-L., Wu, C.-C., Mii, H.-S., MacDonald, J., Shen, C.-C., John, C.M., 2017. Magmatic-like fluid source of the Chingshui geothermal field, NE Taiwan evidenced by carbonate clumped-isotope paleothermometry. Journal of Asian Earth Sciences 149, 124-133. Chingshui geothermal field, a moderate-temperature and water-dominated hydrothermal system, was the site of the first geothermal power plant in Taiwan. Many geological, geophysical and geochemical studies using more than 21 drilled wells have been performed since the 1960s. However, there are still controversies regarding the heat and fluid sources due to the tectonically complicated geological setting. To clarify the heat and fluid sources, we analyzed clumped isotopes with carbon and oxygen isotopic compositions of calcite scaling in geothermal wells and veins on outcrops and calculated the δ18O values of the source fluids. Two populations of δ18O values were calculated: ?5.8 ± 0.8‰ VSMOW from scaling in the well and ?1.0 ± 1.6‰ to 10.0 ± 1.3‰ VSMOW from outcropping calcite veins, indicative of meteoric and magmatic fluid sources, respectively. Meanwhile, two hydrothermal reservoirs at different depths have been identified by magnetotelluric (MT) imaging with micro-seismicity underneath this area. As a result, we propose a two-reservoir model: the shallow reservoir provides fluids from meteoric water for the scaling sampled from wells, whereas the deep reservoir provides magmatic fluids from deep marble decarbonization recorded in outcropping calcite veins.Lu, Y., Liu, Y., Sun, X., Lin, Z., Xu, L., Lu, H., Hao, X., Peckmann, J., 2017. Intensity of methane seepage reflected by relative enrichment of heavy magnesium isotopes in authigenic carbonates: A case study from the South China Sea. Deep Sea Research Part I: Oceanographic Research Papers 129, 10-21. conditions including steep redox gradients result in different Ca-Mg-carbonates forming at methane seeps as a consequence of sulfate-driven anaerobic oxidation of methane (SD-AOM). Since Mg2+ is one of the main cations in Ca-Mg-carbonates, Mg isotope composition may reflect the mode of mineral authigenesis at seeps. Seep carbonates were collected from the Shenhu area and the Southwest (SW) Taiwan basin in the South China Sea. The carbonate phases in Shenhu samples are dolomite accompanied by accessory Mg-calcite, while SW Taiwan samples consist of Mg-calcite and dolomite. Correspondingly, Shenhu carbonates show systematically higher Mg/Ca ratios. Low δ13C values of seep carbonates confirm their derivation from the oxidation of methane, δ18O values reflect formation in equilibrium with coeval seawater. The δ26Mg value of a reference sample of biodetrital carbonate (?4.28‰) is lower than those of seep carbonates (?3.25 to ?2.95‰). Since only little variability of δ26Mg values of pore waters is expected based on previous work, differences in the δ26Mg values of seep carbonates were apparently caused by changing degrees of isotopic fractionation during precipitation. Trends between δ26Mg values and Mg/Ca ratios and between δ26Mg and δ13C values suggest that Mg isotope fractionation was controlled by a kinetic mechanism affecting the incorporation of Mg2+ ions into the carbonate lattice in the course of SD-AOM. By consuming sulfate and by producing sulfide, SD-AOM reduces the energy differences for the dehydration of ions of light and heavy Mg isotopes, lowering isotope fractionation. Additionally, the two trends have been found to be steeper for Shenhu samples, suggesting more pronounced SD-AOM in the Shenhu area. Our study indicates that Mg isotope composition of methane-derived carbonates is affected by the process that drives carbonate precipitation – SD-AOM. Future work is required to confirm the utility of Mg isotopes as a new proxy for this major biogeochemical process.Lu, Y., Zhang, W., 2017. Biogeochemistry of methanogenesis with a specific emphasis on the mineral-facilitating effects. Acta Geochimica 36, 379-384. Earth surface contains various oxic and anoxic environments. The later include natural wetlands, river and lake sediments, paddy field soils and landfills. In the last few decades, the biogeochemical cycle of carbon in anoxic environments, which leads to the production and emission of methane, a potent greenhouse gas in the atmosphere, has drawn great attentions from both scientific and public sectors. New organisms and mechanisms involved in methanogenesis and carbon cycling have been uncovered. Interspecies electron transfer is considered as a crucial step in methanogenesis in anoxic environments. Electron-carrying mediators, like H2 and formate, are known to play the key role in electron transfer. Recently, it has been found that in addition to the conventional electron transfer via chemical mediators, direct interspecies electron transfer (DIET) can occur. In this Review, we describe the ecology and biogeochemistry of methanogenesis and highlight the effect of microbe-mineral interaction on microbial syntrophy. Recent advances in the study of DIET may pave the way towards a mechanistic understanding of methanogenesis and the influence of microbe-mineral interaction on this process.Lugli, F., Brunelli, D., Cipriani, A., Bosi, G., Traversari, M., Gruppioni, G., 2017. C4-plant foraging in northern Italy: Stable isotopes, Sr/Ca and Ba/Ca data of human osteological samples from Roccapelago (16th–18th centuries AD). Archaeometry 59, 1119-1134. osteological samples (n?=?23) taken from different anatomical parts of 11 individuals from the early modern (16th–18th century AD) site of Roccapelago (Modena, Italy) were systematically analysed for δ13C, δ15N and trace elements to investigate their diet. δ13C and δ15N correlate and show a high variability between individuals, attesting to the dietary contribution of C4 plants. This is supported by pollen analysis of the burial site samples, which revealed the presence of maize. δ15N correlates with Sr/Ca, suggesting that the main protein source could have been milk and dairy. We therefore interpret the strong correlation between δ13C and δ15N as evidence for C4-plant foraging practice and the exploitation of livestock for meat and milk, combined with possible direct intake of C4 plants. The Roccapelago site represents an important case study to track the evolution of the post-medieval diet and the introduction of maize cultivation in southern Europe, as also attested by historical sources.Lunn, D.B., Yun, Y.J., Jorgenson, J.W., 2017. Retention and effective diffusion of model metabolites on porous graphitic carbon. Journal of Chromatography A 1530, 112-119. study of metabolites in biological samples is of high interest for a wide range of biological and pharmaceutical applications. Reversed phase liquid chromatography is a common technique used for the separation of metabolites, but it provides little retention for polar metabolites. An alternative to C18 bonded phases, porous graphitic carbon has the ability to provide significant retention for both non-polar and polar analytes. The goal of this work is to study the retention and effective diffusion properties of porous graphitic carbon, to see if it is suitable for the wide injection bands and long run times associated with long, packed capillary-scale separations. The retention of a set of standard metabolites was studied for both stationary phases over a wide range of mobile phase conditions. This data showed that porous graphitic carbon benefits from significantly increased retention (often >100 fold) under initial gradient conditions for these metabolites, suggesting much improved ability to focus a wide injection band at the column inlet. The effective diffusion properties of these columns were studied using peak-parking experiments with the standard metabolites under a wide range of retention conditions. Under the high retention conditions, which can be associated with retention after injection loading for gradient separations, Deff/Dm ～ 0.1 for both the C18-bonded and porous graphitic carbon columns. As C18 bonded particles are widely, and successfully utilized for long gradient separations without issue of increasing peak width from longitudinal diffusion, this suggests that porous graphitic carbon should be amenable for long runtime gradient separations as well.Luo, C.U.I., Pan, B., Reitner, J., 2017. Chambered structures from the Ediacaran Dengying Formation, Yunnan, China: comparison with the Cryogenian analogues and their microbial interpretation. Geological Magazine 154, 1269-1284. chambered structures have been reported forming reef frames in Cryogenian interglacial carbonates, prior to the commonly acknowledged microbial-metazoan reefs at the terminal Ediacaran, and interpreted as fossils of possible sponge-grade organisms. A better constraint on the affinity of these structures is partly hindered by few analogues in other time periods. This study describes similar structures from peritidal dolostones of the Ediacaran Denying Formation from Yunnan, China. Samples were investigated using optical microscopy and three-dimensional (3-D) reconstruction based on grinding tomography. The Dengying chambered structures are comparable with Cryogenian structures in basic construction, but are not frame building, and show variations in overall shape and inhabiting facies. Two-dimensional (2-D) cross-sections show that thin, homogeneous micritic laminae are the basic building blocks of the chamber walls. Thick walls represent parallel accretion of these laminae, and thin walls developed from the angular growth of a single lamina or merging of multiple laminae. In 3-D space, the laminae primarily correspond to continuous surfaces which sometimes contain sub-circular holes, while a few represent filamentous elements connected to the surfaces. The morphological features and growth pattern of the Dengying chambered structures indicate that they are likely to be calcified microbial constructions rather than skeletal remains of basic metazoans. However, aside from the Cryogenian and Dengying examples, comparable chambered constructions with laminae-based architecture are yet unknown from other fossil or extant microbialites. Further work investigating related structures is needed to determine the microbial consortia and controlling environmental factors that produced these chambered structures.Luo, Q., Hao, J., Skovsted, C.B., Luo, P., Khan, I., Wu, J., Zhong, N., 2017. The organic petrology of graptolites and maturity assessment of the Wufeng–Longmaxi Formations from Chongqing, China: Insights from reflectance cross-plot analysis. International Journal of Coal Geology 183, 161-173. Wufeng–Longmaxi Formations (Ordovician-Silurian) contain abundant graptolite-bearing shales, which have proven to be one of the most successful shale gas exploration targets in China and can provide an opportunity to study the organic petrology of graptolites. Organic petrology analysis has been conducted on these organic-rich shales in order to depict the shape of graptolite reflectance indicating surface (GRIS) and their organic maturity. Granular and non-granular graptolites have been observed in the studied sediments, and non-granular graptolites were the major graptolite species. The strong positive correlation between the maximum reflectance (Rmax) and bireflectance of graptolites indicates that the graptolites display stronger anisotropy with maturation. A linear coalification path of graptolite fragments was observed in the studied sediments. A remarkable decrease in the minimum reflectance (Rmin) values of graptolites was observed when Rmax exceeds 6%. The samples with lower thermal maturity (Rmax ≤ 2%) tend to be biaxial neutral, whereas higher rank samples display biaxial negative characteristics. The GRIS shape becomes more oblate with maturation. The Wufeng–Longmaxi shales from the southeastern Chongqing and Wuxi areas of the Chongqing municipality, China, are post mature and in the dry gas zone, whereas samples from the Chengkou area of the Chongqing municipality, China, are still in the oil window. Their different burial and thermal histories controlled their thermal maturity.Luo, W., Hou, M., Liu, X., Huang, S., Chao, H., Zhang, R., Deng, X., 2018. Geological and geochemical characteristics of marine-continental transitional shale from the Upper Permian Longtan formation, Northwestern Guizhou, China. Marine and Petroleum Geology 89, Part 1, 58-67. shale deposited in a marine-continental transitional facies was well developed in the upper Yangtze area during the Late Permian. It is considered to contain a large amount of shale hydrocarbon resources. This paper takes the Upper Permian Longtan shale in the central Guizhou uplift as an example to characterize the transitional shale reservoir. Based on organic geochemistry data, X-ray diffraction (XRD) analysis, and scanning electron microscopy (SEM) observation, the geochemical characteristics of this transitional shale were systematically studied and the shale gas potential was investigated. The results indicate that the Longtan shale has fair to good hydrocarbon potential with high total organic carbon (TOC) and contains type III gas-prone organic matter. Its high thermal maturity favors the generation of gas (Ro, 1.10%–2.74%). XRD analyses show that the mineral components of the transitional shale are dominated by high clay content (58.7 wt%). The clay minerals are dominated by illite (44%) and mixed illite/smectite (43%). SEM observation shows that intra-particle pores, inter-particle pores and microfracture were well developed in the Longtan shale, which can provide reservoir space for the accumulation of shale gas. Organic matter pores appear rare due to its organic type. In summary, the Longtan shale has high organic content, high maturation, and high gas content, all of which demonstrate its great potential as a shale-gas resource. But the high clay content of the Longtan shale may be a challenge to shale-gas production.Luo, X., Wu, Y., Li, X., Chen, D., Wang, Y., Li, F., Liu, T., 2017. The in situ spectral methods for examining redox status of c-type cytochromes in metal-reducing/oxidizing bacteria. Acta Geochimica 36, 544-547. membrane-associated c-type cytochromes (c-Cyts) have been well known as the key enzymes mediating extracellular electron transfer to terminal electron acceptors, resulting in biogeochemical elemental transformation, contaminant degradation, and nutrient cycling. Although c-Cyts-mediated metal reduction or oxidation have been mainly investigated with the purified proteins of metal reducing/oxidizing bacteria, the in vivo behavior of c-Cyts is still unclear, given the difficulty in measuring the proteins of intact cells. Fortunately, the in situ spectroscopy would be ideal for measuring the reaction kinetics of c-Cyts in intact cells under noninvasive physiological conditions. It can also help the establishment of kinetic/thermodynamic models of extracellular electron transfer processes, which are essential to understand the electron transfer mechanisms at the molecular scale. This review briefly summarizes the current advances in spectral methods for examining the c-Cyts in intact cells of dissimilatory metal reducing bacteria and Fe(II)-oxidizing bacteria.Lv, K.-P., Norman, L., Li, Y.-L., 2017. Oxygen-free biochemistry: The putative CHN foundation for exotic life in a hydrocarbon world? Astrobiology 17, 1173-1181. Earth's biochemistry is carbon-based and water-borne, the main strategies for searching for life elsewhere are “follow the carbon” and “follow the water.” Recently, however, there is a growing focus on the prospect that putative exotic life on other planets could rely on unearthly biochemistries. Here, we hypothesize a novel oxygen-free organic chemistry for supporting potential exotic biosystems, which is named CHN biochemistry. This oxygen-free CHN biochemistry starts from simple oxygen-free species (including hydrocarbons, hydrogen cyanide, and nitriles) and produces a range of functional macromolecules that may function in similar ways to terran macromolecules, such as sugars (cyanosugars), acids (cyanoacids), amino acids (amino cyanoacids), and nucleobases (cyanonucleobases). These CHN macromolecules could further interact with each other to generate higher “cyanoester” and “cyanoprotein” systems. In addition, theoretical calculations indicate that the energy changes of some reactions are consistent with their counterparts in Earth's biochemistry. The CHN biochemistry-based life would be applicable in habitats with a low bioavailability of oxygen, such as the alkane lakes of Titan and non-aquatic liquids on extrasolar bodies.Lv, Q., Chen, Z., Wang, M., 2017. An improved elastic-tubes model for the correlation of permeability and stress with correction for the Klinkenberg effect. Journal of Natural Gas Science and Engineering 48, 24-35. correlation of permeability and stress is crucial for correctly predicting the coupled process of fluid flow and solid deformation in geophysical systems. Especially in ultra-low-permeability rocks with nanopores, the apparent permeability becomes sensitive to the properties of fluid and solid. This work presents an improved tubes model, where the correlation of permeability and stress is derived with the Klinkenberg effect correction. Both the in-situ stress effect and the Klinkenberg effect have been carefully considered in current correction of permeability prediction based on Darcy's law. The experimental data can be fitted well by the new model, and the Klinkenberg effect of gas flow in the tight porous media is successfully captured. The predictive ability of the current model has been examined as well and the results are acceptable.Lynch, K.B., Chen, A., Liu, S., 2018. Miniaturized high-performance liquid chromatography instrumentation. Talanta 177, 94-103. high performance liquid chromatography (HPLC) has attracted increasing attention for its potential in high-throughput analyses and point-of-care applications. In this review we highlight the recent advancements in HPLC system miniaturization. We focus on the major components that constitute these instruments along with their respective advantages and drawbacks as well as present a few representative miniaturized HPLC systems. We discuss briefly some of the applications and also anticipate the future development trends of these instrumental platforms.Lyu, Z., Li, Z.-G., He, F., Zhang, Z., 2017. An important role for purifying selection in archaeal genome evolution. mSystems 2, e00112-17; DOI: 10.1128/mSystems.00112-17.: As the null hypothesis of genome evolution, population genetic theory suggests that selection strength controls genome size. Through the process of genetic drift, this theory predicts that compact genomes are maintained by strong purifying selection while complex genomes are enabled by weak purifying selection. It offers a unifying framework that explains why prokaryotic genomes are much smaller than their eukaryotic counterparts. However, recent findings suggest that bigger prokaryotic genomes appear to experience stronger purifying selection, indicating that purifying selection may not dominate prokaryotic genome evolution. Since archaeal genomes were underrepresented in those studies, generalization of the conclusions to both archaeal and bacterial genomes may not be warranted. In this study, we revisited this matter by focusing on archaeal and bacterial genomes separately. We found that bigger bacterial genomes indeed experienced stronger purifying selection, but the opposite was observed in archaeal genomes. This new finding would predict an enrichment of noncoding sequences in large archaeal genomes, which was confirmed by an analysis of coding density. In contrast, coding density remained stable regardless of bacterial genome size. In conclusion, this study suggests that purifying selection may play a more important role in archaeal genome evolution than previously hypothesized, indicating that there could be a major difference between the evolutionary regimes of Archaea and Bacteria.Importance: The evolution of genome complexity is a fundamental question in biology. A hallmark of eukaryotic genome complexity is that larger genomes tend to have more noncoding sequences, which are believed to be minimal in archaeal and bacterial genomes. However, we found that archaeal genomes also possessed this eukaryotic feature while bacterial genomes did not. This could be predicted from our analysis on genetic drift, which showed a relaxation of purifying selection in larger archaeal genomes, also a eukaryotic feature. In contrast, the opposite was evident in bacterial genomes.Ma, M., Liu, X., Wang, W., 2017. Palaeoclimate evolution across the Cretaceous-Palaeogene boundary in the Nanxiong Basin (SE China) recorded by red strata and its correlation with marine records. Climate of the Past Discussions 2017, 1-34. climate during the Cretaceous Period represented one of the greenhouse states of Earth's history. Significant transformation of climate patterns and a mass extinction event characterised by the disappearance of dinosaurs occurred across Cretaceous–Palaeogene boundary. However, most records of this interval are derived from marine sediments. The continuous and well-exposed red strata of the Nanxiong Basin (SE China) provide ideal material to develop continental records. Considerable research into stratigraphic, palaeontological, chronologic, palaeoclimatic, and tectonic aspects has been carried out for the Datang Profile, which is a type section of a non-marine Cretaceous–Palaeogene stratigraphic division in China. For this study, we reviewed previous work and found that: 1) the existing chronological framework of the Datang Profile is flawed; 2) precise palaeoclimatic reconstruction is lacking because of the limitations of sampling resolution (e.g. carbonate samples) and/or the lack of efficient proxies; and 3) comparisons of climate changes between marine and continental records are lacking. To resolve these problems, detailed field observations and sampling, as well as environmental magnetic and rare earth element (REE) measurements, were carried out. The results show that: 1) more accurate ages of the Datang Profile range from 72?Ma to 62.8?Ma, based on a combination of the most recently published radiometric, palaeontological and palaeomagnetic ages; 2) there is considerable evidence of palaeosol generation, which indicates that the red strata formed in a long-term hot, oxidizing environment that lacked of underwater condition; 3) haematite was the dominant magnetic mineral in the red strata, and the variation trend of magnetic susceptibility was consistent with the oxygen isotope records from deep-sea sediments, which indicates that the pedogenic intensity was controlled by global climate; and 4) the palaeoclimate changes from 72?Ma to 62.8?Ma in the Nanxiong Basin were consistent with global patterns, and can be divided into three stages: a relatively hot and wet stage during 72–71.5?Ma, a cool and arid stage during 71.5–66?Ma, and a relatively hot and wet stage again during 66–62.8?Ma with a notable drying and cooling event at 64.7–63.4?Ma. Moreover, there are several sub-fluctuations during each stage. This work provides basic information for further palaeoclimate reconstruction with higher resolution and longer time scales for the Cretaceous to Palaeocene in the Nanxiong Basin, and may even help to test ocean–land climate interactions in the future.Ma, W.-W., Zhu, M.-X., Yang, G.-P., Li, T., 2018. Iron geochemistry and organic carbon preservation by iron (oxyhydr)oxides in surface sediments of the East China Sea and the south Yellow Sea. Journal of Marine Systems 178, 62-74. marine sediments factors that influence iron (Fe) geochemistry and its interactions with other elements are diverse and remain poorly understood. Here we comparatively study Fe speciation and reactive Fe-bound organic carbon (Fe-OC) in surface sediments of the East China Sea (ECS) and the south Yellow Sea (SYS). The objectives are to better understand the potential impacts of geochemically distinct sediment sources and depositional/diagenetic settings on Fe geochemistry and OC preservation by Fe (hydr)oxides in sediments of the two extensive shelf seas around the world. Contents of carbonate- and acid-volatile-sulfide (AVS)-associated Fe(II) (FeAVS + carb) and magnetite (Femag) in the ECS sediments are about 5 and 9 times higher, respectively, than in the SYS. This could be ascribed to the ferruginous conditions of the ECS sediments that favor the formation/accumulation of Fecarb and Femag, a unique feature of marine unsteady depositional regimes. Much lower total Fe(II) contents in the SYS than in the ECS suggest that lower availability of highly reactive Fe (FeHR) and/or weak Fe reduction is a factor limiting Fe(II) formation and accumulation in the SYS sediments. The ratio of FeHR to total Fe is, on average, markedly higher (2.4 times) in the ECS sediments than in the SYS, which may be a combined result of several factors relevant to different sediment sources and depositional/diagenetic settings. In comparison with many other marine sediments, the percent fractions (fFe-OC) of Fe-OC to total organic carbon (TOC) in the ECS and the SYS are low, which can be ascribed to surface adsorption of OC rather than coprecipitation or organic complexation as the dominant binding mechanisms. Based on the fFe-OC in this study, total Fe-OC estimated for global continental shelves is equivalent to 38% of the atmospheric CO2 pool, which indicates the important role of sorptive stabilization of Fe-OC in continental shelf sediments for buffering CO2 release to the atmosphere. In the SYS, consistently less 13C-depleted Fe-OC relative to 13C of non-Fe-bound OC (13Cnon-Fe-OC) suggests selective sequestration of labile marine OC in the marine OC-dominated sediments of the central SYS. In the ECS, however, efficient oxidation of OC and frequent redox cycling of Fe in the unsteady depositional regimes may complicate the isotopic compositions of Fe-OC. A combination of our results and literature data demonstrates that Fe-OC contents are strongly dependent on the availability of TOC and reactive Fe, but the fFe-OC is primarily controlled by the processes of Fe redox cycling in the sediments.Ma, X., Zheng, G., Sajjad, W., Xu, W., Fan, Q., Zheng, J., Xia, Y., 2018. Influence of minerals and iron on natural gases generation during pyrolysis of type-III kerogen. Marine and Petroleum Geology 89, Part 1, 216-224. experiments in a closed system were conducted on kerogen (isolated from a low mature coal sample) either in the presence or absence of clay minerals, iron-bearing minerals, transition metal and their mixture, respectively. The generated gases were collected and analyzed for chemical compositions by using gas chromatography and mass spectrometer; the solid residues were also quantitatively collected and analyzed for iron species using M?ssbauer spectroscopy. These experiments revealed that the hydrocarbon gases generation from kerogen was significantly increased by catalysis of minerals and transition metal (iron). The generation of hydrocarbon gases could be potentially increased by 0.1–1.5 times in the presence of minerals and iron, and the catalytic efficiency was in the order of kerogen + mixed catalysts > kerogen + pyrite > kerogen + smectite > kerogen + iron > kerogen. The dryness ratios, including ethene/ethane, propene/propane, isobutane/n-butane and isopentane/n-pentane, were all decreased due to the catalysis of smectite, pyrite and mixed catalysts, and slightly increased with iron addition. The conversion of pyrite into pyrrhotite and elemental sulfur started at 300 °C during the experiments, for which pyrite might be as an inducer indirectly via sulfur and thus enhance the free radical formation and improve the hydrocarbon yield.Maaten, B., Loo, L., Konist, A., Pihu, T., Siirde, A., 2017. Investigation of the evolution of sulphur during the thermal degradation of different oil shales. Journal of Analytical and Applied Pyrolysis 128, 405-411. paper presents the results of the pyrolytic decomposition of six different oil shale samples with different sulphur contents from Estonia, USA and China using non-isothermal thermogravimetry coupled with a mass spectrometer (TGA-MS). Mass spectrometry (MS) was used to analyse the evaporating gases. The results showed a major difference in the evolution of sulphur containing substances. The sulphur behaviour was found to be in excellent correlation with the composition of the sample. H2S and SO2, the problematic components forming during the pyrolysis process, both exhibited evaporation in two peaks. The kinetic distribution supported the findings of MS ? samples with a higher sulphur content exhibited more parallel reactions that had similar weight percentages. SO2 evolution intensifies above 500 °C. H2S is released in the temperature range of 350–500 °C, depending on the sample. The samples Kentucky, Green River, Estonia and Chinese 2 also have an additional peak at 500–570 °C. This is in good accordance with the aforementioned samples having a relatively high amount of sulphur in the forms of organics and sulphides. Based on the results, an important conclusion is that changing the pyrolysis temperature can reduce the sulphur content of the oil produced. The experimental curves obtained were used to calculate the kinetic parameters using a distributed activation energy model. The obtained activation energy values were in the range of 134–276 kJ/mol with the frequency factors ranging from 1.89E1012 to 1.20E1014 s?1. In order to validate the obtained kinetic parameters, the decomposition curves were compared to modelled ones. The dependence of total conversion on reaction time was calculated at isothermal conditions to show the effect of pyrolysis temperature.Mach, P.M., Winfield, J.L., Aguilar, R.A., Wright, K.C., Verbeck, G.F., 2017. A portable mass spectrometer study targeting anthropogenic contaminants in Sub-Antarctic Puerto Williams, Chile. International Journal of Mass Spectrometry 422, 148-153. into anthropogenic sources of pollutants in the remote region of Puerto Williams, Chile utilized a fieldable portable mass spectrometer for on-site analysis targeting water and atmospheric air. This expedition highlights the benefits of portable instrumentation that is readily taken out into the field, in providing the community with scientific evidence of ongoing contamination. Two notable locations exhibited noticeable quantities of BTEX constituents, while remote regions remain untainted. Correlations between distance to the community and the sampling sites are indicative of sources of pollutants being anthropogenic in nature.Machuca, L.L., Lepkova, K., Petroski, A., 2017. Corrosion of carbon steel in the presence of oilfield deposit and thiosulphate-reducing bacteria in CO2 environment. Corrosion Science 129, 16-25. effect of thiosulphate reducing bacteria (TRB) on the corrosion of carbon steel covered by a complex oilfield deposit has been assessed in CO2-containing seawater at 55° C. TRB were found to significantly accelerate localized corrosion at deposited steels. This effect of TRB on under-deposit corrosion (UDC) was related to metabolic production of corrosive compounds, such as sulphide and acidic species, through biodegradation of organic matter and thiosulfate reduction in the deposit. TRB were also found to promote accumulation of hydrocarbons and metals in the deposit. Results highlight that microbial-deposit interactions are a noteworthy process in corrosion of oilfield facilities.Mafessoni, F., Prüfer, K., 2017. Better support for a small effective population size of Neandertals and a long shared history of Neandertals and Denisovans. Proceedings of the National Academy of Sciences 114, E10256-E10257. et al. (1) compare the sharing of derived alleles among the genomes of Africans, non-Africans, a Neandertal, and a Denisovan to infer the demographic history of archaic humans. They estimate that the effective population size (Ne) of Neandertals was ～15,000 individuals and that Neandertals and Denisovans separated from each other shortly after their ancestor separated from modern humans (～300 generations). These estimates are at odds with previous results (2) that suggested a smaller Ne for Neandertals [ranging from 1,000–5,000 individuals according to pairwise sequentially Markovian coalescent (PSMC) estimates of Ne over time] and a longer common branch for the Neandertal–Denisovan ancestor (5,000–10,000 generations). We note that the difference in assumed mutation rate between the two publications cannot account for the differences … Comment on: Rogers, A.R., Bohlender, R.J., Huff, C.D., 2017. Early history of Neanderthals and Denisovans. Proceedings of the National Academy of Sciences 114, 9859-863.Reply to comment: Rogers, A.R., Bohlender, R.J., Huff, C.D., 2017. Reply to Mafessoni and Prüfer: Inferences with and without singleton site patterns. Proceedings of the National Academy of Sciences 114, E10258-E10260.Magagna, F., Cordero, C., Cagliero, C., Liberto, E., Rubiolo, P., Sgorbini, B., Bicchi, C., 2017. Black tea volatiles fingerprinting by comprehensive two-dimensional gas chromatograph – mass spectrometry combined with high concentration capacity sample preparation techniques: Toward a fully automated sensomic assessment. Food chemistry 225, 276-287. prepared by infusion of dried leaves of Camellia sinensis (L.) Kuntze, is the second world’s most popular beverage, after water. Its consumption is associated with its chemical composition: it influences its sensory and nutritional quality addressing consumer preferences, and potential health benefits.This study aims to obtain an informative chemical signature of the volatile fraction of black tea samples from Ceylon by applying the principles of sensomics. In particular, several high concentration capacity (HCC) sample preparation techniques were tested in combination with GC × GC–MS to investigate chemical signatures of black tea volatiles. This platform, using headspace solid phase microextraction (HS-SPME) with multicomponent fiber as sampling technique, recovers 95% of the key-odorants in a fully automated work-flow. A group 123 components, including key-odorants, technological and botanical tracers, were mapped. The resulting 2D fingerprints were interpreted by pattern recognition tools (i.e. template matching fingerprinting and scripting) providing highly informative chemical signatures for quality assessment.Mairinger, T., Causon, T.J., Hann, S., 2018. The potential of ion mobility–mass spectrometry for non-targeted metabolomics. Current Opinion in Chemical Biology 42, 9-15. analysis of metabolites in hypothesis-generating workflows has proven its potential to answer essential questions that arise when dealing with complex biological systems. Nevertheless, tracking changes in perturbed systems via accurate quantification and the identification process itself represent the most critical challenges in these workflows. Recent advances in ion mobility–mass spectrometry have enabled this technique to increase the confidence of metabolite annotation by introducing a complementary conditional molecular descriptor, that is collision cross section.Makled, W.A., Mostafa, T.F., Mousa, D.A., Abdou, A.A., 2018. Source rock evaluation and sequence stratigraphic model based on the palynofacies and geochemical analysis of the subsurface Devonian rocks in the Western Desert, Egypt. Marine and Petroleum Geology 89, 560-584. Paleozoic rocks are the least explored among the subsurface successions in the Western Desert of Egypt. This contribution submits a significant record for the palynofacies and geochemical analysis for an important division of the subsurface Paleozoic rocks from Faghur-1 and NW-D302-1 boreholes. The palynofacies of the Devonian sediments of Zeitoun Formation extensively verified and classified. The palynofacies classification depended on the statistical techniques of cluster and correspondence analysis. The cluster analysis discriminated four classes of palynofacies in R-mode, which are brown wood palynofacies class R1, spore palynofacies class R2, AOM-opaque phytoclasts palynofacies class R3 and marine phytoplankton palynofacies class R4. In the Q-mode, the cluster analysis revealed three palynofacies types, which are palynofacies type C, palynofacies type B, palynofacies type A. The combination of cluster and correspondence analysis is employed to interpret the evolution of basin dynamics and the mechanisms that controlled the deposition of the Devonian rocks. Three basic environmental settings were recognized and they include 1.) Oxic highly proximal shelf setting, 2.) Oxic proximal shelf setting and 3.) Oxic distal shelf. The high oxygenation levels are confirmed by the inorganic geochemical analysis of Fe%, TS/Fe and TS/TOC in the samples from Faghur-1 borehole. The paleoenvironmental reconstruction is used to identify four 2nd order stratigraphic sequences in the studied sections, which are DevSeq1, DevSeq2, DevSeq3 and DevSeq4. These sequences are systematically described and correlated with their equivalent global Devonian Sequences. The palynofacies investigation is integrated with the inorganic and organic geochemical analysis to evaluate the potentially of hydrocarbon generation from the probable source rocks in the studied sections and its onset timing. The identified kerogen types are mostly mature (TAI range between 2 and 3 and Tmax range between 427 and 439 °C) gas prone type III with poor organic enrichment (TOC <0.9) and low potentiality for hydrocarbon production (PI range between 0.02 and 0.1). The burial history models were constructed for both boreholes; they revealed that the hydrocarbon generation started in the Cretaceous in both boreholes.Malherbe, C., Hutchinson, I.B., Ingley, R., Boom, A., Carr, A.S., Edwards, H., Vertruyen, B., Gilbert, B., Eppe, G., 2017. On the habitability of desert varnish: A combined study by micro-Raman spectroscopy, X-ray diffraction, and methylated pyrolysis–gas chromatography–mass spectrometry. Astrobiology 17, 1123-1137. 2020, the ESA ExoMars and NASA Mars 2020 missions will be launched to Mars to search for evidence of past and present life. In preparation for these missions, terrestrial analog samples of rock formations on Mars are studied in detail in order to optimize the scientific information that the analytical instrumentation will return. Desert varnishes are thin mineral coatings found on rocks in arid and semi-arid environments on Earth that are recognized as analog samples. During the formation of desert varnishes (which takes many hundreds of years), organic matter is incorporated, and microorganisms may also play an active role in the formation process. During this study, four complementary analytical techniques proposed for Mars missions (X-ray diffraction [XRD], Raman spectroscopy, elemental analysis, and pyrolysis–gas chromatography–mass spectrometry [Py-GC-MS]) were used to interrogate samples of desert varnish and describe their capacity to sustain life under extreme scenarios. For the first time, both the geochemistry and the organic compounds associated with desert varnish are described with the use of identical sets of samples. XRD and Raman spectroscopy measurements were used to nondestructively interrogate the mineralogy of the samples. In addition, the use of Raman spectroscopy instruments enabled the detection of β-carotene, a highly Raman-active biomarker. The content and the nature of the organic material in the samples were further investigated with elemental analysis and methylated Py-GC-MS, and a bacterial origin was determined to be likely. In the context of planetary exploration, we describe the habitable nature of desert varnish based on the biogeochemical composition of the samples. Possible interference of the geological substrate on the detectability of pyrolysis products is also suggested.Malik, S.S., Azem-e-Zahra, S., Kim, K.M., Caetano-Anollés, G., Nasir, A., 2017. Do viruses exchange genes across superkingdoms of life? Frontiers in Microbiology 8, 2110. doi: 10.3389/fmicb.2017. can be classified into archaeoviruses, bacterioviruses, and eukaryoviruses according to the taxonomy of the infected host. The host-constrained perception of viruses implies preference of genetic exchange between viruses and cellular organisms of their host superkingdoms and viral origins from host cells either via escape or reduction. However, viruses frequently establish non-lytic interactions with organisms and endogenize into the genomes of bacterial endosymbionts that reside in eukaryotic cells. Such interactions create opportunities for genetic exchange between viruses and organisms of non-host superkingdoms. Here, we take an atypical approach to revisit virus-cell interactions by first identifying protein fold structures in the proteomes of archaeoviruses, bacterioviruses, and eukaryoviruses and second by tracing their spread in the proteomes of superkingdoms Archaea, Bacteria, and Eukarya. The exercise quantified protein structural homologies between viruses and organisms of their host and non-host superkingdoms and revealed likely candidates for virus-to-cell and cell-to-virus gene transfers. Unexpected lifestyle-driven genetic affiliations between bacterioviruses and Eukarya and eukaryoviruses and Bacteria were also predicted in addition to a large cohort of protein folds that were universally shared by viral and cellular proteomes and virus-specific protein folds not detected in cellular proteomes. These protein folds provide unique insights into viral origins and evolution that are generally difficult to recover with traditional sequence alignment-dependent evolutionary analyses owing to the fast mutation rates of viral gene sequences.Malyshev, A.I., 2017. The role of cooling horizons in genesis of hydrocarbon deposits. Doklady Earth Sciences 476, 1152-1154. penetration of fluid flow through cooling horizons resulted in the condensation of the gaseous phase in the course of chemical reactions of natural hydrocarbon synthesis (HS) owing to the occurrence of simple postmagmatic fluid compounds (H2, CO2, H2S). In practice it is possible to use aerospace infrared remote sensing to search for hydrocarbon deposits genetically associated with cooling horizons. Original Russian Text ? A.I. Malyshev, 2017, published in Doklady Akademii Nauk, 2017, Vol. 476, No. 4, pp. 445–447.Mangal, V., Shi, Y.X., Guéguen, C., 2017. Compositional changes and molecular transformations of dissolved organic matter during the arctic spring floods in the lower Churchill watershed (Northern Manitoba, Canada). Biogeochemistry 136, 151-165. spring flood season in Northern aquatic systems is characterized by rapid changes in river discharge and fluxes of organic and inorganic species, yet remains under sampled. In this study, we examine the molecular characteristics and transformations of dissolved organic matter (DOM) during the Arctic spring season at three locations in the lower Churchill River watershed. Characteristics including dissolved organic carbon concentrations, optical properties (i.e. absorbance and, excitation-emission matrix fluorescence coupled with parallel factor analysis, EEM-PARAFAC) and molecular characterization using high resolution mass spectrometry (HR-MS) were assessed. As spring floods progressed, a significant reduction in DOM spectral slope (S275–295) and an increase in absorbance (a270) were observed suggesting an increase in DOM molecular weight and concentrations at all sampled locations. A maximum in HR-MS lignin-class compounds coincided with peak flow at all sampled locations, further validated with an increase in PARAFAC humic-like components and a minimum in S275–295. Principal component analyses revealed that both protein and aromatic humic-like material measured by HR-MS and EEM-PARAFAC, respectively, were significantly correlated (ANOVA, p?<?0.05), demonstrating similarities in both techniques. Based on network analysis of HR-MS assigned formula, the highest peak flow day was characterized by a maximum in homologous DOM of C2H2O and C2H4 additions, suggesting structural similarities in newly deposited lignin and humic material. Overall, the progression of the spring freshet shifted the lower Churchill River watershed from an environment rich in proteins and lipids to an aquatic system more abundant in lignin, aromatic and humic DOM.Mansour, E.M., Desouky, S.M., Aily, M.E., Helmi, M.E., 2018. The effect of asphaltene content on predicting heavy dead oils viscosity: Experimental and modeling study. Fuel 212, 405-411. viscosity of heavy dead oil is one of the most important governing parameters of the fluid flow, either in the porous media or pipelines, so it is of great importance to use accurate empirical correlation to estimate the heavy oil viscosity at various operating temperature. Published heavy oil viscosity correlations resulted in huge errors. The resulted deviations are attributed to the differences in the Asphaltenic content of crude oils and their dependence on operating temperature and density only. Therefore, we need to develop an accurate empirical correlation model that represents the heavy dead crude oil viscosity by adding different effective parameters as Asphaltenic content, oil density at operating temperature and oil molecular weight. In this paper, heavy dead oil empirical correlation has been developed using laboratory data (710 set point) of heavy oil samples that collected from different locations in Egypt. Heavy dead oil viscosity measurements operated at API gravity (22.79?>?API?>?12.36). Efforts are made to build a best-fit correlation by multiple least-square nonlinear regression analysis to find viscosity as a function of (Asphalten, TOper., API gravity, MWT and ρOper.temp.). Both statistical and graphical techniques were applied on hundred data point to evaluate this developed empirical correlation with literature ones and experimental data of Egyptian oil samples. The results show that the developed empirical correlation presents better accuracy and performance for predicting the heavy dead oil viscosity than those correlations in literature.Manz, C., Pagel, K., 2018. Glycan analysis by ion mobility-mass spectrometry and gas-phase spectroscopy. Current Opinion in Chemical Biology 42, 16-24. to the existence of numerous isomers, the in-depth analysis of glycans represents a major challenge. Currently, the majority of glycans are analysed using mass spectrometry (MS)-based techniques, which can provide information on regioisomers but usually fail to differentiate stereoisomers. A promising approach to overcome this limitation is to implement ion mobility spectrometry (IMS) as an additional gas-phase separation dimension. This review highlights recent developments in which IM-MS was used as a tool for comprehensive glycan analysis or as rapid screening method for glycan feature analysis. Furthermore, we summarize a series of very recent investigations in which gas-phase spectroscopy is applied to study glycans and discuss the potential of the hyphenation between IM-MS and infrared (IR) spectroscopy as a future tool for glycomics and glycoproteomics.Mao, H.-K., Hu, Q., Yang, L., Liu, J., Kim, D.Y., Meng, Y., Zhang, L., Prakapenka, V.B., Yang, W., Mao, W.L., 2017. When water meets iron at Earth's core–mantle boundary. National Science Review, Article nwx109. minerals in subducted crust can transport large amounts of water into Earth's deep mantle. Our laboratory experiments revealed the surprising pressure-induced chemistry that, when water meets iron at the core–mantle boundary, they react to form an interlayer with an extremely oxygen-rich form of iron, iron dioxide, together with iron hydride. Hydrogen in the layer will escape upon further heating and rise to the crust, sustaining the water cycle. With water supplied by the subducting slabs meeting the nearly inexhaustible iron source in the core, an oxygen-rich layer would cumulate and thicken, leading to major global consequences in our planet. The seismic signature of the D″ layer may echo the chemical complexity of this layer. Over the course of geological time, the enormous oxygen reservoir accumulating between the mantle and core may have eventually reached a critical eruption point. Very large-scale oxygen eruptions could possibly cause major activities in the mantle convection and leave evidence such as the rifting of supercontinents and the Great Oxidation Event.Mao, S., Peng, Q., Wang, M., Hu, J., Peng, C., Zhang, J., 2017. The PVTx properties of aqueous electrolyte solutions containing Li+, Na+, K+, Mg2+, Ca2+, Cl? and SO42? under conditions of CO2 capture and sequestration. Applied Geochemistry 86, 105-120. on the Pitzer electrolyte theory, an accurate density model of binary sulfate-water systems (Li2SO4-H2O, Na2SO4-H2O, K2SO4-H2O and MgSO4-H2O) has been established. Corresponding model parameters are obtained by the least square method. Compared with reliable experimental data of the Li2SO4-H2O, Na2SO4-H2O, K2SO4-H2O and MgSO4-H2O systems, the average density deviations are 0.046%, 0.036%, 0.051%, 0.038%, respectively, which are within or close to experimental uncertainties. Combined a simple mixing rule with the density models of binary sulfate-water systems and previous chloride-water systems (LiCl-H2O, NaCl-H2O, KCl-H2O, MgCl2-H2O and CaCl2-H2O), a predictive density model is proposed for aqueous mixed electrolyte solutions containing Li+, Na+, K+, Mg2+, Ca2+, Cl? and SO42? under conditions of CO2 capture and sequestration (CCS) (generally less than 473 K and 300 bar). Compared to experimental density data of multi-component water-salt systems, the average density deviation of each system is usually less than 0.1%. The model can be used to calculate the apparent molar volume at infinite dilution and the volumetric properties of CO2-bearing multi-component electrolyte solutions under the CCS conditions. A computer code for the volumetric properties of multi-component aqueous electrolyte solutions can be obtained from the corresponding author.Mao, Y., Zeidouni, M., Duncan, I., 2017. Temperature analysis for early detection and rate estimation of CO2 wellbore leakage. International Journal of Greenhouse Gas Control 67, 20-30. leakage of carbon dioxide (CO2) injected into storage zones can induce significant temperature anomalies. These thermal signals arise from expansion of the leaking CO2 associated with the pressure drop across the leak, known as the Joule-Thomson effect, which has the potential to reveal the nature of leakage and determine the wellbore leakage rate of CO2. We investigate the strength of the temperature signal as a function of leakage rate and develop a control volume analysis to relate these two in the complex two-phase leakage conditions. This analytical thermal model for CO2 leakage enables quick analysis with sufficient accuracy to estimate the leakage rate. The application range of this approach is identified from the results of comprehensive investigations. The nature of the thermal signal is sensitive to the balance between the Joule-Thomson effect and heat conduction. The ratio of these two effects and newly defined JT/cond Number provide general criteria for the applicability of modeling these thermal signals in the range of 40–90% and 1.6-4, respectively. Furthermore, in the case of higher leakage rate, we extend the analytical model to predict the leakage transmissibility with improved accuracy compared to the direct rate estimation from leakage thermal model in this scenario. The general procedure and flow chart to apply the proposed approach to a practical problem are provided, which is suitable for both injection and post-injection periods for a CO2 storage project. This analytical model breaks a new ground to apply recent temperature wellbore monitoring developments for CO2 leakage detection and characterization purposes. Field applications of this model can complement other leakage rate estimation techniques and be an essential part of the CO2 leakage detection tool if other approaches are not viable.Maor, R., Dayan, T., Ferguson-Gow, H., Jones, K.E., 2017. Temporal niche expansion in mammals from a nocturnal ancestor after dinosaur extinction. Nature Ecology & Evolution 1, 1889-1895. modern mammals, including strictly diurnal species, exhibit sensory adaptations to nocturnal activity that are thought to be the result of a prolonged nocturnal phase or ‘bottleneck’ during early mammalian evolution. Nocturnality may have allowed mammals to avoid antagonistic interactions with diurnal dinosaurs during the Mesozoic. However, understanding the evolution of mammalian activity patterns is hindered by scant and ambiguous fossil evidence. While ancestral reconstructions of behavioural traits from extant species have the potential to elucidate these patterns, existing studies have been limited in taxonomic scope. Here, we use an extensive behavioural dataset for 2,415 species from all extant orders to reconstruct ancestral activity patterns across Mammalia. We find strong support for the nocturnal origin of mammals and the Cenozoic appearance of diurnality, although cathemerality (mixed diel periodicity) may have appeared in the late Cretaceous. Simian primates are among the earliest mammals to exhibit strict diurnal activity, some 52–33 million years ago. Our study is consistent with the hypothesis that temporal partitioning between early mammals and dinosaurs during the Mesozoic led to a mammalian nocturnal bottleneck, but also demonstrates the need for improved phylogenetic estimates for Mammalia.Marchand, A., Livet, S., Rosu, F., Gabelica, V., 2017. Drift tube ion mobility: How to reconstruct collision cross section distributions from arrival time distributions? Analytical Chemistry 89, 12674-12681. mobility spectrometry allows one to determine ion collision cross sections, which are related to ion size and shape. Collision cross sections (CCS) are usually discussed based on the peak center, yet the width of each peak contains further information on the distribution of collision cross sections of each conformational ensemble. Here, we analyze how to convert arrival time distributions (ATD) to CCS distributions (CCSD). With a calibration curve taking into account the CCS dependence of the time spent outside the mobility region, one can reconstruct CCS distributions with correct peak center values. However, the peak widths are incorrectly rendered because ion diffusion, which affects the peak width in the time domain, is irrelevant to collision cross sections. For drift tube ion mobility, we describe a new method, coined “FWHMstep”, using a step-field experiment and processing the peak’s full width at half-maximum to reconstruct CCSDs. The width of the CCS distribution helps to characterize the analyte’s structural heterogeneity, and/or its flexibility (i.e., the variety of ways the analyte ions can rearrange following electrospray into kinetically stable gas-phase conformations).Marella, E.R., Holkenbrink, C., Siewers, V., Borodina, I., 2018. Engineering microbial fatty acid metabolism for biofuels and biochemicals. Current Opinion in Biotechnology 50, 39-46. oleochemical industry chemically processes animal fats and plant oils to produce detergents, lubricants, biodiesel, plastics, coatings, and other products. Biotechnology offers an alternative process, where the same oleochemicals can be produced from abundant biomass feedstocks using microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining metabolites with different functionalities. The prospects of commercializing microbial oleochemicals are also discussed.Marshall, C.P., Olcott Marshall, A., Aitken, J.B., Lai, B., Vogt, S., Breuer, P., Steemans, P., Lay, P.A., 2017. Imaging of vanadium in microfossils: A new potential biosignature. Astrobiology 17, 1069-1076. inability to unambiguously distinguish the biogenicity of microfossil-like structures in the ancient rock record is a fundamental predicament facing Archean paleobiologists and astrobiologists. Therefore, novel methods for discriminating biological from nonbiological chemistries of microfossil-like structures are of the utmost importance in the search for evidence of early life on Earth. This, too, is important for the search for life on Mars by in situ analyses via rovers or sample return missions for future analysis here on Earth. Here, we report the application of synchrotron X-ray fluorescence imaging of vanadium, within thermally altered organic-walled microfossils of bona fide biological origin. From our data, we demonstrate that vanadium is present within microfossils of undisputable biological origin. It is well known in the organic geochemistry literature that elements such as vanadium are enriched and contained within crude oils, asphalts, and black shales that have been formed by diagenesis of biological organic material. It has been demonstrated that the origin of vanadium is due to the diagenetic alteration of precursor chlorophyll and heme porphyrin pigment compounds from living organisms. We propose that, taken together, microfossil-like morphology, carbonaceous composition, and the presence of vanadium could be used in tandem as a biosignature to ascertain the biogenicity of putative microfossil-like structures.Martinez, C., Preston, T.M., 2018. Oil and gas development footprint in the Piceance Basin, western Colorado. Science of The Total Environment 616–617, 355-362. long-term implications of energy development on ecosystem function requires establishing regional datasets to quantify past development and determine relationships to predict future development. The Piceance Basin in western Colorado has a history of energy production and development is expected to continue into the foreseeable future due to abundant natural gas resources. To facilitate analyses of regional energy development we digitized all well pads in the Colorado portion of the basin, determined the previous land cover of areas converted to well pads over three time periods (2002–2006, 2007–2011, and 2012–2016), and explored the relationship between number of wells per pad and pad area to model future development. We also calculated the area of pads constructed prior to 2002. Over 21 million m2 has been converted to well pads with approximately 13 million m2 converted since 2002. The largest land conversion since 2002 occurred in shrub/scrub (7.9 million m2), evergreen (2.1 million m2), and deciduous (1.3 million m2) forest environments based on National Land Cover Database classifications. Operational practices have transitioned from single well pads to multi-well pads, increasing the average number of wells per pad from 2.5 prior to 2002, to 9.1 between 2012 and 2016. During the same time period the pad area per well has increased from 2030 m2 to 3504 m2. Kernel density estimation was used to model the relationship between the number of wells per pad and pad area, with these curves exhibiting a lognormal distribution. Therefore, either kernel density estimation or lognormal probability distributions may potentially be used to model land use requirements for future development. Digitized well pad locations in the Piceance Basin contribute to a growing body of spatial data on energy infrastructure and, coupled with study results, will facilitate future regional and national studies assessing the spatial and temporal effects of energy development on ecosystem function.Mashhadi Meighani, H., Ghotbi, C., Jafari Behbahani, T., Sharifi, K., 2018. Evaluation of PC-SAFT model and Support Vector Regression (SVR) approach in prediction of asphaltene precipitation using the titration data. Fluid Phase Equilibria 456, 171-183. deposition in porous media, wellbore and surface facilities has been a severe problem in petroleum industry which causes considerable remediation costs annually. Asphaltenes are heavy and polydisperse fractions of crude oil which are insoluble in n-alkanes such as n-heptane. In this work, three Iranian crude oils were prepared for titration experiments with n-pentane, n-heptane and n-dodecane at different solvent ratios and constant temperature. The experimental data were correlated by perturbed chain form of statistical associating fluid theory (PC-SAFT). The association of asphaltene molecules has been considered in this model with adjusting the uncertain parameters (such as association energy and association volume of asphaltene pseudo component) to match the experimental data. PC-SAFT parameters for other non-associating pseudo components have been calculated using the correlations proposed in literature. The present study also evaluated the performance of SVR method as a supervised learning approach in prediction of asphaltene precipitation. Deviation of proposed models has been validated using the statistical evaluation criteria and graphical analysis. The results show that the proposed models have AAD values less than 0.073 and a high potential in prediction of asphaltene precipitation.Materi?, D., Peacock, M., Kent, M., Cook, S., Gauci, V., R?ckmann, T., Holzinger, R., 2017. Characterisation of the semi-volatile component of dissolved organic matter by Thermal Desorption – Proton Transfer Reaction – Mass Spectrometry. Scientific Reports 7, Article 15936. Transfer Reaction – Mass Spectrometry (PTR-MS) is a sensitive, soft ionisation method suitable for qualitative and quantitative analysis of volatile and semi-volatile organic vapours. PTR-MS is used for various environmental applications including monitoring of volatile organic compounds (VOCs) emitted from natural and anthropogenic sources, chemical composition measurements of aerosols, etc. Here we apply thermal desorption PTR-MS for the first time to characterise the chemical composition of dissolved organic matter (DOM). We developed a clean, low-pressure evaporation/sublimation system to remove water from samples and coupled it to a custom-made thermal desorption unit to introduce the samples to the PTR-MS. Using this system, we analysed waters from intact and degraded peat swamp forest of Kalimantan, Indonesian Borneo, and an oil palm plantation and natural forest in Sarawak, Malaysian Borneo. We detected more than 200 organic ions from these samples and principal component analysis allowed clear separation of the different sample origins based on the composition of organic compounds. The method is sensitive, reproducible, and provides a new and comparatively cheap tool for a rapid characterisation of water and soil DOM.Matthews, A., Azrieli-Tal, I., Benkovitz, A., Bar-Matthews, M., Vance, D., Poulton, S.W., Teutsch, N., Almogi-Labin, A., Archer, C., 2017. Anoxic development of sapropel S1 in the Nile Fan inferred from redox sensitive proxies, Fe speciation, Fe and Mo isotopes. Chemical Geology 475, 24-39. conditions and the mechanisms of redox development are a critical aspect of Eastern Mediterranean sapropels, whose formation in oxygen-depleted waters is closely related to water column stratification at times of global sea level rise and insolation maxima. Sapropels in the Nile Fan formed at relatively shallow water depths under the influence of the monsoon-driven freshwater output from the River Nile. This work evaluates the redox evolution of Holocene sapropel S1 in VALPAMED cruise core MD9509, recovered at 880 mbsl in the NE Nile Fan, using a combination of geochemical element proxies, Fe speciation, Fe and Mo isotopes studies. The productivity and redox proxies (Ba/Al, Mo/Al, U/Al, V/Al, Sb/Al) show well-defined enrichments in the sapropel, but with a marked minimum at ca 8.2 ka indicative of reventilation corresponding to a well known global cooling event. Peak productivity and reducing signals occur close to the initiation of sapropel formation. The proxy signals in sapropel 9509 are stronger and of longer duration than those of a second sapropel S1, recovered at the same depth, but 380 km to the north (MD9501), supporting the notion (suggested in previous studies) of more reduced conditions in the Nile Fan.The MoEF vs. UEF enrichment factor variations in core 9509 infer a transition from open marine suboxic conditions in the enclosing non-sapropel sediments to anoxic non-sulphidic water column conditions in the sapropel. Correspondingly, the highly reactive Fe pool (FeHR) measured in Fe speciation studies is dominated by Fe(oxyhydr) oxide minerals in the background sediments, whereas pyrite (Fepy) becomes the dominant component of the FeHR pool in the sapropel. Maximum Fepy values in the sapropel coincide with peak productivity and reducing conditions, implying a clear link between trace element uptake, diagenetic bacterial sulphate reduction in anoxic porewater and Fe mobilization in the sapropel. Iron isotope compositions (δ56Fe) in the sapropel do not show any departure from primary (marine and detrital) source sediment values, and the absence of an Fe/Al vs. δ56Fe trend strongly argues against an Fe shuttle. Molybdenum isotopes, however, show marked non-conservative fractionation patterns. Background sediment δ98/95Mo values (0.2 to 0.7‰) are compatible with fractionation upon absorptive uptake by Fe (oxyhydr)oxides and pyrite. In contrast, minimum δ98/95Mo values exhibited at peak sapropel (reducing and pyrite producing) conditions are most closely modeled by Mo isotope fractionation during kinetically controlled conversion of aqueous molybdate to thiomolybdate species. The conservative Fe isotope behavior/Mo isotope fractionation minima in the sapropel may be a characteristic of organic-rich sediment diagenesis below an anoxic non-sulphidic water body, without the operation of a benthic Fe shuttle.Mays, C., J., C.D., Bevitt, J.J., 2017. Polar wildfires and conifer serotiny during the Cretaceous global hothouse. Geology 45, 1119-1122. highly effective fire-adaptive traits first evolved among modern plants during the mid-Cretaceous, in response to the widespread wildfires promoted by anomalously high atmospheric oxygen (O2) and extreme temperatures. Serotiny, or long-term canopy seed storage, is a fire-adaptive strategy common among plants living in fire-prone areas today, but evidence of this strategy has been lacking from the fossil record. Deposits of abundant fossil charcoal from sedimentary successions of the Chatham Islands, New Zealand, record wildfires in the south polar regions (75°–80°S) during the mid-Cretaceous (ca. 99–90 Ma). Newly discovered fossil conifer reproductive structures were consistently associated with these charcoal-rich deposits. The morphology and internal anatomy as revealed by neutron tomography exhibit a range of serotiny-associated characters. Numerous related fossils from similar, contemporaneous deposits of the Northern Hemisphere suggest that serotiny was a key adaptive strategy during the high-fire world of the Cretaceous.Mc Keown, L.E., Bourke, M.C., McElwaine, J.N., 2017. Experiments on sublimating carbon dioxide ice and implications for contemporary surface processes on Mars. Scientific Reports 7, Article 14181. dioxide is Mars’ primary atmospheric constituent and is an active driver of Martian surface evolution. CO2 ice sublimation mechanisms have been proposed for a host of features that form in the contemporary Martian climate. However, there has been very little experimental work or quantitative modelling to test the validity of these hypotheses. Here we present the results of the first laboratory experiments undertaken to investigate if the interaction between sublimating CO2 ice blocks and a warm, porous, mobile regolith can generate features similar in morphology to those forming on Martian dunes today. We find that CO2 sublimation can mobilise grains to form (i) pits and (ii) furrows. We have documented new detached pits at the termini of linear gullies on Martian dunes. Based on their geomorphic similarity to the features observed in our laboratory experiments, and on scaling arguments, we propose a new hypothesis that detached pits are formed by the impact of granular jets generated by sublimating CO2. We also study the erosion patterns formed underneath a sublimating block of CO2 ice and demonstrate that these resemble furrow patterns on Mars, suggesting similar formation mechanisms.McCalley, D.V., 2017. Understanding and manipulating the separation in hydrophilic interaction liquid chromatography. Journal of Chromatography A 1523, 49-71. interaction liquid chromatography (HILIC) has emerged as a valuable complimentary technique to reversed-phase (RP), being especially suited for the analysis of polar and ionised solutes, which are difficult to retain in RP. For solutes amenable to both separation mechanisms, HILIC provides a different selectivity to RP, and also offers possibilities as an orthogonal mechanism for 2-dimensional LC when combined with RP. HILIC has further advantages of lower column back pressures, and increased sensitivity with mobile phase evaporative detectors such as electrospray mass spectrometry. This review covers progress in our understanding of the HILIC technique, principally over the last ten years, including the classification of columns, the factors that control retention and selectivity, and attempts to model the separation process and its kinetics.McGovern, P., Jalabadze, M., Batiuk, S., Callahan, M.P., Smith, K.E., Hall, G.R., Kvavadze, E., Maghradze, D., Rusishvili, N., Bouby, L., Failla, O., Cola, G., Mariani, L., Boaretto, E., Bacilieri, R., This, P., Wales, N., Lordkipanidze, D., 2017. Early Neolithic wine of Georgia in the South Caucasus. Proceedings of the National Academy of Sciences 114, E10309-E10318.: The earliest biomolecular archaeological and archaeobotanical evidence for grape wine and viniculture from the Near East, ca. 6,000–5,800 BC during the early Neolithic Period, was obtained by applying state-of-the-art archaeological, archaeobotanical, climatic, and chemical methods to newly excavated materials from two sites in Georgia in the South Caucasus. Wine is central to civilization as we know it in the West. As a medicine, social lubricant, mind-altering substance, and highly valued commodity, wine became the focus of religious cults, pharmacopoeias, cuisines, economies, and society in the ancient Near East. This wine culture subsequently spread around the globe. Viniculture illustrates human ingenuity in developing horticultural and winemaking techniques, such as domestication, propagation, selection of desirable traits, wine presses, suitable containers and closures, and so on. Abstract: Chemical analyses of ancient organic compounds absorbed into the pottery fabrics from sites in Georgia in the South Caucasus region, dating to the early Neolithic period (ca. 6,000–5,000 BC), provide the earliest biomolecular archaeological evidence for grape wine and viniculture from the Near East, at ca. 6,000–5,800 BC. The chemical findings are corroborated by climatic and environmental reconstruction, together with archaeobotanical evidence, including grape pollen, starch, and epidermal remains associated with a jar of similar type and date. The very large-capacity jars, some of the earliest pottery made in the Near East, probably served as combination fermentation, aging, and serving vessels. They are the most numerous pottery type at many sites comprising the so-called “Shulaveri-Shomutepe Culture” of the Neolithic period, which extends into western Azerbaijan and northern Armenia. The discovery of early sixth millennium BC grape wine in this region is crucial to the later history of wine in Europe and the rest of the world. McKenzie, N.R., 2017. Zircons reveal ancient perturbations. Nature Geoscience 10, 884-886. link between CO2 outgassing from carbonatite volcanoes during the Ediacaran and one of the most prominent carbon cycle perturbations in Earth’s history is suggested by an analysis of the trace-element composition of detrital zircons.Today, only a single volcano, Ol Doinyo Lengai in the East African Rift, produces markedly CO2-enriched carbonatite lavas1. Due to their rarity and underlying questions regarding the efficiency of how carbon moves through the mantle2,3, the impacts of carbonatitic magmatism on the long-term carbon cycle are not entirely realized. However, writing in Nature Geoscience, Paulsen et al.4 report that they have used the age and trace-element composition of detrital zircons to identify a pulse of carbonatitic magmatism about 580 million years ago (Ma), coincident with one of the most significant carbon cycle perturbations in Earth’s history — the Shuram negative carbon isotope excursion.Carbonatites, which are comprised of greater than 50 weight percent CaCO3, belong to a suite of alkaline igneous rocks derived from CO2-enriched melts. They generally occur in intraplate settings and continental interiors, as they originate from zones of mantle upwelling rather than the subduction-related magmatism found around plate margins. If this has been the case historically, then the likelihood of finding in situ carbonatites may be low to begin with: rocks formed in continental interiors generally have low preservation potential due to ongoing erosion, and the stability of these settings means that rocks that formed within the subsurface are unlikely to be exhumed and exposed.One way to track rocks that are not readily apparent in outcrops is through detrital zircons. These mineral grains are the products of crustal erosion and are archived in sedimentary basins. As zircon is physically resistant to transport and reworking processes, it has a geologically long residence time in the upper crust. Zircon trace-element data have been shown to reflect parental magmatic compositions5,6,7. Therefore, the combination of the age of detrital zircons and their trace-element geochemistry provides an excellent means to track various magmatic processes throughout Earth's history.Building on this framework, Paulsen et al. created and compiled an exceptionally large dataset of the ages and trace-element compositions of detrital zircons from ancient sedimentary rocks collected in Antarctica. Their data show a pronounced episode of voluminous carbonatite and alkaline magmatism along the Pacific Gondwana margin between 700 and 500 Ma. They also find evidence for substantial and generally coeval alkaline magmatism in other areas, including parts of Australia, India and South Africa. Carbonatite and alkaline volcanism seems to have peaked during the prominent Shuram negative carbon isotopic (δ13C) excursion (Fig. 1a).The Shuram excursion has several unusual features relative to other carbon isotope excursions in the geological record (Fig. 1a). First, carbonate δ13C values reached a low of ?12‰ following a protracted interval of isotopically heavy carbonate δ13C values that hovered around +5‰. Second, the low values are well below average values (?5‰) for material degassed from Earth’s interior; as the solid Earth is the principal source of light carbon, there is a substantial mass-balance problem8. Finally, the inorganic carbonate and organic carbon isotopic records for the Shuram are partially decoupled9, unlike the general covariation seen throughout the past 542 million years10. These collective anomalies have inspired extensive debate about the mechanisms responsible for this excursion8. The protracted interval of positive δ13C values may be explained by an extensive period of organic carbon burial, which can effectively remove isotopically light carbon and drive the reservoir towards heavier isotopic compositions. In contrast, the dramatic negative excursion requires a rapid influx of isotopically light carbon9. Paulsen and colleagues add a new twist to this debate by suggesting deep mantle carbon may be the most likely source, as opposed to changes in carbon fluxes at Earth’s surface.Although the average value of mantle carbon is about ?5‰, it is heterogeneous, with values as light as ?26‰ recorded11. Carbonatite δ13C values mostly range between ?1 and ?8‰, but recent studies have reported carbonatites with δ13C values ranging from ?12 to ?14‰12,13 (Fig. 1b). Thus, it is possible that the major pulse of mantle-derived carbonatite and alkaline magmatism identified by Paulsen et al. may have injected a large amount of isotopically light carbon that contributed to the Shuram anomaly.The proposition for a fundamental restructuring of the carbon cycle due to mantle cooling and changes in associated subduction processes is provocative indeed. Although the spike of carbonatite magmatism identified by Paulsen et al.4 may not explain the overall complexities of the Neoproterozoic carbon cycle, it does offer a new and intriguing piece of the puzzle and sets the stage for future quantitative Earth system modelling.References1. Jones, A. P., Genge, M. & Carmody, L. Rev. Mineral. Geochem. 75, 289–322 (2013).2. Dasgupta, R. Rev. Mineral. Geochem. 75, 183–229 (2013).3. Kelemen, P. B. & Manning, C. E. Proc. Natl Acad. Sci. USA 112, E3997–E4006 (2015).4. Paulsen, T., Deering, C., Sliwinski, J., Bachmann. O. & Guillong, M. Nat. Geosci. (2017).5. Belousova, E. A., Griffin, W. L., O’Reilly, S. Y. & Fisher, N. I. Contrib. Mineral. Petrol. 143, 602–622 (2002).6. Hoskin, P. W. O. & Schaltegger, U. Zircon 53, 27–62 (2003).7. Barth, A. P., Wooden, J. L., Jacobson, C. E. & Economos, R. C. Geology 41, 223–226 (2013).8. Grotzinger, J. P., Fike, D. A. & Fischer, W. W. Nat. Geosci. 4, 285–292 (2011).9. Lee, C., Love, G. D., Fischer, W. W., Grotzinger, J. P. & Halverson, G. P. Geology 43, 1103–1106 (2015).10. Swanson-Hysell, N. L. et al. Science 328, 608–611 (2010).11. Deines, P. Earth Sci. Rev. 58, 247–278 (2002).12. Woodard, J. & Huhma, H. Lithos 236, 311–323 (2015).13. Chen, C. F. et al. Geology 44, 1039–1042 (2016).14. Lyons, T. W., Reinhard, C. T. & Planavsky, N. J. Nature 506, 307–315 (2014).McMahon, K.W., Williams, B., Guilderson, T.P., Glynn, D.S., McCarthy, M.D., 2018. Calibrating amino acid δ13C and δ15N offsets between polyp and protein skeleton to develop proteinaceous deep-sea corals as paleoceanographic archives. Geochimica et Cosmochimica Acta 220, 261-275. stable isotopes of amino acids (CSI-AA) from proteinaceous deep-sea coral skeletons have the potential to improve paleoreconstructions of plankton community composition, and our understanding of the trophic dynamics and biogeochemical cycling of sinking organic matter in the Ocean. However, the assumption that the molecular isotopic values preserved in protein skeletal material reflect those of the living coral polyps has never been directly investigated in proteinaceous deep-sea corals. We examined CSI-AA from three genera of proteinaceous deep-sea corals from three oceanographically distinct regions of the North Pacific: Primnoa from the Gulf of Alaska, Isidella from the Central California Margin, and Kulamanamana from the North Pacific Subtropical Gyre. We found minimal offsets in the δ13C values of both essential and non-essential AAs, and in the δ15N values of source AAs, between paired samples of polyp tissue and protein skeleton. Using an essential AA δ13C fingerprinting approach, we show that estimates of the relative contribution of eukaryotic microalgae and prokaryotic cyanobacteria to the sinking organic matter supporting deep-sea corals are the same when calculated from polyp tissue or recently deposited skeletal tissue. The δ15N values of trophic AAs in skeletal tissue, on the other hand, were consistently 3–4‰ lower than polyp tissue for all three genera. We hypothesize that this offset reflects a partitioning of nitrogen flux through isotopic branch points in the synthesis of polyp (fast turnover tissue) and skeleton (slow, unidirectional incorporation). This offset indicates an underestimation, albeit correctable, of approximately half a trophic position from gorgonin protein-based deep-sea coral skeleton. Together, our observations open the door for applying many of the rapidly evolving CSI-AA based tools developed for metabolically active tissues in modern systems to archival coral tissues in a paleoceanographic context.Medina-Silva, R., de Oliveira, R.R., Pivel, M.A.G., Borges, L.G.A., Sim?o, T.L.L., Pereira, L.M., Trindade, F.J., Augustin, A.H., Valdez, F.P., Eizirik, E., Utz, L.R.P., Groposo, C., Miller, D.J., Viana, A.R., Ketzer, J.M.M., Giongo, A., 2018. Microbial diversity from chlorophyll maximum, oxygen minimum and bottom zones in the southwestern Atlantic Ocean. Journal of Marine Systems 178, 52-61. physicochemical vertical stratification in the deep sea is one of the main forces driving microbial diversity in the oceans. Oxygen and sunlight availability are key factors promoting microbial diversity throughout the water column. Ocean currents also play a major role in the physicochemical stratification, carrying oxygen down to deeper zones as well as moving deeper water masses up towards shallower depths. Water samples within a 50-km radius in a pockmark location of the southwestern Atlantic Ocean were collected and the prokaryotic communities from different water depths - chlorophyll maximum, oxygen minimum and deep-sea bottom (down to 1355 m) - were described. At phylum level, Proteobacteria were the most frequent in all water depths, Cyanobacteria were statistically more frequent in chlorophyll maximum zone, while Thaumarchaeota were significantly more abundant in both oxygen minimum and bottom waters. The most frequent microorganism in the chlorophyll maximum and oxygen minimum zones was a Pelagibacteraceae operational taxonomic unit (OTU). At the bottom, the most abundant genus was the archaeon Nitrosopumilus. Beta diversity analysis of the 16S rRNA gene sequencing data uncovered in this study shows high spatial heterogeneity among water zones communities. Our data brings important contribution for the characterisation of oceanic microbial diversity, as it consists of the first description of prokaryotic communities occurring in different oceanic water zones in the southwestern Atlantic Ocean.Mees, C., Souard, F., Delporte, C., Deconinck, E., Stoffelen, P., Stévigny, C., Kauffmann, J.-M., De Braekeleer, K., 2018. Identification of coffee leaves using FT-NIR spectroscopy and SIMCA. Talanta 177, 4-11. literature has been devoted to coffee beans (green or roasted) chemical description but relatively few studies have been devoted to coffee leaves. Given the fact that coffee leaves are used for food and medicinal consumption, it was of interest to develop a rapid screening method in order to identify coffee leaves taxa. Investigation by Fourier – Transform near infrared spectroscopy (FT-NIRS) was performed on nine Coffea taxa leaves harvested over one year in a tropical greenhouse of the Botanic Garden Meise (Belgium). The only process after leaves harvesting was an effective drying and a homogeneous leaves grinding. FT-NIRS with SIMCA analysis allowed to discriminate the spectral profiles across taxon, aging stage (mature and senescence coffee leaves) and harvest period. This study showed that it was possible (i) to classify the different taxa, (ii) to identify their aging stage and (iii) to identify the harvest period for the mature stage with a correct classification rate of 99%, 100% and 90%, respectively.Meier, A., Kastner, A., Harries, D., Wierzbicka-Wieczorek, M., Majzlan, J., Büchel, G., Kothe, E., 2017. Calcium carbonates: induced biomineralization with controlled macromorphology. Biogeosciences 14, 4867-4878. of (magnesium) calcite and vaterite by bacterial isolates has been known for quite some time. However, the extracellular precipitation has hardly ever been linked to different morphologies of the minerals that are observed. Here, isolates from limestone-associated groundwater, rock and soil were shown to form calcite, magnesium calcite or vaterite. More than 92?% of isolates were indeed able to form carbonates, while abiotic controls failed to form minerals. The crystal morphologies varied, including rhombohedra, prisms and pyramid-like macromorphologies. Different conditions like varying temperature, pH or media components, but also cocultivation to test for collaborative effects of sympatric bacteria, were used to differentiate between mechanisms of calcium carbonate formation. Single crystallites were cemented with bacterial cells; these may have served as nucleation sites by providing a basic pH at short distance from the cells. A calculation of potential calcite formation of up to 2?g?L?1 of solution made it possible to link the microbial activity to geological processes.Menapace, W., V?lker, D., Sahling, H., Zoellner, C., dos Santos Ferreira, C., Bohrmann, G., Kopf, A., 2017. Long-term in situ observations at the Athina mud volcano, Eastern Mediterranean: Taking the pulse of mud volcanism. Tectonophysics 721, 12-27. monitoring on mud volcanoes is fundamental to unravel episodic processes and transient changes that might otherwise be missed by using snapshot observations during time-limited research expeditions. We deployed a pore- and seafloor-pressure observatory close to the main conduit of the Athina mud volcano, south of Turkey (Eastern Mediterranean Sea), for a period of 26months between February 2014 and April 2016. The observatory recorded 32 pore pressure transients related to as many seismic events (out of 625 earthquakes with Mw≥2.5 occurred over the monitoring period in a radius of 1000km) and few pore pressure excursions related to mud volcanism. The data helped to define a threshold for earthquake-triggered changes in mud volcano pore pressure, thus delineating possible pore pressure-distance relationships for different magnitudes ranges. Peak ground accelerations, as representative for earthquakes ground motion at the observatory have been calculated with different ground motion prediction equations. Using a conservative approach, an empirical equation has been identified, which specify the lowermost PGA necessary to induce a change in pore pressure record at the Athina mud volcano. Moreover, internal variations of the mud volcano system recordable through the pore pressure signal have been described for the first time in such a submarine feature.Meyer-Jacob, C., Michelutti, N., Paterson, A.M., Monteith, D., Yang, H., Weckstr?m, J., Smol, J.P., Bindler, R., 2017. Inferring past trends in lake water organic carbon concentrations in northern lakes using sediment spectroscopy. Environmental Science & Technology 51, 13248-13255. lake water total organic carbon (TOC) concentrations are of concern for lake management because of corresponding effects on aquatic ecosystem functioning, drinking water resources and carbon cycling between land and sea. Understanding the importance of human activities on TOC changes requires knowledge of past concentrations; however, water-monitoring data are typically only available for the past few decades, if at all. Here, we present a universal model to infer past lake water TOC concentrations in northern lakes across Europe and North America that uses visible-near-infrared (VNIR) spectroscopy on lake sediments. In the orthogonal partial least-squares model, VNIR spectra of surface-sediment samples are calibrated against corresponding surface water TOC concentrations (0.5–41 mg L–1) from 345 Arctic to northern temperate lakes in Canada, Greenland, Sweden and Finland. Internal model-cross-validation resulted in a R2 of 0.57 and a prediction error of 4.4 mg TOC L–1. First applications to lakes in southern Ontario and Scotland, which are outside of the model’s geographic range, show the model accurately captures monitoring trends, and suggests that TOC dynamics during the 20th century at these sites were primarily driven by changes in atmospheric deposition. Our results demonstrate that the lake water TOC model has multiregional applications and is not biased by postdepositional diagenesis, allowing the identification of past TOC variations in northern lakes of Europe and North America over time scales of decades to millennia.Mi, J., Zhang, B., Shen, Z., Huang, W., Casalins, A., Liu, C., 2017. The experimental study on H2S generation during thermal recovery process for heavy oil from the Eastern Venezuela Basin. Journal of Natural Gas Geoscience 2, 201-208. sulfide (H2S) is toxic, corrosive and environmentally damaging. It is not only found in oil and gas development, but is also often found in heavy oil exploitation. In this study, three heavy oils were selected from the Orinoco Heavy Oil Belt in the southern part of the Eastern Venezuela Basin. Thermal cracking experiments in gold sealed tubes were then conducted using the heavy oils. The objective of the experiment is to unravel the H2S generation mechanism and utility in establishing a development program for heavy oil thermal recovery. The results of the oil isothermal cracking experiments show that the H2S yield increases with the increasing cracking temperature and holding time at 150 °C and 250 °C. Carbon dioxide (CO2) is the main component in gaseous products and its concentration is more than 80% in our experiments. The yields of CO2, H2S and total hydrocarbon gas present similar varying trend that increases with increasing isothermal time. The sulfur contents in group compositions of the original oil from the CJS-48 well and that of the residual oils with different cracking time at 250 °C were then measured. The analytical results show that most sulfur (>75%) exists in aromatics both in original oil and in the residual oils cracked at 250 °C, not to mention, no sulfur was measured in saturates. Although the decrease of sulfur in aromatics with the increased cracking time is low, it has great significance to the H2S generation during thermal recovery of heavy oil for more than 75% sulfur existed in aromatics. The decrease of sulfur content in resin and asphaltene of cracking residues with increased cracking time indicates that the sulfur existed in resin and asphaltene has some contribution to H2S generation during the thermal recovery process of heavy oil.Mi, J., Zhang, S., Su, J., He, K., Zhang, B., Tian, H., Li, X., 2018. The upper thermal maturity limit of primary gas generated from marine organic matters. Marine and Petroleum Geology 89, Part 1, 120-129. composition and chemical structure of 16 kerogen samples concentrated from marine source rocks with maturity levels ranging from 0.65 %Ro to 3.3 %Ro were determined. Pyrolysis experiments of seven samples selected from the 16 kerogen samples were conducted in a gold tube system to clarify the process and determine the upper thermal maturity limit for primary gas generation from marine organic matter (OM). The variation of the H/C atomic ratio of the marine OM appears to evolve through three phases with increasing maturity, including a drastic decreasing phase before 1.3 %Ro, a moderate decreasing phase from 1.3 to 2.0 %Ro and a gradual decreasing phase above 2.0 %Ro. The evolution of the chemical structure measured by FTIR indicates that most oxygen containing functional groups in marine OM appear to be released prior to 0.8 %Ro. Aliphatic groups were still detected in the sample with a maturity of 3.0%Ro, but disappeared in the sample with a maturity of 3.3 %Ro. The variation of aliphatic groups VS aromatic rings (I1) displays a similar three stage pattern as the variation of H/C atomic ratio with increasing maturity. A step-by-step heating method in kerogen pyrolysis experiments was adopted to preclude secondary gas generation. The pyrolysis experimental results for samples with different maturities proved that generally the maximum yield of primary gas generated by the marine OM was not more than 140 ml per gram of total organic carbon (TOC). Only 1.16 ml/g TOC of hydrocarbon gas was generated by the sample with the maturity of 3.3 %Ro. Thus, it can be rationally inferred that the upper thermal maturity limit for gas generation from the marine OM may be around 3.5 %Ro. Nevertheless, the main maturity range for the primary gas generation is suggested to be below 2.0 %Ro. The yield of primary gas generated at the maturity range above 2.0%Ro takes up 10% of maximum yield of the primary gas generated by the marine OM.Mickol, R.L., Kral, T.A., 2017. Low pressure tolerance by methanogens in an aqueous environment: Implications for subsurface life on Mars. Origins of Life and Evolution of Biospheres 47, 511-532. low pressure at the surface of Mars (average: 6?mbar) is one potentially biocidal factor that any extant life on the planet would need to endure. Near subsurface life, while shielded from ultraviolet radiation, would also be exposed to this low pressure environment, as the atmospheric gas-phase pressure increases very gradually with depth. Few studies have focused on low pressure as inhibitory to the growth or survival of organisms. However, recent work has uncovered a potential constraint to bacterial growth below 25?mbar. The study reported here tested the survivability of four methanogen species (Methanothermobacter wolfeii, Methanosarcina barkeri, Methanobacterium formicicum, Methanococcus maripaludis) under low pressure conditions approaching average martian surface pressure (6?mbar – 143?mbar) in an aqueous environment. Each of the four species survived exposure of varying length (3?days – 21?days) at pressures down to 6?mbar. This research is an important stepping-stone to determining if methanogens can actively metabolize/grow under these low pressures. Additionally, the recently discovered recurring slope lineae suggest that liquid water columns may connect the surface to deeper levels in the subsurface. If that is the case, any organism being transported in the water column would encounter the changing pressures during the transport.Moffa-Sánchez, P., Hall, I.R., 2017. North Atlantic variability and its links to European climate over the last 3000 years. Nature Communications 8, Article 1726. subpolar North Atlantic is a key location for the Earth’s climate system. In the Labrador Sea, intense winter air–sea heat exchange drives the formation of deep waters and the surface circulation of warm waters around the subpolar gyre. This process therefore has the ability to modulate the oceanic northward heat transport. Recent studies reveal decadal variability in the formation of Labrador Sea Water. Yet, crucially, its longer-term history and links with European climate remain limited. Here we present new decadally resolved marine proxy reconstructions, which suggest weakened Labrador Sea Water formation and gyre strength with similar timing to the centennial cold periods recorded in terrestrial climate archives and historical records over the last 3000 years. These new data support that subpolar North Atlantic circulation changes, likely forced by increased southward flow of Arctic waters, contributed to modulating the climate of Europe with important societal impacts as revealed in European history.Moghaddam, R.N., Jamiolahmady, M., 2017. Study of slip flow in unconventional shale rocks using lattice Boltzmann method: Effects of boundary conditions and TMAC. Transport in Porous Media 120, 115-139. and production from unconventional resources require understanding of flow mechanisms and rock/fluid interactions, which are different from those in conventional reservoirs. Several flow regimes including slip and transition can be dominated in these reservoirs due to the presence of micro- and nano-pores. Recently the lattice Boltzmann method has been considered as a well-accepted method for simulation of slip flow in shale rocks. In this paper, the two-relaxation-time-based Lattice Boltzmann approach was adopted to simulate the slip flow in a single channel and a simplified 2D and 3D porous media. Different boundary conditions including diffusive reflective and bounce back-specular reflection were used to capture the gas slippage at the wall surface. The simulation results were compared with the experimental data measured on three shale rock samples. The results showed that the gas slippage in the shale samples under study cannot be modelled using the literature tangential momentum accommodation coefficient values. It was also shown that the permeability enhancement was overestimated for Kn?>?0.1 when the gas flow was simulated in a single channel. Furthermore, from the fitted line to the simulation results (up to Kn?=?0.3), the first- and second-order slip coefficients of the N–S boundary conditions were found as 2 and 1.54, respectively.Mohammadi, S., Rashidi, F., Mousavi-Dehghani, S.A., Ghazanfari, M.-H., 2017. Comparison of the effect of temperature on asphaltene destabilisation in light and heavy live oils. International Journal of Oil, Gas and Coal Technology 16, 342-362. main objective of this study is to investigate the effect of temperature on asphaltene destabilisation (precipitation/aggregation) in live oils at elevated pressure conditions. Here, the asphaltene related experiments were performed using solid detection systems, high pressure microscope, and high pressure-high temperature filtration apparatuses in two Iranian light and heavy live oils with different characteristics and stability. The obtained results were interpreted in terms of asphaltene onset pressure, size distribution and average diameter of the aggregates, fractal analysis of the aggregates structures, and the amount of asphaltene precipitation. As well, the results of the experiments for both light and heavy oil samples were compared in detail.Mohammadmoradi, P., Kantzas, A., 2018. Direct geometrical simulation of pore space evolution through hydrate dissociation in methane hydrate reservoirs. Marine and Petroleum Geology 89, 786-798. identification of methane hydrate behavior in porous media is one of the most challenging yet rewarding pore-level visualization and simulation tasks. The hydrate morphology influences the physical characteristics of the host sediments as during the hydrate formation and dissociation processes the pore space and flow pathways constantly evolve. Here, a direct three-phase pore morphological simulation approach is proposed, verified and utilized to simulate hydrate deformities and predict fluid occupancies and absolute and effective permeabilities of hydrate-bearing geological formations. The proposed technique simulates capillary-dominant displacements by applying a set of geomaterial rules directly to the pixels of pore-level porous media images. The case studies are sandy microstructures generated based on the particle size distributions of the Mallik gas hydrate deposit. The fluid occupancy profiles, absolute permeability, and hydraulic tortuosity curves are comparable with the experimental datasets. The sensitivity analysis shows that although the gas relative permeability is less sensitive to the hydrate specifications, the porosity, grain size distribution, and hydrate content and occupancy remarkably influence the rock absolute permeability.M?ller, M., Stukenbrock, E.H., 2017. Evolution and genome architecture in fungal plant pathogens. Nature Reviews Microbiology 15, 756-771. fungal kingdom comprises some of the most devastating plant pathogens. Sequencing the genomes of fungal pathogens has shown a remarkable variability in genome size and architecture. Population genomic data enable us to understand the mechanisms and the history of changes in genome size and adaptive evolution in plant pathogens. Although transposable elements predominantly have negative effects on their host, fungal pathogens provide prominent examples of advantageous associations between rapidly evolving transposable elements and virulence genes that cause variation in virulence phenotypes. By providing homogeneous environments at large regional scales, managed ecosystems, such as modern agriculture, can be conducive for the rapid evolution and dispersal of pathogens. In this Review, we summarize key examples from fungal plant pathogen genomics and discuss evolutionary processes in pathogenic fungi in the context of molecular evolution, population genomics and agriculture.Mori, J.F., Scott, J.J., Hager, K.W., Moyer, C.L., Küsel, K., Emerson, D., 2017. Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov. The Isme Journal 11, 2624-2636. Fe-oxidizing communities are common at diffuse-flow hydrothermal vents throughout the world’s oceans. The foundational members of these communities are the Zetaproteobacteria, a class of Proteobacteria that is primarily associated with ecosystems fueled by ferrous iron, Fe(II). We report here the discovery of two new isolates of Zetaproteobacteria isolated from the Mid-Atlantic Ridge (TAG-1), and the Mariana back-arc (SV-108), that are unique in that they can utilize either Fe(II) or molecular hydrogen (H2) as sole electron donor and oxygen as terminal electron acceptor for growth. Both strains precipitated Fe-oxyhydroxides as amorphous particulates. The cell doubling time on H2 vs Fe(II) for TAG-1 was 14.1 vs 21.8?h, and for SV-108 it was 16.3 vs 20?h, and it appeared both strains could use either H2 or Fe(II) simultaneously. The strains were close relatives, based on genomic analysis, and both possessed genes for the uptake NiFe-hydrogenase required for growth on H2. These two strains belong to Zetaproteobacteria operational taxonomic unit 9 (ZetaOTU9). A meta-analysis of public databases found ZetaOTU9 was only associated with Fe(II)-rich habitats, and not in other environments where known H2-oxidizers exist. These results expand the metabolic repertoire of the Zetaproteobacteria, yet confirm that Fe(II) metabolism is the primary driver of their physiology and ecology.Muangthong-on, T., Wannapeera, J., Jadsadajerm, S., Worasuwannarak, N., Ohgaki, H., Miura, K., 2017. Effect of solvent on the degradative solvent extraction of low rank coal. Energy & Fuels 31, 11954-11962. have proposed a degradative solvent extraction method which upgrades as well as dewaters low rank coals and biomass wastes at 350 °C using 1-methlynaphthalene as a model solvent. The proposed solvent treatment is an effective method to produce high quality extracts having similar physical and chemical properties from several kinds of low rank coals and biomasses. Three solid fractions (Residue, Deposit, and Soluble) were fractionated and recovered after the solvent extraction. Soluble and Deposit are expected to be precursors for producing value added products. In this work the effects of solvent on the degradative solvent extraction of two low-rank coals, Loy Yang (LY) and Pendopo (PD), were examined by using four solvents: 1-methylnaphthalene (1-MN), kerosene, a 1 to 1 mixture of 1-MN and kerosene, and a solvent rich in alkyl benzenes, A150. It was judged that the solvent does not affect the degradation reaction at 350 °C, and hence the performance of this degradative solvent extraction method such as selective deoxygenation and effective dewatering is realized by all of the solvents used. The yield distributions of extracted products were dominated by the solubility of solvent used as expected. The Hildebrand regular solution theory seems to represent the differences in the yields and elemental compositions of Soluble fractions. 1-MN, having 21.3 (J/cm3)1/2 of solubility parameter δ, gave the largest yield of Soluble followed by A150 (δ ? 18.8 (J/cm3)1/2), the mixed solvent (δ ? 19.1 (J/cm3)1/2), and kerosene (δ ? 16.7 (J/cm3)1/2). Preparation of solvent treated coals (STCs) from different solvents gave the yields close to the sum of the yields of Soluble, Deposit, and Residue for all solvents used. Most of the heating values of solid products were over 29 MJ/kg and rather close to subbituminous coal. All Solubles were found to melt completely at rather low temperature. The properties of Solubles can be changed by solvents used. It was found that A150 may be utilized as a practical solvent when Soluble is the target product and that kerosene is expected to be a practical solvent for preparing STC from low-rank coal.Muchowska, K.B., Varma, S.J., Chevallot-Beroux, E., Lethuillier-Karl, L., Li, G., Moran, J., 2017. Metals promote sequences of the reverse Krebs cycle. Nature Ecology & Evolution 1, 1716-1721. reverse tricarboxylic acid (rTCA) cycle (also known as the reverse Krebs cycle) is a central anabolic biochemical pathway whose origins are proposed to trace back to geochemistry, long before the advent of enzymes, RNA or cells, and whose imprint remains intimately embedded in the structure of core metabolism. If it existed, a primordial version of the rTCA cycle would necessarily have been catalysed by naturally occurring minerals at the earliest stage of the transition from geochemistry to biochemistry. Here, we report non-enzymatic promotion of multiple reactions of the rTCA cycle in consecutive sequence, whereby 6 of its 11 reactions were promoted by Zn2+, Cr3+ and Fe0 in an acidic aqueous solution. Two distinct three-reaction sequences were achieved under a common set of conditions. Selectivity was observed for reduction reactions producing rTCA cycle intermediates compared with those leading off-cycle. Reductive amination of ketoacids to furnish amino acids was observed under similar conditions. The emerging reaction network supports the feasibility of primitive anabolism in an acidic, metal-rich reducing environment.Muirhead, D.K., Bowden, S.A., Parnell, J., Schofield, N., 2017. Source rock maturation owing to igneous intrusion in rifted margin petroleum systems. Journal of the Geological Society 174, 979-987. and extrusive volcanism is a common feature associated with many sedimentary basins formed along rifted margins. As a result, igneous intrusions are often found in potential hydrocarbon-producing source rock horizons. Although direct thermal effects on source rocks have been studied in detail, few studies have dealt with understanding the thermal effects on source rocks across a range of different thermal histories prior to intrusion. The metamorphic aureoles of three intrusions have been characterized for source rock maturation using organic geochemistry and Raman spectroscopy. Results show that a unique combination of organic geochemical and Raman spectroscopic techniques adds further insight to intrusion and host rock interactions, with an effective oil window and extended gas window located in the aureole of an immature and mature source rock respectively. Such varied and potentially beneficial geochemical responses further the need to re-evaluate source rock intervals in rifted margin basins.Müller, M., de Sena Oliveira, I., Allner, S., Ferstl, S., Bidola, P., Mechlem, K., Fehringer, A., Hehn, L., Dierolf, M., Achterhold, K., Gleich, B., Hammel, J.U., Jahn, H., Mayer, G., Pfeiffer, F., 2017. Myoanatomy of the velvet worm leg revealed by laboratory-based nanofocus X-ray source tomography. Proceedings of the National Academy of Sciences 114, 12378-12383.: X-ray computed tomography (CT) imaging has become popular for investigating, nondestructively and three-dimensionally, both external and internal structures of various specimens. However, the limited resolution of conventional laboratory-based CT systems (≥500 nm) still hampers the detailed visualization of features on the low nanometer level. We present a laboratory CT device and data processing pipeline to routinely and efficiently generate high-resolution 3D data (≈100 nm) without requiring synchrotron radiation facilities. Our setup is especially relevant for conducting detailed analysis of very small biological samples, as demonstrated for a walking appendage of a velvet worm. Comparative analyses of our CT data with those obtained from other popular imaging methods highlight the advantages and future applicability of the nanoCT setup. Abstract: X-ray computed tomography (CT) is a powerful noninvasive technique for investigating the inner structure of objects and organisms. However, the resolution of laboratory CT systems is typically limited to the micrometer range. In this paper, we present a table-top nanoCT system in conjunction with standard processing tools that is able to routinely reach resolutions down to 100 nm without using X-ray optics. We demonstrate its potential for biological investigations by imaging a walking appendage of Euperipatoides rowelli, a representative of Onychophora—an invertebrate group pivotal for understanding animal evolution. Comparative analyses proved that the nanoCT can depict the external morphology of the limb with an image quality similar to scanning electron microscopy, while simultaneously visualizing internal muscular structures at higher resolutions than confocal laser scanning microscopy. The obtained nanoCT data revealed hitherto unknown aspects of the onychophoran limb musculature, enabling the 3D reconstruction of individual muscle fibers, which was previously impossible using any laboratory-based imaging technique. Munro, J.E., Kimyon, ?., Rich, D.J., Koenig, J., Tang, S., Low, A., Lee, M., Manefield, M., Coleman, N.V., 2017. Co-occurrence of genes for aerobic and anaerobic biodegradation of dichloroethane in organochlorine-contaminated groundwater. FEMS Microbiology Ecology 93, Article fix133. (DCA) is a problematic groundwater pollutant. Factors influencing the distribution and activities of DCA-degrading bacteria are not well understood, which has hampered their application for bioremediation. Here, we used quantitative PCR to investigate the distribution of putative DCA-dehalogenating bacteria at a DCA-impacted site in Sydney (Australia). The dehalogenase genes dhlA, tceA and bvcA were detected in all groundwater samples (n = 15), while vcrA was found in 11/15 samples. The 16S rRNA gene sequences specific to the dehalogenating genera Dehalobacter, Desulfitobacterium and Dehalogenimonas were detected in 15/15, 13/15 and 13/15 samples, respectively, while Dehalococcoides sequences were found in 9/15 samples. The tceA, bvcA and vcrA genes occurred in the same samples as Dehalococcoides and Dehalobacter. Microcosm experiments confirmed the presence of bacteria capable of dechlorination under anoxic conditions. The abundance of the dhlA gene, which is found in hydrolytic DCA degraders, was positively correlated to the DCA concentration, and was unexpectedly most abundant in samples with low oxygen conditions. A dhlA-containing bacterium isolated from the site (Xanthobacter EL8) was capable of anaerobic growth on DCA under denitrifying conditions. The presence of diverse DCA-dehalogenating bacteria at this site indicates that natural attenuation or biostimulation could be valid approaches for site cleanup.Muttoni, G., Scardia, G., Kent, D.V., 2018. Early hominins in Europe: The Galerian migration hypothesis. Quaternary Science Reviews 180, 1-29. updated review of sites bearing hominin remains and/or tools from Europe, including new findings from the Balkans, still indicates that the only compelling evidence of main hominin presence in these regions was only since ～0.9 million years ago (Ma), bracketed by the end of the Jaramillo geomagnetic polarity subchron (0.99 Ma) and the Brunhes-Matuyama polarity chron boundary (0.78 Ma). This time window straddled the late Early Pleistocene climate transition (EPT) at the onset of enhanced glacial/interglacial activity that reverberated worldwide. Europe may have become initially populated during the EPT when, possibly for the first time in the Pleistocene, vast and exploitable ecosystems were generated along the eustatically emergent Po-Danube terrestrial conduit. These newly formed settings, characterized by stable terrestrial lowlands with open grasslands and reduced woody cover especially during glacial/interglacial transitions, are regarded as optimal ecosystems for several large Galerian immigrant mammals such as African and Asian megaherbivores, possibly linked with hominins in a common food web, to expand into en route to Europe. The question of when hominins first arrived in Europe thus places the issue in the context of changes in climate, paleogeography and faunal associations as potential environmental drivers and controlling agents in a specific time frame, a key feature of the Galerian migration hypothesis.Nahidan, S., Nourbakhsh, F., Henneberger, R., Lazzaro, A., Zeyer, J., 2017. Aggregate size distribution of ammonia-oxidizing bacteria and archaea at different landscape positions. Geomicrobiology Journal 34, 895-902. quantify the spatial distribution of ammonia-oxidizing bacteria (AOB) and archaea (AOA) and to determine nitrification activity in soil aggregates along a landscape, soil samples were collected from three landscape positions (shoulder, backslope, and toeslope) at two pasture sites with contrasting climatic conditions. The abundance of AOB and AOA was estimated by quantifying their respective bacterial and archaeal amoA gene copies using real-time polymerase chain reaction. Soil organic C (SOC), total N (TN), and the potential nitrification rate (PNR) were measured in aggregate size ranges (4–1, 1–0.25, and 0.25–0.05 mm). At site 1, a decreasing trend in PNR was observed as the size of aggregates decreased. Both bacterial and archaeal amoA genes were higher in the macroaggregates (4–1 and 1–0.25 mm) than in the microaggregates (0.25–0.05 mm) along the landscape. At site 2, PNR was higher in the smallest size of aggregates. In the 0.25–0.05-mm fraction, the abundance of bacterial and archaeal amoA genes was equal to, or greater than, those found in larger aggregate sizes. The relative abundance of archaeal amoA gene and the PNR correlated with relative SOC and TN contents along the landscapes. The positive relationship between relative archaeal amoA gene abundance and PNR suggests that nitrification in the studied pastures is probably driven by ammonia-oxidizing Thaumarchaeota.Nam, I., Lee, J.K., Nam, H.G., Zare, R.N., 2017. Abiotic production of sugar phosphates and uridine ribonucleoside in aqueous microdroplets. Proceedings of the National Academy of Sciences 114, 12396-12400.: Phosphorylation is essential for life. Phosphorylated molecules play diverse functions in cells, including metabolic (e.g., sugar phosphates), structural (e.g., phospholipids), and instructional (e.g., RNA and DNA). In nature, the phosphorylation of sugars via condensation is thermodynamically and kinetically unfavorable in bulk solution. Thus, a key question arising within prebiotic chemistry concerning the origin of life is, “How was phosphorus incorporated into the biological world?” Here, we show that sugar phosphates and a ribonucleoside form spontaneously in microdroplets, without enzymes or an external energy source. Sugar phosphorylation in microdroplets has a lower entropic cost than in bulk solution. Therefore, thermodynamic obstacles of prebiotic condensation reactions can be circumvented in microdroplets. Abstract: Phosphorylation is an essential chemical reaction for life. This reaction generates fundamental cell components, including building blocks for RNA and DNA, phospholipids for cell walls, and adenosine triphosphate (ATP) for energy storage. However, phosphorylation reactions are thermodynamically unfavorable in solution. Consequently, a long-standing question in prebiotic chemistry is how abiotic phosphorylation occurs in biological compounds. We find that the phosphorylation of various sugars to form sugar-1-phosphates can proceed spontaneously in aqueous microdroplets containing a simple mixture of sugars and phosphoric acid. The yield for d-ribose-1-phosphate reached over 6% at room temperature, giving a ΔG value of ?1.1 kcal/mol, much lower than the +5.4 kcal/mol for the reaction in bulk solution. The temperature dependence of the product yield for the phosphorylation in microdroplets revealed a negative enthalpy change (ΔH = ?0.9 kcal/mol) and a negligible change of entropy (ΔS = 0.0007 kcal/mol·K). Thus, the spontaneous phosphorylation reaction in microdroplets occurred by overcoming the entropic hurdle of the reaction encountered in bulk solution. Moreover, uridine, a pyrimidine ribonucleoside, is generated in aqueous microdroplets containing d-ribose, phosphoric acid, and uracil, which suggests the possibility that microdroplets could serve as a prebiotic synthetic pathway for ribonucleosides. Nangle, S.N., Sakimoto, K.K., Silver, P.A., Nocera, D.G., 2017. Biological-inorganic hybrid systems as a generalized platform for chemical production. Current Opinion in Chemical Biology 41, 107-113. expanding renewable energy market to supplant petrochemicals has motivated synthesis technologies that use renewable feedstocks, such as CO2. Hybrid biological-inorganic systems provide a sustainable, efficient, versatile, and inexpensive chemical synthesis platform. These systems comprise biocompatible electrodes that transduce electrical energy either directly or indirectly into bioavailable energy, such as H2 and NAD(P)H. In combination, specific bacteria use these energetic reducing equivalents to fix CO2 into multi-carbon organic compounds. As hybrid biological-inorganic technologies have developed, the focus has shifted from phenomenological and proof-of-concept discovery towards enhanced energy efficiency, production rate, product scope, and industrial robustness. In this review, we highlight the progress and the state-of-the-art of this field and describe the advantages and challenges involved in designing bio- and chemo- compatible systems.Naraoka, H., Yamashita, Y., Yamaguchi, M., Orthous-Daunay, F.-R., 2017. Molecular evolution of N-containing cyclic compounds in the parent body of the Murchison meteorite. ACS Earth and Space Chemistry 1, 540-550. meteorites contain various classes of organic compounds. Because the molecular distribution in these meteorites is not fully clarified, we do not yet understand the comprehensive formation mechanism(s) of extraterrestrial organic compounds. In this study, diverse and abundant alkylated homologues of N-containing cyclic compounds were identified in the methanol extract of the Murchison meteorite by electrospray ionization using high-performance liquid chromatography/ultrahigh-resolution mass spectrometry. More than 600 positive ions were assigned to CnHmN+ and CnHmN2+, in which saturated and unsaturated alkylated pyridines and alkylimidazoles are predominant. Both can be synthesized from aldehydes and ammonia through aldol condensation and imine formation under an alkaline environment. Further redox reactions could have proceeded to make these molecules evolve to various CHN compounds, including alkylpiperidines and pyridine carboxylic acids. This study indicates that aldol condensation and formose reaction with ammonia are an important mechanism for the molecular evolution of N-containing compounds in the asteroid.Nazina, T.N., Sokolova, D.S., Babich, T.L., Semenova, E.M., Ershov, A.P., Bidzhieva, S.K., Borzenkov, I.A., Poltaraus, A.B., Khisametdinov, M.R., Tourova, T.P., 2017. Microorganisms of low-temperature heavy oil reservoirs (Russia) and their possible application for enhanced oil recovery. Microbiology 86, 773-785. and microbiological characteristics of formation waters low-temperature heavy oil reservoirs (Russia) were investigated. The Chernoozerskoe, Yuzhno-Suncheleevskoe, and Severo-Bogemskoe oilfields, which were exploited without water-flooding, were shown to harbor scant microbial communities, while microbial numbers in the water-flooded strata of the Vostochno-Anzirskoe and Cheremukhovskoe oilfields was as high as 106 cells/mL. The rates of sulfate reduction and methanogenesis were low, not exceeding 1982 ng S2–/(L day) and 9045 nL СН4/(L day), respectively, in the samples from water-flooded strata. High-throughput sequencing of microbial 16S rRNA gene fragments in the community of injection water revealed the sequences of the Proteobacteria (74.7%), including Betaproteobacteria (40.2%), Alphaproteobacteria (20.7%), Gammaproteobacteria (10.1%), Deltaproteobacteria (2.0%), and Epsilonproteobacteria (1.6%), as well as Firmicutes (7.9%), Bacteroidetes (4.1%), and Archaea (0.2%). DGGE analysis of microbial mcrA genes in the community of injection water revealed methanogens of the genera Methanothrix, Methanospirillum, Methanobacterium, Methanoregula, Methanosarcina, and Methanoculleus, as well as unidentified Thermoplasmata. Pure cultures of bacteria of the genera Rhodococcus, Pseudomonas, Gordonia, Cellulomonas, etc., capable of biosurfactant production when grown on heavy oil, were isolated. Enrichment cultures of fermentative bacteria producing significant amounts of volatile organic acids (acetic, propionic, and butyric) from sacchariferous substrates were obtained. These acids dissolve the carbonates of oil-bearing rock efficiently. Selection of the efficient microbial technology for enhanced recovery of heavy oil from terrigenous and carbonate strata requires model experiments with microbial isolates and the cores of oil-bearing rocks. Original Russian Text ? T.N. Nazina, D.Sh. Sokolova, T.L. Babich, E.M. Semenova, A.P. Ershov, S.Kh. Bidzhieva, I.A. Borzenkov, A.B. Poltaraus, M.R. Khisametdinov, T.P. Tourova, 2017, published in Mikrobiologiya, 2017, Vol. 86, No. 6, pp. 748–761.Nelson, J., Yamanaka, M., Lopez-Linares, F., Poirier, L., Rogel, E., 2017. Characterization of dissolved metals and metallic nanoparticles in asphaltene solutions by single-particle inductively coupled plasma mass spectrometry. Energy & Fuels 31, 11971-11976. though evaluating the metal content in asphaltenes is now a routine analysis, determining the nature of the metals present in asphaltenes has continued to be an elusive subject. In this work, we presented, for the first time, the application of single-particle inductively coupled plasma mass spectrometry (spICP–MS) in hydrocarbon media to determine the presence of metal-containing nanoparticles in asphaltene solutions. This method also offers the unique ability to differentiate between metal-containing nanoparticles and dissolved metals. The study of three asphaltene samples from different origins indicates that vanadium and nickel are entirely dissolved probably as part of soluble coordination complexes, such as porphyrins. In clear contrast, we found that molybdenum and iron are forming part of nanoparticles and report nanoparticle distributions. We found that nanoparticle distributions for molybdenum are very similar for the different asphaltenes, while for iron oxide, the size increases as the content of this metal in the sample increases. Relative concentrations of these metals in nanoparticles indicate that most molybdenum is present as soluble compounds in the organic medium, while iron is predominantly forming nanoparticles. This study demonstrates the applicability of spICP–MS in hydrocarbon media as a potential and routine technique to characterize metals in asphaltenes, crude oils, and petroleum-derived materials.Nie, B., Fan, P., Li, X., 2018. Quantitative investigation of anisotropic characteristics of methane-induced strain in coal based on coal particle tracking method with X-ray computer tomography. Fuel 214, 272-284. order to quantify the anisotropic characteristics of coal swelling deformation during the process of methane adsorption, the inner mesoscopic structures of coal are scanned with computerized tomography (CT) and a coal particle tracking method (CPTM) is proposed to quantitatively calculate the strain of coal particulates in view of the pixel gray level matrix of CT image. The results show that the spatio-temporal distribution of coal mesoscopic deformation is inhomogeneous during the process of methane adsorption. From the spatial distribution, some parts of coal swell and other parts shrink. The mineral phase and porosity or fracture inside them are mainly swelling deformation and little shrinkage deformation. The swelling and shrinkage deformation is varying constantly with different gas pressure in the organic lithotypes of varying macerals and pore or fracture inside them. The expansion deformation tends to first squeeze the original pore or fracture inside them for more expansion space. From the temporal distribution, the magnitudes of adsorption deformation is also not uniform along with the decrease of gas pressure. After the adsorption balance, the change magnitudes of strain tend to decrease. The mesoscopic deformation of coal samples is anisotropic and the macroscopic deformation is swelling. This is verified by the cumulative total strain values of coal, which are obtained from the mesoscopic strain calculation results. This study presents mesoscopic CT and strain calculation results images of coal deformation. These data will provide the basis for the study of physical structure and mechanical properties of coal with adsorbing methane.Niggemann, J., Lomstein, B.A., Schubert, C.J., 2018. Diagenesis of amino compounds in water column and sediment of Lake Baikal. Organic Geochemistry 115, 67-77. diagenesis of amino compounds in Lake Baikal was studied in sediment trap material (18 different water depths between 50–1350 m) and underlying sediment (0–40?cm). Total hydrolysable amino acids (THAA), the amino acid (AA) composition including d- and l-enantiomers and amino sugars were analyzed. The study provides information on early diagenesis (<1 year) of settling material as well as on longer-term diagenesis (up to 600 years) occurring in the sediment. AA based diagenetic indicators were successfully applied to reveal changes at the different diagenetic stages. With increasing water and sediment depth, consistent decreases were found in: (1) the contributions of AA to total organic carbon (%TAAC, from 20 to 7%) and total nitrogen (%TAAN, from 54 to 20%); (2) the ratios of protein AA and their respective non-protein degradation products (aspartic acid:β-alanine, from 15 to 2; glutamic acid:γ-aminobutyric acid, from 28 to 2; arginine:ornithine, from 19 to 2); and (3) the AA based degradation index (from 0.7 to ?1.1). There was multiple evidence that diagenesis went along with a progressive transformation of phytoplankton and zooplankton into bacterial organic material. Glycine, which is enriched in bacterial peptidoglycan, increased in relative abundance and bacteria-derived d-AA preferentially accumulated over proteinaceous l-AA. Molar ratios of glucosamine and galactosamine decreased towards a ratio of 1.0?±?0.1 in the sediment, similar to ratios previously reported for detrital marine organic material. The general pattern of amino compound diagenesis in Lake Baikal resembles the pattern observed in marine systems, indicating a universal character of the processes controlling diagenesis in aquatic environments.Nijman, W., Kloppenburg, A., de Vries, S.T., 2017. Archaean basin margin geology and crustal evolution: an East Pilbara traverse. Journal of the Geological Society 174, 1090-1112. palinspastic reconstruction of a 100?km long traverse through Archaean rocks of the East Pilbara, Western Australia, includes new observations of the deformation preceding the now visible greenstone belt pattern. The restoration is time-calibrated with all available U–Pb datings.Between incompletely preserved basin sequences, two superposed Palaeoarchaean volcano-sedimentary basins (the Coongan and Salgash Basins) are separated by an eastwards time-transgressive interface tentatively interpreted as an onlap surface. For over 140?Ma, the basin margin architecture was structurally controlled by superposed extensional growth fault arrays (D1) with associated dyke swarms in a curved pattern spatially not related to that of the actual distribution of granite domes and greenstone belts.The basins are interpreted to have formed by collapse after arching above hotspots due to phase transitions by mini-subduction of slabs of cooled water-saturated basalt towards the base of an originally c. 45?km mafic crust. At c. 3.31?Ga, the extension was replaced by plate-driven regional NW–SE compression (D2) inferred from NW-over-SE shear and ramp-and-flat thrusts, partly reversing offsets of the D1 extension. The recognition of widespread D2 pre-doming compression is important because it triggered the c. 3.18?Ga start of formation of the dome-and-keel pattern (D3) visible today, which culminated at c. 2.9?Ga.Supplementary material: Eight figures, numbered ‘Supplementary material fig. a–h’, and a GPS list of observation sites are available at: , S., Yazdanpanah, M., 2017. Micro-solid phase extraction of benzene, toluene, ethylbenzene and xylenes from aqueous solutions using water-insoluble β-cyclodextrin polymer as sorbent. Journal of Chromatography A 1525, 51-59. β-cyclodextrin polymer was synthesized by chemical cross-linking using epichlorohydrin (EPI) as a cross-linker agent. The produced water-insoluble polymer was used as a sorbent for the micro-solid phase extraction (μ-SPE) of benzene, toluene, ethylbenzene and xylenes (BTEX) from water samples. The μ-SPE device consisted of a sealed tea bag envelope containing 15 mg of sorbent. For the evaluation of the extraction efficiency, parameters such as extraction and desorption time, desorption solvent and salt concentration were investigated. At an extraction time of 30 min in the course of the extraction process, analytes were extracted from a 10 mL aqueous sample solution. The analytes were desorbed by ultrasonication in 200 μL of acetonitrile for 20 min. Analysis of the analytes was done by a gas chromatography-flame ionization detector (GC–FID) system. The enrichment factor (EF) was found to be in the range 23.0–45.4 (EFmax = 50.0). The method provided linearity ranges of between 0.5 and 500.0 ng/mL (depending on the analytes), with good coefficients of determination (r2) ranging between 0.997 and 0.999 under optimized conditions. Detection limits for BTEX were in the range of between 0.15 and 0.60 ng/mL, while corresponding recoveries were in the range of 46.0–90.0%. The relative standard deviation of the method for the analytes at 100.0 ng/mL concentration level ranged from 5.5 to 11.2% (n = 5). The proposed method was concluded to be a cost effective and environmentally-friendly extraction technique with ease of operation and minimal usage of organic solvent.Nooraiepour, M., Haile, B.G., Hellevang, H., 2017. Compaction and mechanical strength of Middle Miocene mudstones in the Norwegian North Sea – The major seal for the Skade CO2 storage reservoir. International Journal of Greenhouse Gas Control 67, 49-59. study has investigated petrophysical, acoustic and geomechanical properties of Middle Miocene mudstones in the Norwegian North Sea as the primary caprock for Skade CO2 storage reservoir. To evaluate the seal properties, we analyzed collected drill cuttings and measured well logs from well 16/4-1, in addition to an extensive well log database in the Northern North Sea. The studied caprock was identified as siliceous ooze-rich mudstones with low bulk density, high shear wave velocity, and low Vp/Vs ratio. The abundance of siliceous skeletal material resulted in a significant shift from the overall trend of mudstones within the Hordaland Group. The estimated scenarios for S-wave velocity depicted that the ooze-rich mudstones have the highest brittleness of the Hordaland Group semi-consolidated rocks. The brittleness indices in well 16/4-1 illustrated that the mineralogical composition-based indices significantly overestimate brittleness compared to the elastic-based indices. While the caprock for Skade CO2 storage reservoir showed an overall ductility, the bottom 30 m demonstrated an increased brittleness profile. The more brittle ooze-rich mudstones also indicated the lowest estimation of fracture pressure compared to other scenarios. The research outcomes emphasize on the influence of mudstone type and microstructure on the macroscale physical properties of shallow semi-compacted CO2 caprocks.Novak, N., Louli, V., Skouras, S., Voutsas, E., 2018. Prediction of dew points and liquid dropouts of gas condensate mixtures. Fluid Phase Equilibria 457, 62-73. modeling of reservoir fluids behavior is of great importance for the oil and gas industry. For design and safe operation purposes, it is necessary to have an accurate, simple and robust model for the prediction of the phase equilibrium of reservoir fluids. In this work, the UMR-PRU model is applied in the prediction of dew points and liquid dropouts of gas condensate mixtures, and is compared with the widely used cubic equations of state Soave-Redlich-Kwong (SRK) and Peng-Robinson (PR) as well as the non-cubic Perturbed Chain Statistical Associating Fluid Theory (PC-SAFT) equation of state. The evaluation of the models was based both on synthetic and real gas condensate mixtures. For real gas condensates, a characterization method for the C7+ fraction based on the one proposed by Pedersen is developed for UMR-PRU. The results reveal that UMR-PRU is a sufficiently accurate model for dew point and liquid dropout predictions of gas condensates.Ogórek, R., Pusz, W., Zago?d?on, P.P., Kozak, B., Bujak, H., 2017. Abundance and diversity of psychrotolerant cultivable mycobiota in winter of a former aluminous shale mine. Geomicrobiology Journal 34, 823-833. paper is a speleomycological report from a former aluminous shale mine in Janowiec, Poland. Fungi were identified morphologically and molecularly. Microclimatic conditions differed significantly between locations of the study. However, the external environment around the mine did not directly increase the community composition and concentration of fungi in the mine. The density of fungi isolated from the air outside the mine was 63.1 colony forming units (CFU) per 1 cm3 of air. Inside the mine, fungal density ranged from 287.5 to 655 CFU per 1 m3 from the air, 28.4 to 131.1 CFU per 1 cm2 from the rock surfaces and 288.1 to 335.1 CFU per 1 cm3 from the water. Pearson correlation analysis showed that the levels of fungi isolated from the air were correlated positively with temperature, relative humidity and CO2 concentration. The concentration of fungi isolated from the rock surfaces showed a positive correlation with air flow. Five species of filamentous fungi were isolated from the sampled external air, 10 species from the internal air, six species from the rock surface and 11 species from the water. The fungi most frequently isolated from the air and water of the mine belonged to Penicillium spp., whereas from the rock surface, Geomyces pannorum was most frequently isolated. Some of the fungi present in the mine can be psychrotolerant and pathogenic for humans and animals, and they can also cause degradation of rocks.Ohkouchi, N., Chikaraishi, Y., Close, H.G., Fry, B., Larsen, T., Madigan, D.J., McCarthy, M.D., McMahon, K.W., Nagata, T., Naito, Y.I., Ogawa, N.O., Popp, B.N., Steffan, S., Takano, Y., Tayasu, I., Wyatt, A.S.J., Yamaguchi, Y.T., Yokoyama, Y., 2017. Advances in the application of amino acid nitrogen isotopic analysis in ecological and biogeochemical studies. Organic Geochemistry 113, 150-174. isotopic analysis of amino acids (CSIA-AA) has emerged in the last decade as a powerful approach for tracing the origins and fate of nitrogen in ecological and biogeochemical studies. This approach is based on the empirical observation that source amino acids (SAAs) (i.e., phenylalanine), fractionate 15N very little (< 0.5‰) during trophic transfer, whereas trophic AAs (TAAs) (i.e., glutamic acid), are greatly (～6–8‰) enriched in 15N during each trophic step. The differential fractionation of these two AA groups can provide a valuable estimate of consumer trophic position that is internally indexed to the baseline δ15N value of the integrated food web. In this paper, we critically review the analytical methods for determining the nitrogen isotopic composition of AAs by gas chromatography–isotope-ratio mass spectrometry. We also discuss methodological considerations for accurate trophic position assessment of organisms using CSIA-AA. We then discuss the advantages and challenges of the CSIA-AA approach using published case studies across a range of topics, including trophic position assessment in various ecosystems, reconstruction of ancient human diets, reconstruction of animal migration and environmental variability, and assessment of marine organic matter dynamics with new classification of microbial fractionation patterns. It is clear that the CSIA-AA approach can provide unique insight into the sources, cycling, and trophic modification of organic nitrogen as it flows through systems. However, this approach will be greatly improved through continued exploration into how biochemical, physiological, and ecological mechanisms affect isotopic fractionation of individual AAs. We end this review with a perspective on future work that will promote the evolution of the rapidly growing field of CSIA-AA.Ojha, S.P., Misra, S., Tinni, A., Sondergeld, C., Rai, C., 2017. Pore connectivity and pore size distribution estimates for Wolfcamp and Eagle Ford shale samples from oil, gas and condensate windows using adsorption-desorption measurements. Journal of Petroleum Science and Engineering 158, 454-468. size distribution and pore connectivity are vital parameters governing the hydrocarbon production of subsurface reservoirs. We estimate pore size distribution and pore connectivity of shale samples by processing the low-pressure nitrogen adsorption-desorption measurements. Our hypothesis is that the connectivity of shale pore structure can be quantified in terms percolation and fractal parameters. The proposed analysis is performed on 35 samples from various maturity windows of Eagle Ford and Wolfcamp formations. The samples were collected from 100 feet interval in the Eagle Ford gas window, 30 feet interval in the Eagle Ford oil window, and 60 feet interval in the Wolfcamp condensate window. Eagle Ford samples were low-temperature plasma ashed to study the impact of removal of organic matter on the pore size distribution and pore connectivity. The estimated pore size distribution of Wolfcamp samples differ significantly from that of Eagle Ford samples that supports the mineralogical differences between the two formations. Wolfcamp samples exhibit higher fractal dimension indicating higher pore complexity. Eagle Ford samples exhibit better long-range pore connectivity and lower pore complexity compared to Wolfcamp samples despite lower porosity.Okere, U.V., Schuster, J.K., Ogbonnaya, U.O., Jones, K.C., Semple, K.T., 2017. Indigenous 14C-phenanthrene biodegradation in "pristine" woodland and grassland soils from Norway and the United Kingdom. Environmental Science: Processes & Impacts 19, 1437-1444. this study, the indigenous microbial mineralisation of 14C-phenanthrene in seven background soils (four from Norwegian woodland and three from the UK (two grasslands and one woodland)) was investigated. ∑PAHs ranged from 16.39 to 285.54 ng g?1 dw soil. Lag phases (time before 14C-phenanthrene mineralisation reached 5%) were longer in all of the Norwegian soils and correlated positively with TOC, but negatively with ∑PAHs and phenanthrene degraders for all soils. 14C-phenanthrene mineralisation in the soils varied due to physicochemical properties. The results show that indigenous microorganisms can adapt to 14C-phenanthrene mineralisation following diffuse PAH contamination. Considering the potential of soil as a secondary PAH source, these findings highlight the important role of indigenous microflora in the processing of PAHs in the environment.Ola, P.S., Aidi, A.K., Bankole, O.M., 2018. Clay mineral diagenesis and source rock assessment in the Bornu Basin, Nigeria: Implications for thermal maturity and source rock potential. Marine and Petroleum Geology 89, 653-664. understanding of the mineral and organic matter modifications during burial are critical in assessments of potential source rocks in petroleum exploration studies. Here, we examined the relationships between clay mineral diagenesis and organic thermal indicators (vitrinite reflectance and Rock-Eval Tmax) to constrain the thermal maturity and hydrocarbon potential of source rocks in the Mbeji-1 well in the northeastern part of the Cretaceous/Tertiary Bornu Basin. X-ray diffraction mineralogical data show that the <2 μm clay-sized fraction consist of mixed layer illite/smectite (I/S), kaolinite, illite, and Fe-chlorite clay mineral assemblages. The major diagenetic changes in the clay mineral evolution are transformation of random (R0) to ordered (R1) illite/smectite (I/S) mixed layer between ～2500 m and ～3640 m depths, decrease in smectite in I/S with burial, and appearance of chlorite at ～2500 m. Total organic carbon and Rock-Eval pyrolysis parameters (HI, S2, Tmax) indicate presence of lean shales consisting of gas prone to inert terrestrial organic matters. Source rocks at shallower depths below 2500 m are immature while those below this level within lower Fika Formation to upper Gongila formations are marginally matured with respect to hydrocarbon generation. The variation between I/S transformation and VR for the Mbeji-1 well shows a delay in illitization process compare to organic matter maturity. We considered that other than temperature, insufficient and variable potassium availability, and short-heating time resulted in retarding the smectite illitization reaction relative to the organic matter parameters (vitrinite reflectance and Tmax). These differences further demonstrates that organic matter responds quickly to increasing temperature than mineral reactions at short heating time in young sedimentary basins.Oldenburg, T.B.P., Jones, M., Huang, H., Bennett, B., Shafiee, N.S., Head, I., Larter, S.R., 2017. The controls on the composition of biodegraded oils in the deep subsurface- Part 4. Destruction and production of high molecular weight non-hydrocarbon species and destruction of aromatic hydrocarbons during progressive in-reservoir biodegradation. Organic Geochemistry 114, 57-80. study extends the analysis of previously well studied biodegraded crude oil case history sample sets. The analytical window is extended into the high molecular weight, aromatic hydrocarbon and non-hydrocarbon fraction of crude oils, using a 12 T ultra-high resolution mass spectrometer (FTICR-MS).Biodegradation is pervasive across compound groups and extent of degradation appears dependent on compound abundance and hence availability. Oil constituents with molecular weights up to m/z 600 (carbon number 44) are affected by in-reservoir biodegradation. Apart from special, specific compound groups possibly related to the active reservoir biomass, all hydrocarbon and single heteroatom-containing compound classes are depleted by biodegradation. Production of various highly alkylated species indicate that transformation of crude oil components often involves derivatization and preservation rather than just complete destruction of high molecular weight compounds. Whereas one case study shows good correlation between depletion of S1 species and a strong increase in SO2 species, a nitrogen enriched oil suite shows an analogous trend in the transformation of N1 species to the corresponding NO2 species. Increase in O2 species are seen in both sample sets indicating partial oxidation is a major overall process in in-situ reservoir biodegradation. These variations are important geochemically but also impact transport, interfacial and corrosion properties of oils.Nitrogen isotope systematics indicate that nitrogen-containing compounds might act as nitrogen nutrient sources or mainly as carbon sources for the microorganisms causing in-situ reservoir biodegradation depending of level of biodegradation. Distributions of some heterocyclic species add a very biodegradation resistant parameter set, to the petroleum geochemists arsenal.Oleinikova, O.V., Shirokova, L.S., Drozdova, O.Y., Lapitskiy, S.A., Pokrovsky, O.S., 2018. Low biodegradability of dissolved organic matter and trace metals from subarctic waters. Science of The Total Environment 618, 174-187. heterotrophic mineralization of dissolved organic matter (DOM) controls the CO2 flux from the inland waters to the atmosphere, especially in the boreal waters, although the mechanisms of this process and the fate of trace metals associated with DOM remain poorly understood. We studied the interaction of culturable aquatic (Pseudomonas saponiphila) and soil (Pseudomonas aureofaciens) Gammaproteobacteria with seven different organic substrates collected in subarctic settings. These included peat leachate, pine crown throughfall, fen, humic lake, stream, river, and oligotrophic lake with variable dissolved organic carbon (DOC) concentrations (from 4 to 60 mg L? 1). The highest removal of DOC over 4 days of reaction was observed in the presence of P. aureofaciens (33 ± 5%, 43 ± 3% and 53 ± 7% of the initial amount in fen water, humic lake and stream, respectively). P. saponiphila degraded only 5% of DOC in fen water but did not affect all other substrates. Trace elements (TE) were essentially controlled by short-term (0 ? 1 h) adsorption on the surface of cells. Regardless of the nature of organic substrate and the identity of bacteria, the degree of adsorption ranged from 20 to 60% for iron (Fe3 +), 15 to 55% for aluminum (Al), 10 to 60% for manganese (Mn), 10 to 70% for nickel (Ni), 20 to 70% for copper (Cu), 10 to 60% for yttrium (Y), 30 to 80% for rare earth elements (REE), and 15 to 50% for uranium (UVI). Rapid adsorption of organic and organo-mineral colloids on bacterial cell surfaces is novel and potentially important process, which deserves special investigation. The long-term removal of dissolved Fe and Al was generally consistent with solution supersaturation degree with respect to Fe and Al hydroxides, calculated by visual Minteq model. Overall, the biomass-normalized biodegradability of various allochthonous substrates by culturable bacteria is much lower than that of boreal DOM by natural microbial consortia.Oliveira, C., Bettencourt, A.M.S., Araújo, A., Gon?alves, L., Ku?niarska-Biernacka, I., Costa, A.L., 2017. Integrated analytical techniques for the study of colouring materials from two megalithic barrows. Archaeometry 59, 1065-1081. have determined the composition of rock art pigments from two megalithic barrows located in the north of Portugal. The use of XRD, SEM–EDS and FT–IR spectroscopy confirmed the presence of hematite and kaolinite in the red pigments from the Eireira barrow, and kaolinite in the white pigment from the Leira das Mamas barrow. The organic composition of the pigments was studied by GC–MS, suggesting that the red sinuous lines and dots from the Eireira barrow were prepared with cooked or heated algae and/or aquatic plants, with egg as binder, while the white pigment from the Leira das Mamas barrow revealed a mixture of vegetable oils for kaolinite moulding, which could be stabilized by temporary exposure to high temperatures. The multi-analytical approach used on this study of megalithic pigments allowed the recovery of important data about north-western prehistoric communities, namely the way in which they exploited existing resources and their ability to transform them.Oliver, P.M., Hugall, A.F., 2017. Phylogenetic evidence for mid-Cenozoic turnover of a diverse continental biota. Nature Ecology & Evolution 1, 1896-1902. climatic change at the beginning of the Oligocene epoch?is concordant with global biotic turnover in the fossil record. However, while Southern Hemisphere geological movement played a key role in shaping these global climatic shifts, given generally poor terrestrial fossil records, evidence for matching turnover in entire Austral biotas is lacking. Emerging comprehensive phylogenetic frameworks provide alternative avenues to explore for signals of mass turnover?or restructuring. Here, we combine phylogenetic data with empirical and simulation-based approaches to understand the temporal dynamics of the origins of a diverse and highly endemic continental biota (Australian lizards and snakes). These analyses indicate that the temporal clustering of major radiation ages in Gondwanan endemic lineages and immigration into Australia is narrower than expected under time-continuous models assuming no overarching external perturbation. Independent phylogenetic dating analyses further indicate that the timing of both processes is concentrated in the period post-dating the Eocene–Oligocene transition (~34 million years ago). Epoch-defining processes around the start of the Oligocene appear to have also played a decisive role in reshaping a diverse Southern Hemisphere biota—by both re-setting Gondwanan endemic diversity and opening the way to successful immigration from the north.Omura, A., Ikehara, K., Arai, K., Udrekh, 2017. Determining sources of deep-sea mud by organic matter signatures in the Sunda trench and Aceh basin off Sumatra. Geo-Marine Letters 37, 549-559. content, optically determined properties, and stable isotope composition of organic carbon in fine-grained sediment cores were analyzed to investigate the origins of deep-sea sediments deposited in the Aceh forearc basin and on the Sunda trench floor off Sumatra from the late Pleistocene to the Holocene. In the Aceh basin, the depositional frequency of turbidite mud decreased as sea level rose during the deglaciation. The terrigenous organic carbon content was high at the end of the last glacial period, whereas during the deglaciation most of the organic carbon was of marine origin. In the Sunda trench, the Holocene turbidites consisted of remobilized slope sediments from two different sources: sediments derived from the old Bengal/Nicobar fan included thermally matured organic fragments, whereas those derived from the trench slope contained little terrigenous organic carbon.Ortiz Cancino, O.P., Peredo Mancilla, D., Pozo, M., Pérez, E., Bessieres, D., 2017. Effect of organic matter and thermal maturity on methane adsorption capacity on shales from the Middle Magdalena Valley Basin in Colombia. Energy & Fuels 31, 11698-11709. methane adsorption isotherms were measured on five shale core samples obtained during exploratory drilling from three boreholes located in the Colombian Middle Magdalena Valley Basin. The experiments were carried out at 50 and 75 °C and for pressures ranging up to 3.5 MPa under dry conditions through the use of a homemade manometric setup. The effect of the total organic carbon (TOC) content, thermal maturity, clay content, and specific surface area (SSA) on methane adsorption capacity has been discussed. The excess adsorption data were fitted to a three-parameter (nL, pL, and ρads) Langmuir model with the value of the adsorbed phase density, ρads, maintained fixed at 421 kg/m3, which corresponds to liquid-phase density of methane at a normal boiling point. An excellent fit to the experimental data was achieved. The results show that the temperature has a negative effect on the adsorption capacity, while TOC has a positive effect, even if no linear regression was found between TOC and methane adsorption capacity. No correlation was observed between the clay content and the TOC-normalized adsorption capacity to methane, which indicates that clay minerals do not significantly contribute to methane adsorption in the case of our samples. In addition, there is not a general trend between TOC normalized and thermal maturity. Among the factors investigated in the present study, TOC has the major contribution to the adsorption uptake. A similar contribution is found for the SSA, which is consistent, considering the positive correlation between TOC and SSA. This set of data represents meaningful information for indirect estimations of the gas in place during the future recovery strategies. This study furthers the ongoing projects on the understanding of the adsorption effect on shale gas production and assessment.Oyo-Ita, O.E., Oyo-Ita, I.O., Elarboui, S., 2017. Reassessment of dibenzothiophene as marker for petroleum and coal contamination in sediments from Imo River, SE Nigeria. Environmental Forensics 18, 285-295. of dibenzothiophene (DBT) and its historical trends of deposition in sediments from Afam, mangrove, estuary, and illegal petroleum refinery sites of Imo River, southeast Nigeria over the past approximately five decades were evaluated in order to reassess the compound's potential as a marker for petroleum and/or coal combustion emission source(s). The spatial distributions in the concentrations of DBT varied from 12.46?ng/g dry weight (dw) to 1,720.42?ng/g dw (mean 454.77±14?ng/g dw), maximizing and minimizing at locations adjacent to an illegal petroleum refinery site. There was no strong geographic element that influenced DBT distribution across the river. The concentrations of DBT down cores ranged from 13.54?ng/g dw at the middle layer (15?20?cm, approximately 1981?1989) of the Afam site to a maximum of 470.43?ng/g dw at near-top layer (5?10?cm) of the illegal petroleum refinery site. The later layer corresponds to a depositional time frame of approximately 1997?2005, coinciding with the period of intensive illegal petroleum refinery operations when coal was used as a refinery fuel in the illegal processing and oil bunkering/pipeline vandalization were at their peaks. The general decline in DBT levels from near-top layers (5?10?cm) to the most recent top layers (0?5?cm) was linked to the recent offer of amnesty to the Niger Delta militant groups by the Nigerian government and subsequent clamp down on economic saboteurs by the Nigerian joint armed forces. Due to its extra stability to microbial degradation relative to polycyclic aromatic hydrocarbons (PAHs), the study illustrated the greater potential of DBT as a marker for petroleum and/or coal combustion emission source contaminations than the commonly used markers such as PAHs.Pachiadaki, M.G., Sintes, E., Bergauer, K., Brown, J.M., Record, N.R., Swan, B.K., Mathyer, M.E., Hallam, S.J., Lopez-Garcia, P., Takaki, Y., Nunoura, T., Woyke, T., Herndl, G.J., Stepanauskas, R., 2017. Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation. Science 358, 1046-1051.: Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean’s interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.Editor's Summary: Dissolved inorganic carbon fixers revealed. Most of the ocean is dark. Yet it is in this darkness, away from photosynthesizing sunlight, that most planetary carbon cycling occurs. Pachiadaki et al. show that nitrite-oxidizing bacteria in one phylum are the predominant fixers of dissolved inorganic carbon in the mesopelagic ocean. The authors sequenced thousands of single amplified genomes of marine prokaryotes. They identified more than 30 nitrite-oxidizing obligate chemoautotrophic bacteria that were unable to transport carbohydrate and that expressed nitrite oxidoreductase. This enzyme provides electrons to drive a reverse tricarboxylic acid cycle that fixes the carbon. Many of the genomes also suggest organisms that have the capacity to produce ammonium and other substrates, possibly to feed nitrite-producing metabolic partners.Pang, X., Maxson, J.K., Cuello Jimenez, W., Singh, J.P., Morgan, R.G., 2017. Microscale characterization of field and laboratory foamed cement by use of X-ray microcomputed tomography. SPE Journal 22, 1690-1703. systems are widely used in deepwater-cementing operations because of their various favorable attributes compared with conventional cement systems. For instance, in the Gulf of Mexico, foamed cement is one of the most commonly used systems for shallow-hazard mitigation. However, because current standard laboratory equipment cannot accurately simulate the foam-cementing process in the field, knowledge of the actual properties of foamed cement produced in field operations is limited.In this study, the microstructure of foamed cement produced by use of field equipment in yard tests is examined in detail. Set foamed-cement samples were analyzed by use of X-ray microcomputed tomography (micro-CT) at different length scales with voxel resolution ranging from 2 to 20 ?m. This study establishes the fundamental criteria and procedures necessary to obtain accurate gas-bubble-size distribution of foamed-cement samples by use of micro-CT technology. The test results suggest that foamed cement should be analyzed at multiple length scales to obtain a better characterization of the gas bubbles in the sample. Although a larger region of analysis is useful to obtain a statistically meaningful size distribution of the larger bubbles, small core samples (diameter smaller than 0.5 in.) and fine scan resolutions (5 ?m or smaller) are typically required to obtain an accurate measure of the small gas bubbles in foamed cement. By comparing foamed cement produced by use of field equipment with that produced by use of the traditional multiblade laboratory blender--i.e., the standard American Petroleum Institute (API) method--this study identifies the key characteristic differences of foamed cement derived from different methods of generation. Analysis of the CT-scan images reveals that gas bubbles in foamed cement generated by field equipment approximately follows a log-normal distribution with a wide size-distribution range, from less than 20 ?m to more than 1000 ?m, and the bubble-size distribution appears to show little dependence on foam quality. Conversely, the gas-bubble-size distribution of foamed cement generated by the API method shows a completely different behavior. It approximately follows a Gaussian distribution, with both distribution range and median varying significantly with foam quality. This research serves as a first step toward predicting the influence of gas-bubble-size distribution on the stability and various other properties of foamed cement to better understand the foam-cementing process in the field.Panza, E., Sessa, E., Agosta, F., Giorgioni, M., 2018. Discrete Fracture Network modelling of a hydrocarbon-bearing, oblique-slip fault zone: Inferences on fault-controlled fluid storage and migration properties of carbonate fault damage zones. Marine and Petroleum Geology 89, 263-279. Fracture Network (DFN) modelling is a useful tool to assess both fluid storage and migration properties of naturally fractured carbonate rocks. This work presents the results of multiple DFN models, which represent the structural network associated with a ca. 100 m–offset, oblique-slip, normal fault zone crosscutting Miocene ramp carbonates of the Majella Mountain, Italy. Specifically, by taking advantage of a previously published conceptual model of fault nucleation and growth, the DFN models are aimed at computing the amount of fracture porosity and equivalent permeability of representative portions of the evolving fault damage zone. In fact, by first considering only background structural elements, those pre-dating the fault nucleation stage, all fault-related structural elements such as joints, small and medium faults are added, one by one, according to their relative time of formation. Small faults are characterized by several cm-offset, whereas the latter ones have several 10's of cm-offset. The following fracture parameters are inputted for each structural element: (i) length; (ii) aspect ratio; (iii) mechanical and hydraulic aperture; (iv) fracture intensity and (v) orientation. A sensitivity analysis is carried out in order to test the seeding procedure of the software, and the input fracture aperture values. Results of DFN modelling are consistent with the small faults forming the main repository for underground geofluids. Differently, the fluid migration paths through the fault damage zone are mainly controlled by opening-mode-related fractures, which mainly form clusters at the extensional quadrants of sheared structural elements. Due to their attitude and distribution, these features mainly enhance fault-parallel fluid migration paths. In fact, the computed values of horizontal equivalent permeability obtained along this direction are about one order of magnitude higher than those along the orthogonal direction. The approach and methodologies applied in this work, together with the results of the multiple DFN model configurations show the relative influence and role of the different structural elements on fluid storage and migration properties of limestone-hosted, fault damage zones.Papale, M., Rizzo, C., Villescusa, J.A., Rochera, C., Camacho, A., Michaud, L., Lo Giudice, A., 2017. Prokaryotic assemblages in the maritime Antarctic Lake Limnopolar (Byers Peninsula, South Shetland Islands). Extremophiles 21, 947-961. potentially metabolically active components within the prokaryotic assemblages inhabiting the Antarctic Lake Limnopolar (Byers Peninsula, Maritime Antarctica) were investigated by a polyphasic approach which included culture-dependent and culture-independent methods (based on RNA molecules). Results support previous observations on the Proteobacteria and Bacteroidetes dominance, followed by Actinobacteria, in Antarctic lakes. In particular, Alpha-, Betaproteobacteria and Bacteroidetes were mainly detected by CARD-FISH and cDNA cloning, whereas Gammaproteobacteria and Actinobacteria dominated within the cultivable fraction. Overall, this study demonstrates the survival potential and physiological heterogeneity of the prokaryotic community in the Lake Limnopolar. The microbial community composition in the lake is affected by external influences (such as marine environment by sea spray and seabird dropping, and microbial mats and mosses of the catchment). However, most external bacteria would be inactive, whereas typical polar taxa dominate the potentially active fraction and are subsidized by external nutrient sources, thus assuming the main biogeochemical roles within the lake.Parada, A.E., Fuhrman, J.A., 2017. Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor. The Isme Journal 11, 2510-2525. archaea are critical contributors to global carbon and nitrogen redox cycles, but their temporal variability and microbial associations across the water column are poorly known. We evaluated seasonal variability of free living (0.2–1?μm size fraction) Thaumarchaea Marine Group I (MGI) and Euryarchaea Marine Group II (MGII) communities and their associations with the microbial community from surface to seafloor (890?m) over 5 years by 16S rRNA V4-V5 gene sequencing. MGI and MGII communities demonstrated distinct compositions at different depths, and seasonality at all depths. Microbial association networks at 150?m, 500?m and 890?m, revealed diverse assemblages of MGI (presumed ammonia oxidizers) and Nitrospina taxa (presumed dominant nitrite oxidizers, completing the nitrification process), suggesting distinct MGI-Nitrospina OTUs are responsible for nitrification at different depths and seasons, and depth- related and seasonal variability in nitrification could be affected by alternating MGI-Nitrospina assemblages. MGII taxa also showed distinct correlations to possibly heterotrophic bacteria, most commonly to members of Marine Group A, Chloroflexi, Marine Group B, and SAR86. Thus, both MGI and MGII likely have dynamic associations with bacteria based on similarities in activity or other interactions that select for distinct microbial assemblages over time. The importance of MGII taxa as members of the heterotrophic community previously reported for photic zone appears to apply throughout the water column.Pardo, P.C., Tilbrook, B., Langlais, C., Trull, T.W., Rintoul, S.R., 2017. Carbon uptake and biogeochemical change in the Southern Ocean, south of Tasmania. Biogeosciences 14, 5217-5237. change in the water masses of the Southern Ocean, south of Tasmania, was assessed for the 16-year period between 1995 and 2011 using data from four summer repeats of the WOCE–JGOFS–CLIVAR–GO-SHIP (Key et al., 2015; Olsen et al., 2016) SR03 hydrographic section (at ～?140°?E). Changes in temperature, salinity, oxygen, and nutrients were used to disentangle the effect of solubility, biology, circulation and anthropogenic carbon (CANT) uptake on the variability of dissolved inorganic carbon (DIC) for eight water mass layers defined by neutral surfaces (γn). CANT was estimated using an improved back-calculation method. Warming (～?0.0352?±?0.0170?°C?yr?1) of Subtropical Central Water (STCW) and Antarctic Surface Water (AASW) layers decreased their gas solubility, and accordingly DIC concentrations increased less rapidly than expected from equilibration with rising atmospheric CO2 (～?0.86?±?0.16??mol?kg?1?yr?1 versus ～?1?±?0.12??mol?kg?1?yr?1). An increase in apparent oxygen utilisation (AOU) occurred in these layers due to either remineralisation of organic matter or intensification of upwelling. The range of estimates for the increases in CANT were 0.71?±?0.08 to 0.93?±?0.08??mol?kg?1?yr?1 for STCW and 0.35?±?0.14 to 0.65?±? 0.21??mol?kg?1?yr?1 for AASW, with the lower values in each water mass obtained by assigning all the AOU change to remineralisation. DIC increases in the Sub-Antarctic Mode Water (SAMW, 1.10?±?0.14??mol?kg?1?yr?1) and Antarctic Intermediate Water (AAIW, 0.40?±?0.15??mol?kg?1?yr?1) layers were similar to the calculated CANT trends. For SAMW, the CANT increase tracked rising atmospheric CO2. As a consequence of the general DIC increase, decreases in total pH (pHT) and aragonite saturation (ΩAr) were found in most water masses, with the upper ocean and the SAMW layer presenting the largest trends for pHT decrease (～??0.0031?±?0.0004?yr?1). DIC increases in deep and bottom layers (～?0.24?±?0.04??mol?kg?1?yr?1) resulted from the advection of old deep waters to resupply increased upwelling, as corroborated by increasing silicate (～?0.21?±?0.07??mol?kg?1?yr?1), which also reached the upper layers near the Antarctic Divergence (～?0.36?±?0.06??mol?kg?1?yr?1) and was accompanied by an increase in salinity. The observed changes in DIC over the 16-year span caused a shoaling (～?340?m) of the aragonite saturation depth (ASD, ΩAr?=??1) within Upper Circumpolar Deep Water that followed the upwelling path of this layer. From all our results, we conclude a scenario of increased transport of deep waters into the section and enhanced upwelling at high latitudes for the period between 1995 and 2011 linked to strong westerly winds. Although enhanced upwelling lowered the capacity of the AASW layer to uptake atmospheric CO2, it did not limit that of the newly forming SAMW and AAIW, which exhibited CANT storage rates (～?0.41?±?0.20?mol?m?2?yr?1) twice that of the upper layers.Pasek, M.A., Gull, M., Herschy, B., 2017. Phosphorylation on the early earth. Chemical Geology 475, 149-170. is an element critical to the formation of several biomolecules, including nucleic acids, the energy transfer molecule ATP, and phospholipids. It hence lies at the heart of several biomolecular functions. However, the formation of these key biomolecules is hindered by the geochemical properties of phosphorus, including its low solubility and poor reactivity. Here we review the approaches that have been taken to overcome some of these difficulties, and place them in the context of the geochemistry of the early earth. We find many experiments rely on phosphate minerals unlikely present on the Hadean earth, or employ conditions that depend on unusual geochemical environments. We propose the most likely routes to forming organophosphate molecules in the context of a plausible prebiotic geochemistry may rely instead on ephemeral phosphate minerals, or redox reactions of phosphorus to form the necessary soluble and reactive phosphorus reagents.Paulsen, T., Deering, C., Sliwinski, J., Bachmann, O., Guillong, M., 2017. Evidence for a spike in mantle carbon outgassing during the Ediacaran period. Nature Geoscience 10, 930-934. cycles in Earth’s climate are thought to be primarily controlled by changes in atmospheric CO2 concentrations. Changes in carbon emissions from volcanic activity can create an imbalance in the carbon cycle. Large-scale changes in volcanic activity have been inferred from proxies such as the age abundance of detrital zircons, but the magnitude of carbon emissions depends on the style of volcanism as well as the amount. Here we analyse U–Pb age and trace element data of detrital zircons from Antarctica and compare the results with the global rock record. We identify a spike in CO2-rich carbonatite and alkaline magmatism during the Ediacaran period. Before the Ediacaran, secular cooling of the mantle and the advent of cooler subduction regimes promoted the sequestration of carbon derived from decarbonation of subducting oceanic slabs in the mantle. We infer that subsequent magmatism led to the extensive release of carbon that may at least in part be recorded in the Shuram–Wonoka carbon isotope excursion. We therefore suggest that this pulse of alkaline volcanism reflects a profound reorganization of the Neoproterozoic deep and surface carbon cycles and promoted planetary warming before the Cambrian radiation.Peng, B., Weintraub, S.T., Coman, C., Ponnaiyan, S., Sharma, R., Tews, B., Winter, D., Ahrends, R., 2017. A comprehensive high-resolution targeted workflow for the deep profiling of sphingolipids. Analytical Chemistry 89, 12480-12487. make up a highly diverse group of biomolecules that not only are membrane components but also are involved in various cellular functions such as signaling and protein sorting. To obtain a quantitative view of the sphingolipidome, sensitive, accurate, and comprehensive methods are needed. Here, we present a targeted reversed-phase liquid chromatography–high-resolution mass spectrometry-based workflow that significantly increases the accuracy of measured sphingolipids by resolving nearly isobaric and isobaric species; this is accomplished by a use of (i) an optimized extraction procedure, (ii) a segmented gradient, and (iii) parallel reaction monitoring of a sphingolipid specific fragmentation pattern. The workflow was benchmarked against an accepted sphingolipid model system, the RAW 264.7 cell line, and 61 sphingolipids were quantified over a dynamic range of 7 orders of magnitude, with detection limits in the low femtomole per milligram of protein level, making this workflow an extremely versatile tool for high-throughput sphingolipidomics.Peng, X., Wang, B., Zhao, Y., 2017. Temporal and spatial characteristics of dissolved organic carbon in the Wujiang River, Southwest China. Acta Geochimica 36, 598-604. systems play an important role in the global carbon cycle. Rivers transport carbon to the ocean and also affect the carbon cycle in the coastal ocean. The flux from land to the ocean is thought to be a very important part of the land carbon budget. To investigate the effect of dam-building on dissolved organic carbon (DOC) in rivers, three reservoirs of different trophic states in the Wujiang basin, Guizhou Province, were sampled twice per month between May 2011 and May 2012. Temporal and spatial distributions of DOC in the reservoirs and their released waters were studied. It was found that different factors controlled DOC in river water, reservoir water, and released water. DOC in the rivers tended to be affected by primary production. For reservoirs, the main controlling factors of DOC concentration varied by trophic state. For the mesotrophic Hongjiadu Reservoir, the effect of primary production on DOC concentration was obvious. For the eutrophic Dongfengdu Reservoir and the hypereutrophic Wujiangdu Reservoir, primary production was not significant and DOC came instead from soil and plant litter.Petts, D.C., Saso, J.K., Diamond, L.W., Aschwanden, L., Al, T.A., Jensen, M., 2017. The source and evolution of paleofluids responsible for secondary minerals in low-permeability Ordovician limestones of the Michigan Basin. Applied Geochemistry 86, 121-137. this study we report on the source and evolution of fluids associated with secondary vein and replacement minerals in low-permeability carbonate units in the Michigan Basin. This petrogenetic information was collected using thermometric data from fluid inclusions combined with C-, O- and Sr-isotope data, and focuses on mm- or cm-wide vein and vug minerals from Ordovician limestones of the Trenton and Black River groups and Cambrian sandstones in SW Ontario, Canada.Primary fluid inclusions in dolomite represent fluid stage I and have the highest trapping temperatures (Ttrap) in the sedimentary succession, between 88 and 128 °C. Primary inclusions in calcite (stage II), and celestine and anhydrite (stage III), represent the final stages of secondary mineral formation and have Ttrap values of 54–78 °C. All three stages of vein minerals formed from brines with salinities of 31–37 wt% [CaCl2+NaCl]eq that were saturated in halite and methane gas at the time of mineral growth. Three subsequent stages of secondary fluid inclusions were observed in the samples (stages IV–VI), however, no secondary vein minerals formed during these stages and they are interpreted as re-mobilization and/or minor fluid ingress along grain boundaries and micro-fractures. Notably, stage IV secondary inclusions are gas-undersaturated with salinities of 32–34 wt% [CaCl2+NaCl]eq and minimum Ttrap values of 57–106 °C, and are interpreted to have formed during a Late Devonian–Mississippian regional heating event.Secondary minerals from the Cambrian units and the Shadow Lake Formation have δ13C values of ?6.1 to ?2.5‰ (VPDB), δ18O values of +14.6 to +24.2‰ (VSMOW) and 87Sr/86Sr of 0.70975–0.71043. Relative shifts of approximately +2 to +3‰ in δ13C, >+4‰ in δ18O and ?0.002 in 87Sr/86Sr are observed upward across the boundary between the Cambrian–Shadow Lake units and the overlying Gull River Formation. Samples from the Gull River and Coboconk formations and the Trenton Group (Kirkfield, Sherman Fall and Cobourg formations) have δ13C values of ?1.0 to +1.9‰, δ18O values of +18.9 to +28.1‰ and 87Sr/86Sr values of 0.70790–0.70990.The combined microthermometric and isotopic data for secondary minerals in the Cambrian–Shadow Lake units suggest they formed from hydrothermal brine with a geochemical signature obtained by interaction with the underlying Precambrian shield, or shield-derived minerals in the Cambrian sandstones. Previous U-Pb dating of vein calcite and Rb-Sr dating of secondary K-feldspar from the region suggests that brine ingress occurred during the Late Ordovician–Silurian. The O- and Sr-isotope variability in vein samples from the Gull River and Coboconk formations is interpreted as localized mixing of 18O-enriched, connate fluids with hydrothermal brine. In comparison, isotopic data for the Trenton Group indicate secondary mineral formation from connate fluids, sourced from 18O-enriched, evolved seawater and/or modified hydrothermal brine that experienced fluid–rock interaction during transit through the underlying stratigraphy.Picard, A., Gartman, A., Clarke, D.R., Girguis, P.R., 2018. Sulfate-reducing bacteria influence the nucleation and growth of mackinawite and greigite. Geochimica et Cosmochimica Acta 220, 367-384. iron sulfide minerals play a key role in maintaining the oxygenation of Earth’s atmosphere over geological timescales; they also record critical geochemical information that can be used to reconstruct paleo-environments. On modern Earth, sedimentary iron sulfide mineral formation takes places in low-temperature environments and requires the production of free sulfide by sulfate-reducing microorganisms (SRM) under anoxic conditions. Yet, most of our knowledge on the properties and formation pathways of iron sulfide minerals, including pyrite, derives from experimental studies performed in abiotic conditions, and as such the role of biotic processes in the formation of sedimentary iron sulfide minerals is poorly understood. Here we investigate the role of SRM in the nucleation and growth of iron sulfide minerals in laboratory experiments. We set out to test the hypothesis that SRM can influence Fe-S mineralization in ways other than providing sulfide through the comparison of the physical properties of iron sulfide minerals precipitated in the presence and in the absence of the sulfate-reducing bacterium Desulfovibrio hydrothermalis AM13 under well-controlled conditions. X-ray diffraction and microscopy analyses reveal that iron sulfide minerals produced in the presence of SRM exhibit unique morphology and aggregate differently than abiotic minerals formed in media without cells. Specifically, mackinawite growth is favored in the presence of both live and dead SRM, when compared to the abiotic treatments tested. The cell surface of live and dead SRM, and the extracellular polymers produced by live cells, provide templates for the nucleation of mackinawite and favor mineral growth. The morphology of minerals is however different when live and dead cells are provided. The transformation of greigite from mackinawite occurred after several months of incubation only in the presence of live SRM, suggesting that SRM might accelerate the kinetics of greigite formation under strict anoxic conditions. Pyrite formation was not observed in any experiments. While SRM provide nearly all the sulfide to the Fe-S system at low temperatures, we also posit that SRM play an additional formative role in the size, morphology and potentially the mineralogy of iron sulfide minerals in sedimentary environments, therefore potentially influencing their reactivity. Attempting to reconstruct modern and ancient biogeochemical cycles based on the geochemistry of iron sulfide minerals formed under purely abiotic conditions should be therefore done with caution.Pierre, C., Blanc-Valleron, M.-M., Boudouma, O., Lofi, J., 2017. Carbonate and silicate cementation of siliciclastic sediments of the New Jersey shelf (IODP Expedition 313): relation with organic matter diagenesis and submarine groundwater discharge. Geo-Marine Letters 37, 537-547. New Jersey continental shelf extends 150 km off the shoreline. During IODP Expedition 313, siliciclastic deposits of late Eocene to late Pleistocene age were drilled down to 631, 669 and 755 m below seafloor at sites 27A, 28A and 29A respectively in very shallow waters (33.5 to 36 m depth). Pore water salinities display multilayered brackish-salty-brine units 10 to 170 m thick, where low-salinity water is preferentially stored in fine-grained sediments. The sharp boundaries of these buried aquifers are often marked by cemented layers a few centimetres thick. The mineralogy and scanning electron microscope observations of these layers show two phases of cementation by authigenic minerals: (1) the early carbonate cement is frequently associated with pyrite, and (2) the late silicate cement infills the residual porosity. The isotopic compositions of the carbonate cements vary widely: ?2.4 < δ18O ‰ VPDB < +2.8; ?15.1 < δ13C ‰ VPDB < +15.6. The δ18O values indicate that the carbonate cements precipitated with pore waters comprising variable mixtures of seawater and 18O-depleted fresh water originating from submarine groundwater discharge. The δ13C values of the carbonate cements are related to organic matter diagenesis, providing 13C-depleted dissolved inorganic carbon during bacterial sulphate reduction and anaerobic oxidation of methane, and 13C-rich dissolved inorganic carbon during methanogenesis. The diagenetic cementation processes included chemical weathering of reactive silicate minerals by the CO2-rich pore waters issued from organic matter diagenesis that released bicarbonate, cations and dissolved silica, which were further precipitated as carbonate and silicate cements. The estimated range of temperature (18±4 °C) during carbonate precipitation is consistent with carbonate cementation at moderate burial depths; however, silicate cementation occurred later during diagenesis at deeper burial depths.Pimienta, L., Esteban, L., Sarout, J., Liu, K., Dautriat, J., Delle Piane, C., Clennell, M.B., 2017. Supercritical CO2 injection and residence time in fluid-saturated rocks: Evidence for calcite dissolution and effects on rock integrity. International Journal of Greenhouse Gas Control 67, 31-48. injection and storage in geological reservoirs is an attractive prospect for mitigating the anthropogenic production of greenhouse gases and global warming. The technology could lead to mineral precipitation and therefore stable storage over geological time scales. This contribution investigates the evolution of three calcite-rich reservoir rock analogues during injection of and exposure to supercritical CO2 (scCO2), i.e., two limestones (Tuffeau and Savonnieres) and a synthetic calcite-cemented sandstone (CIPS). Three types of exposure protocols have been conducted: (i) scCO2 injection and a four-hour residence time in an initially dry rock; (ii) scCO2 injection and a two-hour residence time in an initially brine-saturated rock; and (iii) scCO2 injection and a four-hour residence time in an initially brine-saturated rock. Two aspects are monitored during these experiments: (i) the evolution of the pore fluid chemical composition; and (ii) the evolution of the rocks’ physical properties (i.e. porosity, permeability, P-wave velocity and electrical resistivity). Additionally, some scCO2 injection and exposure experiments in the brine-saturated rocks have been conducted using X-ray tomographic monitoring.X-ray tomographic monitoring suggests that scCO2 first displaces the water, leading to an average water saturation of about 70–90%. Then, scCO2 dissolves in the pore brine, leading to a homogeneous decrease by about 3% in water saturation of the sample. As a result, the pore brine acidifies even after 2 h of exposure only, which leads to calcite dissolution and a significant increase in the brine’s concentration in calcium cations. For the samples and most exposure experiments, evidence of calcite dissolution is inferred from the measured physical properties. For the brine-saturated Tuffeau limestone and CIPS sandstone, calcite dissolution leads to significant mechanical weakening. For the brine-saturated Savonnieres limestone, the sample subject to two-hour residence time shows evidence of calcite dissolution, whereas the sample after four-hour residence time does not. Calcite re-precipitation could be the cause of this unexpected response after four hours.Piotrowski, P.K., Weggler, B.A., Barth-Naftilan, E., Kelly, C.N., Zimmermann, R., Saiers, J.E., Dorman, F.L., 2018. Non-targeted chemical characterization of a Marcellus shale gas well through GC??×?GC with scripting algorithms and high-resolution time-of-flight mass spectrometry. Fuel 215, 363-369. non-targeted study of hydraulic fracturing fluids and corresponding flowback fluids allows for the understanding of the origin of wastewater constituents and provides insight into chemical signatures that may inform wastewater management practices for unconventional gas development. The source water for the hydraulic fracturing fluids, the actual hydraulic fracturing fluids used in four stimulation stages, and four flowback samples were obtained from a single unconventional gas well located in northeastern, PA. The chemical complexity of these fluids required high-resolution non-targeted methodologies. Analyses were therefore performed by GC??×??GC-TOFMS with the use of mass spectral scripting algorithms to expedite data analysis while maintaining a discovery approach. Our results indicate that during the flowback period hydrocarbon concentrations increase with time. The relative chemical composition remains nearly constant, which is hypothesized to be representative of the hydrocarbons present in the native shale that were extracted during the hydraulic fracturing process. Additionally, a comparison of fracturing fluids and flowback with high-resolution time-of-flight mass spectrometry inferred the fate of three common organic modifiers: ethylene glycol, glutaraldehyde, and cinnamaldehyde. It was determined that ethylene glycol is removed from the well within the first four days of flowback, while polymerization reactions are primary mechanisms of glutaraldehyde and cinnamaldehyde transformation.Pirok, B.W.J., Molenaar, S.R.A., van Outersterp, R.E., Schoenmakers, P.J., 2017. Applicability of retention modelling in hydrophilic-interaction liquid chromatography for algorithmic optimization programs with gradient-scanning techniques. Journal of Chromatography A 1530, 104-111. method-development programs require accurate models to describe retention and to make predictions based on a limited number of scouting gradients. The performance of five different retention models for hydrophilic-interaction chromatography (HILIC) is assessed for a wide range of analytes. Gradient-elution equations are presented for each model, using Simpson’s Rule to approximate the integral in case no exact solution exists. For most compound classes the adsorption model, i.e. a linear relation between the logarithm of the retention factor and the logarithm of the composition, is found to provide the most robust performance. Prediction accuracies depended on analyte class, with peptide retention being predicted least accurately, and on the stationary phase, with better results for a diol column than for an amide column. The two-parameter adsorption model is also attractive, because it can be used with good results using only two scanning gradients. This model is recommended as the first-choice model for describing and predicting HILIC retention data, because of its accuracy and linearity. Other models (linear solvent-strength model, mixed-mode model) should only be considered after validating their applicability in specific cases.Pironti, C., Cucciniello, R., Camin, F., Tonon, A., Motta, O., Proto, A., 2017. Determination of the 13C/12C carbon isotope ratio in carbonates and bicarbonates by 13C NMR spectroscopy. Analytical Chemistry 89, 11413-11418. paper is the first study focused on the innovative application of 13C NMR (nuclear magnetic resonance) spectroscopy to determine the bulk 13C/12C carbon isotope ratio, at natural abundance, in inorganic carbonates and bicarbonates. In the past, 13C NMR spectroscopy (irm-13C NMR) was mainly used to measure isotope ratio monitoring with the potential of conducting 13C position-specific isotope analysis of organic molecules with high precision. The reliability of the newly developed methodology for the determination of stable carbon isotope ratio was evaluated in comparison with the method chosen in the past for these measurements, i.e., isotope ratio mass spectrometry (IRMS), with very encouraging results. We determined the 13C/12C ratio of carbonates and bicarbonates (～50–100 mg) with a precision on the order of 1‰ in the presence of a relaxation agent, such as Cr(acac)3, and CH313COONa as an internal standard. The method was first applied to soluble inorganic carbonates and bicarbonates and then extended to insoluble carbonates by converting them to Na2CO3, following a simple procedure and without observing isotopic fractionation. Here, we demonstrate that 13C NMR spectroscopy can also be successfully adopted to characterize the 13C/12C isotope ratio in inorganic carbonates and bicarbonates with applications in different fields, such as cultural heritage and geological studies.Pohlabeln, A.M., Gomez-Saez, G.V., Noriega-Ortega, B.E., Dittmar, T., 2017. Experimental evidence for abiotic sulfurization of marine dissolved organic matter. Frontiers in Marine Science 4, 364. doi: 10.3389/fmars.2017.00364. organic sulfur (DOS) is the largest pool of organic sulfur in the oceans, and as such it is an important component of the global sulfur cycle. DOS in the ocean is resistant against microbial degradation and turns over on a millennium time scale. However, sources and mechanisms behind its stability are largely unknown. Here, we hypothesize that in sulfate-reducing sediments sulfur is abiotically incorporated into dissolved organic matter (DOM) and released to the ocean. We exposed natural seawater and the filtrate of a plankton culture to sulfidic conditions. Already after 1-h at 20°C, DOS concentrations had increased 4-fold in these experiments, and 14-fold after 4 weeks at 50°C, indicating that organic matter does not need long residence times in natural sulfidic environments to be affected by sulfurization. Molecular analysis via ultrahigh-resolution mass spectrometry showed that sulfur was covalently and unselectively bound to DOM. Experimentally produced and natural DOS from sediments were highly similar on a molecular and structural level. By combining our data with published benthic DOC fluxes we estimate that 30–200 Tg DOS are annually transported from anaerobic and sulfate reducing sediments to the oceans. Uncertainties in this first speculative assessment are large. However, this first attempt illustrates that benthic DOS flux is potentially one order of magnitude larger than that via rivers indicating that this could balance the estimated global net removal of refractory DOS.Pollo, S.M.J., Adebusuyi, A.A., Straub, T.J., Foght, J.M., Zhaxybayeva, O., Nesb?, C.L., 2017. Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79?°C. Extremophiles 21, 963-979. is one of the defining parameters of an ecological niche. Most organisms thrive within a temperature range that rarely exceeds ~30?°C, but the deep subsurface bacterium Kosmotoga olearia can grow over a temperature range of 59?°C (20–79?°C). To identify genes correlated with this flexible phenotype, we compared transcriptomes of K. olearia cultures grown at its optimal 65?°C to those at 30, 40, and 77?°C. The temperature treatments affected expression of 573 of 2224 K. olearia genes. Notably, this transcriptional response elicits re-modeling of the cellular membrane and changes in metabolism, with increased expression of genes involved in energy and carbohydrate metabolism at high temperatures and up-regulation of amino acid metabolism at lower temperatures. At sub-optimal temperatures, many transcriptional changes were similar to those observed in mesophilic bacteria at physiologically low temperatures, including up-regulation of typical cold stress genes and ribosomal proteins. Comparative genomic analysis of additional Thermotogae genomes indicates that one of K. olearia’s strategies for low-temperature growth is increased copy number of some typical cold response genes through duplication and/or lateral acquisition. At 77?°C one-third of the up-regulated genes are of hypothetical function, indicating that many features of high-temperature growth are unknown.Pop Ristova, P., Pichler, T., Friedrich, M.W., Bühring, S.I., 2017. Bacterial diversity and biogeochemistry of two marine shallow-water hydrothermal systems off Dominica (Lesser Antilles). Frontiers in Microbiology 8, 2400. doi: 10.3389/fmicb.2017.02400. hydrothermal systems represent extreme environments with unique biogeochemistry and high biological productivity, at which autotrophic microorganisms use both light and chemical energy for the production of biomass. Microbial communities of these ecosystems are metabolically diverse and possess the capacity to transform a large range of chemical compounds. Yet, little is known about their diversity or factors shaping their structure or how they compare to coastal sediments not impacted by hydrothermalism. To this end, we have used automated ribosomal intergenic spacer analysis (ARISA) and high-throughput Illumina sequencing combined with porewater geochemical analysis to investigate microbial communities along geochemical gradients in two shallow-water hydrothermal systems off the island of Dominica (Lesser Antilles). At both sites, venting of hydrothermal fluids substantially altered the porewater geochemistry by enriching it with silica, iron and dissolved inorganic carbon, resulting in island-like habitats with distinct biogeochemistry. The magnitude of fluid flow and difference in sediment grain size, which impedes mixing of the fluids with seawater, were correlated with the observed differences in the porewater geochemistry between the two sites. Concomitantly, individual sites harbored microbial communities with a significantly different community structure. These differences could be statistically linked to variations in the porewater geochemistry and the hydrothermal fluids. The two shallow-water hydrothermal systems of Dominica harbored bacterial communities with high taxonomical and metabolic diversity, predominated by heterotrophic microorganisms associated with the Gammaproteobacterial genera Pseudomonas and Pseudoalteromonas, indicating the importance of heterotrophic processes. Overall, this study shows that shallow-water hydrothermal systems contribute substantially to the biogeochemical heterogeneity and bacterial diversity of coastal sediments.Pozhidaev, V., Kamaev, A., Nuretdinova, A., Kovalchuk, M., Yatsishina, E., Greshnikov, E., Sivitskiy, M., Devlet, E., 2017. Identification of the residue in the Bolgar medieval sphero-conical vessel by gas chromatography – mass spectrometry. Archaeometry 59, 1095-1104. Golden Horde sphero-conical vessel retrieved from the ruins of the medieval city of Bolgar (Russia, Republic of Tatarstan) during archaeological excavations, which contained residue in the form of encrustation on the bottom and the wall, was analysed in the NRC ‘Kurchatov Institute’ by X-ray phase analysis and high-performance liquid and gas chromatography with MS detectors (HPLC–MS, GC–MS). The GC–MS method established that the residue from the sphero-conical vessel was comprised primarily of abietic acid derivatives (around 46%) and retene, which is polycyclic aromatic hydrocarbon (around 27%); this means that turpentine exuded from the stems of certain species of coniferous trees, called resin and subsequently heat-treated, was poured into the vessel. Researchers have been trying to decipher the function of these mysterious vessels for 200?years, and this is the first time that resin stored in a sphero-conical vessel has been documented. Potentially, this vessel was probably used as a personal ‘medical kit’.Pracejus, B., Al-Ansari, A., Al-Battashi, H., 2017. Cyanobacterial mineralisation of posnjakite (Cu4(SO4)(OH)6·H2O) in Cu-rich acid mine drainage at Yanqul, northern Oman. Chemie der Erde - Geochemistry 77, 535-544. is the first detailed account of the copper sulfate posnjakite (Cu4(SO4)(OH)6·H2O) coating cm-long filaments of a microbial consortium of four cyanobacteria and Herminiimonas arsenicoxydans. It was first observed on immersed plant leaves and stalks in a quarry sump of the abandoned Yanqul gold mine in the northern region of Oman; rock surfaces in the immediate vicinity show no immediate evidence of posnjakite. However, a thin unstructured layer without filaments but also containing the brightly coloured turquoise posnjakite covers ferruginous muds in the sump. Although copper is a potent bactericide, the microbes seem to survive even at the extreme heavy metal concentrations that commonly develop in the sump during the dry season (Cu2+ ≈ 2300 ppm; Zn2+ = 750 ppm; Fe2+ ≈ 120 ppm; Ni2+ = 37 ppm; Crtotal = 2.5 ppm; Cl? = 8250 ppm; and SO42? = 12,250 ppm; pH ～2.6), thus leading to the precipitation of posnjakite over a large range of physicochemical conditions. Upon exposure to the prevailing arid climate, dehydration and carbonation quickly replace posnjakite with brochantite (Cu4(SO4)(OH)6) and malachite (Cu2(CO3)(OH)2). To characterise and understand the geochemical conditions in which posnjakite precipitates from undersaturated fluids (according to our thermodynamic modelling of the dominant elements), waters from rainy and dry periods were analysed together with various precipitates and compared with the observed field occurrences. The findings imply that posnjakite should not form in the examined environment through purely inorganic mechanisms and its origin must, therefore, be linked to the encountered microbial activities.Pranesh, V., 2018. Subsurface CO2 storage estimation in Bakken tight oil and Eagle Ford shale gas condensate reservoirs by retention mechanism. Fuel 215, 580-591. paper describes the CO2 geological sequestration process in unconventional reservoirs in northern and southern United States such as Bakken tight oil and Eagle Ford shale gas condensate reservoirs. The hysteresis modelling and retention mechanism was performed in this research and this is one of the efficient and proven method to store CO2 in the subsurface. This can be achieved through CO2 EOR process while injecting CO2, the fluid will be trapped in the pore spaces between the impermeable rocks and oil can be recovered simultaneously. A total of four cases was taken for the analysis, such as the Bakken and Eagle Ford reservoirs with CO2 huff-n-puff process and another two cases with CO2 Flooding. Injection pressure, injection rate, injection time, number of cycles, carbon dioxide soaking time, fracture half-length, fracture conductivity, fracture spacing, porosity, permeability, and initial reservoir pressure as is taken as inputs and cumulative oil production, and oil recovery factor was taken as outputs. The reservoirs were modelled for 30?years of oil production and the factor year was taken as Decision Making Unit (DMU) and the models was calculated at each year. The retention was successfully calculated in all four models and percentage of retention above 90% was observed in all four cases and the injection pressure has the most dominating effect on the CO2 geological sequestration. It was also revealed that the CO2 huff-n-puff performance in Bakken reservoir is not that much more effective since the retention rate decreases during soaking period and flooding was found to be a suitable method in this formation. Even in Eagle Ford formation, the average performance of CO2 flooding process is better than the huff-n-puff, but the latter process was quite effective in this shale gas condensate reservoir.Prangishvili, D., Bamford, D.H., Forterre, P., Iranzo, J., Koonin, E.V., Krupovic, M., 2017. The enigmatic archaeal virosphere. Nature Reviews Microbiology 15, 724-739. of the most prominent features of archaea is the extraordinary diversity of their DNA viruses. Many archaeal viruses differ substantially in morphology from bacterial and eukaryotic viruses and represent unique virus families. The distinct nature of archaeal viruses also extends to the gene composition and architectures of their genomes and the properties of the proteins that they encode. Environmental research has revealed prominent roles of archaeal viruses in influencing microbial communities in ocean ecosystems, and recent metagenomic studies have uncovered new groups of archaeal viruses that infect extremophiles and mesophiles in diverse habitats. In this Review, we summarize recent advances in our understanding of the genomic and morphological diversity of archaeal viruses and the molecular biology of their life cycles and virus–host interactions, including interactions with archaeal CRISPR–Cas systems. We also examine the potential origins and evolution of archaeal viruses and discuss their place in the global virosphere.Key points·Crenarchaeal viruses display a remarkable diversity of unexpected, complex morphologies and have genomes with largely unique content.·The known viruses of extremely halophilic and methanogenic archaea include some morphologies of crenarchaeal viruses and all known morphologies of bacterial dsDNA viruses.·Archaeal viruses display many unique features that have thus far not been observed elsewhere in nature, including A-form DNA in viral particles, virion envelopes containing lipids in a horseshoe conformation and special gateway structures for virion release.·Certain aspects of the virus–host interaction in archaea, such as release of enveloped virions by budding, resemble mechanisms that are employed by eukaryotic enveloped viruses.·Archaeal viruses have a major role in the ocean sediments by killing their hosts, which results in the release of ～0.3 to 0.5 gigatonnes of carbon per year globally.·Comparative genomics analyses revealed close evolutionary relationships between archaeal viruses and capsidless mobile genetic elements.Pretorius, G.N., Bunt, J.R., Gr?bner, M., Neomagus, H., Waanders, F.B., Everson, R.C., Strydom, C.A., 2017. Evaluation and prediction of slow pyrolysis products derived from coals of different rank. Journal of Analytical and Applied Pyrolysis 128, 156-167. coal is heated slowly (<10 °C/min), as in the Lurgi Fixed Bed Dry Bottom (FBDB) gasification process, products formed in the pyrolysis region of the gasifier include gas liquor, condensable tar, oil and non-condensable gases. Knowledge of the temperature profile together with the coal decomposition behaviour is of great importance when designing a fixed bed gasification plant, and although the characterisation of tar and the composition thereof has been reported extensively, there is limited literature available on the prediction of tar composition formed during slow pyrolysis. The focus of this study was to investigate temperature and coal rank effects on pyrolysis product yield, and to predict (using FLASHCHAIN?) the char, tar, water and gas yields when heated at slow heating rates for coals of different rank (ranging from lignite B to bituminous C). A modified Fischer Assay setup was used to investigate pyrolysis at temperatures higher than that of the ISO 647 standard, i.e. 520, 720 and 920 °C and the tar quality was determined via SEC–UV (size exclusion chromatography–ultraviolet), GC–MS (gas chromatography–mass spectrometry), SimDis (simulated distillation) and ultimate analysis. Only the char yield was found to be rank dependent and the average molecular weight of the coal derived tars (212–415 Da) compared well with previous studies. The rank dependence based on the composition of the evolved volatiles (tar and gas), showed a linear relationship with elemental oxygen and carbon contents of the derived tar, as well as for the oxygen containing gases (CO and CO2). FLASHCHAIN? was able to provide a relatively accurate prediction of the char yield, poorer predictions of the tar and water yields and no correlation with the gas yield. The simulated results on tar composition showed poor promise. Statistical regression was also applied in order to determine correlations between coal properties and the pyrolysis product yields and composition. It was found that the mineral elements (Na2O, MgO, CaO, TiO2 and Fe2O3) have strong correlations with tar yield, thus implying that catalytic effects of the mineral matter appear to play a significant role in the formation and decomposition of coal derived tar, which is a limitation in all pyrolysis predictive models.Price, R., Boyd, E.S., Hoehler, T.M., Wehrmann, L.M., Bogason, E., Valt?sson, H.?., ?rlygsson, J., Gautason, B., Amend, J.P., 2017. Alkaline vents and steep Na+ gradients from ridge-flank basalts—Implications for the origin and evolution of life. Geology 45, 1135-1138. may have emerged on early Earth in serpentinizing systems, where ultramafic rocks react with aqueous solutions to generate high levels of dissolved H2 and CH4 and, on meeting seawater, steep redox, ionic, and pH gradients. Most extant life harnesses energy as ion (e.g., H+, Na+) gradients across membranes, and it seems reasonable to suggest that environments with steep ion gradients would have also been important for early life forms. The Strytan Hydrothermal Field (SHF) is a mid-ocean ridge–flank submarine hydrothermal (～70 °C) vent in Iceland that produces steep Na+ (<3–468 mM) and pH (8.1–10.2) gradients, concomitant with enrichments in methane (0.5–1.4 μM) and hydrogen (0.1–5.2 μM), relative to seawater. Large (up to 55 m) saponite towers create ideal “incubators” similar to other proposed origin-of-life analogs (e.g., Lost City hydrothermal field in the mid-Atlantic). However, the SHF is basalt hosted. We suggest that the observed conditions are generated by (1) plagioclase hydrolysis, coupled with calcite precipitation, and (2) hydration of Mg in pyroxene and olivine in basalt. Along with microbial activity, aqueous reactions of Fe in olivine and pyroxene are possible sources of the observed H2. Although the δ13C-CH4 values were highly variable (?53‰ to ?8‰), isotopically heavy CH4 suggests possible abiotic formation or the imprint of methane oxidation. If environments similar to SHF occurred on the early Earth, they should be considered as potential origin-of-life environments.Prokopiev, I.A., Shavarda, A.L., Filippova, G.V., Shein, A.A., 2017. Application of high-performance liquid chromatography to the determination of the concentration of lichen secondary metabolites. Journal of Analytical Chemistry 72, 1178-1183. isolation of aromatic metabolites from lichens of the Cladonia genus (C. stellaris, C. arbuscula, C. amaurocraea, and C. rangiferina) growing in Central Yakutia was carried out. Identification by IR, UV, and time-of-flight mass spectrometry has shown that the isolated compounds belong to the group of lichen substances. It was shown that the component composition of the studied lichens corresponds to the previously described one. At the same time, the concentration of perlatolic and barbatic acids in C. stellaris and C. amaurocrae lichens, respectively, growing in Central Yakutia found by HPLC is higher than in similar types of temperate climatic zones. Original Russian Text ? I.A. Prokopiev, A.L. Shavarda, G.V. Filippova, A.A. Shein, 2017, published in Zhurnal Analiticheskoi Khimii, 2017, Vol. 72, No. 11, pp. 1025–1031.Prud'homme, C., Lécuyer, C., Antoine, P., Hatté, C., Moine, O., Fourel, F., Amiot, R., Martineau, F., Rousseau, D.-D., 2018. δ13C signal of earthworm calcite granules: A new proxy for palaeoprecipitation reconstructions during the Last Glacial in western Europe. Quaternary Science Reviews 179, 158-166. of paleoprecipitation during the Last Glacial is a key element to reconstruct palaeoclimates. Recently, fossil calcite granules have been identified in loess sequences with high contents in specific horizons. In this study, we explored for the first time the potential of this new bio-indicator as a climatic proxy for precipitation in western Europe during the Last Glacial. We extracted 30 granules from eleven samples belonging to three tundra gleys and two brown soils from the Nussloch loess sequence previously dated between 50 and 20 ka. Stable carbon isotope measurements were performed on each granule and duplicated. Throughout the studied section, δ13C values range from ?15.4 to ?10.3‰ for tundra gleys and from ?14.9 to ?9.5‰ for brown soils. By taking into account the fractionation factor between the carbon ingested by the earthworm and the carbon output of the granules, the δ13C values of these granules reflect the composition of the C3 plant vegetation cover. Thus, we estimated the δ13C of the plants with a mean value of ?24.3 ± 0.9‰ for tundra gleys and ?24.1 ± 0.9‰ for brown soils, which are in agreement with values obtained from organic matter preserved in sediments. Palaeoprecipitation range over both tundra gley horizons and brown soils were estimated at about 333[159–574] mm/yr by using an empirical relationship determined between present-day plant leaf isotopic discrimination and the mean annual precipitation. This original preliminary study highlights the potential of earthworm calcite granule δ13C measurements as a new proxy for paleoprecipitation during the Last Glacial interstadials in continental environments.Pulster, E.L., Main, K., Wetzel, D., Murawski, S., 2017. Species-specific metabolism of naphthalene and phenanthrene in 3 species of marine teleosts exposed to Deepwater Horizon crude oil. Environmental Toxicology and Chemistry 36, 3168-3176. 2 most abundant polycyclic aromatic hydrocarbons (PAHs) measured in Deepwater Horizon crude oil, naphthalene and phenanthrene, and their associated homologs have both been shown to be acutely toxic in fish. Although fish have a relatively high metabolic capacity for PAHs, hydroxylated PAH (OH-PAH) derivatives formed during the initial metabolic response can negatively impact the health of fish. Species-specific metabolism of naphthalene and phenanthrene was evaluated in 3 marine teleosts, red drum (Scianops ocellatus), Florida pompano (Trachinotus carolinus), and southern flounder (Paralichthys lethostigma). Fish were exposed to Deepwater Horizon crude oil by intraperitoneal injections at time 0 and 48?h, with bile sampling events at 24 and 72?h post injection. The data suggested metabolic induction in Florida pompano and red drum, whereas southern flounder may have demonstrated metabolic fatigue. By 24?h post injection, overall profiles of red drum and southern flounder were dominated by hydroxylated phenanthrene metabolites; conversely, the Florida pompano profiles were dominated by monohydroxylated naphthalenes. In addition, Florida pompano had faster overall relative biotransformation rates, suggesting their potential decreased susceptibility to adverse effects. Red drum and southern flounder had much lower relative biotransformation rates, indicating their probable susceptibility to adverse outcomes after naphthalene and phenanthrene exposures. To our knowledge, the present study is the first to investigate monohydroxylated PAHs in fish exposed to Deepwater Horizon oil. Putman, J.C., Rowland, S.M., Podgorski, D.C., Robbins, W.K., Rodgers, R.P., 2017. Dual-column aromatic ring class separation with improved universal detection across mobile-phase gradients via eluate dilution. Energy & Fuels 31, 12064-12071. herein described High Performance Liquid Chromatography (HPLC) platform (termed HPLC-3) combines a complex solvent gradient with two electron acceptor columns to provide aromatic ring class (ARC) separation for heavy oils. The separation yields seven major fractions: saturates, monoaromatics (1 ring), diaromatics (2 rings), triaromatics (3 rings), tetra-aromatics (4 rings), polyaromatics and polars (5+ polars), and aliphatic sulfides. The system utilizes a photodiode array detector (PDA) for online measurements of aromaticity in series with an evaporative light scattering detector (ELSD) to provide improved quantitative mass determination across the entire solvent gradient. A new postcolumn dilution strategy was successfully utilized to compensate for solvent effects on the ELSD signal. The method allows for calibration across the entire HPLC-3 solvent gradient and simultaneously diverts ～90% of the sample effluent for fraction collection and further characterization. In addition to the major ARC fractions, the retention characteristics of various heteroatomic functional groups were studied to demonstrate the HPLC-3 system’s ability to further separate polar compounds on the basis of hydrogen bonding.Qiao, H., Hu, N., Bai, J., Ren, L., Liu, Q., Fang, L., Wang, Z., 2017. Encapsulation of nucleic acids into giant unilamellar vesicles by freeze-thaw: A way protocells may form. Origins of Life and Evolution of Biospheres 47, 499-510. are believed to consist of a lipid membrane and encapsulated nucleic acid. As the lipid membrane is impermeable to macromolecules like nucleic acids, the processes by which nucleic acids become encapsulated inside lipid membrane compartments are still unknown. In this paper, a freeze-thaw method was modified and applied to giant unilamellar vesicles (GUVs) and deoxyribonucleic acid (DNA) in mixed solution resulting in the efficient encapsulation of 6.4?kb plasmid DNA and similar length linear DNA into GUVs. The mechanism of encapsulation was followed by observing the effect of freeze-thaw temperatures on GUV morphological change, DNA encapsulation and ice crystal formation, and analyzing their correlation. Following ice crystal formation, the shape of spherical GUVs was altered and membrane integrity was damaged and this was found to be a necessary condition for encapsulation. Heating alone had no effects on DNA encapsulation, but was helpful for restoring the spherical shape and membrane integrity of GUVs damaged during freezing. These results suggested that freeze-thaw could promote the encapsulation of DNA into GUVs by a mechanism: the vesicle membrane was breached by ice crystal formation during freezing, DNA entered into damaged GUVs through these membrane gaps and was encapsulated after the membrane was resealed during the thawing process. The process described herein therefore describes a simple way for the encapsulation of nucleic acids and potentially other macromolecules into lipid vesicles, a process by which early protocells might have formed.Qin, S., Li, F., Li, W., Zhou, Z., Zhou, G., 2018. Formation mechanism of tight coal-derived-gas reservoirs with medium-low abundance in Xujiahe Formation, central Sichuan Basin, China. Marine and Petroleum Geology 89, Part 1, 144-154. Xujiahe Formation source rocks in the central Sichuan Basin, China were determined to have low gas-generation intensity, several large-scale gas fields have been found associated with this formation. Thus origins and formation mechanisms of natural gas in the Xujiahe Formation have attracted attentions of many researchers. In this study, geochemistry techniques were deployed to analyze natural gas and formation water in the Xujiahe Formation tight gas reservoir, central Sichuan Basin. By considering geologic background of the gas reservoir, its formation mechanism was investigated. Research results show that the Xujiahe Formation reservoir contains an independent petroleum system, with its natural gas exclusively originated from coal-measure source rocks in the Xujiahe Formation. The formation water was determined to be CaCl2 type with high salinity. H and O isotope values are largely deviated from those of meteoric water line, indicating favorable preservation conditions for the formation water. The Xujiahe Formation is composed of multiple coal-measure source rocks and superimposed by tight sandstones. The well-developed formation water provides favorable conditions for generating water-dissolved gas. Structural movements during the Himalayan period induced significant uplifting of the central Sichuan Basin with overlying formations denudated. Consequently, natural gas dissolved in formation water experienced depressurization and exsolution. The released natural gas formed free gas phase in structural highs or provided additional natural gas supplies to existing gas reservoirs.Qin, S., Li, F., Zhou, Z., Zhou, G., 2018. Geochemical characteristics of water-dissolved gases and implications on gas origin of Sinian to Cambrian reservoirs of Anyue gas field in Sichuan Basin, China. Marine and Petroleum Geology 89, Part 1, 83-90. Anyue gas field is a supergiant gas field which was discovered recently in the Sichuan Basin, China where the Sinian Dengying Formation and the Cambrian Longwangmiao Formation are principal gas reservoirs. Gas in the Anyue field contains mainly methane (>98%) and a low content of heavy hydrocarbons, with minor H2S component. Reservoirs commonly contain bitumen and produce formation water. It is currently suggested that natural gas in the Anyue field is derived from the secondary cracking of crude oil. However, carbon isotopic ratio of methane is significantly less negative than that of bitumen, which contradicts the isotopic signature oil cracking process would predict. Besides, this phenomenon also cannot be explained by the process of thermochemical sulphate reduction (TSR), because there is no remarkable correlation between the δ13C1 values and H2S contents as suggested in previous studies. Both free gas and water-dissolved gas from the Anyue gas field were analyzed in this study for their stable isotopes. Results show that the δ13C1 of the gas derived from the formation water is much less negative than that of free gas. Therefore, it is inferred that the less negative δ13C1 values in the free gas reservoir are attributable to addition of natural gas that is previously dissolved in formation water. Geological setting of the gas reservoirs in Dengying and Longwangmiao formations of the Anyue gas field is favorable for the formation and preservation of water-dissolved gas. In addition, both formations had experienced significant structural uplifting before the gas reservoirs were formed. Reduced temperature and pressure in the formations by geological uplifting could cause super-saturation of methane in the formation water, and as a consequence, water-dissolved methane gas could exsolve from water phase into gas phase. Therefore, it is concluded that natural gas in the Anyue field is a mixture of free gas and gas exsolved from the formation water. As a result, the carbon isotope of methane gas in the Anyue field became less negative than that of a single free gas component would predict.Qiu, H., Zheng, X., Ge, T., Dorodnikov, M., Chen, X., Hu, Y., Kuzyakov, Y., Wu, J., Su, Y., Zhang, Z., 2017. Weaker priming and mineralisation of low molecular weight organic substances in paddy than in upland soil. European Journal of Soil Biology 83, 9-17. soil organic matter (SOM) and microbial biomass pools in flooded paddy soils are generally larger than they are in upland soils, the processes (i.e., slower mineralisation, other types of C stabilization, and a negative priming effect) underlying higher SOM stocks in paddy soil are unclear. To elucidate these processes, three 13C labelled low molecular weight organic substances (13C-LMWOS) (i.e., glucose, acetic acid, and oxalic acid) were incubated in upland and paddy soils under simulated field conditions. Within 30 days of incubation, acetic acid exhibited the highest mineralisation in both soils. The amount of mineralisation of glucose in upland soil was higher than that of oxalic acid (p < 0.05), whereas the opposite was observed for paddy soil. Mineralisation of all three LMWOS was lower in paddy soil than that in upland soil (p < 0.05), illustrating that the molecular structure of the LMWOS as well as soil management determined the mineralisation rate. The priming effect evoked by oxalic acid and glucose was lower in paddy than in upland soil (p < 0.05). Therefore, the generally weaker mineralisation and priming effect of LMWOS observed in paddy soil contributed to higher carbon accumulation than they did in upland soil. Priming effect was positively correlated with fungal abundance, which was lower in paddy soil than in upland soil. Thus, slow organic C turnover in paddy soil is partly attributed to the suppression of fungal activity by flooding.Qu, L., Zou, C., Lu, Z., Yu, C., Li, N., Zhu, J., Zhang, X., Yue, X., Gao, M., 2017. Elastic-wave velocity characterization of gas hydrate-bearing fractured reservoirs in a permafrost area of the Qilian Mountain, Northwest China. Marine and Petroleum Geology 88, 1047-1058. are two types of gas hydrate-bearing reservoirs in the permafrost area of Qilian Mountain. Most of the gas hydrates occur mainly in the fractured mudstone reservoirs and rarely in the pores of the sandstone reservoirs. In this study, for the acoustic velocity characterization of the fractured gas hydrate reservoirs of the Qilian Mountain permafrost area, some mudstone core samples were collected for physical rock experiments, such as the acoustic experiment and the porosity and permeability experiment. An acoustic velocity numerical simulation of gas hydrate reservoirs was performed according to the Biot theory and the differential effective medium theory, with the conditions of multiple gas hydrate occurrence models, including the suspension model, the semi-cementation model and the cementation model, and considering both infinite and penny-shaped cracks. Fracture porosity was added to the core samples that only contain matrix porosity. With fracture porosity ranging from 0.01% to 5%, the variation laws between acoustic velocity with fractured porosity and hydrate saturation are obtained: (1) In the case of an infinite crack, if the fractured porosity is 0.01%–1%, the P-wave velocity decreases rapidly in the case of the three occurrence models. If the fractured porosity is higher than 1%, the acoustic velocity decreases gradually. If the crack shape is a penny-shaped crack, the P-wave velocity decreases almost linearly with increasing fracture porosity. (2) If the hydrate occurrence model is the suspension model, the P-wave velocity increases slightly with increasing hydrate saturation. If the occurrence model is the semi-cementation model or the cementation model, when the gas hydrate saturation of the infinite crack ranges from 0 to 80%, the acoustic velocity increases approximately linearly, whereas when the gas hydrate saturation ranges from 80% to 100%, the velocity increases rapidly. If the crack is a penny-shaped crack, the velocity increases almost linearly with increasing gas hydrate saturation from 0 to 100%. (3) It is found that the fractured gas hydrate reservoirs of the Qilian Mountain permafrost area contain both penny-shaped and infinite cracks, of which the infinite crack is the main crack shape. The gas hydrate occurrence in the Qilian Mountain permafrost area mainly follows the suspension model. This has significance for the seismic exploration and log evaluation of gas hydrate-bearing fractured reservoirs in the permafrost area of the Qilian Mountain in studying the acoustic velocity characterization, the crack shapes and occurrence models of gas hydrate reservoirs in the study area.Qu, Y., Zhu, S., Whitehouse, M., Engdahl, A., McLoughlin, N., 2018. Carbonaceous biosignatures of the earliest putative macroscopic multicellular eukaryotes from 1630?Ma Tuanshanzi Formation, north China. Precambrian Research 304, 99-109. Paleo- and Mesoproterozoic fossil record of multicellular eukaryotes is scarce but extremely important in studying the evolution of life in the Precambrian Era. Typically, fossils heralded as ‘multicellular eukaryotes’ that are older than the Ediacaran are met with controversy. To confront such debates, we investigate the chemical, isotopic, and molecular structural characteristics of organic matter from carbonaceous compressions in the 1630?Ma Tuanshanzi Formation in northern China, some of the earliest putative macroscopic multicellular eukaryote fossils (Zhu and Chen, 1995). The large-size and relative complexity of these fossils and similar remains from the 1.56?Ga Gaoyuzhuang Formation have led to their interpretation as eukaryotes. Raman spectral parameters give an estimated peak-metamorphic temperature TMax in the range of 202–286?°C, confirming the good preservation of the organic remains. Two-dimensional Raman maps of the carbonaceous compressions show ultrastructural variations that suggest diverse subcellular compounds being consistent with multicellular eukaryotes. The organic matter has carbon isotopic composition δ13Corg-SIMS between ?45.3 and ?32.2‰, and a branching index of carbon chain measured by the micro-FTIR spectral parameter R3/2 between 0.17 and 0.31. Together with their large-size and morphology, the isotopic, geochemical and ultrastructural data supports an interpretation of the Tuanshanzi Formation carbonaceous compressions as derived from phototrophic, multicellular eukaryotic algae. Our data support the early evolution of macroscopic multicellular eukaryotes in the sulfidic and low-oxygen conditions that prevailed in the Paleo- and Mesoproterozoic oceans.Raack, J., Conway, S.J., Herny, C., Balme, M.R., Carpy, S., Patel, M.R., 2017. Water induced sediment levitation enhances downslope transport on Mars. Nature Communications 8, Article 1151. Mars, locally warm surface temperatures (~293?K) occur, leading to the possibility of (transient) liquid water on the surface. However, water exposed to the martian atmosphere will boil, and the sediment transport capacity of such unstable water is not well understood. Here, we present laboratory studies of a newly recognized transport mechanism: “levitation” of saturated sediment bodies on a cushion of vapor released by boiling. Sediment transport where this mechanism is active is about nine times greater than without this effect, reducing the amount of water required to transport comparable sediment volumes by nearly an order of magnitude. Our calculations show that the effect of levitation could persist up to ~48 times longer under reduced martian gravity. Sediment levitation must therefore be considered when evaluating the formation of recent and present-day martian mass wasting features, as much less water may be required to form such features than previously thought.Race, M.S., 2017. Something new: Astrobiology in the real world. Astrobiology 17, 1067-1068., E.J., Parker, C.B., Gilchrist, K.H., Di Dona, S., Russell, Z.E., Hall, S.D., Carlson, J.B., Grego, S., Edwards, S.J., Sperline, R.P., Denton, M.B., Stoner, B.R., Glass, J.T., Amsden, J.J., 2017. A miniature electron ionization source fabricated using microelectromechanical systems (MEMS) with integrated carbon nanotube (CNT) field emission cathodes and low-temperature co-fired ceramics (LTCC). International Journal of Mass Spectrometry 422, 162-169. use of microelectromechanical systems (MEMS) components in miniature mass spectrometers is particularly attractive due to their small size and scalable manufacturing capability. Our group has pioneered the development of miniature electron ionization sources combining MEMS fabricated structures with integrated carbon nanotube (CNT) cold-cathode field emitters. However, until now they have been of limited use due to the limited ability to direct the ions into a mass analyzer. In this work, we design a miniature ion source using a microfabricated MEMS device and a low temperature co-fired ceramic (LTCC) carrier that includes electrical connections, ion optics for directing ions out of the device, and a sample inlet. We present the design and fabrication of the ion source; simulate the energy and angular dispersion; and experimentally determine the energy and angular dispersion.Raes, J., 2017. Crowdsourcing Earth's microbes. Nature 551, 446. large-scale study has been assessing microbial diversity by analysing DNA sequences from samples submitted by scientists around the globe. The initial results are now being used to create an open-access resource. See Article p.457.A simple, though dauntingly ambitious idea of sampling the microbial genetic diversity across Earth is the driving force behind the Earth Microbiome Project. On page 457, Thompson et al.1 report the results of this experimental tour de force.The project began life at a meeting in Snowbird, Utah, in 2010 at which a group of scientists from a wide range of disciplines discussed the goals, challenges and practicalities of such an enterprise2. Seven years on, the authors now report the microbial compositional profiles of a whopping 27,751 samples from 97 independent studies, providing insights into the diversity of microorganisms — from the bacterial and archaeal domains — in a wide range of geographic and environmental ecosystems, both terrestrial and aquatic. From these samples, Thompson and colleagues generated 2.2 billion DNA sequence reads of a highly variable region of a universally evolutionarily conserved gene called 16S rRNA, which encodes a component of the ribosome (the cell's protein-synthesis machinery).The remarkable nature of this study lies not only in its scale and in the breadth of the environmental samples analysed (Fig. 1), but also in its methodology. The project involved a massive, global crowdsourcing effort in which scientists raided their collection freezers for samples to share with the project.The approach was straightforward. A call was made for scientists to contribute well-preserved environmental samples collected during specific research projects, and the Earth Microbiome Project offered to sequence the DNA of the 16S rRNA gene in the microbial samples and to make the data available as open access.This project is a prime example of a trend in the adoption of scientific approaches involving widespread engagement, in which the ease of electronic communication and the power of social media are harnessed to generate useful resources. In the same spirit, in the Polymath Project, mathematicians collaborate to tackle challenging mathematical problems.Such approaches to generating crowdsourced experimental data usually work by first getting the project under way and obtaining funding later as the project gathers momentum, perhaps by crowdfunding. Examples of crowdsourced projects include those analysing bacteria in the human gut, such as the Flemish Gut Flora Project3, or the Personalized Nutrition Project4. Such studies contrast with conventional research collaborations that begin once a grant is obtained from a funding agency.Challenges inevitably arise in the type of work conducted by Thompson et al., particularly from having to handle samples from many collection sites. A common frustration in microbial research is that sampling procedures, storage, transport conditions, DNA extraction and amplification protocols often result in a 'lab-of-origin' effect that makes it difficult to compare data generated by different research groups. To address this, the Earth Microbiome Project developed a range of protocols5 and standards for sample collection, DNA extraction, transport and the formatting of the associated auxiliary data (such as temperature or location), as well as data-analysis procedures. These protocols were used for the project itself, but have been rapidly adopted by the wider research community, and more than 2,000 papers have already been published that use them6. By having a single protocol for all samples, and running all analyses in one laboratory, Thompson and colleagues have tried to remove as many potential technical confounding factors as possible.The results seem to confirm that they have succeeded, revealing that sample microbial profiles cluster by environment — those from a specific type of environment are more similar to each other than to those from other types of environment, irrespective of the research group that collected the sample. This approach also has a drawback, because a single DNA-extraction protocol cannot be expected to perform equally well across the wide chemical and biological variability of the samples collected in this type of broad survey, and might be less effective than a targeted approach in which extraction protocols are optimized for the environment being sampled. Thompson and colleagues have favoured generalizability over sensitivity, a choice that can surely be defended in these circumstances.Another limitation of the study is its lack of hypothesis-driven experimental design, because it deliberately positions itself as an exploratory data analysis across different environments and sample types. This produces certain constraints on the inferences that can be made, because environmental data collected for the samples were not always measured in the same way in different environments.The debate about the relative merits of data-driven and hypothesis-driven experimental approaches is not new, and there are examples of each of these approaches providing scientific insights. This study is an excellent example of the former, even if concessions had to be made regarding the selection of variables that could be used for analyses across all the environments.Thompson and colleagues made several findings. For example, they investigated whether existing theories about the relationship between species richness (as monitored by the diversity of 16S rRNA sequences) and temperature and pH across environments were consistent with their data. For example, there is a model that proposes a steady logarithmic rise of microbial richness with increasing temperature7,8. Surprisingly, in contrast to this theory, the authors found that microbial biodiversity peaks at a relatively narrow pH and temperature range and then drops again.The authors also observed an unexpectedly high amount of 'nestedness' among samples from different environments: samples showing low biodiversity were always present as microbial subsets of other, high-biodiversity samples, irrespective of the sample origin. Notably, this pattern of nestedness was mostly observed for microbial analyses above the level of genus — when analysed at the level of species, or when different strains of the same species were analysed, a strong decrease in nestedness was observed.The value of the Earth Microbiome Project will extend far beyond what is reported in the present paper. The project provides a resource that will keep microbial ecologists and evolutionary biologists busy for years. More than 60 publications have already been published using subsets of the data that had been released previously6. By implementing and fiercely pursuing this open-access model, Thompson and colleagues emphasize the value of collaboration and sharing over competition, which is unfortunately still too frequent in the scientific community.References1. Thompson, L. R. et al. Nature 551, 457–463 (2017).2. Gilbert, J. A., Jansson, J. K. & Knight, R. BMC Biol. 12, 69 (2014).3. Falony, G. et al. Science 352, 560–564 (2016).4. Zeevi, D. et al. Cell 163, 1079–1094 (2015).5. protocols-and-standards6. publications7. Allen, A. P., Brown, J. H. & Gillooly, J. F. Science 297, 1545–1548 (2002).8. Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M. & West, G. B. Ecology 85, 1771–1789 (2004).Rahimi, V., Bidarigh, M., Bahrami, P., 2017. Experimental study and performance investigation of miscible water-alternating-CO2 flooding for enhancing oil recovery in the Sarvak Formation. Oil & Gas Science and Technology - Revue IFP Energies nouvelles 72, Article 35. experimental study is aimed at evaluating the performance of the miscible Water-Alternating-CO2 (CO2-WAG) flooding as a function of slug size and WAG ratio based on the ultimate oil recovery in the Sarvak formation. In this research, initially the slim-tube apparatus was used to determine the Minimum Miscibility Pressure (MMP) of the Sarvak heavy oil and CO2 at the constant reservoir temperature. Then, a total of seven core flooding experiments were performed by using the sandstone core samples collected from the Sarvak formation. These experiments were conducted through respective water flooding, miscible continuous CO2 flooding, and miscible CO2-WAG flooding. In the miscible CO2-WAG flooding, different WAG slug sizes of 0.15, 0.25, and 0.50 Pore Volume (PV) and different WAG ratios of 1:1, 2:1, and 1:2 were applied to investigate their effects on the oil Recovery Factor (RF) in the Sarvak formation. The results showed that, in general, the miscible CO2 Enhanced Oil Recovery (CO2-EOR) process is capable of mobilizing the heavy oil and achieving a high and significant oil RF in the Sarvak formation. The miscible CO2-WAG flooding has the highest oil RF (84.3%) in comparison with water flooding (37.7%), and miscible continuous CO2 flooding (61.5%). In addition, using a smaller WAG slug size for miscible CO2-WAG flooding leads to a higher oil RF. The optimum WAG ratio of the miscible CO2-WAG flooding for the Sarvak formation is approximately 2:1. The results also demonstrated that, more than 50% of the heavy oil is produced in the first two cycles of the miscible CO2-WAG flooding. The optimum miscible CO2-WAG flooding has a much less CO2 consumption than the miscible continuous CO2 flooding.Ramirez-Corredores , M., 2017. The Science and Technology of Unconventional Oils: Finding Refining Opportunities. Academic Press. pp. Science and Technology of Unconventional Oils: Finding Refining Opportunities, intends to report the collective physical and chemical knowledge of unconventional oils (heavy, extra-heavy, sour/acid, and shale oil) and the issues associated with their refining for the production of transportation fuels. It will focus on the discussion of the scientific results and technology activities of the refining of unconventional oils. The presence of reactive and refractory compounds and components that negatively impact refining processing (the "bad actors") are discussed and analyzed. The commercially available technologies, with their reported improvements and emerging ideas, concepts, and technologies, are described. This comprehensive overview constitutes the basis for establishing technology gaps, and in return sets the science and technology needs to be addressed in the future. In summary, this book incorporates the relevant knowledge of processing unconventional crude oils and of the "Bottom-of-the-Barrel" fraction, describing the related commercially available and emerging technologies to contribute to the identification of existing gaps.Relates physicochemical properties and phenomenological behavior of unconventional oils to refining challengesDescribes commercially available technologies and the problems they solveLists recent improvements in various processes and identifies technology gapsExplains emerging new refining technologies and the problems they solveDiscusses future needs and challenges, and suggests further research and development Chapter 1 - Unconventional Oils, Pages 1-40Chapter 2 - Asphaltenes, Pages 41-222Chapter 3 - Metal Compounds, Pages 223-294Chapter 4 - Acidity in Crude Oils: Naphthenic Acids and Naphthenates, Pages 295-385Chapter 5 - Bottom of the Barrel Upgrading Technologies, Pages 387-488Chapter 6 - Emerging Technologies and Ideas with Potential, Pages 489-676Chapter 7 - Shale Oils, Pages 677-693Chapter 8 - Final Remarks and Future Aspirations, Pages 695-741Abbreviations and Acronyms, Pages 743-744Index, Pages 745-761Rao, G.D., Sarma, V.V.S.S., 2017. Influence of river discharge on the distribution and flux of methane in the coastal Bay of Bengal. Marine Chemistry 197, 1-10. are known to be strong sources of methane (CH4) to the atmosphere and their discharges may also enhance its flux from the coastal ocean. In order to examine this, CH4 fluxes to the atmosphere were examined along the coastal Bay of Bengal during peak discharge period. The saturation of CH4 in the Ganges river was relatively lower (208 ± 7%) than that of Indian peninsular rivers (907 ± 136%). The Ganges discharges into the northwestern (NW) while the peninsular rivers discharge into the central and southwestern (SW) regions of the coastal Bay of Bengal and influence the concentration and saturations of CH4 in the western coastal Bay of Bengal. Methane was higher (4.4 ± 0.9 nM) and more supersaturated (208 ± 37%) in the SW coastal Bay of Bengal than in the NW region (2.5 ± 0.1 nM and 116 ± 2.6% respectively). The higher concentrations of CH4 in the SW region were also influenced by mild coastal upwelling. The efflux of CH4 is estimated as 57.4 ± 19.3 and 14.5 ± 2.3 μmol m? 2 d? 1 from SW and NW regions, respectively, and an average of 38.9 ± 11.3 μmol m? 2 d? 1. Our study suggests that the western coastal waters of the Bay of Bengal act as strong source of CH4 to atmosphere. The total flux from Indian coastal waters (estuaries, mangroves and coastal waters) is estimated as 21.9 × 109 g CH4 y? 1 out of which ~ 70% is from the coastal Bay of Bengal and 20% from estuaries.Ratnayake, A.S., Sampei, Y., Kularathne, C.W., 2017. Current status of hydrocarbon exploration in Sri Lanka. International Journal of Oil, Gas and Coal Technology 16, 377-389. offshore investigations in Sri Lanka have identified three oceanic basins (i.e., the Mannar, Cauvery and Southern Basins) for possible oil and gas generation. These sedimentary basins recorded thick sedimentary successions from the Upper Jurassic to recent in age. The Cauvery and Mannar Basins contain a complex sequence of potential source rock beds from the Upper Jurassic to Neogene. An extensive kitchen source can be expected during the Upper Cretaceous. In addition, the basin modelling suggests that the Upper Cretaceous rock entered the maximum gas generation window around 20 Ma ago. The excellence reservoir potential can be expected by channel-levee complexes and slope fans in the Cretaceous and Tertiary sequences. The presence of combined stratigraphic and structural traps such as the Upper Cretaceous stratigraphic pinch-outs, horsts and tilted fault blocks and deepwater turbidites give positive force to the hydrocarbon exploration in Sri Lanka.Ravin, A., Rouchon, V., Blanchet, D., 2017. Determination of organic degradation rates in 100 My old sediments: Application to Cretaceous black shale intervals from Demerara Rise, ODP Leg 207. Organic Geochemistry 113, 128-140. organic-rich, Albian to Santonian, black shale sequences were recovered from Ocean Drilling Program Sites 1261 and 1257 on the Demerara Rise, offshore Surinam, at depths of 564 and 174 m below seafloor (bsf) respectively. Total organic carbon (TOC) concentration varies between 3.9 and 17.3 wt%. Rock-Eval pyrolysis parameters and elemental analysis indicate that the kerogen samples are of Type II, thermally immature and with well preserved organic matter. The hydrogen index (HI) values fluctuate between 608 and 765 mg hydrocarbon (HC)/g TOC and correlate well with C/N and the Sorg/C atomic ratios, indicating varying early diagenesis conditions between samples. Higher C/N and Sorg/C values for kerogen from Site 1261 suggest more reducing depositional conditions than at Site 1257. Long term organic diagenesis is marked by a linear decrease in the oxygen index (OI) at Site 1261, from 34 to 22 mg CO2/g TOC. Ester and carboxyl functional groups are the main target of the degradation as inferred from the decrease in CO and OCC Fourier transform infrared spectroscopy (FTIR) bands as well as in the CHOH and the OCH3/CHxN bands in 13C nuclear magnetic resonance (NMR) spectra. Degradation rate at Site 1261, determined combining quantitative NMR spectra and bulk elemental characterization, is between 1.7 and 12.1 ?mol/m3/yr per 1% TOC, at the lower end of reported rates in a similar context. Kerogen samples from Site 1257 do not show any decrease in oxygen content with depth, indicating significantly lower degradation rate. We propose that the long term exposure to moderate temperature (30 °C) at Site 1261 activated the organic matter, thereby sustaining microbial diagenesis.Rej?ek, J., Vrkoslav, V., Pokorn?, V., P?ibyl, V., Cva?ka, J., 2017. Ion source with laser triangulation for ambient mass spectrometry of nonplanar samples. Analytical Chemistry 89, 11452-11459. analysis of nonplanar samples in ambient mass spectrometry poses a formidable challenge. Here, an ion source equipped with laser triangulation for analyzing nonplanar surfaces was constructed. It was designed as a two-position device, where the sample height was measured using laser triangulation and the target compounds were then analyzed. Thanks to a stage movable in xyz, the ion source maintained an optimal vertical distance between the sample and the sampling capillary for each measured spot during the surface analysis. The xyz-coordinates for the movement of the sample stage were computed using the laser sensor data in such a way as to avoid direct contact of the sampling capillary and the measured surface. The ion source performance and its ability to analyze various morphologies were tested using desorption electrospray ionization with plastic objects coated by 2,5-dimethoxybenzoic acid. The experiments showed excellent performance for nonplanar samples but also revealed some limitations especially on object edges and steep slopes. The applicability of the ion source operated in desorption electrospray ionization and desorption atmospheric pressure photoionization was examined for food and pharmaceutical samples. Chemicals on the surface of nonplanar samples were probed along a line extending across the surface of the measured objects. The device provided high-quality spectra, regardless of the sample height at the measured spot. The automatic adjustments of the sample stage in xyz proved to be beneficial for analyzing nonplanar samples and for simultaneous measurement of samples with various dimensions and shapes.Retallack, G.J., 2018. The oldest known paleosol profiles on Earth: 3.46 Ga Panorama Formation, Western Australia. Palaeogeography, Palaeoclimatology, Palaeoecology 489, 230-248. volcanic flank and floodplain facies of the 3.46 Ga Panorama Formation have been recognized on the basis of trough cross-bedded sandstones, lapilli tuffs, and abundant nodularized barite sand crystals, like those noted in other Archean non-marine facies. These barite-nodular layers are interpreted as alluvial paleosols for the following reasons. They show different degree of bedding disruption scaled to nodule size beneath a sharp upper boundary, like desert soil profiles. They show multiple generations of cracking, clay skins, and up-profile destruction of feldspar and rock fragments, compatible with weathering of labile constituents of the parent material. Loss of alkali and alkaline earth elements and phosphorus up profile are also features of chemical weathering. Geochemical mass balance calculations (tau analysis) shows that the profiles lost mass and labile elements, unlike unaltered sediments and tuffs. Rare earth element analysis also shows light rare earth retention as in weathering, as opposed to sedimentation or hydrothermal alteration. Barite of nodules in the paleosols is mobilized to concentration under very acidic conditions (pH < 3) and is very stable under less acidic conditions. These Archean alluvial paleosols may have formed by acid sulfate weathering by sulfuric acid, rather than the currently more common hydrolysis by carbonic acid. This archaic system of widespread acid sulfate weathering has since been marginalized to a few playa lakes, deep water tables, and sulfur springs.Reyes, C., Schneider, D., Thürmer, A., Kulkarni, A., Lipka, M., Sztejrenszus, S.Y., B?ttcher, M.E., Daniel, R., Friedrich, M.W., 2017. Potentially active iron, sulfur, and sulfate reducing bacteria in Skagerrak and Bothnian bay sediments. Geomicrobiology Journal 34, 840-850. many marine surface sediments, the reduction of manganese (Mn) and iron (Fe) oxides is obscured by sulfate reduction, which is regarded as the predominant anaerobic microbial respiration process. However, many dissimilatory sulfate and sulfur reducing microorganisms are known to utilize alternative electron acceptors such as metal oxides. In this study, we tested whether sulfate and sulfur reducing bacteria are linked to metal oxide reduction based on biogeochemical modeling of porewater concentration profiles of Mn2+ and Fe2+ in Bothnian Bay (BB) and Skagerrak (SK) sediments. Steady-state modeling of Fe2+ and Mn2+ porewater profiles revealed zones of net Fe (0–9 cm BB; ～10 and 20 cm SK) and Mn (0–5 cm BB; 2–8 cm SK) species transformations. 16S rRNA pyrosequencing analysis of the in-situ community showed that Desulfobacteraceae, Desulfuromonadaceae and Desulfobulbaceae were present in the zone of Fe-reduction of both sediments. Rhodobacteraceae were also detected at high relative abundance in both sediments. BB sediments appeared to harbor a greater diversity of potential Fe-reducers compared to SK. Additionally, when the upper 10 cm of sediment from the SK was incubated with lepidocrocite and acetate, Desulfuromonas was the dominant bacteria. Real-time quantitative polymerase chain reaction (qPCR) results showed decreasing dsrA gene copy numbers with depth coincided with decreased Fe-reduction activity. Our results support the idea that sulfur and sulfate reducing bacteria contribute to Fe-reduction in the upper centimeters of both sediments.Richardson, A.E., Danielson, N.D., 2017. Hydrophilic interaction liquid chromatography of hydroxy aromatic carboxylic acid positional isomers. Analytica Chimica Acta 996, 98-105. interaction liquid chromatography (HILIC) has become increasingly popular as an alternative to reversed phase LC due to its ease of separating complex polar compound mixtures and the compatibility of the mobile phase with mass spectrometry (MS). Using a plain silica column (150??mm?×?4.6??mm), we have shown a mixture containing three hydroxybenzoic acid isomers plus syringic and vanillic acid and three hydroxycinnamic acid isomers plus ferulic and sinapic acid can be separated using a mobile phase comprised of 90% acetonitrile (MeCN) and 10% 20?mM ammonium acetate at pH 6 in under 45?min. This method is appropriate when using UV detection at 275?nm. However, for improved MS compatibility, a buffer concentration of 10?mM is recommended but this greatly decreases the analyte retention factors. A second more nonpolar organic solvent component in the mobile phase (particularly pentane which has not been previously considered for HILIC) is found to offset this loss in retention. The optimum mobile phase is found to be 90% MeCN, 5% 10?mM ammonium acetate pH 6, and 5% pentane with resolution of eight of the ten compounds with a separation time of 30?min. Using UV detection, we have shown that detection limits range from 36 to 133 pmole and quantitation limits are spread from 94 to 376 pmole for six of the analytes. Upon testing this method on two other silica columns from different manufacturers, it is found that while resolution is similar, further optimization of the mobile phase is recommended.Ridenhour, B.J., Brooker, S.L., Williams, J.E., Van Leuven, J.T., Miller, A.W., Dearing, M.D., Remien, C.H., 2017. Modeling time-series data from microbial communities. The Isme Journal 11, 2526-2537. sequencing technologies have advanced, the amount of information regarding the composition of bacterial communities from various environments (for example, skin or soil) has grown exponentially. To date, most work has focused on cataloging taxa present in samples and determining whether the distribution of taxa shifts with exogenous covariates. However, important questions regarding how taxa interact with each other and their environment remain open thus preventing in-depth ecological understanding of microbiomes. Time-series data from 16S rDNA amplicon sequencing are becoming more common within microbial ecology, but methods to infer ecological interactions from these longitudinal data are limited. We address this gap by presenting a method of analysis using Poisson regression fit with an elastic-net penalty that (1) takes advantage of the fact that the data are time series; (2) constrains estimates to allow for the possibility of many more interactions than data; and (3) is scalable enough to handle data consisting of thousands of taxa. We test the method on gut microbiome data from white-throated woodrats (Neotoma albigula) that were fed varying amounts of the plant secondary compound oxalate over a period of 22 days to estimate interactions between OTUs and their environment.Rivadeneyra, A., Gonzalez-Martinez, A., Portela, G.R., Martin-Ramos, D.J., Gonzalez-Lopez, J., Rivadeneyra, M.A., 2017. Biomineralisation of carbonate and sulphate by the halophilic bacterium Halomonas maura at different manganese concentrations. Extremophiles 21, 1049-1056. ability of Halomonas maura to bioprecipitate carbonate and sulphate crystals in solid media at different manganese concentrations has been demonstrated in this study for the first time. The precipitated minerals were studied by X-ray diffraction, scanning and transmission electron microscopy, and energy-dispersive X-ray spectroscopy. The precipitated minerals were different based on the manganese concentration present in the medium and the incubation time. In the absence of manganese, H. maura formed pseudokutnahorite crystals; in the presence of manganese, the concentration in the culture medium determined the precipitation carbonates, such as rhodochrosite and dolomites. However, in the presence of low concentrations of manganese chloride (MnCl2) (5?g/l), kutnohorite crystals were also formed. Finally, when H. maura was grown in the presence of manganese, small amounts of sulphate crystals (such as bassanite and gypsum) were detected. Our study of the precipitated minerals showed an active role of H. maura in the biomineralisation process, but the geochemical conditions, and the manganese concentrations in particular, were clearly influential.Rivas-Lamelo, S., Benzerara, K., Lefèvre, C.T., Jézéquel, D., Menguy, N., Viollier, E., Guyot, F., Férard, C., Poinsot, M., Skouri-Panet, F., Trcera, N., Miot, J., Duprat, E., 2017. Magnetotactic bacteria as a new model for P sequestration in the ferruginous Lake Pavin. Geochemical Perspectives Letters 5, 35-41. role of microorganisms in the geochemical cycle of P has received great interest in the context of enhanced biological phosphorus removal and phosphorite formation. Here, we combine scanning and transmission electron microscopies, confocal laser scanning microscopy and synchrotron-based x-ray microfluorescence to analyse the distribution of P at the oxic-anoxic interface in the water column of the ferruginous Lake Pavin. We show that magnetotactic bacteria of the Magnetococcaceae family strongly accumulate polyphosphates and appear as P hotspots in the particulate fraction at this depth. This high accumulation may be characteristic of this family and may also relate to the chemical conditions prevailing in the lake. As a result, these magnetotactic cocci can be considered as new models playing a potentially important role in the P geochemical cycle, similar to sulphide oxidising bacteria such as Thiomargarita and Beggiatoa but thriving in a ferruginous, poorly sulphidic environment. Robroek, B.J.M., Jassey, V.E.J., Payne, R.J., Martí, M., Bragazza, L., Bleeker, A., Buttler, A., Caporn, S.J.M., Dise, N.B., Kattge, J., Zaj?c, K., Svensson, B.H., van Ruijven, J., Verhoeven, J.T.A., 2017. Taxonomic and functional turnover are decoupled in European peat bogs. Nature Communications 8, Article 1161. peatland ecosystems, plant communities mediate a globally significant carbon store. The effects of global environmental change on plant assemblages are expected to be a factor in determining how ecosystem functions?such as carbon uptake will respond. Using vegetation data from 56 Sphagnum-dominated peat bogs across Europe, we show that in these ecosystems plant species aggregate into two major clusters that are each defined by shared response to environmental conditions. Across environmental gradients, we find significant taxonomic turnover in both clusters. However, functional identity and functional redundancy of the community as a whole remain unchanged. This strongly suggests that in peat bogs, species turnover across environmental gradients is restricted to functionally similar species. Our results demonstrate that plant taxonomic and functional turnover are decoupled, which may allow these peat bogs to maintain ecosystem functioning when subject to future environmental change.Rocha, A.C., Murad, M.A., Le, T.D., 2017. A new model for flow in shale-gas reservoirs including natural and hydraulic fractures. Computational Geosciences 21, 1095-1117. this work, we construct a new coupled Multiscale/Discrete Fracture Model for compressible flow in a multiporosity shale gas reservoir containing networks of natural and hydraulic fractures. The geological formation is characterized by four distinct length scales and levels of porosity. The window of observation of the finest (nanoscale) portraits the nanopores within organic matter containing adsorbed gas. At the microscale, the medium is formed by two solid phases: organic, composed by kerogen aggregates, and inorganic (clay, quartz, calcite). Such phases are separated by the network of partially-saturated interparticle pores where microscopic free gas flow influenced by Knudsen effects along with gas diffusion in the immobile water phase occur simultaneously. The upscaling of the local flow to the mesoscale gives rise to a nonlinear homogenized pressure equation in the shale matrix which lies adjacent to the system of natural fractures. Homogenization of the coupled matrix/preexisting fractures to the macroscale leads to a microstructural model of dual porosity type. Such homogenized model is subsequently coupled with the hydrodynamics in the network of induced fractures which, in the context of the discrete fracture modeling, are treated as (n ? 1), (n = 2, 3) lower dimensional objects. In order to handle numerically the nonlinear interaction between the different flow equations, we adopt a superposition argument, firstly proposed by Arbogast (1996), in each iteration of a fixed-point algorithm. The resultant governing equations are discretized by the finite element method and numerical simulations of gas production in stratified arrangements of the fracture networks are presented to illustrate the potential of the multiscale approach.Rodríguez-Maecker, R., Vyhmeister, E., Meisen, S., Rosales Martinez, A., Kuklya, A., Telgheder, U., 2017. Identification of terpenes and essential oils by means of static headspace gas chromatography-ion mobility spectrometry. Analytical and Bioanalytical Chemistry 409, 6595-6603. headspace gas chromatography-ion mobility spectrometry (SHS GC-IMS) is a relatively new analytical technique that has considerable potential for analysis of volatile organic compounds (VOCs). In this study, SHS GC-IMS was used for the identification of the major terpene components of various essential oils (EOs). Based on the data obtained from 25 terpene standards and 50 EOs, a database for fingerprint identification of characteristic terpenes and EOs was generated utilizing SHS GC-IMS for authenticity testing of fragrances in foods, cosmetics, and personal care products. This database contains specific normalized IMS drift times and GC retention indices for 50 terpene components of EOs. Initially, the SHS GC-IMS parameters, e.g., drift gas and carrier gas flow rates, drift tube, and column temperatures, were evaluated to determine suitable operating conditions for terpene separation and identification. Gas chromatography-mass spectrometry (GC-MS) was used as a reference method for the identification of terpenes in EOs. The fingerprint pattern based on the normalized IMS drift times and retention indices of 50 terpenes is presented for 50 EOs. The applicability of the method was proven on examples of ten commercially available food, cosmetic, and personal care product samples. The results confirm the suitability of SHS GC-IMS as a powerful analytical technique for direct identification of terpene components in solid and liquid samples without any pretreatment.Rogers, A.R., Bohlender, R.J., Huff, C.D., 2017. Reply to Mafessoni and Prüfer: Inferences with and without singleton site patterns. Proceedings of the National Academy of Sciences 114, E10258-E10260. and Prüfer (1) (MP) make three points: (i) Low variation among Neanderthal genomes implies a small population, (ii) Neanderthal–Denisovan divergence is small relative to archaic-modern, and (iii) an analysis including singleton site patterns (in which the derived allele appears only once) supports a small Neanderthal population and a more recent Neanderthal–Denisovan separation. Point i assumes that sequenced Neanderthals are representative of all Neanderthals, yet samples come primarily from the north, where DNA preserves well. The global population may have been larger if some unsampled populations were distantly related to those sampled. Point ii is subsidiary to point iii, because divergences can be calculated from site pattern frequencies. We therefore focus on point iii. Our previous estimates (2) were biased, because our modern human data excluded invariant nucleotide sites (3). Mutations in an archaic lineage appear only if that lineage introgressed into moderns, leading … Original paper: Rogers, A.R., Bohlender, R.J., Huff, C.D., 2017. Early history of Neanderthals and Denisovans. Proceedings of the National Academy of Sciences 114, 9859-mented by: Mafessoni, F., Prüfer, K., 2017. Better support for a small effective population size of Neandertals and a long shared history of Neandertals and Denisovans. Proceedings of the National Academy of Sciences 114, E10256-E10257.Rogozin, D.Y., Darin, A.V., Kalugin, I.A., Melgunov, M.S., Meydus, A.V., Degermendzhi, A.G., 2017. Sedimentation rate in Cheko Lake (Evenkia, Siberia): New evidence on the problem of the 1908 Tunguska Event. Doklady Earth Sciences 476, 1226-1228. estimated the age and sedimentation rate of bottom sediments in Cheko Lake located in southern Evenkia, in the territory of Tunguska Nature Reserve, near the supposed epicenter of the so-called 1908 Tunguska Event. The vertical distributions of 137Cs and 210Pb activity and visually counted varves in the core of lake bottom sediments indicate that Cheko Lake is significantly older than the 1908 Tunguska Event; therefore, the lake basin cannot be a crater or a trace of the explosion as was supposed earlier by some researchers. Original Russian Text ? D.Y. Rogozin, A.V. Darin, I.A. Kalugin, M.S. Melgunov, A.V. Meydus, A.G. Degermendzhi, 2017, published in Doklady Akademii Nauk, 2017, Vol. 476, No. 6, pp. 685–687.Rojas-Ruiz, F.A., Bottia-Ramirez, H., Rodríguez-Rodríguez, L., Orrego-Ruiz, J.A., 2017. Exploring compositional changes along in situ combustion and their implications on emulsion stabilization via Fourier transform ion cyclotron resonance mass spectroscopy (FT-ICR MS). Energy & Fuels 31, 11995-12003. situ combustion (ISC) is one of the highest potential enhanced oil recovery (EOR) processes for heavy oils. However, several operational issues, including the formation of highly stable emulsions, have limited its application. Disclosing the physicochemical proprieties of these emulsions, especially the chemical nature of the compounds involved in the stabilization process, has become relevant for the success of ISC projects. In the present work, the physicochemical changes at a laboratory-scale low-temperature oxidation (LTO) regimen performed over a Colombian heavy crude oil were followed by mass spectrometry. The compositional analyses were performed using both positive-ion atmospheric pressure photoionization ((+) APPI) and negative-ion electrospray ionization ((?) ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Further isolation of acidic compounds and surface-active species allowed us to determine that the process incorporates a wide variety of compounds to build up the O/W (oil/water) interface, thus increasing the stabilizing tendency of the emulsions. During the combustion, oxygen is chemically incorporated to the crude over hydrocarbon compounds, as well as over sulfur- and nitrogen-containing compounds, generating classes such as O, O2, O3, O4, OS, NO2, and NO3 that explain the high viscosity and high stability of the emulsions.Romero-Sarmiento, M.-F., Ramiro-Ramirez, S., Berthe, G., Fleury, M., Littke, R., 2017. Geochemical and petrophysical source rock characterization of the Vaca Muerta Formation, Argentina: Implications for unconventional petroleum resource estimations. International Journal of Coal Geology 184, 27-41. Vaca Muerta Formation is currently regarded as the most prolific source rock interval for unconventional petroleum exploration in Argentina. In this study, we integrate recent CT-scanner, nuclear magnetic resonance (NMR) T1-T2 and Rock-Eval Shale Play? analytical techniques, combined with classical geochemical, petrological and petrophysical methods to characterize Vaca Muerta source rocks along a vertical profile. The proposed analytical workflow was tested here on 4 samples derived from one core: the LJE-1010 borehole drilled in the lowermost Jurassic Vaca Muerta member (Neuquén Basin – Argentina), to evaluate the unconventional hydrocarbon potential and pore network attributes. First, entire rock samples were analyzed by dual energy CT scanner to evaluate possible heterogeneities; this also helped in the selection of representative samples. Then the organic matter properties were investigated by open-system pyrolysis techniques, organic petrography and biomarker analyses as a function of the core depth. A comparative approach between open-system pyrolysis methods (e.g. Rock-Eval Basic/Bulk-Rock & Shale Play? methods vs. Source Rock Analyzer) is also illustrated in this work. Finally, petrophysical characteristics and pore network attributes in shale were estimated by gas permeability (steady-state method corrected for Klinkenberg effect), porosity and NMR methods. The investigated samples have oil-window maturity and are characterized by a network of solid bitumen. Based on new Rock-Eval Shale Play? data, the potentially producible oil present in the rock samples was estimated using the modified oil saturation index (OSI = Sh0 + Sh1 peaks × 100/TOC). Results indicate that the oil crossover effect and potential productive oils occur within intervals showing higher TOC values (~ 3 to 8 wt%). We also illustrated here that, for unconventional shale play perspectives, Rock-Eval Shale Play? parameters (Sh0 & Sh1) allow to obtain both a better quantification of free and retained hydrocarbons in source-reservoir rock samples and correct original oil in place (OOIP) estimations in early exploration campaign for shale oil and shale gas assessment. For Vaca Muerta rock samples, OOIP estimations range from 60 to 160 bbl oil/acre-ft, approximately. We also demonstrated that the solid bitumen, oil and organic matter are clearly distinguished in the studied samples using advanced NMR T1-T2 maps obtained at different temperatures. The solid bitumen was clearly evidenced as a peak with T1/T2 ratio ~ 14 on NMR T1-T2 maps. Concerning the matrix bulk rock permeability, the obtained results showed that the most deep sample is characterized by a permeability of about 140 nanoDarcy (nD) whereas the shallower sample containing also higher amounts of organic matter is more permeable (~ 213 nD), indicating that TOC values play a main control on Vaca Muerta poromechanical characteristics. The maximum total porosity values range between 6.5 and 21.8% and were calculated in this work integrating NMR and helium porosity values. Finally, global interpretations of these obtained results suggest that the Vaca Muerta Formation could be considered as a prolific shale play interval for unconventional petroleum exploration in the near future.Rosenthal, K., Oehling, V., Dusny, C., Schmid, A., 2017. Beyond the bulk: disclosing the life of single microbial cells. FEMS Microbiology Reviews 41, 751-780. single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms that organize cellular physiology, unbiased by population heterogeneity or uncontrollable environmental impacts. A holistic description of cellular functions at the single cell level requires analytical concepts beyond the miniaturization of existing technologies, defined but uncontrolled by the biological system itself. This review provides an overview of the latest advances in single cell technologies and demonstrates their potential. Opportunities and limitations of single cell microbiology are discussed using selected application-related examples.Rostami, A., Arabloo, M., Lee, M., Bahadori, A., 2018. Applying SVM framework for modeling of CO2 solubility in oil during CO2 flooding. Fuel 214, 73-87. solubility is one of the most important parameters that affects CO2 flooding, because gas dissolution into crude oil results in oil swelling, viscosity reduction, IFT reduction, oil mobilization, and oil recovery improvement. Therefore, a better understanding of CO2 solubility mechanisms and its influence on physical properties of crude oil are essential to any effective CO2 flooding process. In this study, Least-Square Support Vector Machine (LSSVM) as a newly established soft computing algorithm is applied for developing a new correlative model for CO2 solubility in both dead and live oil systems. CO2 solubility in dead oil is basically affected by the oil saturation pressure (Ps), oil specific gravity (γ), oil molecular weight (MW), and reservoir temperature (T). Moreover, the impact of bubble point pressure is considered in constructing the LSSVM model for the live oil. A number of statistical quality measures are utilized to assess and demonstrate the superior capability of the newly developed LSSVM model in comparison with the previous empirically derived correlations. The average absolute relative deviation (AARD) and coefficient of determination (R2) of 2.2783% and 0.9933 for the dead oil system, and 1.7432% and 0.9958 for the live oil system, respectively, verify the acceptable accuracy and efficient performance of the proposed LSSVM model over a wide range of dataset used in this study within the range of the used databank. However, the impact of CO2 liquefaction pressure is ignored, the LSSVM model gives the best result. In conclusion, it is worth mentioning that the proposed LSSVM model can serve as an accurate correlative tool for fast and effective estimation of CO2 solubility in both dead and live crude oils.Rovere, A., Casella, E., Harris, D.L., Lorscheid, T., Nandasena, N.A.K., Dyer, B., Sandstrom, M.R., Stocchi, P., D’Andrea, W.J., Raymo, M.E., 2017. Giant boulders and Last Interglacial storm intensity in the North Atlantic. Proceedings of the National Academy of Sciences 114, 12144-12149.: The Last Interglacial was the last period of the Earth’s history when climate was warmer than preindustrial, with higher polar temperatures and higher sea levels. Based on geologic evidence in Bermuda and the Bahamas, studies suggest that during this period the North Atlantic was characterized by “superstorms” more intense than any observed historically. Here we present data and models showing that, under conditions of higher sea level, historically observed hurricanes can explain geologic features previously interpreted as evidence for more intense Last Interglacial storm activity. Our results suggest that, even without an increase in the intensity of extreme storms, cliffs and coastal barriers will be subject to significantly higher wave-induced energies under even modestly higher sea levels. Abstract: As global climate warms and sea level rises, coastal areas will be subject to more frequent extreme flooding and hurricanes. Geologic evidence for extreme coastal storms during past warm periods has the potential to provide fundamental insights into their future intensity. Recent studies argue that during the Last Interglacial (MIS 5e, ～128–116 ka) tropical and extratropical North Atlantic cyclones may have been more intense than at present, and may have produced waves larger than those observed historically. Such strong swells are inferred to have created a number of geologic features that can be observed today along the coastlines of Bermuda and the Bahamas. In this paper, we investigate the most iconic among these features: massive boulders atop a cliff in North Eleuthera, Bahamas. We combine geologic field surveys, wave models, and boulder transport equations to test the hypothesis that such boulders must have been emplaced by storms of greater-than-historical intensity. By contrast, our results suggest that with the higher relative sea level (RSL) estimated for the Bahamas during MIS 5e, boulders of this size could have been transported by waves generated by storms of historical intensity. Thus, while the megaboulders of Eleuthera cannot be used as geologic proof for past “superstorms,” they do show that with rising sea levels, cliffs and coastal barriers will be subject to significantly greater erosional energy, even without changes in storm intensity. Rubin, A.E., Ma, C., 2017. Meteoritic minerals and their origins. Chemie der Erde - Geochemistry 77, 325-385. 435 mineral species have been identified in meteorites including native elements, metals and metallic alloys, carbides, nitrides and oxynitrides, phosphides, silicides, sulfides and hydroxysulfides, tellurides, arsenides and sulfarsenides, halides, oxides, hydroxides, carbonates, sulfates, molybdates, tungstates, phosphates and silico phosphates, oxalates, and silicates from all six structural groups. The minerals in meteorites can be categorized as having formed by a myriad of processes that are not all mutually distinct: (1) condensation in gaseous envelopes around evolved stars (presolar grains), (2) condensation in the solar nebula, (3) crystallization in CAI and AOI melts, (4) crystallization in chondrule melts, (5) exsolution during the cooling of CAIs, (6) exsolution during the cooling of chondrules and opaque assemblages, (7) annealing of amorphous material, (8) thermal metamorphism and exsolution, (9) aqueous alteration, hydrothermal alteration and metasomatism, (10) shock metamorphism, (11) condensation within impact plumes, (12) crystallization from melts in differentiated or partially differentiated bodies, (13) condensation from late-stage vapors in differentiated bodies, (14) exsolution, inversion and subsolidus redox effects within cooling igneous materials, (15) solar heating near perihelion, (16) atmospheric passage, and (17) terrestrial weathering.Russell, M.J., 2017. Life is a verb, not a noun. Geology 45, 1143-1144.’s emergence marks one of the last of the cascade of entropy generators that make up the evolutionary structures of the Cosmos. In far-from-equilibrium conditions, one dynamic process issues from another, and both progenitor and descendent remain coupled; e.g., convection and metabolism. Order only derives from order, not from chaos. Immaculate conception and Frankenstein-like origins of life are the stuff of myth, not science. To enable life’s onset, the disequilibria and the materials capable of acting as ‘free energy’ converters must be locally accessible and the gradients appropriately focused. For “life is a verb, not a noun” (Gilman, 1904; Stepney, 2012). Life’s job is to dissipate (the faster) whatever disequilibrium is powering it. It is, however, a construct erected on carbon scaffolds and it fundamentally has to make do with carbon from CO2, which it must therefore hydrogenate as a foundational element of its method. And geologists since Darwin have deduced that, on rainout of the first ocean, CO2 was available in the all-enveloping atmosphere. That is one of the initial conditions for the onset of life.Price et al. (2017, p. 1135 in this issue of Geology) consider another initial condition, that “life may have emerged on early Earth in serpentinizing systems.” They extend the submarine alkaline vent model for life’s emergence to include basalt-hosted alkaline springs derived from meteoric waters issuing into shallow seas lapping volcanic islands. They recruit Iceland as their model, while taking into account another such site in southern New Caledonia, the Prony Bay Hydrothermal Filed (PHF). In their scenario, the entire lithospheric surface of any young, wet, rocky planet hosting a CO2 volatisphere, whether mafic or ultramafic, provides a myriad of possible sites for life’s emergence—an idea enticing to astrobiologists, and one recalling the words of Bernal: “Life, geologically speaking, consists of the interference with secondary lithosphere–atmosphere reactions so as to produce a small but ever-renewed stock of organic molecules” (Bernal 1960, p. 34).While Price et al. acknowledge the fecundity of the submarine alkaline vent model at deep-sea ridge-flank environments such as the Lost City Hydrothermal Field (LCHF, mid-Atlantic), their islands, whether mafic or ultramafic, impose a sodium gradient to the natural proton gradient acting across precipitate membranes to aid the onset of metabolism (de Lorenzo, 2015). Price et al. model their favored environment on the Strytan Hydrothermal Field (SHF, Eyjafjord, Iceland) where maximum values of pH and temperature of the fluid feed reached 10.2 at 78 °C with a Na+ gradient of <3:468 mM. These values are produced through interactions of meteoric waters and basalt in a ridge-flank environment precipitating saponite towers in the shallow sea occupying Eyjafjord (Table 1; Price et al., 2017). They consider that these towers make ideal “incubators” for life’s birth and early evolution. The saponite is accompanied by rare calcite, and possibly stevensite and hisingerite (Table 1; Stanulla et al., 2017). In the case of the PHF, the Mg-hydroxide brucite appears to be the first precipitate, followed by a coating of Mg-carbonate, calcite, and aragonite (Table 1; Pisapia et al., 2017; cf. Okumura et al., 2016).However, the minerals in play in the Hadean/early Archean, both in the deep sea and around putative basaltic islands, while also mostly hydroxides and carbonates, would have been rather different (Table 1). The main chemical sediments at that time comprised the often cherty, banded iron formations. The ferrous iron feeding these was presumably supplied from ～400 °C vents, perhaps at concentrations approaching 80 mM (Kump and Seyfried, 2005; Halevy et al., 2017). In the absence of oxygen, the iron, along with silica, is likely to have remained supersaturated until meeting with alkaline waters, of whatever derivation (Tosca et al., 2016). Indeed, that alkaline springs may have played a part in some of these developments seems inescapable. The precipitates comprised the brucite-structured mixed-valence oxyhydroxide, green rust [～Fe2(OH)5] in place of the true brucite [Mg(OH)2] forming modern chimneys and mounds (Table 1; Arrhenius, 2003; Okumura et al., 2016; Halevy et al., 2017). And when combined with silica, greenalite would have been the Hadean/Archean phyllosilicate precipitated in place of the smectites comprising the mounds and chimneys in the Strytan field, although hisingerite appears to have been common to both the Strytan field and the banded iron formations (Table 1) (Badaut et al. 1985; Meunier et al., 2010; Tosca et al., 2016; Rasmussen et al., 2017; Stanulla et al., 2017; Price et al., 2017). Sulfides, e.g., minor mackinawite, are restricted to the Archean precipitates (Klein, 2005).It is notable in this context that variable-valence green rust, in particular, has been viewed as critical to the emergence of life (Meunier et la 2010). Arrhenius (2003) considered the mineral as exhibiting “primitive cellular metabolic function.” In this regard, it has been recently suggested that green rust and mackinawite, the objet trouvé at the ancient alkaline mounds, could have acted as the multitask protoenzymes, condensers, or nanoengines—the prebiological machinery—to enable the emergence of life (Russell and Nitschke, 2017; Mu?oz-Santiburcio and Marx, 2017). Russell and Nitschke (2017) described a model whereby nitrate in the Hadean Ocean is reduced to nitric oxide, ammonia, and aminogen in the hydrated interlayers of green rust, fed with electrons from hydrothermal hydrogen. The nitric oxide contributes to the hydroxylation of methane to a methyl group, which itself reacts with formate produced in the same milieu to generate acetate, the target molecule of the acetyl coenzyme-A pathway. Carboxylic acids can be aminated to amino acids in the green rust nano-galleries and, thence, in theory, condensed to peptides within water lamella in nanocrysts of mackinawite (Russell and Nitschke, 2017; Mu?oz-Santiburcio and Marx, 2017)—a step toward a ligand-accelerated autocatalytic metabolic pathway to a breakout denitrifying methanotrophic acetogenic metabolism (Russell and Nitschke, 2017; Mu?oz-Santiburcio and Marx, 2017).Of course, testing of ideas associating life’s onset with alkaline vents of various types is a job for the laboratory. However, notwithstanding Price et al.’s (2017) caveat that the modern mounds would not survive in the geological record, a search for the vestiges of alkaline vents in banded iron formations could be rewarding. If found, they would need to be distinguished from the few known ～400 °C vents that discharged the iron into the Archean ocean. What would the precipitates be at an alkaline vent in the Hadean? To my knowledge, there is little to go on in the literature, restricted to the remark made by Goodwin that “beds of extremely carbonaceous mudrock and ironstone beds…had been disrupted by rising volatiles” in the (late Archean) Helen SVOP-IF (shallow-volcanic-platform iron formation) (Kimberley, 1989). Nevertheless, could massive developments of magnetite containing some sulfides bordered by siderite be a giveaway for such exhalative sites? Indeed, are they waiting to be identified?ReferencesArrhenius, G.O., (2003), Crystals and life: Helvetica Chimica Acta , v. 86, p. 1569–1586Badaut, D., , Besson, G., , Decarreau, A., and , Rautureau, R., (1985), Occurrence of a ferrous trioctahedral smectite in recent sediments of Atlantis II Deep Red Sea: Clay Minerals , v. 20, p. 389–404Bernal, J.D., (1960), The problem of stages in biopoesis, in Florkin, M., ed., Aspects of the Origin of Life : New York, Pergamon Press, p. 30–45.Gilman, C.P., (1904), Human Work: Lanham, Maryland, AltaMira Press, 389 p.Halevy, I., , Alesker, M., , Schuster, E.M., , Popovitz-Biro, R., and , Feldman, Y., (2017), A key role for green rust in the Precambrian oceans and the genesis of iron formations: Nature Geoscience , v. 10, p. 135–139.Kimberley, M.M., (1989), Exhalative origins of iron formations: Ore Geology Reviews , v. 5, p. 13–145, Klein, C., (2005), Some Precambrian banded iron-formations (BIFs) from around the world: Their age, geologic setting, mineralogy, metamorphism, geochemistry, and origins: American Mineralogist , v. 90, p.1473–1499.Kump, L.R., and , Seyfried, W.E., (2005), Hydrothermal Fe fluxes during the Precambrian: Effect of low oceanic sulfate concentrations and low hydrostatic pressure on the composition of black smokers: Earth and Planetary Science Letters , v. 235, p. 654–662.de Lorenzo, V., (2015), It’s the metabolism, stupid!: Environmental Microbiology Reports , v. 7, p. 18–19.Meunier, A., , Petit, S., , Cockell, C.S., , El Albani, A., and , Beaufort, D., (2010), The Fe-rich clay microsystems in basalt-komatiite lavas: Importance of Fe-smectites for pre-biotic molecule catalysis during the Hadean Eon: Origins of Life and Evolution of the Biosphere , v. 40, p. 253–272.Mu?oz-Santiburcio, D., and , Marx, D., (2017), Chemistry in nanoconfined water: Chemical Science (Cambridge) , v. 8, p. 3444–3452.Okumura, T., , Ohara, Y., , Stern, R.J., , Yamanaka, T., , Onishi, Y., , Watanabe, H., , Chen, C., , Bloomer, S.H., , Pujana, I., , Sakai, S., and , Ishii, T., (2016), Brucite chimney formation and carbonate alteration at the Shinkai Seep Field, a serpentinite-hosted vent system in the southern Mariana forearc: Geochemistry Geophysics Geosystems , v. 17, p. 3775–3796.Pisapia, C., , Gérard, E., , Gérard, M., , Lecourt, L., , Lang, S.Q., , Pelletier, B., , Payri, C.E., , Monnin, C., , Guentas, L., , Postec, A., and , Quéméneur, M., (2017), Mineralizing filamentous bacteria from the Prony Bay Hydrothermal Field give new insights into the functioning of serpentinization-based subseafloor ecosystems: Frontiers in Microbiology , v. 8, , R., , Boyd, E.S., , Hoehler, T.M., , Wehrmann, L.M., , Bogason, E., , Valt?sson, H.?., , ?rlygsson, J., , Gautason, B., and , Amend, J.P., (2017), Alkaline vents and steep Na+ gradients from ridge-flank basalts—Implications for the origin and evolution of life: Geology , v. 45, , B., , Muhling, J.R., , Suvorova, A., and , Krape?, B., (2017), Greenalite precipitation linked to the deposition of banded iron formations downslope from a late Archean carbonate platform: Precambrian Research , v. 290, p. 49–62, , M.J., and , Nitschke, W., (2017), Methane: Fuel or exhaust at the emergence of life: Astrobiology , v. 17, , R., , Stanulla, C., , Bogason, E., , Pohl, T., and , Merkel, B., (2017), Structural, geochemical, and mineralogical investigation of active hydrothermal fluid discharges at Str?tan hydrothermal chimney, Akureyri Bay, Eyjafj?r?ur region, Iceland: Geothermal Energy , v. 5, p. 8–18.Stepney, S., (2012), Programming unconventional computers: Dynamics, development, self-reference: Entropy (Basel, Switzerland) , v. 14, p. 1939–1952Tosca, N.J., , Guggenheim, S., and , Pufahl, P.K., (2016), An authigenic origin for Precambrian greenalite: Implications for iron formation and the chemistry of ancient seawater: Geological Society of America Bulletin , v. 128, p. 511–530.Sabatino, N., Meyers, S.R., Voigt, S., Coccioni, R., Sprovieri, M., 2018. A new high-resolution carbon-isotope stratigraphy for the Campanian (Bottaccione section): Its implications for global correlation, ocean circulation, and astrochronology. Palaeogeography, Palaeoclimatology, Palaeoecology 489, 29-39. high-resolution carbon isotope record is presented for Campanian strata of the Bottaccione section (Umbria-Marche Basin), through an interval that constitutes the standard reference section for the geomagnetic polarity time scale. The identification of prominent δ13C excursions and high frequency variations allows the establishment of robust stratigraphic markers to link this new Tethyan δ13C record with the Boreal realm (L?gerdorf-Kronsmoor section, Northwest Germany and the Trunch borehole, Norfolk, UK). A decoupling of baseline δ13C values between the Boreal and the Tethyan realm is observed during the mid-Campanian, reflecting a plausible change in intermediate/deep-water mass exchange due to a more restricted Tethyan gateway; this is hypothesized to be a consequence of northward movements of Africa associated with opening of the South Atlantic Ocean. Statistical evaluation of a segment of the δ13C dataset with the TimeOpt method for astrochronologic testing provides strong evidence of astronomical forcing, and underscores the potential for development of a complete astronomically tuned Campanian Stage at Bottaccione, allowing astronomical calibration of key geomagnetic and paleobiologic datums.Saeedi Dehaghani, A.H., 2017. New insight into prediction of phase behavior of natural gas hydrate by different cubic equations of state coupled with various mixing rules. Petroleum Science 14, 780-790. in hydrate thermodynamic study necessitates robust and fast models to be incorporated in reservoir simulation softwares. However, numerous models presented in the literature makes selection of the best, proper predictive model a cumbersome task. It is of industrial interest to make use of cubic equations of state (EOS) for modeling hydrate equilibria. In this regard, this study focuses on evaluation of three common EOSs including Peng–Robinson, Soave–Redlich–Kwong and Valderrama–Patel–Teja coupled with van der Waals and Platteeuw theory to predict hydrate P–T equilibrium?of a real natural gas sample. Each EOS was accompanied with three mixing rules, including van der Waals?(vdW), Avlonitis non-density dependent (ANDD) and general non-quadratic?(GNQ). The prediction of cubic EOSs was in sufficient agreement with experimental data and with overall AARD% of less than unity. In addition, PR plus ANDD proved to be the most accurate model in this study for prediction of hydrate equilibria with AARD% of 0.166. It was observed?that the accuracy of cubic EOSs studied in this paper depends on mixing rule coupled with them, especially at high-pressure conditions. Lastly, the present study does not include any adjustable parameter to be correlated with hydrate phase equilibrium data.Sahoo, P.K., Guimar?es, J.T.F., Souza-Filho, P.W.M., da Silva, M.S., Nascimento, W., Powell, M.A., Reis, L.S., Pessenda, L.C.R., Rodrigues, T.M., da Silva, D.F., Costa, V.E., 2017. Geochemical characterization of the largest upland lake of the Brazilian Amazonia: Impact of provenance and processes. Journal of South American Earth Sciences 80, 541-558. Três Irm?s (LTI), the largest upland lake in the Brazilian Amazonia, located in Serra dos Carajás, was characterized using multi-elemental and isotope geochemistry (δ13C and δ15N) to understand the significance of organic and inorganic sources, weathering and sedimentary processes on the distribution of elements in lake bottom (surficial) sediments. Carbon and nitrogen isotopes from sedimentary organic matter suggest C3 terrestrial plants (forests > canga vegetation), macrophytes and freshwater DOC as the main sources. Sediments are depleted in most of the major oxides (except Fe2O3 and P2O5) when compared to upper continental crust (UCC) and their spatial distribution is highly influenced by catchment lithology. Principal Component Analysis revealed that most of the trace elements (Ba, Sr, Rb, Sc, Th, U, Zr, Hf, Nb, Y, V, Cr, Ga, Co, Ni) and REEs are closely correlated with Al and Ti (PC1; Group-1), so their redistribution is less influenced by post-depositional process. This is due to their relative immobility and being hosted by Al-bearing minerals during laterization. High Chemical Index of Alteration (CIA), Mafic Index of Alteration (MIA) and Index of Laterization (IOL) values indicate intense chemical weathering at source areas, but the weathering transformation was better quantified by IOL. A-CN-K plot along with elemental ratios (Al/K, Ti/K, Ti/Zr, La/Al, Cr/Th, Co/Th, La/Sm, La/Gd, Zr/Y, and Eu/Eu*) as well as chondrite-normalized REE patterns show that the detritic sediments are mainly sourced from ferruginous laterites and soils in the catchment, which may have characteristics similar to mafic rocks.Sailer, Z.R., Harms, M.J., 2017. Molecular ensembles make evolution unpredictable. Proceedings of the National Academy of Sciences 114, 11938-11943.; A long-standing goal in evolutionary biology is predicting evolution. Here, we show that the architecture of macromolecules fundamentally limits evolutionary predictability. Under physiological conditions, macromolecules, like proteins, flip between multiple structures, forming an ensemble of structures. A mutation affects all of these structures in slightly different ways, redistributing the relative probabilities of structures in the ensemble. As a result, mutations that follow the first mutation have a different effect than they would if introduced before. This implies that knowing the effects of every mutation in an ancestor would be insufficient to predict evolutionary trajectories past the first few steps, leading to profound unpredictability in evolution. We, therefore, conclude that detailed evolutionary predictions are not possible given the chemistry of macromolecules. Abstract: Evolutionary prediction is of deep practical and philosophical importance. Here we show, using a simple computational protein model, that protein evolution remains unpredictable, even if one knows the effects of all mutations in an ancestral protein background. We performed a virtual deep mutational scan—revealing the individual and pairwise epistatic effects of every mutation to our model protein—and then used this information to predict evolutionary trajectories. Our predictions were poor. This is a consequence of statistical thermodynamics. Proteins exist as ensembles of similar conformations. The effect of a mutation depends on the relative probabilities of conformations in the ensemble, which in turn, depend on the exact amino acid sequence of the protein. Accumulating substitutions alter the relative probabilities of conformations, thereby changing the effects of future mutations. This manifests itself as subtle but pervasive high-order epistasis. Uncertainty in the effect of each mutation accumulates and undermines prediction. Because conformational ensembles are an inevitable feature of proteins, this is likely universal. Sakai, S., Matsuda, S., Hikida, T., Shimono, A., McManus, J.B., Zahniser, M., Nelson, D., Dettman, D.L., Yang, D., Ohkouchi, N., 2017. High-precision simultaneous 18O/16O, 13C/12C, and 17O/16O analyses for microgram quantities of CaCO3 by tunable infrared laser absorption spectroscopy. Analytical Chemistry 89, 11846-11852. isotope ratios (18O/16O, 13C/12C, and 17O/16O) in carbonates have contributed greatly to the understanding of Earth and planetary systems, climates, and history. The current method for measuring isotopologues of CO2 derived from CaCO3 is primarily gas-source isotope ratio mass spectroscopy (IRMS). However, IRMS has drawbacks, such as mass overlap by multiple CO2 isotopologues and contaminants, the requirement of careful sample purification, and the use of major instrumentation needing permanent installation and a high power electrical supply. Here, we report simultaneous 18O/16O, 13C/12C, and 17O/16O analyses for microgram quantities of CaCO3 using a tunable mid-infrared laser absorption spectroscopy (TILDAS) system, which has no mass overlap problem and yields high sensitivity/precision measurements on small samples, as small as 0.02 μmol of CO2 (equivalent to 2 μg of CaCO3) with standard errors of less than 0.08 ‰ for 18O/16O and 13C/12C (±0.136 ‰ and ±0.387 ‰ repeatability; n = 10). In larger samples of CO2, 0.68 μmol (or 68 μg of CaCO3), standard error is less than 0.04 ‰ for 18O/16O and 13C/12C (< ±0.1 ‰ repeatability; n = 10) and 0.03 ‰ for 17O/16O (±0.069 ‰ repeatability; n = 10). We also show, for the first time, the relationship between 17O/16O ratios measured using the TILDAS system and published δ17O values of international standard materials (NBS-18 and -19) measured by IRMS. The benchtop TILDAS system, with cryogen-free sample preparation vacuum lines for microgram quantities of carbonates, is therefore a significant advance in carbonate stable isotope ratio geochemistry and is a new alternative to conventional IRMS.Sakthipriya, N., Doble, M., Sangwai, J.S., 2018. Kinetic and thermodynamic behavior of the biodegradation of waxy crude oil using Bacillus subtilis. Journal of Petroleum Science and Engineering 160, 412-421. present work investigates the reaction kinetics of biodegradation of waxy crude oil using Bacillus subtilis YB7, a thermophilic organism. Mathematical modeling of the reaction kinetics of microbial growth together with biosurfactant production and hydrocarbon substrate utilization have been attempted. Although various models, such as Monod's, Logistic, Tessier and Contois were investigated for substrate degradation and biomass production, and compared with the experimental studies, none of them could accurately predict the biosurfactant production in the presence of waxy crude oil. In this study, a new model, which is an extension of Monod's equation, has been developed to predict the observed values of biosurfactant production along with substrate degradation and biomass production in the presence of waxy crude oil satisfactorily. The proposed model has also been tested with various experimental studies carried out in the literature. The proposed model is observed to provide satisfactory model predictions when compared to other models available in literature. This shows that the proposed model can be used to study the reaction kinetics of all types of biodegradation studies to find the optimum parameters for maximum possible biodegradation of hydrocarbon substrates and production of biosurfactant. The positive values of activation energy observed in the study indicates that the process of biodegradation is an endothermic process. The negative values of entropy indicates that the reacting molecule underwent an internal rearrangement to give the activated complex, without a change in the number of molecules. It is believed that this study will be suitable for possible model development for biodegradation of hydrocarbons for oil recovery applications or bioremediation methods.Salvadó, J.A., Br?der, L., Andersson, A., Semiletov, I.P., Gustafsson, ?., 2017. Release of black carbon from thawing permafrost estimated by sequestration fluxes in the East Siberian Arctic Shelf recipient. Global Biogeochemical Cycles 31, 1501-1515. carbon (BC) plays an important role in carbon burial in marine sediments globally. Yet the sequestration of BC in the Arctic Ocean is poorly understood. Here we assess the concentrations, fluxes, and sources of soot BC (SBC)—the most refractory component of BC—in sediments from the East Siberian Arctic Shelf (ESAS), the World's largest shelf sea system. SBC concentrations in the contemporary shelf sediments range from 0.1 to 2.1 mg g?1 dw, corresponding to 2–12% of total organic carbon. The 210Pb-derived fluxes of SBC (0.42–11 g m?2 yr?1) are higher or in the same range as fluxes reported for marine surface sediments closer to anthropogenic emissions. The total burial flux of SBC in the ESAS (~4,000 Gg yr?1) illustrates the great importance of this Arctic shelf in marine sequestration of SBC. The radiocarbon signal of the SBC shows more depleted yet also more uniform signatures (?721 to ?896‰; average of ?774 ± 62‰) than of the non-SBC pool (?304 to ?728‰; average of ?491 ± 163‰), suggesting that SBC is coming from an, on average, 5,900 ± 300 years older and more specific source than the non-SBC pool. We estimate that the atmospheric BC input to the ESAS is negligible (~0.6% of the SBC burial flux). Statistical source apportionment modeling suggests that the ESAS sedimentary SBC is remobilized by thawing of two permafrost carbon (PF/C) systems: surface soil permafrost (topsoil/PF; 25 ± 8%) and Pleistocene ice complex deposits (ICD/PF; 75 ± 8%). The SBC contribution to the total mobilized permafrost carbon (PF/C) increases with increasing distance from the coast (from 5 to 14%), indicating that the SBC is more recalcitrant than other forms of translocated PF/C. These results elucidate for the first time the key role of permafrost thaw in the transport of SBC to the Arctic Ocean. With ongoing global warming, these findings have implications for the biogeochemical carbon cycle, increasing the size of this refractory carbon pool in the Arctic Ocean.Salvadó, J.A., Grimalt, J.O., López, J.F., Palanques, A., Heussner, S., Pasqual, C., Sanchez-Vidal, A., Canals, M., 2017. Transfer of lipid molecules and polycyclic aromatic hydrocarbons to open marine waters by dense water cascading events. Progress in Oceanography 159, 178-194. particles were collected by a set of moored sediment traps deployed during one year in the western Gulf of Lion along Cap de Creus and Lacaze-Duthiers submarine canyons and on the adjacent southern open slope. These traps collected particles during periods of pelagic settling and also during events of deep water flushing by dense shelf water cascading (DSWC). Analyses of lipid biomarkers (n-alkanes, n-alkan-1-ols, sterols and C37-C38 alkenones) and polycyclic aromatic hydrocarbons (PAHs) showed much higher transfer of terrestrial lipids and PAHs to open deep waters during DSWC than in the absence of cascading. The area of highest lateral fluxes was mostly located at 1000 m depth but also at 1500 m depth and extended along the canyons and to the adjacent slope. Higher fluxes were observed near the bottom (30 m above bottom; mab) than at intermediate waters (500 mab) which is consistent with the formation and sinking of dense water over the continental shelf, and its transport through the canyons towards the continental slope and deep basin. DSWC involved the highest settling fluxes of terrestrial lipids and PAHs ever described in marine continental slopes and the pelagic domain, as illustrated by peak values of C23-C33 odd carbon numbered alkanes (405 ng·m?2·d?1), C22-C32 even carbon numbered alkan-1-ols (850 ng·m?2·d?1), β-sitosterol+sitostanol (4800 ng·m?2·d?1) and PAHs (55 ?g·m?2·d?1). The algal lipids also showed higher transfer to deep waters during DSWC but to a lower extent than the terrigenous compounds. However, the C37-C38 alkenones constituted an exception and their settling fluxes were not influenced by DSWC. The lack of influence of the DSWC on the C37-C38 alkenone settling is consistent with absence of haptophyte algal inputs from the continental shelf and reinforces the reliability of these molecules for palaeothermometry and palaeoproductivity measurements in pelagic systems.Sandra, K., Steenbeke, M., Vandenheede, I., Vanhoenacker, G., Sandra, P., 2017. The versatility of heart-cutting and comprehensive two-dimensional liquid chromatography in monoclonal antibody clone selection. Journal of Chromatography A 1523, 283-292. recent years, two-dimensional liquid chromatography (2D-LC) has seen an enormous evolution and one of the fields where it is being widely adopted is in the analysis of therapeutic monoclonal antibodies (mAbs). We here further add to the many flavours of this powerful technology. Workflows based on heart-cutting (LC-LC) and comprehensive (LC × LC) 2D-LC are described that allow to guide the clone selection process in mAb and biosimilar development. Combining Protein A affinity chromatography in the first dimension with size exclusion (SEC), cation exchange (CEX) or reversed-phase liquid chromatography-mass spectrometry (RPLC–MS) in the second dimension simultaneously allows to assess mAb titer and critical structural aspects such as aggregation, fragmentation, charge heterogeneity, molecular weight (MW), amino acid sequence and glycosylation. Complementing the LC-LC measurements at intact protein level with LC × LC based peptide mapping provides the necessary information to make clear decisions on which clones to take further into development.Sano, Y., Kinoshita, N., Kagoshima, T., Takahata, N., Sakata, S., Toki, T., Kawagucci, S., Waseda, A., Lan, T., Wen, H., Chen, A.-T., Lee, H., Yang, T.F., Zheng, G., Tomonaga, Y., Roulleau, E., Pinti, D.L., 2017. Origin of methane-rich natural gas at the West Pacific convergent plate boundary. Scientific Reports 7, Article 15646. emission from the geosphere is generally characterized by a radiocarbon-free signature and might preserve information on the deep carbon cycle on Earth. Here we report a clear relationship between the origin of methane-rich natural gases and the geodynamic setting of the West Pacific convergent plate boundary. Natural gases in the frontal arc basin (South Kanto gas fields, Northeast Japan) show a typical microbial signature with light carbon isotopes, high CH4/C2H6 and CH4/3He ratios. In the Akita-Niigata region – which corresponds to the slope stretching from the volcanic-arc to the back-arc –a thermogenic signature characterize the gases, with prevalence of heavy carbon isotopes, low CH4/C2H6 and CH4/3He ratios. Natural gases from mud volcanoes in South Taiwan at the collision zone show heavy carbon isotopes, middle CH4/C2H6 ratios and low CH4/3He ratios. On the other hand, those from the Tokara Islands situated on the volcanic front of Southwest Japan show the heaviest carbon isotopes, middle CH4/C2H6 ratios and the lowest CH4/3He ratios. The observed geochemical signatures of natural gases are clearly explained by a mixing of microbial, thermogenic and abiotic methane. An increasing contribution of abiotic methane towards more tectonically active regions of the plate boundary is suggested.Santos, I.C., Martin, M.S., Reyes, M.L., Carlton, D.D., Stigler-Granados, P., Valerio, M.A., Whitworth, K.W., Hildenbrand, Z.L., Schug, K.A., 2018. Exploring the links between groundwater quality and bacterial communities near oil and gas extraction activities. Science of The Total Environment 618, 165-173. communities in groundwater are very important as they maintain a balanced biogeochemical environment. When subjected to stressful environments, for example, due to anthropogenic contamination, bacterial communities and their dynamics change. Studying the responses of the groundwater microbiome in the face of environmental changes can add to our growing knowledge of microbial ecology, which can be utilized for the development of novel bioremediation strategies. High-throughput and simpler techniques that allow the real-time study of different microbiomes and their dynamics are necessary, especially when examining larger data sets. Matrix-assisted laser desorption-ionization (MALDI) time-of-flight mass spectrometry (TOF-MS) is a workhorse for the high-throughput identification of bacteria. In this work, groundwater samples were collected from a rural area in southern Texas, where agricultural activities and unconventional oil and gas development are the most prevalent anthropogenic activities. Bacterial communities were assessed using MALDI-TOF MS, with bacterial diversity and abundance being analyzed with the contexts of numerous organic and inorganic groundwater constituents. Mainly denitrifying and heterotrophic bacteria from the Phylum Proteobacteria were isolated. These microorganisms are able to either transform nitrate into gaseous forms of nitrogen or degrade organic compounds such as hydrocarbons. Overall, the bacterial communities varied significantly with respect to the compositional differences that were observed from the collected groundwater samples. Collectively, these data provide a baseline measurement of bacterial diversity in groundwater located near anthropogenic surface and subsurface activities.Sanyal, S., Bhui, U.K., Kumar, S.S., Balaga, D., 2017. Designing injection water for enhancing oil recovery from kaolinite laden hydrocarbon reservoirs: A spectroscopic approach for understanding molecular level interaction during saline water flooding. Energy & Fuels 31, 11627-11639. experiments were performed to understand the mechanism(s) behind incremental oil recovery from hydrocarbon reservoirs during low saline water flooding (LSWF). It is believed that the roles of clay minerals present in the hydrocarbon reservoir rocks and the salt concentration in the injected water have a significant effect on the oil recovery during LSWF. Yet, the exact interaction mechanism(s) is still doubtful for designing injection fluids for enhancing oil recovery from subsurface reservoirs. For understanding the interaction between reservoir components explicitly, kaolinite and crude oil, and the interaction between reservoir components and injection saline water, three dead crude oil samples collected from different reservoirs of Cambay basin, India, and two kaolinite powder samples were used in this study. The kaolinites are different on the basis of their exchangeable cations, Fe3+ substitution in octahedral sites, and cation exchange capacity (CEC) values. The three crude oils show differences regarding asphaltene content and the abundance of polycyclic aromatic hydrocarbon in asphatenes. The interaction between reservoir components, particularly, kaolinite and crude oil, was demonstrated by keeping both the kaolinite and crude oil mixtures for two months. Detailed analysis of X-ray diffraction patterns, Fourier transform infrared (FTIR) spectra, and CEC values indicated that the polar oil components are adsorbed onto the interlayer surfaces of kaolinite, making it oil wet, and the interaction depends highly upon the composition of kaolinite and crude oil. The oil removal capacity of three brine concentrations of 500 (low saline), 3000 (intermediate saline), and 8000 ppm (high saline) of NaCl, CaCl2, and MgCl2 from oil adsorbed kaolinites was investigated using UV–visible and fluorescence spectroscopy techniques. The present study demonstrated that low saline water (500 ppm) rich in Na+ ion is more capable of desorbing the maximum amount of 4–6 ring size polycyclic aromatic hydrocarbon (PAH) components from kaolinite interlayer surfaces with respect to Ca2+ and Mg2+ ions. The composition of polar oil components, particularly, asphaltenes enriched with 4–6 ring PAH, greatly influences the recovery of oil from a mixed wet to oil wet kaolinite laden hydrocarbon reservoir during saline water flooding. Thus, apart from the concentration level of the saline water, the type of cation present in the saline water plays the major role during LSWF. The kaolinite composition, its crystallinity, and ring size of PAH in asphaltenes present inside a hydrocarbon reservoir also influence the enhanced oil recovery (EOR). These molecular level insights are valuable for designing effective injection fluids for enhancing oil recovery during LSWF in kaolinite laden hydrocarbon reservoirs.Satherley, J., Cooper, D.L., Schiffrin, D.J., 2018. Surface tension, density and composition in the methane-pentane system at high pressure. Fluid Phase Equilibria 456, 193-202. pressure system is described for measuring the pressure dependence of surface tension using digital image processing techniques on pendant drops in systems where the miscibility changes with both temperature and pressure. Measurements can be performed at pressures up to 40?MPa and temperatures up to 423?K. This high-pressure rig allows, additionally, the simultaneous measurement of both phase density and composition. The system is tested with the methane-pentane system at 313.15?K and pressures up to 15.6?MPa; the results compare well with literature data and with values calculated using the Peng-Robinson equation of state in conjunction with the gradient theory approach to computing surface tension, thus validating the experimental technique. Density profiles of the components through the interfacial layer have also been calculated using gradient theory. The Wegner extended scaling approach has been applied to all of the data sets to estimate the critical pressure for this system, which is found to be 16?MPa?at 313.15?K.Savareear, B., Brokl, M., Wright, C., Focant, J.-F., 2017. Thermal desorption comprehensive two-dimensional gas chromatography coupled to time of flight mass spectrometry for vapour phase mainstream tobacco smoke analysis. Journal of Chromatography A 1525, 126-137. thermal desorption comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry (TD-GC × GC-TOFMS) method has been developed for the analysis of mainstream tobacco smoke (MTS) vapour phase (VP). The selection process of the sample introduction approach involved comparing the results obtained from three different approaches: a) use of gas sampling bag followed by SPME (Tedlar?-SPME), b) gas sampling bag followed by TD (Tedlar?-TD), and c) sampling directly on TD sorbents (Direct-TD). Six different SPME fibers and six different TD sorbent beds were evaluated for the extraction capacities in terms of total number of peaks and related intensities or peak areas. The best results were obtained for the Direct-TD approach using Tenax TA/Carbograph1TD/Carboxen1003 sorbent tubes. The optimisation of TD tube desorption parameters was carried out using a face-centered central composite experimental design and resulted in the use of the Tenax TA/Carbograph 1TD/Carboxen 1003 sorbent with a 7.5 min desorption time, a 60 mL/min tube desorption flow, and a 250 °C tube desorption temperature. The optimised method was applied to the separation of MTS-VP constituents, with 665 analytes detected. The method precision ranged from 1% to 15% for over 99% of identified peak areas and from 0% to 3% and 0% to 1% for both first (1tR) and second (2tR) dimension retention times, respectively. The method was applied to the analyses of two cigarette types differing in their filter construction. Principal component analysis (PCA) allowed a clear differentiation of the studied cigarette types (PC1 describing 94% of the explained variance). Supervised Fisher ratio analysis permitted the identification of compounds responsible for the chemical differences between the two sample types. A set of 91 most relevant compounds was selected by applying a Fisher ratio cut-off approach and most of them were selectively removed by one of the cigarette filter types.Saxena, N., Hofmann, R., Alpak, F.O., Berg, S., Dietderich, J., Agarwal, U., Tandon, K., Hunter, S., Freeman, J., Wilson, O.B., 2017. References and benchmarks for pore-scale flow simulated using micro-CT images of porous media and digital rocks. Advances in Water Resources 109, 211-235. generate a novel reference dataset to quantify the impact of numerical solvers, boundary conditions, and simulation platforms. We consider a variety of microstructures ranging from idealized pipes to digital rocks. Pore throats of the digital rocks considered are large enough to be well resolved with state-of-the-art micro-computerized tomography technology. Permeability is computed using multiple numerical engines, 12 in total, including, Lattice-Boltzmann, computational fluid dynamics, voxel based, fast semi-analytical, and known empirical models. Thus, we provide a measure of uncertainty associated with flow computations of digital media. Moreover, the reference and standards dataset generated is the first of its kind and can be used to test and improve new fluid flow algorithms. We find that there is an overall good agreement between solvers for idealized cross-section shape pipes. As expected, the disagreement increases with increase in complexity of the pore space. Numerical solutions for pipes with sinusoidal variation of cross section show larger variability compared to pipes of constant cross-section shapes. We notice relatively larger variability in computed permeability of digital rocks with coefficient of variation (of up to 25%) in computed values between various solvers. Still, these differences are small given other subsurface uncertainties. The observed differences between solvers can be attributed to several causes including, differences in boundary conditions, numerical convergence criteria, and parameterization of fundamental physics equations. Solvers that perform additional meshing of irregular pore shapes require an additional step in practical workflows which involves skill and can introduce further uncertainty. Computation times for digital rocks vary from minutes to several days depending on the algorithm and available computational resources. We find that more stringent convergence criteria can improve solver accuracy but at the expense of longer computation time.Scherer, S., Wollrab, E., Codutti, L., Carlomagno, T., da Costa, S.G., Volkmer, A., Bronja, A., Schmitz, O.J., Ott, A., 2017. Chemical analysis of a “Miller-Type” complex prebiotic broth. Origins of Life and Evolution of Biospheres 47, 381-403. have analyzed the chemical variety obtained by Miller-Urey-type experiments using nuclear magnetic resonance (NMR) spectroscopy and coherent anti-Stokes Raman scattering (CARS) spectroscopy, gas chromatography followed by mass spectrometry (GC/MS) and two-dimensional gas chromatography followed by mass spectrometry (GCxGC/MS). In the course of a running Miller-Urey-type experiment, a hydrophobic organic layer emerged besides the hydrophilic aqueous phase and the gaseous phase that were initially present. The gas phase mainly consisted of aromatic compounds and molecules containing C≡C?or?C≡N triple bonds. The hydrophilic phase contained at least a few thousands of different molecules, primarily distributed in a range of 50 and 500 Da. The hydrophobic phase is characterized by carbon-rich, oil-like compounds and their amphiphilic derivatives containing oxygen with tensioactive properties. The presence of a wide range of oxidized molecules hints to the availability of oxygen radicals. We suggest that they intervene in the formation of alkylated polyethylene glycol (PEG) in the oil/water interface. CARS spectroscopy revealed distinct vibrational molecular signatures. In particular, characteristic spectral bands for cyanide compounds were observed if the broth was prepared with electric discharges in the gaseous phase. The characteristic spectral bands were absent if discharges were released onto the water surface. NMR spectroscopy on the same set of samples independently confirmed the observation. In addition, NMR spectroscopy revealed overall high chemical variability that suggests strong non-linearities due to interdependent, sequential reaction steps.Schlebusch, C.M., Malmstr?m, H., Günther, T., Sj?din, P., Coutinho, A., Edlund, H., Munters, A.R., Vicente, M., Steyn, M., Soodyall, H., Lombard, M., Jakobsson, M., 2017. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358, 652-655.: Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens. We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.Editor's Summary Ancient DNA pushes human emergence back. Anatomically modern humans evolved in Africa, but pinpointing when has been difficult. Schlebusch et al. sequenced three ancient African genomes from the Stone Age, about 2000 years old, and four from the Iron Age, 300 to 500 years old. One of the oldest samples, sequenced to 13× coverage, appears most closely to resemble individuals from the present-day San population. However, this individual seems to have lacked genetic contributions from other modern African populations, including pastoralists and farmers, which were observed in modern San individuals. Thus, the earliest divergence between human populations may have occurred 350,000 to 260,000 years ago.Schmatz, J., Klaver, J., Jiang, M., Urai, J.L., 2017. Nanoscale morphology of brine/oil/mineral contacts in connected pores of carbonate reservoirs: Insights on wettability from cryo-BIB-SEM. SPE Journal 22, 1374-1384. used broad-ion-beam slope cutting in combination with scanning electron microscopy undertaken under cryogenic conditions (Cryo-BIB-SEM) to study mineral/oil/brine contacts in reservoir carbonates. This direct-imaging method allows pore-scale investigation of in-situ fluids and their distributions down to the nanometer scale.In this study, we compare two types of carbonate reservoirs: a fine-grained Lixhe limestone (Belgium) and a coarse-grained limestone from the Maastricht area (The Netherlands). In both rock types, we first quantify the porosity with BIB-SEM and derive the spatially resolved pore connectivity of the rock from BIB-SEM on Wood’s Metal (WM) injected subsamples. In the second step, subsamples were saturated with the oil analog n-hexadecane, and then flooded with NaCl brine and MgSO4 brine, respectively, to study the effect of the brine chemistry on the microscopic fluid distribution. Cryo-BIB-SEM in combination with high-resolution energy-dispersive-spectroscopy (EDS) imaging and automated image analysis on the saturated samples allowed for a quantification of the oil-droplet size, the lengths of carbonate/oil interfaces, and the 2D contact angle of carbonate with brine and oil. Our results show that these features (e.g., interface length, contact angles, effect of asperities) are present on the scale of a few tens of nanometers to a few micrometers, which is in agreement with numerous theoretical and experimental studies. Lixhe limestone showed relatively less carbonate/oil contacts despite a larger oil fraction in the MgSO4-brine-flooded sample compared with the sample flooded with NaCl brine, indicating a more-hydrophilic nature of the carbonate surface in this experiment. This feasibility study showed that the technique permits the testing of predictions on the morphology and dynamics of contact lines in relation to the mineral properties, which is not possible with other imaging methods, such as X-ray microcomputed tomography (?-CT), because of limits in resolution.Schobben, M., van de Velde, S., Gliwa, J., Leda, L., Korn, D., Struck, U., Ullmann, C.V., Hairapetian, V., Ghaderi, A., Korte, C., Newton, R.J., Poulton, S.W., Wignall, P.B., 2017. Latest Permian carbonate carbon isotope variability traces heterogeneous organic carbon accumulation and authigenic carbonate formation. Climate of the Past 13, 1635-1659. carbon isotope ratios are a widely applied proxy for investigating the ancient biogeochemical carbon cycle. Temporal carbon isotope trends serve as a prime stratigraphic tool, with the inherent assumption that bulk micritic carbonate rock is a faithful geochemical recorder of the isotopic composition of seawater dissolved inorganic carbon. However, bulk-carbonate rock is also prone to incorporate diagenetic signals. The aim of the present study is to disentangle primary trends from diagenetic signals in carbon isotope records which traverse the Permian–Triassic boundary in the marine carbonate-bearing sequences of Iran and South China. By pooling newly produced and published carbon isotope data, we confirm that a global first-order trend towards depleted values exists. However, a large amount of scatter is superimposed on this geochemical record. In addition, we observe a temporal trend in the amplitude of this residual δ13C variability, which is reproducible for the two studied regions. We suggest that (sub-)sea-floor microbial communities and their control on calcite nucleation and ambient porewater dissolved inorganic carbon δ13C pose a viable mechanism to induce bulk-rock δ13C variability. Numerical model calculations highlight that early diagenetic carbonate rock stabilization and linked carbon isotope alteration can be controlled by organic matter supply and subsequent microbial remineralization. A major biotic decline among Late Permian bottom-dwelling organisms facilitated a spatial increase in heterogeneous organic carbon accumulation. Combined with low marine sulfate, this resulted in varying degrees of carbon isotope overprinting. A simulated time series suggests that a 50?% increase in the spatial scatter of organic carbon relative to the average, in addition to an imposed increase in the likelihood of sampling cements formed by microbial calcite nucleation to 1 out of 10 samples, is sufficient to induce the observed signal of carbon isotope variability. These findings put constraints on the application of Permian–Triassic carbon isotope chemostratigraphy based on whole-rock samples, which appears less refined than classical biozonation dating schemes. On the other hand, this signal of increased carbon isotope variability concurrent with the largest mass extinction of the Phanerozoic may provide information about local carbon cycling mediated by spatially heterogeneous (sub-)sea-floor microbial communities under suppressed bioturbation.Schreuder, L.T., Stuut, J.-B.W., Korte, L.F., Sinninghe Damsté, J.S., Schouten, S., 2018. Aeolian transport and deposition of plant wax n-alkanes across the tropical North Atlantic Ocean. Organic Geochemistry 115, 113-123. chain n-alkanes are terrestrial higher plant biomarkers analysed in marine sedimentary archives to reconstruct continental palaeoclimatic and palaeohydrological conditions. Latitudinal variation in their concentration and distribution in marine sediments relatively close to the continent has been widely studied, but little is known on the extent to which this continental signal extends to the ocean. Furthermore, no studies have examined the seasonal variation in the deposition of these biomarkers in marine sediments. Here we studied longitudinal variation in the composition of long chain n-alkanes and two other terrestrial higher plant biomarkers (long chain n-alkanols and long chain fatty acids) in atmospheric particles, as well as longitudinal and seasonal variation in long chain n-alkanes in sinking particles in the ocean at different water depths and in surface sediments, all collected along a 12°N transect across the tropical North Atlantic Ocean. The highest abundance of all three biomarker classes was closest to the African coast, as expected, because they are transported with Saharan dust and the largest part of the dust is deposited close to the source. At this proximal location, the seasonal variability in long chain n-alkane flux and the chain length distribution of the n-alkanes in sinking particles was most pronounced, due to seasonal change in the dust source or to change in vegetation composition in the source area, related to the position of the Intertropical Convergence Zone (ITCZ). In contrast, in the open ocean the seasonal variability in both the long chain n-alkane flux and chain length distribution of the n-alkanes was low. The abundance of the alkanes was also lower, as expected because of the larger source-to-sink distance. At the western part of the transect, close to South America, we found an additional source of the alkanes in the sinking particles during spring and autumn in the year 2013. The δ13C values of the alkanes in the surface sediment closest to the South American continent indicated that the isotope signal was likely derived from C3 vegetation from the Amazon, implying an input from the Amazon River, as there is no significant aeolian input from South America there since the prevailing wind direction is from the east. Finally, the concentration of the alkanes was similar in the material collected from the atmosphere, the particles collected while settling through the marine water column, and in the surface sediments, providing evidence that degradation of long chain n-alkanes from the atmosphere to settling at the sediment–water interface at deep open ocean sites is minimal.Schuhmann, K., Srzenti?, K., Nagornov, K.O., Thomas, H., Gutmann, T., Coskun, ?., Tsybin, Y.O., Shevchenko, A., 2017. Monitoring membrane lipidome turnover by metabolic 15N labeling and shotgun ultra-high-resolution Orbitrap Fourier transform mass spectrometry. Analytical Chemistry 89, 12857-12865. undergo permanent extensive remodeling, but how the turnover rate differs between lipid classes and molecular species is poorly understood. We employed metabolic 15N labeling and shotgun ultra-high-resolution mass spectrometry (sUHR) to quantify the absolute (molar) abundance and determine the turnover rate of glycerophospholipids and sphingolipids by direct analysis of total lipid extracts. sUHR performed on a commercial Orbitrap Elite instrument at the mass resolution of 1.35 × 106 (m/z 200) baseline resolved peaks of 13C isotopes of unlabeled and monoisotopic peaks of 15N labeled lipids (Δm = 0.0063 Da). Therefore, the rate of metabolic 15N labeling of individual lipid species could be determined without compromising the scope, accuracy, and dynamic range of full-lipidome quantitative shotgun profiling. As a proof of concept, we employed sUHR to determine the lipidome composition and fluxes of 62 nitrogen-containing membrane lipids in human hepatoma HepG2 cells.Schure, M.R., Davis, J.M., 2017. Orthogonality measurements for multidimensional chromatography in three and higher dimensional separations. Journal of Chromatography A 1523, 148-161. metrics (OMs) for three and higher dimensional separations are proposed as extensions of previously developed OMs, which were used to evaluate the zone utilization of two-dimensional (2D) separations. These OMs include correlation coefficients, dimensionality, information theory metrics and convex-hull metrics. In a number of these cases, lower dimensional subspace metrics exist and can be readily calculated. The metrics are used to interpret previously generated experimental data. The experimental datasets are derived from Gilar’s peptide data, now modified to be three dimensional (3D), and a comprehensive 3D chromatogram from Moore and Jorgenson.The Moore and Jorgenson chromatogram, which has 25 identifiable 3D volume elements or peaks, displayed good orthogonality values over all dimensions. However, OMs based on discretization of the 3D space changed substantially with changes in binning parameters. This example highlights the importance in higher dimensions of having an abundant number of retention times as data points, especially for methods that use discretization. The Gilar data, which in a previous study produced 21 2D datasets by the pairing of 7 one-dimensional separations, was reinterpreted to produce 35 3D datasets. These datasets show a number of interesting properties, one of which is that geometric and harmonic means of lower dimensional subspace (i.e., 2D) OMs correlate well with the higher dimensional (i.e., 3D) OMs. The space utilization of the Gilar 3D datasets was ranked using OMs, with the retention times of the datasets having the largest and smallest OMs presented as graphs. A discussion concerning the orthogonality of higher dimensional techniques is given with emphasis on molecular diversity in chromatographic separations.In the information theory work, an inconsistency is found in previous studies of orthogonality using the 2D metric often identified as %O. A new choice of metric is proposed, extended to higher dimensions, characterized by mixes of ordered and random retention times, and applied to the experimental datasets. In 2D, the new metric always equals or exceeds the original one. However, results from both the original and new methods are given.Sciarra, A., Cantucci, B., Coltorti, M., 2017. Learning from soil gas change and isotopic signatures during 2012 Emilia seismic sequence. Scientific Reports 7, Article 14187. surveys were performed in Medolla (Italy), a peculiar area characterized by spotty high soil temperature, gas vent, and lack of vegetation, to determine the migration mechanisms and spatial behavior of gas species. Hereby we present soil gas measurements and their isotopic ratios measured between 2008 and 2015, including the 2012 Emilia-Romagna seismic sequence. We found that soil gas concentrations markedly changed during the main shocks of May 20 and 29, 2012 (Mw 6.1 and 6.0, respectively), highlighting the presence of a buried fault intersecting the gas vents. We suggest that crustal dilation associated with seismic activity favored the uprising of geogas towards the surface. Changes in the isotopic signature highlight the contribution of two distinct sources, one deeper, thermogenic and another superficial related to organic-rich layer, whose relative contribution varied before, during and after the earthquake. We suppose an increase of microbial component likely due to the ground shaking of shallower layers linked to seismic sequence, which masks the thermogenic contribution. Although the changes we detect are specific for an alluvial plain, we deduce that analogous processes may be active elsewhere, and that soil gas geochemistry represents an useful tool to discriminate the gas migration related to seismic activity.Selbmann, L., Onofri, S., Coleine, C., Buzzini, P., Canini, F., Zucconi, L., 2017. Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities. Extremophiles 21, 1069-1080. wide sampling of rocks, colonized by microbial epi–endolithic communities, was performed along an altitudinal gradient from sea level to 3600?m asl and sea distance from the coast to 100?km inland along the Victoria Land Coast, Antarctica. Seventy-two rock samples of different typology, representative of the entire survey, were selected and studied using denaturing gradient gel electrophoresis to compare variation in fungal diversity according to environmental conditions along this altitudinal and sea distance transect. Lichenized fungi were largely predominant in all the samples studied and the biodiversity was heavily influenced even by minimal local variations. The n-MDS analysis showed that altitude and sea distance affect fungal biodiversity, while sandstone allows the communities to maintain high biodiversity indices. The Pareto-Lorenz curves indicate that all the communities analyzed are highly adapted to extreme conditions but scarcely resilient, so any external perturbation may have irreversible effects on these fragile ecosystems.Semenov, M.Y., Marinaite, I.I., Golobokova, L.P., Khuriganova, O.I., Khodzher, T.V., Semenov, Y.M., 2017. Source apportionment of polycyclic aromatic hydrocarbons in Lake Baikal water and adjacent air layer. Chemistry and Ecology 33, 977-990. composition of polycyclic aromatic hydrocarbons (PAHs) in Lake Baikal water and adjacent air layer and PAH emission composition profiles of possible sources were investigated. Analysis of emission composition data showed that the source profiles could not be grouped by fuel type or pyrogenic/petrogenic origin. Because of the similarity of source PAH profiles, the drawing of 3D mixing diagrams was the only way to check whether some of the potential PAH sources were the true sources. The mixing diagrams showed that the sources of air pollution were paper mills and wood burning and that the sources of water pollution were coal-fired and oil-fired boilers. The common source for both air and water was only oil and petroleum products. To determine the locations of PAH sources, their contributions to air and water pollution were calculated and mapped. Based on the results, air and water were polluted from both local and regional sources. The location of the zone influenced by a particular source was conditioned by physical properties of source emission, direction of air/water flows that transfer PAHs and temperature differences between mixing air/water flows.Shabani, B., Vilcáez, J., 2018. A fast and robust TOUGH2 module to simulate geological CO2 storage in saline aquifers. Computers & Geosciences 111, 58-66. new TOUGH2 module to simulate geological CO2 storage (GCS) in saline aquifers is developed based on the widely employed ECO2N module of TOUGH2. The newly developed TOUGH2 module uses a new non-iterative fugacity-activity thermodynamic model to obtain the partitioning of CO2 and H2O between the aqueous and gas phases. Simple but robust thermophysical correlations are used to obtain density, viscosity, and enthalpy of the gas phase. The implementation and accuracy of the employed thermophysical correlations are verified by comparisons against the national institute of standards and technology (NIST) online thermophysical database. To assess the computation accuracy and efficiency, simulation results obtained with the new TOUGH2 module for a one-dimensional non-isothermal radial and a three-dimensional isothermal system are compared against the simulation results obtained with the ECO2N module. Treating salt mass fraction in the aqueous phase as a constant, along with the inclusion of a non-iterative fugacity-activity thermodynamic model, and simple thermophysical correlations, resulted in simulations much faster than simulations with ECO2N module, without losing numerical accuracy. Both modules yield virtually identical results. Additional field-scale simulations of CO2 injection into an actual non-isothermal and heterogeneous geological formation confirmed that the new module is much faster than the ECO2N module in simulating complex field-scale conditions. Owing to its capability to handle CO2-CH4-H2S-N2 gas mixtures and its compatibility with TOUGHREACT, this new TOUGH2 module offers the possibility of developing a fast and robust TOUGHREACT module to predict the fate of CO2 in GCS sites under biotic conditions where CO2, CH4, H2S, and N2 gases can be formed.Shaffer, G., Fernández Villanueva, E., Rondanelli, R., Pedersen, J.O.P., Olsen, S.M., Huber, M., 2017. Implementation of methane cycling for deep-time global warming simulations with the DCESS Earth system model (version 1.2). Geoscientific Model Development 10, 4081-4103. records reveal a number of ancient, large and rapid negative excursions of the carbon-13 isotope. Such excursions can only be explained by massive injections of depleted carbon to the Earth system over a short duration. These injections may have forced strong global warming events, sometimes accompanied by mass extinctions such as the Triassic-Jurassic and end-Permian extinctions 201 and 252 million years ago, respectively. In many cases, evidence points to methane as the dominant form of injected carbon, whether as thermogenic methane formed by magma intrusions through overlying carbon-rich sediment or from warming-induced dissociation of methane hydrate, a solid compound of methane and water found in ocean sediments. As a consequence of the ubiquity and importance of methane in major Earth events, Earth system models for addressing such events should include a comprehensive treatment of methane cycling but such a treatment has often been lacking. Here we implement methane cycling in the Danish Center for Earth System Science (DCESS) model, a simplified but well-tested Earth system model of intermediate complexity. We use a generic methane input function that allows variation in input type, size, timescale and ocean–atmosphere partition. To be able to treat such massive inputs more correctly, we extend the model to deal with ocean suboxic/anoxic conditions and with radiative forcing and methane lifetimes appropriate for high atmospheric methane concentrations. With this new model version, we carried out an extensive set of simulations for methane inputs of various sizes, timescales and ocean–atmosphere partitions to probe model behavior. We find that larger methane inputs over shorter timescales with more methane dissolving in the ocean lead to ever-increasing ocean anoxia with consequences for ocean life and global carbon cycling. Greater methane input directly to the atmosphere leads to more warming and, for example, greater carbon dioxide release from land soils. Analysis of synthetic sediment cores from the simulations provides guidelines for the interpretation of real sediment cores spanning the warming events. With this improved DCESS model version and paleo-reconstructions, we are now better armed to gauge the amounts, types, timescales and locations of methane injections driving specific, observed deep-time, global warming events.Shahriman, M.S., Ramachandran, M.R., Zain, N.N.M., Mohamad, S., Manan, N.S.A., Yaman, S.M., 2018. Polyaniline-dicationic ionic liquid coated with magnetic nanoparticles composite for magnetic solid phase extraction of polycyclic aromatic hydrocarbons in environmental samples. Talanta 178, 211-221. this present study, magnetic nanoparticles (MNPs) nanocomposites modified with polyaniline (PANI) coated newly synthesised dicationic ionic liquid (DICAT) forming MNP-PANI-DICAT were successfully synthesised as new generation material for magnetic solid phase extraction (MSPE). MNP-PANI-DICAT was characterised by FT-IR NMR, CHN, BET, SEM, TEM, and VSM techniques and the results were compared with MNP-PANI and native MNP. This new material was applied as a magnetic adsorbent for the pre-concentration and separation of polycyclic aromatic hydrocarbons (PAHs) due to the π–π interaction between polyaniline shell and dicationic ionic liquid (DICAT) with PAHs compounds. Under the optimal conditions, the proposed method was evaluated and applied for the analysis of PAHs in environmental samples using gas chromatography-mass spectrometry (GC-MS). The validation method showed good linearity (0.005–500 ?g L?1) with the coefficient of determination (R2) > 0.999. The limits of detection (LOD) and quantification (LOQ) of the developed method (MNP-PANI-DICAT-MSPE) were in the range of 0.0008–0.2086 ?g L?1 and 0.0024–0.6320 ?g L?1, respectively. The enrichment factor (EF) of PAHs on MNP-PANI-DICAT-MSPE were in the range of 7.546–29.632. The extraction recoveries of natural water, sludge, and soil samples were ranged from 80.2% to 111.9% with relative standard deviation (RSD) less than 5.6%. The newly synthesised MNP-PANI-DICAT possess good sensitivity, reusability, and fast extraction of PAHs under the MSPE procedure in various environmental samples.Shan, C., Zhang, T., Liang, X., Zhang, Z., Zhu, H., Yang, W., Zhang, K., 2018. Influence of chemical properties on CH4 adsorption capacity of anthracite derived from southern Sichuan Basin, China. Marine and Petroleum Geology 89, 387-401. study aimed to determine the effects of high-rank coal chemical properties on CH4 adsorption capacity. A total of 24 core samples of anthracite from 11 coalbed methane wells in southern Sichuan Basin (China) were examined systemically using maceral analysis, proximate and ultimate analyses, total sulfur content test, and CH4 isotherm adsorption experiment. Results show that vitrinite group macerals are the most abundant maceral group, followed by inertinite and inorganic mineral matter of these coals. Vitrinite- and inertinite-rich coals have the similar average Langmuir volume under dry ash-free basis (VLdaf), and no positive or negative correlation was found between VLdaf and vitrinite and inertinite content. In addition, there is a weakly negative relationship between inorganic mineral matter and CH4 adsorption capacity. Effects of coal elements by ultimate analysis, such as C element and the atomic ratios of H/C, O/C and N/C, on CH4 adsorption capacity were studied. CH4 adsorption capacity has positive correlation with C element content, H/C atomic ratio and N/C atomic ratio, respectively, but negative with O/C atomic ratio. Effects of four proximate analysis parameters (moisture, ash, fixed carbon and volatile matter content) on CH4 adsorption capacity were also studied. Moisture, ash and volatile matter content negatively affect CH4 adsorption, respectively, and fixed carbon content has exactly the opposite effect. Principle component regression analyses for the set of elements and proximate analysis parameters show that C, O, ash and fixed carbon content are the important influence factors on CH4 adsorption capacity.Shan, J., Li, M., Allard, L.F., Lee, S., Flytzani-Stephanopoulos, M., 2017. Mild oxidation of methane to methanol or acetic acid on supported isolated rhodium catalysts. Nature 551, 605-608. efficient and direct method of catalytic conversion of methane to liquid methanol and other oxygenates would be of considerable practical value. However, it remains an unsolved problem in catalysis, as typically it involves expensive or corrosive oxidants or reaction media that are not amenable to commercialization. Although methane can be directly converted to methanol using molecular oxygen under mild conditions in the gas phase, the process is either stoichiometric (and therefore requires a water extraction step) or is too slow and low-yielding to be practical. Methane could, in principle, also be transformed through direct oxidative carbonylation to acetic acid, which is commercially obtained through methane steam reforming, methanol synthesis, and subsequent methanol carbonylation on homogeneous catalysts. However, an effective catalyst for the direct carbonylation of methane to acetic acid, which might enable the economical small-scale utilization of natural gas that is currently flared or stranded, has not yet been reported. Here we show that mononuclear rhodium species, anchored on a zeolite or titanium dioxide support suspended in aqueous solution, catalyse the direct conversion of methane to methanol and acetic acid, using oxygen and carbon monoxide under mild conditions. We find that the two products form through independent pathways, which allows us to tune the conversion: three-hour-long batch-reactor tests conducted at 150 degrees Celsius, using either the zeolite-supported or the titanium-dioxide-supported catalyst, yield around 22,000 micromoles of acetic acid per gram of catalyst, or around 230 micromoles of methanol per gram of catalyst, respectively, with selectivities of 60–100 per cent. We anticipate that these unusually high activities, despite still being too low for commercial application, may guide the development of optimized catalysts and practical processes for the direct conversion of methane to methanol, acetic acid and other useful chemicals.Shang, H., Yue, Y., Zhang, J., Wang, J., Shi, Q., Zhang, W., Liu, L., Omar, S., 2018. Effect of microwave irradiation on the viscosity of crude oil: A view at the molecular level. Fuel Processing Technology 170, 44-52. increase in global energy demand and decrease in easily extractable light crude oil has generated a growing interest in heavy oil exploitation. However, the high viscosity of heavy oil leads to exploitation, transportation and refining challenges. In this context, microwave irradiation of crude oil samples from Sudan, China (Liaohe) and Venezuela were carried out to investigate the mechanisms of viscosity reduction. Saturate, aromatic, resin, and asphaltene (SARA) analysis of the crude oils was conducted according to the American Society Test and Materials standard, ASTM D4124-09. The SARA fractionation results demonstrated that microwave irradiation may affect the structure of resin/asphaltene micelles, thus leading to a change in the viscosity of the crude oil. The crude oils were further examined using the combined analytical techniques of electrospray ionization and Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). The results from ESI FT-ICR MS analysis demonstrated that microwave irradiation of crude oil with a high proportion of O2 compounds leads to polymerization, and ultimately an increase in the viscosity of the crude oil after microwave treatment. In other cases, cracking might occur due to the microwave Sharma, A., Gaidamakova, E.K., Grichenko, O., Matrosova, V.Y., Hoeke, V., Klimenkova, P., Conze, I.H., Volpe, R.P., Tkavc, R., Gostin?ar, C., Gunde-Cimerman, N., DiRuggiero, J., Shuryak, I., Ozarowski, A., Hoffman, B.M., Daly, M.J., 2017. Across the tree of life, radiation resistance is governed by antioxidant Mn2+, gauged by paramagnetic resonance. Proceedings of the National Academy of Sciences 114, E9253-E9260.: Decades of functional genomic efforts have failed to predict the ability of cells to survive ionizing radiation (IR). Evidence is mounting that small high-symmetry antioxidant complexes of manganous ions with metabolites (H-Mn2+) are responsible for cellular IR resistance, and that H-Mn2+ protects the proteome, not the genome, from IR-induced reactive oxygen species. We show that the amount of H-Mn2+ in nonirradiated living cells is readily gauged by electron paramagnetic resonance (EPR) spectroscopy and highly diagnostic of their DNA repair efficiency and survival after gamma-radiation exposure. This spectroscopic measure of cellular H-Mn2+ content is the strongest known biological indicator of cellular IR resistance between and within organisms across the three domains of the tree of life, with potential applications including optimization of radiotherapy. Abstract: Despite concerted functional genomic efforts to understand the complex phenotype of ionizing radiation (IR) resistance, a genome sequence cannot predict whether a cell is IR-resistant or not. Instead, we report that absorption-display electron paramagnetic resonance (EPR) spectroscopy of nonirradiated cells is highly diagnostic of IR survival and repair efficiency of DNA double-strand breaks (DSBs) caused by exposure to gamma radiation across archaea, bacteria, and eukaryotes, including fungi and human cells. IR-resistant cells, which are efficient at DSB repair, contain a high cellular content of manganous ions (Mn2+) in high-symmetry (H) antioxidant complexes with small metabolites (e.g., orthophosphate, peptides), which exhibit narrow EPR signals (small zero-field splitting). In contrast, Mn2+ ions in IR-sensitive cells, which are inefficient at DSB repair, exist largely as low-symmetry (L) complexes with substantially broadened spectra seen with enzymes and strongly chelating ligands. The fraction of cellular Mn2+ present as H-complexes (H-Mn2+), as measured by EPR of live, nonirradiated Mn-replete cells, is now the strongest known gauge of biological IR resistance between and within organisms representing all three domains of life: Antioxidant H-Mn2+ complexes, not antioxidant enzymes (e.g., Mn superoxide dismutase), govern IR survival. As the pool of intracellular metabolites needed to form H-Mn2+ complexes depends on the nutritional status of the cell, we conclude that IR resistance is predominantly a metabolic phenomenon. In a cross-kingdom analysis, the vast differences in taxonomic classification, genome size, and radioresistance between cell types studied here support that IR resistance is not controlled by the repertoire of DNA repair and antioxidant enzymes. Shen, B., Xiao, S., Zhou, C., Dong, L.I.N., Chang, J., Chen, Z.H.E., 2017. A new modular palaeopascichnid fossil Curviacus ediacaranus new genus and species from the Ediacaran Dengying Formation in the Yangtze Gorges area of South China. Geological Magazine 154, 1257-1268. Ediacaran macrofossils are rare in carbonate facies, but they offer valuable information about their three-dimensional internal anatomy and can broaden our view about their taphonomy and palaeoecology. In this study, we report a new Ediacaran fossil, Curviacus ediacaranus new genus and species, from bituminous limestone of the Shibantan Member of the Dengying Formation in the Yangtze Gorges area of South China. Curviacus is reconstructed as a benthic modular organism consisting of serially arranged and crescent-shaped chambers. The chambers are confined by chamber walls that are replicated by calcispars, and are filled by micritic sediments. Such modular body construction is broadly similar to the co-occurring Yangtziramulus zhangii and other Ediacaran modular fossils, such as Palaeopascichnus. The preservation style of Curviacus is similar to Yangtziramulus, although the phylogenetic affinities of both genera remain unresolved. The new fossil adds to the diversity of Ediacaran modular organisms.Shettima, B., Abubakar, M.B., Kuku, A., Haruna, A.I., 2018. Facies analysis, depositional environments and paleoclimate of the Cretaceous Bima Formation in the Gongola Sub – Basin, Northern Benue Trough, NE Nigeria. Journal of African Earth Sciences 137, 193-207. analysis of the Cretaceous Bima Formation in the Gongola Sub –basin of the Northern Benue Trough northeastern Nigeria indicated that the Lower Bima Member is composed of alluvial fan and braided river facies associations. The alluvial fan depositional environment dominantly consists of debris flow facies that commonly occur as matrix supported conglomerate. This facies is locally associated with grain supported conglomerate and mudstone facies, representing sieve channel and mud flow deposits respectively, and these deposits may account for the proximal alluvial fan region of the Lower Bima Member. The distal fan facies were represented by gravel-bed braided river system of probably Scot – type model. This grade into sandy braided river systems with well developed floodplains facies, forming probably at the lowermost portion of the alluvial fan depositional gradient, where it inter-fingers with basinal facies. In the Middle Bima Member, the facies architecture is dominantly suggestive of deep perennial sand-bed braided river system with thickly developed amalgamated trough crossbedded sandstone facies fining to mudstone. Couplets of shallow channels are also locally common, attesting to the varying topography of the basin. The Upper Bima Member is characterized by shallow perennial sand-bed braided river system composed of successive succession of planar and trough crossbedded sandstone facies associations, and shallower channels of the flashy ephemeral sheetflood sand – bed river systems defined by interbedded succession of small scale trough crossbedded sandstone facies and parallel laminated sandstone facies. The overall stacking pattern of the facies succession of the Bima Formation in the Gongola Sub – basin is generally thinning and fining upwards cycles, indicating scarp retreat and deposition in a relatively passive margin setting. Dominance of kaolinite in the clay mineral fraction of the Bima Formation points to predominance of humid sub – tropical to tropical climatic conditions. This favors pedogenic activities which are manifested in the several occurrences of paleosols. Pronounced periods of arid climatic conditions are also notable from the subordinate smectite mineralization. Chlorite mineralization at some localities is indicative of elevation of the provenance area, and this is synonymous with deposition of the Bima Formation, because of its syn – depositional tectonics. The absences of lacustrine shales in the syn – rift stratigraphic architecture of the Bima Formation indicates that the lower Cretaceous petroleum system that are common in the West and Central African Rift basins are generally barren in the Gongola Sub – basin of the Northern Benue Trough.Shi, L., Cheng, X., Liu, Q., Liu, Z., 2018. Reaction of volatiles from a coal and various organic compounds during co-pyrolysis in a TG-MS system. Part 1. Reaction of volatiles in the void space between particles. Fuel 213, 37-47. of a coal and low-grade organic matter has been reported to produce tars of higher yield and better quality, but few study explored the detailed reaction of volatiles. This work studies co-pyrolysis of pairs of solid organic compounds and a low rank bituminous coal in a thermal gravimetric analysis coupled online with a mass spectrometer (TG-MS) using specially designed TG crucibles, with or without a vertical baffle to separate the solid matter. The different pyrolysis results, mass loss, mass loss rates and gaseous products yields, from the two crucibles are compared and analyzed, and attributed to the difference in volatiles’ reaction in the void space between the solid particles. The different volatile release behaviors are correlated with the structure of the solid matter, including the presence of aliphatic and aromatic structure and hetero atoms.Shi, L., Cheng, X., Liu, Q., Liu, Z., 2018. Reaction of volatiles from a coal and various organic compounds during co-pyrolysis in a TG-MS system. Part 2. Reaction of volatiles in the free gas phase in crucibles. Fuel 213, 22-36. low rank bituminous coal and four solid organic compounds were co-pyrolyzed in pairs in a thermal gravimetric analysis coupled online with a mass spectrometer (TG-MS) using specially designed TG crucibles which separate the solid matter from each other while allow their volatiles to mix in the free gas space of different volume (or height) above the sample bed. The TG and DTG curves of co-pyrolysis of each pair of the matter are compared with those obtained from pyrolysis of the individual matter in the same crucible and with that calculated from TG and DTG curves of the individual matter by superposition. The gaseous products, including light paraffinic and aromatic compounds in the co-pyrolysis are also studied. It is found that the volatiles’ reaction in all the cases studied decreases volatiles’ yield, and the extent of decrease gets large with increasing free gas space height and is affected by the molecular structure of the organic matter. The nature of the volatiles’ reaction is discussed with respect to adsorption, cracking, condensation and induction.Shi, S., Zhao, H., 2017. Metabolic engineering of oleaginous yeasts for production of fuels and chemicals. Frontiers in Microbiology 8, 2185. doi: 10.3389/fmicb.2017.02185. yeasts have been increasingly explored for production of chemicals and fuels via metabolic engineering. Particularly, there is a growing interest in using oleaginous yeasts for the synthesis of lipid-related products due to their high lipogenesis capability, robustness, and ability to utilize a variety of substrates. Most of the metabolic engineering studies in oleaginous yeasts focused on Yarrowia that already has plenty of genetic engineering tools. However, recent advances in systems biology and synthetic biology have provided new strategies and tools to engineer those oleaginous yeasts that have naturally high lipid accumulation but lack genetic tools, such as Rhodosporidium, Trichosporon, and Lipomyces. This review highlights recent accomplishments in metabolic engineering of oleaginous yeasts and recent advances in the development of genetic engineering tools in oleaginous yeasts within the last 3 years.Shi, Y., Jia, Y., Pan, W., Huang, L., Yan, J., Zheng, R., 2017. Potential evaluation on CO2-EGR in tight and low-permeability reservoirs. Natural Gas Industry B 4, 311-318., i.e. enhanced gas recovery by injecting CO2, is to displace natural gas by injecting CO2 in the supercritical phase. It can both enhance the recovery of gas reservoirs and realize CO2 storage. Currently, this technique is still at its exploring stage. The effect of CO2-EGR is not clarified, the geologic conditions for CO2-EGR are not definite, and the rational working system for CO2-EGR is not available. In this paper, the long-core experiment was conducted to determine whether and how much the recovery of low-permeability reservoirs can be enhanced by injecting CO2. According to the experimental results, the recovery can be enhanced by 12% when CO2 content in produced gas is more than 10%. Moreover, the multi-component seepage mathematical model was built for displacing natural gas by injecting supercritical CO2, and the model accuracy was verified using laboratory data. With this mathematical model, the influence factors for displacing natural gas by injecting supercritical CO2 were analyzed in order to define the conditions for selecting favorable zones. The Well DK13 area in the Daniudi gas field, Ordos Basin, was selected for potential evaluation of CO2-EGR. As indicated by the numerical simulation results, when CO2 content of producing wells in the Well DK13 area is 10% (with a lower cost for corrosion prevention), the ratio of CO2-EGR is 8.0–9.5%, and 31.1% HCPV(hydrocarbon pores volume) of CO2 storage can be realized. It is thus concluded that the CO2-EGR technique can enhance the recovery of gas reservoirs and also store CO2 underground, contributing to the increase of both social and economic benefits.Shibata, M., Nishimasu, H., Kodera, N., Hirano, S., Ando, T., Uchihashi, T., Nureki, O., 2017. Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy. Nature Communications 8, Article 1430. CRISPR-associated endonuclease Cas9 binds to a guide RNA and cleaves double-stranded DNA with a sequence complementary to the RNA guide. The Cas9–RNA system has been harnessed for numerous applications, such as genome editing. Here we use high-speed atomic force microscopy (HS-AFM) to visualize the real-space and real-time dynamics of CRISPR-Cas9 in action. HS-AFM movies indicate that, whereas apo-Cas9 adopts unexpected flexible conformations, Cas9–RNA forms a stable bilobed structure and interrogates target sites on the DNA by three-dimensional diffusion. These movies also provide real-time visualization of the Cas9-mediated DNA cleavage process. Notably, the Cas9 HNH nuclease domain fluctuates upon DNA binding, and subsequently adopts an active conformation, where the HNH active site is docked at the cleavage site in the target DNA. Collectively, our HS-AFM data extend our understanding of the action mechanism of CRISPR-Cas9.Shilla, D., Routh, J., 2017. Using biochemical and isotopic tracers to characterise organic matter sources and their incorporation into estuarine food webs (Rufiji delta, Tanzania). Chemistry and Ecology 33, 893-917. acid biomarkers and stable isotope signatures were used to identify the sources of particulate and sedimentary organic matter and its input into the food web through the dominant consumer within the mangrove-dominated Rufiji estuary, Tanzania. Specific fatty acids were used to identify the preferred basal sources of dominant fauna (i.e. filter feeder bivalves, snails, crabs, shrimps, and three fish species), and their presence in the water and sediment samples in the estuary. Both fatty acid and stable isotope results revealed that food web in the Rufiji estuary depended on a variety of carbon sources (mangroves, allochthonous terrestrial inputs, macroalgae, and phytoplankton), contributing to a different degree into the diets of primary consumers and members of near-shore fish, but none of them were obligatory for the survival of these species. The δ15N values of major primary producers and consumers/predators revealed a trend for δ15N enrichment with increasing trophic level. The ratio of docosahexaenoic acid to eicosapentaenoic acid (DHA:EPA) decreased from pelagic to benthic feeding fish. This indicated that fish with different feeding modes derived their fatty acids from different primary sources of nutrition, and suggested that the DHA:EPA ratio may be a useful indicator of feeding mode.Shuai, Y., Etiope, G., Zhang, S., Douglas, P.M.J., Huang, L., Eiler, J.M., 2018. Methane clumped isotopes in the Songliao Basin (China): New insights into abiotic vs. biotic hydrocarbon formation. Earth and Planetary Science Letters 482, 213-221. hydrocarbon gas, typically generated in serpentinized ultramafic rocks and crystalline shields, has important implications for the deep biosphere, petroleum systems, the carbon cycle and astrobiology. Distinguishing abiotic gas (produced by chemical reactions like Sabatier synthesis) from biotic gas (produced from degradation of organic matter or microbial activity) is sometimes challenging because their isotopic and molecular composition may overlap. Abiotic gas has been recognized in numerous locations on the Earth, although there are no confirmed instances where it is the dominant source of commercially valuable quantities in reservoir rocks. The deep hydrocarbon reservoirs of the Xujiaweizi Depression in the Songliao Basin (China) have been considered to host significant amounts of abiotic methane. Here we report methane clumped-isotope values (Δ18Δ18) and the isotopic composition of C1–C3 alkanes, CO2 and helium of five gas samples collected from those Xujiaweizi deep reservoirs. Some geochemical features of these samples resemble previously suggested identifiers of abiotic gas (13C-enriched CH4; decrease in 13C/12C ratio with increasing carbon number for the C1–C4 alkanes; abundant, apparently non-biogenic CO2; and mantle-derived helium). However, combining these constraints with new measurements of the clumped-isotope composition of methane and careful consideration of the geological context, suggests that the Xujiaweizi depression gas is dominantly, if not exclusively, thermogenic and derived from over-mature source rocks, i.e., from catagenesis of buried organic matter at high temperatures. Methane formation temperatures suggested by clumped-isotopes (167–213?°C) are lower than magmatic gas generation processes and consistent with the maturity of local source rocks. Also, there are no geological conditions (e.g., serpentinized ultramafic rocks) that may lead to high production of H2 and thus abiotic production of CH4 via CO2 reduction. We propose that the Songliao gas is representative of an atypical type of thermogenic gas that can be mistaken for abiotic gas. Such gases may be encountered more frequently in future exploration of deep or over-mature petroleum systems.Si, X., Hu, L., Xu, W., Li, H., Li, C., 2017. A dual-source miniature mass spectrometer with improved sensitivity. International Journal of Mass Spectrometry 423, 15-19., we have reported the development of a miniature mass spectrometer with a continuous atmospheric pressure interface, whose sensitivity was sacrificed due to the limited gas flow rate. In this study, a circular lens was designed and integrated on the ion transfer pathway between the two pumping stages, and a ten-fold sensitivity improvement could be achieved when coupling with external ionization sources. Besides the capability of working with ionization sources in the atmosphere, there is also an in-vacuum plasma ionization source, so that both volatile and non-volatile samples could be analyzed. A 10 ppbv detection sensitivity was achieved for dimethyl methyl phosphonate (DMMP) in air using the plasma ionization source. Furthermore, the miniature mass spectrometer was also demonstrated for the direct analyses of progesterone in drinking water and atrazine in soil samples using paper spray and syringe spray, respectively.Sikes, E.L., Allen, K.A., Lund, D.C., 2017. Enhanced δ13C and δ18O differences between the South Atlantic and South Pacific during the last glaciation: the deep gateway hypothesis. Paleoceanography 32, 1000-1017. vertical gradients in benthic foraminiferal δ13C and δ18O in the Atlantic and Pacific during the last glaciation have revealed that ocean overturning circulation was characterized by shoaling of North Atlantic sourced interior waters; nonetheless, our understanding of the specific mechanisms driving these glacial isotope patterns remains incomplete. Here we compare high-resolution depth transects of Cibicidoides spp. δ13C and δ18O from the Southwest Pacific and the Southwest Atlantic to examine relative changes in northern and southern sourced deep waters during the Last Glacial Maximum (LGM) and deglaciation. During the LGM, our transects show that water mass properties and boundaries in the South Atlantic and Pacific were different from one another. The Atlantic between ~1.0 and 2.5 km was more than 1‰ enriched in δ13C relative to the Pacific and remained more enriched through the deglaciation. During the LGM, Atlantic δ18O was ~0.5‰ more enriched than the Pacific, particularly below 2.5 km. This compositional difference between the deep portions of the basins implies independent deep water sources during the glaciation. We attribute these changes to a “deep gateway” effect whereby northern sourced waters shallower than the Drake Passage sill were unable to flow southward into the Southern Ocean because a net meridional geostrophic transport cannot be supported in the absence of a net east-west circumpolar pressure gradient above the sill depth. We surmise that through the LGM and early deglaciation, shoaled northern sourced waters were unable to escape the Atlantic and contribute to deep water formation in the Southern Ocean.Sikora, M., Seguin-Orlando, A., Sousa, V.C., Albrechtsen, A., Korneliussen, T., Ko, A., Rasmussen, S., Dupanloup, I., Nigst, P.R., Bosch, M.D., Renaud, G., Allentoft, M.E., Margaryan, A., Vasilyev, S.V., Veselovskaya, E.V., Borutskaya, S.B., Deviese, T., Comeskey, D., Higham, T., Manica, A., Foley, R., Meltzer, D.J., Nielsen, R., Excoffier, L., Mirazon Lahr, M., Orlando, L., Willerslev, E., 2017. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358, 659-662.: Present-day hunter-gatherers (HGs) live in multilevel social groups essential to sustain a population structure characterized by limited levels of within-band relatedness and inbreeding. When these wider social networks evolved among HGs is unknown. To investigate whether the contemporary HG strategy was already present in the Upper Paleolithic, we used complete genome sequences from Sunghir, a site dated to ~34,000 years before the present, containing multiple anatomically modern human individuals. We show that individuals at Sunghir derive from a population of small effective size, with limited kinship and levels of inbreeding similar to HG populations. Our findings suggest that Upper Paleolithic social organization was similar to that of living HGs, with limited relatedness within residential groups embedded in a larger mating network.Editor's summary: How early human groups were organized. Sequencing ancient hominid remains has provided insights into the relatedness between individuals. However, it is not clear whether ancient humans bred among close relatives, as is common in some modern human cultures. Sikora et al. report genome sequences from four early humans buried close together in western Russia about 34,000 years ago (see the Perspective by Bergstrom and Tyler-Smith). The individuals clustered together genetically and came from a population with a small effective size, but they were not very closely related. Thus, these people may represent a single social group that was part of a larger mating network, similar to contemporary hunter-gatherers. The lack of close inbreeding might help to explain the survival advantage of anatomically modern humans.Slagter, H.A., Reader, H.E., Rijkenberg, M.J.A., Rutgers van der Loeff, M., de Baar, H.J.W., Gerringa, L.J.A., 2017. Organic Fe speciation in the Eurasian Basins of the Arctic Ocean and its relation to terrestrial DOM. Marine Chemistry 197, 11-25. bio-essential trace metal iron (Fe) has poor inorganic solubility in seawater, and therefore dissolution is dependent on organic complexation. The Arctic Ocean is subject to strong terrestrial influences which contribute to organic solubility of Fe, particularly in the surface. These influences are subject to rapid changes in the catchments of the main contributing rivers. Here we report concentrations and binding strengths of Fe-binding organic ligands in relation to spectral properties of Dissolved Organic Matter (DOM) and concentrations of humic substances. Full-depth profiles of Fe and Fe-binding organic ligands were measured for 11 stations, good agreement to previous studies was found with ligand concentrations between 0.9 and 2.2 equivalent nM of Fe (Eq. nM Fe) at depths > 200 m. We found nutrient-like profiles of Fe in the Atlantic-influenced Nansen basin, surface enrichment in the surface over the Amundsen and Makarov basins and scavenging effects in the deep Makarov basin. A highly detailed surface transect consisting of two sections crossing the surface flow from the Siberian continental shelf to the Fram Strait, the TransPolar Drift (TPD), clearly indicates the flow path of the riverine contribution to Fe and Fe-binding organic ligands with concentrations of 0.7 to 4.4 nM and 1.6 to 4.1 Eq. nM Fe, respectively. This is on average 4.5 times higher in DFe and 1.7 times higher in Fe-binding organic ligands than outside the TPD flow path. Conditional binding strengths of ligands in the entire dataset were remarkably similar at 11.45 ≤ LogK′ ≤ 12.63. Increased organic Fe-binding organic ligand concentrations were evident in the Arctic Ocean surface. To better identify the organic substances responsible for Fe complexation in the Arctic Ocean, diverse analytical approaches and a standard other than Suwannee River Fulvic Acid are recommended.Smidt, E., Tintner, J., Klemm, S., Scholz, U., 2017. FT-IR spectral and thermal characterization of ancient charcoals - A tool to support archeological and historical data interpretation. Quaternary International 457, 43-49., historical, and prehistoric charcoals were characterized using FT-IR spectroscopy and simultaneous thermal analysis to support interpretation of historical and archeological data. Chemical characteristics of aging play a dominant role in terms of the assignment of ancient charcoals. Different periods were differentiated according to the progressing aging process that becomes visible in the spectrum by the asymmetric and symmetric COO, the CH and the CO-stretch vibrations that can be assigned to carboxylates, the methyl- and the carboxyl-group. The increase of these components is paralleled by an increase of hydrophilic properties and therefore confirmed by the OH stretch vibration with a maximum at about 3400 cm?1. Charcoal from combustion residues was distinguished from charcoals produced for energy supply by means of infrared spectral features, classification and PLS-discriminant analysis. Apart from the spectral signature, the thermal behavior of combustion residues unambiguously reveals wood characteristics due to incomplete pyrolysis. Thermal profiles of combustion residues indicate mass losses at several temperatures according to the remaining wood components and a higher mass loss between 80 °C and 120 °C due to water evaporation.Snyder, D.T., Pulliam, C.J., Cooks, R.G., 2017. Extending the mass range of a miniature ion trap mass spectrometer using the inverse Mathieu q scan. International Journal of Mass Spectrometry 422, 154-161. mass/charge range of a mass spectrometer operated in either the boundary or resonance ejection mode is usually limited by the highest radiofrequency (rf) voltage that can be attained, although lowering the resonance ejection Mathieu q value (qeject) can increase this range at the expense of resolution and unintended boundary ejection can result in spectral complexity. High voltage requirements are particularly troublesome for miniature instruments, which have tight electronic constraints and closely-spaced electrodes prone to discharging. Here we demonstrate an alternative approach to mass range extension based on a method of scanning the resonance ejection frequency nonlinearly in the form of an inverse Mathieu q scan. The results show an increase in mass range of up to 3.5 times on both a benchtop LTQ linear ion trap and the Mini 12 miniature linear ion trap mass spectrometer without instrumental modifications, and unit resolution is observed on the benchtop instrument by controlling the scan rate and minimizing space charge effects.Soh, Y., Rangriz-Shokri, A., Babadagli, T., 2018. Optimization of methane use in cyclic solvent injection for heavy-oil recovery after primary production through experimental and numerical studies. Fuel 214, 457-470. cold heavy oil production with sands (CHOPS) is an economically attractive method, ultimate recovery does not exceed 15%. Cyclic solvent injection (CSI) has been under consideration as a follow-up EOR application in the industry. This method targets extracting large amounts of remaining oil in the matrix by solvent diffusion, taking advantage of its high contact area with wormholes. Methane and propane are two potential solvents to be used in this practice. Methane is preferred due to its availability and stronger foaming characteristics, while propane has lower foaming but better mixing capability.A far-reaching -core to field scale- study was conducted in this paper to test out the potential of pure methane and its mixture with propane as well as CO2 as prospective CSI solvents. After the petro-physical properties of the sand-pack (1.5?m-length and 5?cm-diameter) were measured, live oil (saturated with methane and methane-propane mixture at different ratios) production was carried out with certain pressure decline rates: ?0.51?psi/min from 500 to 190?psi and ?0.23?psi/min from 190 to 70?psi. Pressure data with time was monitored through eight equally spaced transducers. The solution GOR from the live oil saturated with methane vs. pressure was matched using the Peng-Robinson EOS (Peng and Robinson, 1976) method. The data points starting injection period (representing equilibrium condition) were fitted to develop K values using the Crookston equation. These matched data were carried to a field scale model to analyze the CSI performance for methane. In field scale modeling, 15-well data from a CHOPS field in Alberta, Canada were history matched and 6-cycle CSI performances were followed as post-CHOPS with different well patterns (central, peripheral, all-wells).As a result of these experiments, methane showed about 14% oil recovery but with additional CO2 huff ‘n’ puff, around 15% recovery was added, totaling 29% recovery. Methane-propane mixture resulted in a lower oil recovery of about 5% due to decreased foamy effect. Valid core-scale simulation was completed by tuning K-values and considering non-equilibrium or equilibrium impact depending on solvent type, showing mostly less than 5% error. In field scale modeling, central and peripheral well patterns yielded oil recoveries consistent with the experiments while all-well huff ‘n’ puff- type pattern showed a slightly higher value.Based on the outcome of the methane and methane-propane mixture experiments, it was of more importance to further study the way to enhance the foaminess in methane-live oil recovery. Different pressure depletion rates, namely ?0.23, ?0.51, and ?1.53?psi/min, were applied and more oil was produced with increasing depletion rates. These experimental results were simulated at the core scale and the change of reaction coefficients was considered with varying decline rates. In field-scale modelling, sensitivity analyses were done with a variety of scenarios by changing injection/soaking period and pressure decline rates. The ratio of injection to soaking period was observed to be more critical than the injection period itself in terms of production efficiency. Also, the influence of pressure depletion rate as a new constraint in the simulation work was studied.Sohn, S.Y., Kuntze, K., Nijenhuis, I., H?ggblom, M.M., 2018. Evaluation of carbon isotope fractionation during anaerobic reductive dehalogenation of chlorinated and brominated benzenes. Chemosphere 193, 785-792. specific stable isotope analysis (CSIA) has been established as a useful tool to evaluate in situ biodegradation. Here, CSIA was used to determine microbial dehalogenation of chloro- and bromobenzenes in microcosms derived from Hackensack River sediments. Gas chromatography-isotope ratio mass spectrometry (GC-IRMS) was used to measure carbon isotope fractionation during reductive dehalogenation of hexachlorobenzene (HCB), pentachlorobenzene (PeCB), 1,2,3,5-tetrachlorobenzene (TeCB), 1,2,3,5-tetrabromobenzene (TeBB), and 1,3,5-tribromobenzene (TriBB). Strong evidence of isotope fractionation coupled to dehalogenation was not observed in the substrate, possibly due to the low solubilities of the highly halogenated benzene substrates and a dilution of the isotope signal. Nonetheless, we could measure a depletion of the δ13C value in the dichlorobenzene product during dechlorination of HCB, the sequential depletion and enrichment of δ13C value for trichlorobenzene in TeCB dechlorinating cultures, and the enrichment of δ13C during debromination of TriBB. This indicates that a measurable isotope fractionation occurred during reductive dehalogenation of highly halogenated chloro- and bromobenzenes in aquatic sediments. Thus, although more quantitative measurements will be needed, the data suggests that CSIA may have application for monitoring in situ microbial reductive dehalogenation of highly halogenated benzenes.Somppi, S., T?rnqvist, H., Topál, J., Koskela, A., H?nninen, L., Krause, C.M., Vainio, O., 2017. Nasal oxytocin treatment biases dogs’ visual attention and emotional response toward positive human facial expressions. Frontiers in Psychology 8, 1854. doi: 10.3389/fpsyg.2017.01854. neuropeptide oxytocin plays a critical role in social behavior and emotion regulation in mammals. The aim of this study was to explore how nasal oxytocin administration affects gazing behavior during emotional perception in domestic dogs. Looking patterns of dogs, as a measure of voluntary attention, were recorded during the viewing of human facial expression photographs. The pupil diameters of dogs were also measured as a physiological index of emotional arousal. In a placebo-controlled within-subjects experimental design, 43 dogs, after having received either oxytocin or placebo (saline) nasal spray treatment, were presented with pictures of unfamiliar male human faces displaying either a happy or an angry expression. We found that, depending on the facial expression, the dogs’ gaze patterns were affected selectively by oxytocin treatment. After receiving oxytocin, dogs fixated less often on the eye regions of angry faces and revisited (glanced back at) more often the eye regions of smiling (happy) faces than after the placebo treatment. Furthermore, following the oxytocin treatment dogs fixated and revisited the eyes of happy faces significantly more often than the eyes of angry faces. The analysis of dogs’ pupil diameters during viewing of human facial expressions indicated that oxytocin may also have a modulatory effect on dogs’ emotional arousal. While subjects’ pupil sizes were significantly larger when viewing angry faces than happy faces in the control (placebo treatment) condition, oxytocin treatment not only eliminated this effect but caused an opposite pupil response. Overall, these findings suggest that nasal oxytocin administration selectively changes the allocation of attention and emotional arousal in domestic dogs. Oxytocin has the potential to decrease vigilance toward threatening social stimuli and increase the salience of positive social stimuli thus making eye gaze of friendly human faces more salient for dogs. Our study provides further support for the role of the oxytocinergic system in the social perception abilities of domestic dogs. We propose that oxytocin modulates fundamental emotional processing in dogs through a mechanism that may facilitate communication between humans and dogs.Song, W., Yao, J., Li, Y., Yang, Y., Sun, H., 2017. New pore size distribution calculation model based on chord length and digital image. Journal of Natural Gas Science and Engineering 48, 111-118. this study, we propose a model to calculate pore size distribution based on the chord length and digital image. First, the chord length cumulative frequency function of the unit circle is deduced. Next, a dimensionless chord length cumulative frequency function of the arbitrary size circle is derived. The chord length data are generated by cutting a combination of the specific step size of the pore size in varying proportions. Conversely, the value of the chord length is also obtained from the segmented CT image data by direct calculation. Using the dimensionless chord length cumulative frequency function, we formulate the balance equation, which indicates that the chord length distribution generated by cutting a combination of the specific step size of the pore size in varying proportions is the same as the chord length distribution that is obtained from direct calculation in the segmented CT image data. By solving the balance equation, the pore size distribution is obtained. Our model calculation results are compared with the max ball model calculation results. Furthermore, the pore size distribution of the shale sample is calculated based on our model. The results indicate that pore radii mostly less than 50?nm and small pores are dominant in shale.Song, W., Yao, J., Ma, J., Li, A., Li, Y., Sun, H., Zhang, L., 2018. Grand canonical Monte Carlo simulations of pore structure influence on methane adsorption in micro-porous carbons with applications to coal and shale systems. Fuel 215, 196-203. and shale are strong heterogeneous anisotropic media involving nanoscale pore size and variance of microstructure. The complexity of methane adsorption is expressed both in diverse chemical properties and confined pore structures. In this study, Grand canonical Monte Carlo simulations were carried out to assess the influence of pore structure on methane adsorption at temperature 318?K, 333?K and pressure up to 20?MPa. The pore radii of physical carbon-based model range from 0.55?nm to 1.15?nm at the step of 0.1?nm. Simulated results indicate that the excess adsorption isotherms and maximum excess adsorption density are notably different for different pore structures. The triangle pore exhibits largest value of maximum excess adsorption density followed by the slit pore, circle pore and square pore. The maximum excess adsorption density is larger than 6?×?103?mol/m3 at simulated temperatures for triangle pore with pore radius less than 1?nm. The excess adsorption amount first increases with the increase of pressure and then decreases when the pressure is larger than 7.5?MPa for slit pore and 5?MPa for the circle pore, triangle pore and square pore. The excess adsorption amount for circle pore and square pore drops down to negative value when the pressure is larger than 12.5?MPa while the excess adsorption amount stays above zero across simulated pressure for the slit pore and triangle pore. The adsorption isotherms of micro-porous carbons were obtained by superposition of simulated adsorption isotherms based on the pore size distribution and were compared with coal samples experimental data gathered from the same temperature. The experimental isotherm is more close to slit pore excess isotherm and predicted excess isotherms based on circle pore and square pore under-estimate excess adsorption capacity.Soriano, M.L., Zougagh, M., Valcárcel, M., Ríos, ?., 2018. Analytical nanoscience and nanotechnology: Where we are and where we are heading. Talanta 177, 104-121. main aim of this paper is to offer an objective and critical overview of the situation and trends in Analytical Nanoscience and Nanotechnology (AN&N), which is an important break point in the evolution of Analytical Chemistry in the XXI century as they were computers and instruments in the second half of XX century. The first part of this overview is devoted to provide a general approach to AN&N by describing the state of the art of this recent topic, being the importance of it also emphasized. Secondly, particular but very relevant trends in this topic are outlined: the analysis of the nanoworld, the so “third way” in AN&N, the growing importance of bioanalysis, the evaluation of both nanosensors and nanosorbents, the impact of AN&N in bioimaging and in nanotoxicological studies, as well as the crucial importance of reliability of the nanotechnological processes and results for solving real analytical problems in the frame of Social Responsibility (SR) of science and technology. Several reflections are included at the end of this overview written as a bird's eye view, which is not an easy task for experts in AN&N.Sreemany, A., Bera, M.K., Sarkar, A., 2017. Rapid and high-resolution stable isotopic measurement of biogenic accretionary carbonate using an online CO2 laser ablation system: Standardization of the analytical protocol. Rapid Communications in Mass Spectrometry 31, 2109-2117.: The elaborate sampling and analytical protocol associated with conventional dual-inlet isotope ratio mass spectrometry has long hindered high-resolution climate studies from biogenic accretionary carbonates. Laser-based on-line systems, in comparison, produce rapid data, but suffer from unresolvable matrix effects. It is, therefore, necessary to resolve these matrix effects to take advantage of the automated laser-based method.Methods: Two marine bivalve shells (one aragonite and one calcite) and one fish otolith (aragonite) were first analysed using a CO2 laser ablation system attached to a continuous flow isotope ratio mass spectrometer under different experimental conditions (different laser power, sample untreated vs vacuum roasted). The shells and the otolith were then micro-drilled and the isotopic compositions of the powders were measured in a dual-inlet isotope ratio mass spectrometer following the conventional acid digestion method.Results: The vacuum-roasted samples (both aragonite and calcite) produced mean isotopic ratios (with a reproducibility of ±0.2 ‰ for both δ18O and δ13C values) almost identical to the values obtained using the conventional acid digestion method. As the isotopic ratio of the acid digested samples fall within the analytical precision (±0.2 ‰) of the laser ablation system, this suggests the usefulness of the method for studying the biogenic accretionary carbonate matrix.Conclusions: When using laser-based continuous flow isotope ratio mass spectrometry for the high-resolution isotopic measurements of biogenic carbonates, the employment of a vacuum-roasting step will reduce the matrix effect. This method will be of immense help to geologists and sclerochronologists in exploring short-term changes in climatic parameters (e.g. seasonality) in geological times.Steiner, Z., Lazar, B., Torfstein, A., Erez, J., 2017. Testing the utility of geochemical proxies for paleoproductivity in oxic sedimentary marine settings of the Gulf of Aqaba, Red Sea. Chemical Geology 473, 40-49. the early stages of sediment diagenesis most of the organic matter reoxidizes, leaving behind a residual fraction of organic carbon which does not typically reflect its original quantities. Paleo-productivity reconstructions are therefore based on changes in the chemical composition of carbonate shells or, alternatively, use the abundances of inorganic elements in the bulk sediments, that have been shown to be proxies for organic matter contents. To examine the applicability of bulk inorganic elements composition for this task, we compare recorded changes in known anthropogenic nutrient fluxes to the oligotrophic and oxygenated Gulf of Aqaba in the north Red Sea, with the sedimentary records of barium, cadmium, copper and nickel over the last decades. Among these elements, nickel and copper strongly correlate with recorded nutrient fluxes and primary productivity in the region. In the present case, nickel is a more reliable proxy since part of the copper is possibly contributed from air-borne pollution sources. The applicability of cadmium to serve as a tracer for nutrient additions could not be reliably tested because contribution of cadmium associated with phosphate ore loading in the adjacent ports may be significant. We do not observe any bulk sediment barium enrichments associated with increased nutrient fluxes. Overall, it appears from these correlations that nickel and probably also copper reliably record past changes in nutrient availability and organic matter fluxes while sedimentary barium and barite, which are commonly attributed to productivity, do not.Stephen, J.L., Periyasamy, B., 2018. Innovative developments in biofuels production from organic waste materials: A review. Fuel 214, 623-633. organic wastes into energy conversion technologies were successful in addressing global challenges such as fossil fuel dependency, production cost optimization, waste management and emission control issues. The utilization of organic wastes for biofuels production is considered as a plausible approach for achieving better energy security, pollution control, process economics, sustainable production, and societal improvements. This work intends to comprehensively review all available technologies for producing biofuels from organic wastes. Besides, it presents a synoptic analysis of the status, prospects and challenges pertinent to each technology. Globally, liquid biofuels are gaining prominence because of their potential to reduce the consumption of fossil fuels in transportation and industrial sectors with comparable performance efficiencies. This review work demonstrates the superiority of biodiesel over other liquid biofuels through a comparative assessment of relevant factors. Some of the main constraints for commercial deployment of biodiesel production using organic wastes include higher production costs, higher energy consumption, longer reaction residence times, and unsystematic feedstock accumulation procedures. The process intensification methods implemented by various researchers to circumvent these biodiesel production challenges are also presented. Moreover, this article recommends a novel concept for intensification of biodiesel production from waste cooking oil using coalescer reactor along with a preliminary scrutiny for justifying further research potential of the approach.Stigall, A.L., 2017. Ordovician oxygen and biodiversity. Nature Geoscience 10, 887-888. oxygen levels may have facilitated the Great Ordovician Biodiversification Event according to a reconstruction of atmospheric oxygen concentrations.The Great Ordovician Biodiversification Event encapsulates the greatest increase in marine family- and genus-level diversity in Earth’s history1. A series of physical and biotic factors have been proposed as causes or drivers of the biodiversification, including meteorite bombardment1, global cooling2, changes in ocean circulation3, increased plankton abundance and predation pressures4. Writing in Nature Geoscience, Edwards et al.5 report the most compelling data yet that atmospheric oxygenation concentrations increased significantly throughout the Ordovician period and argue that increased oxygen availability facilitated diversification.Beginning around 475 million years ago, the Palaeozoic Evolutionary Fauna — which includes brachiopods; bryozoan, rugose and tabulate corals; crinoids and nautloid cephalopods — rapidly diversified. Over the course of 25 million years, the Palaeozoic Evolutionary Fauna grew to contain nearly 1,000 genera (Fig.). Smaller increases occurred within the Cambrian and Modern Evolutionary Faunas, which are characterized by trilobites and archaic molluscs and bivalves, echinoids and bony fishes, respectively. By the Late Ordovician, the total number of genera numbered over 1,800. At the same time, marine ecosystems diversified in terms of functionality, with taxa expanding into niches such as epifaunal suspension-feeding and deep burrowing6. The causes of this diversification remain unclear, partly due to limited data. Increasing oxygen levels have been invoked previously, but the low resolution of these data meant it was difficult to assess the relative timing of oxygen and faunal changes7.Edwards et al.5 instead use a novel and clever approach that capitalizes on the link between photosynthetic fractionation of stable carbon isotopes in marine algae and atmospheric oxygen. Specifically, during photosynthesis, the isotopic fractionation of carbon fixed via the RuBisCo enzyme varies as a function of CO2 and O2 concentrations within the cell. The fractionation factor can be calculated by comparing the carbon isotope ratio (δ13C) of carbonate to the δ13C of bulk organic matter.Edwards et al. assembled 945 paired δ13C values from multiple basins and environmental settings including eastern and mid-continental North America, Anticosti Island (Canada), the Great Basin (western United States) and the Argentine Precordillera, ensuring the global significance of their curve. By combining the resulting fractionation values with known CO2 concentrations from the GEOCARB model7, they were able to calculate O2 concentrations at extremely high temporal resolution and produce a highly detailed O2 curve for the Great Ordovician Biodiversification Event.The reconstruction shows that atmospheric oxygen levels were relatively stable at about 12% during the Early Ordovician. Oxygen concentrations then nearly doubled to about 25%, showing a dramatic linear increase over an interval of only 12 million years during the Middle to Late Ordovician. Notably, this rapid oxygenation increase is coincident with the interval of maximum diversification (Fig.).Links between oxygenation and diversification have been established for other periods. In the case of the Ordovician, the portions of the biota that underwent the greatest radiation were highly skeletonized animals with relatively high metabolic rates, and thus high needs for oxygen. A combination of global cooling and increased oxygen availability would have lowered the metabolic costs for skeletal carbonate biomineralization, and could have established an initiating condition that could promote diversification of these clades.Indeed, both increased skeletal production8 and body size of biomineralized taxa are documented from the diversification interval. Furthermore, an increase in active predation — a metabolically costly behaviour — by cephalopods and fish is also recorded from this interval. Recent analyses have noted that diversification, body size and predation increases are synchronous across palaeocontinents, despite differences in the clades involved9. The synchronicity is consistent with biodiversification facilitated by global environmental changes such as oxygenation.There is, as is typical of such studies, a question of correlation and causation. For instance, it is not immediately clear how increased oxygen would have facilitated the actual splitting of genetic lineages required for speciation and overall diversification. Specifically, speciation requires individuals to undergo reproductive isolation, which is not a process that could clearly be attributed to increased oxygenation alone10.Nevertheless, the correlation between oxygenation and biodiversification identified by Edwards et al. suggests that increasing oxygen levels played a role in the Great Ordovician Biodiversification Event. This significant contribution to the current state of knowledge about the Ordovician Earth system will spur considerable discussion and future research.References1. Harper, D. A. T., Zhan, R.-B. & Jin, J. Palaeoworld 24, 75–85 (2015).2. Trotter, J. A., Williams, I. S., Barnes, C. R., Lécuyer, C. & Nicoll, R. S. Science 321, 550–554 (2008).3. Rasmussen, C. M. ?. et al. Sci. Rep. 6, 18884 (2016).4. Servais, T. et al. Palaeogeogr. Palaeoclimatol. Palaeoecol. 458, 12–28 (2016).5. Edwards, C., Saltzman, M., Royer, D. & Fike, D. Nat. Geosci. (2017).6. Servais, T., Owen, A. W., Harper, D. A. T., Kr?ger, B. & Munnecke, A. Palaeogeogr. Palaeoclimatol. Palaeoecol. 294, 99–119 (2010).7. Berner, R. A. Geochim. Cosmochim. Acta 70, 5653–5664 (2006).8. Pruss, S. B., Finnegan, S., Fischer, W. W. & Knoll, A. H. Palaios 25, 73–84 (2010).9. Trubovitz, S. & Stigall, A. L. Geology 44, 743–746 (2016).10. Stigall, A. L. Lethaia (2017).Stivrins, N., Soininen, J., T?nno, I., Freiberg, R., Veski, S., Kisand, V., 2018. Towards understanding the abundance of non-pollen palynomorphs: A comparison of fossil algae, algal pigments and sedaDNA from temperate lake sediments. Review of Palaeobotany and Palynology 249, 9-15. the increased interest in non-pollen palynomorphs (microscopic objects other than pollen identified from pollen slides) in palaeoecological studies, it is necessary to seek a deeper understanding of the reliability of these results. We combined quantitative information of algal pigments and sedimentary ancient DNA (sedaDNA) of phylotaxonomical resolution to validate the richness and abundance of fossil algae in the sediment of a small temperate lake. For the first time, fossil and sedaDNA algae data were combined in a composite data-set and used to reconstruct algae turnover rates over the last 14,500 years. This comparison serves as both an example of how fossil algae can be used to answer various research questions and as a method of revealing to what extent we can rely on palaeoecological interpretations based solely on the fossil algae record from pollen slides.Stoll, D.R., Sajulga, R.W., Voigt, B.N., Larson, E.J., Jeong, L.N., Rutan, S.C., 2017. Simulation of elution profiles in liquid chromatography ? II: Investigation of injection volume overload under gradient elution conditions applied to second dimension separations in two-dimensional liquid chromatography. Journal of Chromatography A 1523, 162-172. important research direction in the continued development of two-dimensional liquid chromatography (2D-LC) is to improve the detection sensitivity of the method. This is especially important in applications where injection of large volumes of effluent from the first dimension (1D) column into the second dimension (2D) column leads to severe 2D peak broadening and peak shape distortion. For example, this is common when coupling two reversed-phase columns and the organic solvent content of the 1D mobile phase overwhelms the 2D column with each injection of 1D effluent, leading to low resolution in the second dimension. In a previous study we validated a simulation approach based on the Craig distribution model and adapted from the work of Czok and Guiochon [1] that enabled accurate simulation of simple isocratic and gradient separations with very small injection volumes, and isocratic separations with mismatched injection and mobile phase solvents [2]. In the present study we have extended this simulation approach to simulate separations relevant to 2D-LC. Specifically, we have focused on simulating 2D separations where gradient elution conditions are used, there is mismatch between the sample solvent and the starting point in the gradient elution program, injection volumes approach or even exceed the dead volume of the 2D column, and the extent of sample loop filling is varied. To validate this simulation we have compared results from simulations and experiments for 101 different conditions, including variation in injection volume (0.4–80 μL), loop filling level (25–100%), and degree of mismatch between sample organic solvent and the starting point in the gradient elution program (?20 to + 20% ACN). We find that that the simulation is accurate enough (median errors in retention time and peak width of ?1.0 and ?4.9%, without corrections for extra-column dispersion) to be useful in guiding optimization of 2D-LC separations. However, this requires that real injection profiles obtained from 2D-LC interface valves are used to simulate the introduction of samples into the 2D column. These profiles are highly asymmetric ? simulation using simple rectangular pulses leads to peak widths that are far too narrow under many conditions. We believe the simulation approach developed here will be useful for addressing practical questions in the development of 2D-LC methods.Stüeken, E.E., Buick, R., 2018. Environmental control on microbial diversification and methane production in the Mesoarchean. Precambrian Research 304, 64-72. lines of evidence have revealed a thriving marine biosphere capable of diverse metabolic strategies back to at least 3.5?billion years ago (Ga). However, little is known about microbial ecosystems in lakes and rivers during the Mesoarchean and their role in the evolution of life on Earth. Here we report new carbon and nitrogen isotopic data from the fluvio-lacustrine Lalla Rookh Sandstone in Western Australia (～3.0?Ga) – one of the oldest known non-marine sedimentary deposits. Organic δ13C values (?30‰ to ?38‰) are best interpreted as recording carbon fixation by methanogens using the acetyl CoA pathway mixed with organisms using the Calvin cycle, while δ15N data (0‰ to ?1‰) likely reflect biological N2 fixation using FeMo-nitrogenase. When compared with data from the literature, we show that lacustrine habitats of Mesoarchean age (3.2–2.8?Ga) are systematically depleted in δ13C (?37?±?5‰) relative to marginal marine (?32?±?7‰) and open marine settings (?27?±?3‰), suggesting that methanogenesis was relatively more important in lacustrine communities. Our findings highlight: (a) the widespread use of biological N2 fixation by the Mesoarchean biosphere, (b) the potential importance of continental habitats for methane production and perhaps for the formation of a hydrocarbon haze, and (c) the possible role of land masses in driving microbial diversification on the early Earth.Su, Y., Zha, M., Ding, X., Qu, J., Wang, X., Yang, C., Iglauer, S., 2018. Pore type and pore size distribution of tight reservoirs in the Permian Lucaogou Formation of the Jimsar Sag, Junggar Basin, NW China. Marine and Petroleum Geology 89, 761-774. tight reservoir of the Lucaogou Formation in the Jimsar sag, located in the southeastern Junggar Basin, northwest China, has been investigated for its great potential tight oil resources. In this study, petrography and mineralogy, pore microstructures, and pore size distributions of the samples collected from nine wells, were analyzed using X-ray diffraction (XRD), total organic carbon (TOC), thin sections and scanning electron microscopy (SEM). The major rock types were identified as dolomite and siltstone, which had different pore type assemblages and various pore size distribution patterns. Based on the pore origin, pores were identified as: primary mineral pores, dissolved mineral pores, primary organic matter pores and secondary organic matter pores. Their sizes followed a power law distribution, regardless of lithological variability or SEM magnification. However, the power law exponent D was associated with lithology and diagenesis as well as hydrocarbon generation. In dolomite, the decrease in dolomite content and the increase in dolomite particle size were commonly in accordance with the decrease in the power law exponent D. Compaction and cementation were the principal diagenetic processes that had a crucial effect on the pore size distribution with a large D equal to 2.77. In siltstone, the influence of various pore types on the pore size distribution was controlled by diagenesis, in which case dissolution and cementation were compensating for their influence with a fluctuating power law exponent D ranging from 1.5 to 2.7.Subrahmanya, K.R., Prakash Narasimha, K.N., 2017. Kaveri crater – An impact structure in the Precambrian terrain of southern India. Journal of the Geological Society of India 90, 387-395. region to the east of Palghat gap is of low elevation and nearly circular in shape. It forms a part of the Kaveri river basin. The predominantly gneissic terrain is surrounded by the charnockitic hill ranges, prominent among which are Nilgiris and Biligirirangan to the north; and Anaimalai and Kodaikanal to the south. The charnockite massifs have a steep slope facing the circular feature and a gentler slope in the opposite direction. Fractures/faults/shear zones are noticed in many parts. The Bouguer anomaly in the gneissic terrain is elliptical in shape and positive, relative to the surrounding elevated region. The magnetic contours are also elliptical and the magnetic basement is deeper by about one km compared to regions in the periphery. The shallow seismic velocity picture from Chennimalai to Palani indicates a graben structure. The velocity structure also depicts a 4–5 km Moho upwarp near Chennimalai. Junction between the gneissic and charnockitic terrain and even beyond, is marked by the presence of pseudotachylites and breccia. Field and petrographic studies indicate presence of suevite, Planar Deformation Features (PDF), Planar Fractures, diaplectic glass of quartz and plagioclase and spherical inclusion in suevite. These evidences taken together point to an extra-terrestrial impact which created a crater of approximately 120 km in diameter. Several lines of indirect evidences point to Neoproterozoic age for the impact. Kaveri Crater is the fourth largest crater on the surface of the Earth; other larger craters being Vredefort (160 km), Chicxulub (150 km) and Sudbury (130 km).Sun, L., Khan, S., Godet, A., 2018. Integrated ground-based hyperspectral imaging and geochemical study of the Eagle Ford Group in West Texas. Sedimentary Geology 363, 34-47. study used ground-based hyperspectral imaging to map an outcrop of the Eagle Ford Group in west Texas. The Eagle Ford Group consists of alternating layers of mudstone – wackestone, grainstone – packstone facies and volcanic ash deposits with high total organic content deposited during the Cenomanian – Turonian time period. It is one of the few unconventional source rock and reservoirs that have surface representations.Ground-based hyperspectral imaging scanned an outcrop and hand samples at close ranges with very fine spatial resolution (centimeter to sub-millimeter). Spectral absorption modeling of clay minerals and calcite with the modified Gaussian model (MGM) allowed quantification of variations of mineral abundances. Petrographic analysis confirmed mineral identifications and shed light on sedimentary textures, and major element geochemistry supported the mineral quantification. Mineral quantification resulted in mapping of mudstone – wackestone, grainstone – packstone facies and bentonites (volcanic ash beds). The lack of spatial associations between the grainstones and bentonites on the outcrop calls into question the hypothesis that the primary productivity is controlled by iron availability from volcanic ash beds. Enrichment of molybdenum (Mo) and uranium (U) indicated “unrestricted marine” paleo-hydrogeology and anoxic to euxinic paleo-redox bottom water conditions.Hyperspectral remote sensing data also helped in creating a virtual outcrop model with detailed mineralogical compositions, and provided reservoir analog to extract compositional and geo-mechanical characteristics and variations. The utilization of these new techniques in geo-statistical analysis provides a workflow for employing remote sensing in resource exploration and exploitation.Sun, S., Zhao, J., Yu, D., 2018. Dissociation enthalpy of methane hydrate in salt solution. Fluid Phase Equilibria 456, 92-97. dissociation enthalpy of methane hydrate is an important thermal parameter for hydrate-related work. In this paper, the dissociation enthalpies of methane hydrate in various salt solutions are calculated using the previously measured H-LW-V equilibrium data by the Clapeyron equation and the Clausius-Clapeyron equation, respectively. The calculated results by the Clapeyron equation do not show temperature dependence and the order of the dissociation enthalpy of methane hydrate in different salt solutions is 0.5NaCl>0.5MgCl2>0.5CaCl2> 1.0NaCl >1.0CaCl2>2.0NaCl>1.0MgCl2, the corresponding value of which is 52.6 ± 0.1 kJ/mol, 51.3 ± 0.3 kJ/mol, 50.4 ± 0.5 kJ/mol, 49.4 ± 0.3 kJ/mol, 46.0 ± 0.2 kJ/mol, 45.1 ± 0.2 kJ/mol and 44.0 ± 0.3 kJ/mol. Both the values and the errors calculated by the Clausius-Clapeyron equation are bigger than those by the Clapeyron equation. Moreover, the calculated values obtained by the Clausius-Clapeyron equation decrease with the temperature increase. Cations have less effect on the dissociation enthalpy than anions due to the different ability in affecting the ambient water networks. However, how the two effects (the colligative effect and the salting out effect) combine to influence the dissociation enthalpy of hydrate needs to be investigated further.Sun, X.-h., Zhao, Y.-j., Liu, C.-l., Jiao, P.-c., Zhang, H., Wu, C.-h., 2017. Paleoclimatic information recorded in fluid inclusions in halites from Lop Nur, Western China. Scientific Reports 7, Article 16411. homogenization temperature (Th) of primary fluid inclusions in halite can be used for paleoclimate interpretations. Lop Nur, in Central Asia, is an extremely arid zone where large amounts of glauberite were deposited from the late Middle to Late Pleistocene. This deposition was accompanied by formation of large-scale potash-bearing brines. However, quantitative paleotemperature data are still lacking, hindering reconstruction of Quaternary climate conditions and their control over potash formation. We measured the Th of inclusions in halite from the salt field and the top of Upper Pleistocene strata in Lop Nur. The maximum homogenization temperature (ThMAX) of inclusions in halite from the salt field was 41.1?°C, consistent with the maximum ambient temperature (43.4?°C) in the same period. The ThMAX of inclusions in halite from the Upper Pleistocene strata ranged from 35.6?°C to 43?°C, where maximum air temperatures may have reached 37.9?°C to 45.3?°C. The results show that a hot and arid climate prevailed in Lop Nur at the end of the Late Pleistocene. Furthermore, changes of the brine chemical composition due to supply variations instead of climate change, may have caused glauberite deposition to cease at the end of the Late Pleistocene.Sun, Y., Du, Z., Sun, L., Pan, Y., 2017. Phase behavior of SCCO2 sequestration and enhanced natural gas recovery. Journal of Petroleum Exploration and Production Technology 7, 1085-1093. noncommercial gas reservoirs with low reserves are feasible sites for CO2 sequestration. Those gas reservoirs contain natural gas that can take up the potential pore space of SCCO2 sequestration in the reservoir. The solution is to recover the natural gas by active CO2 injection. This idea is carbon sequestration with enhancement gas recovery (CSEGR). In CSEGR, different zones of the formation fluid are formed during the gas migration. In this paper, the sequestration site is a PY gas reservoir. The pressure, volume and temperature properties of the formation fluid are tested by experiments or calculated by the program based on PR-EOS, using a Z-factor, Volume ratio in place (V r.scco 2 Vr.scco2), density and viscosity. We discuss those experimental or simulation results to understand the fluid phase behavior in such a migration during CSEGR in a PY gas reservoir, and we give the suitable site (temperature) and the eligible pressure of the next core-flooding test.Suzuki, S., Ishii, S.i., Hoshino, T., Rietze, A., Tenney, A., Morrill, P.L., Inagaki, F., Kuenen, J.G., Nealson, K.H., 2017. Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars. The Isme Journal 11, 2584-2598. from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (Eh<?550?mV) conditions with low ionic concentrations. These conditions make the springs exceptionally challenging for life. Here, we report the metagenomic data and recovered draft genomes from two different springs, GPS1 and BS5. GPS1, which was fed solely by a deep groundwater source within the serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 (‘Parcubacteria’) and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.Svalova, A., Parker, N.G., Povey, M.J.W., Abbott, G.D., 2017. Determination of asphaltene critical nanoaggregate concentration region using ultrasound velocity measurements. Scientific Reports 7, Article 16125. constitute the heaviest, most polar and aromatic fraction of petroleum crucial to the formation of highly-stable water-in-crude oil emulsions. The latter occur during crude oil production as well as spills and cause difficulties to efficient remediation practice. It is thought that in nanoaggregate form, asphaltenes create elastic layers around water droplets enhancing stability of the emulsion matrix. Ultrasonic characterisation is a high-resolution non-invasive tool in colloidal analysis shown to successfully identify asphaltene nanoaggregation in toluene. The high sensitivity of acoustic velocity to molecular rearrangements and ease in implementation renders it an attractive method to study asphaltene phase properties. Currently, aggregation is thought to correspond to an intersection of two concentration-ultrasonic velocity regressions. Our measurements indicate a variation in the proximity of nanoaggregation which is not accounted for by present models. We attribute this uncertainty to physico-chemical heterogeneity of the asphaltene fraction driven by variation in molecular size and propose a critical nanoaggregation region. We treated asphaltenes from North and South American crude oils with ruthenium ion catalysed oxidation to characterize their n-alkyl appendages attached to aromatic cores. Principal component analysis was performed to investigate the coupling between asphaltene structures and velocity measurements and their impact on aggregation.Sydnes, M., Fjeldskaar, W., L?tveit, I.F., Grunnaleite, I., Cardozo, N., 2018. The importance of sill thickness and timing of sill emplacement on hydrocarbon maturation. Marine and Petroleum Geology 89, 500-514. sills in sedimentary basins can be relatively easy to interpret on seismic data because they stand out due to their high acoustic impedance in relation to the sediments. However, determining sill thickness is challenging unless the sills are drilled. This study explores the influence of magmatic sill thickness and timing of emplacement on temperature and hydrocarbon maturation in sedimentary basins. A 230?km long 2D transect through the V?ring Basin in the Norwegian Sea is modeled and sill thickness and timing of emplacement are the only parameters varied. The transect holds ～40 sills that intruded at ～55 Ma with a temperature of 1000?°C in a shale-dominated sequence. Several sill thickness scenarios were tested, but results for 0?m (no sills), 50?m and 100?m are presented here. Furthermore, the 50?m and 100?m thick sills were tested to intrude as upper and lower clusters separated by time intervals of 10 and 100 kyr. To study the effect of sills below seismic resolution, 1D modeling of well 7316/5-1 in the Barents Sea was performed. This well contains 9 sills distributed in an upper and a lower group. Vitrinite reflectance data from the well allow studying the effect of thin sills on temperature and maturation. The results show a clear connection between sill thickness and the temperature and maturation history of the basin. The largest impact of sill intrusions is at 3–5?km depth. For sills intruding as clusters, there are regionally marginal differences related to timing of emplacement but local differences especially in the close vicinity of the sills occur. This work indicates that the interpretation of sill thickness has a substantial influence on the prediction of the maturation and petroleum potential of sedimentary basins holding magmatic intrusions. Sills below seismic resolution contribute to increased maturation in its surroundings. Differences in the timing of sill emplacement within 10–100?kyr show local effects that may influence the petroleum potential of source rocks between two sill complexes.Tabari, K., Tabari, M., 2017. Characterization of a biodegrading bacterium, Bacillus subtilis, isolated from oil-contaminated soil. International Journal of Environmental Science and Technology 14, 2583-2590. oil and its derivatives because of different events and accidents may cause pollution to the environment. A biological treatment is a novel technique that uses microorganisms to remove or neutralize pollutants from a contaminated site. Oil-contaminated soils were sampled, after isolating of soil bacteria, using quantitative and qualitative screening, biosurfactant-producing bacteria were identified and environmental factors on the growth of bacteria and biosurfactant were investigated. In this study, the Bacillus subtilis was identified as the best biosurfactant-producing strain which has the ability to grow in environments with high salinity and temperature and pH?>?5. The produced biosurfactant from B. subtilis is stable to changes in temperature and salt concentration and pH (in the range of 5–12).The B. subtilis also showed that they are able to biodegrade aliphatic alkanes. The B. subtilis has necessary potential for bioremediation of oil pollution in the environment.Taheri-Shakib, J., Shekarifard, A., Naderi, H., 2017. The experimental investigation of effect of microwave and ultrasonic waves on the key characteristics of heavy crude oil. Journal of Analytical and Applied Pyrolysis 128, 92-101. study examined the effects of microwave (MW) and ultrasonic (US) waves on an heavy crude oil sample from a reservoir in southwest Iran. The waves irradiated the sample from two to 10 min at two-minute steps. MW caused the temperature of the crude-oil sample to rise by selective heating of polar components and creation of hot zones; under US, heating was accompanied by a cavitation effect. MW at 2 and 4 min reduced the sample’s viscosity by inducing hot zones. At 2 min, the viscosity declined 16% due to cracking of heavy components such as asphaltenes, which have a higher capacity to absorb MW. As the radiation time increased after 4 min, the viscosity increased because light components escaped from the sample. However, US reduced the viscosity of the heavy crude oil sample at all time durations. The greatest reduction of viscosity was around 19%, at 4 min. The viscosity increased with irradiation time and then remained constant. Ultrasonic waves altered the viscosity by creating bubbles, which disintegrated the resin intermolecular bonds and cracked the large molecular particles of the asphaltene. The reduction in sulfur content under US was much greater than under MW. At all time durations, sulfur content fell as radiation time increased. Due to its high potential to absorb MW, creates active sulfur that can be emitted from the crude oil as sulfide and hydrogen sulfide, with the sulfur level falling to 0.39%. Furthermore, US waves also reduced sulfur content to around 0.46% as the asphaltene flocks disintegrated. Reduction of sulfur content from asphaltene agglomerates under MW and US was observed using scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). In addition to reducing the effect of sulfur by affecting its nitrogen and oxygen elements, irradiation also reduced the polarity of the asphaltene particles and prevented reaggregation of cracked particles. Results of SARA (saturation, aromatic, resin and asphaltene) analysis showed that asphaltene particles have a higher capacity to absorb MW than resin components, as after the amount of asphaltene components declined in the early stages of irradiation, resin components began to change, falling to 34% at 10 min. The decrease in asphaltene content in samples under US was more evident, reaching 34% at 8 min. According to Fourier transform infrared (FTIR) spectra results, MW irradiation caused cracking of large-chain molecules and drove light components from heavy crude sample. These two phenomena are a function of radiation time. The rate of cracking of heavy components was continuously greater than the rate of light components leaving the sample at early time intervals; ultimately, this resulted in an upgraded heavy oil. In some cases, despite cracking of large-chain molecules and creation of light components, the output values of light components were higher. Under US, the cracking of large-chain molecules occurred, but due to the departure of heavy components from the crude oil, peak intensities increased and the resulting crude oil had purer components.Taheri-Shakib, J., Shekarifard, A., Naderi, H., 2017. The experimental study of effect of microwave heating time on the heavy oil properties: Prospects for heavy oil upgrading. Journal of Analytical and Applied Pyrolysis 128, 176-186. heavy crude oil sample from an oil field in southwest Iran was placed in a Fischer assay and heated by microwave for two-minute time steps until 14 min total heating time had elapsed. Unlike conventional heating technique (CHT), which caused light carbonic components to escape and raised C20+ components in oil samples, the value of light carbonic components increased under microwave heating technique (MHT) up to 6 min. These materials cannot escape the oil sample in MHT because the cracked components approach a superheated state, and in this study a large portion of them remained at 6 min. Moreover, in contrast to the CHT results, the C1–C20 components increased to 13.5 wt% in the analysis of cracked gases during MHT. In MHT, light components increased with heating time, and C7+ components fell. This is indicative of light components escaping after 6 min. Some components escaped as condensate. In CHT, the escape of only small amounts of condensates was observed at 12 and 14 min, while under MHT, this phenomenon started at 8 min and contained larger amounts. This phenomenon is due to secondary cracking in oil, which is created by an abrupt increase in the temperature of some components that have more capacity to absorb microwaves. The sulfur content of heavy oil in MHT tended to decrease over time, approaching 34 wt% at 14 min; in contrast, in CHT it remained constant. Sulfur was removed from the oil sample as H2S and SO2, predominantly in a gas state, but also as condensate, in increasing amounts over time. Sulfur removal from the heavy crude oil sample is highly important in the upgrading process because of its high coefficient of microwave absorption. H2S is produced from the start of MHT, but SO2 is observed only after 6 min, and then only in the produced gas. Saturation, Aromatic, Resin and Asphaltene (SARA) components analysis showed changes in the resin and asphaltene components. The amount of asphaltene components began to decline starting early in the heating process, and approached its lowest amount at 4 min (3.21 wt%). Reduction of resin components in MHT began at 8 min and reached 55% at 14 min. Asphaltenes have a high capability to absorb microwaves due to having SNO (Sulfur, Nitrogen and Oxygen) components that create hot zones in heavy oil; these hot zones enhance cracking and upgrading. Scanning electron microscopy images of asphaltene particles showed that microwaves caused some changes in the structure of these particles. Energy-dispersive spectroscopy analysis of these particles showed that SNO components under MHT declined over heating time. The results also suggest that after sulfur, nitrogen and oxygen have the highest potential to absorb microwaves.Tang, T., Filippino, K.C., Liu, Z., Mulholland, M.R., Lee, C., 2017. Peptide hydrolysis and uptake of peptide hydrolysis products in the James River estuary and lower Chesapeake Bay. Marine Chemistry 197, 52-63. lability of small peptides was investigated along the salinity gradient of the James River estuary and lower Chesapeake Bay using two fluorescent analogs, Lucifer Yellow Anhydride-alanine-valine-phenylalanine-alanine (LYA-AVFA) and LYA-tetraalanine (LYA-AlA4). Hydrolysis rates of these compounds were compared with each other, and with uptake rates of potential hydrolysis products and other smaller derivatives (e.g., glutamic acid and dialanine). Results suggest that rates of peptide hydrolysis and uptake of hydrolysis products were not always correlated with each other along the salinity gradient, or to other environmental parameters measured in the James River and lower Chesapeake Bay. This may be because diverse input and removal processes can influence both peptide hydrolysis and uptake, but not necessarily simultaneously. Rates of both peptide hydrolysis and free amino acid uptake were strongly associated with particles, particularly those freshly produced. This suggests more rapid turnover of enzymatically available organic nitrogen in regions with elevated phytoplankton biomass. Changes in the abundance and composition of dissolved amino acids in these waters were also examined. Dissolved amino acid compositions, but not concentrations, varied with salinity along a gradient from the tidal fresh James River to the mouth of Chesapeake Bay. These compositional variations demonstrate the mixing of terrestrial organic nitrogen and in-situ production along the salinity transect.Tanioka, T., Matsumoto, K., 2017. Buffering of ocean export production by flexible elemental stoichiometry of particulate organic matter. Global Biogeochemical Cycles 31, 1528-1542.: One of the most important factors that determine the ocean-atmosphere carbon partitioning is the sinking of particulate organic matter (POM) from the surface ocean to the deep ocean. The amount of carbon (C) removed from the surface ocean by this POM export production depends critically on the elemental ratio in POM of C to nitrogen (N) and phosphorus (P), two essential elements that limit productivity. Recent observations indicate that P:N:C in marine POM varies both spatially and temporally due to chemical, physical, and ecological dynamics. In a new approach to predicting a flexible P:C ratio, we developed a power law model with a stoichiometry sensitivity factor, which is able to relate P:C of POM to ambient phosphate concentration. The new factor is robust, measurable, and biogeochemically meaningful. Using the new stoichiometry sensitivity factor, we present a first-order estimate that P:C plasticity could buffer against a generally expected future reduction in global carbon export production by up to 5% under a future warming scenario compared to a fixed, Redfield P:C. Further, we demonstrate that our new stoichiometry model can be implemented successfully and easily in a global model to reproduce the large-scale P:N:C variability in the ocean.Plain Language Summary: Sinking of particulate organic carbon (C) from the surface to the deep ocean acts to draw down atmospheric CO2. Essential nutrients such as nitrogen (N) and phosphorus (P) both limit C export production and control its efficiency. The efficiency of C export for a given amount of N or P is expressed by their relative abundances in terms of their elemental ratios in organic matter. This P:N:C ratio is assumed to be fixed (“Redfield ratio”) in the most global biogeochemical models. Here we present a new method for allowing P:C to vary. Using this newly developed model, we quantify how flexible P:C can buffer changes in export production under a future warming scenario.Tao, S., Xu, Y., Tang, D., Xu, H., Li, S., Chen, S., Liu, W., Cui, Y., Gou, M., 2017. Geochemistry of the Shitoumei oil shale in the Santanghu Basin, Northwest China: Implications for paleoclimate conditions, weathering, provenance and tectonic setting. International Journal of Coal Geology 184, 42-56. sequences of organic-rich lacustrine oil shale were deposited in the Middle Permian Lucaogou Formation of the Junggar Basin and the Santanghu Basin. The mineralogy and major, trace and rare earth element geochemistry of the oil shales and mudstones collected from the Lucaogou Formation are discussed. The chondrite-normalized patterns of the studied samples show LREE enrichments, HREE deficits, and generally negative Eu anomalies and positive Ce anomalies. The Paleoclimate indictor (C-value) varies between 0.08 and 0.62, reflecting generally arid to subhumid conditions. In addition, low Rb/Sr (with a mean value of 0.14) and high Sr/Cu (with a mean value of 33.22) values indicate that arid conditions prevailed during the deposition of the Lucaogou Formation. Sr/Ba ratios (0.31–7.73) of the studied samples suggest a paleoenvironment with variable salinity. The salinity of the lake is controlled by climate variations, freshwater replenishment, seawater intrusion, and redox conditions. The studied oil shales in the Lucaogou Formation are mainly derived from a felsic (dacite and rhyolite) to intermediate (andesite) source that formed in the Early Permian and mixed with small amounts of basic rocks (basalt). Volcanic eruptions provided the source rocks for the Lucaogou Formation. The chemical index of alteration (CIA), the plagioclase index of alternation (PIA), and an A-CN-K ternary diagram indicate that the parent rocks of the oil shale experienced weak to moderate chemical weathering.Tchapda, A.H., Krishnamoorthy, V., Yeboah, Y.D., Pisupati, S.V., 2017. Analysis of tars formed during co-pyrolysis of coal and biomass at high temperature in carbon dioxide atmosphere. Journal of Analytical and Applied Pyrolysis 128, 379-396. analysis of tars from the high temperature (1573 K–1773 K) co-pyrolysis of coal (Pittsburgh #8) and biomass (Switchgrass and White Pine) in CO2 has been carried out.The analysis shows that naphthalene content is the maximum in all the tar samples irrespective of biomass and coal blend proportion. Samples with high percentages of coal as well as experiments conducted at 1773 K showed the highest concentration of aromatic compounds. The largest aromatic compound found had five benzene rings (benzo(e)pyrene). Aliphatic hydrocarbons as well as oxygenated hydrocarbons were mostly found in samples containing high percentages of biomass or in experiments conducted at 1573 K. About 100 compounds have been identified in the tars of which 25% account for 90% of the mass of tar.The study indicates that the atomic N/C and S/C ratio increases whereas H/C ratio decreases with pyrolysis temperature. The rate of variation of H/C ratio reduces as the temperature increases. The biomass content in the fuel feed seems to have an impact on the H/C ratio of the tars only at lower temperatures. That is, at lower temperatures, the higher the biomass content of the fuel, the higher the H/C ratio of the resulting tars. These observations also apply to the O/C ratio of the tar. For both switchgrass and pine sawdust, the biomass content of the fuel seems to have no influence on the nitrogen content of the tars. The distribution of sulfur in the tar is inversely proportional to the biomass percentage in the fuel. The higher the biomass content of the fuel, the lower the atomic S/C of the tars.Techtman, S.M., Mahmoudi, N., Whitt, K.T., Campa, M.F., Fortney, J.L., Joyner, D.C., Hazen, T.C., 2017. Comparison of Thaumarchaeotal populations from four deep sea basins. FEMS Microbiology Ecology 93, Article fix128. nitrogen cycle in the marine environment is strongly affected by ammonia-oxidizing Thaumarchaeota. In some marine settings, Thaumarchaeotes can comprise a large percentage of the prokaryotic population. To better understand the biogeographic patterns of Thaumarchaeotes, we sought to investigate differences in their abundance and phylogenetic diversity between geographically distinct basins. Samples were collected from four marine basins (The Caspian Sea, the Great Australian Bight, and the Central and Eastern Mediterranean). The concentration of bacterial and archaeal 16S rRNA genes and archaeal amoA genes were assessed using qPCR. Minimum entropy decomposition was used to elucidate the fine-scale diversity of Thaumarchaeotes. We demonstrated that there were significant differences in the abundance and diversity of Thaumarchaeotes between these four basins. The diversity of Thaumarchaeotal oligotypes differed between basins with many oligotypes only present in one of the four basins, which suggests that their distribution showed biogeographic patterning. There were also significant differences in Thaumarchaeotal community structure between these basins. This would suggest that geographically distant, yet geochemically similar basins may house distinct Thaumarchaeaotal populations. These findings suggest that Thaumarchaeota are very diverse and that biogeography in part contributes in determining the diversity and distribution of Thaumarchaeotes.Tesfamichael, T., Jacobs, B., Tabor, N., Michel, L., Currano, E., Feseha, M., Barclay, R., Kappelman, J., Schmit, M., 2017. Settling the issue of “decoupling” between atmospheric carbon dioxide and global temperature: [CO2]atm reconstructions across the warming Paleogene-Neogene divide. Geology 45, 999-1002. variations in the concentration of atmospheric carbon dioxide ([CO2]atm) have been shown to affect carbon fixation during photosynthesis and are correlated with anatomical and physiological changes observed in leaves of woody dicots. These include changes in stomatal frequency and size and in δ13C values. These attributes can be measured on organically preserved leaf fossils, and therefore can be used as proxies for Earth’s atmospheric CO2 history. This study tests the link between [CO2]atm and global temperature for the late Oligocene and early Miocene using fossil leaves collected from Ethiopia, by estimating [CO2]atm using a leaf gas exchange model. The results of this study show a statistically significant [CO2]atm rise from ～390 ppm in the late Oligocene to ～870 ppm in the early Miocene. These values demonstrate a positive correlation between [CO2]atm and global average temperature, contrary to some previous studies for this time interval. The results of this study have important implications for understanding future climate change driven by rising [CO2]atm.The IceCube Collaboration, 2017. Measurement of the multi-TeV neutrino interaction cross-section with IceCube using Earth absorption. Nature 551-600, 596. interact only very weakly, so they are extremely penetrating. The theoretical neutrino–nucleon interaction cross-section, however, increases with increasing neutrino energy, and neutrinos with energies above 40 teraelectronvolts (TeV) are expected to be absorbed as they pass through the Earth. Experimentally, the cross-section has been determined only at the relatively low energies (below 0.4?TeV) that are available at neutrino beams from accelerators. Here we report a measurement of neutrino absorption by the Earth using a sample of 10,784 energetic upward-going neutrino-induced muons. The flux of high-energy neutrinos transiting long paths through the Earth is attenuated compared to a reference sample that follows shorter trajectories. Using a fit to the two-dimensional distribution of muon energy and zenith angle, we determine the neutrino–nucleon interaction cross-section for neutrino energies 6.3–980?TeV, more than an order of magnitude higher than previous measurements. The measured cross-section is about 1.3 times the prediction of the standard model>, consistent with the expectations for charged- and neutral-current interactions. We do not observe a large increase in the cross-section with neutrino energy, in contrast with the predictions of some theoretical models, including those invoking more compact spatial dimensions or the production of leptoquarks. This cross-section measurement can be used to set limits on the existence of some hypothesized beyond-standard-model particles, including leptoquarks.Thompson, L.R., Sanders, J.G., McDonald, D., Amir, A., Ladau, J., Locey, K.J., Prill, R.J., Tripathi, A., Gibbons, S.M., Ackermann, G., Navas-Molina, J.A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J.T., Mirarab, S., Zech Xu, Z., Jiang, L., Haroon, M.F., Kanbar, J., Zhu, Q., Jin Song, S., Kosciolek, T., Bokulich, N.A., Lefler, J., Brislawn, C.J., Humphrey, G., Owens, S.M., Hampton-Marcell, J., Berg-Lyons, D., McKenzie, V., Fierer, N., Fuhrman, J.A., Clauset, A., Stevens, R.L., Shade, A., Pollard, K.S., Goodwin, K.D., Jansson, J.K., Gilbert, J.A., Knight, R., The Earth Microbiome Project, C., 2017. A communal catalogue reveals Earth’s multiscale microbial diversity. Nature 551, 457-463. growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.Thonusin, C., IglayReger, H.B., Soni, T., Rothberg, A.E., Burant, C.F., Evans, C.R., 2017. Evaluation of intensity drift correction strategies using MetaboDrift, a normalization tool for multi-batch metabolomics data. Journal of Chromatography A 1523, 265-274. recent years, mass spectrometry-based metabolomics has increasingly been applied to large-scale epidemiological studies of human subjects. However, the successful use of metabolomics in this context is subject to the challenge of detecting biologically significant effects despite substantial intensity drift that often occurs when data are acquired over a long period or in multiple batches. Numerous computational strategies and software tools have been developed to aid in correcting for intensity drift in metabolomics data, but most of these techniques are implemented using command-line driven software and custom scripts which are not accessible to all end users of metabolomics data. Further, it has not yet become routine practice to assess the quantitative accuracy of drift correction against techniques which enable true absolute quantitation such as isotope dilution mass spectrometry. We developed an Excel-based tool, MetaboDrift, to visually evaluate and correct for intensity drift in a multi-batch liquid chromatography – mass spectrometry (LC–MS) metabolomics dataset. The tool enables drift correction based on either quality control (QC) samples analyzed throughout the batches or using QC-sample independent methods. We applied MetaboDrift to an original set of clinical metabolomics data from a mixed-meal tolerance test (MMTT). The performance of the method was evaluated for multiple classes of metabolites by comparison with normalization using isotope-labeled internal standards. QC sample-based intensity drift correction significantly improved correlation with IS-normalized data, and resulted in detection of additional metabolites with significant physiological response to the MMTT. The relative merits of different QC-sample curve fitting strategies are discussed in the context of batch size and drift pattern complexity. Our drift correction tool offers a practical, simplified approach to drift correction and batch combination in large metabolomics studies.Tian, J., Li, J., Pan, C., Tan, Z., Zeng, X., Guo, Z., Wang, B., Zhou, F., 2018. Geochemical characteristics and factors controlling natural gas accumulation in the northern margin of the Qaidam Basin. Journal of Petroleum Science and Engineering 160, 219-228. northern margin of the Qaidam Basin is an important area for natural gas exploration that includes the recently discovered Dongping and Niudong gas fields. However, the origins of the natural gas and the primary factors controlling gas accumulation in the region are unclear, particularly in the piedmont zone. Planning and exploration strategies are limited by a lack of knowledge about natural gas accumulation mechanisms. In this study, various comprehensive geochemical, geophysical and geological techniques were applied to investigate the origin and distribution of natural gas in this area, as well as the main factors controlling gas accumulation. The results demonstrate that the gas deposits are dominated by gaseous hydrocarbons with C1/C1–5 ratios in the range 0.76–0.99. The natural gases are characterized by wide variations in δ13C1 values (?19.1‰ to ?36.1‰) and relatively heavy δ13C2 values (?19.82% to ?25.42%). The oil and gas in the investigated area exhibit a zonal spatial distribution and have features typical of coal-generated gases. The locations of major hydrocarbon-generating depressions and source rock maturity exert primary control on the distribution of oil and gas reservoirs. Paleo-uplifts and paleo-slopes controlled the direction of hydrocarbon migration and accumulation, while faults and conducting systems connected to the hydrocarbon source rocks constituted channel systems that controlled the transport of oil and gas. Suggestions for future exploration have been put forward, which will provide significant guidance for gas exploration in the area. Future promising areas for exploration include the paleo-uplifts in the east of the Altun Mountains and the west of the Qilian Mountains front and the Eboliang-Lenghu structural belt in the northern margin of the Qaidam Basin. These results will also provide guidance to natural gas exploration and research efforts in other basins with similar geological settings.Tice, M.M., Quezergue, K., Pope, M.C., 2017. Microbialite biosignature analysis by mesoscale X-ray fluorescence (μXRF) mapping. Astrobiology 17, 1161-1172. part of its biosignature detection package, the Mars 2020 rover will carry PIXL, the Planetary Instrument for X-ray Lithochemistry, a spatially resolved X-ray fluorescence (μXRF) spectrometer. Understanding the types of biosignatures detectable by μXRF and the rock types μXRF is most effective at analyzing is therefore an important goal in preparation for in situ Mars 2020 science and sample selection. We tested mesoscale chemical mapping for biosignature interpretation in microbialites. In particular, we used μXRF to identify spatial distributions and associations between various elements (“fluorescence microfacies”) to infer the physical, biological, and chemical processes that produced the observed compositional distributions.As a test case, elemental distributions from μXRF scans of stromatolites from the Mesoarchean Nsuze Group (2.98 Ga) were analyzed. We included five fluorescence microfacies: laminated dolostone, laminated chert, clotted dolostone and chert, stromatolite clast breccia, and cavity fill. Laminated dolostone was formed primarily by microbial mats that trapped and bound loose sediment and likely precipitated carbonate mud at a shallow depth below the mat surface. Laminated chert was produced by the secondary silicification of microbial mats. Clotted dolostone and chert grew as cauliform, cryptically laminated mounds similar to younger thrombolites and was likely formed by a combination of mat growth and patchy precipitation of early-formed carbonate. Stromatolite clast breccias formed as lag deposits filling erosional scours and interstromatolite spaces. Cavities were filled by microquartz, Mn-rich dolomite, and partially dolomitized calcite. Overall, we concluded that μXRF is effective for inferring genetic processes and identifying biosignatures in compositionally heterogeneous rocks.Tobin, T.S., 2017. Recognition of a likely two phased extinction at the K-Pg boundary in Antarctica. Scientific Reports 7, Article 16317. southernmost Cretaceous – Paleogene (K-Pg) outcrop exposure is the well-studied exposure on Seymour Island, Antarctica. Deposition across the K-Pg boundary there is uninterrupted, and as a consequence the ammonite fossil record is commonly used to test statistical methods of evaluating mass extinctions to account for the incompleteness of the fossil record. Numerous detailed fossil data sets from Seymour Island, comprised dominantly of mollusks, have been published over the last 30 years, but in most cases have not received statistical treatment. Here a previously published statistical technique is modified, automated, and applied to all published macrofossil data sets available from Seymour Island. All data sets reveal likely evidence of two separate multi-species extinctions, one synchronous with bolide impact evidence at the K-Pg boundary, and another 45?±?15 meters (~140–290 ky) below the boundary. The apparent earlier extinction primarily affects benthic mollusks, while the boundary extinction primarily affects ammonites. While there is no unique sedimentological change over the interval where the earlier extinction is identified, it is impossible to exclude the possibility that this pattern is stratigraphically controlled. The automation of this technique allows it to be applied easily to other large fossil data sets.Toli?, N., Liu, Y., Liyu, A., Shen, Y., Tfaily, M.M., Kujawinski, E.B., Longnecker, K., Kuo, L.-J., Robinson, E.W., Pa?a-Toli?, L., Hess, N.J., 2017. Formularity: Software for automated formula assignment of natural and other organic matter from ultrahigh-resolution mass spectra. Analytical Chemistry 89, 12659-12665. resolution mass spectrometry, such as Fourier transform ion cyclotron resonance mass spectrometry (FT ICR MS), can resolve thousands of molecular ions in complex organic matrices. A Compound Identification Algorithm (CIA) was previously developed for automated elemental formula assignment for natural organic matter (NOM). In this work, we describe software Formularity with a user-friendly interface for CIA function and newly developed search function Isotopic Pattern Algorithm (IPA). While CIA assigns elemental formulas for compounds containing C, H, O, N, S, and P, IPA is capable of assigning formulas for compounds containing other elements. We used halogenated organic compounds (HOC), a chemical class that is ubiquitous in nature as well as anthropogenic systems, as an example to demonstrate the capability of Formularity with IPA. A HOC standard mix was used to evaluate the identification confidence of IPA. Tap water and HOC spike in Suwannee River NOM were used to assess HOC identification in complex environmental samples. Strategies for reconciliation of CIA and IPA assignments were discussed. Software and sample databases with documentation are freely available.Trembath-Reichert, E., Morono, Y., Ijiri, A., Hoshino, T., Dawson, K.S., Inagaki, F., Orphan, V.J., 2017. Methyl-compound use and slow growth characterize microbial life in 2-km-deep subseafloor coal and shale beds. Proceedings of the National Academy of Sciences 114, E9206-E9215.: Microbial cells are widespread in diverse deep subseafloor environments; however, the viability, growth, and ecophysiology of these low-abundance organisms are poorly understood. Using single-cell–targeted stable isotope probing incubations combined with nanometer-scale secondary ion mass spectrometry, we measured the metabolic activity and generation times of thermally adapted microorganisms within Miocene-aged coal and shale bed samples collected from 2 km below the seafloor during Integrated Ocean Drilling Program Expedition 337. Microorganisms from the shale and coal were capable of metabolizing methylated substrates, including methylamine and methanol, when incubated at their in situ temperature of 45 °C, but had exceedingly slow growth, with biomass generation times ranging from less than a year to hundreds of years as measured by the passive tracer deuterated water. Abstract: The past decade of scientific ocean drilling has revealed seemingly ubiquitous, slow-growing microbial life within a range of deep biosphere habitats. Integrated Ocean Drilling Program Expedition 337 expanded these studies by successfully coring Miocene-aged coal beds 2 km below the seafloor hypothesized to be “hot spots” for microbial life. To characterize the activity of coal-associated microorganisms from this site, a series of stable isotope probing (SIP) experiments were conducted using intact pieces of coal and overlying shale incubated at in situ temperatures (45 °C). The 30-month SIP incubations were amended with deuterated water as a passive tracer for growth and different combinations of 13C- or 15N-labeled methanol, methylamine, and ammonium added at low (micromolar) concentrations to investigate methylotrophy in the deep subseafloor biosphere. Although the cell densities were low (50–2,000 cells per cubic centimeter), bulk geochemical measurements and single-cell–targeted nanometer-scale secondary ion mass spectrometry demonstrated active metabolism of methylated substrates by the thermally adapted microbial assemblage, with differing substrate utilization profiles between coal and shale incubations. The conversion of labeled methylamine and methanol was predominantly through heterotrophic processes, with only minor stimulation of methanogenesis. These findings were consistent with in situ and incubation 16S rRNA gene surveys. Microbial growth estimates in the incubations ranged from several months to over 100 y, representing some of the slowest direct measurements of environmental microbial biosynthesis rates. Collectively, these data highlight a small, but viable, deep coal bed biosphere characterized by extremely slow-growing heterotrophs that can utilize a diverse range of carbon and nitrogen substrates. Tsizin, S., Bokka, R., Keshet, U., Alon, T., Fialkov, A.B., Tal, N., Amirav, A., 2017. Comparison of electrospray LC–MS, LC–MS with Cold EI and GC–MS with Cold EI for sample identification. International Journal of Mass Spectrometry 422, 119-125. LC–MS, LC–MS with Cold EI and GC–MS with Cold EI (Electron Ionization (EI) of vibrationally cold molecules in supersonic molecular beams (SMB)) are compared in their sample identification capabilities. Two test mixtures were used: (a) acetaminophen, caffeine, sulfadimethoxine, terfenadine and reserpine; and (b) octafluoronaphthalene (OFN), pyrene, cholesterol and agidol 40. The major strength of EI in both LC–MS with Cold EI and GC–MS with Cold EI is its compatibility with library based sample identification that provides samples names and structures at the isomer level. GC–MS with Cold EI alleviates two major downsides of GC–MS with standard EI as it provides enhanced molecular ions that are often weak or missing in standard EI and, it significantly extends the range of compounds that are amenable for analysis. Consequently, reserpine and agidol 40 that are incompatible with standard GC–MS analyses are analyzed by GC–MS with Cold EI and yield effective library based identification. In cases involving sample compounds that are not in the library, ESI–LC–MS provides elemental formula information (when combined with high resolution MS) while GC–MS with Cold EI also provides elemental formula when TAMI software is used for the quadrupole mass accuracy improvement combined with isotope abundance analysis. We found that both LC–MS with Cold EI and GC–MS with Cold EI have broader range of small molecules amenable for analysis than ESI–LC–MS that fails to analyze relatively non-polar compounds and exhibits highly non-uniform and compound dependent ionization yields that span over four orders of magnitude. The total ion mass chromatograms S/N of ESI–LC–MS and LC–MS with Cold EI are comparable while it is better (>100 times per on-column amount) for GC–MS with Cold EI.Tu, T.-H., Wu, L.-W., Lin, Y.-S., Imachi, H., Lin, L.-H., Wang, P.-L., 2017. Microbial community composition and functional capacity in a terrestrial ferruginous, sulfate-depleted mud volcano. Frontiers in Microbiology 8, 2137. doi: 10.3389/fmicb.2017.02137. mud volcanoes (MVs) are an important natural source of methane emission. The role of microbial processes in methane cycling and organic transformation in such environments remains largely unexplored. In this study, we aim to uncover functional potentials and community assemblages across geochemical transitions in a ferruginous, sulfate-depleted MV of eastern Taiwan. Geochemical profiles combined with 16S rRNA gene abundances indicated that anaerobic oxidation of methane (AOM) mediated by ANME-2a group coincided with iron/manganese reduction by Desulfuromonadales at shallow depths deprived of sulfate. The activity of AOM was stimulated either by methane alone or by methane and a range of electron acceptors, such as sulfate, ferrihydrite, and artificial humic acid. Metagenomic analyses revealed that functional genes for AOM and metal reduction were more abundant at shallow intervals. In particular, genes encoding pili expression and electron transport through multi-heme cytochromes were prevalent, suggesting potential intercellular interactions for electron transport involved in AOM. For comparison, genes responsible for methanogenesis and degradation of chitin and plant-derived molecules were more abundant at depth. The gene distribution combined with the enhanced proportions of 16S rRNA genes related to methanogens and heterotrophs, and geochemical characteristics suggest that particulate organic matter was degraded into various organic entities that could further fuel in situ methanogenesis. Finally, genes responsible for aerobic methane oxidation were more abundant in the bubbling pool and near-surface sediments. These methane oxidizers account for the ultimate attenuation of methane discharge into the atmosphere. Overall, our results demonstrated that various community members were compartmentalized into stratified niches along geochemical gradients. These community members form a metabolic network that cascades the carbon transformation from the upstream degradation of recalcitrant organic carbon with fermentative production of labile organic entities and methane to downstream methane oxidation and metal reduction near the surface. Such a metabolic architecture enables effective methane removal under ferruginous, sulfate-depleted conditions in terrestrial MVs.Uno, S., Kokushi, E., A?asco, N.C., Iwai, T., Ito, K., Koyama, J., 2017. Oil spill off the coast of Guimaras Island, Philippines: Distributions and changes of polycyclic aromatic hydrocarbons in shellfish. Marine Pollution Bulletin 124, 962-973. sinking of the Solar 1 tanker caused serious heavy oil pollution around Guimaras Island, Philippines. In the present study, variations of parent polycyclic aromatic hydrocarbons (PAHs) and alkylated PAHs (alkPAHs) in some shellfish were investigated around Guimaras Island and other small islands from 3 months to 5 years after the spill. The total PAHs and alkPAHs in shellfish were detected in high concentrations at 448 and 33,666 ng/g dry weight, respectively, in November 2006. The concentrations of alkPAHs gradually decreased, while the parent PAHs in shellfish degraded more slowly than the alkPAHs, which was likely due to the persistent characteristics of PAHs. The risks based on European Union regulations were insignificant in 2008, but total PAHs in shellfish were still over 8 times higher at the investigated sites in November 2011 than that before the oil spill.Vaida, V., 2017. Prebiotic phosphorylation enabled by microdroplets. Proceedings of the National Academy of Sciences 114, 12359-12361. significant acceleration of reactions in confined environments has recently been reported in the literature (1–7). The reaction environments investigated span a diverse range, including charged microdroplets (1–3), microdiameter emulsions (5), inverted micelles (8), and the surfaces of aerosol particles (9). These experimental results have made the case that the surface of aqueous drops provides a special and unique reaction environment with qualitatively different thermodynamic and kinetic properties from bulk aqueous solutions. In PNAS, Nam et al. (7) report on a compelling application of accelerated reactions in aqueous microdroplets to chemistry that may have occurred prebiotically, in the absence of enzymes. They specifically address the abiotic production of sugar phosphates and uridine ribonucleoside in microdroplets, reactions that do not occur in bulk aqueous solutions. In biology, these reactions are enzyme-catalyzed. Investigations of reactions in confined aqueous environments are especially compelling in prebiotic chemistry, where nonenzymatic pathways must be found to explain the abiotic formation of biopolymers that can be used as building blocks of life (10?–12). It has long been appreciated that phosphorus is important in life (13), yet abiotic phosphorylation remains an area of intense recent activity (14). The contribution of Nam et al. (7) provides a possible route for the formation of prebiotically plausible sugar phosphate in aqueous microdrops. The experiments reported in the literature have used laboratory model systems to show different chemistry at aqueous interfaces than in bulk solutions; however, these model systems have counterparts in the natural environment (10, 15). Therefore, the thermodynamic and kinetic arguments emerging from laboratory model studies can be generalized. On the contemporary and early Earth, Vakhin, A.V., Onishchenko, Y.V., Nazimov, N.A., Kadyrov, R.U., 2017. Thermal transformation of the mobile-hydrocarbon composition of Domanik deposits of Volga-Ural oil-and gas-bearing province. Chemistry and Technology of Fuels and Oils 53, 511-519. mechanisms of the mobile-hydrocarbon composition of rock samples from the Domanik deposits of the Volga-Ural oil-and-gas-bearing province (OGP) are established. IR spectra of extracts obtained from the rock and of resins and asphaltenes after heat treatment are analyzed. The aromaticity of the asphaltenes increases to a maximum at 250°C due to degradation of aliphatic substituents and condensation of aromatic rings under radical-recombination conditions. This correlates with group-analysis results indicating that the maximum asphaltene content is observed at this temperature. Transformation of the mobile-hydrocarbon composition is associated with transformations of the composition and structure of the insoluble organic matter kerogen. The degree of maturity of organic matter of the Domanik deposits is characteristically low, increases steadily with increasing temperature, and reaches a maximum at 350°C. Translated from Khimiya i Tekhnologiya Topliv i Masel, No. 4, pp. 38 – 43, July – August, 2017.Valencia-Chan, L.S., García-Cámara, I., Torres-Tapia, L.W., Moo-Puc, R.E., Peraza-Sánchez, S.R., 2017. Lupane-type triterpenes of Phoradendron vernicosum. Journal of Natural Products 80, 3038-3042. new lupane-type triterpenes, 3α,24-dihydroxylup-20(29)-en-28-oic acid (1), 3α,23-dihydroxy-30-oxolup-20(29)-en-28-oic acid (2), and 3α,23-O-isopropylidenyl-3α,23-dihydroxylup-20(29)-en-28-oic acid (3), together with eight known compounds (4–11) were isolated from a methanol extract of Phoradendron vernicosum aerial parts. The chemical structures of 1–3 were determined on the basis of spectroscopic data interpretation. The isolated compounds were tested against seven human cancer cell lines and two normal cell lines.Valiente, N., Carrey, R., Otero, N., Gutiérrez-Villanueva, M.A., Soler, A., Sanz, D., Casta?o, S., Gómez-Alday, J.J., 2017. Tracing sulfate recycling in the hypersaline Pétrola Lake (SE Spain): A combined isotopic and microbiological approach. Chemical Geology 473, 74-89. (S) plays a significant role in saline environments, and sulfate (SO42 ?) is an important component of the biogeochemical S-cycle since it acts as the main electron acceptor in anoxic sediments. The purpose of this paper is to evaluate the fate of S, its origin, and processes affecting sulfate outcome in the hypersaline Pétrola Lake in the Castilla-La Mancha region (High Segura Basin, SE Spain). The lake is the terminal discharge zone of an endorheic basin with considerable anthropogenic pressures. Anthropogenic activities (mainly agricultural inputs and wastewater discharge), together with bedrock leaching of sulfate and sulfide-rich sediments, increase dissolved SO42 ? in surface and groundwater up to 123,000 mg/L. The source and fate of sulfate in this environment was investigated coupling hydrochemistry, including hydrogen sulfide (H2S) microprofiles, isotopic analyses (δ34S, δ18OSO4, δ2HH2O, δ18OH2O, and tritium), mineralogical determinations, and molecular biology tools (16S rDNA amplification and sequencing). The origin of dissolved SO42 ? in water is related to pyrite oxidation from Lower Cretaceous sediments, and secondary gypsum dissolution. Under the lake, dissolved SO42 ? decreases with depth, controlled by three main processes: (1) seasonal evaporation cycles, (2) hydrodynamic instability caused by the different density-driven groundwater flow, and (3) sulfate-reduction processes, i.e. dissimilatory bacterial sulfate reduction (BSR). These processes control the continuous recycling of sulfur in the system. Lake water and groundwater are in hydraulic connection, and a density-driven flow (DDF) is able to transport reactive organic matter and dissolved SO42 ? towards the underlying aquifer. Hydrochemical evolution in depth, H2S production (up to 0.024 nmol/cm3·s) and the presence of sulfate-reducing bacteria suggest the existence of BSR processes. However, isotope techniques are insufficient to elucidate BSR processes since their isotopic effect is masked by low isotope fractionation and high SO42 ? concentrations. The pattern here described may be found in other saline basins worldwide.van der Meer, F., 2018. Near-infrared laboratory spectroscopy of mineral chemistry: A review. International Journal of Applied Earth Observation and Geoinformation 65, 71-78. is the science concerned with the investigation and measurement of spectra produced when materials interacts with or emits electromagnetic radiation. Commercial infrared spectrometer were designed from the 1950’s onward and found their way into the pharmaceutical and chemical industries. In the 1970’s and 1980’s also natural sciences notably mineralogy and vegetation science started systematically to measure optical properties of leaves and minerals/rocks with spectrometers. In the last decade spectroscopy has made the step from qualitative observations of mineral classes, soil type and vegetation biomass to quantitative estimates of mineral, soil and vegetation chemistry. This resulted in geothermometers used to characterize metamorphic and hydrothermal systems and to the advent of foliar biochemistry. More research is still needed to bridge the gap between laboratory spectroscopy and field spectroscopy. Empirical studies of minerals either as soil or rock constituents (and vegetation parameters) derived from regression analysis of spectra against chemistry is important in understanding the physics of the interaction of electromagnetic radiation and matter which in turn is important in the design of future satellite missions. Physics based models and retrievals are needed to operationalize these relationships and implement them in future earth observation missions as these are more robust and easy to transfer to other areas and data sets.Van Meulebroek, L., De Paepe, E., Vercruysse, V., Pomian, B., Bos, S., Lapauw, B., Vanhaecke, L., 2017. Holistic lipidomics of the human gut phenotype using validated ultra-high-performance liquid chromatography coupled to hybrid Orbitrap mass spectrometry. Analytical Chemistry 89, 12502-12510. lipids are assigned a plethora of biological functions, it is evident that dysregulated lipid metabolism signifies a key element in many pathological conditions. With this rationale, this study presents a validated lipidomics platform to map the fecal lipidome, which integrates unique information about host–gut microbiome interactions, gastrointestinal functionality, and dietary patterns. This particular method accomplished coverage across all eight lipid categories: fatty acyls, glycerolipids, phosphoglycerolipids, polyketides, prenols, saccharolipids, sphingolipids, and sterols. Generic extraction of freeze-dried feces was achieved by solid–liquid extraction using methanol and methyl tert-butyl ether. Extracted components were separated by liquid chromatography, whereby the selected ethylene-bridged hybrid phenyl ultra-high-performance liquid chromatography stationary phase allowed fast separation of both individual lipid species and categories. Detection was achieved by high-resolution full-scan Q-Exactive Orbitrap mass spectrometry and covered a broad m/z scan range (67–2300 Da). Method validation was performed in a targeted fashion to evaluate the analytical performance across all lipid categories, revealing excellent linearity (R2 ≥ 0.9921), acceptable repeatability (coefficients of variance ≤15.6%), and stable recovery (coefficients of variance ≤11.9%). Method suitability for untargeted fingerprinting was verified, demonstrating adequate linearity (R2 ≥ 0.90) for 75.3% and acceptable repeatability (coefficients of variance ≤30%) for 84.5% of about 9000 endogenous fecal compounds. Eventually, the potential of fecal lipidomics was exemplified within a clinical context of type 2 diabetes, thereby revealing significant perturbations [orthogonal partial least-squares discriminant analysis Q2(Y) of 0.728] in the fecal lipidome between participants with normal blood glucose levels (n = 26) and those with type 2 diabetes (n = 17).Vigne, S., Alava, T., Videlier, H., Mahieu, R., Tassetti, C.-M., Duraffourg, L., Progent, F., 2017. Gas analysis using a MEMS linear time-of-flight mass spectrometer. International Journal of Mass Spectrometry 422, 170-176. paper presents the optimization of the ionization, extraction and focalization of our new generation of microfabricated time-of-flight mass spectrometer (μ-TOF). Using electron impact ionization, we show ionization efficiencies in the range of 1.10?6 ion/neutral, which is in the same order of magnitude as macroscale electron impact ionizers. A generated ion current in the range of a few tens of nanoamperes lead to an ionization yield around 0.1%, in the same range as the best microfabricated ionizers. The extracted and focalized ion beam is collected in a Micro Channel Plate detector and used to record mass spectra. Using decreasingly concentrated gas mixtures, we show the ability of the linear microfabricated time-of-flight mass spectrometer to detect up to 100 ppm of alkanes in helium. This work pulls the μ-TOF one step closer towards a fully integrated portable analytical system.Vigneron, A., Alsop, E.B., Cruaud, P., Philibert, G., King, B., Baksmaty, L., Lavallée, D., Lomans, B.P., Kyrpides, N.C., Head, I.M., Tsesmetzis, N., 2017. Comparative metagenomics of hydrocarbon and methane seeps of the Gulf of Mexico. Scientific Reports 7, Article 16015. and gas percolate profusely through the sediments of the Gulf of Mexico, leading to numerous seeps at the seafloor, where complex microbial, and sometimes animal communities flourish. Sediments from three areas (two cold seeps with contrasting hydrocarbon composition and a site outside any area of active seepage) of the Gulf of Mexico were investigated and compared. Consistent with the existence of a seep microbiome, a distinct microbial community was observed in seep areas compared to sediment from outside areas of active seepage. The microbial community from sediments without any influence from hydrocarbon seepage was characterized by Planctomycetes and the metabolic potential was consistent with detrital marine snow degradation. By contrast, in seep samples with methane as the principal hydrocarbon, methane oxidation by abundant members of ANME-1 was likely the predominant process. Seep samples characterized by fluids containing both methane and complex hydrocarbons, were characterized by abundant Chloroflexi (Anaerolinaceae) and deltaproteobacterial lineages and exhibited potential for complex hydrocarbon degradation. These different metabolic capacities suggested that microorganisms in cold seeps can potentially rely on other processes beyond methane oxidation and that the hydrocarbon composition of the seep fluids may be a critical factor structuring the seafloor microbial community composition and function.Vincent, S.G.T., Reshmi, R.R., Hassan, S.J., Nair, K.D., Varma, A., 2017. Predominant terminal electron accepting processes during organic matter degradation: Spatio-temporal changes in Ashtamudi estuary, Kerala, India. Estuarine, Coastal and Shelf Science 198, 508-517. microbial communities in the anoxic zones degrade organic matter in estuarine sediments. Thermodynamic energy yield for the oxidation reactions with various electron acceptors decreases in the order of O2> NO3- > Mn4+> Fe3+> SO42- > CO2. The predominant terminal electron accepting (TEA) process has an influence on the biogeochemical cycles of nutrients as well as the production of important greenhouse gases such as nitrous oxide and methane from estuarine sediments. The research questions of this study were (1) what are the environmental factors (pH, salinity, organic carbon, sulphate, redox potential) explaining variability in TEA activities such as nitrate reduction rate (NRR), iron reduction rate (IRR), sulphate reduction rate (SRR) and methane production rate (MPR) and (2) which is the predominant TEA process during degradation of organic matter. To determine the TEA activities, sediment samples collected from 13 sampling stations of Ashtamudi estuary during monsoon 2014 and summer 2015 were incubated with sulphate depleted artificial seawater, under anaerobic conditions for 72 h, in microcosms. Spatial variations dominated temporal variations for environmental variables. Nevertheless, biogeochemical processes showed a distinct seasonal variation. Total TEA activity was higher during summer than monsoon, indicating the higher heterotrophic microbial activity favored by high temperature. Individually, SRR was the maximum during summer, while NRR, IRR and MPR were the maximum during monsoon. Sulphate reduction was observed to be the predominant electron accepting process in all sampling stations with cumulative values of 3125.79 and 4046.07 nmol cm-3 day-1 during monsoon and summer respectively. This was followed by NRR, IRR and MPR. Although thermodynamically more favorable, NRR could not predominate due to scarcity of nitrate in sediments. Nevertheless, two-fold and five-fold increase in methanogenesis and denitrification were observed respectively during monsoon in sampling stations, which cannot be ignored, owing to the importance of methane and nitrous oxide as a potent greenhouse gas.Vu, H.P., Black, J.R., Haese, R.R., 2018. The geochemical effects of O2 and SO2 as CO2 impurities on fluid-rock reactions in a CO2 storage reservoir. International Journal of Greenhouse Gas Control 68, 86-98. for CO2 capture could be reduced if CO2 gas impurities can be co-injected and do not adversely affect the long-term CO2 containment. This project, as a part of the Callide Oxyfuel Project, investigates the geochemical impacts of the CO2 impurities SO2 and O2 on mineral-fluid reactions in a siliciclastic reservoir. In a single-well push-pull field experiment CO2-saturated water with and without impurities was injected into the reservoir. The injection water was allowed to interact with minerals in the reservoir for three weeks, during which water was back-produced and sampled on three occasions. Four soluble tracers were added to the injection water to estimate the proportions of injection and formation water in the back-produced water. Redox state, speciation and reaction pathway modelling are used as part of the data interpretation. Once injected, SO2 (67 ppm vol/vol, initially as a dissolved impurity in CO2) was dissolved and oxidised, leading to sulphate formation. The alkalinity of the injection water counteracted any substantial decrease in pH, which would otherwise occur due to sulphuric acid formation, thus inhibiting additional mineral dissolution. After being injected, O2 (6150 ppm vol/vol, dissolved impurity in CO2) led to immediate oxidative dissolution of pyrite. Consequently, the SO42? concentration increased rapidly and dissolved iron is predicted to precipitate as hematite. Overall, the impact of CO2 impurities was minimal.Waggoner, D.C., Hatcher, P.G., 2017. Hydroxyl radical alteration of HPLC fractionated lignin: Formation of new compounds from terrestrial organic matter. Organic Geochemistry 113, 315-325. oxygen species (ROS) are thought to play an important, although poorly understood, role in modifying the composition of terrigenous-derived dissolved organic matter (tDOM) upon export to aquatic systems. Of the dominant ROS in natural systems, OH has been shown to substantially modify lignin under laboratory conditions, simulating processes responsible for transformation of DOM in natural waters. Utilizing high performance liquid chromatography (HPLC) in conjunction with ultrahigh resolution mass spectrometry, we examined HPLC fractionated lignin extracts in an effort to establish which fractionated components of the lignin extract were (i) most susceptible to attack by OH and (ii) most likely to be responsible for compounds observed in the DOM. The results indicate that the most polar components of the lignin extract, representing tDOM, could be responsible for a large portion of newly generated formulas observed within DOM in natural waters. This suggests that partially oxidized lignin may be readily altered to compounds observed in DOM which are not typically associated with terrigenous OM, such as alicyclic and condensed aromatic-like compounds.Wahi, R., Zuhaidi, N.F.Q.a., Yusof, Y., Jamel, J., Kanakaraju, D., Ngaini, Z., 2017. Chemically treated microwave-derived biochar: An overview. Biomass and Bioenergy 107, 411-421., a carbon-rich material, can be produced via microwave pyrolysis, as a more energy and cost saving method compared to conventional externally heated pyrolysis. Biochar has versatile applications, for example, for soil amendment purpose and pollutant removal from wastewater. Chemical treatment has been proven to improve the physical and chemical properties of biochar for better applicability. Thus, extensive amount of research has been conducted on chemical treatment of conventional biochar, and several review articles have discussed published works on the chemically treated conventional biochar. However, there has been no review on works involving the chemically treated microwave-derived biochar, by far. This paper presents an overview of the current development and improvement on chemical treatment methods and applications of microwave-derived biochar.Walters, C.C., Wang, F.C., Higgins, M.B., Madincea, M.E., 2018. Universal biomarker analysis using GC×GC with dual FID and ToF-MS (EI/FI) detection. Organic Geochemistry 115, 57-66. and qualitative biomarker analysis using GC-MS or GC-MS/MS is limited by chromatographic separation and variable detector response. Here, we present a GC×GC method that provides absolute quantification and non-targeted pseudo MS-MS for all resolved saturated hydrocarbon components in petroleum. Two innovations make this possible: Agilent capillary flow technology (CFT) and the JEOL JMS-T100GCV 4G ToF-MS capable of electron impact (EI) and field ionization (FI) of the GC×GC effluent. Two sequential chromatograms run using EI- and FI-MS are combined, yielding pseudo parent-daughter spectra. The effluent is split at a constant ratio allowing for easy quantitation by FID and eliminating the need for determining MS-response factors. We demonstrate the technique as offering a means for universal biomarker analysis of saturated hydrocarbon fractions.Wan, K., Ji, P., Miao, Z., Chen, Z., Wan, Y., He, Q., 2017. Analysis of water forms in lignite and pore size distribution measurement utilizing bound water as a molecular probe. Energy & Fuels 31, 11884-11891. on the congelation characteristics, different types of water in lignite and their drying behavior were investigated by using low-temperature differential scanning calorimetry over a temperature range from 25 to ?80 °C. The water in lignite was classified into three types: free water, bound water, and nonfreezable water. It was shown that during drying, the free water in lignite was removed first, and then the bound water began to be evaporated. With the moisture decreasing, the congelation peak of free water moves toward lower temperature, which may be explained by the formed capillary force distribution in the pores driving the free water to flow toward the smaller pores and increasing the confinement effect of the pores. However, for bound water, this mobility was restricted by the stronger coal–water interaction; thus, its congelation peak remained at around ?42 °C. The amounts of three types of water were determined by a new method. It shown that all of the bound water and more than 30% of nonfreezable water needs to be removed in real drying cases. Based on the melting point depression of bound water in lignite, using bound water as a molecular probe, the pore size distribution of lignite was also determined. The maximum and minimum measured pore diameters were 86.47 and 7 nm, respectively.Wan, T., Wang, W., Jiang, J., Zhang, Y., 2018. Pore-scale analysis of gas huff-n-puff enhanced oil recovery and waterflooding process. Fuel 215, 561-571. the complex pore network and fractures are crucial to efficiently producing tight gas and oil reservoirs. A better understanding of gas flooding recovery mechanisms will lead to improved successes of EOR (enhanced-oil-recovery) practices in tight oil formations. In this paper, the gas huff-n-puff efficiency performance in tight oil formations is under surveillance by NMR technology. It is of our interest to estimate the recoverable or movable oil saturation by waterflooding and gas flooding at different types of pore sizes. Fortunately, NMR measurements provide an avenue for calculating the recoverable reserves in different types of pore system (micropores, mesopores and macropores). The NMR T2 relaxation time closely correlates with the pore sizes. The NMR technique was used to analyze the mechanisms of gas flooding and waterflooding in shale formations from a microscopic scale view. In this paper, a series of nitrogen huff-n-puff experiments were conducted on tight cores and NMR was used in the whole huff-n-puff process to observe the gas flooding efficiency at different cycles. The NMR relaxation spectrum reveals that most of the oil production happened in the first few cycles, less oil is recovered in the subsequent cycles. The recoverable oil of this field falls into a range of 1–100?ms?T2 relaxation pore size system. Oil production only occurs in certain type of pores. Due to the nanometer or micrometer scales of the pores and pore throats, cycle depletion time has considerable effect on oil recovery from tight oil reservoirs in the first few cycles. The literature lacks a study of the NMR investigation of gas huff-n-puff effect in tight formations. The purpose of this current study is to illustrate the application of NMR technique in interpreting the effect of cyclic nitrogen injection in tight oil reservoirs.Wang, A.-j., Ye, X., Liu, J.T., Xu, Y.-h., Yin, X.-j., Xu, X.-h., 2017. Sources of settling particulate organic carbon during summer in the northern Taiwan Strait. Estuarine, Coastal and Shelf Science 198, 487-496. settling of particulate organic carbon is significant for the vertical transfer and burial of organic carbon. Using time-series sediment traps, we collected settling particulate matter in the near-bottom layer (8 mab [meters above bed]) over eight continuous days in the continental shelf waters of the northern Taiwan Strait and analyzed the particulate organic carbon content. The observational results indicated that the deposition flux in the continental shelf waters during the summer in the north-eastern Taiwan Strait is 0.86 g/m2·d ～10.68 g/m2·d; the corrected deposition flux is lower than the measured value by approximately 4.5%–30.6%. The particulate organic carbon (POC) content and δ13C org‰ value are 0.589%–0.741% and ?20.74‰～?22.61‰. The δ13C org‰ indicated that the settling particulate matter was primarily from marine sources at a contribution rate of 70%–88%. Settling particulate matter primarily came from the re-suspension of bottom sediment which accounted for 65%–85% of settling particulate matter. The rising thermocline and halocline near the bottom can strengthen the contribution of re-suspension to the settling particulate organic carbon.Wang, B.-B., Liu, X.-T., Chen, J.-M., Peng, D.-C., He, F., 2018. Composition and functional group characterization of extracellular polymeric substances (EPS) in activated sludge: the impacts of polymerization degree of proteinaceous substrates. Water Research 129, 133-142. of extracellular polymeric substances (EPS) in activated sludge strongly depend on wastewater substrates. Proteinaceous substrates (ProS) present in heterogeneous polymeric form are intrinsic and important parts of wastewater substrates for microorganisms in activated sludge systems. However, correlations between ProS and characteristics of EPS are scarce. This study systematically explored the impacts of monomeric (Mono-), low polymeric (LoP-) and high polymeric (HiP-) ProS on compositions and functional groups of EPS in activated sludge. The results showed that the change of polymerization degree of ProS significantly altered the composition of EPS. Compared to EPSMono-ProS, the proportion of proteins in EPSLoP-ProS and EPSHiP-ProS increased by 12.8% and 27.7%, respectively, while that of polysaccharides decreased by 22.9% and 63.6%, respectively. Moreover, the proportion of humic compounds in EPSLoP-ProS and EPSHiP-ProS were ～6 and ～16–fold higher than that in EPSMono-ProS, respectively. The accumulation of humic compounds in EPS increased the unsaturation degree of EPS molecules, and thereby reduced the energy requirement for electrons transition of amide bonds and aromatic groups. Size exclusion chromatography (SEC) analyses detected more molecular clusters in EPSHiP-ProS, indicating more complex composition of EPS in HiP-ProS fed activated sludge. Spectroscopic characterization revealed the dominance of hydrocarbon, protein, polysaccharide and aromatic associated bonds in all three EPS. Nevertheless, with the increase of polymerization degree of ProS, the protein associated bonds (such as CONH, CO, NC, NH) increased, while the polysaccharide associated bonds (such as COC, COH, OCOH) decreased. This paper paves a path to understand the role of ProS in affecting the production and characteristics of EPS in biological wastewater treatment systems.Wang, C., Li, T., Gao, H., Zhao, J., Zhang, M., 2017. Study on the blockage in pores due to asphaltene precipitation during different CO2 flooding schemes with NMR technique. Petroleum Science and Technology 35, 1660-1666. flooding is an effective way in the tertiary oil recovery. While asphaltene often precipitates from the crude oil during the CO2 flooding, and the mechanisms of blockage resulting from asphaltene precipitation is still unclear in different CO2 flooding schemes. In this work, pure-CO2 flooding, water-alternating-CO2 flooding (WAG), and CO2-foam flooding were applied to conduct the core-flooding experiments. Then, as for each flooding scheme, we quantitatively investigated the blockage degree in different pores due to asphaltene precipitation with nuclear magnetic resonance (NMR) technique. Tests results show that CO2-foam flooding has a relatively higher blockage degree both in the smaller pores and the larger pores than WAG and pure-CO2 flooding. Although pure-CO2 flooding has the least asphaltene precipitation and blockage degree among three flooding schemes, its oil recovery degree is far less than the other two flooding schemes. Compared with pure-CO2 flooding and CO2-foam flooding, WAG flooding has the highest oil recovery and an acceptable asphaltene precipitation.Wang, G., Ju, Y., Huang, C., Long, S., Peng, Y., 2017. Longmaxi-Wufeng shale lithofacies identification and 3-D modeling in the northern Fuling Gas Field, Sichuan Basin. Journal of Natural Gas Science and Engineering 47, 59-72. composition and total organic carbon (TOC) content of shale is related with rock brittleness and gas content, respectively. Shale lithofacies defined by them can effectively describe the heterogeneity of shale gas reservoirs. Therefore, a 3-D model of shale lithofacies was constructed for the Longmaxi-Wufeng Shale in Fuling Gas Field, Sichuan Basin. Firstly, three criteria were proposed to define ten shale lithofacies in Longmaxi-Wufeng Shale. The core- and elementary capture spectroscopy (ECS)-defined shale lithofacies with the wireline logs at their location consisted of a training dataset with 1044 sets of data for predicting shale lithofacies by conventional logs. And, artificial neural network and hierarchical decomposition algorithms were developed to achieve this prediction. Due to the instability of horizontal wellbore, a process of quality control was completed to remove all the low-quality data. To construct the 3-D model using data primarily from horizontal wells, it is critical to fix at least two special issues which are not common for the cases using data from only vertical wells. The relationship between horizontal wells and formation surfaces become much more complex, and data from wells was biased and failed to represent the distribution feature of the study area. Methods, including establishing pseudo vertical wells to provide more formation data and constructing 3-D probability trend model, were developed in this research to overcome these issues. The 3-D modeling of shale lithofacies is very helpful for optimizing the design of horizontal well trajectories and hydraulic fracture stimulation strategies.Wang, H., Liang, J., Li, X., Ji, X., Zhang, Q., Huang, R., 2017. Analysis of the geological conditions for shale gas accumulation: Two different Carboniferous marine-continental transitional facies in the Bayanhot Basin, China. Energy & Fuels 31, 11515-11522. sedimentary environment plays an important role in the enrichment of shale gas resources. In this paper, the characteristics of the marine-continental transitional sedimentary environments in the Bayanhot Basin are studied via laboratory analysis, scanning electron microscopy, and comparative analyses of field data. A differential analysis of the shale gas enrichment conditions was conducted by comparing the shale organic geochemical characteristics and performing a petrophysical analysis of the southern and northern sedimentary environments in the Bayanhot Basin. The findings showed that (1) the hydrocarbon-generating potential of the shale in the northern delta sedimentary environment is better than that of the shale in the southern combined sedimentary system based on the total organic carbon content and organic matter type and (2) the shale in the southern Bayanhot Basin, which has better shale petrophysical microcharacteristics, presents superior gas accumulation and fracturing operation characteristics compared to the shale in the northern part.Wang, H., Zeng, Y., Guo, C., Bao, Y., Lu, G., Reinfelder, J.R., Dang, Z., 2018. Bacterial, archaeal, and fungal community responses to acid mine drainage-laden pollution in a rice paddy soil ecosystem. Science of The Total Environment 616–617, 107-116. sufficient clean water, the paddy soils along the Hengshi River have suffered from long-term acid mine drainage (AMD) contamination. The impacted cropland is too heavily contaminated to grow food safely. The microbial communities inhabiting the environment play pivotal roles in the crop growth, health, and ecological services. In this study, the bacterial, archaeal, and fungal communities in the impacted paddy soil were examined using high-throughput Illumina MiSeq sequencing. The results showed that AMD irrigation considerably enriched the bacterial phylum Acidobacteria and the archaeal phylum Crenarchaeota, while the fungal community was more stable. The abundances of Acidobacteria and Crenarchaeota were significantly positively correlated with the AMD-related environmental factors of pH and heavy metals (Cu, Pb, and Zn). In the most contaminated samples, communities were dominated by the bacteria Candidatus Solibacter and Candidatus Koribacter from the Acidobacteria family. Functional gene profile analysis demonstrated that the energy metabolic processes of the microbial communities, especially C/N related pathways, have adjusted and are well-adapted to tolerating AMD contamination. The present study described the structural and functional differentiation of microbial communities in the rice paddy soil under AMD irrigation. The results are useful for the development of bioremediation strategies using native microbes in the cleanup and biorestoration of AMD-contaminated agriculture soil.Wang, J.-X., Xie, W., Zhang, Y.G., Meador, T.B., Zhang, C.L., 2017. Evaluating production of cyclopentyl tetraethers by Marine Group II Euryarchaeota in the Pearl River Estuary and coastal South China Sea: Potential impact on the TEX86 paleothermometer. Frontiers in Microbiology 8, 2077. doi: 10.3389/fmicb.2017.02077. [TetraEther indeX of glycerol dialkyl glycerol tetraethers (GDGTs) with 86 carbon atoms] has been widely applied to reconstruct (paleo-) sea surface temperature. Marine Group I (MG-I) Thaumarchaeota were thought to be the primary source of GDGTs constituting the TEX86 formula; however, recent research has suggested that Marine Group II (MG-II) Euryarchaeota may also contribute significantly to the GDGT pool in the ocean. Little is known regarding the potential impact of MG-II Euryarchaeota-derived GDGTs on TEX86 values recorded in marine sediments. In this study, we assessed the relationship between distributions of GDGTs and MG-II Euryarchaeota and evaluated its potential effect on the TEX86 proxy. Lipid and DNA analyses were performed on suspended particulate matter and surface sediments collected along a salinity gradient from the lower Pearl River (river water) and its estuary (mixing water) to the coastal South China Sea (SCS, seawater). TEX86-derived temperatures from the water column and surface sediments were significantly correlated and both were lower than satellite-based temperatures. The ring index (RI) values in these environments were higher than predicted from the calculated TEX86-RI correlation, indicating that the GDGT pool in the water column of the PR estuary and coastal SCS comprises relatively more cyclopentane rings, which thereby altered TEX86 values. Furthermore, the abundance of MG-II Euryarchaeota 16S rRNA gene in the mixing water was two to three orders of magnitude higher than those observed in the river or seawater. Significant linear correlations were observed between the gene abundance ratio of MG-II Euryarchaeota to total archaea and the fractional abundance of GDGTs with cyclopentane rings. Collectively, these results suggest that MG-II Euryarchaeota likely produce a large proportion of GDGTs with 1–4 cyclopentane moieties, which may bias TEX86 values in the water column and sediments. As such, valid interpretation of TEX86 values in the sediment record, particularly in coastal oceans, should consider the contribution from MG-II Euryarchaeota.Wang, J., He, Y., Zhang, Y., Zhao, X., Peng, Z., Wang, S., Zhang, T., 2018. Research on cationic surfactant adsorption performance on different density lignite particles by XPS nitrogen analysis. Fuel 213, 48-54. is well known for its hard-to-float property. Many surfactants, including anionic, cationic and non-ionic have been applied to improve the floatation efficiency. In this work, cationic dodecylamine was applied to pretreat the lignite samples with different densities, which are ?1.45?g/cm3, 1.45–1.80?g/cm3 and +1.80?g/cm3. The surface charged properties of the raw samples were determined by a zeta potential analyzer. The adsorption performance was characterized by XPS and UV/VIS spectrophotometer methods. From the surface zeta-potential results, three curves of zeta-potential figures versus pH value are similar to each other qualitatively in the pH range 5–8, which indicates that the organic structure has the similar ionization/ protonation ability with inorganic minerals at neutral pH. The negatively charged surfaces attract the cationic dodecylamine molecules at neutral pH for the three density fractions, which is shown by the XPS narrow sweep of heteroatom nitrogen before and after the pretreatment process. On the lignite surface, nitrogen was mainly existed in two forms of pyrrolic and quaternary. After the pretreatment, the quaternary-N peak was increased on the lignite surface due to the adsorption of dodecylamine molecules, especially on the surface of the highest density fraction. Correspondingly, UV/VIS spectrophotometer results showed that the adsorption amounts of dodecylamine molecules were 11.4, 18.7 and 20.0?mg/g on the surface of the samples from low to high density. On the other hand, the flotation result showed that more high ash particles and some low ash ones were both floated with the increase of dodecylamine dosage. Hence, if dodecylamine is to be used in lignite flotation, reagents should be added to selectively depress the adsorption process of cationic dodecylamine on the low or high ash particles.Wang, J., Wen, X., Li, S., 2017. Differentiated correction on the signal intensity dependence of GasBench II-IRMS from blank effect and instrument nonlinear effect. International Journal of Mass Spectrometry 422, 80-87. Isotope Ratio Mass Spectrometry (CF-IRMS) coupled with a GasBench II was designed to rapidly analyze δ13C in carbonate or CO2 in air. The dependence of measured δ13C (δ13Cm) on signal intensity (peak area or peak height) was the main error source resulting from blank effect of samples and/or instrument itself effect. To determine the reasons and origins of signal intensity dependence, eight signal intensity gradients for two carbonate (δ13C values were ?49.64 and 1.61‰, respectively) and a gas mixture of 0.3% CO2 in He (δ13C = ?19.32‰) standards were made respectively. The results showed that there was obvious signal intensity dependence, in particular when sample amount (peak area) was smaller. Given that the dependence was caused by blank effect and/or instrument nonlinear effect, without considering the blank effect, the signal intensity dependence could not be eliminated directly by the instrument nonlinear correction (empirical equation) methods However, it could be eliminated by blank correction (indirect subtraction method). In practice, blank effect should be corrected first, and then the instrument nonlinear effect.Wang, J., Zhu, J., Si, L., Du, Q., Li, H., Bi, W., Chen, D.D.Y., 2017. High throughput screening of phenoxy carboxylic acids with dispersive solid phase extraction followed by direct analysis in real time mass spectrometry. Analytica Chimica Acta 996, 20-28. high throughput, low environmental impact methodology for rapid determination of phenoxy carboxylic acids (PCAs) in water samples was developed by combing dispersive solid phase extraction (DSPE) using velvet-like graphitic carbon nitride (V-g-C3N4) and direct analysis in real time mass spectrometry (DART-MS). Due to the large surface area and good dispersity of V-g-C3N4, the DSPE of PCAs in water was completed within 20 s, and the elution </topics/biochemistry-genetics-and-molecular-biology/elution> of PCAs was accomplished in 20 s as well using methanol. The eluents were then analyzed and quantified using DART ionization source coupled to a high resolution mass spectrometer, where an internal standard was added in the samples. The limit of detection ranged from 0.5 ng L?1 to 2 ng L?1 on the basis of 50 mL water sample; the recovery 79.9–119.1%; and the relative standard deviation 0.23%–9.82% (≥5 replicates). With the ease of use and speed of DART-MS, the whole protocol can complete within mere minutes, including sample preparation , extraction, elution, detection and quantitation. The methodology developed here is simple, fast, sensitive, quantitative, requiring little sample preparation and consuming significantly less toxic organic solvent, which can be used for high throughput screening of PCAs and potentially other contaminants in water.Wang, Q., Lu, H., Wang, T., Liu, D., Peng, P.a., Zhan, X., Li, X., 2018. Pore characterization of Lower Silurian shale gas reservoirs in the Middle Yangtze region, central China. Marine and Petroleum Geology 89, Part 1, 14-26. shales from Lower Silurian are widely distributed in the Middle Yangtze region, central China. However, the lack of fundamental data for shale gas reservoirs increases the difficulty of gas exploration. In this study, 34 core samples were collected to characterize the shale pore structure and conduct a preliminary evaluation of the shale gas reservoir. The TOC (total organic carbon) content of the successively-deposited black shales range from 1.6% to 5.9%, while the total porosity range from 0.5% to 4.2%. The positive correlation between TOC and porosity indicates that TOC is the key factor determining porosity. The major component of the mineral matrix is quartz (content of 21.4%–69.2%), followed by clay minerals (content of 16.7%–44.5%). Field-emission scanning electron microscopy (FE-SEM) and energy dispersive X-ray spectroscopy (EDS) results illustrate that organic matter, mixed with clay minerals, can form an organo-clay complex containing many nanopores. Furthermore, larger organic pores are developed in organo-clay complexes with higher clay content than in those with lower clay content.Correlational analyses between pore volume (or pore surface area) and TOC (or clay content) demonstrate that micropores are associated with organic matter, while mesopores and macropores are probably associated with clay minerals. Many of the clay-related nanopores are organic in nature and are developed in organo-clay complexes containing both organic matter and clay minerals. Overall, the TOC content controls development of nanopores in the shale pore structure, followed by clay content. The DFT-derived PSD indicates that the pore volume is comprised primarily of pores having widths larger than 10 nm, while the surface area is comprised primarily of micropores. When considering the gas in place model and mechanisms of shale gas storage, further shale gas exploration in central China should aim to the deep (>1000 m) and well preserved Longmaxi Shales.Wang, S., Pomerantz, A.E., Xu, W., Lukyanov, A., Kleinberg, R.L., Wu, Y.-S., 2017. The impact of kerogen properties on shale gas production: A reservoir simulation sensitivity analysis. Journal of Natural Gas Science and Engineering 48, 13-23. shales are complex materials with transport occurring over many length scales, from relatively large systems such as natural and induced fractures to relatively small systems including kerogen-hosted pores of nearly molecular size. Here we present results of a sensitivity analysis performed using reservoir simulation designed to test how these different pore space length scales impact gas production. The shale is modeled as a triple porosity system comprising: first, natural and induced fractures; second, kerogen-hosted pores of approximately 25?nm diameter (as are typically observed in SEM images); and third, kerogen-hosted pores of approximately 1?nm diameter (which are below the size detectable by SEM but are typically observed in X-ray diffraction and gas adsorption experiments). In these simulations, the smaller kerogen-hosted pores act as a source term, releasing primarily adsorbed gas. The larger kerogen-hosted pores contribute to storage and transport, serving both as a source of gas on their own and a system through which the gas originating in the smaller pores can flow. As a result, the volume of the smaller pores impacts mainly the later production, when the reservoir pressure is near or below the Langmuir pressure. The volume of the larger pores impacts mainly the early stage of production, when mainly free gas is being produced. The radius of the smaller pores impacts the late stage of production, as smaller pores have greater surface area and therefore larger Langmuir volume. The radius of the larger pores has little impact on the ultimate recovery but instead impacts the production rate, as larger pores correlate with greater permeability. The results suggest that measurements of the variation of kerogen properties—performed potentially using cuttings, cores, or logs—can be used to refine parameters in reservoir simulations.Wang, S., Wang, Z., Zhou, L., Shi, X., Xu, G., 2017. Comprehensive analysis of short-, medium-, and long-chain acyl-coenzyme A by online two-dimensional liquid chromatography/mass spectrometry. Analytical Chemistry 89, 12902-12908. A (CoA) is a pivotal metabolic intermediate in numerous biological processes. However, comprehensive analysis of acyl-CoAs is still challenging as the properties of acyl-CoAs greatly vary with different carbon chains. Here, we designed a two-dimensional liquid chromatography method coupled with high-resolution mass spectrometry (2D LC/HRMS) to cover all short-, medium-, and long-chain acyl-CoAs within one analytical run. Complex acyl-CoAs were separated into two fractions according to their acyl chains by the first dimensional prefractionation. Then, two fractions containing short-chain acyl-CoAs or medium- and long-chain acyl-CoAs were further separated by the two parallel columns in the second dimension. Nineteen representative standards were chosen to optimize the analytical conditions of the 2D LC/HRMS method. Resolution and sensitivity were demonstrated to be improved greatly, and lowly abundant acyl-CoAs and acyl-CoA isomers could be detected and distinguished. By using the 2D LC/HRMS method, 90 acyl-CoAs (including 21 acyl-dephospho-CoAs) were identified from liver extracts, which indicated that our method was one of the most powerful approaches for obtaining comprehensive profiling of acyl-CoAs so far. The method was further employed in the metabolomics study of malignant glioma cells with an isocitrate dehydrogenase 1 (IDH1) mutation to explore their metabolic differences. A total of 46 acyl-CoAs (including 2 acyl-dephospho-CoAs) were detected, and 12 of them were dysregulated in glioma cells with the IDH1 mutation. These results demonstrated the practicability and the superiority of the established method. Therefore, the 2D LC/HRMS method provides a robust and reproducible approach to the comprehensive analysis of acyl-CoAs in tissues, cells, and other biological samples.Wang, X., Hayeck, N., Brüggemann, M., Yao, L., Chen, H., Zhang, C., Emmelin, C., Chen, J., George, C., Wang, L., 2017. Chemical characteristics of organic aerosols in Shanghai: A study by ultrahigh-performance liquid chromatography coupled with Orbitrap mass spectrometry. Journal of Geophysical Research: Atmospheres 122, 11,703-11,722. matter 2.5 (PM2.5) filter samples were collected in July and October 2014 and January and April 2015 in urban Shanghai and analyzed using ultrahigh-performance liquid chromatography coupled to Orbitrap mass spectrometry. The measured chromatogram-mass spectra were processed by a nontarget screening approach to identify significant signals. In total, 810–1,510 chemical formulas of organic compounds in the negative polarity (negative electrospray ionization (ESI?)) and 860–1,790 in the positive polarity (ESI+), respectively, were determined. The chemical characteristics of organic aerosols (OAs) in Shanghai varied among different months and between daytime and nighttime. In the January samples, organics were generally richer in terms of both number and abundance, whereas those in the July samples were far lower. More CHO? (compounds containing only carbon, hydrogen, and oxygen and detected in ESI?) and CHOS? (sulfur-containing organics) were found in the daytime samples, suggesting a photochemical source, whereas CHONS? (nitrogen- and sulfur-containing organics) were more abundant in the nighttime samples, due to nocturnal nitrate radical chemistry. A significant number of monocyclic and polycyclic aromatic compounds, and nitrogen- and sulfur-containing heterocyclic compounds, were detected in all samples, indicating that biomass burning and fossil fuel combustion made important contributions to the OAs in urban Shanghai. Additionally, precursor-product pair analysis indicates that the epoxide pathway is an important formation route for organosulfates observed in Shanghai. Moreover, a similar analysis suggests that 35–57% of nitrogen-containing compounds detected in ESI+ could be formed through reactions between ammonia and carbonyls. Our study presents a comprehensive overview of OAs in urban Shanghai, which helps to understand their characteristics and sources.Wang, X., Kellner, A.W.A., Jiang, S., Cheng, X., Wang, Q., Ma, Y., Paidoula, Y., Rodrigues, T., Chen, H., Say?o, J.M., Li, N., Zhang, J., Bantim, R.A.M., Meng, X., Zhang, X., Qiu, R., Zhou, Z., 2017. Egg accumulation with 3D embryos provides insight into the life history of a pterosaur. Science 358, 1197-1201.: Fossil eggs and embryos that provide unique information about the reproduction and early growth of vertebrates are exceedingly rare, particularly for pterosaurs. Here we report on hundreds of three-dimensional (3D) eggs of the species Hamipterus tianshanensis from a Lower Cretaceous site in China, 16 of which contain embryonic remains. Computed tomography scanning, osteohistology, and micropreparation reveal that some bones lack extensive ossification in potentially late-term embryos, suggesting that hatchlings might have been flightless and less precocious than previously assumed. The geological context, including at least four levels with embryos and eggs, indicates that this deposit was formed by a rare combination of events, with storms acting on a nesting ground. This discovery supports colonial nesting behavior and potential nesting site fidelity in the Pterosauria.Editor's Summary. Even more like birds: Ecological convergence between pterosaurs and birds is often invoked, but to what degree the two groups share behavior is debated. Wang et al. describe a site with more than 100 fossilized pterosaur eggs that reveals that hatchling pterosaurs were likely not as precocial as previously thought (see the Perspective by Deeming). Furthermore, the overlaying of multiple clutches suggests that the pterosaurs may have exhibited breeding site fidelity, similar to rookery-breeding seabirds. Thus, the similarity between these two groups goes beyond wings.Wang, X., Sheng, J., 2017. Gas sorption and non-Darcy flow in shale reservoirs. Petroleum Science 14, 746-754. sorption and non-Darcy flow are two important issues for shale gas reservoirs. The sorption consists of dissolution and adsorption. Dissolved gas and adsorbed gas are different. The former is dissolved in the shale matrix, while the latter is concentrated near the solid walls of pores. In this paper, the Langmuir equation is used to describe adsorption and Henry’s law is used to describe dissolution. The K coefficient in Henry’s law of 0.052?mmol/(MPa?g TOC) is obtained by matching experimental data. The amount of dissolved gas increases linearly when pressure increases. Using only the Langmuir equation without considering dissolution can lead to a significant underestimation of the amount of sorbed gas in shales. For non-Darcy gas flow, the apparent permeability model for free gas is established by combining slip flow and Knudsen flow. For adsorbed gas, the surface diffusion effect is also considered in this model. The surface diffusion coefficient is suggested to be of the same scale as the gas self-diffusion coefficient, and the corresponding effective permeability is derived. When 1/p increases, kapp/kD increases, but the relationship is not linear as the Klinkenberg effect suggests. The effect of adsorption on the gas flow is significant in nanopores ( r ≤ 2nm). Adsorption increases apparent permeability in shales at low pressures and decreases it at high pressures.Wang, X., Wei, G., Li, J., Chen, J., Gong, S., Li, Z., Wang, D., Xie, Z., Yang, C., Wang, Y., Hao, A., 2018. Geochemical characteristics and origins of noble gases of the Kela 2 gas field in the Tarim Basin, China. Marine and Petroleum Geology 89, Part 1, 155-163. on noble gases is important which can provide more information on gas origins and sources due to their special chemical inertness and genesis related to nuclear processes. However, few studies have been carried out on noble gases in the largest un-compartmentalized gas field in the Tarim Basin. In this study, molecular and isotopic compositions of noble gases and hydrocarbon gases in the Kela 2 gas field were analyzed. Hydrocarbon gases are the dominant gases, accompanied by minor N2, CO2 and extremely low contents of noble gases in the Kela 2 gas field. He content is generally 1 order of magnitude higher comparing to that of air, while Ne, Ar, Kr, and Xe contents are 1–3 orders of magnitude lower than corresponding atmospheric values. The δ13C2 value indicates natural gases in the Kela 2 gas field are typical coal-derived gases. Noble gases in the Kela 2 gas field are typical crustal derived source, mainly originating from decay of crustal radioactive elements. Natural gases in the Kela 2 gas field are speculated to be derived from the coal measures source rocks of Triassic to Jurassic with major contribution from coals and secondary contribution from mudstones.Wang, X., Wu, H., Luo, R., Xia, D., Jiang, Z., Han, H., 2017. Separation and detection of free D- and L-amino acids in tea by off-line two-dimensional liquid chromatography. Analytical Methods 9, 6131-6138. acids are currently paid attention to as new physiologically active substances. Foodstuffs and beverages containing D-amino acids are a matter of interest. Until now, the profiles of D-amino acids have not been reported in natural and fermented teas except theanine. In this study, an off-line 2D-HPLC method combining a Gemini C18 column and a CHIRALPAK? IC-3 column or a self-prepared poly(MQD-co-HEMA-co-EDMA) monolithic capillary column was employed for the separation and detection of D-amino acids in tea samples with the co-existence of a large amount of L-amino acids. The free amino acid fractions in longjing, black, oolong, and pu-erh tea samples were separated and collected after pre-column derivatization using 9-fluorenylmethoxycarbonyl (FMOC) chloride in the reversed-phase mode, and then were concentrated and separated to D- and L-forms on a chiral column. Among them, the D-form of isoleucine (Ile) (1.0–1.6%), alanine (Ala) (0.1–0.8%), phenylalanine (Phe) (0.1–0.4%), valine (Val) (0.2–0.3%), serine (Ser) (0.1–0.2%), aspartic acid (Asp) (0.2%), and proline (Pro) (0.1%) were detected in longjing and oolong teas. Differences between natural tea and fermented tea in the profiles of D-amino acids as well as the total amino acids were also observed. The results provided useful information for the bio-function research of D-amino acids in tea.Wang, Y.-P., Zhang, F., Zou, Y.-R., Sun, J.-N., Lin, X.-H., Liang, T., 2018. Oil source and charge in the Wuerxun Depression, Hailar Basin, northeast China: A chemometric study. Marine and Petroleum Geology 89, 665-686. samples collected from the Wuerxun Depression, Hailar Basin, northeast China were analyzed using GC-MS. The K1n Formation (including K1n2 and K1n1 members) consists mainly of argillaceous rock with relatively abundant organic matter and is considered to be the best source rock in the study area, whereas the K1t Formation and K1d1 member (Damoguaihe Formation) provide a limited contribution to the Wuerxun oils. Chemometric methods, i.e., principal component analysis (PCA) and multidimensional scaling (MDS), were used for oil-oil and oil-source rock correlations in this study. Based on PCA and geological evidence, the oils from northern Wuerxun originated primarily from source rocks of the K1n1 member that were charged ca. 100 Ma, whereas those in the southern Wuerxun form separate genetic groups I and II. When combined with trend surface analysis, the MDS technique also revealed variations in the depositional conditions and the maturity of the source rocks and oils. Group I oils, which have relatively higher maturity, are characterized by relatively high saturate/aromatic hydrocarbon ratios, high Pr/Ph ratios (>1), high Ts/(Ts + Tm) ratios, a slight predominance of C29 regular steranes, and more positive δ13C values of saturated and aromatic hydrocarbon fractions, whereas, the lower maturity group II oils have relatively low saturate/aromatic hydrocarbon ratios, low Pr/Ph ratios (<1), low Ts/(Ts + Tm) ratios, high C29 regular steranes and more negative δ13C values of saturated and aromatic hydrocarbon fractions. Analysis indicates that group I oils represent mixtures generated from the K1n1 and K1n2 members during the late hydrocarbon generation stage (ca. 25 Ma), whereas group II oils were primarily generated from the K1n1 member during the early oil generation stage (ca. 93 Ma). The distributions of group I and group II oils are mostly controlled by tectonic development in the southern Wuerxun Depression.Wang, Y., Ju, B., Chen, W., Zhang, K., Ye, Y., 2017. Simulation-assisted gas tracer test study of Tarim Yaha gas-condensate reservoir in China. Journal of Natural Gas Science and Engineering 48, 77-84. enhance oil recovery and optimize a production plan, injected water or gas fluid should be monitored and tracked, which can be realized by gas tracer technology. Tracer test technology has become an effective method for evaluating the flow condition of reservoirs and estimate reservoir properties. Gas tracers, such as chemical and radioactive materials, have been used to identify well-to-well connectivity, reservoir heterogeneity, high-permeability pay zones, sweep efficiency, and residual oil saturation. Moreover, tracer tests have been used to evaluate well interference among multiple hydraulically fractured wells and qualitatively predict possible fracture geometries. Therefore, the accurate quantification of tracer transport is of great importance. However, theoretical study of gas tracers in a condensate gas reservoir has not been thoroughly conducted to date. Current tracer transport models mostly focus on the gas tracer flow in oil reservoirs and cannot be directly applied to condensate gas reservoirs. To the best of our knowledge, the application of a gas tracer to recycle gas injection in gas condensate reservoirs has not been thoroughly studied. In this paper, we propose a mathematical model to quantitatively describe the gas tracer transport mechanism in condensate gas reservoirs. Our mathematical model is based on the mass conservation law and is numerically solved via the Integral Finite Difference method. The results predicted by our model have been compared to and verified by real data collected from the field. The model has been used to optimize the recovery of the Yaha Condensate Gas Field in the Tarim Basin, China. With the assistance of our tracer transport model, the pressure drawdown speed of the Yaha field has been successfully slowed from 0.8?MPa/year to 0.5?MPa/year. Generally, this study not only provides key insights into the transport mechanism of gas tracers but also presents the application of numerical tools to guide the production of gas condensate reservoirs. The technique introduced in this study could be potentially extended to condensate oil production in other fields.Wang, Y., Liao, L., Geng, A., Liu, D., 2018. Trapping pressure estimation of single gaseous inclusion using PVT simulation and its preliminary application in NE Sichuan, China. Marine and Petroleum Geology 89, Part 1, 225-231. this paper, we proposed an alternative way to estimate volumetric vapour: liquid ratio of gaseous or light-petroleum inclusions without fluorescence using regularly-shaped inclusions to estimate volumetric vapour: liquid ratios through geometric methods. The method was applied to the inclusions from the rock samples of the Lower Triassic Feixianguan and Jialingjiang Formations, NE Sichuan (China). The trapping pressures of inclusion fluids were calculated by integrating PVT simulation software, volumetric liquid: vapour ratios determined by the proposed method and homogenization temperatures measured by microthermometry. Fluid densities and gas-oil ratios (GOR) were also estimated. The estimated trapping pressures and temperatures are slightly lower for the Jialingjiang formation (29.69–31.33 MPa, 93.5–105.2 °C) than for the Feixianguan Formation (31.02–34.38 MPa, 98–148 °C), and the trapping time of the inclusions in the Jialingjiang Formation and Feixianguan Formation were estimated at about 173–170 Ma and 178-168 Ma, respectively. The distribution of high pressures correlates with the presence of pyro-bitumen in the reservoir rocks, suggesting the migrated fluid is derived mainly from the secondary cracking of oil. The modeled fluid density and GOR correspond to a typical light oil or condensate, suggesting an origin for the trapped hydrocarbons as an intermediate product in this process.Wang, Y., Wang, L., Wang, J., Jiang, Z., Jin, C., Wang, Y., 2018. Characterization of organic matter pores in typical marine and terrestrial shales, China. Journal of Natural Gas Science and Engineering 49, 56-65. matter (OM) is a significant component in shale and controls gas storage and transportation. Typical marine (JLD sample, NTT sample, WF sample and LMX sample) and terrestrial (C7 sample) OM-rich shale samples from the Sichuan Basin and Erdos Basin in China were investigated using X-ray diffraction and scanning electron microscopy (SEM) to study their mineralogy and OM pore network properties. The X-ray diffraction results indicated that the content of brittle minerals (quartz, plagioclase, calcareous dolomite, dolomite and pyrite) in each shale sample was higher than 60%, providing material in which original matrix pores and microfractures formed during an early stage of diagenesis. The types and contents of clay minerals vary among the shale samples. The main clay mineral in most of the marine shale samples is illite, but the primary clay in the terrestrial shale is an illite–smectite mixed layer. The maturity data of the OM in the marine shale samples suggested a moderate to high stage of maturity, while the terrestrial shale was collected at a relatively low stage of thermal evolution. The SEM observations suggested that the OM was either tight or porous, and the former was the dominant state. The OM pores preserved in the shale consisted of pores within, between and at the interfaces of the OM particles. For the OM pores within the OM particles, the most dominant pore type, type I, exhibits honeycomb-like pores formed by hydrocarbon generation; this type of pore is most developed in the marine LMX shale and NTT shale. Pore type II is related to biogenic residue and is more developed in the JLD shale and LMX shale. Pore type Ⅲ includes mainly elliptical pores or microcracks related to the volume loss of bitumen. The OM pores between the OM particles are narrow and laminar; these structures were inherited from the previous clay mineral structures. The OM pores at the interfaces of the OM particles and the mineral grains are usually observed as microfractures and are more developed in the C7 shale. The lack of pores within the OM in the terrestrial C7 shale was due to low maturity. A combination of SEM results, mineral compositions and carbon analyses indicated a positive correlation between the development of OM pores and the organic carbon content, as well as the thermal maturity. With increasing burial and maturity, migrated OM was squeezed into mineral matrix pores and appears to be continuous, especially along the bedding planes, forming an effective network due to the interconnectivity of the OM.Wang, Y., Zhang, S., Yuce, G., 2018. Gas geochemistry: From conventional to unconventional domains. Marine and Petroleum Geology 89, Part 1, 1-3. geochemistry is developing into a powerful tool to understand geological processes and affirm source origins of geo-fluids. Major and trace gases, including abundances and isotopes, have shown considerable application in natural gas systems. For example, progress in unconventional gases such as shale gas, tight gas, and extreme conditions in the deep oceans represent more emerging areas and application of these novel gas-related techniques. Examples where gas geochemistry continues to place key constraints on the origin and migration characteristics of natural gas, the P-T characteristics of fluids in both subaerial and deep geothermal reservoirs, and the dynamics of the accumulation cycles, to name but a few. This volume will reflect this diversity in scope and application of gas geochemistry, focusing on deeper and broader applications in unconventional domains of novel gas geochemical techniques and applications.Wang, Y., Zhao, Y., Liang, C., Chen, Y., Zhang, Q., Li, X., 2017. Molecular-level modeling investigation of n-decane pyrolysis at high temperature. Journal of Analytical and Applied Pyrolysis 128, 412-422. small-scale molecular reaction model has been established to predict the behavior of thermal cracking n-decane based on the experimental study of n-decane pyrolysis under supercritical conditions (4 MPa, 480–720 °C). A developed experimental method of electrical heating tube (2 mm inner diameter) was used experimentally to obtain the detailed local chemical compositions and temperatures along the reactor tube. Gas chromatography was used to analysis the pyrolysis products, and the calculated density and corresponding residence times along the reactor tube were reported. The overall n-decane decomposition could be represented by a first-order reaction with frequency factor and activation energy of 6.209 × 1015 s?1 and 59.4 kcal/mol, respectively. The experimental products and calculated thermophysical properties along the microchannels of a heat exchanger could be effectively simulated by using the molecular reaction model, consisting of 16 species, a first-order reaction and 21 secondary reactions among the primary products. The performance of the reaction model in reproducing the experimental data was reasonably good even the cracking conversion up to 93%.Wang, Z., Wang, J., Fu, X., Zhan, W., Yu, F., Feng, X., Song, C., Chen, W., Zeng, S., 2017. Organic material accumulation of Carnian mudstones in the North Qiangtang Depression, eastern Tethys: Controlled by the paleoclimate, paleoenvironment, and provenance. Marine and Petroleum Geology 88, 440-457. Late Triassic mudstones are considered to be the most significant hydrocarbon source rocks (TOC: 0.54%–3.29%) in the North Qiangtang Depression, eastern Tethys. Here, we present geochemical data from the Woruo Mountain Carnian mudstones, in order to investigate their paleoclimate, paleoenvironment, and provenance and to analyze the mechanism of organic material accumulation. The paleoclimate condition was warm and humid during the Carnian mudstones deposition, as indicated by moderate chemical index of alteration (CIA; 73–76), which may be connected with the Late Triassic Carnian stage global climate event in the Tethys. The low U/Th (0.17–0.25) and Corg/Ptot (7–33) ratio values and moderate manganese contents, reflect the oxidizing conditions during the Carnian mudstones deposition. The relatively high primary productivity in this study is supported by the relatively high P concentrations. The Al2O3–(CaO* + Na2O)–K2O ternary plot and Th/Sc–Zr/Sc crossplot reflect that the source areas have undergone a medium chemical weathering with weak sedimentary recycling. The TiO2–Zr, Co/Th–La/Sc, La/Th–Hf, and La/Yb–∑REE bivariate diagrams indicate that the provenance of Carnian mudstones was primarily from felsic igneous rocks. The collision setting has been identified based on the multi-major elements discriminate plots in the present study. The Riwanchaka and Mayigangri masses to the southwest and south of the study area consisting mainly of Middle-Triassic granodiorite and Late-Triassic granite are likely responsible for supplying provenance to the Woruo Mountain Carnian mudstones, which have similar REE patterns. The relatively high TOC contents of Carnian mudstones are related to high paleoproductivity and fast sedimentation rates, which will lead to preservation of some organic matter even when bottom waters are completely oxidizing. The detrital input during the Carnian mudstones deposition would result in dilution of organic matter.Wegwerth, A., Eckert, S., Dellwig, O., Schnetger, B., Severmann, S., Weyer, S., Brüske, A., Kaiser, J., K?ster, J., Arz, H.W., Brumsack, H.-J., 2018. Redox evolution during Eemian and Holocene sapropel formation in the Black Sea. Palaeogeography, Palaeoclimatology, Palaeoecology 489, 249-260. Black Sea repeatedly experienced major hydrographic changes during glacial-interglacial transitions, with alternating limnic and brackish stages. While the redox conditions during the present Holocene brackish period (since ~ 9,000 yr BP) have been intensively studied, the redox evolution during the last interglacial, the Eemian (~ 128,000-120,000 yr BP), remains largely unexplored. With its at least 3 °C warmer climate and an up to 10 m higher global sea level, the Eemian could open a window into the future development of the Black Sea. This study provides a detailed comparison of the Black Sea redox evolution during Eemian and Holocene sapropel formation. We show that the redox conditions and associated geochemical processes in the Black Sea water column can strongly deviate from the Holocene when sea level and climate conditions are different. Mo/Al and Re/Mo as well as Mo and Fe isotope proxies record a comparatively uniform rise of the Eemian redoxcline culminating in pronounced euxinia. This scenario strongly contrasts with weaker euxinic conditions during the Holocene Unit II sapropel (~ 8,000-2,500 yr BP). Higher Mo/TOC ratios during the Eemian and Mo inventory considerations suggest a higher Eemian Mo availability, possibly due to an improved connection to the Mediterranean Sea. We conclude that higher temperatures, productivity, sea level-associated salinity changes, and corresponding higher sulphide levels were ultimately responsible for enhanced trace metal enrichment during the Eemian Black Sea sapropel stage.Wei, B., Wu, R., Lu, L., Ning, X., Xu, X., Wood, C., Yang, Y., 2017. Influence of individual ions on oil/brine/rock interfacial interactions and oil–water flow behaviors in porous media. Energy & Fuels 31, 12035-12045. low salinity effect (LSE) in enhanced oil recovery (EOR) is widely accepted. However, its underlying mechanisms remain unclear due in part to the complex interactions at the oil/brine/rock interface. The chemistry of brine largely depends on the ionic composition. Thus, in this work, attention was placed on the roles of individual ions and salinity in LSE through direct measurements of oil/brine/rock interfacial behaviors, oil displacement efficiencies, and oil–water relative permeability in sandstone porous media. The results showed that the oil/water interfacial tensions (IFTs) were weakly dependent on ion and the lowest IFTs were generated at the salinities of 0.2–0.5 wt %. In contrast, the interfacial dilational modulus varied significantly with ion types and salinities due to the adsorption of polar components at the oil/water interface. Moreover, wettability alteration of the sandstone surface was found to be associated with the divalent ions in our work. As a result of the viscoelastic interfaces, the breakage of oil column into oil droplets or ganglia was delayed, which subsequently led to the improvement of the oil–water relative permeability and oil displacement efficiencies. Based on the analysis, it was concluded that HCO3–, Mg2+, and SO42– were potential-determining ions (PDIs) in LSE. The results of the tests, to our knowledge, are the first that particularly emphasize the roles of individual ions at the interfaces and oil–water flow patterns in porous media.Wei, G.-Y., Ling, H.-F., Li, D., Wei, W., Wang, D., Chen, X., Zhu, X.-K., Zhang, F.-F., Yan, B., 2017. Marine redox evolution in the early Cambrian Yangtze shelf margin area: evidence from trace elements, nitrogen and sulphur isotopes. Geological Magazine 154, 1344-1359. is an essential element for biological activity, and nitrogen isotopic compositions of geological samples record information about both marine biological processes and environmental evolution. However, only a few studies of N isotopes in the early Cambrian have been published. In this study, we analysed nitrogen isotopic compositions, as well as trace elements and sulphur isotopic compositions of cherts, black shales, carbonaceous shales and argillaceous carbonates from the Daotuo drill core in Songtao County, NE Guizhou Province, China, to reconstruct the marine redox environment of both deep and surface seawater in the study area of the Yangtze shelf margin in the early Cambrian. The Mo–U covariation pattern of the studied samples indicates that the Yangtze shelf margin area was weakly restricted and connected to the open ocean through shallow water flows. Mo and U concentrations, δ15Nbulk and δ34Spy values of the studied samples from the Yangtze shelf margin area suggest ferruginous but not sulphidic seawater and low marine sulphate concentration (relatively deep chemocline) in the Cambrian Fortunian and early Stage 2; sulphidic conditions (shallow chemocline and anoxic photic zone) in the upper Cambrian Stage 2 and lower Stage 3; and the depression of sulphidic seawater in the middle and upper Cambrian Stage 3. Furthermore, the decreasing δ15N values indicate shrinking of the marine nitrate reservoir during the middle and upper Stage 3, which reflects a falling oxygenation level in this period. The environmental evolution was probably controlled by the changing biological activity through its feedback on the local marine environment.Wei, Y., Babadagli, T., 2017. Alteration of interfacial properties by chemicals and nanomaterials to improve heavy oil recovery at elevated temperatures. Energy & Fuels 31, 11866-11883. oil containing carbonate and sand reservoirs exhibits reverse wettability characteristics. Dependent upon the temperature, phase of injected steam, and rock type, the wettability may be altered to more water-wet. The addition of chemicals to hot water (or steam) may further change the interfacial properties (more water-wet and less interfacial tension). Surfactants were tested extensively for this process in the past, and their temperature resistance was an obstacle. New-generation chemicals need further investigation from a technically and economically success point of view. The objective was to investigate the alteration of interfacial properties induced by different types of chemical agents under high-temperature conditions. To achieve this, four experimental tools (contact angle measurement, interfacial tension measurement, atomic force microscopy, and spontaneous imbibition tests) were applied. High-pressure and high-temperature contact angle measurements enabled a quick method to identify the suitability of the chemicals for wettability modification. Interfacial tension between oil and different chemical solutions was measured with a variation of the temperature. In the imbibition tests, core samples were exposed to heating for longer time periods, so that the temperature resistance of the chemicals was also tested. Imbibition experiments were conducted at ambient pressure and 90 °C. The combination of the contact angle and interfacial tension provided insight into the recovery enhancement mechanisms. Six different chemicals, including an ionic liquid, three nanofluids (silica, aluminum, and zirconium oxides), a cationic surfactant, and a high-pH solution, were chosen based on our screening study. Heavy oil used was obtained from a field in Alberta (6000 cP). Contact angles were measured on mica, calcite, sandstone, and limestone plates. The experimental temperature ranged from 25 to 200 °C, and the pressure was changed to keep the solution in the aqueous phase. Promising modifiers for different rock types under different temperatures were screened separately. Visual data illustrating the deposition of the chemicals on the surface of mica and well-polished calcite substrates and removal of the existing oil layer after the treatment with different chemicals were obtained by atomic force microscopy. Finally, spontaneous imbibition tests were performed on sandstone and limestone cores with screened promising modifiers. Oil recovery in this phase was continuously monitored to evaluate wettability alteration capability, and the mechanism(s) involved were analyzed for different chemicals. Analysis of wettability alteration mechanisms and interfacial tension reduction capabilities is expected to be useful in the selection of suitable and temperature-resistant chemicals for high-temperature applications in different reservoir rocks.Weronika, E., ?ukasz, K., 2017. Tardigrades in space research - past and future. Origins of Life and Evolution of Biospheres 47, 545-553. survive exposure to space conditions, organisms should have certain characteristics including a high tolerance for freezing, radiation and desiccation. The organisms with the best chance for survival under such conditions are extremophiles, like some species of Bacteria and Archea, Rotifera, several species of Nematoda, some of the arthropods and Tardigrada (water bears). There is no denying that tardigrades are one of the toughest animals on our planet and are the most unique in the extremophiles group. Tardigrada are very small animals (50 to 2,100?μm in length), and they inhabit great number of Earth environments. Ever since it was proven that tardigrades have high resistance to the different kinds of stress factors associated with cosmic journeys, combined with their relatively complex structure and their relative ease of observation, they have become a perfect model organism for space research. This taxon is now the focus of astrobiologists from around the world. Therefore, this paper presents a short review of the space research performed on tardigrades as well as some considerations for further studies.Weston, C., Smuts, J., Mao, J.X., Schug, K.A., 2018. Investigation of gas phase absorption spectral similarity for stable-isotopically labeled compounds in the 125–240nm wavelength range. Talanta 177, 41-46. internal standards are commonly incorporated in methods for trace analysis that utilize mass spectrometric detection. They closely mimic the physicochemical properties of the analyte, but their signal is easily differentiable based on a change in molecular mass. To investigate the potential to transfer methods incorporating such internal standards for analysis by vacuum ultraviolet detection, a study was conducted to compare the spectral shape (from 125 to 240 nm) of stable-isotopically-labeled compounds with their non-labeled counterparts. Gas chromatography – vacuum ultraviolet spectroscopic analysis was performed for a series of benzene isotopologues, as well as for clinically- and environmentally-relevant standard compounds and their deuterated counterparts. The absorption characteristics of the benzene isotopologues were evaluated based on similarity (normalized spectra), as well as on their magnitude of absorption. In general, very minor differences in absorption spectra were observed; however, increasing degree of deuteration did generally increase the spectral difference between labeled and non-labeled analytes. Sum of squared residuals were used as quantitative measures to assess spectral similarity (and dissimilarity). Theoretical computation of absorption spectra for benzene using time-dependent density functional theory was also examined; though, further work is needed in this area to extend the analysis to isotopologue analysis.Whelan, N.V., Kocot, K.M., Moroz, T.P., Mukherjee, K., Williams, P., Paulay, G., Moroz, L.L., Halanych, K.M., 2017. Ctenophore relationships and their placement as the sister group to all other animals. Nature Ecology & Evolution 1, 1737-1746., comprising approximately 200 described species, is an important lineage for understanding metazoan evolution and is of great ecological and economic importance. Ctenophore diversity includes species with unique colloblasts used for prey capture, smooth and striated muscles, benthic and pelagic lifestyles, and locomotion with ciliated paddles or muscular propulsion. However, the ancestral states of traits are debated and relationships among many lineages are unresolved. Here, using 27 newly sequenced ctenophore transcriptomes, publicly available data and methods to control systematic error, we establish the placement of Ctenophora as the sister group to all other animals and refine the phylogenetic relationships within ctenophores. Molecular clock analyses suggest modern ctenophore diversity originated approximately 350 million years ago?±?88 million years, conflicting with previous hypotheses, which suggest it originated approximately 65 million years ago. We recover Euplokamis dunlapae—a species with striated muscles—as the sister lineage to other sampled ctenophores. Ancestral state reconstruction shows that the most recent common ancestor of extant ctenophores was pelagic, possessed tentacles, was bioluminescent and did not have separate sexes. Our results imply at least two transitions from a pelagic to benthic lifestyle within Ctenophora, suggesting that such transitions were more common in animal diversification than previously thought.Whitau, R., Balme, J., O'Connor, S., Wood, R., 2017. Wood charcoal analysis at Riwi cave, Gooniyandi country, Western Australia. Quaternary International 457, 140-154. charcoals excavated from archaeological sites provide a useful tool for palaeoenvironmental reconstruction, particularly in arid and semi-arid zones, where suitable catchments for palynological archives are often limited. Preservation of organic material in northern Australia is characteristically poor, and wood charcoal analysis provides a viable alternative to understand shifts in woody vegetation in the past. The analysis of charcoal from matrix contexts at Riwi cave, located in the southern Kimberley region of northern Western Australia, has allowed a reconstruction of the local woody vegetation during occupation over the last 45,000 years. The wood charcoal assemblage from the Holocene stratigraphic units reflects the composition of the modern vegetation, and illustrates that people were occupying the site during periods of relative humidity. The Pleistocene stratigraphic units show a shift in vegetation composition from Eucalyptus spp. to Corymbia sp. dominated savanna, with an understory of secondary shrub, associated with a Late MIS 3 arid event observed in both terrestrial and marine archives, suggesting that activities continued at Riwi during this arid event. Further anthracological analysis of other sites in the Kimberley will help to build a regional picture of woody vegetation change, and will further disentangle local and regional climatic signals, particularly in relation to phases of occupation.Wild, B., Alaei, S., Bengtson, P., Bodé, S., Boeckx, P., Schnecker, J., Mayerhofer, W., Rütting, T., 2017. Short-term carbon input increases microbial nitrogen demand, but not microbial nitrogen mining, in a set of boreal forest soils. Biogeochemistry 136, 261-278. carbon dioxide (CO2) concentrations and temperatures are expected to stimulate plant productivity and ecosystem C sequestration, but these effects require a concurrent increase in N availability for plants. Plants might indirectly promote N availability as they release organic C into the soil (e.g., by root exudation) that can increase microbial soil organic matter (SOM) decomposition (“priming effect”), and possibly the enzymatic breakdown of N-rich polymers, such as proteins, into bio-available units (“N mining”). We tested the adjustment of protein depolymerization to changing soil C and N availability in a laboratory experiment. We added easily available C or N sources to six boreal forest soils, and determined soil organic C mineralization, gross protein depolymerization and gross ammonification rates (using 15N pool dilution assays), and potential extracellular enzyme activities after 1?week of incubation. Added C sources were 13C-labelled to distinguish substrate from soil derived C mineralization. Observed effects reflect short-term adaptations of non-symbiotic soil microorganisms to increased C or N availability. Although C input promoted microbial growth and N demand, we did not find indicators of increased N mobilization from SOM polymers, given that none of the soils showed a significant increase in protein depolymerization, and only one soil showed a significant increase in N-targeting enzymes. Instead, our findings suggest that microorganisms immobilized the already available N more efficiently, as indicated by decreased ammonification and inorganic N concentrations. Likewise, although N input stimulated ammonification, we found no significant effect on protein depolymerization. Although our findings do not rule out in general that higher plant-soil C allocation can promote microbial N mining, they suggest that such an effect can be counteracted, at least in the short term, by increased microbial N immobilization, further aggravating plant N limitation.Williams, G.A., Chadwick, R.A., Vosper, H., 2018. Some thoughts on Darcy-type flow simulation for modelling underground CO2 storage, based on the Sleipner CO2 storage operation. International Journal of Greenhouse Gas Control 68, 164-175. take three flow simulators, all based on Darcy’s Law but with different numerical solver implementations, to assess some of the issues surrounding their use to model underground CO2 storage. We focus on the Sleipner CO2 injection project, which, with its seismic monitoring datasets, provides unique insights into CO2 plume development during a large-scale injection operation. The case studies firstly compare simulator performance in terms of outputs and run-times on carefully matched model scenarios; then we compare numerical with analytical Darcy solutions to explore the potential for modelling simplification; finally we look at the effects of including conservation of energy in the simulations. The initial case-study used simplified axisymmetric model geometry to simulate the upward flux of CO2 through a heterogeneous reservoir, incorporating multiphase flow with coupled CO2 dissolution into formation brine. All three codes produced near-identical results with respect to CO2 migration velocity and total upward CO2 flux at the reservoir top. The second case-study involved 3D modelling of the growth of the topmost layer of CO2 trapped and migrating beneath topseal topography. Again the three codes showed excellent agreement. In the third case-study the simulators were tested against a simplified analytical solution for gravity currents to model the spreading of a single CO2 layer beneath a flat caprock. Neglecting capillary effects, the numerical models showed similar layer migration and geometry to the analytical model, but it was necessary to minimise the effects of numerical dispersion by adopting very fine cell thicknesses. The final case-study was designed to test the non-isothermal effects of injecting CO2 into a reservoir at non-ambient temperature. Only two of the simulators solve for conservation of energy, but both showed a near identical thermal anomaly, dominated by Joule-Thomson effects. These can be significant, particularly where reservoir conditions are close to the critical point for CO2 where property variations can significantly affect plume mobility and also seismic response. In conclusion, the three simulators show robust consistency, any differences far less than would result from geological parameter uncertainty and limitations of model resolution. In this respect the three implementations are significantly different in terms of computing resource requirement and it is clear that approaches with simplified physics will pay rich dividends in allowing more detailed reservoir heterogeneity to be included. Contrary to this, including conservation of energy is heavier on computing time but is likely to be required for storage scenarios where the injectant stream is significantly different in temperature to the reservoir and most critically for shallower storage reservoirs where CO2 is close to its critical point.Woillez, M.-N., Souque, C., Rudkiewicz, J.-L., Willien, F., Cornu, T., 2017. Insights in fault flow behaviour from onshore Nigeria petroleum system modelling. Oil & Gas Science and Technology - Revue IFP Energies nouvelles 72, Article 31. are complex geological features acting either as permeability barrier, baffle or drain to fluid flow in sedimentary basins. Their role can be crucial for over-pressure building and hydrocarbon migration, therefore they have to be properly integrated in basin modelling. The ArcTem basin simulator included in the TemisFlow software has been specifically designed to improve the modelling of faulted geological settings and to get a numerical representation of fault zones closer to the geological description. Here we present new developments in the simulator to compute fault properties through time as a function of available geological parameters, for single-phase 2D simulations. We have used this new prototype to model pressure evolution on a siliciclastic 2D section located onshore in the Niger Delta. The section is crossed by several normal growth faults which subdivide the basin into several sedimentary units and appear to be lateral limits of strong over-pressured zones. Faults are also thought to play a crucial role in hydrocarbons migration from the deep source rocks to shallow reservoirs. We automatically compute the Shale Gouge Ratio (SGR) along the fault planes through time, as well as the fault displacement velocity. The fault core permeability is then computed as a function of the SGR, including threshold values to account for shale smear formation. Longitudinal fault fluid flow is enhanced during periods of high fault slip velocity. The method allows us to simulate both along-fault drainages during the basin history as well as overpressure building at present-day. The simulated pressures are at first order within the range of observed pressures we had at our disposal.Wood, D.A., 2018. Kerogen conversion and thermal maturity modelling of petroleum generation: Integrated analysis applying relevant kerogen kinetics. Marine and Petroleum Geology 89, 313-329. transformation to petroleum and thermal maturity modelling calibrated to vitrinite reflectance utilizing Arrhenius-equation reaction kinetics are important oil and gas exploration tools for conventional and non-conventional resources. The range and correlation between activation energies (E) and frequency factors (A) on a geological scale is presented to support the theory and application of the time-temperature index (∑TTIARR) method of thermal maturity proposed in 1988, with a single set of E-A values (E = 218 kJ/mol (52.1 kcal/mol); A = 5.45E+26/my). The ∑TTIARR method provides a highly-sensitive and transparent thermal maturity index. It is well-correlated with vitrinite reflectance and produces comparable results with models applying theoretically-tenuous distributions of E with single A values. The sensitively-scaled ∑TTIARR methodology has the added benefit of providing detailed insight to petroleum generation via the calculation of related transformation factors (TF) for oil and gas, by applying a range of E-A values referencing the ∑TTIARR thermal maturity scale as a benchmark. This study provides analysis of detailed modelling of the transformation process with representative and realistic kinetics for kerogens, and mixtures of kerogens, for a wide range of heating rates at geological and laboratory scales. The results reveal that novel metrics (such as, maximum transformation gradient and temperature at which it occurs, average transformation gradient between 10% and 90% conversion, and temperature spread from 10% to 90% conversion) can discriminate between the transformation processes of kerogens, and mixtures of kerogens, at geological and laboratory scales. These metrics offer the potential to more-precisely define “sweet spots” of petroleum generation in organic-rich shales. They also have potential at the laboratory scale to assist in the extraction of kinetic information from existing and future pyrolysis test. Furthermore, the analysis suggests that mixtures of kerogens can, in most cases, be more effectively identified and characterized, and their petroleum transformation modelled, with just two or three E-A sets as kinetic inputs. This approach is preferred to the common practice of using a complex distributions of multiple E values linked with a single A value unrelated to the geological-scale E-A trend established for kerogens.Wu, D., Chen, B., Sun, R., Liu, G., 2017. Thermal behavior and Raman spectral characteristics of step-heating perhydrous coal: Implications for thermal maturity process. Journal of Analytical and Applied Pyrolysis 128, 143-155. coal (PHC) had been widely investigated; however, a systematic research on the relationship between the structure of PHC and its thermal reactivity was rarely reported in the previous studies. The PHC was widely developed in the Carboniferous-Permian coal-bearing strata in the northern and eastern regions of the Huainan coalfield. In this study, we chose No. 13-1 PHC as the research object. Based on the macroscopic observation of No. 13-1 PHC of the borehole #9-3 and its logging response, a typical PHC sample was selected and pyrolyzed using a thermogravimetric analyzer (TGA) to acquire a set of coal samples after pyrolysis with wide range of random vitrinite reflectance (% VRo) from 0.86 to 7.79%. The thermal evolution process of PHC before and after pyrolysis was investigated by atomic force microscopy (AFM) and Raman spectroscopy. Research results show that: 1) in the experimental temperature range, the reflectance (VRo) range of PHC varied greatly; 2) with the increase of pyrolysis temperature, the Raman spectra of PHC changed significantly in the D band of disordered structure and the G band of ordered structure and the orderliness of its macromolecule particle arrangement was increasing gradually; 3) the relationship between the thermal reactivity of PHC and its Raman structure parameters was established, the FWHM of G-band can be used as indicators of the degree of thermal evolution of PHC; 4) compared with the G FWHM of normal coal with different rank, the thermal reaction temperature of PHC was advanced. Under the premise of comparable reaction temperature, the thermal maturity of PHC was gradually higher than that of bituminous coal, and slightly lower than anthracite, indicating that the actual PHC thermal maturity was suppressed by a higher amount of hydrogen.Wu, M., Ye, X., Chen, K., Li, W., Yuan, J., Jiang, X., 2017. Bacterial community shift and hydrocarbon transformation during bioremediation of short-term petroleum-contaminated soil. Environmental Pollution 223, 657-664. laboratory study was conducted to evaluate the impact of bioaugmentation plus biostimulation (BR, added both nutrients and bacterial consortia), and natural attenuation (NA) on hydrocarbon degradation efficiency and microflora characterization during remediation of a freshly contaminated soil. After 112 days of remediation, the initial level of total petroleum hydrocarbon (TPH) (61,000 mg/kg soil) was reduced by 4.5% and 5.0% in the NA and BR treatments, respectively. Bioremediation did not significantly enhance TPH biodegradation compared to natural attenuation. The degradation of the aliphatic fraction was the most active with the degradation rate of 30.3 and 28.7 mg/kg/day by the NA and BR treatments, respectively. Soil microbial activities and counts in soil were generally greater for bioremediation than for natural attenuation. MiSeq sequencing indicated that the diversity and structure of microbial communities were affected greatly by bioremediation. In response to bioremediation treatment, Promicromonospora, Pseudomonas, Microcella, Mycobacterium, Alkanibacter, and Altererythrobacter became dominant genera in the soil. The result indicated that combining bioaugmentation with biostimulation did not improve TPH degradation, but soil microbial activities and structure of microbial communities are sensitive to bioremediation in short-term and heavily oil-contaminated soil.Wu, Z.-y., Zeng, Z., Xiao, Z., Kam-Wah Mok, D., Chan, H., 2017. Correlation and uncorrelation between hyphenated chromatographic data with chemometric tools. Chemometrics and Intelligent Laboratory Systems 171, 266-276. studies of chromatographic data are common strategies used to relate complex mixtures of chemical components. The congruence coefficient and correlation coefficient are commonly used to indicate the similarity or correlation between different hyphenated chromatograms. However, these indices typically reduce chromatograms to a single dimension, and information in the other dimensions is not fully utilized. In this work, a new technique is developed to identify possible relationships among related high-dimensional data sets using powerful chemometric tools. First, principal component analysis is used to reduce experimental noise by reconstructing the original data sets. Then, canonical correlation analysis is utilized to obtain the canonical vectors of both data sets for comparison, which makes identification of the possible relationships between the data sets easier. An orthogonal projection operation is then applied to identify both common and different information between the matrix spaces spanned by the canonical vectors. Finally, the correlation and uncorrelation indices are defined from both the chromatographic and spectral directions on the basis of the Euclidean distance of all the elements of the final projection matrices. The new indices are more representative because they are generated via the complete employment of the entire data information that is embedded in hyphenated chromatography. In contrast to the conventional coefficients, the indices proposed in this study provide improved performance in a simulated HPLC-DAD data set and 12 real GC-MS data sets of ginseng, a widely used herbal medicine. The effects of various potential factors on the results are investigated.Wu, Z., Sun, X., Xu, H., Konishi, H., Wang, Y., Lu, Y., Cao, K., Wang, C., Zhou, H., 2018. Microstructural characterization and in-situ sulfur isotopic analysis of silver-bearing sphalerite from the Edmond hydrothermal field, Central Indian Ridge. Ore Geology Reviews 92, 318-347. close Zn-Ag association has been noted recently in several polymetallic sulfide ore deposits from the Indian Ocean. However, the role of nanotextural controls on “invisible” silver distribution within sphalerite (a significant Ag-carrier) is still not well understood. In this study, typical Zn-sulfide samples from the Edmond vent field (Central Indian Ridge) can be roughly classified into three different groups based on their chemical compositions and mineral textures. Among them, sulfosalt-bearing, Fe-poor zinc sulfides in sulfate-dominant outer chimney walls usually contain higher contents of Ag, Cu and Pb (up to wt% levels) than Fe-rich, massive to disseminated sphalerite in Zn-(Fe)-rich chimney fragments coated by silicified crusts. Such sphalerite is represented by colloform/botryoidal aggregates of optically anisotropic ZnS with a strongly disordered structure or hexagonal habit, which are actually formed by coalescence and agglomeration of colloidal nanocrystalline particles. Using high-resolution transmission electron microscopy (HRTEM) and in-situ micro-XRD techniques, we have investigated the ultrastructure and crystal-chemistry of the {1?1?1} twin boundaries and wurtzite-type stacking faults that occur in Ag-rich, colloform or porous dendritic sphalerite. Submicroscopic electrum and Ag nanoparticles appear to nucleate on the micro-/nano-pore walls as cavity-fillings, or occur along grain boundaries between chalcopyrite-tennantite inclusions and the host sphalerite. Interestingly, the inhomogeneous distribution of precious metals and other chalcophile elements is generally concordant with the extent of recrystallization, intragranular porosity as well as various degrees of structural disordering/imperfectness (i.e., bulk defect density) in ZnS domains. Lattice defects and interfaces may play a limited role in promoting the simultaneous introduction of exotic impurities into colloform sphalerite during rapid growth. Even though certain morphological traits and aggregation state at the nanoscale seem to support a biogenic origin of these ZnS particles characterized by admixed polytypic intergrowth structures, the mineralogical and geochemical features of highly-defective sphalerite crystals, in addition to their microscale S-isotope signatures with relatively high δ34S values, exhibit signs of abiologically-mediated, rapid precipitation caused by extensive mixing and cooling at Edmond. The physicochemical conditions and seafloor disequilibrium processes indicated by ZnS formation mechanism might facilitate the incorporation and enrichment of Ag or other trace elements in hydrothermal sphalerite.Xia, D., Zhang, H., Hong, J., Su, X., Liu, X., 2017. Variation in endogenous trace elements during methane generation from different coal ranks. Energy & Fuels 31, 12168-12173. investigate the variation in endogenous trace elements in different coal ranks during methane production, a series of biological gas production experiments were carried out using low- and high-rank coals. Changes in the content and status of occurrence of eight representative beneficial trace elements (i.e., Fe, Co, Ni, Mn, Zn, Cu, and Sn) in the gas production process were analyzed in this study. Under the same conditions, endogenous trace elements were 580.22 ppm in high-rank coal, a higher proportion than in low-rank coal (466.72 ppm). This indicates that the effect of the rank of coal is much more significant than the impact of endogenous trace elements. The average post-reaction rates of trace element content change in low- and high-rank coals are 43.6 and 28.7%, respectively. This result shows that the proportion of trace elements in low-rank coal is more important than that in high-rank coal because of their contribution to response magnitude. Trace elements in different coal ranks exhibit a similar trend during different stages of biogas production. In other words, free and humic states conform to a “increase–decrease–increase” trend, while both the inorganic and macromolecular states exhibit tendencies to decrease. Results show that variation in the occurrence time of trace elements in high-rank coal is backward. Thus, this study addresses trace element variation during the process of biological gas production in different ranks of coal and augments our understanding of the process of coal-derived biogenic methane production. This study also provides a fundamental research basis for a more detailed understanding of the effect of trace elements as degradation substrates in the biogas production process.Xiao, H.-Y., 2017. Effects and underlying mechanisms of damming on carbon and nitrogen cycles and transport in rivers of Southwest China: project introduction. Acta Geochimica 36, 577-580. China is the primary area for damming rivers to produce hydroelectric energy and store water. River damming has changed hydrodynamic, chemical, and biological processes, which are related to sinks and sources of greenhouse gases and carbon and nitrogen fluxes of different interfaces. Here, I provide an introduction to a river damming-related foundation, the National Key R&D Program of China (2016YTA0601000). Supported by the foundation, we carried out research on multi-processes/multi-interfaces of carbon and nitrogen biogeochemical cycles in a dammed river system and have produced important results, as presented in this issue of the journal.Xiao, K., Zou, C., Lu, Z., Deng, J., 2017. Gas hydrate saturations estimated from pore-and fracture-filling gas hydrate reservoirs in the Qilian Mountain permafrost, China. Scientific Reports 7, Article 16258. calculation of gas hydrate saturation is an important aspect of gas hydrate resource evaluation. The effective medium theory (EMT model), the velocity model based on two-phase medium theory (TPT model), and the two component laminated media model (TCLM model), are adopted to investigate the characteristics of acoustic velocity and gas hydrate saturation of pore- and fracture-filling reservoirs in the Qilian Mountain permafrost, China. The compressional wave (P-wave) velocity simulated by the EMT model is more consistent with actual log data than the TPT model in the pore-filling reservoir. The range of the gas hydrate saturation of the typical pore-filling reservoir in hole DKXX-13 is 13.0~85.0%, and the average value of the gas hydrate saturation is 61.9%, which is in accordance with the results by the standard Archie equation and actual core test. The P-wave phase velocity simulated by the TCLM model can be transformed directly into the P-wave transverse velocity in a fracture-filling reservoir. The range of the gas hydrate saturation of the typical fracture-filling reservoir in hole DKXX-19 is 14.1~89.9%, and the average value of the gas hydrate saturation is 69.4%, which is in accordance with actual core test results.Xiao, T., Kweon, H., McPherson, B., Deo, M., 2017. Wormhole generations in Indiana limestone with CO2 intrusion: Numerical simulations based on core flooding experiments. Energy & Fuels 31, 12487-12499. this paper, we examined possible impact factors for calcite dissolution and wormhole generation in limestone formations with CO2 saturated brine intrusion by continuum-scale reactive transport simulations. Previous core-flood experiments that mimic near-wellbore region conditions of Geological CO2 Storage (GCS) fields were used as verification cases. Simulation results reasonably reproduce the experimental results. The results suggest that the initial permeability distribution of the core and pre-existing large permeability zones along the core were key factors for wormhole generation. Porosity distribution also affects wormhole generation, but not significantly. According to our simulation results, CO2 saturated brine injection rate, injection pattern, calcite dissolution rate, and permeability anisotropy do not significantly impact calcite dissolution and wormhole generation. The Damk?hler (Da) numbers were 0.45–0.9 for the experiments at the core scale in this study, which are in accordance with the value for wormhole growth in previous studies. The numerical models would be applicable in further studies at core scale or a larger scale, and the findings that existing levels of high-permeability pathways help drive wormhole generation and the time scale over which the phenomenon occurs are directly applicable in a field injection scenario.Xin, H., Fu, Q., Yuan, Y., Liu, Y., Ke, Y., Jin, Y., Liang, X., 2017. Construction of an off-line two dimensional reversed-phase liquid chromatography/ultra-high performance supercritical fluid chromatography method for rapid and comprehensive analysis of Piper kadsura. The Journal of Supercritical Fluids 127, 9-14. this study, ultra-high performance supercritical fluid chromatography (UHPSFC) was chosen to construct an off-line two dimensional chromatography with reversed-phase liquid chromatography (RPLC) for rapid and comprehensive analysis of Piper kadsura. The sample was firstly divided into a petroleum ether (PE) extract and an ethyl acetate (EA) extract, and then they were separated into 21 and 28 fractions in the first dimensional RPLC, respectively. In the second dimension, the effect of UHPSFC parameters on the analysis speed was investigated. Each PE fraction could be analyzed in 2.0 min, and every EA fraction could be analyzed in 3.0 min. In total, at least 1033 peaks were detected by this method, including 204 peaks from the PE fractions and 829 peaks from the EA fractions. The 2D-RPLC/UHPSFC system with the characteristics of fast separation and high orthogonality has a great potential for the rapid and comprehensive analysis of the complex samples.Xiong, Z., Lin, H., Liu, F., Xiao, P., Wu, Z., Li, T., Li, D., 2017. Flexible PVDF membranes with exceptional robust superwetting surface for continuous separation of oil/water emulsions. Scientific Reports 7, Article 14099. of superwetting surface is the stumbling block of flexible polymeric membranes for continuous separation of water-in-oil or oil-in-water emulsions. Manipulation of rigid superwetting nano-TiO2 on hierarchical poly(vinylidene fluoride) (PVDF) membrane by mimicking the plant roots holding soil behaviour enabled the generation of robust superwetting surface withstanding the harshly physical and chemical torture. The unique interface combination, which fabricated by a compacted nano-layer with the thickness of ~20 μm, was disclosed by systematic structure characterization. As demonstrated by SEM, LSCM and nano-CT, the pristine PVDF membrane with large quantities of cilia-like micro/nano-fibrils can function as the plant roots to capture, cage and confine the nanoparticles to form a robustly rigid nano-coating. The as-prepared membranes showed excellent durable separation performance both in varieties of stabilized water-in-oil and oil-in-water emulsion separation for a long term with few nanoparticles loss in a continuous crossflow mode. The strategy of assembling rigid inorganic nano-particles on flexible surface offers a window of opportunity for preparation of robust organic-inorganic hybrid membranes not only for continuous oil/water emulsion separation, but also for other functional application, such as electric conduction, heat conduction, ion exchange, and in membrane catalytic reactors etc.Xu, H.-H., Berry, C.M., Stein, W.E., Wang, Y., Tang, P., Fu, Q., 2017. Unique growth strategy in the Earth’s first trees revealed in silicified fossil trunks from China. Proceedings of the National Academy of Sciences 114, 12009-12014.: The evolution of trees and forests in the Mid–Late Devonian Period, 393–359 million years ago, profoundly transformed the terrestrial environment and atmosphere. The oldest fossil trees belong to the Cladoxylopsida. Their water-conducting system is a ring of hundreds of individual strands of xylem (water-conducting cells) that are interconnected in many places. Using anatomically preserved trunks, we show how these trees could grow to a large size by the production of large amounts of soft tissues and new wood around the individual xylem strands and by a controlled structural collapse at the expanding base. We have discovered a complex tree growth strategy unique in Earth history, but with some similarity to that of living palms. Abstract: Cladoxylopsida included the earliest large trees that formed critical components of globally transformative pioneering forest ecosystems in the Mid- and early Late Devonian (ca. 393–372 Ma). Well-known cladoxylopsid fossils include the up to ～1-m-diameter sandstone casts known as Eospermatopteris from Middle Devonian strata of New York State. Cladoxylopsid trunk structure comprised a more-or-less distinct cylinder of numerous separate cauline xylem strands connected internally with a network of medullary xylem strands and, near the base, externally with downward-growing roots, all embedded within parenchyma. However, the means by which this complex vascular system was able to grow to a large diameter is unknown. We demonstrate—based on exceptional, up to ～70-cm-diameter silicified fossil trunks with extensive preservation of cellular anatomy from the early Late Devonian (Frasnian, ca. 374 Ma) of Xinjiang, China—that trunk expansion is associated with a cylindrical zone of diffuse secondary growth within ground and cortical parenchyma and with production of a large amount of wood containing both rays and growth increments concentrically around individual xylem strands by normal cambia. The xylem system accommodates expansion by tearing of individual strand interconnections during secondary development. This mode of growth seems indeterminate, capable of producing trees of large size and, despite some unique features, invites comparison with secondary development in some living monocots. Understanding the structure and growth of cladoxylopsids informs analysis of canopy competition within early forests with the potential to drive global processes. Xu, H., Tang, D., Chen, Y., Ming, Y., Chen, X., Qu, H., Yuan, Y., Li, S., Tao, S., 2018. Effective porosity in lignite using kerosene with low-field nuclear magnetic resonance. Fuel 213, 158-163. porosity is a key factor in subsurface fluid flow. However, lignite is soft, may swell in water (depending on saturation state), and is friable. Thus the conventional saturated water NMR method has challenges when applied to lignite (coal swelling, and fragmentation during the centrification process to remove the pore water. Here an improved experimental method for effective porosity is demonstrated for lignite. To prevent sample breakage, the cores were wrapped with a heat shrinkable plastic and kerosene replaced water as the saturated fluid. The kerosene low-field NMR signal and porosity relationship was established and demonstrated for lignites from the Lower Cretaceous Saihantala Formation in the Shengli coalbed reservoirs in the Erlian Basin of Inner Mongolia, China. The lignite had a relatively high total porosity of 37.2–47.0% and an effective porosity of 25.0–34.6%. Thus, from this and additional reservoir considerations, this area is likely conducive to the production of coalbed methane.Xu, H., Zhou, W., Cao, Q., Xiao, C., Zhou, Q., Zhang, H., Zhang, Y., 2018. Differential fluid migration behaviour and tectonic movement in Lower Silurian and Lower Cambrian shale gas systems in China using isotope geochemistry. Marine and Petroleum Geology 89, Part 1, 47-57. geochemistry has been introduced as a means to trace origin of the hydrocarbon and characterize highly productive shale gas systems recently. To assess the impact of tectonic movement and the sealing of shale gas systems, isotope geochemistry, pressure coefficients and the distribution of bitumens are analysed. Many samples yield isotope geochemical data with typical carbon isotopic reversals (δ13C1 > δ13C2) and hydrogen isotopic reversals (δ13DC2H6 > δ13DCH4) in the Lower Silurian shale gas. Isotopically reversed gases are considered to originate in sealed, self-contained petroleum systems. Besides, isotope “reversals order” degree of shale gas has positive correlation with gas production. Isotopically normal gases from the Lower Cambrian indicate that this formation was a continued relatively open petroleum system when oil and gas generated. The pressure coefficients of the Lower Silurian shale gas reservoir range from 1.45 to 2.03, indicating that the reservoir is overpressurized, whereas the Lower Cambrian shale gas reservoir possesses a normal pressure system. Overpressurization of the Lower Silurian shale gas reservoir also indicates that it is a well-sealed system. The distribution and isotope geochemistry of bitumens in the Sinian dolomite and Cambrian shale suggests that the source rock of the Sinian hydrocarbon is the Cambrian shale. An unconformity induced from tectonic movement during the Tongwan period is interpreted to be the fluid migration tunnel and the cause of the differential shale gas content and production. Finally, the isotopic reversals associated with maturity, pressure coefficients and tectonic evolution can both assess the preservation conditions of the reservoir and explain the differential fluid migration behaviour.Xu, J., Zhai, C., Liu, S., Qin, L., Dong, R., 2018. Investigation of temperature effects from LCO2 with different cycle parameters on the coal pore variation based on infrared thermal imagery and low-field nuclear magnetic resonance. Fuel 215, 528-540. coalbed methane (ECBM) achieved by injecting liquid carbon dioxide (LCO2) has been proposed and applied in industrial production for decades and has been demonstrated to be an applicable method to boost CBM production. Most of the studies have concentrated on the gas bursting and flooding effect and have rarely focused on the accompanying “freeze–thaw” phenomenon, and the temperature effect of cyclic LCO2 injection on the pore variation of different coals has been partly investigated. In this paper, the influence of cycle parameters, such as cycle number and cycle time, on the pore variation was studied. Infrared thermal imagery (ITI) and low-field nuclear magnetic resonance (NMR) were used to measure the temperature and pore size distribution (PSD) change, respectively. The results show the following: (1) The gas pressure displayed square cyclicity with different cycle time, the temperature of gasified CO2 was almost 248.15?K, and the end and lateral surface temperatures of a core were in the range from 259.35 to 261.85?K, which could cause the water within the pores to freeze with a 9% volume increase, and the fracturing formula was deduced; (2) The relaxation time spectra obtained by different cycle parameters expressed changeable PSD of cores with increasing cycle parameters, and the magnified proportion of bulk water and capillary water, as well the diminished proportion of adsorbed water, all indicated that the increased number of macropores and mesopores formed a larger free volume; (3) The increased total porosity φt and the decreased T2cutoff of six cores with the increasing cycle parameters meant that the larger cycle number could enhance the porosity due to amount of damage accumulation, and the larger cycle time might make the water freeze completely with larger ice swelling stress; (4) There is a polynomial fitting between relative increase ratio Rφ and cycle time, and the fitting coefficients were all higher than 0.99, and the larger the cycle time was, the greater the Rφ(e/t) increment and Rφ(r/t) decrement were. The interval increase ratio Iφe was positively correlated to cycle time without obvious increase behavior; however, the Iφr variation expressed that the greater the cycle number was, the lesser the Iφr with the increasing cycle time was, which indicates that the increasing cycle parameters might help the proportion of connected pores to increase and provide more pathways for permeable fluid; (5) The NMR permeability kSDR of a core increased as the cycle number increased, and the longer cycle time was superior in terms of permeability enhancement.Xu, Q., Liu, B., Ma, Y., Song, X., Wang, Y., Chen, Z., 2017. Geological and geochemical characterization of lacustrine shale: A case study of the Jurassic Da'anzhai member shale in the central Sichuan Basin, southwest China. Journal of Natural Gas Science and Engineering 47, 124-139. numerous progresses have been achieved in characterizing marine shales, studies that are associated with lacustrine shales are limited. To study lacustrine shales, samples were collected from the Jurassic Da'anzhai Member in the central Sichuan Basin of China, and their mineralogical, reservoir, OM, and paleoenvironmental characteristics were determined, as well as the relationships between them. Analysis of trace elements reveals that the shales formed in paleoenvironments that were oxic to suboxic, dry to humid, had moderate to strong weathering, and were characterized by fresh to salt water conditions. These environments are more variable than those of marine shales. The paleoenvironmental conditions and mineralogy of the shales, particularly the oxic to suboxic paleo-redox conditions, resulted in the relatively low levels (0.11–2.18%, average 0.97%). However, based on evaluation criteria for continental source rocks, the OM is of high quality because of its high level of maturity (Ro: 0.95–1.43; Tmax: 428–500 °C) and favorable kerogen type (II2). There are well-developed intraparticle pores, interparticle pores, and microcracks. The SBET (5.42–10.69 m2/g, average 6.92 m2/g) and VBJH (1.19–4.10 mL/100 g, average 2.97 mL/100 g) values also indicate good nanoscale storage space. Terrestrial minerals (i.e., quartz and clay) and authigenic carbonate minerals (i.e., calcite) are, respectively, positively and negatively correlated with the nanoscale storage space,. Small pores (3–5 nm) dominate the nanoscale storage space. The isotherms and hysteresis loops are of Type Ⅱ and Type H3, respectively, which indicates wedge-shaped pores. However, the hysteresis loops indicate that the lacustrine shale has more dead-end pores and larger pores with more complex microstructures than other lacustrine reservoirs. In general, the Da'anzhai lacustrine shale has the potential for unconventional oil and gas exploration. The lacustrine shale's mineralogy, reservoirs, and OM are closely related to each other, and their differences are mainly caused by the paleoenvironmental conditions in which the shale formed.Xu, T., Bei, K., Tian, H., Cao, Y., 2017. Laboratory experiment and numerical simulation on authigenic mineral formation induced by seabed methane seeps. Marine and Petroleum Geology 88, 950-960. natural gas hydrate marine settings, cold seepage of methane fluid is a widely observed phenomenon, where authigenic minerals serve as an indication of potential gas hydrate-bearing reservoirs at depth. In this study, based on the data from the site HD196 near Dongsha Island, northern continental slope of South China Sea, laboratory experiments and numerical simulation studies were conducted to investigate the biogeochemical processes of authigenic mineral formation induced by methane seepage. The bioreactor experimental results show that in response to methane flux, pH increased to 8.5 after 20 days of reaction, and Eh declined rapidly first and then remained unchanged at about 100 mV. The decrease in SO42?, HS? and HCO3? concentrations indicated the occurrence of anaerobic oxidation of methane coupled with sulfate reduction (AOM-SR). The depletion of Fe2+ implied the formation of iron-bearing minerals, e.g., iron sulfides. Carbonate minerals were also identified in the experimental phase of this study. Most iron sulfides existed as massive pieces, and in some cases as spherical or rod-shape pieces. The calcium carbonates were observed as blocky pieces. Numerical simulations were also performed to reproduce the biogeochemical reactions that occurred in the reactor experiments. Based on experimental data, kinetic parameters associated with the observed reactions were calibrated. The model simulated results are general consistent with those obtained by the experiments conducted in this study. The combination of simulation and experimental studies provided a powerful tool to investigate the biogeochemical processes in the methane leakage environment at different temporal and spatial scales. This study gave a new perspective to understand the formation of cold seep authigenic minerals in marine sediments, and was significant for future investigations on the effects of hydrate decomposition.Yamaguchi, Y.T., McCarthy, M.D., 2018. Sources and transformation of dissolved and particulate organic nitrogen in the North Pacific Subtropical Gyre indicated by compound-specific δ15N analysis of amino acids. Geochimica et Cosmochimica Acta 220, 329-347. study explores the use of compound-specific nitrogen isotopes of amino acids (δ15NAA) of coupled dissolved and particulate organic nitrogen (DON, PON) samples as a new approach to examine relative sources, transformation processes, and the potential coupling of these two major forms of N cycle in the ocean water column. We measured δ15NAA distributions in high-molecular-weight dissolved organic nitrogen (HMW DON) and suspended PON in the North Pacific Subtropical Gyre (NPSG) from surface to mesopelagic depths. A new analytical approach achieved far greater δ15NAA measurement precision for DON than earlier work, allowing us to resolve previously obscured differences in δ15NAA signatures, both with depth and between ON pools. We propose that δ15N values of total hydrolysable amino acids (THAA) represents a proxy for proteinaceous ON δ15N values in DON and PON. Together with bulk δ15N values, this allows δ15N values and changes in bulk, proteinaceous, and “other-N” to be directly evaluated.These novel measurements suggest three main conclusions. First, the δ15NAA signatures of both surface and mesopelagic HMW DON suggest mainly heterotrophic bacterial sources, with mesopelagic HMW DON bearing signatures of far more degraded material compared to surface material. These results contrast with a previous proposal that HMW DON δ15NAA patterns are essentially “pre-formed” by cyanobacteria in the surface ocean, undergo little change with depth. Second, different δ15NAA values and patterns of HMW DON vs. suspended PON in the surface NPSG suggest that sources and cycling of these two N reservoirs are surpisingly decoupled. Based on molecular δ15N signatures, we propose a new hypothesis that production of surface HMW DON is ultimately derived from subsurface nitrate, while PON in the mixed layer is strongly linked to N2 fixation and N recycling. In contrast, the comparative δ15NAA signatures of HMW DON vs. suspended PON in the mesopelagic also suggest a possible PON source for some HMW DON in the mid-water column. Together, these results suggest that conversion of relatively labile ON to less labile DON by heterotrophic bacteria (a “microbial nitrogen pump”) may be the key pathway for production and alteration of DON in both the surface and the mesopelagic oligotrophic ocean. Finally, in contrast to THAA, δ15N values of the other-N were substantially less affected by heterotrophic alteration, which may be consistent with a larger than expected contribution of amino sugars, or other less labile nitrogenous organic molecules.Yamamoto, K., Ueki, T., Higuchi, N., Takahashi, K., Kotani, A., Hakamata, H., 2017. A flow-through column electrolytic cell for supercritical fluid chromatography. Journal of Separation Science 40, 4085-4090. novel flow-through column electrolytic cell was proposed as a detector to obtain current signals for supercritical fluid chromatography. The electrochemical cell consisted of two electrodes and its holder, and a working and a counter electrode were fabricated from 192 carbon strings, which were composed of 400 carbon fibers of 10 μm in diameter filled into a heat-shrinkable tube. These electrodes were placed in the center of a holder made from polyether ether ketone blocks and they were separated by polytetrafluoroethylene membrane filters. To evaluate the sensitivity of this cell, a standard solution of ferrocene was injected into the supercritical fluid chromatography system connected to the electrolytic cell. The ferrocene was eluted through a silica gel column using a mixture of a mobile phase of supercritical CO2 and a modifier of methanol containing ammonium acetate. The current peak area of ferrocene correlated to the ferrocene concentration in the range of 10–400 μmol/L (r = 0.999). Moreover, the limit of detection on the column estimated from a signal-to-noise ratio of 3 was 9.8 × 10?13 mol.Yan, D., Tedone, L., Koutoulis, A., Whittock, S.P., Shellie, R.A., 2017. Parallel comprehensive two-dimensional gas chromatography. Journal of Chromatography A 1524, 202-209. introduce an information rich analytical approach called parallel comprehensive two-dimensional gas chromatography (2GC × 2GC). This parallel chromatography approach splits injected samples into two independent two-dimensional column ensembles and provides two GC × GC separations by using contra-directional thermal modulation. The first-dimension (1D) and second-dimension (2D) columns are connected using planar three-port microchannel devices, which are supplied with supplementary flow via two pressure controller modules. Precise carrier gas flow control at the junction of the 1D and 2D columns permits independent control of flow conditions in each separation column. The 2GC × 2GC approach provides two entirely independent GC × GC separations for each injection. Analysis of hop (Humulus lupulus L.) essential oils is used to demonstrate the capability of the approach. The analytical performance of each GC × GC separation in the 2GC × 2GC experiment is comparable to individual GC × GC separation with matching column configurations. The peak capacity of 2GC × 2GC is about 2 times than that of single GC × GC system. The dual 2D chromatograms produced by this single detector system provide complementary separations and additional identification information by harnessing different selectivity provided by the four separation columns.Yan, Y., Zhou, X., Jiang, L., Luo, Y., 2017. Effects of carbon turnover time on terrestrial ecosystem carbon storage. Biogeosciences 14, 5441-5454. (C) turnover time is a key factor in determining C storage capacity in various plant and soil pools as well as terrestrial C sink in a changing climate. However, the effects of C turnover time on ecosystem C storage have not been well explored. In this study, we compared mean C turnover times (MTTs) of ecosystem and soil, examined their variability to climate, and then quantified the spatial variation in ecosystem C storage over time from changes in C turnover time and/or net primary production (NPP). Our results showed that mean ecosystem MTT based on gross primary production (GPP; MTTEC_GPP?=??Cpool/GPP, 25.0?±?2.7 years) was shorter than soil MTT (MTTsoil?=??Csoil/NPP, 35.5?±?1.2 years) and NPP-based ecosystem MTT (MTTEC_NPP?=??Cpool/NPP, 50.8?±?3 years; Cpool and Csoil referred to ecosystem or soil C storage, respectively). On the biome scale, temperature is the best predictor for MTTEC (R2?=??0.77, p?<?0.001) and MTTsoil (R2?=??0.68, p?<?0.001), while the inclusion of precipitation in the model did not improve the performance of MTTEC (R2?=??0.76, p?<?0.001). Ecosystem MTT decreased by approximately 4 years from 1901 to 2011 when only temperature was considered, resulting in a large C release from terrestrial ecosystems. The resultant terrestrial C release caused by the decrease in MTT only accounted for about 13.5?% of that due to the change in NPP uptake (159.3?±?1.45 vs. 1215.4?±?11.0?Pg?C). However, the larger uncertainties in the spatial variation of MTT than temporal changes could lead to a greater impact on ecosystem C storage, which deserves further study in the future.Yancy-Caballero, D., Ling, L.Y., Archilha, N.L., Ferreira, J.E., Driemeier, C., 2017. Mineral particles in sugar cane bagasse: Localization and morphometry using microtomography analysis. Energy & Fuels 31, 12288-12296. particles are detrimental to lignocellulosic biomass utilization as fuel and feedstock of advanced biorefineries. Minerals may cause corrosion, sintering, and vitrification in boilers, gasifiers, and combustors as well as abrasion and erosion of mechanical equipment used in biomass processing. In this work, we employed synchrotron X-ray computed microtomography to analyze mineral particles in fibers of sugar cane bagasse, the vast lignocellulosic residue of the sugar cane industry. Hundreds of mineral particles with volumes from ～102 to 104 μm3 were observed and analyzed. Mineral particles were found mostly in three regions of the biomass particles: (i) at external surfaces, (ii) at internal surfaces associated with tissue cracks, and (iii) inside parenchyma cells, which were ruptured for extraction of the sugar-rich juice. These results provide novel insights for the development of bagasse cleaning technologies aiming at improving feedstock quality for combustion and biorefining.Yang, C., Li, X.-H., Zhu, M., Condon, D.J., 2017. SIMS U–Pb zircon geochronological constraints on upper Ediacaran stratigraphic correlations, South China. Geological Magazine 154, 1202-1216. Ediacaran successions of South China, the Doushantuo and Dengying formations and their equivalents, are key to understanding bio- and geological evolution at the Neoproterozoic–Cambrian transition. However, their absolute ages, especially the upper Ediacaran successions, are poorly constrained. SIMS zircon U–Pb dating results in this study suggest that ash beds at the basal and middle parts of the Jiucheng Member (middle Dengying Formation) in eastern Yunnan Province were deposited at 553.6 ± 2.7/(3.8) Ma and 546.3 ± 2.7/(3.8) Ma, respectively. These new dates indicate that the age for the base of Dengying Formation in eastern Yunnan Province is similar to the 550.55 ± 0.75 Ma date, which is from an ash bed at the top of the Miaohe Member and has been regarded as the age for the base of Dengying Formation in Yangtze Gorges area. These dates do not permit a clear test of the two correlation models for the chronostratigraphic position of the Miaohe Member (uppermost Doushantuo Formation vs. middle Dengying Formation), implying that further integrated intra-basinal stratigraphic correlations and more high-resolution chronological data from the upper Ediacaran deposits of South China are required. New dates of the Jiucheng Member constrain the age of the fossil biotas in the middle Dengying Formation and extend the stratigraphic range of Rangea, Hiemalora and Charniodiscus to 546.3 ± 2.7/(3.8) Ma. The geochronology of the Dengying Formation implies that Ediacaran-type fossils preserved in this formation are younger than the White Sea Assemblage and temporally overlapping with the Nama Assemblage.Yang, C., Yang, S., Su, N., 2017. The hydrogen and oxygen isotopic compositions of hydroxyl in clay mineral from a weathering profile: New proxies for paleo-climate change? Acta Geochimica 36, 370-373. studies suggest that the hydrogen and oxygen isotopic compositions of clay minerals can indicate paleoclimate. Here, we report mineralogy and stable isotopic records (δD and δ18OOH) of a weathering profile located in the Fujian Province, aiming to validate whether hydroxyl stable isotopes can indicate paleo-precipitation and paleo-temperature. Our results indicate that the δD and δ18OOH changes in the kaolinite hydroxyl of the weathering profile are basically determined by the isotopic composition of paleo-meteoric water and paleo-temperature, respectively. Nevertheless, whether the δD and δ18OOH of kaolinite can quantitatively indicate paleo-precipitation and paleo-temperature needs to be verified further, and especially, the structural oxygen isotopic composition that is the essential element for the kaolinite formation temperature calculation has to be constrained in future work.Yang, F., Hou, Y., Wu, W., Liu, Z., 2017. Structures of aromatic clusters of different coals based on benzene carboxylic acids from coal via oxidation. Energy & Fuels 31, 12072-12080. carboxylic acids (BCAs) are considered to be an important group of chemicals and widely used in the chemical industry. The generation of BCAs from coal via oxidation is widely studied, indicating that the distributions of BCAs are various with different coals and the yields of BCAs with lower numbers of carboxyl groups increase in the process of coalification. However, the relationship between distributions of BCAs and the aromatic clusters of coal is unclear. In this work, combined with the results of distributions of BCAs and 13C NMR, the most probable aromatic clusters in different coals were proposed. The result indicates that, in the process of coalification (from lignite to anthracite), the aromatic cluster size and the degree of condensed aromatic rings both increase with an increase in carbon content or coal rank, but the substituted degree of aromatic rings decreases. When the carbon content of coal is lower than 87%, the aromatic rings in coal are arranged in a linear catenation manner. When the carbon content of coal is more than 87%, aromatic rings in coal are arranged in a circular catenation manner. The substituents of aromatic clusters are distributed uniformly on the aromatic rings. With the increase of coal rank, the average substituted carbon chain length (Ln) decreases; namely, more and more aromatic clusters tend to be directly connected to others. These structural features make the yields of benzene dicarboxylic acids and benzene tricarboxylic acids (BTAs) increase with coal ranks from lignite to anthracite via oxidation. The highest yield of BCAs is benzene tetracarboxylic acids from Xiaolongtan lignite to Xuanzhong bituminous coal via oxidation. With further increasing coal rank, the highest yield of BCAs is BTAs from Pingdingshan bituminous coal to Taixi anthracite via oxidation. The proposed aromatic clusters well explain the reasons that the yields of BCAs with lower numbers of carboxyl group are significantly increased with increasing coal rank.Yang, J., Bondino, I., Regaieg, M., Moncorgé, A., 2017. Pore to pore validation of pore network modelling against micromodel experiment results. Computational Geosciences 21, 849-862. network modelling (PNM) has been widely used to study the multiphase flow and transport in porous media. Although a number of recent papers discussed the PNM validation on core-scale parameters such as permeability, relative permeability and capillary pressure; quantitative predictive potential of PNM on pore by pore basis has rarely been studied. The aim of this paper is to present a direct comparison between PNM simulations and corresponding micro-model experiments at the same scale and the same geometry. A number of well-defined and constrained two-phase flow in porous medium experimental scenarios were utilized to validate the physics solving part in PNM (filling rules, capillary and viscous pressure). This work validates that a dynamic pore network flow solver can predict two-phase flow displacements for these experiments for drainage situations at both pore and plug scales. A glass-etched micro-model is used to quantify the accuracy of a dynamic PNM solver on pore and core levels. Two-phase drainage micro fluidic experiments at different flow conditions are performed on micro-models. PNM simulations are performed on the same pattern and flow conditions as used in micro-model experiments. The two-phase distribution extracted from experiment images is registered onto rsults of PNM simulations for direct pore to pore comparison. Pore-scale matching level is found at around 75 % for all three test cases. The matching level of core-scale parameters such as S w c and oil-phase permeability varies from case to case; the relative error to micro-model experiment measurements varies from 15 to 60 %. Possible reasons leading to discrepancies on core-scale parameters are discussed: missing considerations during validation of the combination of uncertainty in both simulator input parameters and experiments are seen as the principal factors.Yang, K., Zhang, Y., Dong, Y., Li, W., 2017. Selectivity of solid phase extraction for dissolved organic matter in the hypersaline Da Qaidam Lake, China. Environmental Science: Processes & Impacts 19, 1374-1386. organic matter (DOM) was isolated from the hypersaline Da Qaidam Lake using solid-phase extraction (SPE) methods with five different adsorbents: ENVI-Carb (non-porous graphitized carbon), HLB, PPL, and XAD-8 (polymer based), and ENVI-18 (silica based). Structure-selective assessments of SPE-DOM isolated using the different adsorbents were conducted using a combination of complementary analysis techniques, including dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) analysis, as well as elemental analysis, Fourier transformed infrared spectroscopy (FTIR), 1H nuclear magnetic resonance (1H NMR) and pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS). The results indicated that the modified polymer based adsorbents (PPL and HLB) exhibited higher DOC recoveries than the others. The PPL and ENVI-Carb cartridges can recover representative nitrogen-containing organic components from the hypersaline lake. The SPE-DOM isolates obtained using ENVI-18 and XAD-8 adsorbents contained higher proportions of purely aliphatic, alkene, and aromatic compounds; the ENVI-Carb and PPL adsorbents showed higher affinity for polar functionalized aliphatic and nitrogen-containing compounds; HLB isolate was enriched with oxygen-rich organic compounds and sulphur-bearing components. The structural and compositional features of SPE-DOM from the hypersaline Da Qaidam Lake indicated the predominately autochthonous sources of organic matter in the lake.Yang, R., Hu, Q., He, S., Hao, F., Guo, X., Yi, J., He, X., 2018. Pore structure, wettability and tracer migration in four leading shale formations in the Middle Yangtze Platform, China. Marine and Petroleum Geology 89, 415-427. in different sedimentary settings, four leading shale formations (Late Ordovician Wufeng, Early Silurian Longmaxi, Late Permian Dalong, and Early Jurassic Dongyuemiao Shales) are currently the most promising zones for shale gas development in the Middle Yangtze Platform of South China. Based on complementary tests [low pressure gas physisorption, mercury injection capillary pressure (MICP), contact angle measurement, fluid imbibition into initially dry shale, and tracer diffusion into initially fluid-saturated shale followed by tracer mapping with laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS)], this work investigates their pore structure (both geometry and connectivity) and wettability characteristics, as well as the coupled effects of these characteristics on fluid flow and tracer migration. Pores <50?nm account for the majority of the pore volume in these organic shales. The shapes of hysteresis loop from gas physisorption show that the pores are mostly inkbottle-shaped in Wufeng, Longmaxi and Dongyuemiao Shales, while they are mostly narrow plate- or slit-like shaped pores in Dalong Shale. These four organic shales are strongly oil-wetting and moderately water-wetting. According to the imbibition behaviors toward aqueous (deionized water) and oleic (n-decane) phases, hydrophobic pores are better connected than hydrophilic pore networks, which is consistent with the measured contact angles. Diffusion of nano-sized nonsorbing (perrhenate [ReO4?]) and sorbing (cesium [Cs+]) tracers into brine-saturated shales indicates a high spatial variability and limited pore connectivity in these organic shales. The effective diffusion coefficient values are on the order of 10?13?m2/s with an associated geometric tortuosity ranging from 11.1 to 41.4. Due to the limited edge-connected pore spaces and low diffusion coefficients, the migration of hydrocarbons will be very slow from the shale matrix to hydraulically created fractures, with the initially high production of hydrocarbons from connected pore spaces near the sample edge (e.g., fracture face).Yang, S., Winkel, M., Wagner, D., Liebner, S., 2017. Community structure of rare methanogenic archaea: insight from a single functional group. FEMS Microbiology Ecology 93, Article fix126. rare biosphere, the low abundant microbial populations, is suggested to be a conserved way of microbial life. Here we conducted a molecular survey of rare methanogenic archaea in the environment targeting the mcrA gene in order to test if general concepts associated with the structure of the rare bacterial biosphere also apply to single functional groups. Similar to what is known about rare bacterial communities, the contribution of rare methanogens to the alpha diversity is much larger than to Bray-Curtis measures. Moreover, a similar core group of methanogens harbored by the abundant and rare communities suggests similar sources and environmental controls of both groups. Among the communities of different levels of rarity, the conditionally rare methanogenic taxa largely account for the overall community dynamics of the rare biosphere and likely enter the dominant community under favorable environmental conditions. In addition, we observed a positive correlation between the alpha diversity and the production of methane when the rare taxa were taken into account. This supports the concept that increasing microbial biodiversity enhances ecological function. The composition and environmental associations of the rare methanogenic biosphere allow us to conclude that rarity is a conserved way also for single functional groups.Yang, X., Zhao, Y., Babcock, L.E., Peng, J.I.N., 2017. A new vauxiid sponge from the Kaili Biota (Cambrian Stage 5), Guizhou, South China. Geological Magazine 154, 1334-1343. skeleton of a new vauxiid sponge (Order Verongida), Angulosuspongia sinensis gen. et sp. nov., described on the basis of material from calcareous mudstones of the Kaili Formation (Cambrian Stage 5), Jianhe area, Guizhou, South China, is composed of two layers of fused spicules outlining hexagonal or polygonal openings. These vauxiid remains are the first reported from outside Laurentia, and represent only the second genus attributed to the family. Its age is close to but still slightly older than the Burgess Shale Biota, and it appears to be a primitive relative of other members of the Vauxiidae. The morphological differences between Chinese and Laurentian vauxiid sponges may be a result of vicariance. These specimens not only extend the geographic distribution of vauxiids, but also help to fill a chronostratigraphical gap between North Greenland and North American material and provide additional evidence for understanding the evolutionary history of the Demospongiae.Yang, Y., Lin, Y., Chen, Z., Gong, T., Yang, P., Girault, H., Liu, B., Qiao, L., 2017. Bacterial whole cell typing by mass spectra pattern matching with bootstrapping assessment. Analytical Chemistry 89, 12556-12561. typing is of great importance in clinical diagnosis, environmental monitoring, food safety analysis, and biological research. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is now widely used to analyze bacterial samples. Identification of bacteria at the species level can be realized by matching the mass spectra of samples against a library of mass spectra of known bacteria. Nevertheless, in order to reasonably type bacteria, identification accuracy should be further improved. Herein, we propose a new framework to the identification and assessment for MALDI-MS based bacterial analysis. Our approach combines new measures for spectra similarity and a novel bootstrapping assessment. We tested our approach on a general data set containing the mass spectra of 1741 strains of bacteria and another challenging data set containing 250 strains, including 40 strains in the Bacillus cereus group that were previously claimed to be impossible to resolve by MALDI-MS. With the bootstrapping assessment, we achieved much more reliable predictions at both the genus and species level, and enabled to resolve the Bacillus cereus group. To the best of the authors’ knowledge, our method is the first to provide a statistical assessment to MALDI-MS based bacterial typing that could lead to more reliable bacterial typing.Yang, Z., Li, Q., Wu, S., Lin, S., Liu, X., 2017. Evidence of the near-source accumulation of the tight sandstone gas in northern Ordos Basin, north-central China. Acta Geologica Sinica - English Edition 91, 1820-1835. tight sandstone gas in Upper Paleozoic Formation of the northern Ordos Basin is a typical giant unconventional tight gas province. Evidences from geochemistry, reservoir geology and pale-otectonic setting all verify that the present-day tight sandstone gas accumulation in the Ordos Basin is the result of near-source accumulation. The evidences are listed as following: tight sandstone gas is mainly distributed in the area with high gas-generating strength; gas composition was not subjected to fractionation; gas saturation significantly decreases with the distance away from the source rocks; gas isotopes suggest their origin is the same and maturity is consistent with in-place source rocks; reservoirs have experienced three types of densification digenesis, including intense compaction, siliceous cementation and calcareous cementation, which took place before the formation of a large amount of tight sandstone gas, forming tight reservoirs with low porosity and permeability, fine pore throat and great capillary resistance; the paleo-structural gradient ratio is small from the main hydrocarbon generation period to present. It is indicated the present distribution of tight sandstone gas in the northern Ordos Basin is the result of near-source and short-distance migration and accumulation.Yao, B., Wang, L., Yin, X., Wu, Y.-S., 2017. Numerical modeling of cryogenic fracturing process on laboratory-scale Niobrara shale samples. Journal of Natural Gas Science and Engineering 48, 169-177. fracturing is a new fracturing concept that uses cryogenic fluids as fracturing fluids. Its mechanism rests on the effect of a thermal shock (sharp thermal gradient) introduced by cryogen on the hot surface of reservoir rock. Fractures can then be initiated and propagated due to strong local tensile stress. The objective of this research is to simulate the cryogenic fracturing experiments on Niobrara shale samples. The experimental processes are simulated under different conditions and matched with the actual experiment results. The influences of different confining stress, injection pressure and failure criteria are identified by comparing results from modeling and experiments. The simulation tool developed can also predict the distribution of artificial fractured samples.Yao, X., Tao, F., Zhang, K., Tang, H., Xu, P., 2017. Multiple roles for two efflux pumps in the polycyclic aromatic hydrocarbon-degrading Pseudomonas putida strain B6-2 (DSM 28064). Applied and Environmental Microbiology 83.: Microbial bioremediation is a promising approach for the removal of polycyclic aromatic hydrocarbon (PAH) contaminants. Many degraders of PAHs possess efflux pump genes in their genomes; however, their specific roles in the degradation of PAHs have not been clearly elucidated. In this study, two efflux pumps, TtgABC and SrpABC, were systematically investigated to determine their functions in a PAH-degrading Pseudomonas putida strain B6-2 (DSM 28064). The disruption of genes ttgABC or srpABC resulted in a defect in organic solvent tolerance. TtgABC was found to contribute to antibiotic resistance; SrpABC only contributed to antibiotic resistance under an artificial overproduced condition. Moreover, a mutant strain without srpABC did not maintain its activity in long-term biphenyl (BP) degradation, which correlated with the loss of cell viability. The expression of SrpABC was significantly upregulated in the course of BP degradation. BP, 2-hydroxybiphenyl, 3-hydroxybiphenyl, and 2,3-dihydroxybiphenyl (2,3-DHBP) were revealed to be the inducers of srpABC. 2,3-DHBP was verified to be a substrate of pump SrpABC; SrpABC can enhance the tolerance to 2,3-DHBP by pumping it out. The mutant strain B6-2ΔsrpS prolonged BP degradation with the increase of srpABC expression. These results suggest that the pump SrpABC of strain B6-2 plays a positive role in BP biodegradation by pumping out metabolized toxic substances such as 2,3-DHBP. This study provides insights into the versatile physiological functions of the widely distributed efflux pumps in the biodegradation of PAHs. Importance: Polycyclic aromatic hydrocarbons (PAHs) are notorious for their recalcitrance to degradation in the environment. A high frequency of the occurrence of the efflux pump genes was observed in the genomes of effective PAH degraders; however, their specific roles in the degradation of PAHs are still obscure. The significance of our study is in the identification of the function and mechanism of the efflux pump SrpABC of Pseudomonas putida strain B6-2 (DSM 28064) in the biphenyl degradation process. SrpABC is crucial for releasing the toxicity caused by intermediates that are unavoidably produced in PAH degradation, which enables an understanding of how cells maintain the intracellular balance of materials. The findings from this study provide a new perspective on PAH recalcitrance and shed light on enhancing PAH degradation by genetic engineering. Ye, H., Wu, C.-Z., Yang, T., Santosh, M., Yao, X.-Z., Gao, B.-F., Wang, X.-L., Li, W., 2017. Updating the geologic barcodes for South China: Discovery of Late Archean banded iron formations in the Yangtze Craton. Scientific Reports 7, Article 15082. iron formations (BIFs) in Archean cratons provide important “geologic barcodes” for the global correlation of Precambrian sedimentary records. Here we report the first finding of late Archean BIFs from the Yangtze Craton, one of largest Precambrian blocks in East Asia with an evolutionary history of over 3.3 Ga. The Yingshan iron deposit at the northeastern margin of the Yangtze Craton, displays typical features of BIF, including: (i) alternating Si-rich and Fe-rich bands at sub-mm to meter scales; (ii) high SiO2?+?Fe2O3total contents (average 90.6 wt.%) and Fe/Ti ratios (average 489); (iii) relative enrichment of heavy rare earth elements and positive Eu anomalies (average 1.42); (iv) and sedimentary Fe isotope compositions (δ56FeIRMM-014 as low as ?0.36‰). The depositional age of the BIF is constrained at ~2464?±?24?Ma based on U-Pb dating of zircon grains from a migmatite sample of a volcanic protolith that conformably overlied the Yingshan BIF. The BIF was intruded by Neoproterozoic (805.9?±?4.7?Ma) granitoids that are unique in the Yangtze Craton but absent in the North China Craton to the north. The discovery of the Yingshan BIF provides new constraints for the tectonic evolution of the Yangtze Craton and has important implications in the reconstruction of Pre-Nuna/Columbia supercontinent configurations.Yeung, L.Y., 2017. Low oxygen and argon in the Neoproterozoic atmosphere at 815 Ma. Earth and Planetary Science Letters 480, 66-74. evolution of Earth's atmosphere on >106>106-yr timescales is tied to that of the deep Earth. Volcanic degassing, weathering, and burial of volatile elements regulates their abundance at the surface, setting a boundary condition for the biogeochemical cycles that modulate Earth's atmosphere and climate. The atmosphere expresses this interaction through its composition; however, direct measurements of the ancient atmosphere's composition more than a million years ago are notoriously difficult to obtain. Gases trapped in ancient minerals represent a potential archive of the ancient atmosphere, but their fidelity has not been thoroughly evaluated. Both trapping and preservation artifacts may be relevant. Here, I use a multi-element approach to reanalyze recently collected fluid-inclusion data from halites purportedly containing snapshots of the ancient atmosphere as old as 815 Ma. I argue that those samples were affected by the concomitant trapping of air dissolved in brines and contaminations associated with modern air. These artifacts lead to an apparent excess in O2 and Ar. The samples may also contain signals of mass-dependent fractionation and biogeochemical cycling within the fluid inclusions. After consideration of these artifacts, this new analysis suggests that the Tonian atmosphere was likely low in O2, containing ≤10% present atmospheric levels (PAL), not ～50% PAL as the data would suggest at face value. Low concentrations of O2 are consistent with other geochemical constraints for this time period and further imply that the majority of Neoproterozoic atmospheric oxygenation occurred after 815 Ma. In addition, the analysis reveals a surprisingly low Tonian Ar inventory—≤60% PAL—which, if accurate, challenges our understanding of the solid Earth's degassing history. When placed in context with other empirical estimates of paleo-atmospheric Ar, the data imply a period of relatively slow atmospheric Ar accumulation in the Paleo- and Meso-Proterozoic, followed by extensive degassing in the late Neoproterozoic or early Cambrian, before returning to a relatively quiescent state by the Devonian. This two-step structure resembles that for the evolution of atmospheric O2, hinting at a common driving force from the deep Earth. Some caution is warranted, however, because still more enigmatic contaminations than the ones presented here may be relevant. Gases trapped in minerals may offer important constraints on the evolution of Earth's surface, climate, and atmosphere, but potential contaminations and other confounding factors need to be considered carefully before these records can be considered quantitative.Yeung, L.Y., Li, S., Kohl, I.E., Haslun, J.A., Ostrom, N.E., Hu, H., Fischer, T.P., Schauble, E.A., Young, E.D., 2017. Extreme enrichment in atmospheric 15N15N. Science Advances 3, Article eaao6741. nitrogen (N2) comprises three-quarters of Earth’s atmosphere and significant portions of other planetary atmospheres. We report a 19 per mil (‰) excess of 15N15N in air relative to a random distribution of nitrogen isotopes, an enrichment that is 10 times larger than what isotopic equilibration in the atmosphere allows. Biological experiments show that the main sources and sinks of N2 yield much smaller proportions of 15N15N in N2. Electrical discharge experiments, however, establish 15N15N excesses of up to +23‰. We argue that 15N15N accumulates in the atmosphere because of gas-phase chemistry in the thermosphere (>100 km altitude) on time scales comparable to those of biological cycling. The atmospheric 15N15N excess therefore reflects a planetary-scale balance of biogeochemical and atmospheric nitrogen chemistry, one that may also exist on other planets.You, K., Flemings, P.B., 2018. Methane hydrate formation in thick sand reservoirs: 1. Short-range methane diffusion. Marine and Petroleum Geology 89, 428-442. show with a comprehensive hydrate formation model that diffusion of dissolved methane along the local concentration gradient alone cannot transport enough methane to form the concentrated methane hydrates in thick (>= several m) marine sand reservoirs. In this model, methane is generated locally by biodegradation of organic matter in mudstones and diffused into the bounding sandstone where the methane hydrate solubility decreases abruptly and hydrate precipitates from the extra methane in water. Hydrate formed by local diffusion has peak concentrations at the top and base of the sandstone, and it decreases sharply toward the center; salinity is slightly elevated relative to seawater, and its gradient is negligible across the sandstone and adjacent mudstones; dissolved methane concentration decreases from the mudstones to the sandstone. Overpressure is generated in the sediment due to reduction of sediment permeability and volume expansion when hydrate replaces pore water. There is a shallow zone where pore pressure converges toward the lithostatic pressure and fracturing is possible. This study provides further insights into hydrate formation by local diffusion of dissolved methane. In addition, the numerical model we developed in this study fully couples the hydrate-liquid capillary effect, dynamic pore size change, and transient pore pressure-dependent sediment compaction with the multiphase (gas, liquid and hydrate) flow and multicomponent (methane, water and salt) transport. Our model not only predicts pore pressure, but also incorporates the effect of hydrate formation on overpressure generation and subsequent dissipation. These modeling approaches are now at a level of sophistication that we can start to distinguish what physical processes, of the several proposed, are viable explanations for observed hydrate deposits.Yu, K.L., Lau, B.F., Show, P.L., Ong, H.C., Ling, T.C., Chen, W.-H., Ng, E.P., Chang, J.-S., 2017. Recent developments on algal biochar production and characterization. Bioresource Technology 246, 2-11. biomass is known as a promising sustainable feedstock for the production of biofuels and other valuable products. However, since last decade, massive amount of interests have turned to converting algal biomass into biochar. Due to their high nutrient content and ion-exchange capacity, algal biochars can be used as soil amendment for agriculture purposes or adsorbents in wastewater treatment for the removal of organic or inorganic pollutants. This review describes the conventional (e.g., slow and microwave-assisted pyrolysis) and newly developed (e.g., hydrothermal carbonization and torrefaction) methods used for the synthesis of algae-based biochars. The characterization of algal biochar and a comparison between algal biochar with biochar produced from other feedstocks are also presented. This review aims to provide updated information on the development of algal biochar in terms of the production methods and the characterization of its physical and chemical properties to justify and to expand their potential applications.Yu, Q., Zhang, Q., Lu, X., Qian, X., Ni, K., Wang, X., 2017. Developing a vacuum electrospray source to implement efficient atmospheric sampling for miniature ion trap mass spectrometer. Analytical Chemistry 89, 12938-12944. performance of a miniature mass spectrometer in atmospheric analysis is closely related to the design of its sampling system. In this study, a simplified vacuum electrospray ionization (VESI) source was developed based on a combination of several techniques, including the discontinuous atmospheric pressure interface, direct capillary sampling, and pneumatic-assisted electrospray. Pulsed air was used as a vital factor to facilitate the operation of electrospray ionization in the vacuum chamber. This VESI device can be used as an efficient atmospheric sampling interface when coupled with a miniature rectilinear ion trap (RIT) mass spectrometer. The developed VESI-RIT instrument enables regular ESI analysis of liquid, and its qualitative and quantitative capabilities have been characterized by using various solution samples. A limit of detection of 8 ppb could be attained for arginine in a methanol solution. In addition, extractive electrospray ionization of organic compounds can be implemented by using the same VESI device, as long as the gas analytes are injected with the pulsed auxiliary air. This methodology can extend the use of the proposed VESI technique to rapid and online analysis of gaseous and volatile samples.Yuan, B., Wang, W., 2018. Using nanofluids to control fines migration for oil recovery: Nanofluids co-injection or nanofluids pre-flush? -A comprehensive answer. Fuel 215, 474-483. paper provides a comprehensive study to evaluate and optimize the effectiveness of nanofluids to both prevent fines migration and enhance oil recovery using different utilization approaches: nanofluids co-injection and pre-flush. To do that, 1) a comprehensive review of both laboratory experiments and field cases is adopted to confirm the effectiveness of nanoparticles to control fines migration. 2) A novel model of maximum fines retention concentration is then introduced to find out the physical mechanisms on how nanoparticles control fines migration. 3) Through matching with lab experiments, the physical behaviors of fines migration and attachment with the effects of different types of nanofluids are characterized, including fines attachment and straining rates, and breakthrough time of injected fines. 4) As a new criterion, mitigation index (MI) is defined to find out the more excellent performance of nanofluids pre-treatment that of nanofluids co-injection. 5) The pros and cons of fines migration on performance of low-salinity water flooding are discussed comprehensively, in this work, and the success of combining nanofluids with low-salinity water flooding is also confirmed to achieve more oil recovery. The outcomes of this work will help extend the applications of nanofluids in reservoirs suffering from problems of fines migration.Yuan, Y.-S., Jin, Z.-J., Zhou, Y., Liu, J.-X., Li, S.-J., Liu, Q.-Y., 2017. Burial depth interval of the shale brittle–ductile transition zone and its implications in shale gas exploration and production. Petroleum Science 14, 637-647. and ductility of shale are closely related to shale gas exploration and production. How to predict brittleness and ductility of shale is one of the key issues in the study of shale gas preservation and hydraulic fracturing treatments. The magnitude of shale brittleness was often determined by brittle mineral content (for example, quartz and feldspars) in shale gas exploration. However, the shale brittleness is also controlled by burial depth. Shale brittle/ductile properties such as brittle, semi-brittle and ductile can mutually transform with burial depth variation. We established a work flow of determining the burial depth interval of brittle–ductile transition zone for a given shale. Two boundaries were employed to divide the burial depth interval of shale brittle/ductile properties. One is the bottom boundary of the brittle zone (BZ), and the other is the top boundary of the ductile zone (DZ). The brittle–ductile transition zone (BDTZ) is between them. The bottom boundary of BZ was determined by the over-consolidation ratio (OCR) threshold value combined with pre-consolidation stress which the shale experienced over geological time. The top boundary of DZ was determined based on the critical confining pressure of brittle–ductile transition. The OCR threshold value and the critical confining pressure were obtained from uniaxial strain and triaxial compression tests. The BZ, DZ and BDTZ of the Lower Silurian Longmaxi shale in some representative shale gas exploration wells in eastern Sichuan and western Hubei areas were determined according to the above work flow. The results show that the BZ varies with the maximum burial depth and the DZ varies with the density of the overlying rocks except for the critical confining pressure. Moreover, the BDTZ determined by the above work flow is probably the best burial depth interval for marine shale gas exploration and production in Southern China. Shale located in the BDTZ is semi-brittle and is not prone to be severely naturally fractured but likely to respond well to hydraulic fracturing. The depth interval of BDTZ determined by our work flow could be a valuable parameter of shale gas estimation in geology and engineering.Yuan, Y., Bolan, N., Prévoteau, A., Vithanage, M., Biswas, J.K., Ok, Y.S., Wang, H., 2017. Applications of biochar in redox-mediated reactions. Bioresource Technology 246, 271-281. is chemically more reduced and reactive than the original feedstock biomass. Graphite regions, functional groups, and redox-active metals in biochar contribute to its redox characteristics. While the functional groups such as phenolic species in biochar are the main electron donating moieties (i.e., reducers), the quinones and polycondensed aromatic functional groups are the components accepting electrons (oxidants). The redox capacity of biochar depends on feedstock properties and pyrolysis conditions. This paper aims to review and summarize the various synthesis techniques for biochars and the methods for probing their redox characteristics. We review the abiotic and microbial applications of biochars as electron donors, electron acceptors, or electron shuttles for pollutant degradation, metal(loid)s (im)mobilization, nutrient transformation, and discuss the underlying mechanisms. Furthermore, knowledge gaps that exist in the exploration and differentiation of the electron transfer mechanisms involving biochars are also identified.Zaghoo, M., Silvera, I.F., 2017. Conductivity and dissociation in liquid metallic hydrogen and implications for planetary interiors. Proceedings of the National Academy of Sciences 114, 11873-11877.: Liquid metallic hydrogen (LMH) is a fundamental system in condensed matter sciences and the main constituent of gas giant planets. Because of exceptional challenges in experimentation and theory, its transport properties remained poorly understood. We have conducted experimental determination of the optical conductivity of bulk LMH using spectrally resolved reflectance measurements on statically compressed and heated hydrogen. Metallic hydrogen’s mechanism of metallization is largely dissociative to an atomic state, rather than the previously held experimental model, ionization of molecules. We find that LMH’s electrical conductivity is substantially higher, a factor of 6–8, than the only experimentally reported value in the literature, measured in the dc limit. The implications of the current results to Jovian giants planetary models are discussed. Abstract: Liquid metallic hydrogen (LMH) is the most abundant form of condensed matter in our solar planetary structure. The electronic and thermal transport properties of this metallic fluid are of fundamental interest to understanding hydrogen’s mechanism of conduction, atomic or pairing structure, as well as the key input for the magnetic dynamo action and thermal models of gas giants. Here, we report spectrally resolved measurements of the optical reflectance of LMH in the pressure region of 1.4–1.7 Mbar. We analyze the data, as well as previously reported measurements, using the free-electron model. Fitting the energy dependence of the reflectance data yields a dissociation fraction of 65 ± 15%, supporting theoretical models that LMH is an atomic metallic liquid. We determine the optical conductivity of LMH and find metallic hydrogen’s static electrical conductivity to be 11,000–15,000 S/cm, substantially higher than the only earlier reported experimental values. The higher electrical conductivity implies that the Jovian and Saturnian dynamo are likely to operate out to shallower depths than previously assumed, while the inferred thermal conductivity should provide a crucial experimental constraint to heat transport models. Zarghani, M., Parastar, H., 2017. Joint approximate diagonalization of eigenmatrices as a high-throughput approach for analysis of hyphenated and comprehensive two-dimensional gas chromatographic data. Journal of Chromatography A 1524, 188-201. objective of the present work is development of joint approximate diagonalization of eigenmatrices (JADE) as a member of independent component analysis (ICA) family, for the analysis of gas chromatography-mass spectrometry (GC–MS) and comprehensive two-dimensional gas chromatography-mass spectrometry (GC × GC–MS) data to address incomplete separation problem occurred during the analysis of complex sample matrices. In this regard, simulated GC–MS and GC × GC–MS data sets with different number of components, different degree of overlap and noise were evaluated. In the case of simultaneous analysis of multiple samples, column-wise augmentation for GC–MS and column-wise super-augmentation for GC × GC–MS was used before JADE analysis. The performance of JADE was evaluated in terms of statistical parameters of lack of fit (LOF), mutual information (MI) and Amari index as well as analytical figures of merit (AFOMs) obtained from calibration curves. In addition, the area of feasible solutions (AFSs) was calculated by two different approaches of MCR-BANDs and polygon inflation algorithm (FACPACK). Furthermore, JADE performance was compared with multivariate curve resolution-alternating least squares (MCR-ALS) and other ICA algorithms of mean-field ICA (MFICA) and mutual information least dependent component analysis (MILCA). In all cases, JADE could successfully resolve the elution and spectral profiles in GC–MS and GC × GC–MS data with acceptable statistical and calibration parameters and their solutions were in AFSs. To check the applicability of JADE in real cases, JADE was used for resolution and quantification of phenanthrene and anthracene in aromatic fraction of heavy fuel oil (HFO) analyzed by GC × GC–MS. Surprisingly, pure elution and spectral profiles of target compounds were properly resolved in the presence of baseline and interferences using JADE. Once more, the performance of JADE was compared with MCR-ALS in real case. On this matter, the mutual information (MI) values were 1.01 and 1.13 for resolved profiles by JADE and MCR-ALS, respectively. In addition, LOD values (μg/mL) were respectively 1.36 and 1.24 for phenanthrene and 1.26 and 1.09 for anthracene using MCR-ALS and JADE which showed outperformance of JADE over MCR-ALS.Zeng, H.A.N., Zhao, F., Yin, Z., Zhu, M., 2017. Appendages of an early Cambrian metadoxidid trilobite from Yunnan, SW China support mandibulate affinities of trilobites and artiopods. Geological Magazine 154, 1306-1328. anatomy contributes crucial data for understanding the evolution and ecology of Euarthropoda. The Palaeozoic trilobites show a great diversity of exoskeletons in the fossil record. However, soft parts, especially appendages, have only been discovered from a few trilobite species. Here we report extraordinarily preserved appendages in the trilobite species Hongshiyanaspis yiliangensis Zhang & Lin in Zhang et al. 1980 (Redlichiida, Metadoxididae) from a single mudstone layer of the Xiazhuang fossil assemblage within the Hongjingshao Formation (Cambrian Series 2, Stage 3) near Kunming, Yunnan, SW China. The appendages exhibit the common architecture revealed by other trilobites and artiopods by consisting of a pair of uniramous antennae followed by a series of paired homonomous biramous limbs. The antennae in holaspid individuals comprise up to 27 spinous podomeres and their ontogeny occurs by lengthening of the podomeres. The post-antennal biramous limbs are similar to those in other polymerid trilobites and artiopods by having a single-segmented protopodite and an endopodite comprising seven segments, but possess a unique wide tripartite exopodite with long setae. Sophisticated appendage anatomy, including the body–limb junction, fine setae, putative muscle bundles and duct-type tissues, are also revealed. Appendages of trilobites, artiopods and other upper stem-group euarthropods are compared and summarized. The H. yiliangensis appendages highlight the high morphological disparity of exopodites and the conservativeness of endopodites in trilobites and artiopods. This morphological pattern, together with similar body patterning seen in crustaceans but not in chelicerates, supports the mandibulate affinities of trilobites and at least some artiopods.Zeng, Y., Fu, X., Zeng, S., 2017. Organic geochemistry and oil-generating potential of the Oligocene–Early Miocene Dingqinghu Formation sediments in the Lunpola Basin, Tibet. Petroleum Geoscience 23, 440-453. hydrocarbon source rock potential of shales from the Oligocene–Early Miocene Dingqinghu Formation was evaluated using organic geochemistry (Rock-Eval pyrolysis, total organic carbon (TOC) and bitumen extraction) and organic petrology. Forty-one outcrop samples from Lunbori and Jiangria Co shales in the Lunpola Basin were analysed.At Lunbori, in the central part of the basin, the shales have very good source rock potential, and show TOC contents ranging from 3.72 to 11.2?wt%, with an average TOC value of 7.36?wt%, S2 values of 33.4?–?99.5?mg HC/g rock (average 61.8?mg HC/g rock), and extractable organic matter contents varying from 513 to 4525?ppm (average 2105?ppm). The shales have very good source rock potential. Rock-Eval Tmax values of 433?–?437°C (average 435°C) and high carbon preference index (CPI) values (4.76?–?6.70) indicate that the organic matter is immature to early mature for oil generation. The yellow fluorescence of kerogen under UV light is in good agreement with Tmax and CPI data. High hydrogen indices (HI) (635?–?1057?mg HC/g TOC) and H/C ratios (1.60?–?1.72) indicate that the Lunbori shales contain oil-prone organic matter and are characterized by high yellow fluorescing amorphous sapropelite content. The Lunbori shales contain a high content of hydrogen-rich Type II and minor Type I oil-prone kerogen, and have dominant medium to long molecular weight n-alkanes (maximizing at C25 or C27) with marked odd carbon number preference in the n-C23?–?n-C31 range, pristine/phytane (Pr/Ph) ratios of 0.06?–?0.14, high phytane/n-C18 ratios (10.95?–?30.63), abundant gammacerane (gammacerane/C31 hopane: 0.44?–?1.80), and predominant regular sterane C27. These data indicate deposition in stratified, anoxic and saline depositional conditions with a kerogen predominatly formed from a lacustrine biota.The Jiangria Co shales in the western part of the Lunpola Basin contain some hydrogen-rich Type I and II oil-prone kerogens at a marginally mature level. They have TOC contents of up to 2.62?wt%, S2 values of up to 17.2?mg HC/g rock and extractable organic matter contents of up to 1731?ppm, indicating good source rock potential for oil generation. This is supported by their high HI values (420?–?720?mg HC/g TOC) and H/C ratios (1.05?–?1.50). The biomarker distributions of the extracts are characterized by odd carbon number predominance (C23–C31), low Pr/Ph ratios (0.05?–?0.09), high concentrations of phytane and high gammacerane content, indicating lacustrine reducing and saline conditions.Zhang, B., He, Y., Chen, Y., Meng, Q., Yuan, L., 2017. Geochemical characteristics and oil accumulation significance of the high quality saline lacustrine source rocks in the western Qaidam Basin, NW China. Acta Petrolei Sinica 38, 1158-1167. is traditionally believed that the saline lacustrine source rocks in western Qaidam Basin have low organic matter abundance, and the hydrocarbons are mainly sourced from "soluble organic matters". In this study, a certain scale of high quality saline lacustrine source rocks with high organic matter abundance has been discovered for the first time; the TOC value is about 1 % with the maximum above 4 %, the potential of hydrocarbon generation is generally greater than 6 mg/g with the maximum up to 40 mg/g, and the hydrogen index is commonly above 500 mg/g(TOC) with the maximum above 900 mg/g(TOC). The organic matters of Type I and Type II1 are dominant, mixed with a small amount of Type II2, indicating, the oil-prone types. The samples with ultra-low organic matter abundance (TOC<0.5 % ) indicates the poor types, contain a less content of soluble organic matter and a small potential of hydrocarbon generation, belonging to the inactive source rocks. Among the biomarkes of high quality source rocks, the compounds rich in phytane, C28-sterane, gammacerane and C35-hopance revealing the saline environment; the characteristics of high sterane low hopane, high C27-sterane and low C29-sterane, indicating organic matters are mainly derived from hydrobiontic algae. As so-called oil algae, these algae rich in lipid compounds can be directly converted into hydrocarbons in the low mature stage. The saline environment is conductive to the preservation of liquid hydrocarbon directly converted by algae, thus forming "immature-low mature oil". The content of "soluble organic matter" contained in the saline lacustrine source rocks of western Qaidam Basin is significantly higher than that of fresh water lacustrine source rocks, which is the important material source for a batch of immature-low mature oilfields discovered in regional middle-shallow layers in western Qaidam Basin. It is validated by simulation test that organic matters also have a high potential of oil-generation in the mature stage, in accordance with the classic oil-gas generation model. Thus, the oil and gas generated in mature source rocks is the major exploration target for deep layers. In this region, there are two types of hydrocarbon accumulation models for high quality source rocks in Paleogene deep layers. One is outer-source accumulation, i.e., oil and gas migrates towards shallow tectosphere through open faults for accumulation; the other type is inner-source accumulation, i.e., oil and gas is accumulated near the source in the lithological traps adjacent to deep source rocks. So far, significant breakthroughs have been made in these two types of oil-gas reservoir exploration, and two blocks with the reserves up to a hundred million tons are discovered to confirm the enormous exploration potential of oil-gas reservoirs formed in deep high quality source rocks.Zhang, H., Ma, S., Yao, Y., Li, Y., Li, Y., Ou, J., Ye, M., Wei, Y., 2017. Facile preparation of multi-functionalized hybrid monoliths via two-step photo-initiated reactions for two-dimensional liquid chromatography–mass spectrometry. Journal of Chromatography A 1524, 135-142. facile approach was developed to prepare hybrid monoliths with different functions via two-step photo-initiated reactions. Firstly, acrylopropyl polyhedral oligomertic silsesquioxane (acryl-POSS) and propargyl acrylate (PA) were used as precursors to synthesize alkynyl-functionalized hybrid monoliths via photo-initiated free radical polymerization. Secondly, the hybrid monoliths were modified with 1-octadecanethiol (ODT) and sodium 3-mercapto-1-propanesulfonate (SMPS) via photo-initiated thiol-yne click reaction to prepare reversed-phase (RP) and strong cation-exchange (SCX) hybrid monoliths, respectively. The results of chromatographic characterization indicated that the column efficiencies for alkylbenzenes on ODT-modified hybrid monolith reached 84,000–87,700 plates per meter at the velocity of 0.58 mm/s, and also revealed a retention-independent efficient performance of small molecules in isocratic elution. The SMPS-modified hybrid monolith exhibited both hydrophobicity and ion-exchange mechanisms, and the dynamic binding capacity was calculated to be 1.4 × 10?4 μmol/cm. Human Hela cells tryptic digest was well separated on ODT-modified hybrid monolith in one-dimensional RPLC–MS/MS, and 2786 unique peptides and 685 proteins were identified. Furthermore, the SMPS-modified monolith coupled with ODT-modified monolith was used for two-dimensional separation of human Hela cells tryptic digest in SCX-RPLC–MS/MS, and the results showed that 9744 unique peptides and 2749 proteins were identified. Compared to those identified in one-dimensional RP system, the total numbers of unique peptides and proteins identified in SCX-RP system increased by 249.7% and 301.3%, respectively.Zhang, J., Chen, Z., 2017. Metal-organic frameworks as stationary phase for application in chromatographic separation. Journal of Chromatography A 1530, 1-18. frameworks (MOFs) as a subclass of coordination polymers, have attracted wide interest in various field. Herein, we focus on its application in chromatographic separation due to its excellent physical and chemical properties such as large surface area, high porosity, uniform pore sizes and structural diversity. In 2014, a review was published to summarize the most significant advances in MOFs, and their applications in separation science. The present review was an extensive update on applications of MOFs in chromatographic separation from 2014 to the present such as high-performance liquid chromatography (HPLC), capillary electrochromatography (CEC), nano-liquid chromatography (nano-LC), and gas chromatography (GC). Besides, the typical applications of MOFs in solid-phase microextraction (SPME) were also discussed. Except the presentation of experimental data, the limitations and prospects were also summarized in this review, which can offer an outlook and reference on further study of applications of MOFs.Zhang, J., Jia, G., Guo, W., Wang, X., Lei, F., 2017. Isoprenoid tetraether lipids in suspended particulate matter from the East China Sea and implication for sedimentary records. Organic Geochemistry 114, 81-90. total of 90 samples of suspended particulate matter (SPM) collected in surface waters of the East China Sea (ECS) in summer and winter were studied for archaeal isoprenoid glycerol dialkyl glycerol tetraether lipids (iGDGTs) and the derived sea surface temperature (SST) proxy, i.e. TEX86H. Our data showed that in summer SPM TEX86H correlated well with in-situ measured SST, but in winter the relationship became much poorer. We found that the bottom water depth (BWD) of 70?m was a critical depth when studying the TEX86H-SST relationship in winter SPM. In locations with BWD < 70?m, concentrations of iGDGTs in SPM were > 5x higher in winter than in summer, but TEX86H showed a much weaker correlation with in-situ measured SST. This was speculated to be caused by lateral transport of SPM and resuspension of surface sediments in winter due to strong winds. Whereas in locations with BWD > 70?m, TEX86H correlated well with in-situ measured SST, suggesting a minor influence of SPM lateral transport and sediment resuspension. Moreover, although only core iGDGTs were analyzed, we found that both summer and winter TEX86H values correlated better with in-situ measured SST than with seasonal and annual mean SST, suggesting that SPM iGDGTs were dominantly produced around the sampling time rather than encompassing longer time input. The linear relationships of SPM TEX86H with in-situ measured SST were different between winter (BWD > 70?m) and summer, likely due to seasonal archaeal community change. Published sedimentary TEX86H data in the ECS were reexamined here, and a BWD of 70?m was also found to be a critical depth. At sites with BWD > 70?m, TEX86H in sediments correlated well with annual mean SST, whereas the correlation became poor at BWD < 70?m, suggesting that sedimentary GDGTs were also greatly influenced by resuspension and lateral transport, and hence complicating the application of the proxy to shallow locations in the ECS.Zhang, J., Lai, H., Gao, H., Hu, S., Xue, Q., 2018. Prevention and mitigation of paraffin deposition by biosurfactant-producing and paraffin-degrading Bacillus amyloliquefaciens strain 6-2c. Chemical Engineering Journal 335, 510-519. deposition during oil production and transportation results in pipeline blockage and increases the cost of petroleum production. Conventional mechanical, thermal, and chemical methods to clear paraffin deposition are problematic; microbiological approaches are an effective alternative. Bacillus spp. that possesses exceptional survival abilities and can degrade paraffins in the environment of oil wells is often used as potential microbe for paraffin removal. In this study, we investigated a biosurfactant-producing bacterial strain, Bacillus amyloliquefaciens 6-2c that was recently isolated from oil-contaminated soil in the Ansai oilfield, northwest China. The performance of bacterial treatment in prevention and mitigation of paraffin deposition was assessed. Strain 6-2c efficiently improved the solubility of paraffin in n-hexane and the paraffin solubility rate (SR%) reached 79.15%, increased by 5.39% compared to the control. The morphology of paraffin crystals markedly changed after bacterial degradation, having a rough surface and a loose structure. Strain 6-2c produced a biosurfactant that reduced the surface and interfacial tension to 25.51 ± 0.035 mN m?1 and 1.55 ± 0.014 mN m?1, respectively. The biosurfactant formed stable emulsions with a wide range of hydrocarbons, and showed high stability over a wide range of temperature (20–120 °C), pH (2–13), and salinity (0–15%, w/v). The paraffin removal efficiency of strain 6-2c ranged from 50.82% to 95.17%. Interestingly, strain 6-2c cells attached to the surface of steel pipes inhibited paraffin coalescence. These findings indicate the potential of this biosurfactant-producing bacterial strain in paraffin degradation and enhanced oil recovery.Zhang, L., Yao, J., Zhao, J., Li, A., Sun, H., Wan, Y., Su, Y., 2017. The influence of wettability and shut-in time on oil recovery through microscale simulation based on an ideal model. Journal of Natural Gas Science and Engineering 48, 178-185. the oil development, the most common method to enhance recovery is waterflooding. Due to different size of pores existing in reservoirs, some interesting phenomena are observed. In addition, the efficiency of waterflooding is different at different wettability. The shut-in time also has influence on the production rate after water injection while the reason is not clear. In this study, we investigate this problem with lattice Boltzmann method at pore scale, which has many advantages over pore network modeling. The effect of wettability and shut-in time are studied systematically based on an ideal pore-throat model. The whole simulation is divided into three steps: injection, shut-in and flow-back. According to the simulation, the following conclusions can be obtained. (1) In injection simulation, a better efficiency of displacement can be reached as water wettability increases, and it takes less time under weakly wetting situation. The local geometry structure has an impact on invasion order. The wetting phase intrudes into the first pore throat when it flows from pore body to pore throats. (2) In shut-in process, shut-in time has slight influence on the final water saturation, and the water saturation decreases at first, then increases with the shut-in time increasing. It takes more time for capillary pressure to be reflected in the displacement, and it depends on the number of dead end pores and the diameter and length of pore throats that connect the dead end pores. The movement of fluids is quite slow in most pores and is a dynamic balance in a few dead end pores, and the dynamic balance only happens at the beginning of shut-in stage. (3) In flow-back step, as the wettability increases, higher water saturation can be obtained after flow-back process, which leads to a better recovery. The flow-back process takes more time as the wettability decreases. The flow-back time in weakly wetting is six times more than that in highly wetting case. The distribution of oil and water is more concentrated at highly wetting situation. The remaining oil is snapped off in pore body and pore throat. As wettability decreases, the distribution of remaining oil is film-like in the pore space, and less water can invade into the dead end pore. Generally, as the wettability increases, higher recovery can be obtained. It needs take more time for the effect of shut-in to be reflected in the displacement, and even longer time for tight reservoirs.Zhang, M., Tang, Q., Cao, C., Lv, Z., Zhang, T., Zhang, D., Li, Z., Du, L., 2018. Molecular and carbon isotopic variation in 3.5 years shale gas production from Longmaxi Formation in Sichuan Basin, China. Marine and Petroleum Geology 89, Part 1, 27-37. time series of produced shale gas samples from Lower Silurian Longmaxi Formation (Fm.) were collected from six production wells during 3.5 years production period from the Weiyuan and Changning shale gas pilots in Sichuan basin, China. The molecular compositions and carbon isotopes of CH4, C2H6, C3H8 and CO2, and the hydrogen isotope of methane were analyzed for these samples by an integrated method of gas chromatography combined with mass spectrometry. The results showed that the produced shale gases are dominated by CH4 (90.1–99.3%) with minor C2H6 (0.3–0.8%) and non-hydrocarbon gases, and have low wetness (0.3–0.8%). The non-hydrocarbon gases are mainly CO2 and N2, and trace amount of He. The Longmaxi shale gases display completed reversal pattern of carbon isotopic compositions with carbon number (i.e., δ13C1 > δ13C2 > δ13C3) except for Wells W201 and W201-H1 with normal patterns between C2H6 and C3H8 (i.e., δ13C2 < δ13C3), and it is a mixture of oil cracking gas and kerogen cracking gas at high-over level of thermal maturity. Some CO2 (δ13CCO2 ranging from ?2.5 to ?6.0‰) is mainly derived from the decomposition of carbonate minerals.CH4 concentration and the carbon isotopes of methane and ethane during 3.5 years shale gas production from year 2012 to 2016 displayed small fluctuations, which possibly suggested that gas supply from shale matrix to fracture network after hydraulic fracturing is abundant. The Weiyuan shale gases show larger decrease of CH4 content than the Changning shale gases, indicated more adequate supply in the Changning area. The difference in δ13C1 values between horizontal and vertical wells on the same drilling site in the Weiyuan pilot indicated that the vertical heterogeneity of Lower Silurian Longmaxi shale plays an important role to shale gas production. Interestingly, the shale gases in the Weiyuan pilot display much lighter δ13C1 (?34.46 to ?36.82‰) and δ13C2 (?37.59 to ?41.89‰) values than those (δ13C1 = ?27.18–?27.27‰, δ13C2 = ?33.70–?34.14‰) in the Changning pilot. The difference in carbon isotopic compositions in Weiyuan and Changning pilots mainly attributes to mixing between varied proportion of oil cracking gas and kerogen cracking gas because of the regional heterogeneity of the Longmaxi marine shale, in particular amount of residual oil retained in organic matter rich shale. The isotopic difference between Weiyuan and Changning shale gases doesn't disappear in the period about 3.5 years of shale gas development, which further suggests the regional heterogeneity of retained residual oil exists in the Longmaxi Fm. marine shale.Zhang, P., Lu, S., Li, J., Chen, C., Xue, H., Zhang, J., 2018. Petrophysical characterization of oil-bearing shales by low-field nuclear magnetic resonance (NMR). Marine and Petroleum Geology 89, 775-785. are important components of petroleum systems, and it is necessary to reveal their petrophysical properties as reservoirs. Low-field nuclear magnetic resonance (NMR) has proven to be a non-invasive and effective technique for petrophysical characterization of sandstone, carbonate and coal. However, little study has been done using this technique to systematically investigate the petrophysical properties of oil-bearing shales, which is essential for characterizing shale oil reservoirs. In this study, two sets of NMR measurements were performed to reveal the porosity, permeability, movable fluid volume and pore size distribution (PSD) of oil-bearing shales. The results show the following: (1) The NMR T2 spectrum strongly relates to the content of quartz and the amount of dissolution pores within shale. Three T2 spectrum peaks were identified by the relaxation times at 0.03–1 ms, 1–20 ms and >20 ms, corresponding to micropores (<100 nm), mesopores (100–1000 nm) and macropores (>1000 nm), respectively. (2) By combining NMR with centrifugation, both NMR porosity and movable porosity (MP) were calculated. NMR porosity is well consistent with helium porosity, and the MP values strongly relate to the development of mesopores in shales. (3) Based on the T2 spectrum, an effective permeability model was proposed, which can conveniently estimate the permeability of shales. Moreover, two classical permeability models (Coates and SDR) were also used to estimate shale permeability, and the permeability values determined by these models agrees well with helium permeability. (4) In combination with SEM images analyses, an NMR-based PSD was constructed that agrees well with the PSD determined by SEM. The results demonstrate the applicability of NMR relaxation in a systematic investigation of the petrophysical properties of shales, which has potential applications for geophysical logging in shale oil exploration.Zhang, S., Canter, L., Sonnenfeld, M., 2017. Capillary fluid dynamics within unconventional rocks investigated by scanning electron microscopy. American Association of Petroleum Geologists Bulletin 101, 1759-1765. cores from tight-rock samples of subsurface hydrocarbon reservoirs retain mobile fluids. These fluids have complex chemical compositions and a large spectrum of molecules with different diameters and polarities. When investigated using high-resolution field-emission scanning electron microscopy (SEM), the imposed vacuum over hours of time causes pore fluids trapped in the rock sample to flow and interact with the mineral matrix. This paper reports the capillary fluid dynamics effect observed on freshly milled cross sections of tight chalk at high resolution. Multiphase fluid dynamic simulations confirm the aggregation of heavier fluid molecules on the geometrical irregularities of the pore space. As a consequence of this pitfall, the differentiation of solid organic matter versus variably viscous hydrocarbons from SEM data is subject to a fundamental revision.Zhang, S., He, K., Hu, G., Mi, J., Ma, Q., Liu, K., Tang, Y., 2018. Unique chemical and isotopic characteristics and origins of natural gases in the Paleozoic marine formations in the Sichuan Basin, SW China: Isotope fractionation of deep and high mature carbonate reservoir gases. Marine and Petroleum Geology 89, Part 1, 68-82. quantities of natural gases have recently been discovered in the marine carbonate formations in the Sichuan Basin, southern China. The origins and isotopic compositions of the gases are poorly understood and highly controversial. We examined the chemical and isotopic compositions of the carbonate reservoir gases in marine formations from the Sinian to Lower Triassic as well as shale gas from the Silurian and Cambrian Formation in the Sichuan Basin. It is found that the carbon isotopes of the carbonate reservoir gases had been evolved through three stages corresponding to pre-rollover, rollover and post-rollover in the plot of δ13C2 versus wetness, which is consistent with that found in shale gas by Tilley and Muehlenbachs (2013). The unique carbon isotopic compositions indicate that both kerogen and oil-cracking gas have contributed to the accumulation of the carbonate reservoir gases in the Sichuan Basin. A mixing of two thermogenic gases with different maturities can cause the δ13C reversal between methane and ethane, which is commonly observed in the carbonate reservoir gases in the Carboniferous, Permian and Triassic formations, and the shale gas in the Silurian and Cambrian formations in the Sichuan Basin. We established two mixing models for quantitatively determining the contribution of each type gas for the natural gases in different formations. Kinetic extrapolation based on thermal history of the Anyue gas field demonstrates that ethane cracking indeed occurred in the deep reservoir formations, which may explain the disappearance of the 13C reversal for methane and ethane in the carbonate reservoir gases in the post-rollover zone. It is proposed that organic-inorganic interactions may be responsible for the presence of D isotope rollover for methane in carbonate reservoir gases with ultra-high maturity. The organic-inorganic interactions include thermal reactions between water and residual organic matters or carbons and hydrogen isotope exchange between water and methane, and their mechanism needs further investigations in future.Zhang, S., Karthikeyan, R., Fernando, S.D., 2017. Low-temperature biological activation of methane: structure, function and molecular interactions of soluble and particulate methane monooxygenases. Reviews in Environmental Science and Bio/Technology 16, 611-623. aspects of oxidation of methane to methanol by methanotrophic bacteria via methane monooxygenase (MMO) is still not well understood. Elucidating how various molecules pertinent to methane oxidation interact with each other at the MMO active site offers critical insights on low-temperature activation of methane, which is one of the greatest technical challenges in hydrocarbon chemistry. In this review, most recent contributions to the area are analyzed comparing soluble (sMMO) and particulate (pMMO) forms. Initially, the taxonomical, morphological and physiological differences of different methanotrophs are discussed. Then, the structural and functional differences of sMMO and pMMO are analyzed while considering substrate/product-cofactor-active site interactions. A docking analysis was performed using Autodock Vina to uncover interactions between cofactors and corresponding enzymes. With natural gas becoming a significant contributor to the energy continuum, this literature analysis and molecular simulations conducted brings new insights to low-temperature activation of methane.Zhang, S., Liu, C., Liang, H., Wang, J., Bai, J., Yang, M., Liu, G., Huang, H., Guan, Y., 2018. Paleoenvironmental conditions, organic matter accumulation, and unconventional hydrocarbon potential for the Permian Lucaogou Formation organic-rich rocks in Santanghu Basin, NW China. International Journal of Coal Geology 185, 44-60. rocks have received increasing attention for they are essential for evaluating hydrocarbon potential and unravelling the interaction between Earth surface environments and the biosphere. In this paper, we performed a combination of mineralogical, inorganic and organic geochemical analyses on a 200-m core of the Permian Lucaogou Formation organic-rich rocks obtained from Santanghu Basin, NW China, to investigate paleoenvironmental conditions, organic matter accumulation, and hydrocarbon potential. The redox- and salinity-sensitive proxies (e.g. V/Cr, V/(V + Ni) and Sr/Ba, Rb/K, B/Ga, and B content), together with the wide distribution of pyrite and carbonate minerals in these dark, thinly laminated organic-rich rocks, suggest that dysoxic-anoxic, brackish-saline, alkaline conditions prevailed during the deposition of the Lucaogou Formation in the Santanghu Basin. The occurrence of hydrothermal minerals, including strontianite and barite, and enrichments of B (up to 158.0 ppm), Mn (up to 1291 ppm), and certain incompatible elements (Li (up to 923 ppm), Rb (up to 848 ppm), Sr (up to 1760 ppm), Hf (up to 12.7 ppm)) as well as Ni vs. Co vs. Zn and Fe vs. Mn vs. (Cu + Co + Ni) × 10 ternary diagrams demonstrate that the Lucaogou Formation received hydrothermal input during deposition, which suggests hydrothermalism was the source of brine that has caused the salinization of the water column.The positive correlation of HI value and TOC content, together with redox-sensitive proxies, illustrates primary productivity in surface water and preservation in anoxic bottom water collectively contributed to the enrichment of organic matter. Moreover, the positive correlation between silicate mineral content and TOC content and the negative correlation between carbonate content and TOC content suggest that terrigenous input as the main source of nutrients promoted organic matter accumulation, while carbonate constituents acted as a diluent to organic matter accumulation during deposition of the Lucaogou Formation. The faint positive correlation between TOC content and hydrothermal intensity indicator (Cr/Zr) seems to indicate that hydrothermal fluids may provide an additional source of nutrients for organic matter accumulation.In addition, the oil generation capacity of Lucaogou Formation, with abundant oil-prone organic matter (Type I/II1 kerogen with HI values ranging from 421.18–918.41 mg HC/g TOC) in the early mature to mature stage (Tmax values ranging from 435 to 451 °C), is considerable. The Rock-Eval oil saturation index (OSIS1/TOC × 100) values range from 6.04–164.07 mg HC/g TOC, suggesting the Lucaogou Formation contains producible oil. The high brittle mineral (including quartz and carbonates) contents (> 50% wt%) and traces of clay minerals (< 5 wt%) imply that the Lucaogou Formation is likely to respond well to hydraulic stimulation. Consequently, the Lucaogou Formation in Santanghu Basin is expected to be a potential lacustrine shale oil play.Zhang, W., Wirtz, K., 2017. Mutual dependence between sedimentary organic carbon and infaunal macrobenthos resolved by mechanistic modeling. Journal of Geophysical Research: Biogeosciences 122, 2509-2526.: The mutual dependence between sedimentary total organic carbon (TOC) and infaunal macrobenthos is here quantified by a mechanistic model. The model describes (i) the vertical distribution of infaunal macrobenthic biomass resulting from a trade-off between nutritional benefit (quantity and quality of TOC) and the costs of burial (respiration) and mortality, and (ii) the variable vertical distribution of TOC being in turn shaped by bioturbation of local macrobenthos. In contrast to conventional approaches, our model emphasizes variations of bioturbation both spatially and temporally depending on local food resources and macrobenthic biomass. Our implementation of the dynamic interaction between TOC and infaunal macrobenthos is able to capture a temporal benthic response to both depositional and erosional environments and provides improved estimates of the material exchange flux at the sediment-water interface. Applications to literature data for the North Sea demonstrate the robustness and accuracy of the model and its potential as an analysis tool for the status of TOC and macrobenthos in marine sediments. Results indicate that the vertical distribution of infaunal biomass is shaped by both the quantity and the quality of OC, while the community structure is determined only by the quality of OC. Bioturbation intensity may differ by 1 order of magnitude over different seasons owing to variations in the OC input, resulting in a significant modulation on the distribution of OC. Our relatively simple implementation may further improve models of early diagenesis and marine food web dynamics by mechanistically connecting the vertical distribution of both TOC and macrobenthic biomass.Plain Language Summary: Processes for input, transport, and preservation of organic carbon (OC) in seabed surface sediments are pivotal in both regional and global carbon cycles. Among all involved processes, bioturbation by medium- to large-size (body size >0.5 mm) benthic animals is most important for transport of organic carbon in seabed sediments. A key factor controlling distribution of benthic animals is food (OC). Foraging of benthic animals in turn brings down food (OC) into deeper sediments. So far, no quantitative link between vertical distributions of benthic animals and organic carbon has been established. Our study thus aims at filling this knowledge gap by mechanistically linking the two factors together. Our approach is able to improve estimates of carbon fluxes between water column and seabed and especially applicable for dynamic environments with sharp spatial and/or temporal gradients of environmental change.Zhang, X., Du, Z., Luan, Z., Wang, X., Xi, S., Wang, B., Li, L., Lian, C., Yan, J., 2017. In situ Raman detection of gas hydrates exposed on the seafloor of the South China Sea. Geochemistry, Geophysics, Geosystems 18, 3700-3713. hydrates are usually buried in sediments. Here we report the first discovery of gas hydrates exposed on the seafloor of the South China Sea. The in situ chemical compositions and cage structures of these hydrates were measured at the depth of 1,130 m below sea level using a Raman insertion probe (RiP-Gh) that was carried and controlled by a remotely operated vehicle (ROV) Faxian. This in situ analytical technique can avoid the physical and chemical changes associated with the transport of samples from the deep sea to the surface. Natural gas hydrate samples were analyzed at two sites. The in situ spectra suggest that the newly formed hydrate was Structure I but contains a small amount of C3H8 and H2S. Pure gas spectra of CH4, C3H8, and H2S were also observed at the SCS-SGH02 site. These data represent the first in situ proof that free gas can be trapped within the hydrate fabric during rapid hydrate formation. We provide the first in situ confirmation of the hydrate growth model for the early stages of formation of crystalline hydrates in a methane-rich seafloor environment. Our work demonstrates that natural hydrate deposits, particularly those in the early stages of formation, are not monolithic single structures but instead exhibit significant small-scale heterogeneities due to inclusions of free gas and the surrounding seawater, there inclusions also serve as indicators of the likely hydrate formation mechanism. These data also reinforce the importance of correlating visual and in situ measurements when characterizing a sampling site.Zhang, X., Quinn, K., Cruickshank-Quinn, C., Reisdorph, R., Reisdorph, N., 2018. The application of ion mobility mass spectrometry to metabolomics. Current Opinion in Chemical Biology 42, 60-66. spectrometry-based metabolomics is being increasingly utilized in various research fields including investigating human diseases, nutrition, industrial applications, and plant/natural products studies. Although new analytical approaches have enhanced the performance of metabolomic analyses, significant challenges associated with throughput, metabolome coverage, and compound identification still exist. Ion mobility mass spectrometry offers great potential for improving throughput and depth of coverage in metabolomics experiments. For example, multi-dimensional, structural resolution offered by ion mobility enables improved identification of metabolites and chemical classes. This mini-review discusses the advantages, recent developments and limitations of using ion mobility mass spectrometry as part of a metabolomics workflow.Zhang, X., Shi, W., Hu, Q., Zhang, S., Hu, H., Wang, X., Xu, Z., 2017. Geological controls and methane sorption capacity of marine shales of the Fuling shale gas field in the eastern Sichuan Basin, China. Petroleum Geoscience 23, 466-475. methane sorption isotherms were performed on a series of Upper Ordovician Wufeng and Lower Silurian Longmaxi shale samples in the Fuling shale gas field to investigate the effects of organic matter content, thermal maturity, clay minerals, pore structure, temperature and pressure on methane sorption capacity. A large number of micropores with a pore width of less than 10?nm are developed within the organic matter, with its abundant specific surface areas as the fundamental factor to enhance the methane sorption capacity. The total organic carbon (TOC)-normalized sorption capacity increases with an increasing equivalent vitrinite reflectance Ro, but an opposite trend is observed when Ro is in the highly over-mature stage. The TOC-normalized sorption capacity shows no correlation with the total clay content as well as individual clay minerals. Most of the excess sorption capacity of shales increases with an increasing pressure, exhibits a maxima in the pressure range of 15–17?MPa and then decreases. The sorption isotherms show an obvious decrease in excess sorption capacity with increasing temperature. Moreover, the Langmuir pressure exponentially decreases with the reciprocal of temperature. Based on the Langmuir adsorption model, an empirical formula is established to evaluate the absolute sorption capacity of shales as a function of TOC content, pressure and temperature. Additional description of experimental data are available at , X., Tian, G., Gao, J., Han, M., Su, R., Wang, Y., Feng, S., 2017. Prebiotic synthesis of glycine from ethanolamine in simulated archean alkaline hydrothermal vents. Origins of Life and Evolution of Biospheres 47, 413-425. hydrothermal vents are generally considered as the likely habitats for the origin and evolution of early life on Earth. In recent years, a novel hydrothermal system in Archean subseafloor has been proposed. In this model, highly alkaline and high temperature hydrothermal fluids were generated in basalt-hosted hydrothermal vents, where H2 and CO2 could be abundantly provided. These extreme conditions could have played an irreplaceable role in the early evolution of life. Nevertheless, sufficient information has not yet been obtained for the abiotic synthesis of amino acids, which are indispensable components of life, at high temperature and alkaline condition. This study aims to propose a new method for the synthesis of glycine in simulated Archean submarine alkaline vent systems. We investigated the formation of glycine from ethanolamine under conditions of high temperature (80–160?°C) and highly alkaline solutions (pH?=?9.70). Experiments were performed in an anaerobic environment under mild pressure (0.1–8.0?MPa) at the same time. The results suggested that the formation of glycine from ethanolamine occurred rapidly and efficiently in the presence of metal powders, and was favored by high temperatures and high pressures. The experiment provides a new pathway for prebiotic glycine formation and points out the phenomenal influence of high-temperature alkaline hydrothermal vents in origin of life in the early ocean.Zhang, Y., Zeng, J., Dai, Z., Viswanathan, H., Xiao, T., Ma, Y., Feng, X., 2018. Experimental investigation on oil migration and accumulation in tight sandstones. Journal of Petroleum Science and Engineering 160, 267-275. study presents an experimental investigation to simulate and analyze the physical processes of oil migration and accumulation with 19 tight sandstone cores. Characteristic curves of oil migration were obtained by using the experimental results. It shows that the curve variations were mainly influenced by two factors: the permeability of the core and the viscosity of the injected oil. Based on the experimental results, we introduced three important parameters to quantitatively characterize and determine the processes of oil migration and accumulation in tight sandstones. The apparent permeability was introduced to describe the level of oil migration during experiments. The minimum migration pressure gradient (MMPG) and the terminal oil saturation were proposed to evaluate the features of the beginning and final stages of the migration, respectively. The relationships between MMPG, terminal oil saturation and mobility were analyzed, all showed strong linear relationships in the double logarithmic coordinate system. Furthermore, a prediction map of tight oil accumulation was plotted according to the measured oil saturation data, which could be used for estimating the scale and size of oil accumulation in tight reservoirs. The concepts and results in this study provide valuable insight for understanding and quantitatively analyzing the processes of oil migration and accumulation in tight sandstones.Zhao, D., Kumar, S., Zhou, J., Wang, R., Li, M., Xiang, H., 2017. Isolation and complete genome sequence of Halorientalis hydrocarbonoclasticus sp. nov., a hydrocarbon-degrading haloarchaeon. Extremophiles 21, 1081-1090. in hypersaline environments is particularly challenging since the microbes that tolerate such harsh environments and degrade pollutants are quite scarce. Haloarchaea, however, due to their inherent ability to grow at high salt concentrations, hold great promise for remediating the contaminated hypersaline sites. This study aimed to isolate and characterize novel haloarchaeal strains with potentials in hydrocarbon degradation. A haloarchaeal strain IM1011 was isolated from Changlu Tanggu saltern near Da Gang Oilfield in Tianjin (China) by enrichment culture in hypersaline medium containing hexadecane. It could degrade 57?±?5.2% hexadecane (5?g/L) in the presence of 3.6?M NaCl at 37?°C within 24?days. To get further insights into the mechanisms of petroleum hydrocarbon degradation in haloarchaea, complete genome (3,778,989?bp) of IM1011 was sequenced. Phylogenetic analysis of 16S rRNA gene, RNA polymerase beta-subunit (rpoB’) gene and of the complete genome suggested IM1011 to be a new species in Halorientalis genus, and the name Halorientalis hydrocarbonoclasticus sp. nov., is proposed. Notably, with insights from the IM1011 genome sequence, the involvement of diverse alkane hydroxylase enzymes and an intact β-oxidation pathway in hexadecane biodegradation was predicted. This is the first hexadecane-degrading strain from Halorientalis genus, of which the genome sequence information would be helpful for further dissecting the hydrocarbon degradation by haloarchaea and for their application in bioremediation of oil-polluted hypersaline environments.Zhao, H., Lai, Z., Firoozabadi, A., 2017. Sorption hysteresis of light hydrocarbons and carbon dioxide in shale and kerogen. Scientific Reports 7, Article 16209. present adsorption and desorption isotherms of methane, ethane, propane, n-butane and iso-butane as well as carbon dioxide for two shales and isolated kerogens determined by a gravimetric method. The sorption measurements of two shales were performed at three different temperatures, 308.15, 323.15, and 338.15?K. For the isolated kerogens, the measurements were conducted at 338.15?K. Methane and ethane sorption isotherms were measured to 35?bar. Carbon dioxide sorption isotherms were studied to 30?bar. Due to the low vapor pressure at room temperature, the sorption isotherms of propane, n-butane and iso-butane were measured to 8, 2, and 2?bar, respectively. The adsorptions of propane, n-butane, and iso-butane were much higher than methane at the highest pressures where the measurements were conducted. The adsorption of n-butane was 10 times higher than methane by mole at 2?bar, followed by iso-butane and propane. Our data show significant adsorption hysteresis in ethane, propane, n-butane and iso-butane. The most pronounced hysteresis was found in n-butane and iso-butane. Significant hysteresis is attributed to the reversible structural changes of kerogens. Dissolution of adsorbates into organic matter may also affect the hysteresis. This is the first report of propane and butane sorption isotherms in shales.Zhao, J., 2017. Micro-CT scanning of gas hydrate decomposition in model porous media. Chemistry and Technology of Fuels and Oils 53, 600-609. results of investigating gas hydrate decomposition processes in model porous media using a Micro-CT Test System were analyzed. The objects of the study were natural gas hydrates produced at a specified pressure and temperature using porous media consisting of sand with three particle size ranges (0.85-1.18, 1.18-2.85, and 2.85-4.8 mm). The microstructural characteristics and the porosity of the obtained gas hydrates in the decomposition process were studied. The dependence of microstructural characteristics of gas hydrates on the nature of the porous medium, based on which the hydrates were produced, was also investigated. The results indicate that the hydrate is distributed uniformly and fills the pores of the porous media almost completely. Translated from Khimiya i Tekhnologiya Topliv i Masel, No. 4, pp. 94 – 100, July – August, 2017Zhao, J., Tian, Y., Zhao, Y., Liang, W., 2017. Experimental study of gas-hydrate dissociation kinetics at constant temperatures above 0°C. Chemistry and Technology of Fuels and Oils 53, 787-793., gas-hydrate storage technology has been drawing increasing attention as a new means of gas storage and transportation and may in the future become the optimal means of gas storage as compared with LNG technology because of its economic and safety advantages. The main purpose of the present work was to investigate experimentally the hydrate dissociation mechanism using a kinetic model at different temperatures and atmospheric pressure in the range 5-15°C. The obtained results have great significance for gas-hydrate storage technology and its application in industry. Translated from Khimiya i Tekhnologiya Topliv i Masel, No. 5, pp. 96-99, September-October, 2017.Zhao, X., Zhang, L., Jin, F., Wang, Q., Bai, G., Li, Z., Wang, J., 2017. Hydrocarbon charging and accumulation history in the Niudong Buried Hill Field in the Baxian Depression, eastern China. Marine and Petroleum Geology 88, 343-358. Niudong Buried Hill Field, which lies in the Baxian Depression of the Bohai Bay Basin, is the deepest oil/gas accumulation in eastern China. Its Precambrian dolomite reservoir occurs at burial depths of 5860 m–6027 m. This paper attempts to document the hydrocarbon charging and accumulation history in this field, which could greatly enhance the understanding of the mechanisms for the formation of deep hydrocarbon accumulations. Our previous study of oil trapped in fluid inclusions has demonstrated that the ratio parameters of the fluorescence spectral intensities at 425 nm and 433 nm (Q425/433 ratio), and at 419 nm and 429 nm (Q419/429 ratio) can be more effective for revealing hydrocarbon charging history than the previously-used fluorescence parameters such as Lambda max and red/green quotient as well as fluorescence colors. The hydrocarbon charging and accumulation history in the Niudong Buried Hill Field was studied with an integrated approach involving the application of these two spectral parameters of petroleum inclusion fluorescence as well as utilization of other data including homogenization temperatures of aqueous inclusions coeval with petroleum inclusions, and cross-cutting relationships of cements and “oil veins” in pores and fractures. The results indicate that the dolomite reservoir in the Niudong Buried Hill Field experienced three episodes of hydrocarbon charging. In the first two episodes (between 38.5Ma and 25Ma), the low mature and mature oils, which were derived from source rocks in the Sha-4 Member of the Eocene Shahejie Formation, migrated into the reservoir, but part of them leaked out due to normal faulting at the updip margin of the buried hill. These early-charged oils were preserved mainly in small pores in micritic dolomites by oil-wettability and capillary pressure. In the Neogene, the basin subsided as a whole and local faults at the updip margin became inactive and played a sealing role. By approximately 13Ma, the source rocks became highly mature and the generated hydrocarbons then migrated into the reservoir and accumulated. Therefore, the last charging is the most important for hydrocarbon accumulation in the Niudong Buried Hill Field.Zhao, Y., Sun, Y., Liu, S., Chen, Z., Yuan, L., 2018. Pore structure characterization of coal by synchrotron radiation nano-CT. Fuel 215, 102-110. the significant impact of pore structure on gas storage and transport in coal seams, research on coal pore structure characterization has been a hotspot. Benefited from the high spatial resolution synchrotron-based nano-CT instrument, pore structure characterization of coal is investigated in nano scale. Image alignment and 3D reconstruction were completed at the platform designed by National Synchrotron Radiation Laboratory and Chinese Academy of Sciences. The segmentation of the unimodal grey-scale value histograms is solved by Between-class Variance Maximisation (BCVM) algorithm and the nano-CT images are segmented into three components, pore, organic components and mineral components. Based on the voxel number, components fraction is computed. Pore size distribution (PSD) presents bimodality. Pores with equivalent radius less than 60?nm account for 84% of the total pore number. Throats with equivalent radius less than 60?nm account for 89% of the total throat number. Throats with length less than 100?nm account for 58% of the total throat number and throats with length less than 400?nm account for 84% of the total throat number. Pore number decreases with the increase of coordination number. There are over 50% of pores without coordination pore and pore connectivity was analysed. Nanopore structure-based computational fluid dynamics (CFD) simulation was explored. The permeability in three coordinate axes directions presents anisotropy.Zheng, G., Ma, X., Guo, Z., Hilton, D.R., Xu, W., Liang, S., Fan, Q., Chen, W., 2017. Gas geochemistry and methane emission from Dushanzi mud volcanoes in the southern Junggar Basin, NW China. Journal of Asian Earth Sciences 149, 184-190. are many mud volcanoes in the southern margin of the Junggar Basin, northwest China, of which the Dushanzi area is the most typical and active one, emitting large amount of greenhouse gases associated with water and mud. The emitted gas is dominated by methane (average 90.1%), together with other gases, such as ethane (4.84–5.46%), propane (0.06–0.90%), CO2 (0.67–1.0%), and N2 (2.8–3.3%). The carbon (δ13C1) and hydrogen (δD) isotopic ratios of methane are in the ranges of ?40.6‰ to ?45.0‰ and ?221‰ to ?249‰, respectively, whereas carbon isotope ratios of ethane (δ13C2) are ?25.2‰ to ?27.6‰. Based on δ13C values, the released gas is characterized as a thermogenic coal-type and possibly originated from the middle-low Jurassic coal-bearing sequences according to the gas-source correlation and regional geology. Helium isotopes show a crustal source. The methane flux of Dushanzi mud volcanoes from both macro-seepage (craters/vents) and micro-seepage (ground soil exhalation) ranged over the orders of magnitude, from 0.4–2.7 kg d?1 and 4950 mg m?2 d?1 on average, respectively. Positive CH4 fluxes from dry soil were widespread throughout the investigated areas. The total CH4 emission from Dushanzi mud volcanoes is estimated to be at least 22.6 tons a?1, of which about 89% is from micro-seepage surrounding the mud volcano vents.Zheng, G., Xu, W., Etiope, G., Ma, X., Liang, S., Fan, Q., Sajjad, W., Li, Y., 2018. Hydrocarbon seeps in petroliferous basins in China: A first inventory. Journal of Asian Earth Sciences 151, 269-284. hydrocarbon seepage is a widespread phenomenon in sedimentary basins, with important implications in petroleum exploration and emission of greenhouse gases to the atmosphere. China has vast petroleum (oil and gas) bearing sedimentary basins, but hydrocarbon seepage has rarely been the object of systematic studies and measurements. Based on the available Chinese literature, we report a first inventory of 932 hydrocarbon seeps or seepage zones (710 onshore seeps and 222 offshore seeps), including 81 mud volcanoes, 449 oil seeps, 215 gas seeps, and 187 solid seeps (bitumen outcrops). The seeps are located within the main 20 Mesozoic-Cenozoic petroliferous sedimentary basins, especially along the marginal, regional and local faults. The type of manifestations (oil, gas or mud volcano) reflects the type and maturity of the subsurface petroleum system and the sedimentary conditions of the basin. Oil seeps are particularly abundant in the Junggar Basin. Gas seeps mostly developed in the Lunpola Basin, in smaller basins of the eastern Guizhou and Yunnan provinces, onshore Taiwan and in the offshore Yinggehai Basin. Mud volcanoes developed in basins (Junggar, Qaidam, Qiangtang, onshore and offshore Taiwan) that experienced rapid sedimentation, which induced gravitative instability of shales and diapirism. In comparison to available global onshore seep data-bases, China results to be the country with the highest number of seeps in the world. The massive gas seepage in China could represent a considerable natural source of methane to the atmosphere, and a key process that may drive future hydrocarbon exploration.Zheng, L., Jing, C., Liu, J., Zhang, L., 2017. Change of the chemical and physical properties of heavy oil before and after CO2 treatment. Petroleum Science and Technology 35, 1724-1730. order to improve the heavy oil displacement effect by CO2 flooding, the change of the chemical and physical properties of heavy oil before and after CO2 treatment is systematically investigated by indoor simulation experiment. Experimental results show that CO2 treatment can decrease the amount of the saturates but increase that of the aromatics, and yet has little impact on those of resins and asphaltenes. Besides, the corresponding consequence is that there has an increase in the viscosity of the heavy oil and the particle size of the asphaltene micelle, and a decrease in the conductivity of the heavy oil and n-heptane systems and the stability of the asphaltene micelle after CO2 treatment. The conclusions can provide a certain guidance for high-efficiency development of heavy oil reservoir by CO2 flooding.Zheng, N., Xiao, H., Zhang, Z., Gao, X., Zhao, J., 2017. Rapid and sensitive method for determining free amino acids in plant tissue by high-performance liquid chromatography with fluorescence detection. Acta Geochimica 36, 680-696. paper describes a reliable and rapid method for the complete separation and quantitation of twenty-five amino acids typically found in plants, based on reversed phase high-performance liquid chromatography–linked fluorescence detector using a 150?×?4.6?mm Zorbax Eclipse AAA column. Plant tissue free amino acids (FAA) were extracted by ultrasonication with 5% (v/v) aqueous trifluoroacetic acid followed by ultrafiltration of extracts. The following analysis of amino acids was performed through programmed precolumn derivatization with ortho-phthalaldehyde and 9-fluorenylmethyl chloroformate reagents and efficient elution of derivatives within 26?min using binary gradient scheme. The method was validated over a concentration range of 4.5–450?μmol?L?1 (μM). Separation analysis showed good selectivity (resolution?>?1.5) for most amino acids. The average repeatability (RSD%, relative standard deviation) of the analysis at seven calibration concentrations was below 4% and ranged from 1.13% to 12.04%. The intra-day mean coefficient of variation at two concentrations (22.5 and 90?μM) was within 2%, and the intermediate precision was less than 4%. The limits of detection were between 0.012 and 6.68?μM. The coefficients of determination (R2) of the linear calibration curves were from 0.9989 to 0.9999. When the method was applied to plant samples, the FAA recoveries at two spiked levels (25 and 100?μM) ranged from 67.0% to 108.9% with an average of 94.4%, and the precision was 0.26%–12.31% RSD. A specific application combining this method with optimized extraction and interference removal procedures was successfully used to determine the FAA pools in different plant tissues. Finally, a PLS-DA multivariate statistics model was validated for the classification of three plant species according to their FAA profiles.Zheng, S., Wang, B., Liu, F., Wang, O., 2017. Magnetite production and transformation in the methanogenic consortia from coastal riverine sediments. Journal of Microbiology 55, 862-870. that contain ferric iron, such as amorphous Fe(III) oxides (A), can inhibit methanogenesis by competitively accepting electrons. In contrast, ferric iron reduced products, such as magnetite (M), can function as electrical conductors to stimulate methanogenesis, however, the processes and effects of magnetite production and transformation in the methanogenic consortia are not yet known. Here we compare the effects on methanogenesis of amorphous Fe (III) oxides (A) and magnetite (M) with ethanol as the electron donor. RNA-based terminal restriction fragment length polymorphism with a clone library was used to analyse both bacterial and archaeal communities. Iron (III)-reducing bacteria including Geobacteraceae and methanogens such as Methanosarcina were enriched in iron oxide-supplemented enrichment cultures for two generations with ethanol as the electron donor. The enrichment cultures with A and non-Fe (N) dominated by the active bacteria belong to Veillonellaceae, and archaea belong to Methanoregulaceae and Methanobacteriaceae, Methanosarcinaceae (Methanosarcina mazei), respectively. While the enrichment cultures with M, dominated by the archaea belong to Methanosarcinaceae (Methanosarcina barkeri). The results also showed that methanogenesis was accelerated in the transferred cultures with ethanol as the electron donor during magnetite production from A reduction. Powder X-ray diffraction analysis indicated that magnetite was generated from microbial reduction of A and M was transformed into siderite and vivianite with ethanol as the electron donor. Our data showed the processes and effects of magnetite production and transformation in the methanogenic consortia, suggesting that significantly different effects of iron minerals on microbial methanogenesis in the iron-rich coastal riverine environment were present.Zhou, C., Li, X.-H., Xiao, S., Lan, Z., Ouyang, Q., Guan, C., Chen, Z.H.E., 2017. A new SIMS zircon U–Pb date from the Ediacaran Doushantuo Formation: age constraint on the Weng'an biota. Geological Magazine 154, 1193-1201. a well-known phosphatized Lagerst?tte, the Ediacaran Weng'an biota in central Guizhou Province of South China contains diverse acanthomorphic acritarchs, algal thalli, tubular microfossils as well as various spheroidal fossils. These fossils provide crucial palaeontological evidence for the radiation of multicellular eukaryotes after the termination of the Neoproterozoic global glaciation. While the Weng'an biota is generally considered as early Ediacaran in age on the basis of phosphorite Pb–Pb isochron ages ranging from 572 Ma to 599 Ma, the reliability and accuracy of these age data have been questioned and some geologists have proposed that the Weng'an biota may be younger than 580 Ma instead. Here we report a SIMS zircon U–Pb age of 609 ± 5 Ma for a tuffaceous bed immediately above the upper phosphorite unit in the Doushantuo Formation at Zhangcunping, Yichang, South China. Litho-, bio- and chemostratigraphic correlations suggest that the upper phosphorite unit at Zhangcunping can be well correlated with the upper phosphorite unit at Weng'an, which is the main horizon of the Weng'an biota. We therefore conclude that the Weng'an biota could be as old as 609 ± 5 Ma.Zhou, E., Li, H., Yang, C., Wang, J., Xu, D., Zhang, D., Gu, T., 2018. Accelerated corrosion of 2304 duplex stainless steel by marine Pseudomonas aeruginosa biofilm. International Biodeterioration & Biodegradation 127, 1-9. influenced corrosion (MIC) in the marine environment is a serious threat to the service life of marine materials. MIC pitting corrosion rate is usually much faster than the general corrosion process. The 2304 duplex stainless steel (DSS) is an excellent alternative to 316L SS in marine applications, while its MIC behavior is barely known. In this work, surface analysis and electrochemical techniques were used to study the corrosion behavior of 2304 DSS caused by the ubiquitous marine aerobe Pseudomonas aeruginosa. Compared with the abiotic control, the largest pit depth showed that the P. aeruginosa biofilm greatly accelerated the pitting corrosion (11.0 μm vs. 4.8 μm for the abiotic control). The presence of P. aeruginosa biofilm oxidized the passive film of 2304 DSS from Cr2O3 to CrO3, which was a water-soluble compound, resulting in the decrease of the relative Cr content and destruction of the passive film. The linear polarization resistance (LPR), electrochemical frequency modulation (EFM), electrochemical impedance spectroscopy (EIS) and polarization curve analyses all demonstrated that 2304 DSS was susceptible to MIC.Zhou, L., Pang, X., Wu, L., Kuang, L., Pang, H., Jiang, F., Bai, H., Peng, J., Pan, Z., Zheng, D., 2017. Petroleum generation and expulsion in middle Permian Lucaogou Formation, Jimusar Sag, Junggar Basin, northwest China: assessment of shale oil resource potential. Geological Journal 52, 1032-1048. oil exploration of the Permian Lucaogou Formation (P2l) has greatly advanced in the Jimusar Sag in the Junggar Basin. However, despite the strong exploration prospects of shale oil resources, the potential of shale oil resources in the Junggar Basin has been insufficiently assessed. This study performs systematical evaluation of P2l source rocks in the Jimusar Sag and proposes an improved hydrocarbon generation potential method to assess the hydrocarbon generation and expulsion characteristics and evaluates the shale oil resource potential of the P2l source rocks in the Jimusar Sag. The results show that the P2l source rocks are thick (up to 200?m) and are distributed over a wide area (up to 1200?km2) in the study region. It contains high TOC (2%–5%), characterized by dominantly type I and type II kerogen. The source rocks are in the low mature–mature stage, and possess good conditions for generation of hydrocarbons. The P2l source rocks reached the hydrocarbon expulsion threshold at a thermal maturity of 0.8% vitrinite reflectance. The efficiency of hydrocarbon expulsion of the source rock is 34%. The amounts of hydrocarbons generated and expelled were 65?×?108?t. Based on the above information, the shale oil resources potential is calculated to be 43?×?108?t, indicating very good shale oil resource prospect in the P2l source rocks of the Jimusar Sag.Zhou, Z., Meng, H., Liu, Y., Gu, J.-D., Li, M., 2017. Stratified bacterial and archaeal community in mangrove and intertidal wetland mudflats revealed by high throughput 16S rRNA gene sequencing. Frontiers in Microbiology 8, 2148. doi: 10.3389/fmicb.2017.02148. stratified distribution of bacterial and archaeal communities has been detected in many sediment profiles from various natural environments. A better understanding of microbial composition and diversity pattern in coastal mangrove wetlands in relation to physicochemical and spatial-temporal influences could provide more insights into the ecological functions of microbes in coastal wetlands. In this study, seasonal variations of microbial communities within sediment profiles from two sediment types (mangrove forest and intertidal mudflats) at three sampling locations in coastal Mai Po wetland were characterized using MiSeq high throughput sequencing and 16S rRNA quantitative PCR methods. Bacterial 16S rRNA gene abundance showed clear decreasing trends with increasing depth for all sites, seasonality and sediment types. There is a weak seasonal dynamic of bacterial and archaeal community abundance in both seasons. Seasonality imposed more influence on the beta diversity pattern of bacterial community than archaeal community. The five most abundant phyla within bacterial and archaeal community remain stable between two distinctive seasons. Sediment depth and seasonality are the most influential factors affecting bacterial community composition and diversity. The pH is the most influential factor on shaping the archaeal community. Stratified distribution of bacterial community including aerobic and anaerobic bacterial taxa is largely represented in the surface layers and the subsurface layers, respectively. For archaeal stratification, Thaumarchaeota Marine Group I is the dominant member in surface sediments while Bathyarchaeota and MBG-B dominate in subsurface sediments. Such stratified distribution patterns are irrespective of sediment types, sampling locations or seasonality, but significantly correlated to the sediment depth, which might be shaped by oxygen availability and the distribution of other terminal electron accepters along the depth profile.Zhou, Z., Tu, J., Zhu, Z.-J., 2018. Advancing the large-scale CCS database for metabolomics and lipidomics at the machine-learning era. Current Opinion in Chemical Biology 42, 34-41. and lipidomics aim to comprehensively measure the dynamic changes of all metabolites and lipids that are present in biological systems. The use of ion mobility–mass spectrometry (IM–MS) for metabolomics and lipidomics has facilitated the separation and the identification of metabolites and lipids in complex biological samples. The collision cross-section (CCS) value derived from IM–MS is a valuable physiochemical property for the unambiguous identification of metabolites and lipids. However, CCS values obtained from experimental measurement and computational modeling are limited available, which significantly restricts the application of IM–MS. In this review, we will discuss the recently developed machine-learning based prediction approach, which could efficiently generate precise CCS databases in a large scale. We will also highlight the applications of CCS databases to support metabolomics and lipidomics.Zhu, B.I., Jiang, S.-Y., 2017. A LA-ICP-MS analysis of rare earth elements on phosphatic grains of the Ediacaran Doushantuo phosphorite at Weng'an, South China: implication for depositional conditions and diagenetic processes. Geological Magazine 154, 1381-1397. Ediacaran Doushantuo Formation at Weng'an, South China hosts well-preserved phosphatized microfossils known as the Weng'an biota. A laser ablation ICP-MS analysis of rare earth element (REE) characteristics of the fossil-bearing black phosphorite unit of the Doushantuo Formation at Weng'an was conducted, with the aim of unravelling the depositional conditions and diagenetic processes during formation of the phosphorites. Spherical phosphatized microfossils and phosphatic clasts were analysed, and the REE data display middle REE (MREE) -enriched shale-normalized REE patterns. The spherical phosphatized microfossils show an increase in total REE contents (∑REE) from core to rim. Negative correlations between ∑REE and the extent of MREE enrichment over the other REE (indicated by LaN/SmN, YbN/SmN) are observed for analysed spots within individual phosphatic grains, which may be due to complex diagenetic history of the phosphatic grains, with fluctuations in REE sources and chemical parameters in a high-energy shallow-water environment being additional factors. The LaN/YbN and LaN/SmN characteristics of the phosphatic grains suggest they were mostly influenced by early diagenetic alteration rather than late extensive recrystallization. The negative Ce anomalies in the samples suggest they formed under oxic-bottom-water conditions. Positive Eu anomalies are present in all samples, and are likely to reflect involvement of hydrothermal fluids rather than changes in redox conditions of porewater. Overall this study has major implications for phosphorites as important archives for the study of geochemical proxies, the Ediacaran period and also evolutionary changes.Zhu, G., Milkov, A.V., Chen, F., Weng, N., Zhang, Z., Yang, H., Liu, K., Zhu, Y., 2018. Non-cracked oil in ultra-deep high-temperature reservoirs in the Tarim basin, China. Marine and Petroleum Geology 89, 252-262. stability of liquid petroleum in the subsurface is closely linked to reservoir temperature. Most oil accumulations occur at temperatures <120?°C. Oil cracks into gas at temperatures >150–160?°C leading to the dominance of gas condensate and free gas accumulations in ultra-deep high-temperature reservoirs. The recently drilled Fuyuan-1 exploration well (northern Tarim basin) produced high-quality non-cracked single-phase (black) oil from a carbonate reservoir located at maximum depth 7711?m and temperature 172?°C. This is the deepest oil discovery in China to date and among the deepest in the world. The oil density (0.825?g/cm3 at 20?°C or API gravity 40°), relatively low gas/oil ratio (135?m3/m3 or 758 scf/bbl), low variety and abundance of adamantanes as well as lack of thiaadamantanes and dibenzothiophenes indicate that the oil was expelled from a source rock at moderate thermal maturity and has not been cracked. The molecular and isotopic composition of oil-associated gases are consistent with this interpretation. We suggest that the oil remained uncracked because the residence time at temperatures >150-160°C was relatively short (<5 my based on 1D modeling) and apparently insufficient for cracking. We conclude that there is potential for finding unaltered liquid petroleum in other high-temperature reservoirs with relatively low geothermal gradient and recent burial in the Tarim basin and around the world.Zhu, H., Liu, P., Chen, P., Kang, J., 2017. Analysis of coalbed methane occurrence in Shuicheng Coalfield, southwestern China. Journal of Natural Gas Science and Engineering 47, 140-153. article is the result of authors’ long-term efforts to evaluate the occurrence of coalbed methane (CBM) for CBM exploration and coal gas disaster prevention in Shuicheng Coalfield (SCC). A relatively large program of exploratory drilling to determine the content of CBM, geological surveys and laboratory experiments, including coal proximate analysis, coal physical properties analysis and methane adsorption were conducted. The results show that the coals from the SCC contain 21.42–41.34% volatile, 0.24–1.44% moisture and 6.27–38.1% ash yield, with coal porosity in the range of 5.97–14.89%. The type of coal structure ranges from II to IV. The sedimentary characteristics, tectonic evolution, geological structure, coal reservoir conditions and hydrodynamics were studied via geological surveys, field research and laboratory tests. The relationships between these factors and gas content are explained and analyzed in this present paper. The formation of the Shuicheng coal basin was formed under the control of the Ziyun fracture and the Luoping fracture. Ejective folds and synclines that evolved from inverted geological structures in the stage of Yanshan movement affect CBM occurrence. Folds generated in coal bearing strata play an important role in methane accumulation in the period of Himalayan movement. A positive relationship is observed between gas content and coal burial depth, coal thickness, and hydrodynamics. CBM easily concentrates because of the separation between coal bearing strata and Maokou enrich aquifer. We divide the SCC into three methane geological units, the Ertang syncline unit, the Dahebian syncline unit and the Xiaohebian syncline unit. Furthermore, gas content spatial distributions were predicted in the SCC. The probability of CBM exploration was evaluated based on coal permeability and gas flow attenuation coefficient. These research results could contribute to CBM exploration and coal gas disaster prevention in the SCC.Zhu, M., Li, X.-H., 2017. Introduction: from snowball Earth to the Cambrian explosion–evidence from China. Geological Magazine 154, 1187-1192. Neoproterozoic–Palaeozoic transition (NPT) around 600 Ma ago was a critical time interval when the Earth experienced fundamental change, manifested as climatic extremes – ‘snowball Earth’ – followed by the emergence and rapid diversification of animals – ‘Cambrian explosion’. How animals and environments co-evolved, and what caused these fundamental changes to the Earth system during the NPT, is a great scientific puzzle, which has been a rapidly developing frontier of interdisciplinary research between bio- and geosciences. South China preserves a complete stratigraphic succession of the NPT developed in various facies ranging from shallow to deep marine realms with extraordinarily well-preserved, successive fossil biotas in various taphonomic settings (Zhu, 2010; Fig. 1), making it a key area and global focus of studies in the field over recent decades. Indeed, the current narrative of early animal evolution has largely been based on the fossil biotas from South China. These include: (1) the world's oldest microscopic animal fossils with cellular details from the early Ediacaran Weng'an biota (Doushantuo Formation); (2) putative macroscopic animal fossils preserved as carbonaceous imprints from the early Ediacaran Lantian, Wenghui and Miaohe biotas (also Doushantuo Formation); (3) typical late Ediacaran faunas, preserved in dark limestone (Shibantan biota) and as large and poorly mineralized tubular animal fossils (Gaojiashan biota), both from the Dengying Formation; (4) phosphatized small shelly and soft-bodied animal fossils from the early Cambrian Meishucun and Kuanchuanpu faunas; and (5) Cambrian fossil Lagerst?tten (Chengjiang, Guanshan and Kaili faunas) with typical Burgess Shale-type soft-bodied preservation.Zhu, W., Liu, L., Liu, J., Wei, C., Peng, Y., 2018. Impact of gas adsorption-induced coal damage on the evolution of coal permeability. International Journal of Rock Mechanics and Mining Sciences 101, 89-97. the injection of CO2 into coalbed for geologic sequestration, CO2 is likely both adsorbed and dissolved in coals, and swells them slightly. When coal is swollen due to the adsorption and dissolution, the induced strain is relieved as the coal structure rearranges to a lower free energy state, causing coal damage and resulting in permeability change. This adsorption- and dissolution- induced coal damage is usually ignored in the permeability model, even though this kind of damage has been observed and detected in the past CO2 injection experiments. In a previous study we generated a sequence of coal permeability profiles from the “V” shape as observed in experiments through a newly dual-permeability model. Based on this work, in this paper, the dual-permeability model is extended to take the coal damage induced by gas adsorption and dissolution into account according to the principle of damage mechanics, and this model is used to examine the permeability evolution during the injections of different gases, including CO2, CH4 and N2, into coal specimen. Numerical simulation indicates that the model predicts well the permeability increase during the high injected gas pressure. In addition, since the highest gas adsorption into coal occurs for CO2, the coal permeability during CO2 injection decreases most pronounced, in contrast, the permeability reduction during N2 injection is the smallest. Also, it is confirmed that the adsorption-induced coal damage is dominated by tensile damage of coal during the injection of CO2.Zimmerman, A.R., Mitra, S., 2017. Trial by fire: On the terminology and methods used in pyrogenic organic carbon research. Frontiers in Earth Science 5, 95. doi: 10.3389/feart.2017.00095. understanding of the cycling of fire-derived, i.e. pyrogenic organic matter (pyOM), as well as the goals of the community of researchers who study it, may be inhibited by the many terms and methods currently used in its quantification and characterization. Terms currently used for pyOM have evolved by convention, but are often poorly defined. Further, each of the different methods now used to quantify solid and dissolved pyrogenic carbon (pyC) comes with its own biases and artifacts. That is, each detects only a fraction of the total pyrogenic products produced by fire, while, at the same time, include some fraction of non-pyrogenic OM. This may be evident in the commonly observed correlations between pyC and total organic C reported for both soils and dissolved OM in many different systems. We suggest that our research area can be placed on a stronger footing by: 1) agreement upon a common set of terms tied to the method used for detection (e.g. of the form pyCmethod), 2) implementation of another ‘ring trial’ study with a wider set of natural soil and water samples that cross-compare more recently developed methods, and 3) further investigation of the processes which preserve/degrade/transport pyOM in the environment.Zou, J., Rezaee, R., Liu, K., 2017. Effect of temperature on methane adsorption in shale gas reservoirs. Energy & Fuels 31, 12081-12092. adsorption isotherms on shale were investigated at 25, 45, 60, and 80 °C with pressure up to 7 MPa (1015 psi). A total of six shale samples with low total organic carbon (TOC) from the Perth Basin and Canning Basin (Western Australia) were studied to quantify the effect of temperature on methane adsorption in shale gas reservoirs. The pore structure of the shale samples was measured using low-pressure nitrogen and carbon dioxide adsorption. At low temperature (25 °C), the methane adsorption isotherms show a general increase of methane adsorption with the TOC. However, the trend is not in line with methane adsorption at high temperature (80 °C). At 80 °C, sample AC-2 with 0.64% TOC has a larger maximum methane adsorption capacity than sample AC-4 with 1.03% TOC, indicating that the effects of temperature on methane adsorption for different shale samples are different. As the temperature increases, the decrease rate of methane adsorption on low TOC samples is smaller than that on the samples with a high TOC content. All the experimental methane adsorption isotherms fit well with the Langmuir equation. The Langmuir volumes of samples AC-2 (0.64% TOC), AC-4 (1.03% TOC), and AC-5 (0.23% TOC) are very close to each other at high temperature (80 °C). The thermodynamic parameters of methane adsorption on shale samples were determined. For the studied shale samples, the heat of adsorption and the standard entropy range from 4.5 to 14.5 kJ/mol and from 42.0 to 74.7 J mol–1 K–1, respectively.Zupanska, A.K., Schultz, E.R., Yao, J., Sng, N.J., Zhou, M., Callaham, J.B., Ferl, R.J., Paul, A.-L., 2017. ARG1 functions in the physiological adaptation of undifferentiated plant cells to spaceflight. Astrobiology 17, 1077-1111. access to spaceflight and especially the International Space Station has revealed that physiological adaptation to spaceflight is accompanied or enabled by changes in gene expression that significantly alter the transcriptome of cells in spaceflight. A wide range of experiments have shown that plant physiological adaptation to spaceflight involves gene expression changes that alter cell wall and other metabolisms. However, while transcriptome profiling aptly illuminates changes in gene expression that accompany spaceflight adaptation, mutation analysis is required to illuminate key elements required for that adaptation.Here we report how transcriptome profiling was used to gain insight into the spaceflight adaptation role of Altered response to gravity 1 (Arg1), a gene known to affect gravity responses in plants on Earth. The study compared expression profiles of cultured lines of Arabidopsis thaliana derived from wild-type (WT) cultivar Col-0 to profiles from a knock-out line deficient in the gene encoding ARG1 (ARG1 KO), both on the ground and in space. The cell lines were launched on SpaceX CRS-2 as part of the Cellular Expression Logic (CEL) experiment of the BRIC-17 spaceflight mission. The cultured cell lines were grown within 60?mm Petri plates in Petri Dish Fixation Units (PDFUs) that were housed within the Biological Research In Canisters (BRIC) hardware. Spaceflight samples were fixed on orbit. Differentially expressed genes were identified between the two environments (spaceflight and comparable ground controls) and the two genotypes (WT and ARG1 KO). Each genotype engaged unique genes during physiological adaptation to the spaceflight environment, with little overlap. Most of the genes altered in expression in spaceflight in WT cells were found to be Arg1-dependent, suggesting a major role for that gene in the physiological adaptation of undifferentiated cells to spaceflight. ................
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