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GEOCHEMISTRY ARTICLES – January 2018?Analytical ChemistryClark, K.D., Emaus, M.N., Varona, M., Bowers, A.N., Anderson, J.L., 2018. Ionic liquids: solvents and sorbents in sample preparation. Journal of Separation Science 41, 209-235.de Toffoli, A.L., Maciel, E.V.S., Fumes, B.H., Lan?as, F.M., 2018. The role of graphene-based sorbents in modern sample preparation techniques. Journal of Separation Science 41, 288-302.Ferreira, S.L.C., Bezerra, M.A., Santos, A.S., dos Santos, W.N.L., Novaes, C.G., de Oliveira, O.M.C., Oliveira, M.L., Garcia, R.L., 2018. Atomic absorption spectrometry – A multi element technique. TrAC Trends in Analytical Chemistry 100, 1-6.Gouilleux, B., Rouger, L., Giraudeau, P., 2018. Ultrafast 2D NMR: Methods and applications, in: Webb, G.A. (Ed.), Annual Reports on NMR Spectroscopy. Academic Press, pp. 75-144.Maya, F., Palomino Cabello, C., Ghani, M., Turnes Palomino, G., Cerdà, V., 2018. Emerging materials for sample preparation. Journal of Separation Science 41, 262-287.Meier, T., 2018. At its extremes: NMR at giga-pascal pressures, in: Webb, G.A. (Ed.), Annual Reports on NMR Spectroscopy. Academic Press, pp. 1-74.Ncube, S., Madikizela, L., Cukrowska, E., Chimuka, L., 2018. Recent advances in the adsorbents for isolation of polycyclic aromatic hydrocarbons (PAHs) from environmental sample solutions. TrAC Trends in Analytical Chemistry 99, 101-116.Ng, N.-T., Kamaruddin, A.F., Wan Ibrahim, W.A., Sanagi, M.M., Abdul Keyon, A.S., 2018. Advances in organic–inorganic hybrid sorbents for the extraction of organic and inorganic pollutants in different types of food and environmental samples. Journal of Separation Science 41, 195-208.Ojeda, C.B., Rojas, F.S., 2018. Vortex-assisted liquid–liquid microextraction (VALLME): The latest applications. Chromatographia 81, 89-103.Olivares, I.R.B., Souza, G.B., Nogueira, A.R.A., Toledo, G.T.K., Marcki, D.C., 2018. Trends in developments of certified reference materials for chemical analysis - Focus on food, water, soil, and sediment matrices. TrAC Trends in Analytical Chemistry 100, 53-64.Reyes-Garcés, N., Gionfriddo, E., Gómez-Ríos, G.A., Alam, M.N., Boyac?, E., Bojko, B., Singh, V., Grandy, J., Pawliszyn, J., 2018. Advances in solid phase microextraction and perspective on future directions. Analytical Chemistry 90, 302-360.Shvartsburg, A.A., Haris, A., Andrzejewski, R., Entwistle, A., Giles, R., 2018. Differential ion mobility separations in the low-pressure regime. Analytical Chemistry 90, 936-943.Simpson, A.J., Simpson, M.J., Soong, R., 2018. Environmental nuclear magnetic resonance spectroscopy: An overview and a primer. Analytical Chemistry 90, 628-639.Sugiyama, I., Williams-Jones, A.E., 2018. An approach to determining nickel, vanadium and other metal concentrations in crude oil. Analytica Chimica Acta 1002, 18-25.Timofeeva, I.I., Vakh, C.S., Bulatov, A.V., Worsfold, P.J., 2018. Flow analysis with chemiluminescence detection: Recent advances and applications. Talanta 179, 246-270.Wang, Y., Rui, M., Lu, G., 2018. Recent applications of metal–organic frameworks in sample pretreatment. Journal of Separation Science 41, 180-194.Wiesheu, A.C., Brejcha, R., Mueller, C.W., K?gel-Knabner, I., Elsner, M., Niessner, R., Ivleva, N.P., 2018. Stable-isotope Raman microspectroscopy for the analysis of soil organic matter. Analytical and Bioanalytical Chemistry 410, 923-931.Xiao, L., Schultz, Z.D., 2018. Spectroscopic imaging at the nanoscale: Technologies and recent applications. Analytical Chemistry 90, 440-458.Zhang, B., Daigle, H., 2018. Oil-soluble contrast agents for NMR. Journal of Petroleum Science and Engineering 162, 180-189.Gas Chromatography/GC×GC/GC-MSBeccaria, M., Mellors, T.R., Petion, J.S., Rees, C.A., Nasir, M., Systrom, H.K., Sairistil, J.W., Jean-Juste, M.-A., Rivera, V., Lavoile, K., Severe, P., Pape, J.W., Wright, P.F., Hill, J.E., 2018. Preliminary investigation of human exhaled breath for tuberculosis diagnosis by multidimensional gas chromatography – Time of flight mass spectrometry and machine learning. Journal of Chromatography B 1074-1075, 46-50.Hua, Y., Hawryluk, M., Gras, R., Shearer, R., Luong, J., 2018. Flow injection gas chromatography with sulfur chemiluminescence detection for the analysis of total sulfur in complex hydrocarbon matrixes. Journal of Separation Science 41, 469-474.Mani-Varnosfaderani, A., Kanginejad, A., Yamini, Y., 2018. Exploring the effects of sparsity constraint on the ranges of feasible solutions for resolution of GC-MS data. Chemometrics and Intelligent Laboratory Systems 173, 30-40.Nalin, F., Sander, L.C., Wilson, W.B., Wise, S.A., 2018. Gas chromatographic retention behavior of polycyclic aromatic hydrocarbons (PAHs) and alkyl-substituted PAHs on two stationary phases of different selectivity. Analytical and Bioanalytical Chemistry 410, 1123-1137.Prebihalo, S.E., Berrier, K.L., Freye, C.E., Bahaghighat, H.D., Moore, N.R., Pinkerton, D.K., Synovec, R.E., 2018. Multidimensional gas chromatography: Advances in instrumentation, chemometrics, and applications. Analytical Chemistry 90, 505-532.Santos, N.A., Cacique, A.P., Barbosa, ?.S., Silvério, F.O., Pinho, G.P.d., 2017. Validation of a method for extraction of polycyclic aromatic hydrocarbons from sewage sludge and analysis by GC-MS. International Journal of Environmental Analytical Chemistry 97, 1393-1404.Schedl, A., Zweckmair, T., Kikul, F., Bacher, M., Rosenau, T., Potthast, A., 2018. Pushing the limits: Quantification of chromophores in real-world paper samples by GC-ECD and EI-GC-MS. Talanta 179, 693-699.Song, X., Li, H., Yin, M., Ma, Y., 2018. Determination of 16 polycyclic aromatic hydrocarbons in marine sediments by gas chromatography-tandem mass spectrometry with accelerated solvent extraction. Chinese Journal of Chromatography 36, 43-50.?pánik, I., Machyňáková, A., 2018. Recent applications of gas chromatography with high-resolution mass spectrometry. Journal of Separation Science 41, 163-179.Yan, J., Kim, M., Haberl, M., Kwok, H., Brunswick, P., MacInnis, C., van Aggelen, G., Shang, D., 2018. Determination of polycyclic aromatic hydrocarbons in surface water using simplified liquid-liquid micro-extraction and pseudo-MRM GC/MS/MS. Analytical Methods 10, 405-416.Zhou, R., Zhou, Y., Mao, T., Jiang, J., 2018. Determination of fatty acids in natural cream and artificial cream by comprehensive two-dimensional gas chromatography-mass spectrometry Chinese Journal of Chromatography 36, 43-50.Imagine: SEM, TEM, HIM, AFMBurch, M.J., Ievlev, A.V., Mahady, K., Hysmith, H., Rack, P.D., Belianinov, A., Ovchinnikova, O.S., 2018. Helium ion microscopy for imaging and quantifying porosity at the nanoscale. Analytical Chemistry 90, 1370-1375.Chukwuma, K., Bordy, E.M., Coetzer, A., 2018. Evolution of porosity and pore geometry in the Permian Whitehill Formation of South Africa – A FE-SEM image analysis study. Marine and Petroleum Geology 91, 262-278.Crawford, A.J., Baker, S.J., Belcher, C.M., 2018. Fossil charcoals from the Lower Jurassic challenge assumptions about charcoal morphology and identification. Palaeontology 61, 49-56.Deirieh, A., Casey, B., Germaine, J.T., Xu, G., 2018. The integration of magnifications: A novel approach to obtain representative information about the pore space of mudrocks from SEM images. Applied Clay Science 154, 73-82.Karayi?it, A.?., Mastalerz, M., Oskay, R.G., Gayer, R.A., 2018. Coal petrography, mineralogy, elemental compositions and palaeoenvironmental interpretation of Late Carboniferous coal seams in three wells from the Kozlu coalfield (Zonguldak Basin, NW Turkey). International Journal of Coal Geology 187, 54-70.Kreisserman, Y., Emmanuel, S., 2018. Release of particulate iron sulfide during shale-fluid interaction. Environmental Science & Technology 52, 638-643.Kremer, B., Ka?mierczak, J., ?rodoń, J., 2018. Cyanobacterial-algal crusts from Late Ediacaran paleosols of the East European Craton. Precambrian Research 305, 236-246.Medeiros, J.M., B?ck, D., Pilhofer, M., 2018. Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography. Current Opinion in Microbiology 43, 62-68.Ngo, A.T., Skeini, T., Iancu, V., Redfern, P.C., Curtiss, L.A., Hla, S.W., 2018. Manipulation of origin of life molecules: Recognizing single-molecule conformations in β-carotene and chlorophyll-a/β-carotene clusters. ACS Nano 12, 217-225.Sánchez-Espa?a, J., Wang, K., Falagán, C., Yusta, I., Burgos, W.D., 2018. Microbially mediated aluminosilicate formation in acidic anaerobic environments: A cell-scale chemical perspective. Geobiology 16, 88-103.Shen, B., Qin, J., Tenger, B., Pan, A., Yang, Y., Bian, L., 2018. Identification of bacterial fossils in marine source rocks in South China. Acta Geochimica 37, 68-79.Sun, Z., Zhang, H., Wei, Z., Wang, Y., Wu, B., Zhuo, S., Zhao, Z., Li, J., Hao, L., Yang, H., 2018. Effects of slick water fracturing fluid on pore structure and adsorption characteristics of shale reservoir rocks. Journal of Natural Gas Science and Engineering 51, 27-36.Taheri-Shakib, J., Shekarifard, A., Naderi, H., 2018. Characterization of the wax precipitation in Iranian crude oil based on Wax Appearance Temperature (WAT): Part 1. The influence of electromagnetic waves. Journal of Petroleum Science and Engineering 161, 530-540.Tahmasebi, P., 2018. Nanoscale and multiresolution models for shale samples. Fuel 217, 218-225.Walder, R., Van Patten, W.J., Adhikari, A., Perkins, T.T., 2017. Going vertical to improve the accuracy of atomic force microscopy based single-molecule force spectroscopy. ACS Nano 12, 198–207.Xiao, L., Schultz, Z.D., 2018. Spectroscopic imaging at the nanoscale: Technologies and recent applications. Analytical Chemistry 90, 440-458.Yan, G., Wei, C., Song, Y., Luo, J., Zhang, J., 2018. Quantitative description of shale pore structure using image analysis and determination of controls on shape, size and orientation complexity. Arabian Journal of Geosciences Article 11, 11.Yoshida, K., Orozbaev, R., Hirajima, T., Miyake, A., Tsuchiyama, A., Bakirov, A., Takasu, A., Sakiev, K., 2018. Micro-excavation and direct chemical analysis of individual fluid inclusion by cryo-FIB-SEM-EDS: Application to the UHP talc-garnet-chloritoid schist from the Makbal Metamorphic Complex, Kyrgyz Tian-Shan. Geochemical Journal, 52, 59-67.Yu, X., Granados-Focil, S., Tao, M., Burnham, N.A., 2018. Time- and composition-dependent evolution of distinctive microstructures in bitumen. Energy & Fuels 32, 67-80.Yu, X., H?rst, S.M., He, C., McGuiggan, P., Bridges, N.T., 2017. Direct measurement of interparticle forces of Titan aerosol analogs (“tholin”) using atomic force microscopy. Journal of Geophysical Research: Planets 122, 2610-2622.Imagine: ?-Xray CTDesmond, P., Best, J.P., Morgenroth, E., Derlon, N., 2018. Linking composition of extracellular polymeric substances (EPS) to the physical structure and hydraulic resistance of membrane biofilms. Water Research 132, 211-221.Erofeev, A.A., Pachezhercev, A.A., Karpov, I.A., Morozov, N.V., Kalmykov, A.G., Cheremisin, A.N., Kozlova, E.V., Bychkov, A.Y., 2017. Estimation of the heat-impact potential for stimulating the development of the deposits of the Bazhenov Formation according to the results of experimental studies. Moscow University Geology Bulletin 72, 339-348.Shabaninejad, M., Middlelton, J., Fogden, A., 2018. Systematic pore-scale study of low salinity recovery from Berea sandstone analyzed by micro-CT. Journal of Petroleum Science and Engineering 163, 283-294.Yang, Y., Wu, J., Zhao, S., Han, Q., Pan, X., He, F., Chen, C., 2018. Assessment of the responses of soil pore properties to combined soil structure amendments using X-ray computed tomography. Scientific Reports 8, Article 695.D’AnielloLiquid Chromatography/LC-MS/SFCAhmed, A., Skinley, K., Herodotou, S., Zhang, H., 2018. Core–shell microspheres with porous nanostructured shells for liquid chromatography. Journal of Separation Science 41, 99-124.Eddhif, B., Allavena, A., Liu, S., Ribette, T., Abou Mrad, N., Chiavassa, T., d’Hendecourt, L.L.S., Sternberg, R., Danger, G., Geffroy-Rodier, C., Poinot, P., 2018. Development of liquid chromatography high resolution mass spectrometry strategies for the screening of complex organic matter: Application to astrophysical simulated materials. Talanta 179, 238-245.Fornells, E., Barnett, B., Bailey, M., Hilder, E.F., Shellie, R.A., Breadmore, M.C., 2018. Evaporative membrane modulation for comprehensive two-dimensional liquid chromatography. Analytica Chimica Acta 1000, 303-309.Gupta, V., Beirne, S., Nesterenko, P.N., Paull, B., 2018. Investigating the effect of column geometry on separation efficiency using 3D printed liquid chromatographic columns containing polymer monolithic phases. Analytical Chemistry 90, 1186-1194.Jandera, P., Hájek, T., 2018. Mobile phase effects on the retention on polar columns with special attention to the dual hydrophilic interaction–reversed-phase liquid chromatography mechanism, a review. Journal of Separation Science 41, 145-162.López-Ure?a, S., Torres-Lapasió, J.R., Donat, R., García-Alvarez-Coque, M.C., 2018. Gradient design for liquid chromatography using multi-scale optimization. Journal of Chromatography A 1534, 32-42.Massei, R., Byers, H., Beckers, L.-M., Prothmann, J., Brack, W., Schulze, T., Krauss, M., 2018. A sediment extraction and cleanup method for wide-scope multitarget screening by liquid chromatography–high-resolution mass spectrometry. Analytical and Bioanalytical Chemistry 410, 177-188.McAdams, B.C., Aiken, G.R., McKnight, D.M., Arnold, W.A., Chin, Y.-P., 2018. High pressure size exclusion chromatography (HPSEC) determination of dissolved organic matter molecular weight revisited: Accounting for changes in stationary phases, analytical standards, and isolation methods. Environmental Science & Technology 52, 722-730.Mitra, V., Smilde, A.K., Bischoff, R., Horvatovich, P., 2018. Tutorial: Correction of shifts in single-stage LC-MS(/MS) data. Analytica Chimica Acta 999, 37-53.Phong, D.D., Hur, J., 2018. Using two-dimensional correlation size exclusion chromatography (2D-CoSEC) and EEM-PARAFAC to explore the heterogeneous adsorption behavior of humic substances on nanoparticles with respect to molecular sizes. Environmental Science & Technology 52, 427-435.Pirok, B.W.J., Gargano, A.F.G., Schoenmakers, P.J., 2018. Optimizing separations in online comprehensive two-dimensional liquid chromatography. Journal of Separation Science 41, 68-98.Subraveti, S.G., Nikrityuk, P., Rajendran, A., 2018. Computational fluid dynamics study of viscous fingering in supercritical fluid chromatography. Journal of Chromatography A 1534, 150-160.Svan, A., Hedeland, M., Arvidsson, T., Pettersson, C.E., 2018. The differences in matrix effect between supercritical fluid chromatography and reversed phase liquid chromatography coupled to ESI/MS. Analytica Chimica Acta 1000, 163-171.Taraji, M., Haddad, P.R., Amos, R.I.J., Talebi, M., Szucs, R., Dolan, J.W., Pohl, C.A., 2018. Chemometric-assisted method development in hydrophilic interaction liquid chromatography: A review. Analytica Chimica Acta 1000, 20-40.Xu, C., Wang, B., Pu, Y., Tao, J., Zhang, T., 2018. Techniques for the analysis of pentacyclic triterpenoids in medicinal plants. Journal of Separation Science 41, 6-19.Yuan, X., Oleschuk, R.D., 2018. Advances in microchip liquid chromatography. Analytical Chemistry 90, 283-301.Zhang, L., Liu, C.-W., Zhang, Q., 2018. Online 2D-LC-MS/MS platform for analysis of glycated proteome. Analytical Chemistry 90, 1081–1086.Zhao, Y., Fu, D., Liu, Y., Liang, X., Xue, H., 2018. Separation of chemical compositions in root of Rumex patientia L. with off-line two-dimensional liquid chromatography. Chinese Journal of Chromatography 36, 37-42.Zhu, Z., Chen, H., Ren, J., Lu, J.J., Gu, C., Lynch, K.B., Wu, S., Wang, Z., Cao, C., Liu, S., 2018. Two-dimensional chromatographic analysis using three second-dimension columns for continuous comprehensive analysis of intact proteins. Talanta 179, 588-593.Mass Spectroscopy/FTICR-MSAbdulla, H.A., Burdige, D.J., Komada, T., 2018. Accumulation of deaminated peptides in anoxic sediments of Santa Barbara Basin. Geochimica et Cosmochimica Acta 223, 245-258.Aizpurua-Olaizola, O., Sastre Tora?o, J., Falcon-Perez, J.M., Williams, C., Reichardt, N., Boons, G.J., 2018. Mass spectrometry for glycan biomarker discovery. TrAC Trends in Analytical Chemistry 100, 7-14.Bokhart, M.T., Nazari, M., Garrard, K.P., Muddiman, D.C., 2018. MSiReader v1.0: Evolving open-source mass spectrometry imaging software for targeted and untargeted analyses. Journal of The American Society for Mass Spectrometry 29, 8-16.Buchberger, A.R., DeLaney, K., Johnson, J., Li, L., 2018. Mass spectrometry imaging: A review of emerging advancements and future insights. Analytical Chemistry 90, 240-265.Chacón-Pati?o, M.L., Rowland, S.M., Rodgers, R.P., 2018. Advances in asphaltene petroleomics. Part 2: Selective separation method that reveals fractions enriched in island and archipelago structural motifs by mass spectrometry. Energy & Fuels 32, 314-328.Chandler, S.A., Benesch, J.L.P., 2018. Mass spectrometry beyond the native state. Current Opinion in Chemical Biology 42, 130-137.Chen, B., Brown, K.A., Lin, Z., Ge, Y., 2018. Top-down proteomics: Ready for prime time? Analytical Chemistry 90, 110-127.D'Atri, V., Causon, T., Hernandez-Alba, O., Mutabazi, A., Veuthey, J.-L., Cianferani, S., Guillarme, D., 2018. Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry? Journal of Separation Science 41, 20-67.Graham, E.B., Tfaily, M.M., Crump, A.R., Goldman, A.E., Bramer, L.M., Arntzen, E., Romero, E., Resch, C.T., Kennedy, D.W., Stegen, J.C., 2017. Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes. Journal of Geophysical Research: Biogeosciences 122, 3188-3205.Guan, M., Zhang, Z., Li, S., Liu, J.a., Liu, L., Yang, H., Zhang, Y., Wang, T., Zhao, Z., 2018. Silver nanoparticles as matrix for MALDI FTICR MS profiling and imaging of diverse lipids in brain. Talanta 179, 624-631.Habchi, B., Alves, S., Jouan-Rimbaud Bouveresse, D., Appenzeller, B., Paris, A., Rutledge, D.N., Rathahao-Paris, E., 2018. Potential of dynamically harmonized Fourier transform ion cyclotron resonance cell for high-throughput metabolomics fingerprinting: control of data quality. Analytical and Bioanalytical Chemistry 410, 483-490.Idowu, I., Francisco, O., Thomas, P.J., Johnson, W., Marvin, C., Stetefeld, J., Tomy, G.T., 2018. Validation of a simultaneous method for determining polycyclic aromatic compounds and alkylated isomers in biota. Rapid Communications in Mass Spectrometry 32, 277-287.Laskin, J., Laskin, A., Nizkorodov, S.A., 2018. Mass spectrometry analysis in atmospheric chemistry. Analytical Chemistry 90, 166-189.Lewis, S.A., Connatser, R.M., Olarte, M.V., Keiser, J.R., 2018. Determining aromatic and aliphatic carboxylic acids in biomass-derived oil samples using 2,4-dinitrophenylhydrazine and liquid chromatography-electrospray injection-mass spectrometry/mass spectrometry. Biomass and Bioenergy 108, 198-206.Li, X., Ma, W., Li, H., Ai, W., Bai, Y., Liu, H., 2018. Sampling and analyte enrichment strategies for ambient mass spectrometry. Analytical and Bioanalytical Chemistry 410, 715-724.Liu, H., Zhou, Y., Wang, J., Xiong, C., Xue, J., Zhan, L., Nie, Z., 2018. N-phenyl-2-naphthylamine as a novel MALDI matrix for analysis and in situ imaging of small molecules. Analytical Chemistry 90, 729-736.Molnárné Guricza, L., Schrader, W., 2018. Optimized asphaltene separation by online coupling of size exclusion chromatography and ultrahigh resolution mass spectrometry. Fuel 215, 631-637.Nyadong, L., Lai, J., Thompsen, C., LaFrancois, C.J., Cai, X., Song, C., Wang, J., Wang, W., 2018. High-field Orbitrap mass spectrometry and tandem mass spectrometry for molecular characterization of asphaltenes. Energy & Fuels 32, 294-305.Oya, M., Suzuki, H., Anas, A.R.J., Oishi, K., Ono, K., Yamaguchi, S., Eguchi, M., Sawada, M., 2018. LC-MS/MS imaging with thermal film-based laser microdissection. Analytical and Bioanalytical Chemistry 410, 491-499.Rahman, M.M., Jiang, T., Tang, Y., Xu, W., 2018. A simple desorption atmospheric pressure chemical ionization method for enhanced non-volatile sample analysis. Analytica Chimica Acta 1002, 62-69.Sans, M., Feider, C.L., Eberlin, L.S., 2018. Advances in mass spectrometry imaging coupled to ion mobility spectrometry for enhanced imaging of biological tissues. Current Opinion in Chemical Biology 42, 138-146.Teng, F., Zhu, Q., Wang, Y., Du, J., Lu, N., 2018. Enhancing reproducibility of SALDI MS detection by concentrating analytes within laser spot. Talanta 179, 583-587.Valle, J., Gonsior, M., Harir, M., Enrich-Prast, A., Schmitt-Kopplin, P., Bastviken, D., Conrad, R., Hertkorn, N., 2018. Extensive processing of sediment pore water dissolved organic matter during anoxic incubation as observed by high-field mass spectrometry (FTICR-MS). Water Research 129, 252-263.Veli?kovi?, D., Chu, R.K., Carrell, A.A., Thomas, M., Pa?a-Toli?, L., Weston, D.J., Anderton, C.R., 2018. Multimodal MSI in conjunction with broad coverage spatially resolved MS2 increases confidence in both molecular identification and localization. Analytical Chemistry 90, 702-707.Wang, H., Fei, Z., Li, Z., Xing, R., Liu, Z., Zhang, Y., Ding, H., 2018. Coupling laser desorption with corona beam ionization for ambient mass spectrometric analysis of solution and powder samples. Talanta 179, 364-368.Yang, B., Zhang, H., Shu, J., Ma, P., Zhang, P., Huang, J., Li, Z., Xu, C., 2018. Vacuum-ultraviolet-excited and CH2Cl2/H2O-amplified ionization-coupled mass spectrometry for oxygenated organics analysis. Analytical Chemistry 90, 1301-1308.Metabolomics/LipidomicsAthenaki, M., Gardeli, C., Diamantopoulou, P., Tchakouteu, S.S., Sarris, D., Philippoussis, A., Papanikolaou, S., 2018. Lipids from yeasts and fungi: physiology, production and analytical considerations. Journal of Applied Microbiology 124, 336-367.Boysen, A.K., Heal, K.R., Carlson, L.T., Ingalls, A.E., 2017. Best-matched internal standard normalization in liquid chromatography–mass spectrometry metabolomics applied to environmental samples. Analytical Chemistry 90, 1363-1369.D'Atri, V., Causon, T., Hernandez-Alba, O., Mutabazi, A., Veuthey, J.-L., Cianferani, S., Guillarme, D., 2018. Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry? Journal of Separation Science 41, 20-67.Domingo-Almenara, X., Montenegro-Burke, J.R., Benton, H.P., Siuzdak, G., 2018. Annotation: A computational solution for streamlining metabolomics analysis. Analytical Chemistry 90, 480-489.Hillyer, K.E., Dias, D., Lutz, A., Roessner, U., Davy, S.K., 2017. 13C metabolomics reveals widespread change in carbon fate during coral bleaching. Metabolomics 14, Article 12.Hu, T., Zhang, J.-L., 2018. Mass-spectrometry-based lipidomics. Journal of Separation Science 41, 351-372.Lippens, G., Cahoreau, E., Millard, P., Charlier, C., Lopez, J., Hanoulle, X., Portais, J.C., 2018. In-cell NMR: from metabolites to macromolecules. Analyst 143, 620-629.Liu, M., Hilty, C., 2018. Metabolic measurements of nonpermeating compounds in live cells using hyperpolarized NMR. Analytical Chemistry 90, 1217-1222.Poad, B.L.J., Zheng, X., Mitchell, T.W., Smith, R.D., Baker, E.S., Blanksby, S.J., 2018. Online ozonolysis combined with ion mobility-mass spectrometry provides a new platform for lipid isomer analyses. Analytical Chemistry 90, 1292-1300.Prebihalo, S.E., Berrier, K.L., Freye, C.E., Bahaghighat, H.D., Moore, N.R., Pinkerton, D.K., Synovec, R.E., 2018. Multidimensional gas chromatography: Advances in instrumentation, chemometrics, and applications. Analytical Chemistry 90, 505-532.Reyes-Garcés, N., Gionfriddo, E., Gómez-Ríos, G.A., Alam, M.N., Boyac?, E., Bojko, B., Singh, V., Grandy, J., Pawliszyn, J., 2018. Advances in solid phase microextraction and perspective on future directions. Analytical Chemistry 90, 302-360.Richardson, S.D., Ternes, T.A., 2018. Water analysis: Emerging contaminants and current issues. Analytical Chemistry 90, 398-428.Rustam, Y.H., Reid, G.E., 2018. Analytical challenges and recent advances in mass spectrometry based lipidomics. Analytical Chemistry 90, 374-397.Sans, M., Feider, C.L., Eberlin, L.S., 2018. Advances in mass spectrometry imaging coupled to ion mobility spectrometry for enhanced imaging of biological tissues. Current Opinion in Chemical Biology 42, 138-146.Schrimpe-Rutledge, A.C., Sherrod, S.D., McLean, J.A., 2018. Improving the discovery of secondary metabolite natural products using ion mobility–mass spectrometry. Current Opinion in Chemical Biology 42, 160-166.Wang, J., Wang, C., Han, X., 2018. 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Reconstruction of prehistoric pottery use from fatty acid carbon isotope signatures using Bayesian inference. Organic Geochemistry 117, 31-42.Forte, V., Nunziante Cesaro, S., Medeghini, L., 2018. Cooking traces on Copper Age pottery from central Italy: An integrated approach comprising use wear analysis, spectroscopic analysis and experimental archaeology. Journal of Archaeological Science: Reports 18, 121-138.Itahashi, Y., Tsuneki, A., Dougherty, S.P., Chikaraishi, Y., Ohkouchi, N., Yoneda, M., 2018. Dining together: Reconstruction of Neolithic food consumption based on the δ15N values for individual amino acids at Tell el-Kerkh, northern Levant. Journal of Archaeological Science: Reports 17, 775-784.Kendall, C., Eriksen, A.M.H., Kontopoulos, I., Collins, M.J., Turner-Walker, G., 2018. Diagenesis of archaeological bone and tooth. Palaeogeography, Palaeoclimatology, Palaeoecology 491, 21-37.Leclerc, M., Taché, K., Bedford, S., Spriggs, M., Lucquin, A., Craig, O.E., 2018. 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Enrichment conditions and favorable zone prediction of Wufeng–Longmaxi shale gas reservoirs in the northern Yunnan–Guizhou provinces, China Natural Gas Industry 37, 26-34.AbstractsAamir, A., Matee, U., Matloob, H., Bhatti, A.S., Khaista, R., 2017. Estimation of the shale oil/gas potential of a Paleocene–Eocene succession: A case study from the Meyal area, Potwar Basin, Pakistan. Acta Geologica Sinica - English Edition 91, 2180-2199. successful exploration and production of shale-gas resources in the United States and Canada sets a new possible solution towards the energy crisis presently affecting most countries of Asia. This study focuses on the use of well log and 2D seismic data for the characterization of the shale oil/gas potential of a Paleocene-Eocene succession — the Meyal area in the Potwar Basin of Pakistan. Two shaly plays are identified in Paleocene-Eocene strata in well logs using Δ LogR and modified Δ LogR cross-plot techniques. The results indicate that Paleocene shale (the Patala Formation) and the lower shaly part of Eocene limestone (Sakesar Formation) can be potentially mature source rocks. However, the thermal maturity modelling proves that only the Paleocene shale is mature. Our results also suggest that the maturity responses on Δ LogR models for the lower shaly part of the Eocene limestone are due to trapped hydrocarbons in the intra-formational fractures. Petroelastic/petrophysical analysis of the Patala Formation reveals two potential shale oil/gas zones on the basis of Young's modulus, Poisson's ratio, Brittleness index and Total Organic Content at an exploitation depth of 3980–3988 m. This work can provide valuable insight for estimating shale oil/gas potential in highly deformed basins not only in Asia but in other parts of the world.Abby, S.S., Melcher, M., Kerou, M., Krupovic, M., Stieglmeier, M., Rossel, C., Pfeifer, K., Schleper, C., 2018. Candidatus Nitrosocaldus cavascurensis, an ammonia oxidizing, extremely thermophilic archaeon with a highly mobile genome. Frontiers in Microbiology 9, 28. doi: 10.3389/fmicb.2018.00028. oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in moderate environments but their occurrence and activity has also been demonstrated in hot springs. Here we present the first enrichment of a thermophilic representative with a sequenced genome, which facilitates the search for adaptive strategies and for traits that shape the evolution of Thaumarchaeota. Candidatus Nitrosocaldus cavascurensis has been enriched from a hot spring in Ischia, Italy. It grows optimally at 68°C under chemolithoautotrophic conditions on ammonia or urea converting ammonia stoichiometrically into nitrite with a generation time of approximately 23 h. Phylogenetic analyses based on ribosomal proteins place the organism as a sister group to all known mesophilic AOA. The 1.58 Mb genome of Ca. N. cavascurensis harbors an amoAXCB gene cluster encoding ammonia monooxygenase and genes for a 3-hydroxypropionate/4-hydroxybutyrate pathway for autotrophic carbon fixation, but also genes that indicate potential alternative energy metabolisms. Although a bona fide gene for nitrite reductase is missing, the organism is sensitive to NO-scavenging, underlining the potential importance of this compound for AOA metabolism. Ca. N. cavascurensis is distinct from all other AOA in its gene repertoire for replication, cell division and repair. Its genome has an impressive array of mobile genetic elements and other recently acquired gene sets, including conjugative systems, a provirus, transposons and cell appendages. Some of these elements indicate recent exchange with the environment, whereas others seem to have been domesticated and might convey crucial metabolic traits.Abdelsayed, V., Shekhawat, D., Smith, M.W., Link, D., Stiegman, A.E., 2018. Microwave-assisted pyrolysis of Mississippi coal: A comparative study with conventional pyrolysis. Fuel 217, 656-667. conditions greatly affect the structure-reactivity relationship of char during coal gasification. This work investigated the effect of temperature and microwave heating on the structural properties of the chars generated during pyrolysis, as well as gaseous and tar products. Results showed that microwave pyrolysis of Mississippi coal produced more gaseous products and less tars compared to conventional pyrolysis. Higher CO/CO2 ratio (>1) was observed under microwave pyrolysis compared to conventional pyrolysis (CO/CO2?<?1), which may be explained by a greater extent of gasification between solid carbon and the CO2 formed during microwave pyrolysis. Additionally, in microwave pyrolysis, the oil tars generated exhibited lower concentrations of polar oxygenates, while the wax tars showed higher concentrations of non-polar alkanes, as observed from the intensity of C-H vibrations in FTIR. The product compositions and FTIR analysis of the tars (oils and waxes) suggest that the microwave interacted preferentially with these polar species, which have relatively higher dielectric properties compared to alkanes. The structure–reactivity relationship of the chars produced was also investigated using a variety of characterization tools such as XRD, BET, SEM, EDS, and FTIR. Finally, the char reactivity towards combustion suggested that microwave-produced chars have a higher thermal stability, likely due to lower O/C ratios, and could be utilized in the metallurgical industry.Abdulla, H.A., Burdige, D.J., Komada, T., 2018. Accumulation of deaminated peptides in anoxic sediments of Santa Barbara Basin. Geochimica et Cosmochimica Acta 223, 245-258. represent the most abundant class of biomolecules in marine sinking particles and microbial biomass, yet their cycling in marine sediments is not fully understood. To investigate whether some portion of hydrolyzed proteins escapes complete remineralization and accumulate in the pore waters, we analyzed dissolved organic matter from the anoxic sediments of Santa Barbara Basin, California, by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS). The results showed an increase in the molecular diversity and abundance of dissolved organic nitrogen (DON) formulas with depth. A comparison of the detected DON formulas to a database of small peptides (2–4 amino acid sequences) returned 119 matches, and these formulas were most abundant near the sediment surface. When we compared our detected formulas to all possible structures that would result from deamination of peptides in the database, we found 680 formula matches. However, these molecular formulas can represent hundreds of different structural isomers (in the present case as many as 3257 different deaminated peptide structures), which cannot be distinguished by the FTICR-MS settings that were used. Analysis of amino acid sequences suggests that these deaminated peptides may be the products of selective degradation of source proteins in marine sediments. We hypothesize that these deaminated peptides accumulate in the pore waters due to extracellular proteinases being inhibited from completely hydrolyzing specific peptides to free amino acids. We suggest that anaerobic microbes deaminate peptides largely to produce H2, which is ultimately used as a reducing agent by other sediment microbes (e.g. CO2 reduction by methanogens). Simple calculations suggest that deaminated peptides may represent ～25–45% of DOC accumulating in these sediment pore waters. Unlike rapid remineralization of free amino acids, peptide deamination leaves behind the peptide carbon skeleton. Molecular structures of these remnant carbon skeletons may hold important clues about specific microbial processes influencing organic matter remineralization and accumulation.Abou El-Anwar, E.A., 2017. Mineralogical, petrographical, geochemical, diageneses and provenance of the Cretaceous Black Shales, Duwi Formation at Quseir-Safaga, Red Sea, Egypt. Egyptian Journal of Petroleum 26, 915-926. Duwi Formation in the Quseir-Safaga area is conformably overlain by the Quseir variegated shales and underlain by the Dakhla shales. Detailed mineralogical and geochemical studies were carried out on the middle member of the black shales of the Duwi Formation in Quseir-Safaga province to infer their source rocks, paleo-weathering and provenance of the sources. The studied black shales are highly fossiliferous and fissile. They are texturally classified as phosphatic marly mudstone microfacies. Mineralogically, they are composed mainly of calcite, apatite, quartz, pyrite and clay minerals. The studied clay fraction reveals that the well-crystalline Na-montmorillonite is the dominating clay mineral with mixed layer montmorillonite-illite and minor kaolinite. These shales could be used as a source for the sodium bentonite. The studied black shales are highly mature, detrital and authigenic in origin. They are most probably derived from basic volcanic rocks by intensive chemical weathering. The provenance constituted a part of passive and active continental margins similar to those the Devonian/Mississippian shales in USA. The Cretaceous black shales of the Duwi Formation in Quseir-Safaga area are part of Mes-Neoarchean Shales, and are typically comparable to the Archean Shale Average.The average values of Cu, Ni, Zn, Cr, V, As and Se and, with the ratios Rb/Sr and Cr/Ni, are enriched with respect to those of the PAAS values. This could be attributed to the abundance of mafic components. The felsic source rocks were considered as an added source similar to Cretaceous and Cambrian black shales in India and China; respectively. The ratios V/Cr, V/(V + Ni) and Mo/Al and the high concentrations of the redox sensitive elements revealed that the studied black shales were deposited under relatively euxinic to anoxic reducing marine environments coupled with hydrothermal solutions. They were found comparable to the Cretaceous Gulf of California, Posidonia, Cretaceous/Tertiary black shales, and those in the Black Sea. The studied black shales can be classified as good to excellent source of oil and trace elements. The chemical composition of the studied black shales of the Duwi Formation (Cretaceous) was correlated to published data at different localities and ages.Adam, Z.R., Hongo, Y., Cleaves, H.J., Yi, R., Fahrenbach, A.C., Yoda, I., Aono, M., 2018. Estimating the capacity for production of formamide by radioactive minerals on the prebiotic Earth. Scientific Reports 8, Article 265. creates special problems for prebiotic chemistry, as it is thermodynamically favorable for amide and phosphodiester bonds to hydrolyze. The availability of alternative solvents with more favorable properties for the formation of prebiotic molecules on the early Earth may have helped bypass this so-called “water paradox”. Formamide (FA) is one such solvent, and can serve as a nucleobase precursor, but it is difficult to envision how FA could have been generated in large quantities or accumulated in terrestrial surface environments. We report here the conversion of aqueous acetonitrile (ACN) via hydrogen cyanide (HCN) as an intermediate into FA by γ-irradiation under conditions mimicking exposure to radioactive minerals. We estimate that a radioactive placer deposit could produce 0.1?0.8?mol FA km?2 year?1. A uraninite fission zone comparable to the Oklo reactors in Gabon can produce 0.1?1?mol?m?2 year?1, orders of magnitude greater than other scenarios of FA production or delivery for which reaching sizeable concentrations of FA are problematic. Radioactive mineral deposits may be favorable settings for prebiotic compound formation through emergent geologic processes and FA-mediated organic chemistry.Ahmed, A., Skinley, K., Herodotou, S., Zhang, H., 2018. Core–shell microspheres with porous nanostructured shells for liquid chromatography. Journal of Separation Science 41, 99-124. development of new stationary phases has been the key aspect for fast and efficient high-performance liquid chromatography separation with relatively low backpressure. Core–shell particles, with a solid core and porous shell, have been extensively investigated and commercially manufactured in the last decade. The excellent performance of core–shell particles columns has been recorded for a wide range of analytes, covering small and large molecules, neutral and ionic (acidic and basic), biomolecules and metabolites. In this review, we first introduce the advance and advantages of core–shell particles (or more widely known as superficially porous particles) against non-porous particles and fully porous particles. This is followed by the detailed description of various methods used to fabricate core–shell particles. We then discuss the applications of common silica core–shell particles (mostly commercially manufactured), spheres-on-sphere particles and core–shell particles with a non-silica shell. This review concludes with a summary and perspective on the development of stationary phase materials for high-performance liquid chromatography applications.Aizpurua-Olaizola, O., Sastre Tora?o, J., Falcon-Perez, J.M., Williams, C., Reichardt, N., Boons, G.J., 2018. Mass spectrometry for glycan biomarker discovery. TrAC Trends in Analytical Chemistry 100, 7-14. association between aberrant glycosylation of proteins and many cancers, and autoimmune and inflammatory diseases has been known for many years. Altered glycosylation can occur at the onset and during disease progression and identifying these changes at an early stage may greatly increase survival and improve quality of life. However, the identification of these biomarkers has not been easy, mainly due to the structural diversity and numerous possible glycan isomers. Fortunately, glycomics is becoming more feasible due to major improvements in mass spectrometry and separation science. The present review discusses recent methods for mass-spectrometry (MS) based glycomics for the identification of glycan biomarkers. Recent MS techniques with and without coupling to liquid chromatography, capillary electrophoresis or ion mobility spectrometry are described, and the most recent glycan biomarker studies are presented and future prospects discussed.Ajayi, T., Anderson, B.J., Seol, Y., Boswell, R., Myshakin, E.M., 2018. Key aspects of numerical analysis of gas hydrate reservoir performance: Alaska North Slope Prudhoe Bay Unit “L-Pad” hydrate accumulation. Journal of Natural Gas Science and Engineering 51, 37-43. previous work, we reported the development of the 3D geostatistical hydrate reservoir model of "L-Pad" (Myshakin et al., 2016). In this paper, gas production sensitivity on key reservoir parameters are studied. Hydraulic communication with an aquifer and optimal depressurization strategies are subjects of investigation. Uncertainty in initial in situ permeability within 0.1–10 mD range leads to 2.0?×?108–3.5?×?108 ST m3 of gas produced over 10 years. Accounting for reservoir quality and irreducible water saturation leads to noticeable change in productivity. Sequential depressurization of hydrate-bearing units was found to be more attractive versus simultaneous depressurization.Aleklett, K., Kiers, E.T., Ohlsson, P., Shimizu, T.S., Caldas, V.E.A., Hammer, E.C., 2018. Build your own soil: exploring microfluidics to create microbial habitat structures. The Isme Journal 12, 312-319. is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats.Almendros, G., Hernández, Z., Sanz, J., Rodríguez-Sánchez, S., Jiménez-González, M.A., González-Pérez, J.A., 2018. Graphical statistical approach to soil organic matter resilience using analytical pyrolysis data. Journal of Chromatography A 1533, 164-173. chromatography-mass spectrometry (Py-GC-MS) of humic acids (HAs) from 30 agricultural soils from a volcanic island (Tenerife, Spain) was used to discern the molecular characteristics of soil organic matter (SOM) associated to resilience. For faster perceptual identification of the results, the yields of the pyrolysis products in the form of surface density plots were compared in an update of the Van Krevelen graphical statistical method. This approach, with respect to data reduction and visualization, was also used to collectively represent statistical indices that were obtained after simple and partial least squares (PLS) regression. The resulting plots illustrate different SOM structural domains (for example, carbohydrate- and lignin-derived and condensed lipid). The content of SOM and total mineralization coefficient (TMC) values can be well estimated from the relative abundance of 57 major pyrolysis compounds: SOM content and composition parallels the accumulation of lignin- and carbohydrate-derived structures (lignocellulosic material) and the depletion of condensed polyalkyl structures. In other words, in the volcanic ash soils that were studied, we found that the higher the amount of SOM, the lower its quality in terms of resilience. Although no cause-and-effect is inferred from this fact, it is evident that the resistance to biodegradation of the SOM is related to its molecular composition.Alwmark, C., Bleeker, W., LeCheminant, A., Page, L., Scherstén, A., 2017. An Early Ordovician 40Ar-39Ar age for the ～50 km Carswell impact structure, Canada. Geological Society of America Bulletin 129, 1442-1449. formation age of the large (～50 km) Carswell impact structure, Canada, has been a matter of debate ever since its discovery five decades ago, with proposed ages ranging from Mesoproterozoic to Early Cretaceous. Here, we present new 40Ar-39Ar data for aliquots of euhedral adularia, separated from vesicles in an impact melt rock from the central uplift of the structure. The analyses of the adularia yielded a statistically robust Early Ordovician crystallization age of 481.5 ± 0.8 Ma (2σ, mean square of weighted deviates = 1.06, P = 0.30). The most plausible explanation for the formation of vesicle-filling adularia is through low-temperature mineral precipitation during residual hydrothermal circulation that followed the impact, as no other known major intrusive, extrusive, or thermal events have occurred in the Carswell region in the Phanerozoic. The new age of the Carswell impact structure overlaps within uncertainty with the most precise Ar-Ar ages proposed for the L-chondrite parent body breakup event, but not with the age of the stratigraphic sequence from which the meteorites and micrometeorites from this event were recovered. Thus, either the Carswell impact represents a separate, unrelated impact event, or the dynamic evolution of the L-chondrite parent body breakup is more complicated than presently understood, and Carswell represents one of the earliest and largest known impacts of this event on Earth.Amato del Monte, A., Antonielli, E., De Tomasi, V., Luchetti, G., Paparozzi, E., Gambacorta, G., 2018. Methods for source rock identification on seismic data: An example from the Tanezzuft Formation (Tunisia). Marine and Petroleum Geology 91, 108-124. rocks occurrence, extension and quality in the subsurface are usually characterized directly from well data. Seismic characterization is however becoming an emerging technique for extending source rock properties beyond well locations and an effective tool for mapping their lateral and vertical heterogeneities. The Tanezzuft Formation in Tunisia, an extremely organic-rich source rock, was used as a test for applying and comparing different seismic methods aimed at organic-rich sequences characterization. The data used consist of a 2D seismic line shot in the northern flank of the Ghadames Basin (Tunisia), pre-stack gathers extracted from an inline of a 3D survey and four wells with a complete set of wireline and petrophysical logs. Impedance inversion, AVO and seismic attributes were computed on the seismic lines and compared to well data. Impedance inversion together with a rock physics model of the formation generated a quantitative estimate of total organic carbon (TOC) content in the studied 2D seismic line. AVO analysis showed a Class IV and a Base Class IV response for the upper and lower reflectors delimiting the organic-rich interval respectively. Seismic attributes analyzed the formation by exploiting its high impedance contrast and intrinsic anelastic attenuation. The three methods here discussed showed coherent results both when compared each other and when compared with the well data and the regional geological model. In particular, AVO and seismic attribute analysis are methods that can be applied without the need of well information, and are then feasible methods for the investigation of source rock properties in undrilled basins.Andrault, D., Mu?oz, M., Pesce, G., Cerantola, V., Chumakov, A., Kantor, I., Pascarelli, S., Rüffer, R., Hennet, L., 2018. Large oxygen excess in the primitive mantle could be the source of the Great Oxygenation Event. Geochemical Perspectives Letters 6, 5-10. the Archean to Proterozoic Transition (APT) the tectonic regime was dominated by microplates floating on a low viscosity mantle. Such a regime restricted chemical exchange between the shallow and deeper mantle reservoirs. After the APT, a more global convection regime led to deep subduction of slabs. We propose that the improved vertical mixing of the mantle favoured the release to the Earth’s surface of an oxygen excess initially trapped in the deep mantle. This excess built up when the primordial lower mantle was left with a high Fe3+/(Fe2++Fe3+) ratio (#Fe3+), after metallic iron segregated down into the core. Our synchrotron-based in situ experiments suggest a primordial Fe3+excess of ~20 % for the mantle iron. By comparison with the #Fe3+ of the present mantle, this Fe3+excess would correspond to 500–1000 times the O2 content in the Earth’s atmosphere. The tectonic transition greatly facilitated the ascent of oxidised lower mantle material towards the Earth’s surface, inducing a continuous arrival of O2 at the Earth’s surface and into the atmosphere. Andreani, J., Khalil, J.Y.B., Baptiste, E., Hasni, I., Michelle, C., Raoult, D., Levasseur, A., La Scola, B., 2018. Orpheovirus IHUMI-LCC2: A new virus among the giant viruses. Frontiers in Microbiology 8, 2643. doi: 10.3389/fmicb.2017.02643. viruses continue to invade the world of virology, in gigantic genome sizes and various particles shapes. Strains discoveries and metagenomic studies make it possible to reveal the complexity of these microorganisms, their origins, ecosystems and putative roles. We isolated from a rat stool sample a new giant virus “Orpheovirus IHUMI-LCC2,” using Vermamoeba vermiformis as host cell. In this paper, we describe the main genomic features and replicative cycle of Orpheovirus IHUMI-LCC2. It possesses a circular genome exceeding 1.4 Megabases with 25% G+C content and ovoidal-shaped particles ranging from 900 to 1300 nm. Particles are closed by at least one thick membrane in a single ostiole-like shape in their apex. Phylogenetic analysis and the reciprocal best hit for Orpheovirus show a connection to the proposed Pithoviridae family. However, some genomic characteristics bear witness to a completely divergent evolution for Orpheovirus IHUMI-LCC2 when compared to Cedratviruses or Pithoviruses.Andrieu, S., Brigaud, B., Barbarand, J., Lasseur, E., 2018. The complex diagenetic history of discontinuities in shallow-marine carbonate rocks: New insights from high-resolution ion microprobe investigation of δ18O and δ13C of early cements. Sedimentology 65, 360-399. gaps are a major obstacle in the reconstruction of a carbonate platform's history. In order to improve the understanding of the early diagenesis and the succession of events occurring during the formation of discontinuity surfaces in limestones, secondary ion mass spectrometry was used for the first time to measure the δ18O and δ13C signatures of 11 early cement and fabric stages in several discontinuity surfaces from the Jurassic carbonate platform of the Paris Basin, France. Pendant cements show a high variability in δ18O, which was impossible to detect by the less precise microdrilling method. The morphology of a given cement can be produced in various environments, and dogtooth cements especially can precipitate in marine phreatic and meteoric phreatic to vadose environments. Marine dogtooth cements and micritic microbially induced fabrics precipitated directly as low-magnesium calcite in marine waters, as attested to by the preservation of their initial δ18O and δ13C signals. Five discontinuity types are recognized based on high-resolution geochemical analyses, and their palaeoenvironmental history can be reconstructed. Two exposure surfaces with non-ferroan pendant or meniscus cements formed in the oxidizing vadose zone. A hardground displays marine fibrous cements and non-ferroan dogtooth cements that formed in a subtidal environment in oxidizing water. Two composite surfaces have undergone both marine and subaerial lithification. Composite surface 1 displays non-luminescent ferroan dogtooth cements that precipitated in reduced conditions in seawater, followed by brown-luminescent dogtooth cements characteristic of a meteoric phreatic environment. Composite surface 2 exhibits microbially induced fabrics that formed in marine water with abundant organic matter. The latter discontinuity, initially formed in a subtidal environment, was subsequently exposed to meteoric conditions, as evidenced by ferroan geopetal cements. A high-resolution ion microprobe study is essential to precisely document the successive diagenetic environments that have affected carbonate rocks and discontinuities with a polygenic and intricate history.Arab, D., Kantzas, A., Bryant, S.L., 2018. Nanoparticle stabilized oil in water emulsions: A critical review. Journal of Petroleum Science and Engineering 163, 217-242. recovery techniques and solvent-based EOR methods are not applicable in many of thin post cold heavy oil production with sands (CHOPS) heavy oil reservoirs in Western Canada. Therefore, alkaline-surfactant flood has been suggested as an alternative to develop these reservoirs. The main mechanism behind these processes has been attributed to the effect of synthetic surfactant and natural soap, created due to the reaction of alkaline with acidic crude, to form an oil in water emulsion. The created emulsions can plug the very high permeable wormholes in post CHOPS heavy oil reservoirs to improve sweep efficiency. In these processes the efficiency of the process is improved with increasing the stability of the emulsions. Therefore, this review was aimed to investigate the potential application of nanoparticles, with the main focus on silica nanoparticles as the most cost-effective ones, along with synthetic or natural surfactants created by alkaline-surfactant flooding to boost the stability of oil in water emulsions.It was found that very hydrophilic silica nanoparticles (NP) tend not to adsorb at the oil-water interface and so they need to be surface activated to be able to work as emulsifiers. Different techniques including in-situ (i.e. surfactant-assisted) versus ex-situ (i.e. either surface-coating the nanoparticles or physically-enforced attachment of NP to the interface) techniques have been used to reduce nanoparticles hydrophilicity among which in-situ methods seem to be more practical in oil field applications. All types of surfactants and their effects on the hydrophilicity of silica NP were discussed in detail. All the literature discusses NPs effects to emulsify simple oils like decane, dodecane, 1-octadecene, n-hexane, kerosene, toluene, mineral oil, vegetable oil, paraffin, etc. in water. There is very little research done with crude oil, which is not comparable to the corresponding ideal systems work.It is concluded that although there are some clues in the literature addressing the emulsion stability due to mixing of surfactant with NPs of similar charge, the most stable oil in water emulsions can be obtained when the system contains oppositely-charged surfactants and NPs i.e., anionic NPs along with cationic surfactants or cationic NPs along with anionic surfactants. Therefore, it seems that the most influential factor is having two emulsifiers with different charges and the system chemistry is of less importance. In these cases, at specific surfactant concentrations the electrostatic interactions between NPs and surfactant molecules result in the least stable and most flocculated NPs which is reported as the most suitable condition (corresponding to the most favorable state for NPs hydrophobicity) to stabilize oil in water emulsions. Furthermore, adding a large amount of energy into the system by ultrasonication decreases the size of oil droplets which in turn, increases their surface area on which NPs have a higher chance to adsorb.Arai, K., Wada, S., Shimotori, K., Omori, Y., Hama, T., 2018. Production and degradation of fluorescent dissolved organic matter derived from bacteria. Journal of Oceanography 74, 39-52. of fluorescent dissolved organic matter (FDOM) in ocean environments has received attention over the past few decades. Although it has appeared that in situ production of oceanic FDOM is mainly due to bacteria, the production and bio- and photodegradation processes of bacterial FDOM have not been elucidated. In this study, a culture experiment with bacteria was carried out to assess the production and biodegradation processes of bacterial FDOM. Photodegradation of bacterial FDOM and dissolved organic carbon (DOC) was also examined by exposure to a solar simulator. Bacterial FDOM consists of six components which were determined by parallel factor analysis (PARAFAC). Fluorescence intensities of protein-like FDOM increased with the bacterial biomass, but the increases of humic-like FDOM lagged behind the protein-like FDOM by 5–10?days. Exposure to simulated sunlight caused significant decreases in fluorescence intensities of all components; 52–94% of the initial intensities were lost during 24?h. While, the DOC concentration exhibited a small decrease through the experiment (1.9–11.1%). These results showed that photodegradability of bacteria derived DOC was much less than the fluorescence, indicating that the lifetime of bacteria-derived DOC is much longer than the length estimated by the fluorescence. The role of photobleached FDOM derived from bacteria may be significant in the biogeochemical cycle at the surface layer.Ardelean, C.F., Israde-Alcántara, I., González-Hernández, R., Arroyo-Cabrales, J., Solis-Rosales, C., Rodríguez-Ceja, M., Pears, B.R., Watling, J., Macías-Quintero, J.I., Ocampo-Díaz, Y.Z.E., 2018. The Younger Dryas black mat from Ojo de Agua, a geoarchaeological site in Northeastern Zacatecas, Mexico. Quaternary International 463, 140-152. explorations in the desert of northeastern Zacatecas, in central-northern Mexico, revealed dozens of archaeological and geoarchaeological sites. One of them, Ojo de Agua, contains the remains of a Pleistocene spring-fed hydrographic system located at the southeastern end of a large elongated endorheic basin. The locality yielded a particularly dark, highly organic stratigraphic layer commonly known in the Americas as Black Mat (BM), exposed on the natural profiles of a creek, but not associated with cultural materials. Several radiocarbon assessments confirmed the formation of the Ojo de Agua Black Mat during the Younger Dryas chronozone, with ten calibrated results clustering between 12,700–12,100?cal BP. This multi-proxy study confirmed the peculiarity of the deposit and found similarities and differences with other contexts of Younger Dryas age. The Ojo de Agua Black Mat (stratum C2) is far richer in charcoal specks than the related strata, but lacks phytoliths, diatoms or ostracods. No further biological remains were found in it, except for intrusive capillary roots. Clearly water-lain in a shallow pond, the stratum qualifies as a clayey silt with an acidic-to-neutral pH. Rich in heavy metals and with high contents of titanium, the Ojo de Agua Black Mat yielded significant indicators of intense wildfires during the Younger Dryas, but produced no carbon spherules or nanodiamonds supposedly linked to the impact theory.Arkhipova, K., Skvortsov, T., Quinn, J.P., McGrath, J.W., Allen, C.C.R., Dutilh, B.E., McElarney, Y., Kulakov, L.A., 2018. Temporal dynamics of uncultured viruses: a new dimension in viral diversity. The Isme Journal 12, 199-211. work has vastly expanded the known viral genomic sequence space, but the seasonal dynamics of viral populations at the genome level remain unexplored. Here we followed the viral community in a freshwater lake for 1 year using genome-resolved viral metagenomics, combined with detailed analyses of the viral community structure, associated bacterial populations and environmental variables. We reconstructed 8950 complete and partial viral genomes, the majority of which were not persistent in the lake throughout the year, but instead continuously succeeded each other. Temporal analysis of 732 viral genus-level clusters demonstrated that one-fifth were undetectable at specific periods of the year. Based on host predictions for a subset of reconstructed viral genomes, we for the first time reveal three distinct patterns of host–pathogen dynamics, where the viruses may peak before, during or after the peak in their host’s abundance, providing new possibilities for modelling of their interactions. Time series metagenomics opens up a new dimension in viral profiling, which is essential to understand the full scale of viral diversity and evolution, and the ecological roles of these important factors in the global ecosystem.Arruda-Santos, R.H.d., Schettini, C.A.F., Yogui, G.T., Maciel, D.C., Zanardi-Lamardo, E., 2018. Sources and distribution of aromatic hydrocarbons in a tropical marine protected area estuary under influence of sugarcane cultivation. Science of The Total Environment 624, 935-944. estuary is a well preserved marine protected area (MPA) located on the northeastern coast of Brazil. Despite its current state, human activities in the watershed represent a potential threat to long term local preservation. Dissolved/dispersed aromatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) were investigated in water and sediments across the estuarine salt gradient. Concentration of aromatic hydrocarbons was low in all samples. According to results, aromatic hydrocarbons are associated to suspended particulate matter (SPM) carried to the estuary by river waters. An estuarine turbidity maximum (ETM) was identified in the upper estuary, indicating that both sediments and contaminants are trapped prior to an occasional export to the adjacent sea. PAHs distribution in sediments were associated with organic matter and mud content. Diagnostic ratios indicated pyrolytic processes as the main local source of PAHs that are probably associated with sugarcane burning and combustion engines. Low PAH concentrations probably do not cause adverse biological effects to the local biota although their presence indicate anthropogenic contamination and pressure on the Goiana estuary MPA.Ashtari Larki, S., Banashooshtari, H., Shokrollahzadeh Behbahani, H., Najafi-Marghmaleki, A., 2018. Effect of acid number of crude oil on oil recovery of smart water coupled with silica nanoparticles. Petroleum Science and Technology 36, 343-349. imbibition (SI) is one of the most important mechanisms in reservoir engineering. In order to activate of this mechanism completely in carbonate reservoirs, wettability of these oil wet rocks should be altered to water-wet. Multi-step spontaneous imbibition tests were designed and conducted in this study. Results indicated that mixture of smart water and nano silica could increase oil recovery up to 5 percent. Effect of acid number of crude oil on oil recovery of this mixture was investigated by using three samples of crude oil during SI tests: A (0.38?mg KOH/g), B (0.25?mg KOH/g) and C (0.18?mg KOH/g). Maximum oil recovery of SI tests was recorded for oil sample C which had lowest acid number. Ion analysis of imbibing fluids indicated sharp reductions in concentration of sulfate ion in each step of SI tests which confirmed occurrence of ion exchange mechanism in the rock surface of core samples.Asmala, E., Haraguchi, L., Jakobsen, H.H., Massicotte, P., Carstensen, J., 2018. Nutrient availability as major driver of phytoplankton-derived dissolved organic matter transformation in coastal environment. Biogeochemistry 137, 93-104. experiments were performed to examine the processing of fresh autochthonous dissolved organic matter (DOM) produced by coastal plankton communities in spring and autumn. The major driver of observed DOM dynamics was the seasonally variable inorganic nutrient status and characteristics of the initial bulk DOM, whereas the characteristics of the phytoplankton community seemed to have a minor role. Net accumulation of dissolved organic carbon (DOC) during the 18-days experiments was 3.4 and 9.2??mol?l?1 d?1 in P-limited spring and N-limited autumn, respectively. Bacterial bioassays revealed that the phytoplankton-derived DOC had surprisingly low proportions of biologically labile DOC, 12.6% (spring) and 17.5% (autumn). The optical characteristics of the DOM changed throughout the experiments, demonstrating continuous heterotrophic processing of the DOM pool. However, these temporal changes in optical characteristics of the DOM pool were not the same between seasons, indicating seasonally variable environmental drivers. Nitrogen and phosphorus availability is likely the main driver of these seasonal differences, affecting both phytoplankton extracellular release of DOM and its heterotrophic degradation by bacteria. These findings underline the complexity of the DOM production and consumption by the natural planktonic community, and show the importance of the prevailing environmental conditions regulating the DOM pathways.Athenaki, M., Gardeli, C., Diamantopoulou, P., Tchakouteu, S.S., Sarris, D., Philippoussis, A., Papanikolaou, S., 2018. Lipids from yeasts and fungi: physiology, production and analytical considerations. Journal of Applied Microbiology 124, 336-367. last years there has been a significant rise in the number of publications in the international literature that deal with the production of lipids by microbial sources (the ‘single cell oils; SCOs’ that are produced by the so-called ‘oleaginous’ micro-organisms). In the first part of the present review article, a general overview of the oleaginous micro-organisms (mostly yeasts, algae and fungi) and their potential upon the production of SCOs is presented. Thereafter, physiological and kinetic events related with the production of, mostly, yeast and fungal lipids when sugars and related substrates like polysaccharides, glycerol, etc. (the de novo lipid accumulation process) or hydrophobic substrates like oils and fats (the ex novo lipid accumulation process) were employed as microbial carbon sources, are presented and critically discussed. Considerations related with the degradation of storage lipid that had been previously accumulated inside the cells, are also presented. The interplay of the synthesis of yeast and fungal lipids with other intracellular (i.e. endopolysaccharides) or extracellular (i.e. citric acid) secondary metabolites synthesized is also presented. Finally, aspects related with the lipid extraction and lipidome analysis of the oleaginous micro-organisms are presented and critically discussed.Aurepatipan, N., Champreda, V., Kanokratana, P., Chitov, T., Bovonsombut, S., 2018. Assessment of bacterial communities and activities of thermotolerant enzymes produced by bacteria indigenous to oil-bearing sandstone cores for potential application in Enhanced Oil Recovery. Journal of Petroleum Science and Engineering 163, 295-302. Oil Recovery (EOR) is a potential approach to improve oil yield in petroleum production. In this research, indigenous bacterial communities residing in oil-bearing sandstone cores, taken from oil wells in Fang oil field in Northern Thailand, were investigated using the Ion Torrent PGM sequencing method. Based on 16rRNA gene sequences, Proteobacteria and Firmicutes were found to be the predominant phyla, and Bacillus, Sinomonas, Paenibacillus and Hydrogenophaga were the major genera. Thermotolerant lipase-esterase and urease producing bacteria were also isolated from the oil-bearing sandstone core samples. One lipase-esterase producing isolate, Bacillus licheniformis L3-2, produced the enzyme with highest activity at 80?°C. The enzyme retained up to 50% of its activity after incubation at 60?°C for 4?h. The results suggest the possibility of applying an in situ EOR approach using a combination of Enzyme Enhanced Oil Recovery (EEOR) and Microbial Enhanced Oil Recovery (MEOR) methods, with this lipase-esterase producing Bacillus licheniformis isolate, which is indigenous to one of the wells in this oil field.Ayranci, K., Harris, N.B., Dong, T., 2018. Sedimentological and ichnological characterization of the Middle to Upper Devonian Horn River Group, British Columbia, Canada: Insights into mudstone depositional conditions and processes below storm wave base. Journal of Sedimentary Research 88, 1-23. Middle and Upper Devonian Horn River Group in northeastern British Columbia, Canada, consists predominantly of organic-rich mudstones that are typically described as black shales. This stratigraphic unit has seen substantial exploration and development for natural gas during the last decade. Although black shales such as the Horn River Group have historically been interpreted as deposited in anoxic deep-water basins, detailed sedimentological and ichnological analyses of eleven Horn River Group cores indicate that the depositional conditions varied significantly with respect to paleoenvironments, redox conditions, and physical processes, resulting in distinctive sedimentary facies. This study integrates data on lithology and physical and biogenic sedimentary structures from detailed core descriptions combined with total-organic-carbon content to better understand depositional processes and conditions.Ten mudstone lithofacies and three lithofacies associations are identified. Massive mudstones and pyrite-rich mudstones display very rare planar lamination and graded beds and scarce bioturbation (BI 0–1), and are interpreted to represent anoxic waters, below storm wave base (SWB), with conditions of relatively low to moderate energy. Heterolithic, laminated, and more bioturbated lithofacies are interpreted to represent oxygenated waters below SWB with relatively high-energy conditions. Overall bioturbation intensity varies between moderate to intense (BI 3–6). Where these lithofacies are not intensely bioturbated, oxygenated lithofacies show combinations of well-preserved physical sedimentary structures, including horizontal parallel lamination, soft-sediment deformation, double mud drapes, graded beds, and current ripples. A third lithofacies association represents conditions intermediate between anoxic and oxygenated lithofacies associations, mainly based on local changes in the ichnological characteristics. These lithofacies show either intense or sparse bioturbation (BI 4–6 or BI 0–1, respectively) depending on the core location, possibly indicating local changes in the depositional conditions and processes (e.g., variations in the oxygen content and/or sedimentation rate). They can also be found in thick anoxic and oxygenated deposits. These lithofacies display intervals of faint lamination, amalgamated current ripples, and normally graded bedding.The cores collectively display significant spatial and stratigraphic heterogeneity in lithology, sedimentary structures, and bioturbation that are related to relative water depth, oxygen content, sediment input, and deep-water currents. We interpreted bioturbation intensity to vary mainly as a function of oxygen content related to proximity to the basin margin and sea–level fluctuations, although secondary stress conditions (e.g., nutrient content and sedimentation rate) may also be important. Unbioturbated and massive fabrics represent anoxic to dysoxic conditions. Current-generated structures are present, mainly in the central and distal parts of the basin, and are interpreted to represent the presence of contour currents. In the proximal parts of the basin, laminated and heterolithic units are more common and more bioturbated than in the central and distal basin. This study thus can provide significant insights into other shale basins that show similar lateral and vertical variations. Integration of multidisciplinary studies, particularly sedimentology, ichnology, and total organic carbon aids in understanding and modeling the complexity of these systems.Baioumy, H., Ahmed Salim, A.M., Arifin, M.H., Akmal Anuar, M.N., Musa, A.A., 2018. Geochemical characteristics of the Paleogene-Neogene coals and black shales from Malaysia: Implications for their origin and hydrocarbon potential. Journal of Natural Gas Science and Engineering 51, 73-88. coals are widespread in Malaysia, cover a wide age spectrum and are considered the source rock of hydrocarbons in Malaysia. However, they have not been studied systematically up to now. Moreover, the black shales associated with these coals were not taken into consideration in previous studies. Therefore, this study presents systematic inorganic and Rock-Eval analyses of the Paleogene-Neogene coals and their associated black shales to examine their origin, depositional environment and hydrocarbon potential.With the exception of coals from the Tanjong Formation, Sabah, the Paleogene-Neogene coals are characterized by very low ash yields and low concentrations of trace and rare earth elements including hazardous trace elements. The black shales are composed of quartz, illite, kaolinite and traces of pyrite in some samples. Al2O3/TiO2 ratios in the coals (6–62) and black shales (16–34) suggest a mixture of felsic and intermediate igneous rocks as sources for their detrital fractions, which is supported by the Zr-Ti binary plot. V/(V+Ni) ratios average between 0.8 and 0.7, V/Ni between 13.5 and 3, and Ni/Co between 1.7 and 3.8 for coal and black shale samples; respectively, indicating suboxic to anoxic depositional conditions for both groups of samples. Rock-Eval analysis indicates that coal and black shale samples contain mixed Type II–III kerogens, which suggest similar organic input from terrestrial high plants. The samples also contain immature to mature organic matter and can produce gas and oil. These characteristics along with the high TOC contents (very good to excellent) indicate that the Paleogene-Neogene coals and black shales are potential source rocks for oil and gas fields in Malaysia. The coals and black shales from different ages and localities were shown to have similar source area composition, climate conditions during their deposition, terrestrial organic input as well as suboxic to anoxic depositional conditions. However, coals and black shales from the early-middle Miocene Tanjong Formation exhibit higher Al2O3/SiO2 ratios than the rest of coals and black shales suggesting a prevalence of wetter climatic conditions during formation. In addition, coals and black shales from the early-middle Miocene Tanjong Formation and upper Pliocene Liang Formation show higher values for redox proxies such as V/(V+Ni), V/Ni, Ni/Co and Ce* compared with other formations, indicating the dominance of reducing conditions during the deposition of these formations.Bakhtiari Manesh, P., shahryari, S., Bemani, A., 2018. Utilization of Grid partitioning based Fuzzy inference system approach as a novel method to estimate solubility of hydrocarbons in carbon dioxide. Petroleum Science and Technology 36, 350-355. due to increasing demand for energy and declination of oil reservoir the researchers have been encouraged to investigate the enhancement of oil recovery (EOR) approaches. One of popular and wide applicable processes in EOR is carbon dioxide injection which is attractive for researchers and industries due to environmentally aspects, good efficiency in displacement and low cost. The carbon dioxide injection causes the hydrocarbons extracted from crude oil so the solubility of hydrocarbon in carbon dioxide which is one of the critical parameters affects this phenomenon becomes interesting topic for researchers. In the present work Grid partitioning based Fuzzy inference system approach as a new method for prediction of solubility of hydrocarbons in carbon dioxide as function of temperature, pressure and carbon number of alkane was applied. To show the accuracy of the model the coefficients of determination were determined as 0.9902 and 0.9584 for training and testing phases respectively.Balbi, A., 2018. The impact of the temporal distribution of communicating civilizations on their detectability. Astrobiology 18, 54-58. used a statistical model to investigate the detectability (defined by the requirement that causal contact has been initiated with us) of communicating civilizations within a volume of the Universe surrounding our location. If the civilizations are located in our galaxy, the detectability requirement imposes a strict constraint on their epoch of appearance and their communicating life span. This, in turn, implies that our ability to gather empirical evidence of the fraction of civilizations within range of detection strongly depends on the specific features of their temporal distribution. Our approach illuminates aspects of the problem that can escape the standard treatment based on the Drake equation. Therefore, it might provide the appropriate framework for future studies dealing with the evolutionary aspects of the search for extraterrestrial intelligence (SETI).Baled, H.O., Gamwo, I.K., Enick, R.M., McHugh, M.A., 2018. Viscosity models for pure hydrocarbons at extreme conditions: A review and comparative study. Fuel 218, 89-111. is a critical fundamental property required in many applications in the chemical and oil industries. In this review the performance of seven select viscosity models, representative of various predictive and correlative approaches, is discussed and evaluated by comparison to experimental data of 52 pure hydrocarbons including straight-chain alkanes, branched alkanes, cycloalkanes, and aromatics. This analysis considers viscosity data to extremely high-temperature, high-pressure conditions up to 573?K and 300?MPa. Unsatisfactory results are found, particularly at high pressures, with the Chung-Ajlan-Lee-Starling, Pedersen-Fredenslund, and Lohrenz-Bray-Clark models commonly used for oil reservoir simulation. If sufficient experimental viscosity data are readily available to determine model-specific parameters, the free volume theory and the expanded fluid theory models provide generally comparable results that are superior to those obtained with the friction theory, particularly at pressures higher than 100?MPa. Otherwise, the entropy scaling method by L?tgering-Lin and Gross is recommended as the best predictive model.Ba?ados, E., Venemans, B.P., Mazzucchelli, C., Farina, E.P., Walter, F., Wang, F., Decarli, R., Stern, D., Fan, X., Davies, F.B., Hennawi, J.F., Simcoe, R.A., Turner, M.L., Rix, H.-W., Yang, J., Kelson, D.D., Rudie, G.C., Winters, J.M., 2017. An 800-million-solar-mass black hole in a significantly neutral Universe at a redshift of 7.5. Nature 553, 473-476. are the most luminous non-transient objects known and as a result they enable studies of the Universe at the earliest cosmic epochs. Despite extensive efforts, however, the quasar ULAS J1120?+?0641 at redshift z?=?7.09 has remained the only one known at z?>?7 for more than half a decade>. Here we report observations of the quasar ULAS J134208.10?+?092838.61 (hereafter J1342?+?0928) at redshift z?=?7.54. This quasar has a bolometric luminosity of 4?×?1013 times the luminosity of the Sun and a black-hole mass of 8?×?108 solar masses. The existence of this supermassive black hole when the Universe was only 690 million years old—just five per cent of its current age—reinforces models of early black-hole growth that allow black holes with initial masses of more than about 104 solar masses or episodic hyper-Eddington accretion. We see strong evidence of absorption of the spectrum of the quasar redwards of the Lyman α emission line (the Gunn–Peterson damping wing), as would be expected if a significant amount (more than 10 per cent) of the hydrogen in the intergalactic medium surrounding J1342?+?0928 is neutral. We derive such a significant fraction of neutral hydrogen, although the exact fraction depends on the modelling. However, even in our most conservative analysis we find a fraction of more than 0.33 (0.11) at 68 per cent (95 per cent) probability, indicating that we are probing well within the reionization epoch of the Universe.Baniak, G.M., Kingsmith, K.G., 2018. Sedimentological and stratigraphic characterization of Cretaceous upper McMurray deposits in the southern Athabasca oil sands, Alberta, Canada. American Association of Petroleum Geologists Bulletin 102, 309-332. Lower Cretaceous McMurray Formation located in northeastern Alberta, Canada, is host to one of the largest bitumen resources in the world. In this paper, we provide an integrated sedimentological and stratigraphic analysis of the upper McMurray member located in the Pike and Jackfish project areas (Townships 73–76 and Ranges 4–7 W4M) of the southern Athabasca oil sands. Using core data, geophysical well logs, and seismic data, two main facies associations (embayment and fluvial) are evident. The embayment deposits were likely sourced by up-dip distributary channels and are commonly expressed in the subsurface as a series of coarsening-upward parasequences. The facies expressions in core range from bioturbated mudstones to wave-rippled sandstones. Noticeable, however, is the fact that there are areas where strata within the parasequences are instead substituted with sand, inclined heterolithic stratification, and mud. These deposits, in the form of fluvial channels with brackish-water overprint, occur at three different parasequence horizons within the study area. The removal of these embayment deposits is believed to be initiated, in part, by halite dissolution of the Middle Devonian Prairie Evaporite Formation deposits during upper McMurray deposition. Notably, the halite dissolution edge on the eastern half of the study area is believed to have created a subregional shelf–slope break during upper McMurray deposition. As such, the distributary channels likely re-equilibrated themselves to the slope created by the salt dissolution edge and thus proceeded to incise into previously deposited upper McMurray parasequence and underlying middle McMurray deposits.Bao, R., Strasser, M., McNichol, A.P., Haghipour, N., McIntyre, C., Wefer, G., Eglinton, T.I., 2018. Tectonically-triggered sediment and carbon export to the Hadal zone. Nature Communications 9, Article 121. in deep ocean trenches may contain crucial information on past earthquake history and constitute important sites of carbon burial. Here we present 14C data on bulk organic carbon (OC) and its thermal decomposition fractions produced by ramped pyrolysis/oxidation for a core retrieved from the >7.5?km-deep Japan Trench. High-resolution 14C measurements, coupled with distinctive thermogram characteristics of OC, reveal hemipelagic sedimentation interrupted by episodic deposition of pre-aged OC in the trench. Low δ13C values and diverse 14C ages of thermal fractions imply that the latter material originates from the adjacent margin, and the co-occurrence of pre-aged OC with intervals corresponding to known earthquake events implies tectonically triggered, gravity-flow-driven supply. We show that 14C ages of thermal fractions can yield valuable chronological constraints on sedimentary sequences. Our findings shed new light on links between tectonically driven sedimentological processes and marine carbon cycling, with implications for carbon dynamics in hadal environments.Barman, S.R., Banerjee, P., Mukhopadhayay, A., Das, P., 2017. Biodegradation of acenapthene and naphthalene by Pseudomonas mendocina: Process optimization, and toxicity evaluation. Journal of Environmental Chemical Engineering 5, 4803-4812. of poly aromatic hydrocarbons (PAHs) from waste water is a challenging task due to their hydrophobic and persistent nature. The present study investigated the efficiency of Pseudomonas mendocina for PAH biodegradation. Biodegradation of PAHs acenapthene and naphthalene was studied and the process was optimized with the Central Composite Design (CCD) feature of Response Surface Methodology (RSM). Toxicity analysis of the untreated and bio treated solutions were conducted on a comparative scale using Cicer arietinum (chickpea) in terms of oxidative stress, germination studies and biochemical parameters. Almost 98.8% and 98.6% degradation of acenaphthene and naphthalene respectively by Pseudomonas mendocina was recorded under RSM optimized conditions. Results of the toxicity analysis further indicated that the bio-treated solutions were fit to be reused or discharged, thereby establishing the potential of Pseudomonas mendocina for biodegradation applications in wide scale.Basha, W.A., Lamb, A.L., Zaki, M.E., Kandeel, W.A., Fares, N.H., Chamberlain, A.T., 2018. Dietary seasonal variations in the Medieval Nubian population of Kulubnarti as indicated by the stable isotope composition of hair. Journal of Archaeological Science: Reports 18, 161-168.: The island of Kulubnarti is located in Sudanese Nubia and contains two cemeteries, named R and S, which are dated to AD 550–800. In order to provide more detailed dietary information for this population and examine seasonality of diet, we analyzed the carbon isotope composition of hair samples from both cemeteries.Materials and methods: Forty seven separate hair samples from 8 adults, 29 adolescents, 7 infants and 3 individuals with unknown age were analyzed. Long hair samples were cut transversely and divided into 2?cm longitudinal segments, to examine temporal variations in the dietary carbon sources.Results: The average carbon isotope value for the whole population was ?17.95‰ (SD?=?1.8). A significant difference between the two cemeteries was found with variances in the amount of C4 dietary carbon sources consumed.Discussion: The results of hair isotope compositions concur with previous soft tissue investigations of Kulubnarti population which suggested that the dietary regimen contains a mix of C3 and C4 plant-based sources. A seasonal variation in diet can be inferred from the sequential hair segments of Kulubnarti individuals. These suggest a dietary transition between dominant C3 plant-based sources in winter to dominant C4 ones in summer with a small contribution of the non-harvested, alternative, crop.Batchelor, M.T., Burne, R.V., Henry, B.I., Li, F., Paul, J., 2018. A biofilm and organomineralisation model for the growth and limiting size of ooids. Scientific Reports 8, Article 559. are typically spherical sediment grains characterised by concentric layers encapsulating a core. There is no universally accepted explanation for ooid genesis, though factors such as agitation, abiotic and/or microbial mineralisation and size limitation have been variously invoked. Here we examine the possible influence of microbial organomineralisation on the formation of some naturally occurring ooids. We develop a mathematical model for ooid growth, inspired by work on avascular brain tumours, that assumes mineralisation in a biofilm to form a central core which then nucleates the progressive growth of concentric laminations. The model predicts a limiting size with the sequential width variation of growth rings comparing favourably with those observed in experimentally grown ooids generated from biomicrospheres. In reality, this model pattern may be complicated during growth by syngenetic aggrading neomorphism of the unstable mineral phase, followed by diagenetic recrystallisation that further complicates the structure. Our model provides a potential key to understanding the genetic archive preserved in the internal structures of some ooids.Beccaria, M., Mellors, T.R., Petion, J.S., Rees, C.A., Nasir, M., Systrom, H.K., Sairistil, J.W., Jean-Juste, M.-A., Rivera, V., Lavoile, K., Severe, P., Pape, J.W., Wright, P.F., Hill, J.E., 2018. Preliminary investigation of human exhaled breath for tuberculosis diagnosis by multidimensional gas chromatography – Time of flight mass spectrometry and machine learning. Journal of Chromatography B 1074-1075, 46-50. (TB) remains a global public health malady that claims almost 1.8 million lives annually. Diagnosis of TB represents perhaps one of the most challenging aspects of tuberculosis control. Gold standards for diagnosis of active TB (culture and nucleic acid amplification) are sputum-dependent, however, in up to a third of TB cases, an adequate biological sputum sample is not readily available. The analysis of exhaled breath, as an alternative to sputum-dependent tests, has the potential to provide a simple, fast, and non-invasive, and ready-available diagnostic service that could positively change TB detection. Human breath has been evaluated in the setting of active tuberculosis using thermal desorption-comprehensive two-dimensional gas chromatography–time of flight mass spectrometry methodology. From the entire spectrum of volatile metabolites in breath, three random forest machine learning models were applied leading to the generation of a panel of 46 breath features. The twenty-two common features within each random forest model used were selected as a set that could distinguish subjects with confirmed pulmonary M. tuberculosis infection and people with other pathologies than TB.Bereiter, B., Shackleton, S., Baggenstos, D., Kawamura, K., Severinghaus, J., 2018. Mean global ocean temperatures during the last glacial transition. Nature 553, 39-44. is known about the ocean temperature’s long-term response to climate perturbations owing to limited observations and a lack of robust reconstructions. Although most of the anthropogenic heat added to the climate system has been taken up by the ocean up until now, its role in a century and beyond is uncertain. Here, using noble gases trapped in ice cores, we show that the mean global ocean temperature increased by 2.57?±?0.24 degrees Celsius over the last glacial transition (20,000 to 10,000 years ago). Our reconstruction provides unprecedented precision and temporal resolution for the integrated global ocean, in contrast to the depth-, region-, organism- and season-specific estimates provided by other methods. We find that the mean global ocean temperature is closely correlated with Antarctic temperature and has no lead or lag with atmospheric CO2, thereby confirming the important role of Southern Hemisphere climate in global climate trends. We also reveal an enigmatic 700-year warming during the early Younger Dryas period (about 12,000 years ago) that surpasses estimates of modern ocean heat uptake.Bergauer, K., Fernandez-Guerra, A., Garcia, J.A.L., Sprenger, R.R., Stepanauskas, R., Pachiadaki, M.G., Jensen, O.N., Herndl, G.J., 2018. Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics. Proceedings of the National Academy of Sciences 115, E400-E408,.: Circumstantial evidence indicates that especially deep-ocean heterotrophic microbes rely on particulate organic matter sinking through the oceanic water column and being solubilized to dissolved organic matter (DOM) prior to utilization rather than on direct uptake of the vast pool of DOM in the deep ocean. Comparative metaproteomics allowed us to elucidate the vertical distribution and abundance of microbially mediated transport processes and thus the uptake of solutes throughout the oceanic water column. Taken together, our data suggest that, while the phylogenetic composition of the microbial community is depth stratified, the composition and substrate specificities of transporters considered in this study are ubiquitous while their relative abundance changes with depth. Abstract: The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ～39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm. Berggren, M., Klaus, M., Selvam, B.P., Str?m, L., Laudon, H., Jansson, M., Karlsson, J., 2018. Quality transformation of dissolved organic carbon during water transit through lakes: contrasting controls by photochemical and biological processes. Biogeosciences 15, 457-470. organic carbon (DOC) may be removed, transformed, or added during water transit through lakes, resulting in changes in DOC composition and pigmentation (color). However, the process-based understanding of these changes is incomplete, especially for headwater lakes. We hypothesized that because heterotrophic bacteria preferentially consume noncolored DOC, while photochemical processing removes colored fractions, the overall changes in DOC color upon water passage through a lake depend on the relative importance of these two processes, accordingly. To test this hypothesis we combined laboratory experiments with field studies in nine boreal lakes, assessing both the relative importance of different DOC decay processes (biological or photochemical) and the loss of color during water transit time (WTT) through the lakes. We found that influence from photo-decay dominated changes in DOC quality in the epilimnia of relatively clear headwater lakes, resulting in systematic and selective net losses of colored DOC. However, in highly pigmented brown-water lakes (absorbance at 420?nm??>?7?m?1) biological processes dominated, and there was no systematic relationship between color loss and WTT. Moreover, in situ data and dark experiments supported our hypothesis on the selective microbial removal of nonpigmented DOC, mainly of low molecular weight, leading to persistent water color in these highly colored lakes. Our study shows that brown headwater lakes may not conform to the commonly reported pattern of the selective removal of colored constituents in freshwaters, as DOC can show a sustained degree of pigmentation upon transit through these lakes.Bergmann, K.D., Finnegan, S., Creel, R., Eiler, J.M., Hughes, N.C., Popov, L.E., Fischer, W.W., 2018. A paired apatite and calcite clumped isotope thermometry approach to estimating Cambro-Ordovician seawater temperatures and isotopic composition. Geochimica et Cosmochimica Acta 224, 18-41. secular increase in δ18O values of both calcitic and phosphatic marine fossils through early Phanerozoic time suggests either that (1) early Paleozoic surface temperatures were high, in excess of 40?°C (tropical MAT), (2) the δ18O value of seawater has increased by 7–8‰ VSMOW through Paleozoic time, or (3) diagenesis has altered secular trends in early Paleozoic samples. Carbonate clumped isotope analysis, in combination with petrographic and elemental analysis, can deconvolve fluid composition from temperature effects and therefore determine which of these hypotheses best explain the secular δ18O increase. Clumped isotope measurements of a suite of calcitic and phosphatic marine fossils from late Cambrian- to Middle-late Ordovician-aged strata–the first paired fossil study of its kind–document tropical sea surface temperatures near modern temperatures (26–38?°C) and seawater oxygen isotope ratios similar to today’s ratios.Beulig, F., R?y, H., Glombitza, C., J?rgensen, B.B., 2018. Control on rate and pathway of anaerobic organic carbon degradation in the seabed. Proceedings of the National Academy of Sciences 115, 367-372.: The subsurface seabed is a great anaerobic bioreactor where organic matter deposited from the ocean’s water column is slowly being degraded by microorganisms. It is uncertain how rates of organic matter degradation progress through different geochemical zones, and the deep production of methane and CO2 in the global seabed therefore remains poorly constrained. With highly depth-resolved analyses of geochemistry and microbial activities, we demonstrate that rates of organic matter degradation decrease continuously with sediment age, irrespective of the prevailing redox zonation and associated changes in the degradation pathway. Moreover, our results show that the microbial food chain leading to methane does not proceed directly through the general key intermediate acetate, but rather through an additional, as of yet unidentified, syntrophic step. Abstract: The degradation of organic matter in the anoxic seabed proceeds through a complex microbial network in which the terminal steps are dominated by oxidation with sulfate or conversion into methane and CO2. The controls on pathway and rate of the degradation process in different geochemical zones remain elusive. Radiotracer techniques were used to perform measurements of sulfate reduction, methanogenesis, and acetate oxidation with unprecedented sensitivity throughout Holocene sediment columns from the Baltic Sea. We found that degradation rates transition continuously from the sulfate to the methane zone, thereby demonstrating that terminal steps do not exert feedback control on upstream hydrolytic and fermentative processes, as previously suspected. Acetate was a key intermediate for carbon mineralization in both zones. However, acetate was not directly converted into methane. Instead, an additional subterminal step converted acetate to CO2 and reducing equivalents, such as H2, which then fed autotrophic reduction of CO2 to methane. Bischoff, N., Mikutta, R., Shibistova, O., Dohrmann, R., Herdtle, D., Gerhard, L., Fritzsche, F., Puzanov, A., Silanteva, M., Grebennikova, A., Guggenberger, G., 2018. Organic matter dynamics along a salinity gradient in Siberian steppe soils. Biogeosciences 15, 13-29. soils will become more frequent in the next decades as arid and semiarid ecosystems are predicted to expand as a result of climate change. Nevertheless, little is known about organic matter (OM) dynamics in these soils, though OM is crucial for soil fertility and represents an important carbon sink. We aimed at investigating OM dynamics along a salinity and sodicity gradient in the soils of the southwestern Siberian Kulunda steppe (Kastanozem, non-sodic Solonchak, Sodic Solonchak) by assessing the organic carbon (OC) stocks, the quantity and quality of particulate and mineral-associated OM in terms of non-cellulosic neutral sugar contents and carbon isotopes (δ13C, 14C activity), and the microbial community composition based on phospholipid fatty acid (PLFA) patterns. Aboveground biomass was measured as a proxy for plant growth and soil OC inputs. Our hypotheses were that (i) soil OC stocks decrease along the salinity gradient, (ii) the proportion and stability of particulate OM is larger in salt-affected Solonchaks compared to non-salt-affected Kastanozems, (iii) sodicity reduces the proportion and stability of mineral-associated OM, and (iv) the fungi?:?bacteria ratio is negatively correlated with salinity. Against our first hypothesis, OC stocks increased along the salinity gradient with the most pronounced differences between topsoils. In contrast to our second hypothesis, the proportion of particulate OM was unaffected by salinity, thereby accounting for only ?<??10?% in all three soil types, while mineral-associated OM contributed ?>??90?%. Isotopic data (δ13C, 14C activity) and neutral sugars in the OM fractions indicated a comparable degree of OM transformation along the salinity gradient and that particulate OM was not more persistent under saline conditions. Our third hypothesis was also rejected, as Sodic Solonchaks contained more than twice as much mineral-bound OC than the Kastanozems, which we ascribe to the flocculation of OM and mineral components under higher ionic strength conditions. Contrary to the fourth hypothesis, the fungi?:?bacteria ratio in the topsoils remained fairly constant along the salinity gradient. A possible explanation for why our hypotheses were not affirmed is that soil moisture covaried with salinity along the transect, i.e., the Solonchaks were generally wetter than the Kastanozems. This might cause comparable water stress conditions for plants and microorganisms, either due to a low osmotic or a low matric potential and resulting in (i) similar plant growth and hence soil OC inputs along the transect, (ii) a comparable persistence of particulate OM, and (iii) unaffected fungi?:?bacteria ratios. We conclude that salt-affected soils contribute significantly to the OC storage in the semiarid soils of the Kulunda steppe, while most of the OC is associated with minerals and is therefore effectively sequestered in the long term.Blum, P.W., Hershey, A.E., Tsui, M.T.-K., Hammerschmidt, C.R., Agather, A.M., 2018. Methylmercury and methane production potentials in North Carolina Piedmont stream sediments. Biogeochemistry 137, 181-195. mercury (MeHg) can be produced by all microbes possessing the genes hgcA and hgcB, which can include sulfate-reducing bacteria (SRB), iron-reducing bacteria (FeRB), methane-producing archaea (MPA), and other anaerobic microbes. These microbial groups compete for substrates, including hydrogen and acetate. When sulfate is in excess, SRB can outcompete other anaerobic microbes. However, low concentrations of sulfate, which often occur in stream sediments, are thought to reduce the relative importance of SRB. Although SRB are regarded as the primary contributors of MeHg in many aquatic environments, their significance may not be universal, and stream sediments are poorly studied with respect to microbial Hg methylation. We evaluated suppression of methanogenesis by SRB and the potential contributions from SRB, MPA and other MeHg producing microbes (including FeRB) to the production of MeHg in stream sediments from the North Carolina Piedmont region. Lower methanogenesis rates were observed when SRB were not inhibited, however, application of a sulfate-reduction inhibitor stimulated methanogenesis. Greater MeHg production occurred when SRB were active. Other MeHg producing microbes (i.e., FeRB) contributed significantly less MeHg production than SRB. MPA produced MeHg in negligible amounts. Our results suggest that SRB are responsible for the majority of MeHg production and suppress methanogenesis in mid-order stream sediments, similar to other freshwater sediments. Further investigation is needed to evaluate the generality of these findings to streams in other regions, and to determine the mechanisms regulating sulfate and electron acceptor availability and other potential factors governing Hg methylation and methane production in stream sediments.Bodewits, D., Farnham, T.L., Kelley, M.S.P., Knight, M.M., 2018. A rapid decrease in the rotation rate of comet 41P/Tuttle–Giacobini–Kresák. Nature 553, 186-188. outgassing can produce torques that change the spin state of the cometary nucleus, which in turn influences the evolution and lifetime of the comet. If these torques increase the rate of rotation to the extent that centripetal forces exceed the material strength of the nucleus, the comet can fragment. Torques that slow down the rotation can cause the spin state to become unstable, but if the torques persist the nucleus can eventually reorient itself and the rotation rate can increase again. Simulations predict that most comets go through a short phase of rapid changes in spin state, after which changes occur gradually over longer times. Here we report observations of comet 41P/Tuttle–Giacobini–Kresák during its close approach to Earth (0.142 astronomical units, approximately 21 million kilometres, on 1 April 2017) that reveal a rapid decrease in rotation rate. Between March and May 2017, the apparent rotation period of the nucleus increased from 20 hours to more than 46 hours—a rate of change of more than an order of magnitude larger than has hitherto been measured. This phenomenon must have been caused by the gas emission from the comet aligning in such a way that it produced an anomalously strong torque that slowed the spin rate of the nucleus. The behaviour of comet 41P/Tuttle–Giacobini–Kresák suggests that it is in a distinct evolutionary state and that its rotation may be approaching the point of instability.Bokhart, M.T., Nazari, M., Garrard, K.P., Muddiman, D.C., 2018. MSiReader v1.0: Evolving open-source mass spectrometry imaging software for targeted and untargeted analyses. Journal of The American Society for Mass Spectrometry 29, 8-16. major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time.Bosshart, N.W., Azzolina, N.A., Ayash, S.C., Peck, W.D., Gorecki, C.D., Ge, J., Jiang, T., Dotzenrod, N.W., 2018. Quantifying the effects of depositional environment on deep saline formation CO2 storage efficiency and rate. International Journal of Greenhouse Gas Control 69, 8-19. an effort to reduce carbon dioxide (CO2) emissions from large stationary sources, carbon capture and storage (CCS) is being investigated as one approach in a portfolio of greenhouse gas (GHG) reduction strategies. This work assesses CO2 storage rates and efficiency of saline formations classified by interpreted depositional environment at the regional scale over a 100-year time frame. The focus of this study was placed on developing results applicable to future commercial-scale CO2 storage operations in which an array of injection wells would be used to optimize storage in saline formations. The results of this work suggest future investigations of prospective storage resource in closed or semiclosed formations that may focus less heavily on interpretation of depositional processes. However, the results illustrate the relative importance of depositional environment, aquifer depth, structural geometry, and boundary conditions on the rate of CO2 storage in closed or semiclosed systems.Botha, J., Mizrachi, E., Myburg, A.A., Cowan, D.A., 2018. Carbohydrate active enzyme domains from extreme thermophiles: components of a modular toolbox for lignocellulose degradation. Extremophiles 22, 1-12. biomass is a promising feedstock for the manufacture of biodegradable and renewable bioproducts. However, the complex lignocellulosic polymeric structure of woody tissue is difficult to access without extensive industrial pre-treatment. Enzyme processing of partly depolymerised biomass is an established technology, and there is evidence that high temperature (extremely thermophilic) lignocellulose degrading enzymes [carbohydrate active enzymes (CAZymes)] may enhance processing efficiency. However, wild-type thermophilic CAZymes will not necessarily be functionally optimal under industrial pre-treatment conditions. With recent advances in synthetic biology, it is now potentially possible to build CAZyme constructs from individual protein domains, tailored to the conditions of specific industrial processes. In this review, we identify a ‘toolbox’ of thermostable CAZyme domains from extremely thermophilic organisms and highlight recent advances in CAZyme engineering which will allow for the rational design of CAZymes tailored to specific aspects of lignocellulose digestion.Boysen, A.K., Heal, K.R., Carlson, L.T., Ingalls, A.E., 2017. Best-matched internal standard normalization in liquid chromatography–mass spectrometry metabolomics applied to environmental samples. Analytical Chemistry 90, 1363-1369. goal of metabolomics is to measure the entire range of small organic molecules in biological samples. In liquid chromatography–mass spectrometry-based metabolomics, formidable analytical challenges remain in removing the nonbiological factors that affect chromatographic peak areas. These factors include sample matrix-induced ion suppression, chromatographic quality, and analytical drift. The combination of these factors is referred to as obscuring variation. Some metabolomics samples can exhibit intense obscuring variation due to matrix-induced ion suppression, rendering large amounts of data unreliable and difficult to interpret. Existing normalization techniques have limited applicability to these sample types. Here we present a data normalization method to minimize the effects of obscuring variation. We normalize peak areas using a batch-specific normalization process, which matches measured metabolites with isotope-labeled internal standards that behave similarly during the analysis. This method, called best-matched internal standard (B-MIS) normalization, can be applied to targeted or untargeted metabolomics data sets and yields relative concentrations. We evaluate and demonstrate the utility of B-MIS normalization using marine environmental samples and laboratory grown cultures of phytoplankton. In untargeted analyses, B-MIS normalization allowed for inclusion of mass features in downstream analyses that would have been considered unreliable without normalization due to obscuring variation. B-MIS normalization for targeted or untargeted metabolomics is freely available at <, A.L., Goordial, J., Sun, H.J., Whyte, L.G., Slater, G.F., 2018. Variability in carbon uptake and (re)cycling in Antarctic cryptoendolithic microbial ecosystems demonstrated through radiocarbon analysis of organic biomarkers. Geobiology 16, 62-79. lichens and cyanobacteria living in porous sandstone in the high-elevation McMurdo Dry Valleys are purported to be among the slowest growing organisms on Earth with cycles of death and regrowth on the order of 103–104 years. Here, organic biomarker and radiocarbon analysis were used to better constrain ages and carbon sources of cryptoendoliths in University Valley (UV; 1,800 m.a.s.l) and neighboring Farnell Valley (FV; 1,700 m.a.s.l). Δ14C was measured for membrane component phospholipid fatty acids (PLFA) and glycolipid fatty acids, as well as for total organic carbon (TOC). PLFA concentrations indicated viable cells comprised a minor (<0.5%) component of TOC. TOC Δ14C values ranged from ?272‰ to ?185‰ equivalent to calibrated ages of 1,100–2,550 years old. These ages may be the result of fractional preservation of biogenic carbon and/or sudden large-scale community death and extended period(s) of inactivity prior to slow recolonization and incorporation of 14C-depleted fossil material. PLFA Δ14C values were generally more modern than the corresponding TOC and varied widely between sites; the FV PLFA Δ14C value (+40‰) was consistent with modern atmospheric CO2, while UV values ranged from ?199‰ to ?79‰ (calibrated ages of 1,665–610 years). The observed variability in PLFA Δ14C depletions is hypothesized to reflect variations in the extent of fixation of modern atmospheric CO2 and the preservation and recycling of older organic carbon by the community in various stages of sandstone recolonization. PLFA profiles and microbial community compositions as determined by molecular genetic characterizations and microscopy differed between the two valleys (e.g., predominance of biomarker 18:2 [>50%] in FV compared to UV), representing microbial communities that may reflect distinct stages of sandstone recolonization and/or environmental conditions. It is thus proposed that Dry Valley cryptoendolithic microbial communities are faster growing than previously estimated.Bravo-Linares, C., Schuller, P., Castillo, A., Ovando-Fuentealba, L., Mu?oz-Arcos, E., Alarcón, O., de los Santos-Villalobos, S., Cardoso, R., Muniz, M., Meigikos dos Anjos, R., Bustamante-Ortega, R., Dercon, G., 2018. First use of a compound-specific stable isotope (CSSI) technique to trace sediment transport in upland forest catchments of Chile. Science of The Total Environment 618, 1114-1124. degradation is a problem affecting the sustainability of commercial forest plantations. The identification of critical areas prone to erosion can assist this activity to better target soil conservation efforts. Here we present the first use of the carbon-13 signatures of fatty acids (C14 to C24) in soil samples for spatial and temporal tracing of sediment transport in river bodies of upland commercial forest catchments in Chile. This compound-specific stable isotope (CSSI) technique was tested as a fingerprinting approach to determine the degree of soil erosion in pre-harvested forest catchments with surface areas ranging from 12 to 40 ha. For soil apportionment a mixing model based on a Bayesian inference framework was used (CSSIAR v.2.0). Approximately four potential sediment sources were used for the calculations of all of the selected catchments. Unpaved forestry roads were shown to be the main source of sediment deposited at the outlet of the catchments (30–75%). Furthermore, sampling along the stream channel demonstrated that sediments were mainly comprised of sediment coming from the unpaved roads in the upper part of the catchments (74–98%). From this it was possible to identify the location and type of primary land use contributing to the sediment delivered at the outlet of the catchments. The derived information will allow management to focus efforts to control or mitigate soil erosion by improving the runoff features of the forest roads. The use of this CSSI technique has a high potential to help forestry managers and decision makers to evaluate and mitigate sources of soil erosion in upland forest catchments. It is important to highlight that this technique can also be a good complement to other soil erosion assessment and geological fingerprinting techniques, especially when attempting to quantify (sediment loads) and differentiate which type of land use most contributes to sediment accumulation.Breitburg, D., Levin, L.A., Oschlies, A., Grégoire, M., Chavez, F.P., Conley, D.J., Gar?on, V., Gilbert, D., Gutiérrez, D., Isensee, K., Jacinto, G.S., Limburg, K.E., Montes, I., Naqvi, S.W.A., Pitcher, G.C., Rabalais, N.N., Roman, M.R., Rose, K.A., Seibel, B.A., Telszewski, M., Yasuhara, M., Zhang, J., 2018. Declining oxygen in the global ocean and coastal waters. Science 359, eaam7240.. Oxygen is fundamental to life. Not only is it essential for the survival of individual animals, but it regulates global cycles of major nutrients and carbon. The oxygen content of the open ocean and coastal waters has been declining for at least the past half-century, largely because of human activities that have increased global temperatures and nutrients discharged to coastal waters. These changes have accelerated consumption of oxygen by microbial respiration, reduced solubility of oxygen in water, and reduced the rate of oxygen resupply from the atmosphere to the ocean interior, with a wide range of biological and ecological consequences. Further research is needed to understand and predict long-term, global- and regional-scale oxygen changes and their effects on marine and estuarine fisheries and ecosystems.Structured AbstractBackground: Oxygen concentrations in both the open ocean and coastal waters have been declining since at least the middle of the 20th century. This oxygen loss, or deoxygenation, is one of the most important changes occurring in an ocean increasingly modified by human activities that have raised temperatures, CO2 levels, and nutrient inputs and have altered the abundances and distributions of marine species. Oxygen is fundamental to biological and biogeochemical processes in the ocean. Its decline can cause major changes in ocean productivity, biodiversity, and biogeochemical cycles. Analyses of direct measurements at sites around the world indicate that oxygen-minimum zones in the open ocean have expanded by several million square kilometers and that hundreds of coastal sites now have oxygen concentrations low enough to limit the distribution and abundance of animal populations and alter the cycling of important nutrients.Advances: In the open ocean, global warming, which is primarily caused by increased greenhouse gas emissions, is considered the primary cause of ongoing deoxygenation. Numerical models project further oxygen declines during the 21st century, even with ambitious emission reductions. Rising global temperatures decrease oxygen solubility in water, increase the rate of oxygen consumption via respiration, and are predicted to reduce the introduction of oxygen from the atmosphere and surface waters into the ocean interior by increasing stratification and weakening ocean overturning circulation.In estuaries and other coastal systems strongly influenced by their watershed, oxygen declines have been caused by increased loadings of nutrients (nitrogen and phosphorus) and organic matter, primarily from agriculture; sewage; and the combustion of fossil fuels. In many regions, further increases in nitrogen discharges to coastal waters are projected as human populations and agricultural production rise. Climate change exacerbates oxygen decline in coastal systems through similar mechanisms as those in the open ocean, as well as by increasing nutrient delivery from watersheds that will experience increased precipitation.Expansion of low-oxygen zones can increase production of N2O, a potent greenhouse gas; reduce eukaryote biodiversity; alter the structure of food webs; and negatively affect food security and livelihoods. Both acidification and increasing temperature are mechanistically linked with the process of deoxygenation and combine with low-oxygen conditions to affect biogeochemical, physiological, and ecological processes. However, an important paradox to consider in predicting large-scale effects of future deoxygenation is that high levels of productivity in nutrient-enriched coastal systems and upwelling areas associated with oxygen-minimum zones also support some of the world’s most prolific fisheries.Outlook: Major advances have been made toward understanding patterns, drivers, and consequences of ocean deoxygenation, but there is a need to improve predictions at large spatial and temporal scales important to ecosystem services provided by the ocean. Improved numerical models of oceanographic processes that control oxygen depletion and the large-scale influence of altered biogeochemical cycles are needed to better predict the magnitude and spatial patterns of deoxygenation in the open ocean, as well as feedbacks to climate. Developing and verifying the next generation of these models will require increased in situ observations and improved mechanistic understanding on a variety of scales. Models useful for managing nutrient loads can simulate oxygen loss in coastal waters with some skill, but their ability to project future oxygen loss is often hampered by insufficient data and climate model projections on drivers at appropriate temporal and spatial scales. Predicting deoxygenation-induced changes in ecosystem services and human welfare requires scaling effects that are measured on individual organisms to populations, food webs, and fisheries stocks; considering combined effects of deoxygenation and other ocean stressors; and placing an increased research emphasis on developing nations. Reducing the impacts of other stressors may provide some protection to species negatively affected by low-oxygen conditions. Ultimately, though, limiting deoxygenation and its negative effects will necessitate a substantial global decrease in greenhouse gas emissions, as well as reductions in nutrient discharges to coastal waters.The global map indicates coastal sites where anthropogenic nutrients have exacerbated or caused O2 declines to <2 mg liter?1 (<63 μmol liter?1) (red dots), as well as ocean oxygen-minimum zones at 300 m of depth (blue shaded regions). [Map created from data provided by R. Diaz, updated by members of the GO2NE network, and downloaded from the World Ocean Atlas 2009].Editor's summary. Beneath the waves, oxygen disappears. As plastic waste pollutes the oceans and fish stocks decline, unseen below the surface another problem grows: deoxygenation. Breitburg et al. review the evidence for the downward trajectory of oxygen levels in increasing areas of the open ocean and coastal waters. Rising nutrient loads coupled with climate change—each resulting from human activities—are changing ocean biogeochemistry and increasing oxygen consumption. This results in destabilization of sediments and fundamental shifts in the availability of key nutrients. In the short term, some compensatory effects may result in improvements in local fisheries, such as in cases where stocks are squeezed between the surface and elevated oxygen minimum zones. In the longer term, these conditions are unsustainable and may result in ecosystem collapses, which ultimately will cause societal and economic harm.Brenner, D.C., Passey, B.H., Stolper, D.A., 2018. Influence of water on clumped-isotope bond reordering kinetics in calcite. Geochimica et Cosmochimica Acta 224, 42-63. self-diffusion in calcite and many other minerals is considerably faster under wet conditions relative to dry conditions. Here we investigate whether this “water effect” also holds true for solid-state isotope exchange reactions that alter the abundance of carbonate groups with multiple rare isotopes (‘clumped’ isotope groups) via the process of solid-state bond reordering. We present clumped-isotope reordering rates for optical calcite heated under wet, high-pressure (100?MPa) conditions. We observe only modest increases in reordering rates under such conditions compared with rates for the same material reacted in dry CO2 under low-pressure conditions. Activation energies under wet, high-pressure conditions are indistinguishable from those for dry, low-pressure conditions, while rate constants are resolvably higher (up to ～3 times) for wet, high-pressure relative to dry, low-pressure conditions in most of our interpretations of experimental results. This contrasts with the water effect for oxygen self-diffusion in calcite, which is associated with lower activation energies, and diffusion coefficients that are ≥103 times higher compared with dry (pure CO2) conditions in the temperature range of this study (385–450?°C). The water effect for clumped-isotopes leads to calculated apparent equilibrium temperatures (“blocking temperatures”) for typical geological cooling rates that are only a few degrees higher than those for dry conditions, while O self-diffusion blocking temperatures in calcite grains are ～150–200?°C lower in wet conditions compared with dry conditions. Since clumped-isotope reordering is a distributed process that occurs throughout the mineral volume, our clumped-isotope results support the suggestion of Labotka et al. (2011) that the water effect in calcite does not involve major changes in bulk (volume) diffusivity, but rather is primarily a surface phenomenon that facilitates oxygen exchange between the calcite surface and external fluids. We explore the mechanism(s) by which clumped isotope reordering rates may be modestly increased under wet, high-pressure conditions, including changes in defect concentrations in the near surface environment due to reactions at the water–mineral interface, and lattice deformation resulting from pressurization of samples.Brüchert, V., Br?der, L., Sawicka, J.E., Tesi, T., Joye, S.P., Sun, X., Semiletov, I.P., Samarkin, V.A., 2018. Carbon mineralization in Laptev and East Siberian sea shelf and slope sediment. Biogeosciences 15, 471-490. Siberian Arctic Sea shelf and slope is a key region for the degradation of terrestrial organic material transported from the organic-carbon-rich permafrost regions of Siberia. We report on sediment carbon mineralization rates based on O2 microelectrode profiling; intact sediment core incubations; 35S-sulfate tracer experiments; pore-water dissolved inorganic carbon (DIC); δ13CDIC; and iron, manganese, and ammonium concentrations from 20 shelf and slope stations. This data set provides a spatial overview of sediment carbon mineralization rates and pathways over large parts of the outer Laptev and East Siberian Arctic shelf and slope and allows us to assess degradation rates and efficiency of carbon burial in these sediments. Rates of oxygen uptake and iron and manganese reduction were comparable to temperate shelf and slope environments, but bacterial sulfate reduction rates were comparatively low. In the topmost 50?cm of sediment, aerobic carbon mineralization dominated degradation and comprised on average 84?% of the depth-integrated carbon mineralization. Oxygen uptake rates and anaerobic carbon mineralization rates were higher in the eastern East Siberian Sea shelf compared to the Laptev Sea shelf. DIC?∕?NH4+ ratios in pore waters and the stable carbon isotope composition of remineralized DIC indicated that the degraded organic matter on the Siberian shelf and slope was a mixture of marine and terrestrial organic matter. Based on dual end-member calculations, the terrestrial organic carbon contribution varied between 32 and 36?%, with a higher contribution in the Laptev Sea than in the East Siberian Sea. Extrapolation of the measured degradation rates using isotope end-member apportionment over the outer shelf of the Laptev and East Siberian seas suggests that about 16?Tg?C?yr?1 is respired in the outer shelf seafloor sediment. Of the organic matter buried below the oxygen penetration depth, between 0.6 and 1.3?Tg?C?yr?1 is degraded by anaerobic processes, with a terrestrial organic carbon contribution ranging between 0.3 and 0.5?Tg?yr?1.Bucha, M., J?drysek, M.-O., Kufka, D., Ple?niak, ?., Marynowski, L., Kubiak, K., B?aszczyk, M., 2018. Methanogenic fermentation of lignite with carbon-bearing additives, inferred from stable carbon and hydrogen isotopes. International Journal of Coal Geology 186, 65-79. from the Konin area (Poland) was used as a substrate for incubation experiments to evaluate its potential for simulation of biogenic methane production. Lignite was incubated with a bacterial inoculum enriched from lake sediments, mineral media, and various supplemental components for microbial life. Additives, such as acetate, methanol, glucose, nutrient broth, and yeast extract, can significantly increase methane production. At the same time, biodegradation of these additional carbon sources leads to overestimation of methane yield. In this paper, selected geochemical properties (total organic carbon content; stable isotopic composition of carbon δ13C) were analyzed in order to evaluate changes in the organic matter of fermented lignite. Stable isotope analysis of carbon and hydrogen was applied in order to identify sources of methane and carbon dioxide formation. TOC decreased in range from 1.4 to 9.6% in lignite after fermentation. The δ13C value of lignite used in the experiments (?25.2‰) decreased after incubation to values in range from ?27.1 to ?26.2‰. Methane yield per g of TOC (lignite + organic carbon in nutrients) ranged from 0.47 to 2.60 mM/g. Glucose, acetate, and methanol significantly increased biogas production. Nutrient broth and yeast extract were not a source of organic carbon for methane formation, but their presence enhanced biogas production. Values of δ13C(CH4) and δ2H(CH4) across incubation conditions ranged from ?70.2 to ?24.2‰ and from ?396.6 to ?290.5‰, respectively. Values of δ13C(CO2) ranged from –55.2 to 45.0‰. The high level of variation of δ13C(CH4) and δ13C(CO2) suggests mixing of gases from different carbon sources during incubation, but can also be caused by mixing of metabolic modes by the microbial community. Understanding the δ2H(CH4) variation is even more difficult than the δ13C(CH4) and δ13C(CO2), since many substrates often contain exchangeable hydrogen (e.g. in water, lignite, and elements of nutrients). The combined values of δ13C(CH4) and δ13C(CO2) suggests that the dominant methanogenesis pathway in our experiments may be acetate fermentation. In biodegraded lignite, high relative concentrations of p-cresol (one of the most abundant in the sample) and n-(2-acetylphenyl)formamide were identified. These compounds are most probably lignin decomposition products, or, in the case of the latter, bacterial by-products or remnants. Organic compounds with low molecular weights, n-alkanes, and biomolecules including ferruginol, sugiol, and 6,7-dehydroferruginol, as well as amyrins and tocopherols, were preferentially degraded. The potential for methane production from lignite spiked with carbon-bearing additives is at least one magnitude lower than that from agricultural wastes. The lignite utilization as the single substrate for methanogenic fermentation is economically unprofitable. Mixing of lignite with the external substrate as biomass may be an alternative for consideration and future research.Buchberger, A.R., DeLaney, K., Johnson, J., Li, L., 2018. Mass spectrometry imaging: A review of emerging advancements and future insights. Analytical Chemistry 90, 240-265. spectrometry imaging (MSI) is a powerful tool that enables untargeted investigations into the spatial distribution of molecular species in a variety of samples. It has the capability to image thousands of molecules, such as metabolites, lipids, peptides, proteins, and glycans, in a single experiment without labeling. The combination of information gained from mass spectrometry (MS) and visualization of spatial distributions in thin sample sections makes this a valuable chemical analysis tool for biological specimen characterization. A summary workflow is depicted in Figure 1. After minimal but careful sample preparation, the general setup of an MSI experiment involves defining an (x, y) grid over the surface of the sample, with the grid area chosen by the user. The mass spectrometer then ionizes the molecules on the surface of the sample and collects a mass spectrum at each pixel on the section with the resulting spatial resolution defined by the pixel size. After collecting the spectra, computational software can be used to select an individual mass-to-charge (m/z) value, and the intensity of the m/z is extracted from each pixel’s spectrum. These intensities are then combined into a heat map image depicting the relative distribution of that m/z value throughout the sample’s surface. In order to determine the identity of a specific m/z value, tandem MS (MS/MS) fragmentation can be performed on ions from each pixel, and the fragments can be used to piece together the structure of the unknown molecule. Otherwise, the molecule can be identified based on its intact mass by accurate mass matching to databases of known molecules within a certain mass error range.With the numerous technological advances in recent years, MSI is becoming a more established tool in clinical practice and the pharmaceutical industry. Advances include improvements in reproducible sample preparation to ensure reliable interpretation of data and instrumentation that allows for high acquisition speeds and enhanced spatial resolution improving throughput and depth. The credibility of MSI experiments has further been enhanced by the development of methods for absolute quantitation of detected molecules. To help with large computational endeavors, statistical workflows and machine learning algorithms have been implemented to handle the large imaging data sets being produced with modern instrumentation. MSI can also be combined with other complementary imaging modalities, such as microscopy, Raman spectroscopy, and MRI, to strengthen any biological conclusions. With both hardware and software improvements, 3-dimensional (3D) renderings and even single-cell resolution using MSI are emerging as future frontiers. With all the advances in this field, MSI is rapidly evolving and requires continuous development to match the current demand. Overall, the aim of this review is to provide an informative resource for those in the MSI community who are interested in improving MSI data quality and analysis or using MSI for novel applications. Particularly, we discuss advances from the last 2 years in sample preparation, instrumentation, quantitation, statistics, and multimodal imaging that have allowed MSI to emerge as a powerful technique in various biomedical applications including clinical settings. Also, several novel biological applications are highlighted to demonstrate the potential for the future of the MSI field.Burch, M.J., Ievlev, A.V., Mahady, K., Hysmith, H., Rack, P.D., Belianinov, A., Ovchinnikova, O.S., 2018. Helium ion microscopy for imaging and quantifying porosity at the nanoscale. Analytical Chemistry 90, 1370-1375. materials are key components in a vast number of applications from energy to drug delivery and to agriculture. However, the number of ways to analytically quantify the salient features of these materials, for example: surface structure, pore shape, and size, remain limited. The most common approach is gas absorption, where volumetric gas absorption and desorption are measured. This technique has some fundamental drawbacks such as low sample throughput and a lack of direct surface visualization. In this work, we demonstrate Helium Ion Microscopy (HIM) as a tool for imaging and quantification of pores in industrially relevant SiO2 catalyst supports. We start with the fundamental principles of ion-sample interaction, and build on this knowledge to experimentally observe and quantify surface pores by using the HIM and image data analytics. We contrast our experimental results to gas absorption and demonstrate full statistical agreement between two techniques. The principles behind the theoretical, experimental, and analytical framework presented herein offer an automated framework for visualization and quantification of pore structures in a wide variety of materials.Butterfield, N.J., 2018. Oxygen, animals and aquatic bioturbation: An updated account. Geobiology 16, 3-16.. No abstractCabrol, N.A., 2017. The coevolution of life and environment on Mars: An ecosystem perspective on the robotic exploration of biosignatures. Astrobiology 18, 1-27.'s biological and environmental evolution are intertwined and inseparable. This coevolution has become a fundamental concept in astrobiology and is key to the search for life beyond our planet. In the case of Mars, whether a coevolution took place is unknown, but analyzing the factors at play shows the uniqueness of each planetary experiment regardless of similarities. Early Earth and early Mars shared traits. However, biological processes on Mars, if any, would have had to proceed within the distinctive context of an irreversible atmospheric collapse, greater climate variability, and specific planetary characteristics. In that, Mars is an important test bed for comparing the effects of a unique set of spatiotemporal changes on an Earth-like, yet different, planet. Many questions remain unanswered about Mars' early environment. Nevertheless, existing data sets provide a foundation for an intellectual framework where notional coevolution models can be explored. In this framework, the focus is shifted from planetary-scale habitability to the prospect of habitats, microbial ecotones, pathways to biological dispersal, biomass repositories, and their meaning for exploration. Critically, as we search for biosignatures, this focus demonstrates the importance of starting to think of early Mars as a biosphere and vigorously integrating an ecosystem approach to landing site selection and exploration.Cam, N., Benzerara, K., Georgelin, T., Jaber, M., Lambert, J.F., Poinsot, M., Skouri-Panet, F., Moreira, D., López-García, P., Raimbault, E., Cordier, L., Jézéquel, D., 2018. Cyanobacterial formation of intracellular Ca-carbonates in undersaturated solutions. Geobiology 16, 49-61. have long been thought to induce the formation of Ca-carbonates as secondary by-products of their metabolic activity, by shifting the chemical composition of their extracellular environment to conditions favoring mineral precipitation. Some cyanobacterial species forming Ca-carbonates intracellularly were recently discovered. However, the environmental conditions under which this intracellular biomineralization process can occur and the impact of cyanobacterial species forming Ca-carbonates intracellularly on extracellular carbonatogenesis are not known. Here, we show that these cyanobacteria can form Ca-carbonates intracellularly while growing in extracellular solutions undersaturated with respect to all Ca-carbonate phases, that is, conditions thermodynamically unfavorable to mineral precipitation. This shows that intracellular Ca-carbonate biomineralization is an active process; that is, it costs energy provided by the cells. The cost of energy may be due to the active accumulation of Ca intracellularly. Moreover, unlike cyanobacterial strains that have been usually considered before by studies on Ca-carbonate biomineralization, cyanobacteria forming intracellular carbonates may slow down or hamper extracellular carbonatogenesis, by decreasing the saturation index of their extracellular solution following the buffering of the concentration of extracellular calcium to low levels.Cantera, S., Mu?oz, R., Lebrero, R., López, J.C., Rodríguez, Y., García-Encina, P.A., 2018. Technologies for the bioconversion of methane into more valuable products. Current Opinion in Biotechnology 50, 128-135., with a global warming potential twenty five times higher than that of CO2 is the second most important greenhouse gas emitted nowadays. Its bioconversion into microbial molecules with a high retail value in the industry offers a potential cost-efficient and environmentally friendly solution for mitigating anthropogenic diluted CH4-laden streams. Methane bio-refinery for the production of different compounds such as ectoine, feed proteins, biofuels, bioplastics and polysaccharides, apart from new bioproducts characteristic of methanotrophic bacteria, has been recently tested in discontinuous and continuous bioreactors with promising results. This review constitutes a critical discussion about the state-of-the-art of the potential and research niches of biotechnologies applied in a CH4 biorefinery approach.Canul-Chan, M., Sánchez-González, M., González-Burgos, A., Zepeda, A., Rojas-Herrera, R., 2018. Population structures shift during the biodegradation of crude and fuel oil by an indigenous consortium. International Journal of Environmental Science and Technology 15, 1-16. and fuel oil are complex mixtures of recalcitrant hydrocarbons. The biodegradation of these hydrocarbons needs the action of a vast variety of enzymatic capacities. A microbial consortium offers the capability to degrade complex substrates through the assembly of different biochemical reactions, providing a metabolic versatility superior to axenic cultures. In this work, the microbial population dynamics, taxonomy, and the catabolic capacity of a stabilized consortium exposed to fuel and crude oil was analyzed through metagenomics. The stabilized consortium degraded 59% of crude oil components after 8?days, and 34% of fuel oil components after 130?days. Population dynamics analysis indicates that in fuel oil the biodiversity richness was higher; however, denaturing gradient gel electrophoresis similarity dendrogram shows significant changes in the microbial population during crude oil degradation. Taxonomy studies indicate a great genera divergence; only eight microbial genera were common in both samples. In crude oil, the Limnobacter sp. was the most abundant specie (15.6%), while Sphingomonas wittichii (7.9%) and Novosphingobium aromaticivorans (7.6%) were abundant in fuel oil. These microorganisms have been reported to participate in the degradation of aliphatic and aromatic hydrocarbons. Functional analysis suggests that fuel and crude oil components changed the interactions between the consortium members affecting the collective metabolic functionality.Cao, J., Song, T., Zhu, Y., Wang, S., Wang, X., Lv, F., Jiang, L., Sun, M., 2018. Application of amino-functionalized nanosilica in improving the thermal stability of acrylamide-based polymer for enhanced oil recovery. Energy & Fuels 32, 246-254. nanosilica (ANS) was prepared from nanosilica (NS) modified by 3-aminopropyltriethoxysilane. The amine groups on the ANS surface could be positively charged at acidic environment. As a result, compared to NS, ANS presented better dispersion stability and stronger interaction with functional groups on acrylamide-based polymer. Three systems, such as nanoparticle free polymer (PAS), NS/polymer (PAS-S), and ANS/polymer (PAS-AS), were prepared, and the thermal degradations of these systems in distilled water after deoxygenation were carried out at 100 and 140 °C. The variations of apparent viscosity, degree of hydrolysis, and average hydrodynamic radius in the aging process were investigated, and the results indicated that ANS could both inhibit the hydrolysis of amide groups and protect the polymer backbone to avoid the rupture of polymer molecule. As a result, PAS-AS exhibited much better thermal stability at harsh environment. The relative viscosity for PAS-AS after 12 h degradation at 140 °C was 58.0%; however, it was only 14.9% for PAS. The long-term thermal degradations of three systems were also performed under a simulated oilfield condition. PAS-AS also presented the best thermal stability under low or high residual oxygen situations. Additionally, core flooding experiments show that PAS-AS solution has a higher oil recovery factor than PAS solution.Cao, J., Yang, R., Hu, G., Hu, W., Yao, S., Xie, X., Gao, Y., Gao, J., 2018. Hydrocarbon potential of the Lower Cretaceous mudstones in coastal southeastern China. American Association of Petroleum Geologists Bulletin 102, 333-366. Cretaceous hosts the highest hydrocarbon potential among all geological stratigraphic sequences worldwide, and the Lower Cretaceous in coastal southeastern China, with the development of black mudstones and shales, has potential for hydrocarbon generation. This potential, therefore, is of significance to regional hydrocarbon exploration both onshore and offshore; however, it has not been investigated in detail. Here, we address this issue based on the results of integrated organic geochemistry and petrology of four representative outcrop sections in the region. Results show that there are two possible source rock sequences in the Lower Cretaceous of coastal southeastern China, that is, a lower sequence represented by the Bantou Formation black mudstones in the Fujian Province and an upper interval represented by the Guantou Formation black mudstones or calcareous mudstones in the Zhejiang Province. The organic matter abundance of these two formations reaches levels of poor to good source rocks. The kerogen is dominated by type III, whereas type II can also be found locally in the northwestern Fujian Province. Most samples are highly mature to overmature, except for the samples with less influence of volcanism in the northern Guangdong Province. Comparatively, the organic matter abundance of the early-stage source rocks is higher than for the late-stage rocks, and the kerogen type is less favorable; however, the maturity shows little correlation with age and is largely related to volcanism. Therefore, the Lower Cretaceous in coastal southeastern China seems to have hydrocarbon potential (gas in particular) in local areas, including the northern Guangdong Province and its analog in offshore basins for the early stage and the northwestern Fujian Province and its analog in offshore basins for the late stage. These results and understanding provide insights for expanding new hydrocarbon exploration targets in southeastern China both onshore and offshore and may also have implications for understanding the regional Cretaceous geology.Carr, S.A., Schubotz, F., Dunbar, R.B., Mills, C.T., Dias, R., Summons, R.E., Mandernack, K.W., 2018. Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments. The Isme Journal 12, 330-342. accounting for the majority of sedimentary methane, the physiology and relative abundance of subsurface methanogens remain poorly understood. We combined intact polar lipid and metagenome techniques to better constrain the presence and functions of methanogens within the highly reducing, organic-rich sediments of Antarctica’s Adélie Basin. The assembly of metagenomic sequence data identified phylogenic and functional marker genes of methanogens and generated the first Methanosaeta sp. genome from a deep subsurface sedimentary environment. Based on structural and isotopic measurements, glycerol dialkyl glycerol tetraethers with diglycosyl phosphatidylglycerol head groups were classified as biomarkers for active methanogens. The stable carbon isotope (δ13C) values of these biomarkers and the Methanosaeta partial genome suggest that these organisms are acetoclastic methanogens and represent a relatively small (0.2%) but active population. Metagenomic and lipid analyses suggest that Thaumarchaeota and heterotrophic bacteria co-exist with Methanosaeta and together contribute to increasing concentrations and δ13C values of dissolved inorganic carbon with depth. This study presents the first functional insights of deep subsurface Methanosaeta organisms and highlights their role in methane production and overall carbon cycling within sedimentary environments.Carradec, Q., Pelletier, E., Da Silva, C., Alberti, A., Seeleuthner, Y., Blanc-Mathieu, R., Lima-Mendez, G., Rocha, F., Tirichine, L., Labadie, K., Kirilovsky, A., Bertrand, A., Engelen, S., Madoui, M.-A., Méheust, R., Poulain, J., Romac, S., Richter, D.J., Yoshikawa, G., Dimier, C., Kandels-Lewis, S., Picheral, M., Searson, S., Jaillon, O., Aury, J.-M., Karsenti, E., Sullivan, M.B., Sunagawa, S., Bork, P., Not, F., Hingamp, P., Raes, J., Guidi, L., Ogata, H., de Vargas, C., Iudicone, D., Bowler, C., Wincker, P., 2018. A global ocean atlas of eukaryotic genes. Nature Communications 9, Article 373. our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry.Cecchi, G., Marescotti, P., Di Piazza, S., Lucchetti, G., Mariotti, M.G., Zotti, M., 2018. Gypsum biomineralization in sulphide-rich hardpans by a native Trichoderma harzianum Rifai strain. Geomicrobiology Journal 35, 209-214. acid mine drainage affects abandoned sulfide mines worldwide, causing hardpan formation and heavy metal leaching. Hardpans are characterized by very low permeability, thus representing a significant limiting factor for oxygen and water circulation in the rhizosphere. Our work shows the results concerning the gypsum biomineralization capability of a native Trichoderma harzianum Rifai strain in sulfide -rich hardpans. Two months after the fungal inoculum, hardpan clasts resulted, completely covered by T. harzianum mycelium, where newly formed gypsum crystals occur. Our study provided the first evidence about interaction between T. harzianum and sulfide -mineralized hardpans as well as about its influence on gypsum genesis.Cesar, J., Grice, K., 2018. Drimane-type compounds in source rocks and fluids from fluvial-deltaic depositional settings in the North-West Shelf of Australia. Organic Geochemistry 116, 103-112. petroleum systems with gas-prone source rocks are difficult to assess because the released fluids generally lack biomarkers and this limits the implementation of traditional organic geochemistry screening. However, there are a number of compound classes yet to be investigated in order to establish novel parameters for correlation studies in fluvial-deltaic geological settings. In this study we have focused on drimane-skeleton molecules (C15-decalins), particularly the compounds 1,2,2,5,5-pentamethyl-trans-decalin and 1,1,2,5,5-pentamethyl-trans-decalin (termed herein as rearranged drimanes RD1 and RD2, respectively) and drimane (D), in source rock extracts and fluids from fluvial-deltaic petroleum systems in the Carnarvon Basin, North-West Shelf of Australia (NWS). We have calculated the ratio (RD1?+?RD2)/D as proposed by Ji et al. (Ji, L., He, C., Zhang, M., Wu, Y., Li, X. [2016]. Bicyclic alkanes in source rocks of the Triassic Yanchang Formation in the Ordos Basin and their inconsistency in oil-source correlation. Marine and Petroleum Geology 72, 359–373) and compared their results with samples from the NWS. Our compilation of rearranged drimane ratios for a variety of lithologies suggests clay-catalysed rearrangement of C15-decalins in siliciclastic source rocks from fluvial-deltaic depositional environments. Therefore, the mineral content seems to be a key factor controlling the isomerisation of decalins. Samples with higher clay content, such as claystone from the Brigadier Formation, have higher (RD1?+?RD2)/D ratios (～6) and higher C29 diasterane/C29 sterane (～1.1) compared to silty claystone from the Legendre Formation (～2 and ～0.8 respectively). The effects exerted by thermal maturity of the source rock and redox conditions of the depositional environment require further investigation, although samples from the Yanchang Fomation and La Luna Formation, where deposition occurred under more reducing conditions, exhibit lower rearranged drimane ratios (<?2).Chacón-Pati?o, M.L., Rowland, S.M., Rodgers, R.P., 2018. Advances in asphaltene petroleomics. Part 2: Selective separation method that reveals fractions enriched in island and archipelago structural motifs by mass spectrometry. Energy & Fuels 32, 314-328. in high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) enable molecular-level characterization of ultracomplex asphaltene samples. Such analyses most often reveal compounds that are highly aromatic but alkyl-deficient in nature and, thus, support the classical “island” model of asphaltene architecture. However, recent works that combine chromatographic separations with mass spectrometry for the analysis of crude oils have shown that differences in ionization may greatly affect the analysis of complex mixtures (known as the matrix effect). Simply, compounds that ionize with greater efficiency are preferentially observed and mask the detection of poorly ionized compounds. Asphaltenes are not immune to this phenomenon. In the first of this series, it was demonstrated that asphaltenes generated by different precipitants showed greatly varied monomer ion yields (ionization efficiencies). This work focuses on the development of an extrography fractionation method that selectively targets the removal of asphaltene species that exhibit high monomer ion yields and, thus, restrict mass spectral characterization of less efficiently ionized species. Silica gel was used as the stationary phase, and a unique solvent series separated asphaltenes based on their interaction with the silica surface, which was later determined to depend heavily upon the structure as well as monomer ion yield. The first two solvents (acetone and acetonitrile) isolated compounds that most efficiently produce monomeric asphaltene ions and, thus, cause bias in mass spectrometric analyses of whole asphaltenes. A solvent polarity gradient was then used, with n-heptane, toluene, tetrahydrofuran, and methanol, to separate remnant asphaltene compounds on the basis of polarity and structure. Our results demonstrate that mass spectrometry of whole asphaltenes does not reveal the complete molecular composition but rather preferentially exposes highly aromatic, alkyl-deficient, island-type structures. Early eluting fractions are shown to resemble the composition of the whole asphaltene and are enriched in island structures, whereas the analysis of later-eluting fractions reveals archipelago structural motifs as well as species with atypical asphaltene molecular compositions. We also demonstrate that, as molecular weight increases, the asphaltenes exhibit increased contributions of archipelago structural motifs. Higher mass ions (m/z > 550), even from asphaltene fractions enriched in island structures, exhibit fragmentation pathways that originate from archipelago structures. Thus, positive-ion atmospheric pressure photoionization (APPI) FT-ICR MS provides molecular-level data that suggest that the island model is not the dominant structure of asphaltenes. It coexists with abundant archipelago structures, and the ratios of each are sample-dependent.Chan, Q.H.S., Zolensky, M.E., Kebukawa, Y., Fries, M., Ito, M., Steele, A., Rahman, Z., Nakato, A., Kilcoyne, A.L.D., Suga, H., Takahashi, Y., Takeichi, Y., Mase, K., 2018. Organic matter in extraterrestrial water-bearing salt crystals. Science Advances 4, Article eaao3521. evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body. Associated with these trapped brines are organic compounds exhibiting wide chemical variations representing organic precursors, intermediates, and reaction products that make up life’s precursor molecules such as amino acids. The organic compounds also contain a mixture of C-, O-, and N-bearing macromolecular carbon materials exhibiting a wide range of structural order, as well as aromatic, ketone, imine, and/or imidazole compounds. The enrichment in 15N is comparable to the organic matter in pristine Renazzo-type carbonaceous chondrites, which reflects the sources of interstellar 15N, such as ammonia and amino acids. The amino acid content of the Zag halite deviates from the meteorite matrix, supporting an exogenic origin of the halite, and therefore, the Zag meteorite contains organics synthesized on two distinct parent bodies. Our study suggests that the asteroidal parent body where the halite precipitated, potentially asteroid 1 Ceres, shows evidence for a complex combination of biologically and prebiologically relevant molecules.Chandler, S.A., Benesch, J.L.P., 2018. Mass spectrometry beyond the native state. Current Opinion in Chemical Biology 42, 130-137. mass spectrometry allows the study of proteins by probing in vacuum the interactions they form in solution. It is a uniquely useful approach for structural biology and biophysics due to the high resolution of separation it affords, allowing the concomitant interrogation of multiple protein components with high mass accuracy. At its most basic, native mass spectrometry reports the mass of intact proteins and the assemblies they form in solution. However, the opportunities for more detailed characterisation are extensive, enabled by the exquisite control of ion motion that is possible in vacuum. Here we describe recent developments in mass spectrometry approaches to the structural interrogation of proteins both in, and beyond, their native state.Chang, C.-Y., 2018. Surface sensing for biofilm formation in Pseudomonas aeruginosa. Frontiers in Microbiology 8, 2671. doi: 10.3389/fmicb.2017.02671. and forming biofilms on biotic or abiotic surfaces are ubiquitous bacterial behaviors under various conditions. In clinical settings, persistent presence of biofilms increases the risks of healthcare-associated infections and imposes huge healthcare and economic burdens. Bacteria within biofilms are protected from external damage and attacks from the host immune system and can exchange genomic information including antibiotic-resistance genes. Dispersed bacterial cells from attached biofilms on medical devices or host tissues may also serve as the origin of further infections. Understanding how bacteria develop biofilms is pertinent to tackle biofilm-associated infections and transmission. Biofilms have been suggested as a continuum of growth modes for adapting to different environments, initiating from bacterial cells sensing their attachment to a surface and then switching cellular physiological status for mature biofilm development. It is crucial to understand bacterial gene regulatory networks and decision-making processes for biofilm formation upon initial surface attachment. Pseudomonas aeruginosa is one of the model microorganisms for studying bacterial population behaviors. Several hypotheses and studies have suggested that extracellular macromolecules and appendages play important roles in bacterial responses to the surface attachment. Here, I review recent studies on potential molecular mechanisms and signal transduction pathways for P. aeruginosa surface sensing.Chaudhary, D.K., Kim, J., 2018. Sphingopyxis nepalensis sp. nov., isolated from oil-contaminated soil. International Journal of Systematic and Evolutionary Microbiology 68, 364-370. a study of oil-degrading bacteria, three yellow-coloured, Gram-stain-negative, non-motile and rod-shaped bacteria, designated strains Ktm-14T, Ktm-17 and Ktm-18, were isolated from oil-contaminated soil of Biratnagar, Morang, Nepal. The strains were able to grow at 15–37?°C, pH 4.5–10.0 and 0–2?% (w/v) NaCl concentration. Strains Ktm-14T, Ktm-17 and Ktm-18 were characterized by multiple taxonomic approaches. Based on 16S rRNA gene sequence analysis, strains Ktm-14T, Ktm-17 and Ktm-18 belonged to the genus Sphingopyxis and shared highest sequence similarity with Sphingopyxis ginsengisoli Gsoil 250T (98.94?%). The only respiratory quinone was ubiquinone-10 and the predominant polyamine was spermidine. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and sphingoglycolipids. The predominant fatty acids were C17?:?1ω6c, summed feature 8 (C18?:?1ω7c and/or C18?:?1ω6c), summed feature 3 (C16?:?1ω7c and/or C16?:?1ω6c) and C16?:?0. The DNA G+C?content values of strains Ktm-14T, Ktm-17 and Ktm-18 were 65.8, 65.9 and 65.6?mol%, respectively. The DNA–DNA relatedness between Ktm-14T and Ktm-17 and Ktm-18 were higher than 70?% but with closely related reference strains were less than 40?%. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished strain Ktm-14T from its closest phylogenetic neighbours. Thus, strain Ktm-14T represents a novel species of the genus Sphingopyxis , for which the name Sphingopyxis nepalensis sp. nov. is proposed. The type strain is Ktm-14T (=KEMB 9005-694T=KACC 19389T=JCM 32250T), and strains Ktm-17 and Ktm-18 represent two additional strains. The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene sequence of strains Ktm-14T, Ktm-17, and Ktm-18 are MF405104, MF405105, and MF405106, respectively.Chen, B., Brown, K.A., Lin, Z., Ge, Y., 2018. Top-down proteomics: Ready for prime time? Analytical Chemistry 90, 110-127. the posshetgenomics era, the study of proteins is critical for understanding cellular functions at the molecular level. Beyond the genetic code, the human proteome is greatly diversified by genetic variations, alternative splicing of RNA transcripts, and post-translational modifications (PTMs). In 2013, the term “proteoform” was designated to describe “all of the different molecular forms in which the protein product of a single gene can be found”, clearing up the confusion in nomenclature and joining research efforts to develop methodologies for proteoform characterization. Top-down proteomics, which analyzes intact proteins without digestion, has proved to be a premier mass spectrometry (MS) technology for global and comprehensive analysis of proteoforms. The top-down approach retains intact protein mass information, providing a “bird’s-eye” view of the proteome and allowing for identification of novel proteoforms, in-depth sequence characterization, and quantitation of disease-associated PTMs.Although some technical challenges remain, development over the past 5 years has expanded top-down proteomics from a mostly targeted approach to one capable of proteoform-profiling across multiple samples. Now, thousands of proteoforms can be identified, characterized, and quantified using high-throughput top-down proteomics approaches. Moreover, developments in instrumentation and fragmentation have positioned top-down proteomics in the fast lane for future progression. With the successful development of commercial high-resolution mass spectrometers such as the solariX XR Fourier transform ion cyclotron resonance (FTICR) (Bruker), Orbitraps (Thermo), and quadrupole time-of-flight (Q-TOFs) (Bruker and Waters), these instruments are now widely available in academic and industrial laboratories for top-down proteomics. Moreover, the 21 T FTICR mass spectrometers equipped with state-of-the-art fragmentation methods at the Pacific Northwest National Laboratory and National High Magnetic Field Laboratory have demonstrated unprecedented resolving power, acquisition rate, and flexible tandem MS (MS/MS) capabilities, providing enormous potential for top-down proteomics practitioners to probe complicated proteomics applications. Reciprocally, the methodological and technological gains from developing large-scale and high-throughput workflow have further empowered targeted analysis, from which top-down proteomics roots and thrives. As a result, interest in top-down MS has grown considerably and many studies have already underscored the potential of top-down proteomics for unraveling disease mechanisms and discovering novel biomarkers.A number of recent reviews have already given an overview of the technical requirements for top-down proteomics and delineated the history and fundamentals of the field as well as its application to biomedical research. With a special emphasis on publications in the past 2 years (2015–2017), this review examines recent technological trends and developments in the areas of intact protein sample preparation, separation, MS/MS, data acquisition strategies, data analysis, native MS, and quantitation. We also highlight recent applications for global and targeted top-down proteomics applications and conclude with outlooks in the field.Chen, J., Yang, H., Zeng, Y., Guo, J., Song, Y., Ding, W., 2018. Combined use of radiocarbon and stable carbon isotope to constrain the sources and cycling of particulate organic carbon in a large freshwater lake, China. Science of The Total Environment 625, 27-38. concentrations and isotopic compositions of dissolved inorganic carbon (DIC) and particulate organic carbon (POC) were measured in order to better constrain the sources and cycling of POC in Lake Fuxian, the largest deep freshwater lake in China. Model results based on the combined δ13C and Δ14C, showed that the average lake-wide contributions of autochthonous POC, terrestrial POC, and resuspended sediment POC to the bulk POC in Lake Fuxian were 61%, 22%, and 17%, respectively. This indicated autochthonous POC might play a dominant role in sustaining large oligotrophic lake ecosystem. A mean 17% contribution of resuspended sediment POC to the bulk POC implied that sediment might have more significant influence on aquatic environment and ecosystem than previously recognized in large deep lakes. The contributions of different sources POC to the water-column POC were a function of the initial composition of the source materials, photosynthesis, physical regime of the lake, sediment resuspension, respiration and degradation of organic matter, and were affected indirectly by environmental factors such as light, temperature, DO, wind speed, turbidity, and nutrient concentration.This study is not only the first systematic investigation on the radiocarbon and stable isotope compositions of POC in large deep freshwater lake in China, but also one of the most extensive radiocarbon studies on the ecosystem of any great lakes in the world. The unique data constrain relative influences of autochthonous POC, terrestrial POC, and resuspended sediment POC, and deepen the understanding of the POC cycling in large freshwater lakes. This study is far from comprehensive, but it serves to highlight the potential of combined radiocarbon and stable carbon isotope for constraining the sources and cycling of POC in large lake system. More radiocarbon investigations on the water-column POC and the aquatic food webs are necessary to illuminate further the fate of autochthonous POC, terrestrial POC, and resuspended sediment POC, and their eco-environmental effects.Chen, S., Tang, D., Tao, S., Xu, H., Li, S., Zhao, J., Cui, Y., Li, Z., 2018. Characteristics of in-situ stress distribution and its significance on the coalbed methane (CBM) development in Fanzhuang-Zhengzhuang Block, southern Qinshui Basin, China. Journal of Petroleum Science and Engineering 161, 108-120. stress is a vital index on the coal reservoir permeability and coalbed methane (CBM) development. Based on 41 sets of well test data at depths (h) of 353–1273 m in Fanzhuang-Zhengzhuang Block, the distribution of in-situ stress was analyzed systematically and its effect on coal permeability was also addressed. Results show that stress fields could convert in the vertical and four ranges corresponding to the certain depth can be characterized: the σH > σv > σh type mainly occurs in the shallow and deep coal seams (<600 m and > 825 m); From 600 to 725 m, a stress transition zone can be observed (σH ≈ σv > σh); The σv > σH > σh type is dominant within depth from 725 to 825 m. With the increase of depth, well testing permeability (k) exhibits a trend of decrease (h < 600 m, 0.055 < k < 0.91mD) - increase (600 < h < 825 m, 0.02 < k < 1.13 mD) - decrease (h > 825 m, k < 0.1 mD), the essence of which is the open and closure of pores and fractures under the control of stress regime and vertical belting. Meanwhile, the correlation between gas content and depth was also illustrated, which shows two trends at the depth of 200–825 m (increase) and 825–1400 m (decrease), respectively. Generally, the coal reservoir deeper than 825 m is characterized by high in situ stress, low permeability and low gas resource, meaning that the geological conditions for CBM development deteriorate. The gas/water production of 500 CBM wells also indicates that the gas recovery rate in deeper coal seams is poorer than that in shallower coal seams. Therefore, a series of corresponding methods for these deep CBM (>825 m) should be taken in the future CBM development strategy.Chen, X.D., Zhang, C.K., Zhou, Z., Gong, Z., Zhou, J.J., Tao, J.F., Paterson, D.M., Feng, Q., 2017. Stabilizing effects of bacterial biofilms: EPS penetration and redistribution of bed stability down the sediment profile. Journal of Geophysical Research: Biogeosciences 122, 3113-3125., consisting of microorganisms and their secreted extracellular polymeric substances (EPSs), serve as “ecosystem engineers” stabilizing sedimentary environments. Natural sediment bed provides an excellent substratum for biofilm growth. The porous structure and rich nutrients allow the EPS matrix to spread deeper into the bed. A series of laboratory-controlled experiments were conducted to investigate sediment colonization of Bacillus subtilis and the penetration of EPS into the sediment bed with incubation time. In addition to EPS accumulation on the bed surface, EPS also penetrated downward. However, EPS distribution developed strong vertical heterogeneity with a much higher content in the surface layer than in the bottom layer. Scanning electron microscope images of vertical layers also displayed different micromorphological properties of sediment-EPS matrix. In addition, colloidal and bound EPSs exhibited distinctive distribution patterns. After the full incubation, the biosedimentary beds were eroded to test the variation of bed stability induced by biological effects. This research provides an important reference for the prediction of sediment transport and hence deepens the understanding of the biologically mediated sediment system and broadens the scope of the burgeoning research field of “biomorphodynamics.”Plain Language Summary: In many studies, biofilms have been developed on synthetic material such as glass slides. However, natural sediment beds are very different from impermeable surfaces and provide a more extensive substratum for biofilm growth: the porous structure and rich nutrients allow the biofilm and related extracellular polymeric substance (EPS) matrix to extend deeper into the matrix. A sample of field observation on tidal flats proves this: the biosedimentary layer can be found several centimeters below the surface. Therefore, the biological effects on the sediment bed should not be restricted to simply “surficial protection” such as increasing the erosion threshold. Instead, the EPS expansion into the depth profile alters the properties of a layer of sediment, and thus will certainly have an even greater impact on sediment transport. In the light of this, coastal engineers and morphological prediction modelers are concerned with the following: (1) how do these bioeffects change with depth and time? And (2) what will be the changes to bed stability in response? Therefore, the penetration of bacterial EPS down sediment profile and the depth potential of biostabilization are further investigated in this study.Chen, Y., Zheng, F., Chen, S., Liu, H., Phelps, T.J., Zhang, C., 2018. Branched GDGT production at elevated temperatures in anaerobic soil microcosm incubations. Organic Geochemistry 117, 12-21. glycerol dialkyl glycerol tetraethers (bGDGTs) are unique ether-linked bacterial membrane lipids, which occur in diverse environments. Acidobacteria are considered to produce them in acidic soils and peat bogs. However, the biological source(s) of bGDGTs other than acidobacteria in alkaline soils and their response to environmental changes are obscure. We designed a 1?year incubation experiment under elevated temperature conditions (30?°C, 45?°C and 85?°C) in order to accelerate the growth of mesophilic and thermophilic bacteria that may potentially produce bGDGTs and to understand the mechanisms underlying the changes in bGDGT composition. The soil we selected was alkaline (pH?>?8) with a small population of acidobacteria being detected using high throughput sequencing. The medium contained nutrients and organic carbon and samples were incubated under anaerobic conditions with pH of 7.5, in order to stimulate the growth of heterotrophic and anaerobic bacteria from the soil. Quantitative polymerase chain reaction (qPCR) was employed to monitor the growth status of bacteria at the beginning and the end of the experiment. The results showed multiple lines of evidence for bGDGT biosynthesis, including: (1) increased total abundance of both PL-bGDGTs (polar lipid-derived bGDGTs, “living”) and CL-bGDGTs (core lipid bGDGTs, “dead”) at 30?°C and 45?°C, but not 85?°C; (2) changes in bGDGT distribution at 30?°C and 45?°C; and (3) increased temperature inferred by the bGDGT-based proxy at an incubation temperature at 45?°C. Estimated turnover time of both PL- and CL-bGDGTs was 1–8?months at 30?°C or 45?°C under these laboratory conditions, which agrees with previous studies. Our study suggests that raising temperature may stimulate growth of bGDGT-producing bacteria that likely includes some anaerobic heterotrophs other than acidobacteria.Chiriac, C.M., Baricz, A., Szekeres, E., Rudi, K., Drago?, N., Coman, C., 2018. Microbial composition and diversity patterns in deep hyperthermal aquifers from the western plain of Romania. Microbial Ecology 75, 38-51. limited number of studies have investigated the biodiversity in deep continental hyperthermal aquifers and its influencing factors. Here, we present the first description of microbial communities inhabiting the Pannonian and Triassic hyperthermal aquifers from the Western Plain of Romania, the first one being considered a deposit of “fossilized waters,” while the latter is embedded in the hydrological cycle due to natural refilling. The 11 investigated drillings have an open interval between 952 and 3432?m below the surface, with collected water temperatures ranging between 47 and 104?°C, these being the first microbial communities characterized in deep continental water deposits with outflow temperatures exceeding 80?°C. The abundances of bacterial 16S rRNA genes varied from approximately 105–106?mL?1 in the Pannonian to about 102–104?mL?1 in the Triassic aquifer. A 16S rRNA gene metabarcoding analysis revealed distinct microbial communities in the two water deposits, especially in the rare taxa composition. The Pannonian aquifer was dominated by the bacterial genera Hydrogenophilus and Thermodesulfobacterium, together with archaeal methanogens from the Methanosaeta and Methanothermobacter groups. Firmicutes was prevalent in the Triassic deposit with a large number of OTUs affiliated to Thermoanaerobacteriaceae, Thermacetogenium, and Desulfotomaculum. Species richness, evenness, and phylogenetic diversity increased alongside with the abundance of mesophiles, their presence in the Triassic aquifer being most probably caused by the refilling with large quantities of meteoric water in the Carpathian Mountains. Altogether, our results show that the particular physico-cheminal characteristics of each aquifer, together with the water refilling possibilities, seem to determine the microbial community structure.Choquette-Levy, N., Zhong, M., MacLean, H., Bergerson, J., 2017. COPTEM: A model to investigate the factors driving crude oil pipeline transportation emissions. Environmental Science & Technology 52, 337-345. transportation fuel life cycle assessment studies have not fully accounted for the full variability in the crude oil transport stage, for example, transporting a light crude through a high-diameter pipeline, vs transporting a heavy crude through a small-diameter pipeline. We develop a first-principles, fluid mechanics-based crude oil pipeline transportation emissions model (COPTEM) that calculates the greenhouse gas (GHG) emissions associated with pipeline transport as a function of crude oil parameters, pipeline dimensions, and external factors. Additionally, we estimate the emissions associated with the full life cycle of pipeline construction, maintenance, and disposal. This model is applied to an inventory of 62 major Canadian and U.S. pipelines (capacity greater than 100?000 barrels/day) to estimate the variability of GHG emissions associated with pipeline transportation. We demonstrate that pipeline GHG emissions intensities range from 0.23 to 20.3 g CO2e/(bbl·km), exhibiting considerably greater variability than data reported in other studies. A sensitivity analysis demonstrates that the linear velocity of crude transport and pipeline diameter are the most impactful parameters driving this variability. To illustrate one example of how COPTEM can be used, we develop an energy efficiency gap analysis to investigate the possibilities for more efficient pipeline transport of crude oil.Chrachri, A., Hopkinson, B.M., Flynn, K., Brownlee, C., Wheeler, G.L., 2018. Dynamic changes in carbonate chemistry in the microenvironment around single marine phytoplankton cells. Nature Communications 9, Article 74. by marine diatoms plays a major role in the global carbon cycle, although the precise mechanisms of dissolved inorganic carbon (DIC) uptake remain unclear. A lack of direct measurements of carbonate chemistry at the cell surface has led to uncertainty over the underlying membrane transport processes and the role of external carbonic anhydrase (eCA). Here we identify rapid and substantial photosynthesis-driven increases in pH and [CO32?] primarily due to the activity of eCA at the cell surface of the large diatom Odontella sinensis using direct simultaneous microelectrode measurements of pH and CO32? along with modelling of cell surface inorganic carbonate chemistry. Our results show that eCA acts to maintain cell surface CO2 concentrations, making a major contribution to DIC supply in O. sinensis. Carbonate chemistry at the cell surface is therefore highly dynamic and strongly dependent on cell size, morphology and the carbonate chemistry of the bulk seawater.Christakis, C.A., Polymenakou, P.N., Mandalakis, M., Nomikou, P., Kristoffersen, J.B., Lampridou, D., Kotoulas, G., Magoulas, A., 2018. Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc. Extremophiles 22, 13-27. the last decades, there has been growing interest about the ecological role of hydrothermal sulfide chimneys, their microbial diversity and associated biotechnological potential. Here, we performed dual-index Illumina sequencing of bacterial and archaeal communities on active and inactive sulfide chimneys collected from the Kolumbo hydrothermal field, situated on a geodynamic convergent setting. A total of 15,701 OTUs (operational taxonomic units) were assigned to 56 bacterial and 3 archaeal phyla, 133 bacterial and 16 archaeal classes. Active chimney communities were dominated by OTUs related to thermophilic members of Epsilonproteobacteria, Aquificae and Deltaproteobacteria. Inactive chimney communities were dominated by an OTU closely related to the archaeon Nitrosopumilus sp., and by members of Gammaproteobacteria, Deltaproteobacteria, Planctomycetes and Bacteroidetes. These lineages are closely related to phylotypes typically involved in iron, sulfur, nitrogen, hydrogen and methane cycling. Overall, the inactive sulfide chimneys presented highly diverse and uniform microbial communities, in contrast to the active chimney communities, which were dominated by chemolithoautotrophic and thermophilic lineages. This study represents one of the most comprehensive investigations of microbial diversity in submarine chimneys and elucidates how the dissipation of hydrothermal activity affects the structure of microbial consortia in these extreme ecological niches.Christel, S., Herold, M., Bellenberg, S., El Hajjami, M., Buetti-Dinh, A., Pivkin, I.V., Sand, W., Wilmes, P., Poetsch, A., Dopson, M., 2018. Multi-omics reveals the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilumT. Applied and Environmental Microbiology 84, Article e02091-17.: Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647T (here referred to as Leptospirillum ferriphilumT) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilumT obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). Adaptations of Leptospirillum ferriphilumT to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced. Importance: Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilumT coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilumT for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction. Chukwuma, K., Bordy, E.M., Coetzer, A., 2018. Evolution of porosity and pore geometry in the Permian Whitehill Formation of South Africa – A FE-SEM image analysis study. Marine and Petroleum Geology 91, 262-278. the advent of technologically efficient exploitation of economic hydrocarbon reservoirs in shales, increasingly more research has been devoted to identifying and characterizing pore systems within shales. However, only a handful of these studies focused on the development of porosity in thermally mature unconventional reservoirs. In this study, the evolution of porosity and pore geometry in the Permian Whitehill Formation is addressed with the aid of ultrathin sections (2?×?3 cm, 10–20?μm thick) and field-emission scanning electron microscopy (FE-SEM) on samples with mean random vitrinite reflectance values ranging from 1.03 to 4.07 %Ro. We document a strong positive covariation of porosity and total organic carbon content (TOC) in all localities. However for samples with vitrinite reflectance values greater than 2.88 %Ro porosity per unit TOC decreased by over 25% relative to samples with lower thermal maturities. The positive covariation of thermal maturity and total porosity recorded here is unsurprising and have been documented previously in many gas shales. However, the dramatic decrease in porosity restricted to samples from localities that experienced advanced maturation (Ro?>?2.88%) is viewed as an evidence that porosity decrease is directly related to late thermal decarboxylation of organic matter. This is supported by the presence of pores and micro-fractures infilled by fibrous grains, including carbonates, clays, silicates, and phosphates, and residual fluid inclusions. These grains were likely generated from re-precipitation of framework grains previously dissolved by organic acids (carboxylic, phenolic) that were generated during thermochemical decarboxylation of the OM. Our findings do not only fill important gaps in the understanding of organic pore development, including processes that create, preserve, and destroy porosity, the porosities described here are also key to gas transfer from shale matrix to induced fractures during fracture stimulation programs.Clancy, S.A., Worrall, F., Davies, R.J., Gluyas, J.G., 2018. An assessment of the footprint and carrying capacity of oil and gas well sites: The implications for limiting hydrocarbon reserves. Science of The Total Environment 618, 586-594. estimate the likely physical footprint of well pads if shale gas or oil developments were to go forward in Europe and used these estimates to understand their impact upon existing infrastructure (e.g. roads, buildings), the carrying capacity of the environment, and how the proportion of extractable resources maybe limited. Using visual imagery, we calculate the average conventional well site footprints to be 10,800 m2 in the UK, 44,600 m2 in The Netherlands and 3000 m2 in Poland. The average area per well is 541 m2/well in the UK, 6370 m2/well in The Netherlands, and 2870 m2/well in Poland. Average access road lengths are 230 m in the UK, 310 m in The Netherlands and 250 m in Poland.To assess the carrying capacity of the land surface, well pads of the average footprint, with recommended setbacks, were placed randomly into the licensed blocks covering the Bowland Shale, UK. The extent to which they interacted or disrupted existing infrastructure was then assessed. For the UK, the direct footprint would have a 33% probability of interacting with immovable infrastructure, but this would rise to 73% if a 152 m setback was used, and 91% for a 609 m setback. The minimum setbacks from a currently producing well in the UK were calculated to be 21 m and 46 m from a non-residential and residential property respectively, with mean setbacks of 329 m and 447 m, respectively. When the surface and sub-surface footprints were considered, the carrying capacity within the licensed blocks was between 5 and 42%, with a mean of 26%. Using previously predicted technically recoverable reserves of 8.5 × 1011 m3 for the Bowland Basin and a recovery factor of 26%, the likely maximum accessible gas reserves would be limited by the surface carrying capacity to 2.21 × 1011 m3.Clark, K.D., Emaus, M.N., Varona, M., Bowers, A.N., Anderson, J.L., 2018. Ionic liquids: solvents and sorbents in sample preparation. Journal of Separation Science 41, 209-235. applications of ionic liquids (ILs) and IL-derived sorbents are rapidly expanding. By careful selection of the cation and anion components, the physicochemical properties of ILs can be altered to meet the requirements of specific applications. Reports of IL solvents possessing high selectivity for specific analytes are numerous and continue to motivate the development of new IL-based sample preparation methods that are faster, more selective, and environmentally benign compared to conventional organic solvents. The advantages of ILs have also been exploited in solid/polymer formats in which ordinarily nonspecific sorbents are functionalized with IL moieties in order to impart selectivity for an analyte or analyte class. Furthermore, new ILs that incorporate a paramagnetic component into the IL structure, known as magnetic ionic liquids (MILs), have emerged as useful solvents for bioanalytical applications. In this rapidly changing field, this Review focuses on the applications of ILs and IL-based sorbents in sample preparation with a special emphasis on liquid phase extraction techniques using ILs and MILs, IL-based solid-phase extraction, ILs in mass spectrometry, and biological applications.Clery, D., 2018. Earth-based planet finders power up. Science 359, 18-19. it comes to finding new worlds, NASA's Kepler spacecraft hogs the headlines, having racked up thousands of exoplanet discoveries since its launch in 2009. But before Kepler, the workhorses of exoplanet identification were ground-based instruments that measure tiny stellar wobbles caused by the gravity of an orbiting planet. They are now undergoing a quiet renaissance. The new generation of these devices may be precise enough to find a true Earth twin: a planet with the same mass as ours, orbiting a sunlike star once a year. That's something Kepler—sensitive to planet size, but not mass—can't do.On 9 December 2017, the Extreme Precision Spectrometer (EXPRES) took its first view of the sky on the Discovery Channel Telescope in Arizona. And in October 2017, the Echelle Spectrograph for Rocky Exoplanet and Stable Spectroscopic Observations (ESPRESSO) began operating at the European Southern Observatory's (ESO's) Very Large Telescope in Chile. Nearly two dozen other instruments are either under construction or have recently begun service. “It's now clear that exoplanets are a major part of astronomy,” says astronomer Jason Wright of Pennsylvania State University in State College. “So every major observatory needs a high-resolution spectrograph.”Such spectrographs spread starlight out into its array of spectral colors, which contains dark lines at wavelengths where gases in the star's atmosphere absorb light. Astronomers then look for tiny oscillating Doppler shifts in these lines over time, caused by planetary tugging.The technique works best for a massive planet orbiting close to its star, because its gravitational tug will be stronger. As a result, early discoveries—such as the first exoplanet to be found, in 1995—were usually “hot Jupiters,” giant planets in tight orbits. Then came the High Accuracy Radial velocity Planet Searcher (HARPS) at ESO's La Silla Observatory in Chile in 2003, a second-generation spectrograph that enabled astronomers to find smaller planets in wider orbits. (It has spotted about 130 to date.)In recent years, however, a new “transit” technique, led by Kepler, began to dominate. Kepler stared at 145,000 stars in one part of the sky and looked for dips in stellar brightness when a planet passed in front. Although Kepler has been prolific, identifying thousands of exoplanets and gauging their sizes, the planets and their stars are mostly too far away for ground-based spectrographs to determine their masses. Over the coming year, the launch of Kepler's successor, the Transiting Exoplanet Survey Satellite (TESS), along with Europe's Characterising Exoplanets Satellite (CHEOPS), will change all that. They will scour the sky for transits of nearby bright stars—perfect for ground-based follow-up. “To understand them we have to know their mass, that's absolutely fundamental,” says René Doyon of the University of Montreal in Canada.The new spectrographs should be able to weigh many of the planets found by TESS and CHEOPS. Astronomers boosted the instruments' precision in part by isolating them from mechanical and thermal noise—mounting them inside vacuum vessels that are separated from the telescope and piping in light through optical fibers. They also improved the reference spectrum against which the slow shifts in the spectral lines are gauged.Instruments such as HARPS rely on reference spectra produced by a thorium-argon lamps. But these produce a jumble of spectral lines of varying brightness. The new wave of spectrographs, including ESPRESSO and EXPRES, instead use laser frequency combs, which duplicate a single spectral line from a laser to form an ultraprecise reference grid, with lines of equal brightness spaced at regular intervals.With these improvements, says lead scientist Francesco Pepe of the University of Geneva in Switzerland, ESPRESSO aims to measure stellar movements as slow as 10 centimeters per second (roughly the speed of a giant tortoise). That would be a factor of 10 better than HARPS, and is exactly the motion expected to be caused by an Earth twin in an Earth-size orbit around a sunlike star.At this sort of precision, pulsing gases in the star's atmosphere can swamp the signal of any wobble. With some of the new spectrographs, researchers hope to disentangle the wobble from the noise by comparing spectral shifts across a range of wavelengths. But Pepe expects the noise to limit ESPRESSO to planets that are about three or four times as heavy as Earth. Only if the star is much less massive and more susceptible to a planet's tug might ESPRESSO see Earth-size planets.Other spectrographs aim for increased sensitivity to small planets by focusing on some of the smallest stars: red dwarfs. Red dwarfs emit most of their light in the infrared. Yet Earth's atmosphere allows only a narrow range of near-infrared wavelengths to reach the ground, posing a challenge for instrument builders. “There is a big push to develop instruments,” says Doyon, who leads a team building the Near-InfraRed Planet Searcher to work alongside HARPS on ESO's 3.6-meter telescope in Chile.The new instruments could even enhance transit studies. Besides searching for the spectral wobbles, they might see additional spectral lines caused by starlight passing through the atmosphere of a transiting planet. Transit spectroscopy with existing instruments has already revealed gases such as water and carbon dioxide in exoplanet atmospheres, and astronomers are now using it to look for signs of life (Science, 3 November 2017, p. 578). If the new spectrographs can characterize planets as well as find them, the renaissance could become a revolution.Clog, M., Lawson, M., Peterson, B., Ferreira, A.A., Santos Neto, E.V., Eiler, J.M., 2018. A reconnaissance study of 13C–13C clumping in ethane from natural gas. Geochimica et Cosmochimica Acta 223, 229-244. is the second most abundant alkane in most natural gas reservoirs. Its bulk isotopic compositions (δ13C and δD) are used to understand conditions and progress of cracking reactions that lead to the accumulation of hydrocarbons. Bulk isotopic compositions are dominated by the concentrations of singly-substituted isotopologues (13CH3–12CH3 for δ13C and 12CDH2–12CH3 for δ D). However, multiply-substituted isotopologues can bring additional independent constraints on the origins of natural ethane. The 13C2H6 isotopologue is particularly interesting as it can potentially inform the distribution of 13C atoms in the parent biomolecules whose thermal cracking lead to the production of natural gas. This work presents methods to purify ethane from natural gas samples and quantify the abundance of the rare isotopologue 13C2H6 in ethane at natural abundances to a precision of ±0.12‰‰ using a high-resolution gas source mass spectrometer. To investigate the natural variability in carbon-carbon clumping, we measured twenty-five samples of thermogenic ethane from a range of geological settings, supported by two hydrous pyrolysis of shales experiments and a dry pyrolysis of ethane experiment. The natural gas samples exhibit a range of ‘clumped isotope’ signatures (Δ13C2H6) at least 30 times larger than our analytical precision, and significantly larger than expected for thermodynamic equilibration of the carbon-carbon bonds during or after formation of ethane, inheritance from the distribution of isotopes in organic molecules or different extents of cracking of the source. However we show a relationship between the Δ13C2H6 and the proportion of alkanes in natural gas samples, which we believe can be associated to the extent of secondary ethane cracking. This scenario is consistent with the results of laboratory experiments, where breaking down ethane leaves the residue with a low Δ13C2H6 compared to the initial gas. Carbon-carbon clumping is therefore a new potential tracer suitable for the study of kinetic processes associated with natural gas.Cobain, S.L., Hodgson, D.M., Peakall, J., Wignall, P.B., Cobain, M.R.D., 2018. A new macrofaunal limit in the deep biosphere revealed by extreme burrow depths in ancient sediments. Scientific Reports 8, Article 261. is known to inhabit the top few 10s?cm of marine sediments, with rare burrows up to two metres below the seabed. Here, we provide evidence from deep-water Permian strata for a previously unrecognised habitat up to at least 8 metres below the sediment-water interface. Infaunal organisms exploited networks of forcibly injected sand below the seabed, forming living traces and reworking sediment. This is the first record that shows sediment injections are responsible for hosting macrofaunal life metres below the contemporaneous seabed. In addition, given the widespread occurrence of thick sandy successions that accumulate in deep-water settings, macrofauna living in the deep biosphere are likely much more prevalent than considered previously. These findings should influence future sampling strategies to better constrain the depth range of infaunal animals living in modern deep-sea sands. One Sentence Summary: The living depth of infaunal macrofauna is shown to reach at least 8 metres in new habitats associated with sand injections.Colman, D.R., Poudel, S., Hamilton, T.L., Havig, J.R., Selensky, M.J., Shock, E.L., Boyd, E.S., 2018. Geobiological feedbacks and the evolution of thermoacidophiles. The Isme Journal 12, 225-236. microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past. Comparative genomic analyses indicated that archaeal thermoacidophiles from independent lineages are enriched in similar protein-coding genes, consistent with convergent evolution aided by horizontal gene transfer. Because the generation of acidic environments and their successful habitation characteristically require O2, these results suggest that thermoacidophilic Archaea and the acidity of their habitats co-evolved after the evolution of oxygenic photosynthesis. Moreover, it is likely that dissolved O2 concentrations in thermal waters likely did not reach levels capable of sustaining aerobic thermoacidophiles and their acidifying activity until ~0.8?Ga, when present day atmospheric levels were reached, a time period that is supported by our estimation of divergence times for archaeal thermoacidophilic clades.Copado, J.A.?., Sandoval, R.Z., Castellanos, A.D., Padilla-Vaca, F., Franco, B., 2018. A protein complex bearing an oxidase with napthalene dihydrodiol dehydrogenase activity is induced in Mucor circinelloides strain YR-1 during growth on polycyclic aromatic compounds. Antonie van Leeuwenhoek 111, 297-309. are organisms capable of growing in a myriad of conditions and respond to counteract environmental cues. Several locations in the world are polluted with oil and its derivatives, and some microorganisms tolerant to these compounds have been isolated. Some fungi can grow in the presence of molecules such as polycyclic aromatic hydrocarbons as sole carbon sources. In this report, we further characterized the induced enzymes with phenanthrene from Mucor circinelloides YR-1 strain, isolated from a polluted field near a petrochemical facility in México. We identified a putative oxidase that is induced when growth with phenanthrene as sole carbon source at a pH of 8.5 and is NADP+ dependent. We show that this enzyme bears naphthalene dihydrodiol dehydrogenase activity with substrate preference for the cis-naphthalene over the trans-naphthalene, with an optimal pH in the range of 8–10. Mass spectrometry analysis revealed that the induced enzyme belongs to the NADP+ oxidase family enzymes with the typical Rossmann-fold for NADP+ binding. This enzyme seems to form a high molecular weight structure (~?541?kDa) and with a monomer of 57?kDa, suggesting that the multimer is constituted of 10 subunits. Our findings contribute to understanding of the roles that dihydrodiol dehydrogenases have in organisms exposed to toxic compounds in the environment and can regulate their expression.Corlies, P., Hayes, A.G., Birch, S.P.D., Lorenz, R., Stiles, B.W., Kirk, R., Poggiali, V., Zebker, H., Iess, L., 2017. Titan's topography and shape at the end of the Cassini mission. Geophysical Research Letters 44, 11,754-11,761. the conclusion of the Cassini mission, we present an updated topographic map of Titan, including all the available altimetry, SARtopo, and stereophotogrammetry topographic data sets available from the mission. We use radial basis functions to interpolate the sparse data set, which covers only ～9% of Titan's global area. The most notable updates to the topography include higher coverage of the poles of Titan, improved fits to the global shape, and a finer resolution of the global interpolation. We also present a statistical analysis of the error in the derived products and perform a global minimization on a profile-by-profile basis to account for observed biases in the input data set. We find a greater flattening of Titan than measured, additional topographic rises in Titan's southern hemisphere and better constrain the possible locations of past and present liquids on Titan's surface.Cotovicz, L.C., Knoppers, B.A., Brandini, N., Poirier, D., Costa Santos, S.J., Cordeiro, R.C., Abril, G., 2018. Predominance of phytoplankton-derived dissolved and particulate organic carbon in a highly eutrophic tropical coastal embayment (Guanabara Bay, Rio de Janeiro, Brazil). Biogeochemistry 137, 1-14. investigate the carbon dynamics in Guanabara Bay, an eutrophic tropical coastal embayment surrounded by the megacity of Rio de Janeiro (southeast coast of Brazil). Nine sampling campaigns were conducted for dissolved, particulate and total organic carbon (DOC, POC and TOC), dissolved inorganic carbon (DIC), partial pressure of CO2 (pCO2), chlorophyll a (Chl a), pheo-pigments and ancillary parameters. Highest DOC, POC and Chl a concentrations were found in confined-shallow regions of the bay during the summer period with strong pCO2 undersaturation, and DOC reached 82 mg L?1, POC 152 mg L?1, and Chl a 800 μg L?1. Spatially and temporally, POC and DOC concentrations varied positively with total pigments, and negatively with DIC. Strong linear correlations between these parameters indicate that the production of TOC translates to an equivalent uptake in DIC, with 85% of the POC and about 50% of the DOC being of phytoplanktonic origin. Despite the shallow depths of the bay, surface waters were enriched in POC and DOC relative to bottom waters in periods of high thermohaline stratification. The seasonal accumulation of phytoplankton-derived TOC in the surface waters reached about 105 g C m?2 year?1, representing between 8 and 40% of the net primary production. The calculated turnover time of organic carbon was 117 and 34 days during winter and summer, respectively. Our results indicate that eutrophication of coastal bays in the tropics can generate large stocks of planktonic biomass and detrital organic carbon which are permanently being produced and partially degraded and buried in sediments.Crawford, A.J., Baker, S.J., Belcher, C.M., 2018. Fossil charcoals from the Lower Jurassic challenge assumptions about charcoal morphology and identification. Palaeontology 61, 49-56. morphometry is increasingly employed in the analysis of Quaternary sediments, but has not been applied in studies of earlier sediments. We present findings relating to charcoal morphometry and morphotypes in a Toarcian sequence, which contains a preponderance of highly elongate forms, and morphometric values well outside expected ranges. SEM imaging reveals elongate particles of two distinct kinds. One originates in conifer xylem, and may be associated with formation at high levels of heating. It is proposed that the other may derive from tree ferns, or from plants with similar growth forms. Our results show the importance of recognizing the wide morphological variation that exists in sedimentary charcoal. Failing to do so may result in serious errors in its identification, interpretation and quantification.Crosby, C.H., Bailey, J.V., 2018. Experimental precipitation of apatite pseudofossils resembling fossil embryos. Geobiology 16, 80-87. phosphatic grains preserved in the rock record are interpreted as microfossils representing a diversity of microorganisms from bacteria to fossil embryos. In addition to bona fide primary biological features, phosphatic microfossils and fossil embryos commonly exhibit features that result from abiotic precipitation or diagenetic alteration. Distinguishing between abiotic and primary biological features can be difficult, and some features thought to represent biological tissue could instead be artifacts that are unrelated to the original morphology of a preserved organism. Here, we present experimentally generated, abiotically produced mineral precipitates that morphologically resemble biologically produced features, some of which may be observed in the rock record or noted in extant organisms, including embryos. These findings extend the diversity of biomorphic features known to result from abiotic precipitation.Crutchley, G.J., Kroeger, K.F., Pecher, I.A., Mountjoy, J.J., Gorman, A.R., 2017. Gas hydrate formation amid submarine canyon incision: Investigations from New Zealand's Hikurangi subduction margin. Geochemistry, Geophysics, Geosystems 18, 4299-4316. investigate gas hydrate system dynamics beneath a submarine canyon on New Zealand's Hikurangi subduction margin using seismic reflection data and petroleum systems modeling. High seismic velocities just above the base of gas hydrate stability (BGHS) indicate that concentrated gas hydrates exist beneath the canyon. Two-dimensional gas hydrate formation modeling shows how the process of canyon incision at this location alters the distribution and concentration of gas hydrate. The key modeling result is that free gas is trapped beneath the gas hydrate layer and then “captured” into a concentrated gas hydrate deposit as a result of a downward-shift in the BGHS driven by canyon incision. Our study thus provides new insight into the functioning of this process. From our data, we also conceptualize two other models to describe how canyons could significantly change gas hydrate distribution and concentration. One scenario is related to deflection of fluid flow pathways from over-pressured regions at the BGHS toward the canyon, and the other is based on relationships between simultaneous seafloor uplift and canyon incision. The relationships and processes described are of global relevance because of considerations of gas hydrate as an energy resource and the influence of both submarine canyons and gas hydrate systems on seafloor biodiversity.Cuadrado, D.G., Pan, J., 2018. Field observations on the evolution of reticulate patterns in microbial mats in a modern siliciclastic coastal environment. Journal of Sedimentary Research 88, 24-37. patterns often found in siliciclastic rocks as wrinkle structures may have been associated with or the product of biological activity. They are also present in modern environments, and laboratory experiments have elucidated the role of filamentous cyanobacteria in their formation, thus considering these microbes putatively as ecosystem engineers. The present study traces the evolution of reticulate structures in situ in a modern siliciclastic coastal sedimentary basin for over a year, under different hydrodynamic conditions. The results give new insights on the parameters involved in the formation and preservation of these microbial structures. Field observations documented the development of millimeter-size microbial reticulate structures with specific geometries. They were found in ephemeral ponds starting from two-dimensional submerged laminated cyanobacterial mats, and ultimately created three-dimensional protruding tufts and pinnacles in junctional positions after their desiccation. Reticulate patterns were formed on top of microbial mats four days after a storm flooding and two days after seawater vacated the area under calm conditions, by virtue of the motility of filamentous cyanobacteria. Through their subsequent consolidation they can be maintained in the form of reticulate structures and tufts for extended periods (months). These structures were found sharing an area with deformation sedimentary structures such as microbial folds, roll-ups, and ripped mats, formed under high energy. Therefore, calm settings such as those created by a shallow-water lamina seem to be a requisite for the formation of reticulate structures in the microbial mats, but once they become established, the microbial mats withstand high-energy hydrodynamic regimes. Our observations of modern structures and the sequential in situ study of their evolution provide linking references to laboratory and rock-record microbial reticulates, aiding in paleoenvironmental reconstruction.Cui, X., Bianchi, T.S., Kenney, W.F., Wang, J., Curtis, J.H., Xu, K., Savage, C., 2017. Carbon dynamics along a temperate fjord-head delta: Linkages with carbon burial in fjords. Journal of Geophysical Research: Biogeosciences 122, 3419-3430. used seven 210Pb-dated sediment cores from the Gaer Arm in the Doubtful Sound fjord complex, Fiordland, New Zealand to evaluate organic carbon (OC) dynamics in a temperate fjord-head delta. The highly dynamic spatial features of this delta were clearly evident in the observed sediment properties such as mass accumulation rates that varied by a factor of 14, sediment grain size by a factor 5, and sedimentary OC content by a factor 6. Low lignin concentrations (e.g., 2.95 mg (100 mg OC)?1) and syringic/vanillic ratios of lignin phenols (S/V; e.g., 0.44) at the upper deltaic stations were representative of substantial autochthonous OC contributions to delta sediments. Significantly higher acid/aldehyde ratios of vanillic phenols [(Ad/Al)v] at the deltaic stations (0.45–0.82) than the surface grabs (0.26–0.30) indicated rapid degradation of OC within the delta. Despite being a “hot spot” for OC oxidation, the delta likely improves OC preservation in the adjacent fjord by filtering out coarse-grained particles and exporting fine-grained particles to fjord sediments. Our results showed that fjord-head deltas can influence sedimentation and OC dynamics in select regions of fjords and thus warrant more examination of fjord-head processes, particularly in areas where they are expanding. In particular, as Earth warms and glaciers retreat, the newly exposed fjord-head platforms in high-latitude environments may evolve into similar “hot spots” of OC oxidation, thereby altering the dynamics of OC burial in these systems.D'Atri, V., Causon, T., Hernandez-Alba, O., Mutabazi, A., Veuthey, J.-L., Cianferani, S., Guillarme, D., 2018. Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry? Journal of Separation Science 41, 20-67. mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products, metabolites, glycans, lipids) to large biomolecules (proteins, protein complexes, biopharmaceuticals, oligonucleotides).D’Aniello, B., Semin, G.R., Alterisio, A., Aria, M., Scandurra, A., 2017. Interspecies transmission of emotional information via chemosignals: from humans to dogs (Canis lupus familiaris). Animal Cognition 21, 67-78. report a study examining interspecies emotion transfer via body odors (chemosignals). Do human body odors (chemosignals) produced under emotional conditions of happiness and fear provide information that is detectable by pet dogs (Labrador and Golden retrievers)? The odor samples were collected from the axilla of male donors not involved in the main experiment. The experimental setup involved the co-presence of the dog’s owner, a stranger and the odor dispenser in a space where the dogs could move freely. There were three odor conditions [fear, happiness, and control (no sweat)] to which the dogs were assigned randomly. The dependent variables were the relevant behaviors of the dogs (e.g., approaching, interacting and gazing) directed to the three targets (owner, stranger, sweat dispenser) aside from the dogs’ stress and heart rate indicators. The results indicated with high accuracy that the dogs manifested the predicted behaviors in the three conditions. There were fewer and shorter owner directed behaviors and more stranger directed behaviors when they were in the “happy odor condition” compared to the fear odor and control conditions. In the fear odor condition, they displayed more stressful behaviors. The heart rate data in the control and happy conditions were significantly lower than in the fear condition. Our findings suggest that interspecies emotional communication is facilitated by chemosignals.Dai, C., Xue, L., Wang, W., Li, X., 2017. Analysis of the influencing factors on the well performance in shale gas reservoir. Geofluids 2017, Article 7818346. to the ultralow permeability of shale gas reservoirs, stimulating the reservoir formation by using hydraulic fracturing technique and horizontal well is required to create the pathway of gas flow so that the shale gas can be recovered in an economically viable manner. The hydraulic fractured formations can be divided into two regions, stimulated reservoir volume (SRV) region and non-SRV region, and the produced shale gas may exist as free gas or adsorbed gas under the initial formation condition. Investigating the recovery factor of different types of shale gas in different region may assist us to make more reasonable development strategies. In this paper, we build a numerical simulation model, which has the ability to take the unique shale gas flow mechanisms into account, to quantitatively describe the gas production characteristics in each region based on the field data collected from a shale gas reservoir in Sichuan Basin in China. The contribution of the free gas and adsorbed gas to the total production is analyzed dynamically through the entire life of the shale gas production by adopting a component subdivision method. The effects of the key reservoir properties, such as shale matrix, secondary natural fracture network, and primary hydraulic fractures, on the recovery factor are also investigated.Dalai, P., Ustriyana, P., Sahai, N., 2018. Aqueous magnesium as an environmental selection pressure in the evolution of phospholipid membranes on early earth. Geochimica et Cosmochimica Acta 223, 216-228. compartmentalization of simple biomolecules by membrane bilayers was, presumably, a critical step in the emergence of the first cell-like entities, protocells. Their membranes were likely composed of single chain amphiphiles (SCAs), but pure SCA membranes especially those with short-chains are highly unstable towards divalent cations, which are ubiquitous in aqueous environments. The prebiotic synthesis of phospholipids (PLs), even in only trace amounts, may also have been possible. PL membranes are much more stable towards divalent cations. Here, we show the transition of fatty acid membranes to mixed fatty acid-PL and, finally, to PL membranes in the presence of Mg2+, which acts as an environmental selection pressure, and we propose different mechanisms for the observed increased Mg2+-immunity. The “fatal” concentration ([Mg2+]fatal) at which vesicles are disrupted increased dramatically by an order of magnitude from OA to mixed to POPC vesicles. Two mechanisms for the increasing immunity were determined. The negative charge density of the vesicles decreased with increasing POPC content, so more Mg2+ was required for disruption. More interestingly, Mg2+ preferentially bound to and abstracted OA from mixed lipid membranes, resulting in relatively POPC-enriched vesicles compared to the initial ratio. The effect was the most dramatic for the largest initial OA-POPC ratio representing the most primitive protocells. Thus, Mg2+ acted to evolve the mixed membrane composition towards PL enrichment. To the best of our knowledge, this is the first report of selective lipid abstraction from mixed SCA-PL vesicles. These results may hold implications for accommodating prebiotic Mg2+-promoted processes such as non-enzymatic RNA polymerization on early Earth.Darvish, H., Ghani, P., Zare, M., Rezaei, H., 2018. Application of fuzzy c-means algorithm as a novel method to predict density of mixtures of Athabasca bitumen and heavy n-alkane. Petroleum Science and Technology 36, 338-342. significant number of oil reservoir are bitumen and heavy oil. One of the approaches to enhance oil recovery of these types of reservoir is dilution of reservoir oil by injection of a solvent such as tetradecane into the reservoirs to modify viscosity and density of reservoir fluids. In this investigation, an effective and robust estimating algorithm based on fuzzy c-means (FCM) algorithm was developed to predict density of mixtures of Athabasca bitumen and heavy n-alkane as function of temperature, pressure and weight percent of the solvent. The model outputs were compared to experimental data from literature in different conditions. The coefficients of determination for training and testing datasets are 0.9989 and 0.9988. The comparisons showed that the proposed model can be an applicable tool for predicting density of mixtures of bitumen and heavy n-alkane.Daryasafar, A., Shahbazi, K., 2018. The effect of different solvents on the density of undersaturated Athabasca bitumen: Application in VAPEX and ES-SAGD. Petroleum Science and Technology 36, 222-226. the density of bitumen after solvent injection is highly required in solvent-based recovery techniques like expanding solvent-steam assisted gravity drainage (ES-SAGD) and vapor extraction (VAPEX) in order to estimate the cumulative oil recovery by these processes. Using experimental procedures for this purpose is so expensive and time-consuming; therefore, it is crucial to propose a rapid and accurate model for predicting the effect of various solvents on the dilution of bitumen. In this study, an adaptive neuro-fuzzy interference system is introduced to estimate the effect of methane, ethane, propane, butane, carbon dioxide, and n-hexane on the density of undersaturated Athabasca bitumen in wide ranges of operating conditions. The obtained results were in an excellent agreement with experimental data with coefficients of determination (R2) of 0.99997 and 0.99948 for training and testing datasets, respectively. Statistical analyses illustrate the superiority of the proposed model in predicting the bitumen density at different conditions.Daryasafar, A., Shahbazi, K., 2018. Prediction of dynamic viscosity of n-alkanes at high pressures using a rigorous approach. Petroleum Science and Technology 36, 333-337. adaptive neuro-fuzzy interference system has been developed for estimating the dynamic viscosity of n-alkanes in a wide range of operating conditions. In this study, for the first time, a simple predictive model is proposed for viscosity prediction of n-pentane, n-octane, n-nonane, n-decane and dodecane at various pressures and temperatures, especially at high pressures, without needing to measurement or estimation of density. This tool predicts the dynamic viscosity of the n-alkanes as function of pressure, temperature and n-alkanes' molecular weight. The obtained results of the model were in an excellent agreement with experimental data with an acceptable coefficient of determination of 0.999 for both training and testing datasets. Moreover, the validity of the proposed model for viscosity trends prediction at various conditions was demonstrated and it showed a very good match with actual data. This model is simple to use and can be of massive evaluation for better understanding the behavior of fluids under reservoir conditions.Daryasafar, N., Borazjani, O., Daryasafar, A., 2018. Adsorption kinetics of natural surfactants on carbonate minerals in enhanced oil recovery processes. Petroleum Science and Technology 36, 371-377. of the most promising methods for improving oil recovery from carbonate reservoirs is surfactant flooding in which the trapped oil can be mobilized by alteration in the wettability of rock surfaces and also reduction in the interfacial tension between oil and water. Adsorption of surfactants on carbonate minerals plays a key role in designing this process and may make it less effective for enhancing oil recovery. Natural surfactants have been proposed by many researchers since they have lower cost and also less detrimental environmental effects compared to the industrial surfactants. Well-established predictive models for predicting the adsorption of natural surfactants have some issues which need to be addressed. Therefore, developing an accurate, rapid and simple model is crucial. In this study, a least square support vector machine (LSSVM) optimized with coupled simulated annealing (CSA) algorithm is developed for accurate prediction of natural surfactants kinetic adsorption on carbonate minerals. Obtained results by this model were in a very good agreement with experimental results. Additionally, the results showed that the proposed model has the highest accuracy and performance in comparison to the previous kinetic models. Afterward, the effect of natural surfactants adsorption on the amount of oil recovery and also the quality of the produced oil was investigated via core flooding tests for showing the importance of determining the adsorption of surfactants before any surfactant flooding. Results demonstrated that lower surfactants adsorption yields higher oil recovery factor and oil with higher viscosity.Davies, N.S., Liu, A.G., Gibling, M.R., Miller, R.F., 2018. Reply to comment on the paper by Davies et al. “Resolving MISS conceptions and misconceptions: A geological approach to sedimentary surface textures generated by microbial and abiotic processes” (Earth Science Reviews, 154 (2016), 210–246). Earth-Science Reviews 176, 384-386. thank Noffke (2017) for her comment and for providing an opportunity to clarify our classification of “sedimentary surface textures”. We accord great credit to Dr. Noffke and other dedicated researchers whose detailed work has brought microbially induced sedimentary structures (MISS) to the widespread attention of geoscientists. However, we stand by our assertion that attributing structures observed in practical field and laboratory studies to processes of formation is much more problematic than Noffke (2017) indicates. Indeed, points in the Comment confirm the need for a classification system that categorises the degree of certainty attributed to a given interpretation. We stress that our paper was not designed as a critique of previous studies of MISS but rather was designed to encourage a reasonable assessment of uncertainty in assigning sedimentary surface textures to physical processes or to MISS.While the contribution of Noffke (2017) raises valid points of discussion, to which we respond below, we first emphasise that in several places the Comment inaccurately reflects the conclusions of Davies et al. (2016). Furthermore, Noffke (2017) attributes to us a large number of statements and assumptions that do not appear in the original paper (e.g., “the paper by Davies et al. regards microbial mats simply as coherent layers that develop at random atop of clastic deposits”, “Davies et al. article assumes that stages of mat development were never considered in MISS research”, “Davies et al.'s statement that crinkled surfaces are now ‘routineously [sic] described as wrinkle structures’ is therefore incorrect”; “they are not interference ripple marks, as the article of Davies et al. assumes”; “The unusual statement by Davies et al. that Noffke (2014) [sic] claims to have detected fossil life on Mars is a misrepresentation of the conclusions presented”; plus other instances). In these and other respects, the Comment published by Noffke (2017) is an erroneous precis of Davies et al. (2016), and we make no attempt here to argue against statements in which our conclusions have been misrepresented.Fully testing Noffke's (2015) hypothesis requires the return of specimens from Mars. However, had the same Martian features been studied by a researcher employing our classification scheme, they could have initially classified the features as ‘Ba’ or ‘ab’. Subsequent like-for-like comparison of rocks on Earth and Mars (Fig. 1), would reveal to the researcher that abiotic processes can sculpt rock outcrops with superficial similarity to living microbial mats. The pragmatic flexibility of our scheme (Davies et al., 2016) means that they would now be able to classify these particular Martian features as ‘Ab’, or even ‘A’.Davudov, D., Moghanloo, R.G., 2018. Scale-dependent pore and hydraulic connectivity of shale matrix. Energy & Fuels 32, 99-106. resources have distinctive characteristics compared to conventional reservoirs, including microsized pores (IUPAC definition), ultralow permeability, several gas storage mechanisms, and complex fluid flow behavior. Prediction of productivity and deliverability of shale systems requires knowledge about in situ porosity and permeability. In this study, we evaluate pore and hydraulic connectivity of matrix for Barnett and Haynesville shale plays based on mercury injection capillary pressure (MICP) data and percolation theory. Using MICP porosity values measured at the laboratory for different sample size, accessible porosity and permeability for Barnett and Haynesville shale samples are reported. Next, pore and hydraulic connectivity for both Barnett and Haynesville samples are evaluated based on percolation theory. Moreover, permeability values that have been calculated based on MICP data are used to estimate the average coordination number as a function of sample size. Our results indicate that accessible porosity and matrix permeability decreases with increasing sample size, which predicts lower connectivity for shale matrix in large scale. Consistent with percolation theory, results suggest that accessible porosity decreases with increasing sample size, following a power law function. Furthermore, results show that sample size has a significant impact on the estimated coordination number; this is expected, because interconnected porosity is a strong function of the average coordination number. The main contribution of this work is the evaluation of accessible porosity and pore connectivity for different sample sizes from two shale plays. The new insight about scale-dependent pore connectivity and interconnected porosity may lead to improved predictions of production performance and project economics.de la Fuente, M., Calvo, E., Skinner, L., Pelejero, C., Evans, D., Müller, W., Povea, P., Cacho, I., 2017. The evolution of deep ocean chemistry and respired carbon in the eastern Equatorial Pacific over the last deglaciation. Paleoceanography and Paleoclimatology 32, 1371-1385. has been shown that the deep Eastern Equatorial Pacific (EEP) region was poorly ventilated during the Last Glacial Maximum (LGM) relative to Holocene values. This finding suggests a more efficient biological pump, which indirectly supports the idea of increased carbon storage in the deep ocean contributing to lower atmospheric CO2 during the last glacial. However, proxies related to respired carbon are needed in order to directly test this proposition. Here we present Cibicides wuellerstorfi B/Ca ratios from Ocean Drilling Program Site 1240 measured by laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) as a proxy for deep water carbonate saturation state (Δ[CO32?], and therefore [CO32?]), along with δ13C measurements. In addition, the U/Ca ratio in foraminiferal coatings has been analyzed as an indicator of oxygenation changes. Our results show lower [CO32?], δ13C, and [O2] values during the LGM, which would be consistent with higher respired carbon levels in the deep EEP driven, at least in part, by reduced deep water ventilation. However, the difference between LGM and Holocene [CO32?] observed at our site is relatively small, in accordance with other records from across the Pacific, suggesting that a “counteracting” mechanism, such as seafloor carbonate dissolution, also played a role. If so, this mechanism would have increased average ocean alkalinity, allowing even more atmospheric CO2 to be “sequestered” by the ocean. Therefore, the deep Pacific Ocean very likely stored a significant amount of atmospheric CO2 during the LGM, specifically due to a more efficient biological carbon pump and also an increase in average ocean alkalinity.de Moor, J.M., Kern, C., Avard, G., Muller, C., Aiuppa, A., Saballos, A., Ibarra, M., LaFemina, P., Protti, M., Fischer, T.P., 2017. A new sulfur and carbon degassing inventory for the southern Central American volcanic arc: The importance of accurate time-series data sets and possible tectonic processes responsible for temporal variations in arc-scale volatile emissions. Geochemistry, Geophysics, Geosystems 18, 4437-4468. work presents a new database of SO2 and CO2 fluxes from the Southern Central American Volcanic Arc (SCAVA) for the period 2015–2016. We report ～300 SO2 flux measurements from 10 volcanoes and gas ratios from 11 volcanoes in Costa Rica and Nicaragua representing the most extensive available assessment of this ～500 km arc segment. The SO2 flux from SCAVA is estimated at 6,240?±?1,150 T/d, about a factor of three higher than previous estimations (1972–2013). We attribute this increase in part to our more complete assessment of the arc. Another consideration in interpreting the difference is the context of increased volcanic activity, as there were more eruptions in 2015–2016 than in any period since ～1980. A potential explanation for increased degassing and volcanic activity is a change in crustal stress regime (from compression to extension, opening volcanic conduits) following two large (Mw?>?7) earthquakes in the region in 2012. The CO2 flux from the arc is estimated at 22,500?±?4,900 T/d, which is equal to or greater than estimates of C input into the SCAVA subduction zone. Time-series data sets for arc degassing need to be improved in temporal and spatial coverage to robustly constrain volatile budgets and tectonic controls. Arc volatile budgets are strongly influenced by short-lived degassing events and arc systems likely display significant short-term variations in volatile output, calling for expansion of nascent geochemical monitoring networks to achieve spatial and temporal coverage similar to traditional geophysical networks.de Toffoli, A.L., Maciel, E.V.S., Fumes, B.H., Lan?as, F.M., 2018. The role of graphene-based sorbents in modern sample preparation techniques. Journal of Separation Science 41, 288-302. application of graphene-based sorbents in sample preparation techniques has increased significantly since 2011. These materials have good physicochemical properties to be used as sorbent and have shown excellent results in different sample preparation techniques. Graphene and its precursor graphene oxide have been considered to be good candidates to improve the extraction and concentration of different classes of target compounds (e.g., parabens, polycyclic aromatic hydrocarbon, pyrethroids, triazines, and so on) present in complex matrices. Its applications have been employed during the analysis of different matrices (e.g., environmental, biological and food). In this review, we highlight the most important characteristics of graphene-based material, their properties, synthesis routes, and the most important applications in both off-line and on-line sample preparation techniques. The discussion of the off-line approaches includes methods derived from conventional solid-phase extraction focusing on the miniaturized magnetic and dispersive modes. The modes of microextraction techniques called stir bar sorptive extraction, solid phase microextraction, and microextraction by packed sorbent are discussed. The on-line approaches focus on the use of graphene-based material mainly in on-line solid phase extraction, its variation called in-tube solid-phase microextraction, and on-line microdialysis systems.De Vleeschouwer, D., Da Silva, A.-C., Sinnesael, M., Chen, D., Day, J.E., Whalen, M.T., Guo, Z., Claeys, P., 2017. Timing and pacing of the Late Devonian mass extinction event regulated by eccentricity and obliquity. Nature Communications 8, Article 2268. Late Devonian envelops one of Earth’s big five mass extinction events at the Frasnian–Famennian boundary (374?Ma). Environmental change across the extinction severely affected Devonian reef-builders, besides many other forms of marine life. Yet, cause-and-effect chains leading to the extinction remain poorly constrained as Late Devonian stratigraphy is poorly resolved, compared to younger cataclysmic intervals. In this study we present a global orbitally calibrated chronology across this momentous interval, applying cyclostratigraphic techniques. Our timescale stipulates that 600?kyr separate the lower and upper Kellwasser positive δ13C excursions. The latter excursion is paced by obliquity and is therein similar to Mesozoic intervals of environmental upheaval, like the Cretaceous Ocean-Anoxic-Event-2 (OAE-2). This obliquity signature implies coincidence with a minimum of the 2.4?Myr eccentricity cycle, during which obliquity prevails over precession, and highlights the decisive role of astronomically forced “Milankovitch” climate change in timing and pacing the Late Devonian mass extinction.Dehaghani, A.H.S., Karami, B., 2018. A new predictive thermodynamic framework for phase behavior of gas hydrate. Fuel 216, 796-809. study presents a thermodynamic framework for predicting hydrate equilibrium pressure of gas species including methane, ethane, propane, nitrogen, carbon dioxide and hydrogen sulfide and their mixtures. For this purpose, Peng–Robinson–Stryjek–Vera equation of state (PRSV-EOS) along with modified Huron-Vidal (MHV1) mixing rule and UNIQUAC model were employed to calculate fugacity and activity coefficient of water in equilibrated fluid phases. To represent phase behavior of solid hydrate, a modified version of van der Waals and Platteeuw (vWd-P) model was utilized which accounts for guest interaction with water molecules beyond first shell of cavity and also asymmetry of encapsulated molecules and cage structure. In addition, dissolution of gas compounds in aqueous phase and subsequent non-ideality of water was taken into account. It was realized that both physical phenomena are of marked influence on the prediction accuracy.In contrast to conventional modelling approaches which scarify some part of equilibrium data to regress some adjustable parameters, advantageously, our model does not require any pre-matching. It was observed that present framework gives accurate prediction for equilibrium pressure of hydrates of CH4, C2H6, C3H8, CO2, N2 and H2S with overall average absolute percent deviation (AAPD) 3.2, 3.4, 3.7, 1.5, 2.8 and 1.3, respectively. Also, incipient pressure of hydrate formed by binary gas mixtures comprised of aforementioned single components could accurately be predicted by proposed approach, which is detailed in the manuscript. Overall, formation pressures predicted by proposed modelling approach are more accurate (or at least comparable) to outstanding models presented in the hydrate literature.Deirieh, A., Casey, B., Germaine, J.T., Xu, G., 2018. The integration of magnifications: A novel approach to obtain representative information about the pore space of mudrocks from SEM images. Applied Clay Science 154, 73-82. resolution Scanning Electron Microscopy (SEM) imaging has been widely used to characterize the pore space of mudrocks. However, obtaining representative microfabric information has been limited by the highly heterogeneous microstructure of mudrocks, which contains pores and particles spanning several length scales. The integration of magnifications (IOM) method was developed to obtain representative information about the pore space of mudrocks. This method combines information from SEM images acquired at different magnifications to characterize the pore space. High magnification images with high resolution are used to quantify small pores and low magnification images with lower resolution are used to quantify large pores. These different scales are then mathematically combined to obtain a complete pore space representation. The method was validated using 2D Monte Carlo simulations applied on a synthetic 2D microstructure with a prescribed porosity and pore size distribution. The applicability of the method was illustrated by computing the porosity and pore size distribution of two naturally resedimented mudrocks. The IOM method provides a practical and economical alternative to the current cumbersome methodology that stitches together hundreds to thousands of SEM images to obtain large representative mosaics.Delgado-Baquerizo, M., Oliverio, A.M., Brewer, T.E., Benavent-González, A., Eldridge, D.J., Bardgett, R.D., Maestre, F.T., Singh, B.K., Fierer, N., 2018. A global atlas of the dominant bacteria found in soil. Science 359, 320-325.: The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa. Our study narrows down the immense number of bacterial taxa to a “most wanted” list that will be fruitful targets for genomic and cultivation-based efforts aimed at improving our understanding of soil microbes and their contributions to ecosystem functioning.Editor's summary: A global map of soil bacteria. Soil bacteria play key roles in regulating terrestrial carbon dynamics, nutrient cycles, and plant productivity. However, the natural histories and distributions of these organisms remain largely undocumented. Delgado-Baquerizo et al. provide a survey of the dominant bacterial taxa found around the world. In soil collections from six continents, they found that only 2% of bacterial taxa account for nearly half of the soil bacterial communities across the globe. These dominant taxa could be clustered into ecological groups of co-occurring bacteria that share habitat preferences. The findings will allow for a more predictive understanding of soil bacterial diversity and distribution.Dement’ev, V.A., 2018. Origin of the simplest genetic code as an evolutionary stage of the Earth. Geochemistry International 56, 65-70. minimal set of conditions is found under which a primitive genetic code can be formed in the chemical world in which polypeptides and polynucleotides can be produced. Molecular modeling demonstrates that multiple cycles of synthesis and thermal destruction of biopolymers result in spontaneous complication of their structure. This evolutionary progressive complication of polypeptides and polynucleotides coding them results in certain specific functions of the polypeptides, which are similar to properties of enzymes. Computer simulations confirm the internal logical consistency of the simplified scenario suggested for the origin of a genetic code as a process of transferring information on the structure of biomolecules to the historical future, in spite of the continuous thermal decomposition of these structures. Original Russian Text ? V.A. Dement’ev, 2018, published in Geokhimiya, 2018, No. 1, pp. 70–76.Deshmukh, S.K., Prakash, V., Ranjan, N., 2018. Marine fungi: A source of potential anticancer compounds. Frontiers in Microbiology 8, 2536. doi: 10.3389/fmicb.2017.02536. from marine fungi have hogged the limelight in drug discovery because of their promise as therapeutic agents. A number of metabolites related to marine fungi have been discovered from various sources which are known to possess a range of activities as antibacterial, antiviral and anticancer agents. Although, over a thousand marine fungi based metabolites have already been reported, none of them have reached the market yet which could partly be related to non-comprehensive screening approaches and lack of sustained lead optimization. The origin of these marine fungal metabolites is varied as their habitats have been reported from various sources such as sponge, algae, mangrove derived fungi, and fungi from bottom sediments. The importance of these natural compounds is based on their cytotoxicity and related activities that emanate from the diversity in their chemical structures and functional groups present on them. This review covers the majority of anticancer compounds isolated from marine fungi during 2012–2016 against specific cancer cell lines.Desmond, P., Best, J.P., Morgenroth, E., Derlon, N., 2018. Linking composition of extracellular polymeric substances (EPS) to the physical structure and hydraulic resistance of membrane biofilms. Water Research 132, 211-221. effect of extracellular polymeric substances (EPS) on the meso-scale physical structure and hydraulic resistance of membrane biofilms during gravity driven membrane (GDM) filtration was investigated. Biofilms were developed on the surface of ultrafiltration membranes during dead-end filtration at ultra-low pressure (70?mbar). Biofilm EPS composition (total protein, polysaccharide and eDNA) was manipulated by growing biofilms under contrasting nutrient conditions. Nutrient conditions consisted of (i) a nutrient enriched condition with a nutrient ratio of 100:30:10 (C: N: P), (ii) a phosphorus limitation (C: N: P ratio: 100:30:0), and (iii) a nitrogen limitation (C: N: P ratio: 100:0:10). The structure of the biofilm was characterised at meso-scale using Optical Coherence Tomography (OCT). Biofilm composition was analysed with respect to total organic carbon, total cellular mass and extracellular concentrations of proteins, polysaccharides, and eDNA. 2D-confocal Raman mapping was used to characterise the functional group composition and micro-scale distribution of the biofilms EPS. Our study reveals that the composition of the EPS matrix can determine the meso-scale physical structure of membrane biofilms and in turn its hydraulic resistance. Biofilms grown under P limiting conditions were characterised by dense and homogeneous physical structures with high concentrations of polysaccharides and eDNA. Biofilm grown under nutrient enriched or N limiting conditions were characterised by heterogeneous physical structures with lower concentrations of polysaccharides and eDNA. For P limiting biofilms, 2D-confocal Raman microscopy revealed a homogeneous spatial distribution of anionic functional groups in homogeneous biofilm structures with higher polysaccharide and eDNA concentrations. This study links EPS composition, physical structure and hydraulic resistance of membrane biofilms, with practical relevance for the hydraulic performances of GDM ultrafiltration.DeVries, T., 2018. New directions for ocean nutrients. Nature Geoscience 11, 15-16. elemental ratios of marine phytoplankton and organic matter vary widely across ocean biomes, according to a catalogue of biogeochemical data, suggesting that climate change may have complex effects on the ocean’s elemental cycles.In the surface ocean, phytoplankton use carbon and nutrients such as nitrogen and phosphorus to synthesize organic compounds. A portion of this biomass sinks into the deep ocean, where it can be sequestered for months to centuries. The efficiency of this biological carbon pump is determined in part by the relative proportions of carbon and nutrients assimilated by plankton. Writing in Nature Geoscience in 2013, Martiny and co-workers1 demonstrated large latitudinal variations in the C:N:P ratio of marine organic matter, highlighting the role of the environment in shaping the elemental composition of plankton communities. Spurred by the findings of Martiny et al. and others, scientists are still unravelling how this variability may affect the ocean’s elemental cycles as anthropogenic climate change unfolds.In 1934, Alfred Redfield2 proposed that the major biochemical elements (namely carbon, nitrogen and phosphorus) accumulate in inorganic forms in the ocean in the same proportion as they accumulate in plankton biomass. Redfield found that the proportions of C:N:P derived from respired organic matter in the sea, and that found from averaging a wide variety of marine plankton, were almost identical at roughly 140:20:1. In the decades that followed, these ratios, or stoichiometries, were refined somewhat to arrive at the ‘Redfield ratio’ — a C:N:P ratio in marine organic matter of 106:16:1 (ref. 3). The Redfield ratio was later adopted by biogeochemical models to tie the biological cycling of carbon in the ocean to that of the macronutrients. These models found that changes in the ocean’s biological carbon pump are driven by high-latitude oceans where surface macronutrients are abundant: a phenomenon known as high-latitude dominance4. Later global climate models and Earth system models were developed that included more sophisticated representations of ocean biogeochemistry, but these models still adopted a constant and uniform Redfield ratio5.Outside of the model world, marine biologists (among them Redfield himself) had long recognized the variability of C:N:P ratios in marine plankton6,7. In the early 2000s the underpinnings of this variability were being unravelled. Culture-based studies demonstrated that C:N:P stoichiometry differed markedly in phytoplankton descended from different evolutionary lineages: members of the ancient Green superfamily had much higher C:P ratios than members of the more recently evolved Red superfamily8. These differences could be traced to the relative proportions of certain biochemicals within plankton cells9. Plankton adapted to low-nutrient conditions act as ‘survivalists’: they stock up on N-rich proteins and pigments such as chlorophyll, which results in high cellular N:P ratios10. Plankton adapted to nutrient-rich environments take advantage of abundant nutrients to engage in exponential growth: their cells are enriched in P-rich nucleic acids and they have lower N:P ratios10. However, it remained unclear whether large-scale patterns of C:N:P variability existed in the ocean that could be matched to the phylogenetic or phenotypic variability observed in the lab.Martiny and co-workers filled this observational gap by providing a global-scale view of C:N:P variations in marine organic matter. With a compilation of both old and new observations, they identified patterns of C:N:P variability across a wide range of ocean biomes (Fig. 1). Their results demonstrated clear and coherent variations in organic matter stoichiometry. In the nutrient-starved subtropical gyres, organic matter C:N:P ratios were as high as 226:37:1, whereas in nutrient-rich high-latitude regions they were as low as 66:11:1, consistent with the conclusions drawn from culture experiments. Thus, the global-scale variations in organic matter C:N:P appear to reflect shifts in the composition of plankton communities: fast-growing plankton with low C:N:P such as diatoms dominate in nutrient-replete waters, while slow-growing plankton with high C:N:P survive in the deserts of the subtropical gyres. The patterns of C:P variability in organic matter observed by Martiny and co-workers were subsequently confirmed by inversions of global nutrient and carbon data11, and by analyses of nutrient and oxygen data12, adding to previous models that had demonstrated large regional variability in plankton N:P ratios13,14.The work of Martiny and co-workers ignited interest in the implications of flexible plankton C:N:P stoichiometry for the ocean’s carbon cycle. Model simulations that included flexible C:P stoichiometry of phytoplankton did not show the high-latitude dominance of the biological pump that characterized previous constant-stoichiometry models15. Because low-latitude plankton have higher C:P ratios than their high-latitude counterparts, any changes in the delivery of nutrients to low-latitude oceans can have a much greater impact on the biological pump than comparable changes in the high latitudes. Flexible plankton C:N:P stoichiometry also tends to buffer the biological pump response to climate change. As the oceans warm and become more stratified, nutrient supply to the surface ocean is cut off, and productivity declines. If the ratio of carbon to nutrients in the plankton increases in response, the productivity loss is counteracted16.Anthropogenic climate change is affecting ocean ecosystems in ways that will cause substantial stoichiometric shifts in plankton. In addition to expansion of low-nutrient regions that favour survivalist plankton with high C:N:P ratios, warmer ocean temperatures promote higher C:P and N:P ratios of plankton17,18, and enhance the activity of C-mobilizing enzymes, further contributing to increased C:N:P of plankton19. Rising CO2 levels may also help shift plankton C:N and C:P ratios higher20. The overall effects of climate change thus appear to favour a stoichiometric shift toward more C-rich and nutrient-poor organic matter (Fig. 1).The effects of this stoichiometric shift will cascade into other elemental cycles, such as ocean oxygen and nitrogen cycling. Many regions of the ocean are subject to hypoxic or even anoxic conditions. Multiple forces conspire to push oxygen levels even lower, including rising temperatures, stagnating circulation and coastal eutrophication. If stoichiometric shifts make organic matter increasingly C-rich and nutrient-poor, this will exacerbate the deoxygenation problem as microbes consume more oxygen to metabolize nutrients. A higher plankton N:P ratio will also affect the balance of the ocean’s nitrogen cycle: as nitrogen is drawn out of the surface ocean, the ecological niche of nitrogen-fixing phytoplankton will expand14, in turn pushing the total nitrogen inventory of the ocean higher (Fig. 1).The interactions of these perturbations to elemental cycles are complex and difficult to predict. Thanks to the work of Martiny et al.1 and others, we are beginning to develop a process-level understanding of plankton elemental composition that can be integrated into biogeochemical models, yielding more accurate predictions of ocean CO2 uptake, ocean nutrient balance, and ocean deoxygenation.References1. Martiny, A. C. et al. Nat. Geosci. 6, 279–283 (2013).2. Redfield, A. C. On the Proportions of Organic Derivatives in Sea Water and Their Relation to the Composition of Plankton 176–192 (James Johnstone Memorial Volume, Liverpool Univ. Press, Liverpool, 1934).3. Redfield, A. C. Amer. Scientist 46, 205–221 (1958).4. Sarmiento, J. S. & Toggweiler, R. J. Nature 308, 621–624 (1984).5. Sarmiento, J. S., Hughes, T. M. C. & Manabe, S. Nature 393, 245–249 (1998).6. Copin-Montegut, C. & Copin-Montegut, G. Deep-Sea Res. 30, 31–46 (1983).7. Karl, D., Letelier, R., Tupas, L., Dore, J., Christian, J. & Hebel, D. Nature 38, 533–538 (1997).8. Quigg, A. et al. Nature 425, 291–294 (2003).9. Geider, R. J. & La Roche, J. European J. Phycology 37, 1–17 (2002).10. Klausmeier, C. A., Litchman, E., Dufresne, T. & Levin, S. A. Nature 429, 171–174 (2004).11. Teng, Y.-C. et al. Nat. Geosci. 7, 895–898 (2014).12. DeVries, T. & Deutsch, C. Nat. Geosci. 7, 890–895 (2014).13. Weber, T. S. & Deutsch, C. Nature 467, 550–554 (2010).14. Weber, T. S. & Deutsch, C. Nature 467, 419–422 (2012).15. Galbraith, E. D. & Martiny, A. C. Proc. Natl Acad. Sci. USA 112, 8199–8204 (2015).16. Tanioka, T. & Matsumoto, K. Glob. Biogeochem. Cycles 31, 1–15 (2017).17. Toseland, A. et al. Nat. Clim. Change 3, 979–984 (2013).18. Yvon-Durocher, G., Schaum, C.-E. & Trimmer, M. Frontiers Microbiol. 8, 1–14 (2017).19. Ayo, B. et al. Global Change Biol. 23, 4084–4093 (2017).20. van de Wall, D. B., Vershoor, A. M. & Huisman, J. Front. Ecol. Environ. 8, 145–212 (2010).Ding, W., Hou, D., Zhang, W., He, D., Cheng, X., 2018. A new genetic type of natural gases and origin analysis in Northern Songnan-Baodao Sag, Qiongdongnan Basin, South China Sea. Journal of Natural Gas Science and Engineering 50, 384-398. the typical coal-type gas of neighboring Lingshui and Ya'nan Sags in the Qiongdongnan Basin and farther Yinggehai Basin, most gases in the Songnan-Baodao Sag have much lighter δ13C1 and δ13C2 values, which are in the range of ?54.68‰～-33.68‰ and ?31.03‰～-23.50‰, respectively. The differences are attributed to the following aspects: (1) lighter gas from the preferential cracking of 12C-12C bond in aliphatic acid decarboxylation and polycondensation under catalysis of clay minerals in lower temperature, and (2) greater proportion of sapropelinite in strata overlying 1st member of Lingshui Formation with corresponding Ro less than 0.6%. The natural gases are classified into three genetic types: (1) Bio-thermocatalytic Transition Zone Gas generated from shale overlying 1st member of Lingshui Formation, (2) Thermal Catalytic Gas generated from lower Lingshui Formation and Yacheng Formation, (3) Mixed gas. Bio-thermocatalytic Transition Zone Gas shows lighter δ13C1 (δ13C1 <?44‰), a wider range of δ13C2 (>-31‰), a relatively lower dry coefficient (0.65–0.91), and abundant organic CO2 with δ13CCO2 ranging from ?28.9‰ to ?7.61‰. Thermal Catalytic Gas is typical coal-type gas (δ13C2 >?28‰) with higher maturity and dominating inorganic CO2. Mixed gas is mixture of above two gases. Compared with the condensate in the Yinggehai Basin, n-alkane mono-isomer and whole oil of condensate in study area are isotopically lighter, which are similar to the lighter Bio-thermocatalytic Transition Zone Gas. Attributed to mixed input of increasing proportion of alga and decreasing terrigenous higher plants in low-mature shale, contents of terrestrial biomarkers such as oleanane, cadinane, bicadinane, etc, are very low. Oil-source correlation analyzed from characteristics of mass chromatograms and C7 system, n-heptane, isoheptane value of light hydrocarbons of Bio-thermocatalytic Transition Zone Gas and Mixed gas show genetic relation with abundant sapropelinite in the low-mature shale in study area. This study provides a new insight to recognize potential gas and condensate resources generated from the previously neglected low-mature shale overlying 1st member of Lingshui Formation of Songnan-Baodao Sag and adjacent deep waters in Qiongdongnan Basin.Domingo-Almenara, X., Montenegro-Burke, J.R., Benton, H.P., Siuzdak, G., 2018. Annotation: A computational solution for streamlining metabolomics analysis. Analytical Chemistry 90, 480-489. aim of any untargeted metabolomics experiment is to identify and quantify dysregulated compounds relevant to a particular phenotype. However, metabolite identification is still considered an imposing bottleneck in untargeted metabolomics. Untargeted data analysis workflows for liquid chromatography/electrospray ionization/mass spectrometry (LC/ESI/MS) usually consists of applying peak-picking algorithms,(1-6) aligning those peaks across multiple samples to obtain the so-called peak features (defined as a peak or a set of aligned peaks across samples with a unique m/z and a specific retention time), and subsequently discovering statistically significant variations between phenotypes. Once features of interest are prioritized, these can be annotated by searching their mass values against metabolite libraries.(7-9) Next, features can be putatively identified via fragmentation experiments (tandem MS or MS/MS), usually with quadrupole-time-of-flight (Q-TOF) instrumentation, by comparing experimental fragmentation patterns with spectral libraries.(10) Ultimately, unambiguous identification, according to the Metabolomics Standards Initiative (MSI) guidelines,(11) can only be achieved by comparing the experimental tandem MS spectra with standard materials analyzed under identical conditions. Although untargeted metabolomics data analysis workflows are well-defined, metabolite annotation still remains a computational bottleneck, and only a small fraction of the thousands of metabolites that can be present in a sample can be annotated with an acceptable confidence level.(12) We can attribute this to different facts. First, there is a high redundancy of features representing the same metabolite due to the presence of adducts, in-source fragments, and isotopes, and library searching of all statistically significant features without prior knowledge of monoisotopic accurate masses might lead to missanotations.(13) Second, accurate mass library searches, considering expected adducts, can lead to a large number of potential molecular formulas and thus, molecular entities. Computational feature grouping and annotation is therefore a necessary step to reduce the number of putative identities. In this context, annotation is defined as the process of “noting” each observed feature with a putative identity, but it also includes assigning each observed feature with identity of formed adducts, neutral losses, isotopes, and in-source fragments. This, ultimately facilitates the accurate characterization and identification of annotated adduct peaks via tandem mass spectrometry (MS/MS). This computational annotation process ideally consists in (i) grouping features stemming from the same compound such as adducts, isotopes, and in-source fragments, which gives valuable chemical information for metabolite identification, and (ii) determining monoisotopic or neutral molecular mass of each metabolite by annotation of formed adduct peaks, neutral losses, etc. Additional strategies have been proposed which attempt to increase the annotation confidence. These strategies take into account biological information such as pathways, tandem MS/MS data, and retention time prediction and calibration. This review provides an overview of LC/ESI/MS based untargeted metabolomics data from a computational perspective to understand the characteristics of LC/MS data and its challenges for accurate computational annotation. We focused on the occurrence of in-source dissociation phenomena in metabolomics data, and the pitfalls of using accurate mass search without a priori feature annotation. Moreover, we provide an overview of the state of the art computational annotation strategies for LC/MS data. Despite different computational tools being cited throughout the paper, we focused on their algorithms and strategies rather than providing a comprehensive list of all available annotation tools. For more in depth reviews focused on tools and resources, we encourage the readers to read the following literature.(14-16)Dong, C., Jin, M., Lingam, M., Airapetian, V.S., Ma, Y., van der Holst, B., 2018. Atmospheric escape from the TRAPPIST-1 planets and implications for habitability. Proceedings of the National Academy of Sciences 115, 260-265.: The search for exoplanets has rapidly emerged as one of the most important endeavors in astronomy. This field received a major impetus with the recent discovery of seven temperate Earth-sized exoplanets orbiting the nearby ultracool dwarf star TRAPPIST-1. One of the most crucial requirements for conventional (surface-based) planetary habitability is the presence of an atmosphere over long timescales. We determine the atmospheric escape rates numerically and analytically for the planets of the TRAPPIST-1 system and show that the outer planets are potentially likely to retain their atmospheres over billion-year timescales. Our work has far-reaching and profound implications for atmospheric escape and the habitability of terrestrial exoplanets around M dwarfs. Abstract: The presence of an atmosphere over sufficiently long timescales is widely perceived as one of the most prominent criteria associated with planetary surface habitability. We address the crucial question of whether the seven Earth-sized planets transiting the recently discovered ultracool dwarf star TRAPPIST-1 are capable of retaining their atmospheres. To this effect, we carry out numerical simulations to characterize the stellar wind of TRAPPIST-1 and the atmospheric ion escape rates for all of the seven planets. We also estimate the escape rates analytically and demonstrate that they are in good agreement with the numerical results. We conclude that the outer planets of the TRAPPIST-1 system are capable of retaining their atmospheres over billion-year timescales. The consequences arising from our results are also explored in the context of abiogenesis, biodiversity, and searches for future exoplanets. In light of the many unknowns and assumptions involved, we recommend that these conclusions must be interpreted with due caution. Dong, S., Xie, J.-W., Zhou, J.-L., Zheng, Z., Luo, A., 2018. LAMOST telescope reveals that Neptunian cousins of hot Jupiters are mostly single offspring of stars that are rich in heavy elements. Proceedings of the National Academy of Sciences 115, 266-271.: Hot Jupiters are Jupiter-size planets at ?1/10 of the Sun–Earth distance, and even though they were the first exoplanet population discovered around sun-like stars, their origins still remain elusive. Using data from NASA’s Kepler satellite and China’s Large Sky Area Multi-Object Fiber Spectroscopic Telescope, we discover a population of close-in Neptune-size planets (called “Hoptunes”) that share key similarities with hot Jupiters. Like hot Jupiters, Hoptunes prefer to reside around stars with higher metal abundance than the Sun. Nearly half of the Kepler planets are discovered in systems with multiple transiting planets, but both hot Jupiters and Hoptunes are preferentially found in single-transiting planet systems. The “kinship” between hot Jupiters and Hoptunes suggests likely common origins and offers fresh clues into the formation of these exotic close-in planets. Abstract: We discover a population of short-period, Neptune-size planets sharing key similarities with hot Jupiters: both populations are preferentially hosted by metal-rich stars, and both are preferentially found in Kepler systems with single-transiting planets. We use accurate Large Sky Area Multi-Object Fiber Spectroscopic Telescope (LAMOST) Data Release 4 (DR4) stellar parameters for main-sequence stars to study the distributions of short-period (1 d <P <10 d) (1d<P<10d) Kepler planets as a function of host star metallicity. The radius distribution of planets around metal-rich stars is more “puffed up” compared with that around metal-poor hosts. In two period–radius regimes, planets preferentially reside around metal-rich stars, while there are hardly any planets around metal-poor stars. One is the well-known hot Jupiters, and the other one is a population of Neptune-size planets (2R ⊕ ? R p ?6R ⊕ 2R⊕?Rp?6R⊕), dubbed “Hoptunes.” Also like hot Jupiters, Hoptunes occur more frequently in systems with single-transiting planets although the fraction of Hoptunes occurring in multiples is larger than that of hot Jupiters. About 1% 1% of solar-type stars host Hoptunes, and the frequencies of Hoptunes and hot Jupiters increase with consistent trends as a function of [Fe/H]. In the planet radius distribution, hot Jupiters and Hoptunes are separated by a “valley” at approximately Saturn size (in the range of 6R ⊕ ? R p ?10R ⊕ 6R⊕?Rp?10R⊕), and this “hot-Saturn valley” represents approximately an order-of-magnitude decrease in planet frequency compared with hot Jupiters and Hoptunes. The empirical “kinship” between Hoptunes and hot Jupiters suggests likely common processes (migration and/or formation) responsible for their existence. Drosou, K., Price, C., Brown, T.A., 2018. The kinship of two 12th Dynasty mummies revealed by ancient DNA sequencing. Journal of Archaeological Science: Reports 17, 793-797. resolve a longstanding question regarding the kinship of two high-status Egyptians from the 12th Dynasty, Nakht-Ankh and Khnum-Nakht, whose mummies were discovered in 1907 by Egyptian workmen directed by Flinders Petrie and Ernest Mackay. Although their coffin inscriptions indicate that Nakht-Ankh and Khnum-Nakht were brothers, when the mummies were unwrapped in 1908 the skeletal morphologies were found to be quite different, suggesting an absence of family relationship. We extracted ancient DNA from the teeth of the two mummies and, following hybridization capture of the mitochondrial and Y chromosome fractions, sequenced the DNA by a next generation method. Analysis of single nucleotide polymorphisms showed that both Nakht-Ankh and Khnum-Nakht belonged to mitochondrial haplotype M1a1, suggesting a maternal relationship. The Y chromosome sequences were less complete but showed variations between the two mummies, indicating that Nakht-Ankh and Khnum-Nakht had different fathers. Our study emphasizes the importance of kinship in ancient Egypt, and represents the first successful typing of both mitochondrial and Y chromosomal DNA in Egyptian mummies.Du, Y., Chen, X., Li, L., Wang, P., 2018. Characteristics of methane desorption and diffusion in coal within a negative pressure environment. Fuel 217, 111-121. study the characteristics of gas diffusion and changes in the dynamic parameters of coal under a negative pressure environment, experiments were performed to constrain the desorption process under different negative pressures in coal samples at (0.5, 1.5 and 2.5)?MPa adsorption equilibrium pressures. The experimental results demonstrate that the relation curves between time and the desorption quantities of coal samples with different negative pressures have shapes similar to that of Langmuir’s adsorption isotherm. In addition, all coal samples with different negative pressures have a maximum regarding methane desorption. As the negative pressure increases from 10?kPa to 40?kPa, the limitation gas desorption amount increases from 8.73 to 10.93?mL/g, from 14.91 to 17.75?mL/g, and from 18.30 to 23.27?mL/g, respectively, under 0.5?MPa, 1.5?Mpa and 2.5?Mpa adsorption equilibrium pressure. Moreover, under the same adsorption pressure, the larger the negative pressure becomes, the greater the gas desorption velocity of the first minute (V1) is. The change of gas desorption velocity with negative pressure during the first minute is an exponential function. The performance under different adsorption equilibrium pressures demonstrates the same regularity. With the increase of negative pressure, interfacial mass transfer resistance also decreases, and the diffusion coefficient and Fourier’s criterion of mass transmission increase. This indicates that the negative pressure environment changes the desorption kinetic-parameters of the coal mass and increases the amounts of methane desorption and desorption velocity, which are advantageous for desorption and diffusion of coal methane.Duan, J., Liu, W., Zhao, X., Han, Y., O’Reilly, S.E., Zhao, D., 2017. Study of residual oil in Bay Jimmy sediment 5 years after the Deepwater Horizon oil spill: Persistence of sediment retained oil hydrocarbons and effect of dispersants on desorption. Science of The Total Environment 618, 1244-1253. 2010 Deepwater Horizon (DwH) oil spill contaminated ~ 1,773 km of the Gulf of Mexico shorelines. Yet, few field data are available on the long-term fate and persistency of sediment-retained oil. While an unprecedented amount of oil dispersants was applied, the effects of oil dispersants on desorption of field aged oil remain unknown. This study aimed to investigate the abundance, distributions and physico-chemical availability of the oil retained in Bay Jimmy sediment, Louisiana, five years after the DwH oil spill, and to determine the effects of two model oil dispersants on the desorption potential of the residual oil. Total petroleum hydrocarbons (TPHs), n-alkanes and polycyclic aromatic hydrocarbons (PAHs) in the sediment were analyzed and compared with those in the crude oil and the pre-DwH levels, and batch desorption kinetic tests were carried out to quantify the dispersant effects on the desorption rate and extent. The biomarker hopanes profile and diagnostic ratio were analyzed, which confirmed the origin and persistence of the sediment-retained oil. After five-year natural weathering, the oil level in the sediment remained orders of magnitude higher than the pre-spill level. Nearly all low-molecular-weight n-alkanes and 2-ring PAHs had been degraded. Oil dispersants, SPC 1000 and Corexit EC9500A, were able to enhance solubilization of the sediment-retained oil upon resuspension of the sediment. Successive desorption experiments indicated that 71.6% of TPHs, 74.8% of n-alkanes, and 91.9% of PAHs in the sediment remained highly stable and hardly desorbable by seawater; yet, addition of 18 mg/L of SPC 1000 enhanced the desorption and lowered these fractions to 57.3%, 68.1%, and 81.4%, respectively. The findings are important for understanding the natural weathering rate and persistence of oil residual and the effects of dispersants on the physical and biological availabilities of aged oil in coastal sediments.Duarte, B., Carreiras, J., Pérez-Romero, J.A., Mateos-Naranjo, E., Redondo-Gómez, S., Matos, A.R., Marques, J.C., Ca?ador, I., 2018. Halophyte fatty acids as biomarkers of anthropogenic-driven contamination in Mediterranean marshes: Sentinel species survey and development of an integrated biomarker response (IBR) index. Ecological Indicators 87, 86-96. environments are extremely affected by anthropogenic-driven contamination, namely heavy metals. In the recent years, several organisms have been studied to be used as sentinel species providing a wide range of biomarkers for estuarine contamination. Only recently non-traditional biomarkers, such as fatty acids, were included in animal ecotoxicology and impact assessment studies. Nevertheless, there is a wide lack of knowledge regarding to its application in estuarine plants. Considering this the present work aimed to evaluate the application of fatty acid profiling in Mediterranean halophytic species chronically exposed to different degrees of metal contamination, while incorporating these fatty acid biomarkers into an unifying index. From the fatty acids analysis two different types of sentinel halophytes could be identified: the contamination sensitive Halimione portulacoides (sea purslane), Sarcocornia fruticosa (glasswort) and Spartina patens (saltmeadow cordgrass), and the contamination-tolerant Spartina maritima (small cordgrass). In sensitive species the most evident changes in the fatty acid profiles were the decrease in the 18:3 and the increase in the 16:0 fatty acid relative concentrations, while the inverse trend was recorded in the tolerant S. maritima under chronic contamination. Beyond the evident physiological importance, these shifts in the halophyte fatty acid profiles provide some understanding on their use as biomarkers of metal contamination. After application of an integrated biomarker response (IBR) index it was possible to conclude that in sensitive halophytes (H. portulacoides, S. fruticosa and S. patens) the samples collected from the contaminated site produce had higher IBR values than the tolerant species S. maritima being these lower values linked with an adaptation mechanism towards contamination. Furthermore, the fatty acid-based IBR index was intrinsically connected with the bioavailable metals concentrations in the rhizosediments, which make that it could be used in future impact assessment and/or ecotoxicology studies. In summary, the data showed that two of the most abundant halophytes in the Mediterranean eco-region (S. fruticosa and H. portulacoides) are potential sentinel species of metal contamination, whereas its fatty acid profile is an efficient biomarker of the degree of environmental contamination.Dundas, C.M., Bramson, A.M., Ojha, L., Wray, J.J., Mellon, M.T., Byrne, S., McEwen, A.S., Putzig, N.E., Viola, D., Sutton, S., Clark, E., Holt, J.W., 2018. Exposed subsurface ice sheets in the Martian mid-latitudes. Science 359, 199-201.: Thick deposits cover broad regions of the Martian mid-latitudes with a smooth mantle; erosion in these regions creates scarps that expose the internal structure of the mantle. We investigated eight of these locations and found that they expose deposits of water ice that can be >100 meters thick, extending downward from depths as shallow as 1 to 2 meters below the surface. The scarps are actively retreating because of sublimation of the exposed water ice. The ice deposits likely originated as snowfall during Mars’ high-obliquity periods and have now compacted into massive, fractured, and layered ice. We expect the vertical structure of Martian ice-rich deposits to preserve a record of ice deposition and past climate.Editor's summary: Water ice cliffs on Mars. Some locations on Mars are known to have water ice just below the surface, but how much has remained unclear. Dundas et al. used data from two orbiting spacecraft to examine eight locations where erosion has occurred. This revealed cliffs composed mostly of water ice, which is slowly sublimating as it is exposed to the atmosphere. The ice sheets extend from just below the surface to a depth of 100 meters or more and appear to contain distinct layers, which could preserve a record of Mars' past climate. They might even be a useful source of water for future human exploration of the red planet.Dunhill, A.M., Foster, W.J., Sciberras, J., Twitchett, R.J., 2018. Impact of the Late Triassic mass extinction on functional diversity and composition of marine ecosystems. Palaeontology 61, 133-148 extinctions have profoundly influenced the history of life, not only through the death of species but also through changes in ecosystem function and structure. Importantly, these events allow us the opportunity to study ecological dynamics under levels of environmental stress for which there are no recent analogues. Here, we examine the impact and selectivity of the Late Triassic mass extinction event on the functional diversity and functional composition of the global marine ecosystem, and test whether post-extinction communities in the Early Jurassic represent a regime shift away from pre-extinction communities in the Late Triassic. Our analyses show that, despite severe taxonomic losses, there is no unequivocal loss of global functional diversity associated with the extinction. Even though no functional groups were lost, the extinction event was, however, highly selective against some modes of life, in particular sessile suspension feeders. Although taxa with heavily calcified skeletons suffered higher extinction than other taxa, lightly calcified taxa also appear to have been selected against. The extinction appears to have invigorated the already ongoing faunal turnover associated with the Mesozoic Marine Revolution. The ecological effects of the Late Triassic mass extinction were preferentially felt in the tropical latitudes, especially amongst reefs, and it took until the Middle Jurassic for reef ecosystems to fully recover to pre-extinction levels.Eddhif, B., Allavena, A., Liu, S., Ribette, T., Abou Mrad, N., Chiavassa, T., d’Hendecourt, L.L.S., Sternberg, R., Danger, G., Geffroy-Rodier, C., Poinot, P., 2018. Development of liquid chromatography high resolution mass spectrometry strategies for the screening of complex organic matter: Application to astrophysical simulated materials. Talanta 179, 238-245. present work aims at developing two LC-HRMS setups for the screening of organic matter in astrophysical samples. Their analytical development has been demonstrated on a 100-?g residue coming from the photo-thermo chemical processing of a cometary ice analog produced in laboratory.The first 1D-LC-HRMS setup combines a serially coupled columns configuration with HRMS detection. It has allowed to discriminate among different chemical families (amino acids, sugars, nucleobases and oligopeptides) in only one chromatographic run without neither a priori acid hydrolysis nor chemical derivatisation. The second setup is a dual-LC configuration which connects a series of trapping columns with analytical reverse-phase columns. By coupling on-line these two distinct LC units with a HRMS detection, high mass compounds (350 < m/z < 600) have been efficiently preconcentrated, separated and detected.Our strategies demonstrate a real interest for the analysis of astrophysical samples coming in minute quantities and allowing only few analytical runs. Besides its relevance for astrobiological studies, this work points out the suitability of these two novel LC-HRMS strategies for untargeted analysis of complex environmental samples.El-Sabagh, S.M., Rashad, A.M., El-Naggar, A.Y., El Nady, M.M., Badr, I.A., Ebiad, M.A., Abdullah, E.S., 2018. API gravities, vanadium, nickel, sulfur, and their relation to gross composition: Implications for the origin and maturation of crude oils in Western Desert, Egypt. Petroleum Science and Technology 36, 1-8. the present study, the geochemical analyses of API gravities, vanadium, nickel, sulfur, and bulk composition were performed on eight samples from productive wells in Gindi, South Deep Abu-gharadig, Abu-gharadig, Dahab-Merier, and Faghure basins locates in the North Western Desert. The results were used to describe the source organic matter input, depositional environment, assess the degree of thermal maturity, and to correlate between crude oils to determine the genetic relationship between hydrocarbon generation and their source rock for the studied oil samples. The results showed that a wide range of crude oil parameters exists in this data, indicating that a variety of oil types is represented. Crude oils range from unaltered to altered by vanadium, nickel, and sulfur concentrations, V/Ni and saturate fraction were used to classify the oils. Oils are classified into two groups. Group I contains oil samples from Gindi, South deep Abu-gharadig and Abu-gharadig, and Dahab-Merier that are generated from organic matter input deposited in marine environment under anoxic to suboxic conditions. Group II from Faghur basin possess high Pr/Ph ratios suggesting high contribution of terreginous organic matter deposited under relatively oxic conditions.El Bassoussi, A.A., El-sabagh, S.M., Harb, F.M., El Nady, M.M., 2018. Characterization and correlation of crude oils from some wells in the North Western Desert, Egypt. Petroleum Science and Technology 36, 384-391. and correlation of crude oils from some wells in the North Western Desert, based on six crude oil samples, were studied by different analytical techniques, including API gravity, sulfur content, nickel and vanadium, bulk compositions and saturated fraction obtained from gas chromatography have been studied. The results show that the crude oils are normal to medium aromatic oils, with high API gravity and high sulfur content. V, Ni, V/Ni and V/(V + Ni) reflecting oils might be sourced from non-clastic source rocks, possibly carbonates, deposited under anoxic-suboxic conditions. Bulk compositions revealing that the crude oils were derived from marine organic sources. While, the paraffins and naphthenes percent indicates that the oils belong to paraffinic to naphthenic oil types, deposited in slightly anoxic to suboxic conditions and contained marine organic matter. Thermal maturity data showed that the oil samples were generated from mature source rocks. This indicates the studied oil samples are well correlated with each other, where they are similar in their oil type maturation and source depositional environments.Elfadly, A.A., Ahmed, O.E., El Nady, M.M., 2017. Assessing of organic content in surface sediments of Suez Gulf, Egypt depending on normal alkanes, terpanes and steranes biological markers indicators. Egyptian Journal of Petroleum 26, 969-979. Semi-enclosed Suez Gulf records various signals of high anthropic pressures from surrounding regions and the industrialized Suez countries. The sedimentary hydrocarbons have been studied in 6 coastal stations located in the Gulf of Suez. Non-aromatic hydrocarbons were analyzed by GC/FID and GC/MS to assess organic content in surface sediments of Suez Gulf, Egypt depending on alkanes, terpanes and steranes biological markers indicators. The results showed that the hydrocarbons are originated from multiple terrestrial inputs, biogenic, pyrolytic. Several ratios of hydrocarbons indicated the predominance of petrogenic in combination with biogenic hydrocarbons. Al-Attaqa harbor, Suez oil processing company, Al-Nasr Oil Company, AL-Kabanon and EL-Sukhna of Loloha Beach are the main sources of petroleum contamination.Eltom, H.A., Abdullatif, O.M., Babalola, L.O., 2018. The elemental geochemistry of Lower Triassic shallow-marine carbonates from central Saudi Arabia: Implications for redox conditions in the immediate aftermath of the latest Permian mass extinction. Journal of African Earth Sciences 139, 283-306. southern margin of the Tethys Ocean was occupied by a broad, shallow continental shelf during the Permian-Triassic boundary interval, with the area of present-day Saudi Arabia located from 10° to 30° south of the paleo-equator. The strata deposited in modern Saudi Arabia in the aftermath of the latest Permian mass extinction (LPME) are dominated by oolitic microbialite limestone (OML), which are overlain by skeletal oolitic limestones (SOL) capped by dolostones and dolomitic limestones (DDL). This succession reflects changes in depositional setting, which can be potentially tied to redox conditions using redox sensitive trace elements and rare earth elements (REEs). Statistical analyses reveals that trace elements and REEs are associated with detrital material, and possibly with diagenetic minerals as well. Proxies such as the Y/Ho, Pr/Pr*, Smn/Ybn, Lan/Smn and Lan/Ybn ratios indicate that REEs do not record a seawater-like pattern, and cannot be used as redox indicator. The presence of a normal marine fauna implies oxic conditions during deposition of the DDL and SOL units. However, the OML unit, which represents the immediate aftermath of LPME, lacks both a normal marine fauna and reliable geochemical signals, making it difficult to infer redox conditions in the depositional environment. Similar to published data from sections that reflect shallow marine condition in the LPME of the Tethys Ocean, chemical index of alteration values are consistently high throughout the study succession, suggesting globally intense chemical weathering in the aftermath of the LPME. As a result, geochemical redox proxies in shallow marine carbonates of the Tethys Ocean are likely to be contaminated by detrital material that have been generated by chemical weathering, and thus, other methods are required to determine depositional redox conditions.Eltom, H.A., Gonzalez, L.A., Hasiotis, S.T., Rankey, E.C., Cantrell, D.L., 2018. Paleogeographic and paleo-oceanographic influences on carbon isotope signatures: Implications for global and regional correlation, Middle-Upper Jurassic of Saudi Arabia. Sedimentary Geology 364, 89-102. isotope data (δ13C) can provide an essential means for refining paleogeographic and paleo-oceanographic reconstructions, and interpreting stratigraphic architecture within complex carbonate strata. Although the primary controls on global δ13C signatures of marine carbonates are well understood, understanding their latitudinal and regional variability is poor. To better constrain the nature and applications of δ13C stratigraphy, this study: 1) presents a new high-resolution δ13C stratigraphic curve from Middle to Upper Jurassic carbonates in the upper Tuwaiq Mountain, Hanifa, and lower Jubaila formations in central Saudi Arabia; 2) explores their latitudinal and regional variability; and 3) discusses their implications for stratigraphic correlations.Analysis of δ13C data identified six mappable units with distinct δ13C signatures (units 1–6) between up-dip and down-dip sections, and one unit (unit 7) that occurs only in the down-dip section of the study succession. δ13C data from the upper Tuwaiq Mountain Formation and the lower Hanifa Formation (units 1, 2), which represent Upper Callovian to Middle Oxfordian strata, and record two broad positive δ13C excursions. In the upper part of the Hanifa Formation (units 3–6, Early Oxfordian–Late Kimmeridgian), δ13C values decreased upward to unit 7, which showed a broad positive δ13C excursion. Isotopic data suggest similar δ13C trends between the southern margin of the Tethys Ocean (Arabian Plate; low latitude, represented by the study succession) and northern Tethys oceans (high latitude), despite variations in paleoclimatic, paleogeographic, and paleoceanographic conditions. Variations in the δ13C signal in this succession can be attributed to the burial of organic matter and marine circulation at the time of deposition. Our study uses δ13C signatures to provide independent data for chronostratigraphic constraints which help in stratigraphic correlations within heterogeneous carbonate successions.Erkkil?, K.M., Ojala, A., Bastviken, D., Biermann, T., Heiskanen, J.J., Lindroth, A., Peltola, O., Rantakari, M., Vesala, T., Mammarella, I., 2018. Methane and carbon dioxide fluxes over a lake: comparison between eddy covariance, floating chambers and boundary layer method. Biogeosciences 15, 429-445. bring a notable contribution to the global carbon budget by emitting both carbon dioxide (CO2) and methane (CH4) to the atmosphere. Global estimates of freshwater emissions traditionally use a wind-speed-based gas transfer velocity, kCC (introduced by Cole and Caraco, 1998), for calculating diffusive flux with the boundary layer method (BLM). We compared CH4 and CO2 fluxes from BLM with kCC and two other gas transfer velocities (kTE and kHE), which include the effects of water-side cooling to the gas transfer besides shear-induced turbulence, with simultaneous eddy covariance (EC) and floating chamber (FC) fluxes during a 16-day measurement campaign in September 2014 at Lake Kuivaj?rvi in Finland. The measurements included both lake stratification and water column mixing periods. Results show that BLM fluxes were mainly lower than EC, with the more recent model kTE giving the best fit with EC fluxes, whereas FC measurements resulted in higher fluxes than simultaneous EC measurements. We highly recommend using up-to-date gas transfer models, instead of kCC, for better flux estimates. BLM CO2 flux measurements had clear differences between daytime and night-time fluxes with all gas transfer models during both stratified and mixing periods, whereas EC measurements did not show a diurnal behaviour in CO2 flux. CH4 flux had higher values in daytime than night-time during lake mixing period according to EC measurements, with highest fluxes detected just before sunset. In addition, we found clear differences in daytime and night-time concentration difference between the air and surface water for both CH4 and CO2. This might lead to biased flux estimates, if only daytime values are used in BLM upscaling and flux measurements in general. FC measurements did not detect spatial variation in either CH4 or CO2 flux over Lake Kuivaj?rvi. EC measurements, on the other hand, did not show any spatial variation in CH4 fluxes but did show a clear difference between CO2 fluxes from shallower and deeper areas. We highlight that while all flux measurement methods have their pros and cons, it is important to carefully think about the chosen method and measurement interval, as well as their effects on the resulting flux.Erlykin, A.D., Harper, D.A.T., Sloan, T., Wolfendale, A.W., 2018. Periodicity in extinction rates. Palaeontology 61, 149-158. report a reinvestigation of the peak at a period of 27 myr in the Fourier periodogram of Phanerozoic mass extinction data. This peak is interesting since it implies a repetitive cause of the extinctions such as might be expected from an astronomical source. In a previous paper, we showed that the peak had insufficient statistical significance to be considered a real effect. A recent paper in Palaeontology by Melott & Bambach (2017) disagreed with our conclusion, mainly on the grounds that the peak has a higher statistical significance than we considered. Here we re-examine the data and demonstrate that Melott & Bambach overstated the statistical precision of their Fourier analysis. Hence Fourier analysis alone is insufficient evidence for extinctions occurring repetitively. We show that the peak is fragile and disappears if 5 events with large extinction proportions are excluded from the sample of 136 events. Since the causes of these 5 events are unlikely to have a repetitive nature we conclude that the peak is most probably caused by a statistical fluctuation.The case for periodicity in mass extinctions and its relationship to astronomical drivers is not new but it remains controversial. In the light of a series of recent studies, essentially reviving the exciting discoveries of the 1980s, our paper (Erlykin et al. 2017) sought to present an alternative view. In that paper, we showed that the oscillation of the Solar System about the galactic plane is probably too variable in time to account for the possibly observed periodicity of 27 myr. Hence it is implausible as a cause of the periodicity, as has been claimed (e.g. Rampino & Stothers 1984; Fox 1987). We further showed that the statistical significance of the observed 27 myr periodicity could be poorer than has been previously thought so that the possibility that it is a statistical fluctuation cannot be excluded.In the lack of such periodicity, it is difficult then to relate the key astronomical processes that may have matched this pattern and thus driven mass extinctions. In a series of detailed papers, Melott & Bambach (2017) have espoused the opposing view and they offered a critique of our position. They focused mainly on the statistical significance of the observed peak, claiming a higher statistical significance than we deduced in Erlykin et al. (2017). Moreover, they challenged our study on a number of grounds. Here we focus on the core of the argument: Is the 27 myr cycle real or a statistical artefact?In the present paper, we examine the work reported in Melott & Bambach (2017). We show that they have overestimated the statistical significance of the observed 27 myr peak. Firstly, we show that the statistical significance cannot be determined precisely enough to draw the firm conclusion that the peak is highly significant. This is due to statistical fluctuations from the small number of extinction events (136 in total). Secondly, we show that the noise power is much closer to white noise than the red noise assumed in Melott & Bambach (2017). This reduces considerably the statistical significance of the peak. Thirdly, we show that the peak disappears if 5 of the 136 extinctions are excluded. Four of these events have terrestrial origins which are unlikely, in our view, to be repetitive in nature. This provides further evidence that the peak is caused by a statistical fluctuation in a small data sample.Erofeev, A.A., Pachezhercev, A.A., Karpov, I.A., Morozov, N.V., Kalmykov, A.G., Cheremisin, A.N., Kozlova, E.V., Bychkov, A.Y., 2017. Estimation of the heat-impact potential for stimulating the development of the deposits of the Bazhenov Formation according to the results of experimental studies. Moscow University Geology Bulletin 72, 339-348. influence of temperature on rock samples of the Bazhenov Formation is shown. The samples underwent pyrolysis at 300–480°C, as well as in closed autoclaves in the presence of water under formation pressure. The temperature impact at 400°C resulted in a decrease in the S2 pyrolytic peak by 90–95% and almost complete formation of the generation potential of the rocks. Microtomographic studies of samples combined with raster electron microscopy revealed a correlation between the variable reservoir properties of the rocks. At 350°C, the rocks are characterized by a system of fractures; as a result of impacts, the porosity and permeability can increase from several to several tens of times. Our results will allow more precise modeling of the influence of tertiary processes on the rocks of the Bazhenov Formation in order to increase the final oil recovery of the bed. Original Russian Text ? A.A. Erofeev, A.A. Pachezhercev, I.A. Karpov, N.V. Morozov, A.G. Kalmykov, A.N. Cheremisin, E.V. Kozlova, A.Yu. Bychkov, 2017, published in Vestnik Moskovskogo Universiteta, Seriya 4: Geologiya, 2017, No. 4, pp. 39–47.Espínola, F., Dionisi, H.M., Borglin, S., Brislawn, C.J., Jansson, J.K., Mac Cormack, W.P., Carroll, J., Sj?ling, S., Lozada, M., 2018. Metagenomic analysis of subtidal sediments from polar and subpolar coastal environments highlights the relevance of anaerobic hydrocarbon degradation processes. Microbial Ecology 75, 123-139. this work, we analyzed the community structure and metabolic potential of sediment microbial communities in high-latitude coastal environments subjected to low to moderate levels of chronic pollution. Subtidal sediments from four low-energy inlets located in polar and subpolar regions from both Hemispheres were analyzed using large-scale 16S rRNA gene and metagenomic sequencing. Communities showed high diversity (Shannon’s index 6.8 to 10.2), with distinct phylogenetic structures (<40% shared taxa at the Phylum level among regions) but similar metabolic potential in terms of sequences assigned to KOs. Environmental factors (mainly salinity, temperature, and in less extent organic pollution) were drivers of both phylogenetic and functional traits. Bacterial taxa correlating with hydrocarbon pollution included families of anaerobic or facultative anaerobic lifestyle, such as Desulfuromonadaceae, Geobacteraceae, and Rhodocyclaceae. In accordance, biomarker genes for anaerobic hydrocarbon degradation (bamA, ebdA, bcrA, and bssA) were prevalent, only outnumbered by alkB, and their sequences were taxonomically binned to the same bacterial groups. BssA-assigned metagenomic sequences showed an extremely wide diversity distributed all along the phylogeny known for this gene, including bssA sensu stricto, nmsA, assA, and other clusters from poorly or not yet described variants. This work increases our understanding of microbial community patterns in cold coastal sediments, and highlights the relevance of anaerobic hydrocarbon degradation processes in subtidal environments.Esteban, J., García-Coca, M., 2018. Mycobacterium biofilms. Frontiers in Microbiology 8, 2651. doi: 10.3389/fmicb.2017.02651. genus Mycobacterium includes human pathogens (Mycobacterium tuberculosis and Mycobacterium leprae) and environmental organisms known as non-tuberculous mycobacteria (NTM) that, when associated with biomaterials and chronic disease, can cause human infections. A common pathogenic factor of mycobacteria is the formation of biofilms. Various molecules are involved in this process, including glycopeptidolipids, shorter-chain mycolic acids, and GroEL1 chaperone. Nutrients, ions, and carbon sources influence bacterial behavior and have a regulatory role in biofilm formation. The ultrastructure of mycobacterial biofilms can be studied by confocal laser scanning microscopy, a technique that reveals different phenotypic characteristics. Cording is associated with NTM pathogenicity, and is also considered an important property of M. tuberculosis strains. Mycobacterial biofilms are more resistant to environmental aggressions and disinfectants than the planktonic form. Biofilm-forming mycobacteria have been reported in many environmental studies, especially in water systems. NTM cause respiratory disease in patients with underlying diseases, such as old tuberculosis scars, bronchiectasis, and cystic fibrosis. Pathogens can be either slowly growing mycobacteria, such as Mycobacterium avium complex, or rapidly growing species, such as Mycobacterium abscessus. Another important biofilm-related group of infections are those associated with biomaterials, and in this setting the most frequently isolated organisms are rapidly growing mycobacteria. M. tuberculosis can develop a biofilm which plays a role in the process of casseous necrosis and cavity formation in lung tissue. M. tuberculosis also develops biofilms on clinical biomaterials. Biofilm development is an important factor for antimicrobial resistance, as it affords protection against antibiotics that are normally active against the same bacteria in the planktonic state. This antibiotic resistance of biofilm-forming microorganisms may result in treatment failure, and biofilms have to be physically eradicated to resolve the infection. New strategies with potential antibiofilm molecules that improve treatment efficacy have been developed. A novel antibiofilm approach focuses on Methylobacterium sp. An understanding of biofilm is essential for the appropriate management of patients with many NTM diseases, while the recent discovery of M. tuberculosis biofilms opens a new research field.Eun, Y.-J., Ho, P.-Y., Kim, M., LaRussa, S., Robert, L., Renner, L.D., Schmid, A., Garner, E., Amir, A., 2018. Archaeal cells share common size control with bacteria despite noisier growth and division. Nature Microbiology 3, 148-154. nature, microorganisms exhibit different volumes spanning six orders of magnitude. Despite their capability to create different sizes, a clonal population in a given environment maintains a uniform size across individual cells. Recent studies in eukaryotic and bacterial organisms showed that this homogeneity in cell size can be accomplished by growing a constant size between two cell cycle events (that is, the adder model). Demonstration of the adder model led to the hypothesis that this phenomenon is a consequence of convergent evolution. Given that archaeal cells share characteristics with both bacteria and eukaryotes, we investigated whether and how archaeal cells exhibit control over cell size. To this end, we developed a soft-lithography method of growing the archaeal cells to enable quantitative time-lapse imaging and single-cell analysis, which would be useful for other microorganisms. Using this method, we demonstrated that Halobacterium?salinarum, a hypersaline-adapted archaeal organism, grows exponentially at the single-cell level and maintains a narrow-size distribution by adding a constant length between cell division events. Interestingly, the archaeal cells exhibited greater variability in cell division placement and exponential growth rate across individual cells in a population relative to those observed in Escherichia?coli. Here, we present a theoretical framework that explains how these larger fluctuations in archaeal cell cycle events contribute to cell size variability and control.Faboya, O.L., Ojo, A.A., Bello, H., Osasona, I., 2018. Geochemical investigation of trace elements in crude oils from two different depobelts in the Niger Delta basin, Nigeria. Petroleum Science and Technology 36, 130-135. concentrations of trace elements in crude oil samples from the Northern and Central swamps depobelts in the Niger Delta basin were investigated using Flame Atomic Absorption Spectrometer. The origin, source facies, and depositional environment of organic matter that produced the oils were determined based on the trace elements concentrations. The concentrations of the trace elements (Cr, Cu, Fe, Mn, Ni and V) ranged from 0.04 to 5.71?ppm. Iron is the most abundant element in the samples while Cr has the least concentration. The results from trace metal geochemistry showed that the Niger Delta oils were derived predominantly from terrestrial organic matter deposited in the oxic depositional environment. The concentrations and ratios of nickel and vanadium grouped the oils into two distinct families reflecting the depobelt the oils belong. This observation indicates that the source rocks in the two depobelts were formed from organic matter of different source facies.Fallon, J.A., Smith, E.P., Schoch, N., Paruk, J.D., Adams, E.A., Evers, D.C., Jodice, P.G.R., Perkins, C., Schulte, S., Hopkins, W.A., 2018. Hematological indices of injury to lightly oiled birds from the Deepwater Horizon oil spill. Environmental Toxicology and Chemistry 37, 451-461. mortality events are common following large-scale oil spills. However, the sublethal effects of oil on birds exposed to light external oiling are not clearly understood. We found that American oystercatchers (area of potential impact n?=?42, reference n?=?21), black skimmers (area of potential impact n?=?121, reference n?=?88), brown pelicans (area of potential impact n?=?91, reference n?=?48), and great egrets (area of potential impact n?=?57, reference n?=?47) captured between 20 June 2010 and 23 February 2011 following the Deepwater Horizon oil spill experienced oxidative injury to erythrocytes, had decreased volume of circulating erythrocytes, and showed evidence of a regenerative hematological response in the form of increased reticulocytes compared with reference populations. Erythrocytic inclusions consistent with Heinz bodies were present almost exclusively in birds from sites impacted with oil, a finding pathognomonic for oxidative injury to erythrocytes. Average packed cell volumes were 4 to 19% lower and average reticulocyte counts were 27 to 40% higher in birds with visible external oil than birds from reference sites. These findings provide evidence that small amounts of external oil exposure are associated with hemolytic anemia. Furthermore, we found that some birds captured from the area impacted by the spill but with no visible oiling also had erythrocytic inclusion bodies, increased reticulocytes, and reduced packed cell volumes when compared with birds from reference sites. Thus, birds suffered hematologic injury despite no visible oil at the time of capture. Together, these findings suggest that adverse effects of oil spills on birds may be more widespread than estimates based on avian mortality or severe visible oiling.Fan, J., Bailey, T.P., Sun, Z., Zhao, P., Uher, C., Yuan, F., Zhao, M., 2018. Preparation and properties of ultra-low density proppants for use in hydraulic fracturing. Journal of Petroleum Science and Engineering 163, 100-109., environmental pollution in hydraulic fracturing operations in the petroleum and gas industry has drawn more and more attention. As a result, research in non-toxic, ultra-low density and high pressure proppants, which do not rely on the environmentally harmful suspending agents used in most fracturing fluids, has become a hot topic. Here, we report the successful preparation of porous proppants with an ultra-low density of 1.25?g/cm3, a breakage ratio of 6.9%, a short-term fracture conductivity of 102.15?μm2?cm and a permeability of 163.57?μm2?at 52?MPa synthesized by instant sintering through thermal plasma and closed-external pore sintering using a rotary kiln. The mechanism of forming porous proppants with hard shells and closed pores is described. The concentration of micro-silica, sodium metasilicate, and nano-silica, as well as the sintering temperature in the process of post-sintering, are discussed in terms of their effects on the structure and constituency of the proppant, which determine its mechanical properties. Our study demonstrates that porous proppants without toxic suspending agents are a viable technology for the hydraulic fracturing fluid.Fan, S., Wang, X., Lang, X., Wang, Y., 2017. Energy efficiency simulation of the process of gas hydrate exploitation from flue gas in an electric power plant. Natural Gas Industry B 4, 470-476. is a safe and environmentally-friendly method to exploit natural gas hydrates (“hydrate”) by using flue gas (mainly including CO2 and N2) from electric power plants. So far, however, its energy consumption and energy efficiency has not been investigated thoroughly. In this paper, the process to exploit hydrates from flue gas was established. Firstly, flue gas is injected into hydrate reservoirs after it is pressurized. The hydrates in reservoirs partially experience thermal decomposition while the rest is replaced with flue gas, so CH4CO2N2 mixture is formed. Secondly, the concentrated CH4CO2 mixture is got after N2 is separated and removed by using membrane component. And thirdly, the CH4CO2 mixture is delivered to the original electric power plant. This process was simulated by using the software Aspen Plus to analyze the production/injection ratio in the process of flue gas replacement under different injection pressures, the methane replacement ratio, and the energy consumption and energy efficiency in the whole process. It is indicated that the energy in the process of hydrate exploitation from flue gas is mainly consumed at the pressurized injection stage, and the injection pressure increase correspondingly results in the increase of energy consumption at pressurization and membrane separation stages, and to some extent improves the recovery ratio of pressure energy. Besides, when the injection pressure is 5–16 MPa, the production/injection ratio in the process of flue gas replacement is 0.03–0.26, the methane replacement ratio is 19.9–56.2%, the unit energy consumption in the whole process is 2.15–1.05 (kW·h)/kgCH4, and the energy return on investment (EROI) is 7.2–14.7. It is concluded that the energy efficiency of hydrate exploitation from flue gas can be effectively improved by increasing the injection pressure in the range of 5–10 MPa.Farhangian, H., Abrishamifar, S.M., Palizian, M., Janghorban Lariche, M., Baghban, A., 2018. The application of nanofluids for recovery of asphaltenic oil. Petroleum Science and Technology 36, 287-292. the recent years, requirement of suitable enhanced oil recovery (EOR) technique as a more proficient technology becomes significant because of increasing demand for energy. Nanofluids have great potential in order to improve oil recovery. In our study, the effect of SiO2, Al2O3, and MgO nanoparticles on oil recovery was investigated by using core flooding apparatus. Zeta potential and particle size distribution measurements were carried out to investigate the stability of nano particles and results showed SiO2 has more stability than other ones. Interfacial tension and contact angle measurements between nanofluids and crude oil used to demonstrate that how nanoparticles enhance oil recovery. Experimental data reveals that SiO2 nanoparticles introduce as the greatest agent among these nanoparticles for enhanced oil recovery. Lowest damage for SiO2 nanofluids was observed and also it was observed that the concentration and injection rate have straight effects on permeability reductions.Faroughi, S.A., Pruvot, A.J.-C.J., McAndrew, J., 2018. The rheological behavior of energized fluids and foams with application to hydraulic fracturing: Review. Journal of Petroleum Science and Engineering 163, 243-263. use of aqueous energized fluids and foams for hydraulic fracturing reduces water consumption and formation damage, while improving proppant transport and placement. Thus, coupling an improvement in well productivity with a reduction in environmental impact appears possible. However, several advances in scientific understanding of these complex fluids, e.g., fracture-induced shear thinning, elasticity and osmotic effects, have not been fully integrated into the engineering practice of well stimulation. These properties may lead to an optimized fracturing fluid that can be tuned to satisfy both sides of the stimulation design spectrum - better fracturing and efficient proppant transport. This review aims to progress in that direction by reviewing recent advancements in combination with earlier and more engineering-oriented works, and to connect the complex rheology and mechanics of energized fluids and foams with practical usage in hydraulic fracturing.Feng, W., Wang, F., Guan, J., Zhou, J., Wei, F., Dong, W., Xu, Y., 2018. Geologic structure controls on initial productions of lower Silurian Longmaxi shale in south China. Marine and Petroleum Geology 91, 163-178. Lower Silurian Longmaxi shale is the most important marine shale gas play in South China. Several hundred wells have been drilled to date, of which more than 150 wells have obtained high initial production (IP). Outside of the Sichuan Basin, however, wells drilled in the Lower Silurian Longmaxi shale do not reach flow rates that are commercial. Developing an understanding of the key factors controlling the IPs of Longmaxi shale is important in screening shale-resource plays. In this study, the TOC, thermal maturity, porosity, and gas saturation data obtained from Longmaxi shale of southeastern Chongqing area outside Sichuan Basin have been compared with that of Sichuan Basin. The results of this study show that the shales encountered display similar properties including TOC (>2%), thermal maturity (2.5–3.5% EqRo), and total porosity (3–6%). A good correlation between IPs and pressure coefficient suggest that the free gas content of gas shale controls on IPs. Porosity and gas saturation of gas shale are the main factors to control its free gas volume. The gas saturations in Longmaxi shale from high initial production wells in Sichuan Basin mainly range between 50 and 90%, however, that of shale in the southeastern Chongqing area are decreased to 10–30%. This is the directly reason for low IPs of wells. The contrasting gas saturation of Longmaxi shale between Sichuan Basin and the adjacent fold-thrust belts are interpreted to reflect, in part, differences in sealed condition of fluid system. Intensive tectonic movements caused the exhumation, faulting and fracturing, that reduced or destroyed the sealed ability of shale fluid system, which are the major factors for enhancing water saturation, decreasing fluid pressure and IPs. Finally, the study proposes several most favorable zones for Longmaxi shale gas exploration and development.Fernandes, R., Eley, Y., Brabec, M., Lucquin, A., Millard, A., Craig, O.E., 2018. Reconstruction of prehistoric pottery use from fatty acid carbon isotope signatures using Bayesian inference. Organic Geochemistry 117, 31-42. isotope measurements of individual fatty acids (C16:0 and C18:0) recovered from archaeological pottery vessels are widely used in archaeology to investigate past culinary and economic practices. Typically, such isotope measurements are matched with reference to food sources for straightforward source identification, or simple linear models are used to investigate mixing of contents. However, in cases where multiple food sources were processed in the same vessel, these approaches result in equivocal solutions. To address this issue, we tested the use of a Bayesian mixing model to determine the proportional contribution of different food sources to a series of different mixed food compositions, using data generated both by simulation and by experiment. The model was then applied to previously published fatty acid isotope datasets from pottery from two prehistoric sites: Durrington Walls, near Stonehenge in southern Britain and Neustadt in northern Germany. We show that the Bayesian approach to the reconstruction of pottery use offers a reliable probabilistic interpretation of source contributions although the analysis also highlights the relatively low precision achievable in quantifying pottery contents from datasets of this nature. We suggest that, with some refinement, the approach outlined should become standard practice in organic residue analysis, and also has potential application to a wide range of geological and geochemical investigations.Fernandez, A., Müller, I.A., Rodríguez-Sanz, L., van Dijk, J., Looser, N., Bernasconi, S.M., 2017. A reassessment of the precision of carbonate clumped isotope measurements: Implications for calibrations and paleoclimate reconstructions. Geochemistry, Geophysics, Geosystems 18, 4375-4386. clumped isotopes offer a potentially transformational tool to interpret Earth's history, but the proxy is still limited by poor interlaboratory reproducibility. Here, we focus on the uncertainties that result from the analysis of only a few replicate measurements to understand the extent to which unconstrained errors affect calibration relationships and paleoclimate reconstructions. We find that highly precise data can be routinely obtained with multiple replicate analyses, but this is not always done in many laboratories. For instance, using published estimates of external reproducibilities we find that typical clumped isotope measurements (three replicate analyses) have margins of error at the 95% confidence level (CL) that are too large for many applications. These errors, however, can be systematically reduced with more replicate measurements. Second, using a Monte Carlo-type simulation we demonstrate that the degree of disagreement on published calibration slopes is about what we should expect considering the precision of Δ47 data, the number of samples and replicate analyses, and the temperature range covered in published calibrations. Finally, we show that the way errors are typically reported in clumped isotope data can be problematic and lead to the impression that data are more precise than warranted. We recommend that uncertainties in Δ47 data should no longer be reported as the standard error of a few replicate measurements. Instead, uncertainties should be reported as margins of error at a specified confidence level (e.g., 68% or 95% CL). These error bars are a more realistic indication of the reliability of a measurement.Ferreira, S.L.C., Bezerra, M.A., Santos, A.S., dos Santos, W.N.L., Novaes, C.G., de Oliveira, O.M.C., Oliveira, M.L., Garcia, R.L., 2018. Atomic absorption spectrometry – A multi element technique. TrAC Trends in Analytical Chemistry 100, 1-6. the past, many types of researches have been performed to allow multi-element determinations using atomic absorption spectrometry. The first spectrometers developed for this purpose were proposed in the 1970s, using flame and furnace atomizers.In the early 2000s, a spectrometer equipped with software that allows a fast selection of the hollow cathode lamps was introduced commercially. This equipment operates in a sequential mode, and it enables the determination of up to 16 elements. Many publications have reported its performance.Over the years, many spectrometers were built adding new technologies, but they were discontinued due to low sensitivity, difficulty for background corrections, etc. However, all the efforts of the past have contributed to the development and consolidation of the high-resolution continuum source atomic absorption spectrometry (HR-CS AAS) using flame and furnace atomizers. This technique allows the establishment of sequential and simultaneous methods for determinations of many elements with high sensitivity and efficient background correction.Figueroa, I.A., Barnum, T.P., Somasekhar, P.Y., Carlstr?m, C.I., Engelbrektson, A.L., Coates, J.D., 2018. Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway. Proceedings of the National Academy of Sciences 115, E92-E101.: Phosphite (HPO32?) is the most energetically favorable biological electron donor known, but only one organism capable of growing by phosphite oxidation has been previously identified. Here, we describe a phosphite-oxidizing bacterium that can grow with CO2 as its sole electron acceptor, and we propose a metabolic model in which inorganic carbon is assimilated via the reductive glycine pathway. Although the reductive glycine pathway has previously been identified as a “synthetic” carbon fixation pathway, this study provides evidence that it may actually function as a natural autotrophic pathway. Our results suggest that phosphite may serve as a driver of microbial growth and carbon fixation in energy-limited environments, particularly in aphotic environments lacking alternative terminal electron acceptors. Abstract: Dissimilatory phosphite oxidation (DPO), a microbial metabolism by which phosphite (HPO32?) is oxidized to phosphate (PO43?), is the most energetically favorable chemotrophic electron-donating process known. Only one DPO organism has been described to date, and little is known about the environmental relevance of this metabolism. In this study, we used 16S rRNA gene community analysis and genome-resolved metagenomics to characterize anaerobic wastewater treatment sludge enrichments performing DPO coupled to CO2 reduction. We identified an uncultivated DPO bacterium, Candidatus Phosphitivorax (Ca. P.) anaerolimi strain Phox-21, that belongs to candidate order GW-28 within the Deltaproteobacteria, which has no known cultured isolates. Genes for phosphite oxidation and for CO2 reduction to formate were found in the genome of Ca. P. anaerolimi, but it appears to lack any of the known natural carbon fixation pathways. These observations led us to propose a metabolic model for autotrophic growth by Ca. P. anaerolimi whereby DPO drives CO2 reduction to formate, which is then assimilated into biomass via the reductive glycine pathway. Fornells, E., Barnett, B., Bailey, M., Hilder, E.F., Shellie, R.A., Breadmore, M.C., 2018. Evaporative membrane modulation for comprehensive two-dimensional liquid chromatography. Analytica Chimica Acta 1000, 303-309. evaporative membrane modulator was developed, built and evaluated to avoid loss of performance in the second dimension when coupling two-dimensional liquid chromatography systems. The automated interface reduces the volume after 1D elution on-line by a pre-determined factor, regardless of the separation gradient. This volume reduction ensures that the injection volume in the 2D is appropriate for the second column, avoiding the detrimental effects of overloading. In addition, the fraction solvent composition is constant over the length of the separation increasing reproducibility of 2D separations. The evaporative membrane modulator was demonstrated with a 10-fold reduction, reducing the injection volume from 50 to 5 μL. A consequence of the EMM device is a reduction in the capacity of the first dimension, which is decreased by a factor of 2.4, but the peak width at half maximum was reduced by up to 22% in the second dimension. When band broadening is considered, the corrected peak capacity with the modulator was only 10% lower than that without the modulator, but with a gain in peak height of 2–3, and a decrease in retention time between subsequent peak-slices reduced from 4s to be negligible. This improves peak shape and shows potential to facilitate peak identification and quantification in more complex applications.Forte, V., Nunziante Cesaro, S., Medeghini, L., 2018. Cooking traces on Copper Age pottery from central Italy: An integrated approach comprising use wear analysis, spectroscopic analysis and experimental archaeology. Journal of Archaeological Science: Reports 18, 121-138. contribution discusses the results of an integrated approach of use wear analysis, spectroscopic analysis and experimental archaeology, applied for the investigation of the actual use of selected ceramic vessels, taken from domestic Copper Age contexts in the modern Rome area.This study is based upon the consideration of a vessel as a tool, used during everyday life and thus reflecting human activities and social behaviours. To this end, the paper here presented proposes an interpretation of the actual use activities which led to the modification of prehistoric vessels. The methodology of this study integrates the traditional approach to ceramic use wear studies, based on experimental and ethnoarchaeological studies, with principles of tribology, along with the application of a dedicated experimental framework which enabled the development of a detailed collection of comparative use wear. Moreover, the application of spectroscopic analysis provided preliminary data related to the charred encrustations found inside the archaeological specimens. These data, when combined with use wear, palaeobotanical remains and archaeological preserved structures, aided interpretation of the archaeological ceramic vessels as cooking pots.Foster, C.S., Crosman, E.T., Holland, L., Mallia, D.V., Fasoli, B., Bares, R., Horel, J., Lin, J.C., 2017. Confirmation of elevated methane emissions in Utah's Uintah Basin with ground-based observations and a high-resolution transport model. Journal of Geophysical Research: Atmospheres 122, 13,026-13,044. CH4 leak rates have been observed in the Uintah Basin of eastern Utah, an area with over 10,000 active and producing natural gas and oil wells. In this paper, we model CH4 concentrations at four sites in the Uintah Basin and compare the simulated results to in situ observations at these sites during two spring time periods in 2015 and 2016. These sites include a baseline location (Fruitland), two sites near oil wells (Roosevelt and Castlepeak), and a site near natural gas wells (Horsepool). To interpret these measurements and relate observed CH4 variations to emissions, we carried out atmospheric simulations using the Stochastic Time-Inverted Lagrangian Transport model driven by meteorological fields simulated by the Weather Research and Forecasting and High Resolution Rapid Refresh models. These simulations were combined with two different emission inventories: (1) aircraft-derived basin-wide emissions allocated spatially using oil and gas well locations, from the National Oceanic and Atmospheric Administration (NOAA), and (2) a bottom-up inventory for the entire U.S., from the Environmental Protection Agency (EPA). At both Horsepool and Castlepeak, the diurnal cycle of modeled CH4 concentrations was captured using NOAA emission estimates but was underestimated using the EPA inventory. These findings corroborate emission estimates from the NOAA inventory, based on daytime mass balance estimates, and provide additional support for a suggested leak rate from the Uintah Basin that is higher than most other regions with natural gas and oil development.Franco-Aguirre, M., Zabala, R.D., Lopera, S.H., Franco, C.A., Cortés, F.B., 2018. Interaction of anionic surfactant-nanoparticles for gas - Wettability alteration of sandstone in tight gas-condensate reservoirs. Journal of Natural Gas Science and Engineering 51, 53-64. of the most common sources of formation damage in tight reservoirs of gas-condensate is condensate banking. The condensate level on the porous media reduces the effective permeability to gas, decreasing the gas production primarily because the pressure reaches values that are lower than dew point pressure or because there is a sharp pressure drop in the near wellbore. The primary objective of this study is to develop a nanofluid, based on the interaction between an anionic surfactant and silica (SiO2) nanoparticles, to alter the reservoir wettability from a liquid-wet state to gas-wettability. The SiO2 nanoparticles were modified by an incipient method using a solution of anionic commercial surfactant Silnyl?FSJ (SY) at various concentrations from 3.0 to 7.0?wt%. Posteriorly, the nanofluids were prepared with modified SiO2 nanoparticles that were dispersed in an SY solution in deionized water. Nanofluids were initially evaluated at room conditions by contact angle and imbibition tests on oil-wet and water-wet sandstone samples for the wettability alteration to obtain the best concentration ratio of modified nanoparticles and SY in the nanofluid. Different combinations and individual effects of the nanoparticles and SY surfactant were evaluated. Better performance in changing the wettability of the system was achieved for a nanofluid at a concentration of 500?mg/L of SiO2 nanoparticles, which were functionalized with 5.0?wt% of SY and dispersed in an SY solution at 0.46?wt% in deionized water. In water-wet samples, contact angles changed from 0° to 118° and from 32° to 95° for water/rock/air and oil/rock/air systems, respectively. Similarly, for oil-wet samples, the contact angles were modified from 123° to 115° and from 0° to 93°.Coreflooding tests were performed under tight gas-condensate reservoir temperature and pressure conditions. Through the permeability curves and oil recovery, the synthesized nanofluid was observed to alter the wettability of the system from a strongly liquid-wet to a gas-wet condition. Additionally, according to the results, the use of the synthesized nanofluids can reduce the formation damage caused by the condensate banking, favoring the mobility of liquid and leading to a considerable improvement in oil and gas production. The oil recovery increases from 46.6% in the base system to 78.4% after treatment. Additionally, residual saturation of oil was reduced from 29.2% to 17.8% in the base and treated systems, respectively.Franek, P., Plaza-Faverola, A., Mienert, J., Buenz, S., Ferré, B., Hubbard, A., 2017. Microseismicity linked to gas migration and leakage on the western Svalbard shelf. Geochemistry, Geophysics, Geosystems 18, 4623-4645. continental margin off Prins Karls Forland, western Svalbard, is characterized by widespread natural gas seepage into the water column at and upslope of the gas hydrate stability zone. We deployed an ocean bottom seismometer integrated into the MASOX (Monitoring Arctic Seafloor-Ocean Exchange) automated seabed observatory at the pinch-out of this zone at 389 m water depth to investigate passive seismicity over a continuous 297 day period from 13 October 2010. An automated triggering algorithm was applied to detect over 220,000 short duration events (SDEs) defined as having a duration of less than 1 s. The analysis reveals two different types of SDEs, each with a distinctive characteristic seismic signature. We infer that the first type consists of vocal signals generated by moving mammals, likely finback whales. The second type corresponds to signals with a source within a few hundred meters of the seismometer, either due east or west, that vary on short (～tens of days) and seasonal time scales. Based on evidence of prevalent seafloor seepage and subseafloor gas accumulations, we hypothesize that the second type of SDEs is related to subseafloor fluid migration and gas seepage. Furthermore, we postulate that the observed temporal variations in microseismicity are driven by transient fluid release and due to the dynamics of thermally forced, seasonal gas hydrate decomposition. Our analysis presents a novel technique for monitoring the duration, intensity, and periodicity of fluid migration and seepage at the seabed and can help elucidate the environmental controls on gas hydrate decomposition and release.Freymond, C.V., Kündig, N., Stark, C., Peterse, F., Buggle, B., Lupker, M., Pl?tze, M., Blattmann, T.M., Filip, F., Giosan, L., Eglinton, T.I., 2018. Evolution of biomolecular loadings along a major river system. Geochimica et Cosmochimica Acta 223, 389-404. the transport history and fate of organic carbon (OC) within river systems is crucial in order to constrain the dynamics and significance of land–ocean interactions as a component of the global carbon cycle. Fluvial export and burial of terrestrial OC in marine sediments influences atmospheric CO2 over a range of timescales, while river-dominated sedimentary sequences can provide valuable archives of paleoenvironmental information. While there is abundant evidence that the association of organic matter (OM) with minerals exerts an important influence on its stability as well as hydrodynamic behavior in aquatic systems, there is a paucity of information on where such associations form and how they evolve during fluvial transport. Here, we track total organic carbon (TOC) and terrestrial biomarker concentrations (plant wax-derived long-chain fatty acids (FA), branched glycerol dialkyl glycerol tetraethers (brGDGTs) and lignin-derived phenols) in sediments collected along the entire course of the Danube River system in the context of sedimentological parameters. Mineral-specific surface area-normalized biomarker and TOC concentrations show a systematic decrease from the upper to the lower Danube basin. Changes in OM loading of the available mineral phase correspond to a net decrease of 70–80% of different biomolecular components. Ranges for biomarker loadings on Danube River sediments, corresponding to 0.4–1.5?μgFA/m2 for long-chain (n-C24–32) fatty acids and 17–71?ngbrGDGT/m2 for brGDGTs, are proposed as a benchmark for comparison with other systems. We propose that normalizing TOC as well as biomarker concentrations to mineral surface area provides valuable quantitative constraints on OM dynamics and organo-mineral interactions during fluvial transport from terrigenous source to oceanic sink.Frieling, J., Reichart, G.J., Middelburg, J.J., R?hl, U., Westerhold, T., Bohaty, S.M., Sluijs, A., 2018. Tropical Atlantic climate and ecosystem regime shifts during the Paleocene–Eocene Thermal Maximum. Climate of the Past 14, 39-55. Paleocene–Eocene Thermal Maximum (PETM, 56?Ma) was a phase of rapid global warming associated with massive carbon input into the ocean–atmosphere system from a 13C-depleted reservoir. Many midlatitude and high-latitude sections have been studied and document changes in salinity, hydrology and sedimentation, deoxygenation, biotic overturning, and migrations, but detailed records from tropical regions are lacking. Here, we study the PETM at Ocean Drilling Program (ODP) Site 959 in the equatorial Atlantic using a range of organic and inorganic proxies and couple these with dinoflagellate cyst (dinocyst) assemblage analysis. The PETM at Site 959 was previously found to be marked by a ?～??3.8?‰ negative carbon isotope excursion (CIE) and a ?～??4?°C surface ocean warming from the uppermost Paleocene to peak PETM, of which ?～??1?°C occurs before the onset of the CIE. We record upper Paleocene dinocyst assemblages that are similar to PETM assemblages as found in extratropical regions, confirming poleward migrations of ecosystems during the PETM. The early stages of the PETM are marked by a typical acme of the tropical genus Apectodinium, which reaches abundances of up to 95?%. Subsequently, dinocyst abundances diminish greatly, as do carbonate and pyritized silicate microfossils. The combined paleoenvironmental information from Site 959 and a close-by shelf site in Nigeria implies the general absence of eukaryotic surface-dwelling microplankton during peak PETM warmth in the eastern equatorial Atlantic, most likely caused by heat stress. We hypothesize, based on a literature survey, that heat stress might have reduced calcification in more tropical regions, potentially contributing to reduced deep sea carbonate accumulation rates, and, by buffering acidification, also to biological carbonate compensation of the injected carbon during the PETM. Crucially, abundant organic benthic foraminiferal linings imply sustained export production, likely driven by prokaryotes. In sharp contrast, the recovery of the CIE yields rapid (??10?kyr) fluctuations in the abundance of several dinocyst groups, suggesting extreme ecosystem and environmental variability.Fu, K., Bohn, P.W., 2018. Nanopore electrochemistry: A nexus for molecular control of electron transfer reactions. ACS Central Science 4, 20-29. structures occur widely in living organisms. Ion channels embedded in cell membranes, for example, provide pathways, where electron and proton transfer are coupled to the exchange of vital molecules. Learning from mother nature, a recent surge in activity has focused on artificial nanopore architectures to effect electrochemical transformations not accessible in larger structures. Here, we highlight these exciting advances. Starting with a brief overview of nanopore electrodes, including the early history and development of nanopore sensing based on nanopore-confined electrochemistry, we address the core concepts and special characteristics of nanopores in electron transfer. We describe nanopore-based electrochemical sensing and processing, discuss performance limits and challenges, and conclude with an outlook for next-generation nanopore electrode sensing platforms and the opportunities they present.Fu, M., Li, N., Huang, Q., Liu, L., 2017. Shoreline-neritic mixed sedimentation response to sea level change and paleoclimate: A case study from Carboniferous in Tarim Basin. Acta Sedimentologica Sinica 35, 1110-1120. characteristics of siliciclastic-carbonate mixed sedimentary environment still remains unknown, resulting in poor understanding of distribution of mixed rock. In this study, the sedimentary environments and environmental parameters of Carboniferous in Bamai area, Tarim Basin are deeply studied, using observation of thin sections, measurement of minerals composition, and elements composition. The mixed rocks were deposited, carbonate restricted platform and open platform. The concentrations of Ti, Rb, K, Al are used to divide the degrees of mixed sedimentation into four levels due to their good relationship with the degree of mixing. The salinity was reflected by Na content and Na/Ca. The depth of water was reflected by Mn/Fe and Sr content. The redox condition was reflected by V/(V+Ni). And, the paleoclimate was analyzed from Ti/Al and Mg/Sr. The result of geochemical indices shows the mixed sedimentation beyond Ⅱ level occurred at humid climate, while there was no obvious mixing at arid climate. Meanwhile, most mixed sedimentation accompanied by sea level fall. On the open platform, there was only I level mixed sedimentation, while Ⅲ-IV level mixed sedimentation developed on the barrier coast and restricted platform. The mixed sedimentation in each depositional environment can record the change of sea level and paleoclimate.Fu, P., Settgast, R.R., Hao, Y., Morris, J.P., Ryerson, F.J., 2017. The influence of hydraulic fracturing on carbon storage performance. Journal of Geophysical Research: Solid Earth 122, 9931-9949. principles of the design and operation of geologic carbon storage (GCS) require injecting CO2 below the caprock fracturing pressure to ensure the integrity of the storage complex. In nonideal storage reservoirs with relatively low permeability, pressure buildup can lead to hydraulic fracturing of the reservoir and caprock. While the GCS community has generally viewed hydraulic fractures as a key risk to storage integrity, a carefully designed stimulation treatment under appropriate geologic conditions could provide improved injectivity while maintaining overall seal integrity. A vertically contained hydraulic fracture, either in the reservoir rock or extending a limited height into the caprock, provides an effective means to access reservoir volume far from the injection well. Employing a fully coupled numerical model of hydraulic fracturing, solid deformation, and matrix fluid flow, we study the enabling conditions, processes, and mechanisms of hydraulic fracturing during CO2 injection. A hydraulic fracture's pressure-limiting behavior dictates that the near-well fluid pressure is only slightly higher than the fracturing pressure of the rock and is insensitive to injection rate and mechanical properties of the formation. Although a fracture contained solely within the reservoir rock with no caprock penetration, would be an ideal scenario, poroelastic principles dictate that sustaining such a fracture could lead to continuously increasing pressure until the caprock fractures. We also investigate the propagation pattern and injection pressure responses of a hydraulic fracture propagating in a caprock subjected to heterogeneous in situ stress. The results have important implications for the use of hydraulic fracturing as a tool for managing storage performance.Fukumoto, A., Kamada, K., Sato, T., Oyama, H., Torii, H., Kiyono, F., Nagao, J., Temma, N., Narita, H., 2018. Numerical simulation of pore-scale formation of methane hydrate in the sand sediment using the phase-field model. Journal of Natural Gas Science and Engineering 50, 269-281. hydrate is considered as a promising energy resource for the near future. To predict the gas productivity from the methane hydrate in the subsea sand-sediment, it is important to know effective permeability accurately of the sediment bearing methane hydrate. Hence, the hydrate morphological distribution: namely, what is the shape and morphology of hydrate, in the sediment should be elucidated, because the permeability is strongly affected by the hydrate distribution. In this study, to know where hydrate is formed in the pore of porous media, we proposed a numerical model for estimating the microscopic distribution of methane hydrate in sand sediment, using the classical nucleation theory and the phase-field model. The former theory gave the probabilities of hydrate nucleation positions in the gas-water-sand three-phases and the latter method provided the mobility of the front of the hydrate formation. A necessary hydrate formation rate constant was determined by history-matching with an experiment in the literature. Using the obtained rate constant, we numerically simulated hydrate formations within the microscopic computational domains.Gall, D.L., Kontur, W.S., Lan, W., Kim, H., Li, Y., Ralph, J., Donohue, T.J., Noguera, D.R., 2018. In vitro enzymatic depolymerization of lignin with release of syringyl, guaiacyl, and tricin units. Applied and Environmental Microbiology 84, Article e02076-17.: New environmentally sound technologies are needed to derive valuable compounds from renewable resources. Lignin, an abundant polymer in terrestrial plants comprised predominantly of guaiacyl and syringyl monoaromatic phenylpropanoid units, is a potential natural source of aromatic compounds. In addition, the plant secondary metabolite tricin is a recently discovered and moderately abundant flavonoid in grasses. The most prevalent interunit linkage between guaiacyl, syringyl, and tricin units is the β-ether linkage. Previous studies have shown that bacterial β-etherase pathway enzymes catalyze glutathione-dependent cleavage of β-ether bonds in dimeric β-ether lignin model compounds. To date, however, it remains unclear whether the known β-etherase enzymes are active on lignin polymers. Here we report on enzymes that catalyze β-ether cleavage from bona fide lignin, under conditions that recycle the cosubstrates NAD+ and glutathione. Guaiacyl, syringyl, and tricin derivatives were identified as reaction products when different model compounds or lignin fractions were used as substrates. These results demonstrate an in vitro enzymatic system that can recycle cosubstrates while releasing aromatic monomers from model compounds as well as natural and engineered lignin oligomers. These findings can improve the ability to produce valuable aromatic compounds from a renewable resource like lignin. Importance: Many bacteria are predicted to contain enzymes that could convert renewable carbon sources into substitutes for compounds that are derived from petroleum. The β-etherase pathway present in sphingomonad bacteria could cleave the abundant β–O–4-aryl ether bonds in plant lignin, releasing a biobased source of aromatic compounds for the chemical industry. However, the activity of these enzymes on the complex aromatic oligomers found in plant lignin is unknown. Here we demonstrate biodegradation of lignin polymers using a minimal set of β-etherase pathway enzymes, the ability to recycle needed cofactors (glutathione and NAD+) in vitro, and the release of guaiacyl, syringyl, and tricin as depolymerized products from lignin. These observations provide critical evidence for the use and future optimization of these bacterial β-etherase pathway enzymes for industrial-level biotechnological applications designed to derive high-value monomeric aromatic compounds from lignin. Galperin, M.Y., Shalaeva, D.N., 2018. A bacterial coat that is not pure cotton. Science 359, 276-277., a linear polymer of glucose residues, is the main component of plant cell walls and the most abundant biomolecule on the planet. Cellulose fibers from wood, cotton, and linen are mostly used as such, but can also be chemically modified to make rayon, viscose, and other textiles. Many bacteria also synthesize cellulose. Cellulose fibers produced by the model organism Komagataeibacter (Gluconacetobacter) xylinus are very similar to those found in plants (1) and are increasingly used in biotechnology and nanotechnology (2, 3). Escherichia coli and many other bacteria produce cellulose as a key component of the extracellular matrix that coats the cells to form a biofilm, a complex multicellular community consisting of numerous bacteria, exopolysaccharides (like cellulose), protein fibers, and DNA (4–6). The cellulose in biofilms was assumed to be the same as that produced by G. xylinus, owing to the same pattern of staining with Congo red dye and the same cellulose synthase enzyme (4–6). However, on page 334 of this issue, Thongsomboon et al. (7) report that E. coli and Salmonella enterica serovar Typhimurium produce modified cellulose, in which every other glucosyl residue carries an additional phosphoethanolamine (pEtN) group. These findings have important implications for a wide variety of disciplines, from microbiology to materials science.It appears that previous studies simply overlooked the presence of this cellulose modification. Bacterial cellulose is a stable polymer that is resistant to a variety of harsh treatments. When such treatments were used to purify cellulose fibers from microbial biofilms, the pEtN group was lost. Thongsomboon et al. used mass spectrometry and several versions of solid-state nuclear magnetic resonance spectroscopy to detect and study the pEtN modification in vivo. They also showed that the pEtN group comes from the cell membrane lipid phosphatidylethanolamine and identified BcsG, a subunit of the cellulose synthase complex, as the pEtN transferase responsible for catalyzing the pEtN modification.Microbiologists might be most interested in the wide phylogenetic distribution of the pEtN modification. In addition to E. coli and Salmonella, BcsG is encoded in cellulose synthase operons of some important pathogens, including certain species of Klebsiella, Shigella, Enterobacter, and Burkholderia, as well as the plant pathogen Erwinia spp. (4). Thus, biofilms formed by these organisms might also contain pEtN-modified cellulose. This is important because the addition of the pEtN group is likely to change biofilm properties. Thongsomboon et al. show that pEtN-modified cellulose forms a more compact biofilm mesh that is more resistant to shear forces. However, the presence of the pEtN group probably makes the cellulose fibers less rigid and less inert than those consisting of pure cellulose. This warrants reexamination of the sensitivity of E. coli and Salmonella biofilms to detergents and enzymes that do not affect standard cellulose fibers but that might be active on pEtN-modified cellulose. Thus, the goal of preventing infection by disrupting such biofilms might be within closer reach.The work by Thongsomboon et al. should also help with understanding the exact role of the cellulose-containing biofilm as a virulence factor. Curiously, some of the worst disease-causing strains of E. coli and Shigella do not produce biofilms in acute infections (4, 8). It appears that the ability to form a biofilm allows these pathogens to better adapt to the host environment and shifts the infection from an acute to chronic state. Thus, improved understanding of pEtN cellulose biosynthesis is an important step toward fighting bacterial diseases.More generally, Thongsomboon et al. provide insight into the regulation of polymer export in bacteria. Bacterial cellulose biosynthesis depends on the second messenger cyclic diguanosine monophosphate (c-di-GMP) (4, 9–11). The structure of cellulose synthase (10) showed that c-di-GMP is required to allow the substrate access to the enzyme active site. The amount of cellulose produced by E. coli also depends on the expression of the bcsEFG operon and one of its products, BcsE, which binds c-di-GMP (12). However, the exact roles of these proteins have remained obscure. The finding that the catalytic domain of BcsG is located in the periplasm (between the inner and outer membranes) and modifies glucosyl residues of the nascent cellulose chain (7) allowed Thongsomboon et al. to predict the organization of the entire membrane-bound cellulose synthase complex (see the figure). This not only resolves the role of the bcsEFG operon, but also highlights the complexity of c-di-GMP-mediated regulatory processes. At least in E. coli and Salmonella, c-di-GMP seems to regulate cellulose formation at several different levels. This multilevel regulation of important life-cycle decisions, such as biofilm formation, has been dubbed “sustained sensing” (13). It appears to be common in the microbial world but is difficult to disentangle without a detailed analysis of regulatory interactions.Finally, the work by Thongsomboon et al. will benefit efforts to find new applications for bacterially synthesized cellulose and develop new cellulose-based compounds. Gluconacetobacter-produced cellulose microfibers and crystals, commonly referred to as nanocellulose, have numerous applications (2). The apparent biocompatibility—lack of toxicity, immunogenicity, and proinflammatory response—of unmodified cellulose makes it an attractive choice for a variety of biomedical applications, such as drug delivery, wound dressing, replacement of blood vessels, and tissue engineering of bone and cartilage (2, 3). Thus, pEtN-modified cellulose would have to undergo rigorous biocompatibility testing. Nevertheless, the availability of genetic tools to manipulate E. coli opens numerous possibilities for using cellulose synthase genes for synthetic biology. A particularly interesting development could be the ability to produce entirely new kinds of cellulose films for applications ranging from optoelectronics to packaging.In principle, one could imagine production of cellulose microfibers with new modifications. The catalytic domain of BcsG is a metalloenzyme of the alkaline phosphatase and sulfatase superfamily (14), which is anchored in the membrane by five predicted transmembrane helices (see the figure). Replacing the catalytic domain of BcsG with a different enzyme, such as an acyltransferase or a glycosyltransferase, could allow biosynthesis of cellulose nanocrystals with new optical properties, increased conductivity, or the ability to bind metal ions.References1. P. Ross, R. Mayer, M. Benziman, Microbiol. Rev. 55, 35 (1991).2. N. Lin, A. Dufresne, Eur. Polymer. J. 59, 302 (2014).3. T. Abitbol et al., Curr. Opin. Biotechol. 39, 76 (2016).4. U. R?mling, M. Y. Galperin, Trends Microbiol. 23, 545 (2015).5. X. Zogaj, M. Nimtz, M. Rohde, W. Bokranz, U. R?mling, Mol. Microbiol. 39, 1452 (2001).6. D. O. Serra, A. M. Richter, R. Hengge, J. Bacteriol. 195, 5540 (2013).7. W. Thongsomboon et al., Science 359, 334 (2018).8. A. M. Richter, T. L. Povolotsky, L. H. Wieler, R. Hengge, EMBO Mol. Med. 6, 1622 (2014).9. U. R?mling, M. Y. Galperin, M. Gomelsky, Microbiol. Mol. Biol. Rev. 77, 1 (2013).10. J. L. Morgan et al., Nature 531, 329 (2016).11. P. V. Krasteva et al., Nat. Commun. 8, 2065 (2017).12. X. Fang et al., Mol. Microbiol. 93, 439 (2014).13. M. W. Orr, M. Y. Galperin, V. T. Lee, Curr. Opin. Microbiol. 34, 119 (2016).14. M. Y. Galperin, A. Bairoch, E. V. Koonin, Protein Sci. 7, 1829 (1998).15. M. A. Lomize, I. D. Pogozheva, J. Joo, H. I. Mosberg, A. L. Lomize, Nucleic Acids Res. 40, D370 (2012).Gao, G., Yang, S., Ren, J., Zhang, W., Xiang, B., 2018. Geochemistry and depositional conditions of the carbonate-bearing lacustrine source rocks: A case study from the Early Permian Fengcheng Formation of Well FN7 in the northwestern Junggar Basin. Journal of Petroleum Science and Engineering 162, 407-418. of TOC, Rock-Eval pyrolysis, carbon isotope composition, solvent extract, extract fractionation, and the gas chromatography-mass spectrum (GC-MS) of the saturated fraction were conducted on the Lower Permian Fengcheng Formation carbonate-bearing shales and argillaceous dolomites of Well FN7 in the northwestern Junggar Basin to understand the geochemistry and depositional environmental evolution of the carbonate-bearing lacustrine source rocks. The results indicate that the Fengcheng Formation carbonate-bearing shales are fair to good source rocks with Type II kerogen for generating oil and minor gas, and the argillaceous dolomites are poor source rocks. The thermal mature shales contain more residually generated hydrocarbon, whereas the argillaceous dolomites contain more migrated hydrocarbon. This property is favorable for shale oil or tight oil accumulation in the Fengcheng Formation. Biomarker analyses indicate that the Fengcheng Formation source rocks were formed in the anoxic reducing lacustrine depositional environment with a stratified water column and high salinity. The source rock organic matter has major aquatic phytoplankton and algae input and less terrestrial organic matter input. During the Fengcheng Formation period, oxidation had a weak increasing tendency and salinity had a weak decreasing tendency from the early to late periods under the background of a reducing environment. Except for poor source rocks in upper and lower parts, the good source rocks are primarily in the middle part of the Fengcheng Formation.Gao, X., Ma, Y., Jiang, Q., Shi, K., Li, Y., Shen, Y., 2018. Wave processes in relation to the tectono-sedimentary of the Tarim basin: A?new method for basin study. Journal of Petroleum Science and Engineering 161, 248-258. study gives insights into the tectonic and sedimentary evolution of the Tarim basin, the largest petroleum-bearing basin in Western China, by analyzing sedimentary wave process using multi-scale decomposition of the wavelet transform method, and the mathematical defects of sliding-window method in the process of sedimentary wave analysis was discussed. The filtering analysis, in the time domain, was carried out on cores collected from 14 wells in the Tarim basin. The results show that the evolution of the Tarim basin was controlled by various wave processes. The periods of 212 ± Ma, 102 ± Ma and 33 ± Ma indicated a strong sedimentary rhythm, which displayed a spatial and temporal evolution of wave characteristics. The 33 ± Ma period represented a third-order sequence of the stratigraphic division, which identified with the unconformities of the Tarim basin; 102 ± Ma period corresponded to an important period of sedimentation and the plate collision around the Tarim basin, which marked a second-order period of the basin evolution. The centers of subsidence showed periodic shifts since the Cambrian, and the time for periodic migration (completing a circle) of the depocenters or the centers of subsidence is traced as 212 ± Ma, which corresponded to the first-order period of the basin evolution. The coupling relationships between the wave processes and the evolution and distribution of source, reservoir and cap rocks in the basin were given by three kinds of patterns, which were important in predicting the space-time distribution of source, reservoir and cap rocks. This study gives a new insight on predicting the formation and distribution of petroleum, which could be used for selecting petroleum exploration targets effectively.Ghiasi, M.M., Noorollahi, Y., Aslani, A., 2018. CO2 hydrate: Modeling of incipient stability conditions and dissociation enthalpy. Petroleum Science and Technology 36, 259-265. this study, CO2 hydrate incipient stability zone in pure water is modelled employing an empirical tool, classification and regression tree, least squares support vector machine, and adaptive neuro-fuzzy inference system. Furthermore, a new semi-theoretical model is developed to estimate CO2 hydrate dissociation enthalpy. Moreover, the quality of CO2 hydrate's experimental data is assessed through a thermodynamic-based and Leverage approaches. Results revealed that: (1) the proposed models provide satisfactory predictions; (2) there are some doubtful data in the database; (3) outcomes of the developed semi-theoretical model for estimating the CO2 hydrate dissociation enthalpy are in good agreement with previous works.Ghosh, S., Bal, B., Das, A.P., 2018. Enhancing manganese recovery from low-grade ores by using mixed culture of indigenously isolated bacterial strains. Geomicrobiology Journal 35, 242-246. leaching methods for manganese (Mn) recovery require strong acids and are threatening to the environment. Alternatively, the use of microbes for Mn recovery is environment friendly in nature. The present investigation compares the capacity of pure and mixed cultures of native bacterial strains for bioleaching of low-grade Mn ores. The ability of the isolated microorganisms to recover Mn was evaluated in shake flasks for 20 days under optimized conditions of pulp density (2%), sucrose concentration (2 g/100 mL), initial pH 6.5, and 30°C incubation temperature. In pure culture form, Acinetobacter sp. MSB 5 (70%) was found to have a higher bioleaching potential than Lysinibacillus sp. MSB 11 (67%). Mixed culture of Acinetobacter sp. MSB 5 and Lysinibacillus sp. MSB 11 was found to perform better than the pure cultures with 74% extraction of Mn. The presence of mixed culture increased the dissolution rate and the recovery percentage of Mn. The respective growth pattern of the cultures was in synchronization to their Mn bioleaching performances. This study underlines the importance of mixed cultures and Mn solubilizing activity of native bacterial strains for efficient Mn biorecovery.Gibtan, A., Song, H.S., Kim, J.Y., Kim, Y.B., Park, N., Park, K., Lee, S.-J., Kwon, J., Roh, S.W., Lee, H.-S., 2018. Halorubrum aethiopicum sp. nov., an extremely halophilic archaeon isolated from commercial rock salt. International Journal of Systematic and Evolutionary Microbiology 68, 416-422. novel extremely halophilic archaeon, designated SAH-A6T, was isolated from a sample of commercial rock salt in Ethiopia. Cells of SAH-A6T were aerobic and pleomorphic. The strain was able to grow at concentrations of 15–30?% (w/v) NaCl (optimum 20–25?%?NaCl), at pH 6.0–9.0 (optimum pH 7.0) and in a temperature range of 30–55?°C (optimum 37–45?°C). Mg2+ was not required for growth of SAH-A6T cells. On the basis of 16S rRNA gene sequence analysis, strain SAH-A6T was closely related to Halorubrum halodurans Cb34T (99.1?%), Halorubrum rubrum YC87T (98.9?%), Halorubrum aquaticum EN-2T (98.7?%), Halorubrum cibi JCM 15757T (98.4?%), Halorubrum luteum CGSA15T (97.3?%), Halorubrum lipolyticum 9-3T (97.1?%), Halorubrum tibetense 8W8T (97.1?%), Halorubrum kocurii JCM 1478T (97.1?%), Halorubrum halophilum B8T (97.0?%) and Halorubrum persicum C49T (97.0?%). Phylogenetic analysis based on the rpoB' gene sequences showed that strain SAH-A6T was closely related to Hrr. halodurans Cb34T (99.7?%), Hrr. aquaticum JCM 14031T (99.3?%) and other members of the genus Halorubrum (<99.0?%). The DNA G+C?content of the strain was 68.0?mol%. DNA–DNA hybridization between strain SAH-A6T and the most closely related members of the genus Halorubrum were below 55?%, suggesting that the new isolate constitutes a different genospecies. On the bases of chemotaxonomic, phenotypic and genotypic data, strain SAH-A6T (=KCCM 43215T=JCM 31519T) represents a novel species of the genus Halorubrum , for which the name Halorubrum aethiopicum sp. nov. is proposed. The GenBank/EMBL/DDBJ accession numbers of the 16S rRNA and rpoB′ gene sequence of strain SAH-A6T are KX150521 and MF039476, respectively.Gomes, M.L., Fike, D.A., Bergmann, K.D., Jones, C., Knoll, A.H., 2018. Environmental insights from high-resolution (SIMS) sulfur isotope analyses of sulfides in Proterozoic microbialites with diverse mat textures. Geobiology 16, 17-34. modern microbial mats, hydrogen sulfide shows pronounced sulfur isotope (δ34S) variability over small spatial scales (~50‰ over <4 mm), providing information about microbial sulfur cycling within different ecological niches in the mat. In the geological record, the location of pyrite formation, overprinting from mat accretion, and post-depositional alteration also affect both fine-scale δ34S patterns and bulk δ34Spyrite values. We report μm-scale δ34S patterns in Proterozoic samples with well-preserved microbial mat textures. We show a well-defined relationship between δ34S values and sulfide mineral grain size and type. Small pyrite grains (<25 μm) span a large range, tending toward high δ34S values (?54.5‰ to 11.7‰, mean: ?14.4‰). Larger pyrite grains (>25 μm) have low but equally variable δ34S values (?61.0‰ to ?10.5‰, mean: ?44.4‰). In one sample, larger sphalerite grains (>35 μm) have intermediate and essentially invariant δ34S values (?22.6‰ to ?15.6‰, mean: ?19.4‰). We suggest that different sulfide mineral populations reflect separate stages of formation. In the first stage, small pyrite grains form near the mat surface along a redox boundary where high rates of sulfate reduction, partial closed-system sulfate consumption in microenvironments, and/or sulfide oxidation lead to high δ34S values. In another stage, large sphalerite grains with low δ34S values grow along the edges of pore spaces formed from desiccation of the mat. Large pyrite grains form deeper in the mat at slower sulfate reduction rates, leading to low δ34Ssulfide values. We do not see evidence for significant 34S-enrichment in bulk pore water sulfide at depth in the mat due to closed-system Rayleigh fractionation effects. On a local scale, Rayleigh fractionation influences the range of δ34S values measured for individual pyrite grains. Fine-scale analyses of δ34Spyrite patterns can thus be used to extract environmental information from ancient microbial mats and aid in the interpretation of bulk δ34Spyrite records.Gougherty, S.W., Bauer, J.E., Pohlman, J.W., 2018. Exudation rates?and δ13C signatures of tree root soluble organic carbon in a riparian forest. Biogeochemistry 137, 235-252. root exudation (TRE) of water soluble organic carbon (WSOC) is an important but under-assessed component of net primary production, and is thought to strongly influence rhizosphere biogeochemistry. Riparian systems in particular are often viewed as biogeochemical hot spots fueled partially by root exudate WSOC. However, TRE rates have not been previously reported for these systems. The δ13C signatures of exudates may provide important insights into plant physiology and inform isotope-based methods to identify sources of soil CO2 fluxes, but this information is also generally lacking. In the present study, root exudate WSOC was collected in situ to assess both net exudation rates and exudate δ13C values in a temperate riparian forest. Net TRE rates were found to be most strongly related to a combination of tree species, root characteristics and net ecosystem exchange (Adj. R2 = 0.73; p < 0.001). In contrast, exudate δ13C values were correlated to time-lagged vapor pressure deficit (Adj. R2 = 0.21; p < 0.05) and air temperature (Adj. R2 = 0.43; p < 0.05), suggesting a rapid transfer of photosynthate from the canopy to the rhizosphere. Extrapolation of mean net TRE rates (13 ?mol C g root?1 day?1) from a root mass basis to the entire sampling area suggests that TRE may account for as much as 3% of net annual C uptake and represents an important input of organic matter to riparian soils. Our findings of predictable TRE rates and exudate δ13C values in the present study suggest that future studies examining δ13C values of different plant components, soil organic matter and respired soil CO2 would benefit by accounting for the impact of root exudates.Gouilleux, B., Rouger, L., Giraudeau, P., 2018. Ultrafast 2D NMR: Methods and applications, in: Webb, G.A. (Ed.), Annual Reports on NMR Spectroscopy. Academic Press, pp. 75-144. NMR (nD NMR) has become one of the most powerful spectroscopic tools to deliver diverse structural and functional insights into organic and biomolecules as well as on raw materials. A long-standing concern of nD NMR is related to its long experiment duration, arising from the need to sample the indirect dimension(s) in a multistep fashion. For decades, the NMR community has been developing numerous strategies to speed up nD NMR experiments and therefore extend their scope of applications. Among them is the ultrafast (UF) NMR methodology, capable of delivering arbitrary homo- or heteronuclear multidimensional spectra in a single scan. Since the initial concept was published in 2002, the performance of this subsecond 2D NMR approach has been greatly improved so that UF NMR is nowadays a relevant analytical tool used in broad variety of situations whereby the experiment duration is crucial. Following a description of the principles of UF NMR, the present review aims at emphasizing the numerous methodological developments that this approach has undergone so far in 2017. Thereafter, the high versatility of UF NMR is highlighted through the review of the applications that have been reported in a variety of settings and disciplines, in isotropic as well as anisotropic media.Graeber, D., Poulsen, J.R., Heinz, M., Rasmussen, J.J., Zak, D., Gücker, B., Kronvang, B., Kamjunke, N., 2018. Going with the flow: Planktonic processing of dissolved organic carbon in streams. Science of The Total Environment 625, 519-530. large part of the organic carbon in streams is transported by pulses of terrestrial dissolved organic carbon (tDOC) during hydrological events, which is more pronounced in agricultural catchments due to their hydrological flashiness. The majority of the literature considers stationary benthic biofilms and hyporheic biofilms to dominate uptake and processing of tDOC. Here, we argue for expanding this viewpoint to planktonic bacteria, which are transported downstream together with tDOC pulses, and thus perceive them as a less variable resource relative to stationary benthic bacteria. We show that pulse DOC can contribute significantly to the annual DOC export of streams and that planktonic bacteria take up considerable labile tDOC from such pulses in a short time frame, with the DOC uptake being as high as that of benthic biofilm bacteria. Furthermore, we show that planktonic bacteria efficiently take up labile tDOC which strongly increases planktonic bacterial production and abundance. We found that the response of planktonic bacteria to tDOC pulses was stronger in smaller streams than in larger streams, which may be related to bacterial metacommunity dynamics. Furthermore, the response of planktonic bacterial abundance was influenced by soluble reactive phosphorus concentration, pointing to phosphorus limitation. Our data suggest that planktonic bacteria can efficiently utilize tDOC pulses and likely determine tDOC fate during downstream transport, influencing aquatic food webs and related biochemical cycles.Graham, E.B., Tfaily, M.M., Crump, A.R., Goldman, A.E., Bramer, L.M., Arntzen, E., Romero, E., Resch, C.T., Kennedy, D.W., Stegen, J.C., 2017. Carbon inputs from riparian vegetation limit oxidation of physically bound organic carbon via biochemical and thermodynamic processes. Journal of Geophysical Research: Biogeosciences 122, 3188-3205. light of increasing terrestrial carbon (C) transport across aquatic boundaries, the mechanisms governing organic carbon (OC) oxidation along terrestrial-aquatic interfaces are crucial to future climate predictions. Here we investigate the biochemistry, metabolic pathways, and thermodynamics corresponding to OC oxidation in the Columbia River corridor using ultrahigh-resolution C characterization. We leverage natural vegetative differences to encompass variation in terrestrial C inputs. Our results suggest that decreases in terrestrial C deposition associated with diminished riparian vegetation induce oxidation of physically bound OC. We also find that contrasting metabolic pathways oxidize OC in the presence and absence of vegetation and—in direct conflict with the “priming” concept—that inputs of water-soluble and thermodynamically favorable terrestrial OC protect bound-OC from oxidation. In both environments, the most thermodynamically favorable compounds appear to be preferentially oxidized regardless of which OC pool microbiomes metabolize. In turn, we suggest that the extent of riparian vegetation causes sediment microbiomes to locally adapt to oxidize a particular pool of OC but that common thermodynamic principles govern the oxidation of each pool (i.e., water-soluble or physically bound). Finally, we propose a mechanistic conceptualization of OC oxidation along terrestrial-aquatic interfaces that can be used to model heterogeneous patterns of OC loss under changing land cover distributions.Granold, M., Hajieva, P., To?a, M.I., Irimie, F.-D., Moosmann, B., 2018. Modern diversification of the amino acid repertoire driven by oxygen. Proceedings of the National Academy of Sciences 115, 41-46.: All life uses the same 20 amino acids, but only 7–13 early amino acids seem to be indispensable to build functional proteins. Thus, what triggered the introduction of the additional amino acids? Employing quantum chemical calculations and biochemical experiments, we find that the additional amino acids have become systematically “softer” (Ralph G. Pearson) over time, more redox-reactive, and more capable of protecting cells from destruction by oxygen free radicals. Hence, it appears that molecular oxygen forced life to incorporate novel amino acids with augmented redox properties into the genetic code. The present study provides a plausible scenario for a more than 80-y-old problem of fundamental biochemistry: Why these 20 amino acids? Abstract: All extant life employs the same 20 amino acids for protein biosynthesis. Studies on the number of amino acids necessary to produce a foldable and catalytically active polypeptide have shown that a basis set of 7–13 amino acids is sufficient to build major structural elements of modern proteins. Hence, the reasons for the evolutionary selection of the current 20 amino acids out of a much larger available pool have remained elusive. Here, we have analyzed the quantum chemistry of all proteinogenic and various prebiotic amino acids. We find that the energetic HOMO–LUMO gap, a correlate of chemical reactivity, becomes incrementally closer in modern amino acids, reaching the level of specialized redox cofactors in the late amino acids tryptophan and selenocysteine. We show that the arising prediction of a higher reactivity of the more recently added amino acids is correct as regards various free radicals, particularly oxygen-derived peroxyl radicals. Moreover, we demonstrate an immediate survival benefit conferred by the enhanced redox reactivity of the modern amino acids tyrosine and tryptophan in oxidatively stressed cells. Our data indicate that in demanding building blocks with more versatile redox chemistry, biospheric molecular oxygen triggered the selective fixation of the last amino acids in the genetic code. Thus, functional rather than structural amino acid properties were decisive during the finalization of the universal genetic code. Greenwood, P.F., Mohammed, L., Grice, K., McCulloch, M., Schwark, L., 2018. The application of compound-specific sulfur isotopes to the oil–source rock correlation of Kurdistan petroleum. Organic Geochemistry 117, 22-30. concentrations and δ34S values of thioaromatic compounds of a suite of oils from several major oil fields in Kurdistan and their corresponding regional Type II-S source rocks have been measured to investigate their source relationship. The oils of three fields (Khabbaz, Jambur, Ajeel) and the bitumen extracted from specific rock formations (Alan, Sargelu, Naokelekan, Chia Gara) showed particularly high abundances of thioaromatics consistent with a carbonate source deposited in a restricted sulfate-rich marine platform setting. The δ34S [V-CDT] values of the major organosulfur compounds (OSCs) in these petroleum samples were measured with a gas chromatograph coupled to a multi-collector inductively coupled plasma mass spectrometer. δ34S values of dibenzothiophenes and methyldibenzothiophenes were consistently in the range ?4‰ to ?12‰ and ?9‰ to ?18‰ for the oils and rocks, respectively. Separate groupings of oils and rocks were distinguishable by >?2‰ difference, given an analytical reproducibility of <?0.8‰. OSCs from rocks were consistently ～2–4‰ depleted than in oils, reflecting a similar trend to previous bulk δ34S studies from which an initial evolution of 34S depleted H2S during diagenesis and thermal maturation had been proposed. Distinctive δ34SOSC data of the oils and rocks with particularly high thioaromatic abundances did suggest several oils–source rock relationships: the Ajeel and Jambur oils and sediments from the Chia Gara formation yielded relatively enriched δ34SOSC values, whereas consistently depleted δ34SOSC values were observed for the Khabbaz oil and Naokelekan source rocks. Results suggest that compound-specific S isotope analysis can help establish oil–source rock relationships of S-rich petroleum.Grimm, R.E., Marchi, S., 2018. Direct thermal effects of the Hadean bombardment did not limit early subsurface habitability. Earth and Planetary Science Letters 485, 1-8. bombardment is considered characteristic of the Hadean and early Archean eons, yet some detrital zircons indicate that near-surface water was present and thus at least intervals of clement conditions may have existed. We investigate the habitability of the top few kilometers of the subsurface by updating a prior approach to thermal evolution of the crust due to impact heating, using a revised bombardment history, a more accurate thermal model, and treatment of melt sheets from large projectiles (>100 km diameter). We find that subsurface habitable volume grows nearly continuously throughout the Hadean and early Archean (4.5–3.5 Ga) because impact heat is dissipated rapidly compared to the total duration and waning strength of the bombardment. Global sterilization was only achieved using an order of magnitude more projectiles in 1/10 the time. Melt sheets from large projectiles can completely resurface the Earth several times prior to ～4.2 Ga but at most once since then. Even in the Hadean, melt sheets have little effect on habitability because cooling times are short compared to resurfacing intervals, allowing subsurface biospheres to be locally re-established by groundwater infiltration between major impacts. Therefore the subsurface is always habitable somewhere, and production of global steam or silicate-vapor atmospheres are the only remaining avenues to early surface sterilization by bombardment.Gu, Y., Ding, W., Yin, S., Yin, M., Xiao, Z., 2018. Adsorption characteristics of clay minerals in shale. Petroleum Science and Technology 36, 108-114. on the adsorption potential theory, this paper describes the adsorption characteristics of four kinds of clay minerals, i.e. Montmorillonite, Kaolinite, Chlorite, and Illite, in clay shales, meanwhile adding quartzite as control sample. We focus on adsorption amount a, differential adsorption work A, characteristic energy E, characteristic coefficient n in adsorption potential analysis. The results show that the differential adsorption work decreases as the adsorption energy increases, which can generally represent the change features during each stage; the optimum value of n is around 1.5 for five kinds of inorganic minerals; E slightly decreases as the temperature increases. For clay minerals, the absolute values of adsorption heat and the result of maximum adsorption can meet that Montmorillonite> Kaolinite> Chlorite> Illite.Guan, M., Zhang, Z., Li, S., Liu, J.a., Liu, L., Yang, H., Zhang, Y., Wang, T., Zhao, Z., 2018. Silver nanoparticles as matrix for MALDI FTICR MS profiling and imaging of diverse lipids in brain. Talanta 179, 624-631. to the diversity of lipids, profiling and imaging multiple classes of lipids in one analysis by matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) is a great challenge. In this work, polyvinylpyrrolidone (PVP) capped silver nanoparticles (AgNPs) was used as the matrix for MALDI MSI for the first time to simultaneously analyze 10 classes of lipids from the brain. This analysis included fatty acids and their derivatives, sterols, CPAs, LPA and PAs, LPE and PEs, LPC and PCs, PS, Cers, SMs, and MAGs and DAGs, and other small metabolites. Owing to the abundant silver ions on the surface of PVP-capped AgNPs, compounds with poor ionization efficiency such as FAs and sterols can be detected. The PVP-capped AgNPs based MALDI MSI analysis of mouse brain showed that lipid distributions in the substructures of the mouse brain can be connected with their biological functions. The brain lipids in rats with middle cerebral artery occlusion (MCAO) were also investigated. Most unsaturated FAs, prostaglandins, CPAs, vitamin A, neuraminic acid, 5-OH-tryptophan and the K+ adducts of most phospholipids (PAs, LPE, PEs, PCs, PS) and SMs were extremely down regulated in the ischemic region and saturated FA, Cers, hexanoylcarnitine, stearaldehyde, the Na+ adduct of phospholipids (LPA, PAs, LPE, PEs, LPC, PCs) and SMs were highly expressed in the damaged section. These novel findings could be very significant for elucidating the disease mechanism. MALDI MSI using PVP-capped AgNPs as a matrix can be a powerful tool in histopathology and pathology studies.Guo, W., Xie, W., Li, X., Wang, P., Hu, A., Zhang, C.L., 2018. Environmental factors shaping the archaeal community structure and ether lipid distribution in a subtropic river and estuary, China. Applied Microbiology and Biotechnology 102, 461-474. are widespread and abundant in aquatic and terrestrial habitats and play fundamental roles in global biogeochemical cycles. Archaeal lipids, such as isoprenoid glycerol diakyl glycerol tetraethers (iGDGTs), are important biomarkers tracing changes in archaeal community structure and biogeochemical processes in nature. However, the linkage between the archaeal populations and the GDGT distribution in the natural environment is poorly examined, which hindered the application and interpretation of GDGT-based climate or environmental proxies. We addressed this question by investigating changes in archaeal lipid composition and community structure in the context of environmental variables along the subtropical Jiulong River Watershed (JRW) and Jiulong River Estuary (JRE) in southern China. The results showed that both the archaeal cells and the polar GDGTs (P-GDGTs) in the JRW and JRE were mostly autochthonous rather than exogenous input from surrounding soils. We further found that only five (Methanobacteriales, Ca. Bathyarchaeota, Marine Benthic Groups A (MBGA), Marine Benthic Groups B (MBGB), and Marine Benthic Groups D (MBGD)) out of sixteen lineages showed significant impacts on the composition of P-GDGTs, suggesting the significant contribution of those archaea to the changes of P-GDGT compositions. Salinity and total phosphorus (TP) showed significant impact on the distribution of both genetic and P-GDGTs compositions of archaea; whereas, sand and silt contents only had significant impact on the P-GDGTs. MBGD archaea, which occur widely in marine sediments, showed positive correlations with P-TEX86 in the JRW and JRE, suggesting that uncultivated MBGD might also contribute to the variations in TEX86 signals in marine sediments. This study provided insight into the sources of P-GDGTs and the factors controlling their distributions in river-dominated continental margins, which has relevance to applications of GDGT-based proxies in paleoclimate studies.Guo, Z., Peng, X., Czaja, A.D., Chen, S., Ta, K., 2018. Cellular taphonomy of well-preserved Gaoyuzhuang microfossils: A window into the preservation of ancient cyanobacteria. Precambrian Research 304, 88-98. ～1500?Ma Gaoyuzhuang microfossils, a representative Mesoproterozoic cyanobacteria assemblage, are crucial for understanding and searching for early Precambrian life on Earth. The cellular taphonomy of fossils in this assemblage is poorly known, however. Here we combined in situ microscopic and microanalytical techniques to study the detailed taphonomy of these microfossils. Light microscopy (LM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations show that Gaoyuzhuang microfossils are mainly preserved in black chert layers and that silica particles can be found within fossilized cell walls and sheaths. Raman spectra show the characteristic first-order bands (at ～1350 and ～1605?cm?1) of carbonaceous material comprising microfossils, indicating that they have experienced peak temperatures of ～215 to 308?°C. Raman maps show the spatial distribution of the carbonaceous matter as well as that of the silica matrix, consistent with nano-scale secondary ion mass spectrometry (NanoSIMS) analyses. Variations in 13C versus 12C and 34S versus 32S within individual microfossils are likely the result of original differences in the isotopic compositions of cellular components. Confocal laser scanning microscopy (CLSM) analyses provide fluorescence-based 2-D and 3-D images of the cellular components of such microfossils at high spatial resolution. The micro-scale chemical, isotopic and structural heterogeneities together with the subcellular morphological features support the preferential preservation of cyanobacterial cell walls and sheaths over cell contents in Precambrian chert. We proposed a potential taphonomic model, perhaps responsible for the high fidelity of preservation, for such microfossils permineralized in Precambrian rocks. The integrated approach has potential for deciphering the enigmatic nature of Mesoproterozoic microorganisms preserved in stromatolitic cherts, with significant implications for microbial preservation in the geological record.Gupta, V., Beirne, S., Nesterenko, P.N., Paull, B., 2018. Investigating the effect of column geometry on separation efficiency using 3D printed liquid chromatographic columns containing polymer monolithic phases. Analytical Chemistry 90, 1186-1194. of column geometry on the liquid chromatographic separations using 3D printed liquid chromatographic columns with in-column polymerized monoliths has been studied. Three different liquid chromatographic columns were designed and 3D printed in titanium as 2D serpentine, 3D spiral, and 3D serpentine columns, of equal length and i.d. Successful in-column thermal polymerization of mechanically stable poly(BuMA-co-EDMA) monoliths was achieved within each design without any significant structural differences between phases. Van Deemter plots indicated higher efficiencies for the 3D serpentine chromatographic columns with higher aspect ratio turns at higher linear velocities and smaller analysis times as compared to their counterpart columns with lower aspect ratio turns. Computational fluid dynamic simulations of a basic monolithic structure indicated 44%, 90%, 100%, and 118% higher flow through narrow channels in the curved monolithic configuration as compared to the straight monolithic configuration at linear velocities of 1, 2.5, 5, and 10 mm s–1, respectively. Isocratic RPLC separations with the 3D serpentine column resulted in an average 23% and 245% (8 solutes) increase in the number of theoretical plates as compared to the 3D spiral and 2D serpentine columns, respectively. Gradient RPLC separations with the 3D serpentine column resulted in an average 15% and 82% (8 solutes) increase in the peak capacity as compared to the 3D spiral and 2D serpentine columns, respectively. Use of the 3D serpentine column at a higher flow rate, as compared to the 3D spiral column, provided a 58% reduction in the analysis time and 74% increase in the peak capacity for the isocratic separations of the small molecules and the gradient separations of proteins, respectively.Gustitus, S.A., Clement, T.P., 2017. Formation, fate, and impacts of microscopic and macroscopic oil-sediment residues in nearshore marine environments: A critical review. Reviews of Geophysics 55, 1130-1157. oil that is spilled in marine environments often interacts with suspended sediments to form residues that can impact the recovery of the affected nearshore ecosystems. When spilled oil and sediment interact, they can form either small microscopic aggregates, commonly referred to as oil-particle aggregates, or large macroscopic agglomerates, referred to as sediment-oil agglomerates or sediment-oil mats. Although these different sized oil-sediment residues have similar compositions, they are formed under different conditions and have different fates in nearshore environments; the goal of this review is to synthesize our current understanding of these two types of residues. We believe that researchers who focus solely on studying either microscopic aggregates or macroscopic agglomerates could benefit from understanding the research findings available in the other field. In this study, we compare and contrast various processes that control the formation, fate, and impacts of these two types of residues in nearshore environments and point out some of the knowledge gaps in this field. Additionally, these residues have been referred to by many names in the past, leading to confusion and misconceptions at times. In this effort, we recommend a uniform nomenclature to distinguish them based on their physical size. Our overall aim is to bridge the gap between microscopic and macroscopic oil-sediment residue literature to foster a robust exchange of ideas, which we believe can lead to the development of efficient strategies for managing oil spills that affect nearshore environments.Habchi, B., Alves, S., Jouan-Rimbaud Bouveresse, D., Appenzeller, B., Paris, A., Rutledge, D.N., Rathahao-Paris, E., 2018. Potential of dynamically harmonized Fourier transform ion cyclotron resonance cell for high-throughput metabolomics fingerprinting: control of data quality. Analytical and Bioanalytical Chemistry 410, 483-490. to the presence of pollutants in the environment and food, the assessment of human exposure is required. This necessitates high-throughput approaches enabling large-scale analysis and, as a consequence, the use of high-performance analytical instruments to obtain highly informative metabolomic profiles. In this study, direct introduction mass spectrometry (DIMS) was performed using a?Fourier transform ion cyclotron resonance (FT-ICR) instrument equipped with a dynamically harmonized cell. Data quality was evaluated based on mass resolving power (RP), mass measurement accuracy, and ion intensity drifts from the repeated injections of quality control sample (QC) along the analytical process. The large DIMS data size entails the use of bioinformatic tools for the automatic selection of common ions found in all QC injections and for robustness assessment and correction of eventual technical drifts. RP values greater than 106 and mass measurement accuracy of lower than 1?ppm were obtained using broadband mode resulting in the detection of isotopic fine structure. Hence, a very accurate relative isotopic mass defect (RΔm) value was calculated. This reduces significantly the number of elemental composition (EC) candidates and greatly improves compound annotation. A very satisfactory estimate of repeatability of both peak intensity and mass measurement was demonstrated. Although, a non negligible ion intensity drift was observed for negative ion mode data, a normalization procedure was easily applied to correct this phenomenon. This study illustrates the performance and robustness of the dynamically harmonized FT-ICR cell to perform large-scale high-throughput metabolomic analyses in routine conditions.Hajimohammadi, R., Johari-ahar, S., 2018. Determination of optimal parameters of rhamnolipid biosurfactant production: An agent for emulsification of heavy crude oil. Petroleum Science and Technology 36, 186-192. oil and petroleum industries, emulsification process is important to transfer and upgrade heavy oil. Rhamnolipids are the essential molecules of biosurfactants that used for this goal and they are often produced from various types of Pseudomonas aeroginosa bacteria. In this research, rhamnolipid biosurfactant produced from Pseudomonas aeroginosa ATCC 9027. The goal of this study was to optimize the effective parameters in production of rhamnolipid in order to reach the minimum water droplet size using Taguchi method. The evaluated parameters include incubation temperature, RPM of incubation, C/N ratio and pH of aqueous phase. Response parameters were yield, cost and water droplet size in water in oil (w/o) microemulsion. The results illustrated that the temperature of incubation and pH of the aqueous phase were the most effective factors in the production of rhamnolipid. Optimum operation condition including yield, cost and water droplet size, were 5.2 ± 0.1 g/l, 2.4 ± 0.14 $/g and 70 ± 5%, respectively. Dynamic light scattering (DLS) analysis was used for determination of water droplet size. Also the emulsification index (E24) of (w/o) emulsion was 98% ± 4. The results of this study could reduce the cost of rhamnolipid production for the applications in oil industries.Hamilton, A., Taylor, D., 2018. Palynological evidence for abrupt climatic cooling in equatorial Africa at about 43,000–40,000 cal BP. Review of Palaeobotany and Palynology 250, 53-59. same basal sequence of two pollen zones is found in three previously published pollen diagrams for widely separated sites situated along highlands adjacent to the Albertine Rift in equatorial Africa. Here evidence is presented that is supportive of the hypothesis that the transition between the zones was contemporaneous at all sites and dates to about 43,000–40,000 cal BP. Environmental interpretation of the sequence indicates that there was a major fall in temperature, depressed temperature thereafter persisting until the transition to the postglacial at 14,000–11,500 cal BP. The climate also became drier. Well-dated sediments of this age are rare in equatorial Africa, so comparisons are scarce. However, there is some evidence from the Eastern Arc Mountains, Tanzania, of a similar climatic event at about the same time. Farther afield, there is good evidence for abrupt climatic deterioration at ~ 40,000 cal BP in western Eurasia, where there was accompanying cultural change. Sedimentary basins along the Albertine Rift-margin highlands are especially well suited for palynologically-based investigations of past temperatures. Their relatively well-defined catchment areas result in reduced inputs of pollen derived from vegetation growing under different climatic conditions.Hamilton, T.L., Klatt, J.M., de Beer, D., Macalady, J.L., 2018. Cyanobacterial photosynthesis under sulfidic conditions: insights from the isolate Leptolyngbya sp. strain hensonii. The Isme Journal 12, 568-584. report the isolation of a pinnacle-forming cyanobacterium isolated from a microbial mat covering the sediment surface at Little Salt Spring—a flooded sinkhole in Florida with a perennially microoxic and sulfidic water column. The draft genome of the isolate encodes all of the enzymatic machinery necessary for both oxygenic and anoxygenic photosynthesis, as well as genes for methylating hopanoids at the C-2 position. The physiological response of the isolate to H2S is complex: (i) no induction time is necessary for anoxygenic photosynthesis; (ii) rates of anoxygenic photosynthesis are regulated by both H2S and irradiance; (iii) O2 production is inhibited by H2S concentrations as low as 1?μM and the recovery rate of oxygenic photosynthesis is dependent on irradiance; (iv) under the optimal light conditions for oxygenic photosynthesis, rates of anoxygenic photosynthesis are nearly double those of oxygenic photosynthesis. We hypothesize that the specific adaptation mechanisms of the isolate to H2S emerged from a close spatial interaction with sulfate-reducing bacteria. The new isolate, Leptolyngbya sp. strain hensonii, is not closely related to other well-characterized Cyanobacteria that can perform anoxygenic photosynthesis, which further highlights the need to characterize the diversity and biogeography of metabolically versatile Cyanobacteria. The isolate will be an ideal model organism for exploring the adaptation of Cyanobacteria to sulfidic conditions.Hand, E., 2018. Mars methane rises and falls with the seasons. Science 359, 16-17. the pasture to the swamp, methane emissions on Earth are the effluvia of life. So what are whiffs of the gas doing on barren Mars? Trace detections of the stuff, alongside glimpses of larger spikes, have fueled debates about biological and nonbiological sources of the gas. Last month, at a meeting of the American Geophysical Union (AGU) in New Orleans, Louisiana, NASA scientists announced a new twist in the tale: a seasonal cycle in the abundance of martian methane, which regularly rises to a peak in late northern summer.“The thing that's so shocking here is this large variation,” said Chris Webster, who leads the methane-sensing instrument on NASA's Curiosity rover. “We're left trying to imagine how we can create this seasonal variation,” says Webster, who is at the Jet Propulsion Laboratory in Pasadena, California.It is a variation on a very faint theme. Since landing in 2012, Curiosity has on 30 occasions opened a few valves to the martian night and taken a sniff of the thin, frigid air. In a small, mirrored chamber, it shines a laser through the air sample and measures the absorption at specific wavelengths that indicate methane. At the meeting, Webster reported vanishingly small background levels of the gas: 0.4 parts per billion (ppb), compared with Earth's 1800 ppb.Where that whiff comes from is the heart of the mystery. Microbes (including those that live in the guts of cows and sheep) are responsible for most of Earth's methane, and Mars's could conceivably come from microbes as well—either contemporary microbes or ancient ones, if the methane they produced was trapped underground. But methane can also be made in ways that have nothing to do with biology. Hydrothermal reactions with olivine-rich rocks underground can generate it, as can reactions driven by ultraviolet (UV) light striking the carbon-containing meteoroids and dust that constantly rain down on the planet from space.Now, add to the methane puzzle the seasonal variation Curiosity has detected, with levels cycling between about 0.3 ppb and 0.7 ppb over more than two martian years. Some seasonality is expected in an atmosphere that is mostly carbon dioxide (CO2), says Fran?ois Forget, who models the climate of Mars at the Laboratory of Dynamical Meteorology in Paris. In the southern winter, some of that CO2 freezes out onto the large southern polar cap, making the overall atmosphere thinner. That boosts the concentration of any residual methane, which doesn't freeze, and by the end of northern summer this methane-enriched air makes its way north to Curiosity's location, Forget says. Seasonal variations in dust storms and levels of UV light could also affect the abundance of methane, if interplanetary dust is its primary source.But, Webster said at the meeting, the seasonal signal is some three times larger than those mechanisms could explain. Maybe the methane—whatever its source—is absorbed and released from pores in surface rocks at rates that depend on temperature, he said. Another explanation, “one that no one talks about but is in the back of everyone's mind,” is biological activity, says Mike Mumma, a planetary scientist at Goddard Space Flight Center in Greenbelt, Maryland. “You'd expect life to be seasonal.”The seasonal wiggles are a mystery within a larger mystery: claims of occasional methane spikes an order of magnitude or two higher than the background. Mumma and his colleagues reported one of the largest in 2009, when they detected spectral signs of a 45-ppb methane plume through a telescope in Hawaii. Curiosity, too, has detected a handful of spikes, to about 7 ppb. For these events, Webster favors the idea of a sudden release from a deep underground source.Other scientists are looking skyward. Marc Fries, the cosmic dust curator at Johnson Space Center in Houston, Texas, says the source of methane spikes could be the hail of tiny meteors that falls when a planet crosses a comet's orbit and sweeps up carbon-rich dust and debris shed by the comet. Fries says that as the dust particles vaporize at altitudes of tens of kilometers, the same chemical reaction that produces methane from interplanetary dust at the surface would take place more quickly, driven by the stronger UV light at high altitudes. All the claimed methane spikes over the past 2 decades occurred within about 2 weeks of a known martian meteor shower, Fries and his colleagues found. “It could be a cause, and it could be a coincidence,” he says.Skeptics say the atmospheric reactions may not occur quickly enough and that meteor showers don't deposit much more material than the background flux of interplanetary dust. In 2014, when Mars nearly collided with comet Siding Spring, NASA's Mars Atmosphere and Volatile Evolution Mission (MAVEN) spacecraft was watching, monitoring magnesium ions as a proxy for dust dumped in the upper atmosphere. The MAVEN team reckons the encounter put 16 tons of material into the martian atmosphere—not much more than the 3 tons of interplanetary dust estimated to fall daily, and much less than the tens of thousands of tons that Fries says are needed to make a large methane plume. “I don't see how it's possible to produce the methane abundance he needs,” says Matteo Crismani, a MAVEN science team member and postdoctoral researcher at the Laboratory for Atmospheric and Space Physics at the University of Colorado in Boulder. But Fries contends that meteor showers are highly variable, and just because the Siding Spring encounter was close does not mean it was rich in dust and debris.It happens that Fries will have a chance to test the hypothesis. On 24 January, Mars will have a close brush—less than a tenth of the Earth-moon distance—with the orbit of comet C/2007 H2 Skiff. Mumma is skeptical about Fries's idea, but he will nevertheless be watching for methane with his telescope in Hawaii in the days after the encounter. The MAVEN and Curiosity teams also plan to watch. “This is a great opportunity to test this hypothesis,” Crismani says.One spacecraft won't quite be ready to participate—even though it is best positioned overall to resolve the methane debate. In April, the European Space Agency's ExoMars Trace Gas Orbiter (TGO) will settle into its final orbit and begin science observations, mapping concentrations of methane across the planet. Atmospheric dust will probably prevent the orbiter from reaching its originally advertised sensitivity of several tens of parts per trillion, says Geronimo Villanueva, a science team member at Goddard. But he expects the TGO to approach Curiosity's sensitivity—and its ability to hunt for methane sources in space and time will be unrivaled. The “TGO will allow us to search for this molecule with new eyes,” he says.Hao, Y., Li, X., Tao, S., Wei, X., Liu, Y., 2017. Heat conduction and convection of thermal front movement during natural gas hydrate heat injection exploitation. Natural Gas Industry 37, 47-52. main heat transfer mode that controls the thermal front movement in the process of natural gas hydrate (NGH) exploitation by heat injection was discussed and whether it is reliable that most analytical models only consider the heat conduction but neglect the effect of heat convection was determined through NGH thermal stimulation experiments and the experimental results were compared with the calculation results of the Selim's thermal mathematical model. And the following findings were obtained. First, the movement rate of thermal front increases with the rise of hot water injection rate, but changes little with the rise of the temperature of the injected hot water. It is indicated that heat convection is the key factor promoting the thermal front movement and NGH dissociation. Second, the thermal front movement rate measured in the experiments is about 10 times that by the Selim's thermal mathematical model, the reason for which is that the Selim's thermal mathematical model only takes the heat conduction into account. And third, based on the calculation, the heat transfer by conduction only accounts for 6.04% of the total heat transfer in the process of NGH thermal stimulation and that by convection accounts for 93.96%, which shows that heat transfer by convection is 15.56 times that by conduction. It is concluded that heat convection is the main heat transfer mode that controls the thermal front movement in the process of NGH thermal stimulation, and its influence should never be neglected in those analytical models.Hare, V.J., Loftus, E., Jeffrey, A., Ramsey, C.B., 2018. Atmospheric CO2 effect on stable carbon isotope composition of terrestrial fossil archives. Nature Communications 9, Article 252. 13C/12C ratio of C3 plant matter is thought to be controlled by the isotopic composition of atmospheric CO2 and stomatal response to environmental conditions, particularly mean annual precipitation (MAP). The effect of CO2 concentration on 13C/12C ratios is currently debated, yet crucial to reconstructing ancient environments and quantifying the carbon cycle. Here we compare high-resolution ice core measurements of atmospheric CO2 with fossil plant and faunal isotope records. We show the effect of pCO2 during the last deglaciation is stronger for gymnosperms (?1.4?±?1.2‰) than angiosperms/fauna (?0.5?±?1.5‰), while the contributions from changing MAP are ?0.3?±?0.6‰ and ?0.4?±?0.4‰, respectively. Previous studies have assumed that plant 13C/12C ratios are mostly determined by MAP, an assumption which is sometimes incorrect in geological time. Atmospheric effects must be taken into account when interpreting terrestrial stable carbon isotopes, with important implications for past environments and climates, and understanding plant responses to climate change.Harkness, J.S., Warner, N.R., Ulrich, A., Millot, R., Kloppmann, W., Ahad, J.M.E., Savard, M.M., Gammon, P., Vengosh, A., 2018. Characterization of the boron, lithium, and strontium isotopic variations of oil sands process-affected water in Alberta, Canada. Applied Geochemistry 90, 50-62. sands operations in Alberta, Canada generate large volumes (>840?×?106?m3) of oil sands process-affected water (OSPW) that contains contaminants that are toxic to aquatic life. OSPW is stored in open tailings ponds and leakage from the ponds presents a potential long-term environmental risk. However, the presence of naturally occurring saline water in the oil sands region in Alberta presents a challenge for delineating the impact of OSPW in cases where OSPW is leaked to the environment. Here, we characterize the inorganic chemistry and isotopic variations of boron (δ11B), lithium (δ7Li), and strontium (εSrSW) of OSPW from tailings ponds in order to evaluate the source of salinity in OSPW and the potential utilization of these isotope ratios as forensic tracers of OSPW migration in the environment. In addition to generating new data, we compiled published data to build a comprehensive dataset of the geochemical composition of different water sources in the oil sands region of Alberta. OSPW is brackish (TDS?～?1800?mgL?1), with elevated chloride (392?±?184?mg?L?1), boron (2.2?±?0.4?mg?L?1), and lithium (0.12?±?0.11?mg?L?1) concentrations relative to the Athabasca River that is used for bitumen extraction. OSPW is characterized by narrow ranges of δ11B (23.7?±?1.8‰), δ7Li (16.3?±?1.7‰), and 87Sr/86Sr ratios (εSrSW=-3.9?±?19.2). The geochemical and isotope ratios in OSPW reflect mixing of residual, saline formation water from Lower Cretaceous units with fresh surface water that has been modified by interactions with the solid oil sands. The elevated boron and lithium concentrations and δ11B, δ7Li and εSrSW variations we observed are distinct from the compositions of a shallow freshwater aquifer in the area (8.1?±?5.0‰, 11.3?±?0.9‰ and 9.7?±?5.6, respectively) and the local rivers (15.6?±?4.7‰, 15.1?±?1.4‰ and 30.3?±?16.0). However, groundwater and saline springs in the region presents a wider range of geochemical and isotopic values that are not always distinguishable from OSPW. The integration of boron, lithium, and strontium isotopes provides a potential monitoring tool for tracing OSPW release to local freshwater sources.Harris, H.W., Sánchez-Andrea, I., McLean, J.S., Salas, E.C., Tran, W., El-Naggar, M.Y., Nealson, K.H., 2018. Redox sensing within the genus Shewanella. Frontiers in Microbiology 8, 2568. doi: 10.3389/fmicb.2017.02568. novel bacterial behavior called congregation was recently described in Shewanella oneidensis MR-1 as the accumulation of cells around insoluble electron acceptors (IEA). It is the result of a series of “run-and-reversal” events enabled by modulation of swimming speed and direction. The model proposed that the swimming cells constantly sense their surroundings with specialized outer membrane cytochromes capable of extracellular electron transport (EET). Up to this point, neither the congregation nor attachment behavior have been studied in any other strains. In this study, the wild type of S. oneidensis MR-1 and several deletion mutants as well as eight other Shewanella strains (Shewanella putrefaciens CN32, S. sp. ANA-3, S. sp. W3-18-1, Shewanella amazonensis SB2B, Shewanella loihica PV-4, Shewanella denitrificans OS217, Shewanella baltica OS155, and Shewanella frigidimarina NCIMB400) were screened for the ability to congregate. To monitor congregation and attachment, specialized cell-tracking techniques, as well as a novel cell accumulation after photo-bleaching (CAAP) confocal microscopy technique were utilized in this study. We found a strong correlation between the ability of strain MR-1 to accumulate on mineral surface and the presence of key EET genes such as mtrBC/omcA (SO_1778, SO_1776, and SO_1779) and gene coding for methyl-accepting protein (MCPs) with Ca+ channel chemotaxis receptor (Cache) domain (SO_2240). These EET and taxis genes were previously identified as essential for characteristic run and reversal swimming around IEA surfaces. CN32, ANA-3, and PV-4 congregated around both Fe(OH)3 and MnO2. Two other Shewanella spp. showed preferences for one oxide over the other: preferences that correlated with the metal content of the environments from which the strains were isolated: e.g., W3-18-1, which was isolated from an iron-rich habitat congregated and attached preferentially to Fe(OH)3, while SB2B, which was isolated from a MnO2-rich environment, preferred MnO2.Hayes, A.G., Birch, S.P.D., Dietrich, W.E., Howard, A.D., Kirk, R.L., Poggiali, V., Mastrogiuseppe, M., Michaelides, R.J., Corlies, P.M., Moore, J.M., Malaska, M.J., Mitchell, K.L., Lorenz, R.D., Wood, C.A., 2017. Topographic constraints on the evolution and connectivity of Titan's lacustrine basins. Geophysical Research Letters 44, 11,745-11,753. topography provided by altimetry, synthetic aperture radar-topography, and stereo radargrammetry has opened new doors for Titan research by allowing for quantitative analysis of morphologic form. Using altimetry measurements, we show that Titan's Maria are consistent with an equipotential surface but that several filled lakes are found to be hundreds of meters above this sea level, suggesting that they exist in isolated or perched basins. Within a given drainage basin, empty lake floors are typically higher than the liquid elevation of nearby lakes/seas, suggesting local subsurface connectivity. The majority of Titan's lakes reside in topographically closed, sharp-edged depressions whose planform curvature suggests lateral expansion through uniform scarp retreat. Many, but not all, empty lake basins exhibit flat floors and hectometer-scale raised rims that present a challenge to formation models. We conclude that dissolution erosion can best match the observed constraints but that challenges remain in the interpretation of formation processes and materials.Hazra, B., Wood, D.A., Varma, A.K., Sarkar, B.C., Tiwari, B., Singh, A.K., 2018. Insights into the effects of matrix retention and inert carbon on the petroleum generation potential of Indian Gondwana shales. Marine and Petroleum Geology 91, 125-138. Rock-Eval pyrolysis and total organic carbon (TOC) analysis technique is widely used for organic geochemistry screening of source rocks and potential unconventional petroleum reservoirs. The Rock-Eval-derived parameters, the Hydrogen Index (HI), which is the ratio between hydrocarbons released under the S2 curve (hydrocarbon formed by thermal pyrolysis; S2 is an indicator of petroleum generation potential) and total organic carbon (TOC) can be used to infer the type of organic matter present in a rock. However, HI is often under-estimated due to retention of some hydrocarbons included under the S2 curve by the rock matrix, and the presence of inert carbon within the rock. Here we describe and correct the matrix retention and inert carbon effects on hydrocarbon generation from a suite of shale samples from Indian Gondwana shale reservoirs. Removal of the petrographically-identified inert carbon component from the samples tested leads to less scatter in the TOC-S2 relationship obtained. The ratio of volume percentage of organic matter identified through optical microscopy to TOC is calculated, and that ratio was least in the one heat-affected sample, but higher in low-TOC shales (<12.5%) compared to high-TOC shales (>12.5%). With decreasing TOC content in the sample set analyzed, the corrected HI values calculated using the S2-TOC intercept, increase significantly. This correction can therefore lead to false indications about the type of organic matter present. A key novel finding of this work is the need while correcting HI for matrix retention effects, to consider samples with a specific range of TOC contents, and to match them to the kerogen types present (e.g. Types III and IV in the samples analyzed). Filters should also be applied to adjust for the degree of thermal maturity and organic facies.Hershkovitz, I., Weber, G.W., Quam, R., Duval, M., Grün, R., Kinsley, L., Ayalon, A., Bar-Matthews, M., Valladas, H., Mercier, N., Arsuaga, J.L., Martinón-Torres, M., Bermúdez de Castro, J.M., Fornai, C., Martín-Francés, L., Sarig, R., May, H., Krenn, V.A., Slon, V., Rodríguez, L., García, R., Lorenzo, C., Carretero, J.M., Frumkin, A., Shahack-Gross, R., Bar-Yosef Mayer, D.E., Cui, Y., Wu, X., Peled, N., Groman-Yaroslavski, I., Weissbrod, L., Yeshurun, R., Tsatskin, A., Zaidner, Y., Weinstein-Evron, M., 2018. The earliest modern humans outside Africa. Science 359, 456-459.: To date, the earliest modern human fossils found outside of Africa are dated to around 90,000 to 120,000 years ago at the Levantine sites of Skhul and Qafzeh. A maxilla and associated dentition recently discovered at Misliya Cave, Israel, was dated to 177,000 to 194,000 years ago, suggesting that members of the Homo sapiens clade left Africa earlier than previously thought. This finding changes our view on modern human dispersal and is consistent with recent genetic studies, which have posited the possibility of an earlier dispersal of Homo sapiens around 220,000 years ago. The Misliya maxilla is associated with full-fledged Levallois technology in the Levant, suggesting that the emergence of this technology is linked to the appearance of Homo sapiens in the region, as has been documented in Africa.Editor's Summary: Earliest modern humans out of Africa. Recent paleoanthropological studies have suggested that modern humans migrated from Africa as early as the beginning of the Late Pleistocene, 120,000 years ago. Hershkovitz et al. now suggest that early modern humans were already present outside of Africa more than 55,000 years earlier (see the Perspective by Stringer and Galway-Witham). During excavations of sediments at Mount Carmel, Israel, they found a fossil of a mouth part, a left hemimaxilla, with almost complete dentition.The sediments contain a series of well-defined hearths and a rich stone-based industry, as well as abundant animal remains. Analysis of the human remains, and dating of the site and the fossil itself, indicate a likely age of at least 177,000 years for the fossil—making it the oldest member of the Homo sapiens clade found outside Africa.Hillyer, K.E., Dias, D., Lutz, A., Roessner, U., Davy, S.K., 2017. 13C metabolomics reveals widespread change in carbon fate during coral bleaching. Metabolomics 14, Article 12.: Rising seawater temperatures are threatening the persistence of coral reefs; where above critical thresholds, thermal stress results in a breakdown of the coral-dinoflagellate symbiosis and the loss of algal symbionts (coral bleaching). As symbiont-derived organic products typically form a major portion of host energy budgets, this has major implications for the fitness and persistence of symbiotic corals.Objectives: We aimed to determine change in autotrophic carbon fate within individual compounds and downstream metabolic pathways in a coral symbiosis exposed to varying degrees of thermal stress and bleaching.Methods: We applied gas chromatography–mass spectrometry coupled to a stable isotope tracer (13C), to track change in autotrophic carbon fate, in symbiont and host individually, following exposure to elevated water temperature.Results: Thermal stress resulted in partner-specific changes in carbon fate, which progressed with heat stress duration. We detected modifications to carbohydrate and fatty acid metabolism, lipogenesis, and homeostatic responses to thermal, oxidative and osmotic stress. Despite pronounced photodamage, remaining in hospite symbionts continued to produce organic products de novo and translocate to the coral host. However as bleaching progressed, we observed minimal 13C enrichment of symbiont long-chain fatty acids, also reflected in 13C enrichment of host fatty acid pools.Conclusion: These data have major implications for our understanding of coral symbiosis function during bleaching. Our findings suggest that during early stage bleaching, remaining symbionts continue to effectively translocate a variety of organic products to the host, however under prolonged thermal stress there is likely a reduction in the quality of these products.Holden, S., 2018. Probing the mechanistic principles of bacterial cell division with super-resolution microscopy. Current Opinion in Microbiology 43, 84-91. cell division takes place almost entirely below the diffraction limit of light microscopy, making super-resolution microscopy ideally suited to interrogating this process. I review how super-resolution microscopy has advanced our understanding of bacterial cell division. I discuss the mechanistic implications of these findings, propose physical models for cell division compatible with recent data, and discuss key outstanding questions and future research directions.Horodyskyj, L.B., Mead, C., Belinson, Z., Buxner, S., Semken, S., Anbar, A.D., 2018. Habitable Worlds: Delivering on the promises of online education. Astrobiology 18, 86-99. thinking and scientific reasoning are central to higher education in the United States, but many courses (in-person and online) teach students information about science much more than they teach the actual process of science and its associated knowledge and skills. In the online arena specifically, the tools available for course construction exacerbate this problem by making it difficult to build the types of active learning activities that research shows to be the most effective. Here, we present a report on Habitable Worlds, offered by Arizona State University for 12 semesters over the past 6 years. This is a unique online course that uses an array of novel technologies to deliver an active, inquiry-driven learning experience. Learning outcomes and quantitative data from more than 3000 students demonstrate the success of our approach but also identify several remaining challenges. The design and development of this course offers valuable lessons for instructional designers and educators who are interested in fully capitalizing on the capabilities of 21st-century technology to achieve educational goals.Hou, L., Xu, G., Han, S., Li, Z., Jiang, C., 2018. Characteristics of gaseous hydrocarbons generated from asphaltene pyrolysis and the geochemical significance. Petroleum Science and Technology 36, 48-54. order to study the mechanism of gas generation from the asphaltene, the thermal pyrolysis simulation experiment of the asphaltene is carried out by using high temperature and high pressure closed system. During asphaltene pyrolysis, the amount of methane is constantly increased but those of ethane, propane, and butane + pentane are all first increased and then decreased and eventually go to zero with the increase of the experiment temperature. And the dynamic parameters of gaseous hydrocarbon generation can be used to analyze the dynamic procedure of the asphaltene pyrolysis at the geological scale. The experimental results can perfect the theory of the origin of natural gas and provide an evidence for source judgment and resource evaluation of natural gas in marine strata in China.Hsu, C.S., Robinson, P.R., 2017. Springer Handbook of Petroleum Technology. Springer International Publishing, p. 1238. handbook provides a comprehensive but concise reference resource for the vast field of petroleum technology. Built on the successful book "Practical Advances in Petroleum Processing" published in 2006, it has been extensively revised and expanded to include upstream technologies. The book is divided into four parts: The first part on petroleum characterization offers an in-depth review of the chemical composition and physical properties of petroleum, which determine the possible uses and the quality of the products. The second part provides a brief overview of petroleum geology and upstream practices. The third part exhaustively discusses established and emerging refining technologies from a practical perspective, while the final part describes the production of various refining products, including fuels and lubricants, as well as petrochemicals, such as olefins and polymers. It also covers process automation and real-time refinery-wide process optimization. Two key chapters provide an integrated view of petroleum technology, including environmental and safety issues.Written by international experts from academia, industry and research institutions, including integrated oil companies, catalyst suppliers, licensors, and consultants, it is an invaluable resource for researchers and graduate students as well as practitioners and professionals.Robinson, Paul R. et al., Introduction to Petroleum Technology, 1-83Robinson, Paul R., Safety and the Environment, 85-147Hsu, Chang Samuel, Molecular Science, Engineering and Management, 151-172Hur, Manhoi (et al.), Petroinformatics, 173-198Andersson, Jan T., Separations in the Sample Preparation for Sulfur Compound Analysis, 199-219Mullins, Oliver C. (et al.), Asphaltenes, 221-250Fujisawa, Go (et al.), Reservoir Evaluation by DFA Measurements and Thermodynamic Analysis, 251-271Shaw, John M. (et al.), Phase Behavior and Properties of Heavy Oils, 273-318Ali, Hendratta N., Fundamentals of Petroleum Geology, 321-357Walters, Clifford C., Origin of Petroleum, 359-379Peters, Kenneth E. (et al.), Basin and Petroleum System Modeling. 381-417Ganssle, Graham, Seismic Explorations, 419-431Hill, Donald G., Formation Evaluation, 433-500Chen, Shengnan, Petroleum Production Engineering, 501-516Maksimova, Ekaterina V. (et al.), Offshore Production. 517-530Hsu, Chang Samuel (et al.), Petroleum Distillation, 533-550Hsu, Chang Samuel (et al.), Gasoline Production and Blending, 551-587Goff, Pierre-Yves (et al.), Catalytic Reforming, 589-616Speight, James G., Fluid-Bed Catalytic Cracking, 617-648Robinson, Paul R., Sulfur Removal and Recovery, 649-673Park, Joo-Il (et al.), Modern Approaches to Hydrotreating Catalysis, 675-712Robinson, Paul R. (et al.), Hydrocracking, 713-776Bingham, F. Emmett (et al.), Hydroprocessing Reactor Internals, 777-786Crews, M. Andrew (et al.), Hydrogen Production, 787-816Hallale, Nick (et al.), Hydrogen Network Optimization, 817-831Robinson, Paul R. (et al.), Model-Predictive Control Fundamentals, 833-839Ho, Teh C., Modeling Refining Processes, 841-864Mudt, Dale R. (et al.), Refinery-Wide Optimization, 865-877Meixell, Milo D., Rigorous Kinetics Modeling of Hydrogen Synthesis, 879-901Wisecarver, Keith, Delayed Coking, 903-913Gonzalez, Martin R., Transitioning Refineries from Sweet to Extra Heavy Oil, 915-930Al-Salem, Sultan M. (et al.), Carbon Dioxide Mitigation, 931-953Beasley, Brent E., Conventional Lube Base Stock, 957-1013Lee, Stephen K. (et al.), Premium Lubricant Base Stocks by Hydroprocessing, 015-1042Wu, Margaret M. (et al.), Synthetic Lubricant Base Stock, 1043-1061Zhu, Genquan (et al.), Catalytic Processes for Light Olefin Production, 1063-1079Fiscus, David (et al.), Polyolefins, 1081-1116Brodeur, Gary (et al.), Biomass to Liquid (BTL) Fuels, 1117-1132Rasmussen, Henrik, Renewable Diesel and Jet Fuels, 1133-1140Gentile, Adam A. (et al.), Small Scale Catalytic Syngas Production with Plasma, 1141-1162Wandell, Robert J. (et al.), Hydrocarbon Processing by Plasma, 1163-1182Hu, D., Clarke, J.A., Eliason, C.M., Qiu, R., Li, Q., Shawkey, M.D., Zhao, C., D’Alba, L., Jiang, J., Xu, X., 2018. A bony-crested Jurassic dinosaur with evidence of iridescent plumage highlights complexity in early paravian evolution. Nature Communications 9, Article 217. Jurassic Yanliao theropods have offered rare glimpses of the early paravian evolution and particularly of bird origins, but, with the exception of the bizarre scansoriopterygids, they have shown similar skeletal and integumentary morphologies. Here we report a distinctive new Yanliao theropod species bearing prominent lacrimal crests, bony ornaments previously known from more basal theropods. It shows longer arm and leg feathers than Anchiornis and tail feathers with asymmetrical vanes forming a tail surface area even larger than that in Archaeopteryx. Nanostructures, interpreted as melanosomes, are morphologically similar to organized, platelet-shaped organelles that produce bright iridescent colours in extant birds. The new species indicates the presence of bony ornaments, feather colour and flight-related features consistent with proposed rapid character evolution and significant diversity in signalling and locomotor strategies near bird origins.Hu, T., Zhang, J.-L., 2018. Mass-spectrometry-based lipidomics. Journal of Separation Science 41, 351-372., which have a core function in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases. Mass-spectrometry-based analytical techniques are currently the most widely used and most effective tools for lipid profiling and quantification. In this review, the field of mass-spectrometry-based lipidomics was discussed. Recent progress in all essential steps in lipidomics was carefully discussed in this review, including lipid extraction strategies, separation techniques and mass-spectrometry-based analytical and quantitative methods in lipidomics. We also focused on novel resolution strategies for difficult problems in determining C=C bond positions in lipidomics. Finally, new technologies that were developed in recent years including single-cell lipidomics, flux-based lipidomics and multiomics technologies were also reviewed.Hua, Y., Hawryluk, M., Gras, R., Shearer, R., Luong, J., 2018. Flow injection gas chromatography with sulfur chemiluminescence detection for the analysis of total sulfur in complex hydrocarbon matrixes. Journal of Separation Science 41, 469-474. fast and reliable analytical technique for the determination of total sulfur levels in complex hydrocarbon matrices is introduced. The method employed flow injection technique using a gas chromatograph as a sample introduction device and a gas phase dual-plasma sulfur chemiluminescence detector for sulfur quantification. Using the technique described, total sulfur measurement in challenging hydrocarbon matrices can be achieved in less than 10?s with sample-to-sample time <2?min. The high degree of selectivity and sensitivity toward sulfur compounds of the detector offers the ability to measure low sulfur levels with a detection limit in the range of 20?ppb w/w S. The equimolar response characteristic of the detector allows the quantitation of unknown sulfur compounds and simplifies the calibration process. Response is linear over a concentration range of five orders of magnitude, with a high degree of repeatability. The detector's lack of response to hydrocarbons enables direct analysis without the need for time-consuming sample preparation and chromatographic separation processes. This flow injection-based sulfur chemiluminescence detection technique is ideal for fast analysis or trace sulfur analysis.Huang, J.H., 2018. Impact of competitive adsorption on microbial arsenate reduction at the water-goethite interface. Applied Geochemistry 88, 59-67. adsorption between arsenate, extracellular polymeric substances (EPS), phosphate and sulphate and resulting impacts on microbial arsenate reduction was investigated at the water-goethite interface at 10 μM arsenate with Shewanella putrefaciens strain CN-32 at pH 7. Addition of phosphate and S. putrefaciens EPS to 2 g L?1 goethite suspensions increased dissolved arsenate concentrations and enhanced arsenate reduction rates. The half-life of first order kinetics was 343 h without competitive species, whereas adding 50–500 μM phosphate and 0.28 g L?1 EPS decreased half-lives to 141–177 and 223 h, respectively. Phosphate and EPS addition did not increase arsenate reduction rates at 10 and 0.4 L?1 goethite, reflecting stronger effect of arsenate mobilisation induced by microbe-mineral interaction than competitive adsorption, respectively. Addition of 100 μM sulphate did not accelerate arsenate reduction, reflecting its weak competitive adsorption. Moreover, phosphate may slow down but EPS accelerate arsenate reduction in solution. Addition of 300–700 μM phosphate increased half-life of dissolved arsenate reduction in solution from 21.3 to 29.4–32.2 h but the presence of 1.4 g L?1 EPS decreased half-life to 2.2 h. Depending on surface coverage and the nature and concentrations of competitive species, competitive adsorption may enhance arsenate reduction kinetics and cause arsenic mobilisation.Huang, S., Ding, G., Wu, Y., Huang, H., Lan, X., Zhang, J., 2018. A semi-analytical model to evaluate productivity of shale gas wells with complex fracture networks. Journal of Natural Gas Science and Engineering 50, 374-383. the increasing of clean energy demands and the maturing of shale gas extraction technology, multiple fractured horizontal well (MFHW) has become the most key technology for shale gas development. After hydraulic fracturing, fracture networks, which consist of natural fractures, hydraulic fractures and secondary fractures, are formed around the wellbore. Compared to conventional gas reservoirs, shale gas reservoirs are characterized by the complex fracture networks and gas adsorptions in shale matrix. Therefore, it is essential to propose a new productivity evaluation method for shale gas wells to handle these characteristics.In this paper, to account for special characteristics of MFHW, a complex fracture model for shale gas reservoirs is established. With the new method, shale reservoirs are depicted by De Swaan dual porosity model, where the secondary fractures and hydraulic fractures are characterized by discrete units. Therefore, together with micro-seismic data, fracture networks can be exactly described using this new model. With a well-depicted facture network, Green function and superposition method are then adopted to model the flow in the reservoir, and finite difference method is used to solve the equations of one-dimensional flow in fracture system. Besides, to deal with the complex flow in the fracture intersection, star-delta transformation is applied Finally, the equations of reservoir and fracture system, the solution in Laplace domain is obtained, which can then be transferred to real domain using the Stehfest parisons were made between the results of the proposed model and that of a numerical model accomplished by commercial simulator Eclipse for a specific case to verify the accuracy of the model. Results show that the semi-analytical method is more efficient than numerical method by reducing the computing time without losing accuracy. Moreover, the semi-analytical productivity evaluation method can describe fracture networks more exactly. Then, a field case from Sichuan Basin of China is applied in the analysis. The results shows that desorption gas takes up 10%-30% of the total production in this case. Besides, the effects of storage capacity ratio and inter-porosity flow coefficient on type curves were analyzed based on the production decline curves. In addition, pressure profiles of different production times are obtained by the superposition of pressure potential.Huang, X., Liu, Q., Gao, W., Wang, Y., Nie, Z., Yao, S., Jiang, G., 2018. Fast screening of short-chain chlorinated paraffins in indoor dust samples by graphene-assisted laser desorption/ionization mass spectrometry. Talanta 179, 575-582. an important class of emerging chemical contaminants, short-chain chlorinated paraffins (SCCPs) are considered as one of the most challenging groups of compounds to analyze. In this paper, we report a new method for fast screening of SCCPs based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with graphene as a matrix and 2,5,6,9-tetrachlorodecane as an internal standard. We found that the use of graphene as MALDI matrix generated high peak intensities for SCCPs while producing few background noises. The ion fragmentation mechanisms of SCCPs in MALDI are discussed in detail. Under the optimized conditions, much lower detection limits of SCCP congeners (0.1–5 ng/mL) than those reported previously were obtained. Other distinct advantages such as short analysis time and simplified sample preparation procedures are also demonstrated. The method was successfully applied in fast screening of SCCPs in indoor dust samples and monitoring of human exposure levels to SCCPs, and the results were verified by gas chromatography coupled to negative chemical ionization quadrupole time-of-flight high-resolution mass spectrometry. This work not only offers a new promising tool for SCCP studies, but also further demonstrates the promise of graphene as a new generation of MALDI matrix.Hui, R., Ding, A., 2017. The role of microorganisms in the oil generation (I): The degradation of macromolecular organic matter and the elimination of oxygen-containing groups. Acta Sedimentologica Sinica 35, 1274-1283. microbiology has achieved rapid progress in the past 20 to 30 years and about 70 genera (140 species) of thermophilic bacteria have been found. The optimum growth temperature range for these bacteria is generally above 60℃ or 80℃, and the maximum temperature is 110℃~113℃. Anaerobic microorganisms, including a variety of bacteria like decomposition microorganisms, hydrogenogens and methanogens, are widely distributed from low temperature to high temperature in both shallow and deep deposits. They can be distributed in the deep water or on the surface of rock. The temperature at which these species live is close to the main temperature of oil formation (60℃~100℃). Microorganisms are unicellular organisms, which have small individuals and simple structures. Each of their cells can directly feel the environmental stimuli when the environment changes. Then, they are more capable of adaptation and easier to generate genetic variations. A hypersaline environment of high temperature, high pressure is suitable for the thermophilic bacteria. The large number discoveries about the thermophilic bacterium provide a solid theoretical basis for understanding the origin of life and the formation of the oil and gas reservoirs. The conversion of sedimentary organic matter into petroleum is related to the process of degradation of macromolecular organic matter (molecular weight can reach tens of thousands to hundreds of thousands) into middle and low molecular compounds and the process of elimination of oxygen-containing (and other heteroatoms-containing) groups. These processes are mainly carried out by the microorganisms. Carbon is the core atom that constitutes life. Microorganisms need to draw the carbon source from the organic matter to form the cellular material, such as cell wall, cell membrane, cytoplasm, and cell nucleus. Macromolecular organic matter can be absorbed by microorganisms when they are gradually broken down into simple organic matter, such as dipeptides from the decomposition of protein and simple sugars from the hydrolysis of carbohydrates. Anaerobic microorganisms will constantly obtain carbons and can help to turn the organic matter into simple compounds gradually. Anaerobic respiration of microorganisms leads to a reduction of the oxygen-containing compounds, forming the compounds that are more reduced than the original ones. As the final electron acceptor material in the anaerobic respiration of sediments, the organic matter containing groups such as hydroxyl, carboxyl, etc. then form the hydrocarbons by elimination of the oxygen-containing groups.Hurley, S.J., Lipp, J.S., Close, H.G., Hinrichs, K.-U., Pearson, A., 2018. Distribution and export of isoprenoid tetraether lipids in suspended particulate matter from the water column of the Western Atlantic Ocean. Organic Geochemistry 116, 90-102. TEX86 paleotemperature proxy is based on the distribution of archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids preserved in marine sediments, yet both the influence of different physiological factors on the structural distribution of GDGTs and the mechanism(s) by which GDGTs is(are) exported to marine sediments remain(s) unresolved. We investigated the abundance and structural distribution of GDGTs in the South-west and Equatorial Atlantic Ocean in four water column profiles spanning 48 degrees of latitude. The depth distribution was consistent with production by ammonia-oxidizing Thaumarchaeota; maximum GDGT concentration occurred at the base of the NO2? maximum, core GDGTs dominated the structural distribution in surface waters above the NO2? maximum, and intact polar GDGTs – potentially indicating live cells – were more abundant below the NO2? maximum. Between 0 and1000 m, > 98% of the integrated GDGT inventory was present in waters at and below the NO2? maximum. Depth profiles of TEX86 temperature values displayed local minima at the NO2? maximum, while the ratio of GDGT-2:GDGT-3 increased with depth. A model based on the results predicts an average depth of origin for GDGTs exported to sediments between ca. 80–250?m. In the model, exported TEX86 values are remarkably insensitive to change in the average depth of origin of GDGTs. However, TEX86 values exported from the water column appear to reflect euphotic zone productivity, possibly due to the correlative intensity of organic matter remineralization providing substrates for ammonia oxidation. Predicting the influence of these regional controls on sedimentary TEX86 records requires a better understanding of the interaction between GDGT production, particle dynamics, and the depth of origin for exported organic matter.Husnik, F., McCutcheon, J.P., 2017. Functional horizontal gene transfer from bacteria to eukaryotes. Nature Reviews Microbiology 16, 67-79. influence eukaryotic biology as parasitic, commensal or beneficial symbionts. Aside from these organismal interactions, bacteria have also been important sources of new genetic sequences through horizontal gene transfer (HGT) for eukaryotes. In this Review, we focus on gene transfers from bacteria to eukaryotes, discuss how horizontally transferred genes become functional and explore what functions are endowed upon a broad diversity of eukaryotes by genes derived from bacteria. We classify HGT events into two broad types: those that maintain pre-existing functions and those that provide the recipient with new functionality, including altered host nutrition, protection and adaptation to extreme environments.Idowu, I., Francisco, O., Thomas, P.J., Johnson, W., Marvin, C., Stetefeld, J., Tomy, G.T., 2018. Validation of a simultaneous method for determining polycyclic aromatic compounds and alkylated isomers in biota. Rapid Communications in Mass Spectrometry 32, 277-287.: There is a need for a validated method to improve detection limits and simultaneously quantify polycyclic aromatic compounds (PACs, both parent and alkylated homologues) in biota by gas chromatography/tandem mass spectrometry because of their environmental significance. The validation of the method was performed in accordance to the Eurachem Guide to Quality in Analytical Chemistry.Methods: Gas chromatography coupled with a triple quadrupole mass spectrometer used in multiple reaction monitoring (MRM) mode was used for detection and quantification. Retention time windows and selective MRM ion transitions were optimized for a suite of PACs. The developed method was validated by comparing our measurements made on a reference material of freeze-dried mussel tissue (Mytilus edulis) with the certified values.Results: Linearity was observed between 10–1000 pg/μL (PAHs) and 2-500 pg/μL (alkyl-PACs including S-based PACs). The overall mean (±SD) for the limits of detection of 43 PACs studied were 0.305 ± 0.276 and 2.69 ± 1.10 ng/g, respectively. For the 14 certified target analytes, the percent relative error ranged from 1.3 to 33%. With the exception of benzo(a)pyrene, the between-day and within-day repeatability for all target analytes was lower than 15% RSD.Conclusions: This is the first report of a fully validated method to simultaneously quantify PACs in biota performed in an ISO accredited laboratory.Imhoff, J.F., Rahn, T., Künzel, S., Neulinger, S.C., 2018. Photosynthesis is widely distributed among proteobacteria as demonstrated by the phylogeny of PufLM reaction center proteins. Frontiers in Microbiology 8, 2679. doi: 10.3389/fmicb.2017.02679. different photosystems for performing bacteriochlorophyll-mediated photosynthetic energy conversion are employed in different bacterial phyla. Those bacteria employing a photosystem II type of photosynthetic apparatus include the phototrophic purple bacteria (Proteobacteria), Gemmatimonas and Chloroflexus with their photosynthetic relatives. The proteins of the photosynthetic reaction center PufL and PufM are essential components and are common to all bacteria with a type-II photosynthetic apparatus, including the anaerobic as well as the aerobic phototrophic Proteobacteria. Therefore, PufL and PufM proteins and their genes are perfect tools to evaluate the phylogeny of the photosynthetic apparatus and to study the diversity of the bacteria employing this photosystem in nature. Almost complete pufLM gene sequences and the derived protein sequences from 152 type strains and 45 additional strains of phototrophic Proteobacteria employing photosystem II were compared. The results give interesting and comprehensive insights into the phylogeny of the photosynthetic apparatus and clearly define Chromatiales, Rhodobacterales, Sphingomonadales as major groups distinct from other Alphaproteobacteria, from Betaproteobacteria and from Caulobacterales (Brevundimonas subvibrioides). A special relationship exists between the PufLM sequences of those bacteria employing bacteriochlorophyll b instead of bacteriochlorophyll a. A clear phylogenetic association of aerobic phototrophic purple bacteria to anaerobic purple bacteria according to their PufLM sequences is demonstrated indicating multiple evolutionary lines from anaerobic to aerobic phototrophic purple bacteria. The impact of pufLM gene sequences for studies on the environmental diversity of phototrophic bacteria is discussed and the possibility of their identification on the species level in environmental samples is pointed out.Ino, K., Hernsdorf, A.W., Konno, U., Kouduka, M., Yanagawa, K., Kato, S., Sunamura, M., Hirota, A., Togo, Y.S., Ito, K., Fukuda, A., Iwatsuki, T., Mizuno, T., Komatsu, D.D., Tsunogai, U., Ishimura, T., Amano, Y., Thomas, B.C., Banfield, J.F., Suzuki, Y., 2018. Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. The Isme Journal 12, 31-47. single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with 13C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.Israde-Alcántara, I., Domínguez-Vázquez, G., Gonzalez, S., Bischoff, J., West, A., Huddart, D., 2018. Five Younger Dryas black mats in Mexico and their stratigraphic and paleoenvironmental context. Journal of Paleolimnology 59, 59-79. Younger Dryas interval (YD) was a period of widespread, abrupt climate change that occurred between 12,900 and 11,700?cal?yr BP (10,900–10,000 14C BP). Many sites in the Northern Hemisphere preserve a sedimentary record across the onset of the YD interval, including sites investigated in sedimentary basins located in central Mexico (Chapala, Cuitzeo, Acambay), the Basin of Mexico (Tocuila), and northern Mexico (El Cedral). Deposits consist of lacustrine or marginal lake sediments that were deposited during the Pleistocene and the Holocene. At the Tocuila and Acambay sites, Pleistocene fossil vertebrate assemblages, mainly mammoths (Mammuthus columbi), are found in association with a distinctive organic layer, sometimes called the black mat that formed during the YD. At the Chapala, Cuitzeo, Acambay, and Tocuila sites the black mats contain a suite of distinctive microscopic and mineralogical signatures and are accompanied by a sharp change in the depositional environments as supported by diatom and pollen studies reported here. The signatures include magnetic, Fe-rich microspherules, silica melted droplets with aerodynamic shapes (tektites), large amounts of charcoal, and sometimes nanodiamonds (Cuitzeo), all of which were deposited at the onset of the YD. The geochemistry of the microspherules indicates that they are not anthropogenic, authigenic or of cosmic or volcanic origin, and instead, were produced by melting and quenching of terrestrial sediments. Here, we present the stratigraphy at five field sites, the analyses of magnetic microspherules, including major element composition and scanning electron microscopy images. All of these materials are associated with charcoal and soot, which are distinctive stratigraphic markers for the YD layer at several sites in Mexico.Itahashi, Y., Tsuneki, A., Dougherty, S.P., Chikaraishi, Y., Ohkouchi, N., Yoneda, M., 2018. Dining together: Reconstruction of Neolithic food consumption based on the δ15N values for individual amino acids at Tell el-Kerkh, northern Levant. Journal of Archaeological Science: Reports 17, 775-784. report here stable nitrogen isotope values of amino acids and stable carbon and nitrogen isotope values of collagen in human (n = 18) and faunal remains from Tell el-Kerkh, which was a large settlement in the northern Levant during the Neolithic period. A unique outdoor communal cemetery involving &gt; 240 individual burials was found in the Pottery Neolithic levels at Tell el-Kerkh. To test the hypothesis that the burial locations of individuals within the cemetery were determined by household units sharing food resources, we separated individuals from one layer into seven groups within the cemetery, and compared the isotope values of collagen, glutamic acid, and phenylalanine. The results of analysis of individual skeletons in the cemetery suggest that the early farmers had different isotope values based on their burial locations, perhaps indicating distinct household burial spaces.Jandera, P., Hájek, T., 2018. Mobile phase effects on the retention on polar columns with special attention to the dual hydrophilic interaction–reversed-phase liquid chromatography mechanism, a review. Journal of Separation Science 41, 145-162. interaction liquid chromatography on polar columns in aqueous–organic mobile phases has become increasingly popular for the separation of many biologically important compounds in chemical, environmental, food, toxicological, and other samples. In spite of many new applications appearing in literature, the retention mechanism is still controversial. This review addresses recent progress in understanding of the retention models in hydrophilic interaction liquid chromatography. The main attention is focused on the role of water, both adsorbed by the column and contained in the bulk mobile phase. Further, the theoretical retention models in the isocratic and gradient elution modes are discussed. The dual hydrophilic interaction liquid chromatography reversed-phase retention mechanism on polar columns is treated in detail, especially with respect to the practical use in one- and two-dimensional liquid chromatography separations.Jia, H., Lian, P., Liang, Y., Zhu, Y., Huang, P., Wu, H., Leng, X., Zhou, H., 2018. Systematic investigation of the effects of zwitterionic surface-active ionic liquids on the interfacial tension of a water/crude oil system and their application to enhance crude oil recovery. Energy & Fuels 32, 154-160. zwitterionic surface-active ionic liquids (SAILs), 3-(1-hexadecyl-3-imidazolio) propanesulfonate (C16IPS) and 3-(1-hexadecyl-3-imidazolio) propanesulfonate β-naphthalenesulfonate (C16IPS-Nsa), were evaluated for their potential application in chemical enhanced oil recovery. It was found that the zwitterionic SAILs had a higher interfacial activity than the traditional SAILs. Interestingly, the C16IPS-Nsa molecule with the large hydrophobic group β-naphthalenesulfonate had a greater ability for reducing the interfacial tension (IFT) of water/crude oil. Moreover, the systematic investigations of the dynamic IFT and the salt and temperature effects further confirmed the proposed mechanism of two zwitterionic SAIL effects on the IFT. The C16IPS-Nsa system exhibited a satisfactory displacement performance (15.3% of initial oil in place), which may be attributed to the transient minimum value (～1 × 10–3 mN/m) in its dynamic IFT curve.Jia, J., Sang, S., Cao, L., Liu, S., 2018. Characteristics of CO2/supercritical CO2 adsorption-induced swelling to anthracite: An experimental study. Fuel 216, 639-647. reservoirs especially deep unminable coal reservoirs, are viable geological target formations for CO2 storage to mitigate greenhouse gas emissions. However, CO2 storage in deep coal seam faces many difficulties, such as low initial injectivity and further permeability loss during injection, induced by the volumetric swelling effects of coal. This paper presents a set of measurements on anthracite cores exposed to CO2/supercritical CO2 (ScCO2) under temperature and pressure condition. Testing includes the measurements of CO2 adsorption amount and volumetric swelling ratio, and these measurements are conducted by a novel experimental apparatus, which design base on the methodology of coal swelling-induced confining pressure liquid flowing. Noteworthy, we have measured the CO2 adsorption-induced swelling to anthracite cores at temperatures between 35?°C and 55?°C and adsorption equilibrium pressures up to 9.3?MPa. The results indicate that the anthracite in Qinshui basin capable of adsorbing a large amount of CO2 then inducing a large swelling ratio, the absolute adsorption amount is between 54.4?mL/g and 69.5?mL/g, and swelling ratio is between 2.32% and 3.45%. The Langmuir-like equation is not suit to the data fitting between excess adsorption amount and adsorption equilibrium pressure. The growth of micropores and ultramicro-fracture increase the specific surface area of anthracite for adsorbing CO2. The apparatus, by the liquid-displacement method, capable of directly observing CO2/ScCO2 adsorption-induced swelling to the whole anthracite core, which reduces the effect of heterogeneous minerals distribution on the swelling measurement.Jiang, Y., Gu, Y., Liu, F., Liu, D., Chen, W., Liao, Y., Zhang, W., Jiang, C., 2017. Discovery and exploration significance of Permian-Triassic trough and platform margin facies in Zhongxian-Yuchi area, eastern Sichuan Basin. Acta Petrolei Sinica 38, 1343-1355. Kaijiang-Liangping trough and the Chengkou-western Hubei trough were developed in the Late Permian-Early Triassic eastern Sichuan Basin-western Hubei area. To determine the distribution of platform margin and sedimentary facies surrounding the trough has an important realistic significance for guiding the exploration and development in Permian-Triassic reef and shoal gas reservoirs. Based on the field measurement and systematic sampling analysis of Changxing-Feixianguan Formation on Yaochang, Qianyecaochang, Nanmuya and Sandengpo outcrops in Zhongxian-Yuchi area, eastern Sichuan Basin, in combination with the well drilling data and early research achievement of Jiannan area, Dachigan-Shibaozhai-Gaofengchang block is considered as the opening platform facies sediment, while the main body of Kaijiang-Liangping trough has not extended to this area. The trough facies deep-water sediment is developed in Zhongxian-Yuchi area, and the Kaijiang-Liangping trough is directly connected with the shallow shelf in Jiannan area, directly contacting the main body of Chengkou-western Hubei trough eastwards with platform edge facies reef and shoal sediment on both sides. Through determining the plane distribution rule of platform margin, the platform margin distribution range in the study area has been further extended, which reveals a brand new field for the exploration and development in the Permian-Triassic reef and shoal gas reservoirs of eastern Sichuan Basin.Jiang, Y., Xing, H., 2018. Theoretical research of pressure propagation in pulsating hydraulic fracturing for coal permeability enhancement. International Journal of Oil, Gas and Coal Technology 17, 91-112. hydraulic fracturing (PHF) technology has been regarded as one of the most effective method to improve both coal permeability and extraction rate of coal seam gas (CSG). However, proper theories for pressure loading and its propagation are still poorly understood, and thus the optimal fracturing conditions cannot be determined. In this paper, functions of pulsating pressure are analysed with the structure of pulsating apparatus and other engineering parameters. A positive correlation between pulsating frequency and loading pressure that observed in existing laboratory experiments is explained. Furthermore, an advanced mathematical approach is proposed and analytical/semi-analytical solutions are obtained to describe the law of pressure ripple propagation inside a loading pipe and coal cleat during fracturing progress. Finally, effects of both boundary conditions and crucial factors (e.g., length of loading pipe, pulsating frequency and injection scheme) on pressure changing pattern are analysed and discussed. The results demonstrated the usefulness of proposed algorithm for a better understanding of the basic mechanism and practical application of PHF technology in coal reservoirs.Jiao, K., Ye, Y., Liu, S., Ran, B., Deng, B., Li, Z., Li, J., Yong, Z., Sun, W., 2018. Characterization and evolution of nanoporosity in superdeeply buried shales: A case study of the Longmaxi and Qiongzhusi shales from MS Well #1, north Sichuan Basin, China. Energy & Fuels 32, 191-203. nanopore characteristics of shale samples from the superdeeply buried Longmaxi Shale (drillcore recovered from 6604–6920 m below ground level), Wufeng Shale (6920–6926 m), and Qiongzhusi Shale (7960–8044 m) were studied from MS Well #1, Sichuan Province, China, which was completed in March 2016 and is the deepest onshore well yet drilled in Asia. To gain a better understanding of the influence of burial depth on the pore system of shales and to aid in the study of nanopore characteristics, the samples were analyzed by FESEM and N2 gas adsorption. Samples of Sichuan Basin shales recovered from depths ranging from 0 to 5000 m were selected as a control group. The results show similar nanopore characteristics in all 32 superdeeply buried shale samples from the three formations. The dominant pore types in the superdeeply buried shales are organic matter pores and interparticle pores, along with minor intraparticle pores. The dominant pore morphology is slit-like in shape. Low-pressure N2 adsorption analysis shows that the isotherms of all samples are type IV with an H3 hysteresis pattern. The quenched solid density functional theory (QSDFT) pore size distribution is dominantly in the range of 4–16 nm, and the BET surface area ranges between 8.63 and 16.13 m2/g. In comparison with nonsuperdeeply buried shales, superdeeply buried shales in MS Well #1 have a more dispersed pore-size distribution, lower micropore volume and micropore surface area, and higher mesopore volume and mesopore surface area. Thus, the mesopore/micropore volume and mesopore/micropore surface area ratios of the superdeeply buried shales are several orders of magnitude higher than those of the nonsuperdeeply buried shales. Compaction related to burial depth may compress the pores to reduce the pore sizes and change the pore shapes from round or elliptical-shaped to slit-shaped. Given their relatively small pore sizes, micropores are most easily destroyed during the superdeep burial stage.Jin, Y., Li, S., Yang, D., Jiang, X., 2018. Determination of dissociation front and operational optimization for hydrate development by combining depressurization and hot brine stimulation. Journal of Natural Gas Science and Engineering 50, 215-230. have been developed to determine dissociation front (i.e., the boundary where hydrate saturation is decreased to 0) for hydrate development by combining depressurization and hot brine stimulation. Experimentally, hydrate dissociation is determined with a one-dimensional (1D) model by gradually injecting hot brine to examine gas and water production. Theoretically, simulation techniques are employed to determine the decay rate and relative permeability by fitting the experimental measurements. Subsequently, the numerical techniques are well matched with field test data and then extended to field applications by applying two different development methods (i.e., depressurization and combining it with hot brine injection). It is found that the combination method not only greatly improves gas recovery by approximately 35.00%, but also results in higher water production rate and lower gas water ratio compared with those of depressurization alone. The orthogonal design method is then used to perform sensitivity analysis and optimize operational parameters by maximizing energy efficiency as the objective function. The most sensitive parameters are found to be the brine temperature, producer bottomhole pressure, brine injection rate, and injection time. Two dissociation fronts are formed separately near the producer and injector, while the dissociation front of the producer is found to move slower than that of the injector due to the different driving mechanisms for the movement of two dissociation fronts.Joblin, C., Cernicharo, J., 2018. Detecting the building blocks of aromatics. Science 359, 156-157. clouds are sites of active organic chemistry (1). Many small, gasphase molecules are found in the dark parts of the clouds that are protected from ultraviolet (UV) photons, but these molecules photodissociate in the external layers of the cloud that are exposed to stellar radiation (see the photo). These irradiated regions are populated by large polycyclic aromatic hydrocarbons (PAHs) with characteristic infrared (IR) emission features. These large aromatics are expected to form from benzene (C6H6), which is, however, difficult to detect because it does not have a permanent dipole moment and can only be detected via its IR absorption transitions against a strong background source (2). On page 202 of this issue, McGuire et al. (3) report the detection of benzonitrile (c-C6H5CN) with radio telescopes. Benzonitrile likely forms in the reaction of CN with benzene; from its observation, it is therefore possible to estimate the abundance of benzene itself.Chemical models that include molecular formation and destruction processes, both in the gas phase and at the surface of dust grains, can account reasonably well for the observed abundances of a number of molecular species (4). The situation is different for large aromatics, for which no individual species have been identified, with the exception of the C60 molecule (5). Although PAHs are large molecules, they are considered by astronomers as very small dust particles. They are therefore generally thought to form in the dense and hot environments of the envelopes of evolved stars. Chemical models have been developed that are based on chemical networks in flames (6). More recently, the possibility to form PAHs at the very low temperatures of molecular clouds has been discussed (7) following the demonstration that the reaction CCH + C4H6 leading to benzene (C6H6) is barrierless and therefore efficient at low temperature (8).In both hot and cold gas-phase chemistry, benzene derivatives—such as C6H4 and C6H5—that can lead to further growth toward larger aromatic species are involved. Observations of benzene-type species are therefore crucial for constraining these chemical models.McGuire et al. were able to detect benzonitrile in a cold molecular cloud of the Taurus region thanks to an elegant spectral-stacking procedure (9) that increases the chance of detecting molecules with aromatic rings. Among the species that they searched for, only benzonitrile was identified as a promising candidate. The authors confirmed its detection after identification of individual rotational lines, including their hyperfine structure, through detailed spectroscopic work in the laboratory. The presence of a CN side group leads to a substantial dipole moment and thus facilitates detection of benzonitrile. Calculated benzonitrile abundances from a chemical model that includes different gas-phase reactions at low temperature are lower than those observed by a factor of four. The authors suggest that alternative mechanisms involving cosmic-ray radiation-induced chemistry at the surface of grains produce the missing benzonitrile. The mismatch between observations and models shows that, despite the low observed abundance of benzonitrile, its detection remains important in constraining chemical models.Is there any relation between the detection of the first aromatic ring in dark clouds and the presence of PAHs, the carriers of the mid-IR aromatic emission bands, in the external UV-irradiated regions of the clouds? In addition to the gas-phase chemical reactions mentioned above, these PAHs and related species, such as C60, could be produced through UV processing of dust grains (10). Other scenarios have also been proposed. For instance, large hydrocarbons, including PAHs, could be formed by chemical processing on the surface of silicon carbide grains, a mechanism that could be efficient in the envelopes of carbon-rich red giant stars (11, 12).It remains unclear how many of the PAHs and their precursors are synthesized in the dense and hot envelopes of evolved stars and how many arise from photo- or radiative chemistry in interstellar environments. The detection by McGuire et al. of a benzene derivative in a cold molecular cloud indicates that it can form even at very low temperatures and without UV radiation. The authors did not detect larger species with two or three cycles, but the species they selected have lower dipole moments compared to benzonitrile, which reduces the chance for their detection unless they have an anomalously large abundance.Among the ～200 molecules detected in space, many are organic species. Studying their composition and chemical networks is key for understanding molecular complexity in protoplanetary disks surrounding young stars (13). The search for complex molecules has mainly been performed in the millimeter and submillimeter domains. The work of McGuire and collaborators (3, 14) shows the potential of centimeter-wave instruments for chemical complexity studies. This opens avenues for research at the upcoming Square Kilometer Array, which will operate in this spectral range.Knowledge of astrochemical networks also helps in understanding the nucleation and growth of interstellar dust (including PAHs) and its role in star and planet formation. However, the detection of benzonitrile in the Taurus region is not sufficient to conclude on the possibility to form PAHs in cold molecular clouds. It also remains to be shown whether the detection of benzonitrile indicates that PAHs could contain nitrogen (15). More insights into the chemistry of PAHs and related species are expected from combining data from radio and infrared waves with the James Webb Space Telescope, due to launch in 2019. In addition to observations, guidelines from laboratory astrophysics studies are key to progress in this area. These include spectroscopic and kinetic studies but also experimental simulations in reactors in order to provide scenarios that can explain the building of molecular complexity in cosmic conditions.References1. astro.uni-koeln.de/cdms/moleculesGoogle2. J. Cernicharo et al., Astrophys. J. 546, L123 (2001).3. B. A. McGuire et al., Science 359, 202 (2018).4. E. Herbst, E. F. van Dishoeck, Annu. Rev. Astron. Astrophys. 47, 427 (2009).5. K. Sellgren et al., Astrophys. J. 722, L54 (2010).6. M. Frenklach, E. D. Feigelson, Astrophys. J. 341, 372 (1989).7. R. I. Kaiser, D. S. N. Parker, A. M. Mebel, Annu. Rev. Phys. Chem. 66, 43 (2015).8. B. M. Jones et al., Proc. Natl. Acad. U.S.A. 108, 452 (2011).9. S. V. Kalenskii, in Proceedings of the Russian-Indian Workshop on Radio Astronomy and Star Formation, I. Zinchenko, P. Zemlyanukha, Eds. (Institute of Applied Physics, Russian Academy of Sciences, 2017), vol. 43.10. P. Pilleri, C. Joblin, F. Boulanger, T. Onaka, Astron. Astrophys. 577, A16 (2015).11. P. Merino et al., Nat. Commun. 5, 3054 (2014).12. T. Q. Zhao et al., Phys. Chem. Chem. Phys. 18, 3489 (2016).13. T. Henning, D. Semenov, Chem. Rev. 113, 9016 (2013).14. B. A. McGuire et al., Science 352, 1449 (2016)15. D. M. Hudgins, C. W. Bauschlicher Jr., L. J. Allamandola, Astrophys. J. 632, 316 (2005).Jokinen, S.A., Virtasalo, J.J., Jilbert, T., Kaiser, J., Dellwig, O., Arz, H.W., H?nninen, J., Arppe, L., Collander, M., Saarinen, T., 2018. A 1500-year multiproxy record of coastal hypoxia from the northern Baltic Sea indicates unprecedented deoxygenation over the 20th century. Biogeosciences Discussions 2018, 1-52. anthropogenically forced expansion of coastal hypoxia is a major environmental problem affecting coastal ecosystems and biogeochemical cycles throughout the world. The Baltic Sea is a semi-enclosed shelf sea whose central deep basins have been highly prone to deoxygenation during its Holocene history, as shown previously by numerous paleoenvironmental studies. However, long-term data on past fluctuations in the intensity of hypoxia in the coastal zone of the Baltic Sea are largely lacking, despite the significant role of these areas in retaining nutrients derived from the catchment. Here we present a 1500-year multiproxy record of near-bottom water redox changes from the coastal zone of the northern Baltic Sea, encompassing the climatic phases of the Medieval Climate Anomaly (MCA), the Little Ice Age (LIA), and the Modern Warm Period (MoWP). Our reconstruction shows that although multicentennial climate variability has modulated depositional conditions and delivery of organic matter (OM) to the basin the modern aggravation of coastal hypoxia is unprecedented, and besides gradual changes in the basin configuration, it must have been forced by excess human-induced nutrient loading. The progressive deoxygenation since the beginning of 1900s was originally triggered by the combined effects of gradual shoaling of the basin and warming climate, which amplified sediment focusing and increased the vulnerability to hypoxia. Importantly, the anthropogenic eutrophication of coastal waters in our study area began decades earlier than previously thought, leading to a marked aggravation of hypoxia in the 1950s through fueling primary productivity, while we find no evidence of anthropogenic forcing during the MCA. These results have implications for the assessment of reference conditions for coastal water quality. Furthermore, this study highlights the need for combined use of sedimentological, ichnological, and geochemical proxies in order to robustly reconstruct subtle redox shifts especially in dynamic, non-euxinic coastal settings with strong seasonal contrasts in the bottom water quality.Jumat, N., Shalaby, M.R., Haque, A.K.M.E., Islam, M.A., Lee Hoon, L., 2018. Geochemical characteristics, depositional environment and hydrocarbon generation modeling of the Upper Cretaceous Pakawau group in Taranaki Basin, New Zealand. Journal of Petroleum Science and Engineering 163, 320-339. oil, gas and condensate province of the Upper Cretaceous to Cenozoic Taranaki Basin is very important as it has become the sole commercially-producing sedimentary basin in New Zealand. An understanding of burial/thermal geo-histories of Taranaki Basin is essential for modeling hydrocarbon generation. In the present study, data from subsurface samples from selected wells have been analyzed and interpreted for characterizing source rock of the Pakawau Group along with thermal geohistory of the basin. The Upper Cretaceous Pakawau Group, made up of Rakopi (87-75 Ma) and North Cape (75-65 Ma) formations, is the eldest and most prolific organic rich hydrocarbon source rock in the basin. Their lithologies vary between carbonaceous mudstone and coal from alluvial to coastal plain depositional environments with marginal marine influence. Most samples that are interpreted contain kerogen Types II and II-III, with few samples of Type-III kerogen. This is validated by the biomarkers results, where the assessed data shows that the organic source ranges from terrestrial to marine origin. The Pakawau Group source is immature to mature, as reflected by the distribution of vitrinite reflectance (%Ro), pyrolysis Tmax from pyrolysis data and biomarkers data. Vitrinite reflectance distribution shows that the Rakopi Formation is mostly within the mature oil window for hydrocarbon generation with values ranging generally between 0.5% and 0.95% Ro. Using two selected wells, the models have been interpreted to generate hydrocarbons from the Pakawau Group between Upper Paleocene and Middle Eocene. Interpretations of the burial models confirm that hydrocarbons of Pakawau Group has not yet attained peak generation and is still being expelled from the source rock to-date.Kaiser, K.E., McGlynn, B.L., Dore, J.E., 2018. Landscape analysis of soil methane flux across complex terrain. Biogeosciences Discussions 2018, 1-42. between methane (CH4) fluxes and environmental conditions have been extensively explored in saturated soils, while in aerated soils, the relatively small magnitudes of CH4 fluxes have made research less prevalent. Our study builds on previous carbon cycle research at Tenderfoot Creek Experimental Forest, Montana to identify how environmental conditions reflected by topographic metrics can be leveraged to estimate watershed scale CH4 fluxes from point scale measurements. Here, we measured soil CH4 concentrations and fluxes across a range of landscape positions (7 riparian, 25 upland), utilizing topographic and seasonal gradients to examine the relationships between environmental variables, hydrologic dynamics, and CH4 emission and uptake. Riparian areas emitted small fluxes of CH4 throughout the study (median: 0.186??g?CH4-C?m?2?h?1) and uplands increased in sink strength with dry down of the watershed (median: ?22.9??g?CH4-C?m?2?h?1). Locations with volumetric water content (VWC) below 38?% were methane sinks, and uptake increased with decreasing VWC. Above 43?% VWC, net CH4 efflux occurred, and at intermediate VWC net fluxes were near zero. Riparian sites had near neutral cumulative seasonal flux, and cumulative uptake of CH4 in the uplands was significantly related to topographic indices. These relationships were used to model the net seasonal CH4 flux of the upper Stringer Creek watershed (?1.75?kg?CH4-C?ha?1). This spatially distributed estimate was 111?% larger than that obtained by simply extrapolating the mean CH4 flux to the entire watershed area. Our results highlight the importance of quantifying the space-time variability of net CH4 fluxes as predicted by the frequency distribution of landscape positions when assessing watershed scale greenhouse gas balances.Kalenitchenko, D., Le Bris, N., Dadaglio, L., Peru, E., Besserer, A., Galand, P.E., 2018. Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. The Isme Journal 12, 367-379. ecosystems host chemosynthetic bacteria that use hydrogen sulfide as an electron donor. The production of hydrogen sulfide from decaying wood in the deep-sea has long been suspected to rely on the activity of wood-boring bivalves, Xylophaga spp. However, recent mesocosm experiments have shown hydrogen sulfide production in the absence of wood borers. Here, we combined in situ chemical measurements, amplicon sequencing and metagenomics to test whether the presence of Xylophaga spp.-affected hydrogen sulfide production and wood microbial community assemblages. During a short-term experiment conducted in a deep-sea canyon, we found that wood-fall microbial communities could produce hydrogen sulfide in the absence of Xylophaga spp. The presence of wood borers had a strong impact on the microbial community composition on the wood surface but not in the wood centre, where communities were observed to be homogeneous among different samples. When wood borers were excluded, the wood centre community did not have the genetic potential to degrade cellulose or hemicellulose but could use shorter carbohydrates such as sucrose. We conclude that wood centre communities produce fermentation products that can be used by the sulfate-reducing bacteria detected near the wood surface. We thus demonstrate that microorganisms alone could establish the chemical basis essential for the recruitment of chemolithotrophic organisms in deep-sea wood falls.Kandanelli, R., Meesala, L., Kumar, J., Raju, C.S.K., Peddy, V.C.R., Gandham, S., Kumar, P., 2018. Cost effective and practically viable oil spillage mitigation: Comprehensive study with biochar. Marine Pollution Bulletin 128, 32-40. is carbonaceous mass that is produced from pyrolysis or gasification of biomass. It is so far majorly explored for soil remediation application, but recently it has attracted a lot of interest because of its unexplored applications in the area of adsorption. In this work, detailed study on biochars produced from two different feeds (rice husk and saw dust), at two different temperatures (450 and 550 °C) and two different rates (fast and slow) of pyrolysis are discussed for oil spill mitigation. Biochar is characterized in detail by various techniques such as FTIR, 13C CPMAS, FESEM, RAMAN, TGA to determine the structural composition and observe the extent of pyrolysis. Tests to assess the performance of produced biochars as sorbents for oil spill mitigation have been demonstrated. The as produced biochars selectively absorbed crude oil from oil/water biphasic mixtures in various capacities.Kang, J., Liang, Q., Wang, J., Lin, Y., He, X., Xia, Z., Zheng, X., Wang, Y., 2018. Size structure of biomass and primary production of phytoplankton: environmental impact analysis in the Dongsha natural gas hydrate zone, northern South China Sea. Acta Oceanologica Sinica 37, 97-107. size-fractionated biomass and primary production of phytoplankton, and the influence of environmental factors on it were studied in the Dongsha natural gas hydrate zone of the northern South China Sea in May 2013. Low nutrient, low chlorophyll a (Chl a) and primary productivity characteristics were found in these waters. The phenomena of subsurface Chl a maximum layers (SCMLs) and primary production maximum layers (SPMLs) were observed in the Dongsha waters. There were significant differences in the size-fractionated biomass and primary production that showed picophytoplankton>nanophytoplankton>microphytoplankton in terms of biomass and degree of contribution to production. Vertical biomass distribution indicated there were considerable differences among different phytoplankton within the euphotic zone (Zeu) in spring. For example, microphytoplankton was distributed evenly in the euphotic layer and nanophytoplankton was mainly distributed in the subsurface or in the middle of the euphotic layer, while picophytoplankton was mainly distributed in the middle or bottom of the euphotic layer. Smaller cell size and larger relative surface area allow picophytoplankton to benefit from nutrient competition and to hold a dominant position in the tropical oligotrophic waters of low latitudes. There was a positive correlation between size-fractionated biomass and temperature with pH and a negative correlation between size-fractionated biomass and silicate with phosphate. There was a positive correlation between size-fractionated primary production and temperature and a negative correlation between size-fractionated biomass and salinity with phosphate. Phosphate was an important factor influencing the size structure of phytoplankton. Meanwhile, irradiation and the euphotic layer were more important in regulating the vertical distribution of size-fractionated phytoplankton in the Dongsha natural gas hydrate zone.Kao, N.-H., Su, M.-C., Chang, C.-C., Yen, C.-C., 2018. Revealing minor terpane biomarkers in lubricants and soils using the customized cleanup method. Journal of Soils and Sediments 18, 136-147.: Lubricant oils are popularly applied and the spill incidents are seen ubiquitously in the environment, in which the terpane biomarkers are the most abundant compounds and which are the essential compounds in the contaminated soils. We studied the traditional and modified cleanup protocols and developed a negative pressure cleanup device and proposed a more suitable internal standard in the quantitation of biomarkers, wherein the main terpane compounds in a lubricant and soil samples were identified.Materials and methods: Surface soil samples were collected in an oil dispatch center where no major spill accidents have been reported in the past decades. Soil samples were studied based on their dry weight quantity and then extracted by using a microwave digestion system. The extracted sample solution was placed in a filter paper and eluted with n-hexane three times and then concentrated by using a nitrogen purge concentration workstation to 1 mL. A lubricant sample was taken without the step of extraction, 0.1 g of lubricants was diluted with 10 mL of hexane, spiked with the surrogate standard, and then concentrated to 1 mL before silica column cleanup procedures. The characteristic fragment ions of terpanes were determined by m/z 177 and 191 in the gas chromatography mass spectrometry (GC/MS) analysis.Results and discussion: In the lubricant sample, besides the 17 dominated compounds, another 20 minor terpanes with a concentration ratio (individual/total) of below 1% were also identified using the modified method. In the soil sample study, the result shows that the quantified major terpane concentrations can be increased up to five times by using the modified method. The soil data also shows that the lower molecular weight compound has higher concentration ratios than the other compounds that were eluted at a later time. The results indicated that for the real environmental samples as for the studied soil, the modified method could enhance the detection probability for those weathering effected compounds.Conclusions: The modified cleanup method has successfully improved the identification technology and many overlooked minor biomarkers were revealed in the samples and the minor biomarkers may including the compound that has been popularly used as the surrogate standard. In quantitation, we proposed a more proper internal standard for future research. The results can also be applied to identify other kinds of biomarkers to plan a suitable remediation program for a contaminated site.Karayi?it, A.?., Mastalerz, M., Oskay, R.G., Gayer, R.A., 2018. Coal petrography, mineralogy, elemental compositions and palaeoenvironmental interpretation of Late Carboniferous coal seams in three wells from the Kozlu coalfield (Zonguldak Basin, NW Turkey). International Journal of Coal Geology 187, 54-70. number of coal seams of Late Carboniferous age in the coal-bearing Karadon, Kozlu, and Alacaa?z? formations have been mined in several deep underground mines in the Zonguldak Basin (NW Turkey). For this study, a total of 154 coal core samples were collected from three research wells that were drilled in the tectonically complex settings of the Kozlu coalfield. All the coal samples were studied by means of coal petrography, mineralogy, and geochemistry. Special attention was given to the compositions and origins of fracture/cleat-filling minerals that were identified by SEM-EDX on polished blocks. The coal seams investigated are of bituminous rank. They are characterized by low total sulphur contents (≤ 1.0%, on dry basis) and high gross calorific values (22.5–40.2 MJ/kg, on dry, ash-free basis), whereas ash yields and volatile matter contents are variable. X-ray powder diffraction data indicate that the mineralogical compositions of the studied coal seams are rather similar, and clay minerals, along with quartz and carbonate minerals, were identified in almost all seams. The statistical evaluations and SEM data show that some elements such as Mg, Ti, Zr, Nb, and Th are generally affiliated with silicate minerals, whereas elements like Cu, Zn, Mo, and Pb are mainly associated with sulphide minerals. The silicate minerals are generally detrital, and the majority of carbonate minerals are of epigenetic origin. The epigenetic carbonate and sulphide minerals suggest that circulated solutions within coal seams were mainly derived from Ca2 +-rich solutions leached from overlying formations such as Cretaceous aged Zonguldak formations and from hydrothermal solutions that likely were derived from andesitic dykes within the basin. The regional tectonic activities during coalification seem to have deformed coal-bearing formations and, therefore, intra-basinal solutions could have penetrated into the studied coal seams. The epigenetic mineralisation also resulted in elemental enrichments and elevated ash yields, total sulphur, and volatile matter contents in some coal seams. Thus, deformation during coalification controlled some coal quality parameters in the studied wells. The coal facies diagrams suggest that palaeomires mostly accumulated under limno-telmatic conditions, whereas a telmatic environment was more common in palaeomires of the Kozlu Formation. Coal petrography suggests that peat-forming vegetation and water tables in palaeomires were changeable during the Late Carboniferous.Karimi, E., Yazdian, F., Rasekh, B., Jeffryes, C., Rashedi, H., Sepahi, A.A., Shahmoradi, S., Omidi, M., Azizi, M., Bidhendi, M.E., Hatamian, A., 2018. DBT desulfurization by decorating bacteria using modified carbon nanotube. Fuel 216, 787-795. food, fossil fuel is humanity’s most important source of energy. Sulfur oxides are produced by the oxidation of the available sulfur in the fuel. Biodesulfurization (BDS) could be an alternative technology to hydrodesulfurization (HDS) to remove sulfur from the recalcitrant organic compounds dissolved in crude oil fractions. It can be seen that all carbon nanotubes (CNTs) exhibited excellent catalytic performance for dibenzothiophene (DBT) oxidation when using molecular oxygen. In this study, chemical modification of Multiple Wall Carbon Nanotubes (MWCNTs) via oxidation followed by side wall functionalization using polyethylene glycol (PEG) was performed to improve the solubility of MWCNTs in aqueous solution. TEM, SEM, FT-IR spectra and Raman spectra were done for characterization of modified MWCNTs. Solubility of the modified MWCNTs studied using different solvents; deionized water, ethanol, and dimethyl sulfoxide (DMSO). Biodesulfurization capability investigated for Rodococcus erythropolis IGTS8 and Gordona rubropertinctus PTCC 1604 of DBT as sole sulfur source in basal salts medium. The results indicated in the presence of carbon nanotubes growth rate of R. erythropolis IGTS8 around 8% increases and G. rubropertinctus PTCC 1604 5% reduction was observed after 96?h. Gibb's assay results in the presence of carbon nanotubes showed desulfurization activity of R. erythropolis IGTS8 an increase of about 12% and for G. rubropertinctus PTCC 1604 was estimated about 15%.Karwautz, C., Kus, G., St?ckl, M., Neu, T.R., Lueders, T., 2018. Microbial megacities fueled by methane oxidation in a mineral spring cave. The Isme Journal 12, 87-100. biofilms have been discovered in the cave of an iodine-rich former medicinal spring in southern Germany. The biofilms completely cover the walls and ceilings of the cave, giving rise to speculations about their metabolism. Here we report on first insights into the structure and function of the biofilm microbiota, combining geochemical, imaging and molecular analytics. Stable isotope analysis indicated that thermogenic methane emerging into the cave served as an important driver of biofilm formation. The undisturbed cavern atmosphere contained up to 3000?p.p.m. methane and was microoxic. A high abundance and diversity of aerobic methanotrophs primarily within the Methylococcales (Gammaproteobacteria) and methylotrophic Methylophilaceae (Betaproteobacteria) were found in the biofilms, along with a surprising diversity of associated heterotrophic bacteria. The highest methane oxidation potentials were measured for submerged biofilms on the cavern wall. Highly organized globular structures of the biofilm matrix were revealed by fluorescent lectin staining. We propose that the extracellular matrix served not only as an electron sink for nutrient-limited biofilm methylotrophs but potentially also as a diffusive barrier against volatilized iodine species. Possible links between carbon and iodine cycling in this peculiar habitat are discussed.Kashefi, S., Lotfollahi, M.N., Shahrabadi, A., 2018. Investigation of asphaltene adsorption onto zeolite beta nanoparticles to reduce asphaltene deposition in a silica sand pack. Oil & Gas Science and Technology – Revue d’IFP Energies nouvelles 73, Article 2. beta nanoparticles were used as a new asphaltene adsorbent for reducing asphaltene deposition during fluid injection into a silica sand pack. At first, the asphaltene adsorption efficiency and capacity of zeolite beta nanoparticles were determined by UV-Vis spectrophotometer. It was found that the proper concentration of nanoparticles for asphaltene adsorption was 10?g/L and the maximum asphaltene adsorption onto zeolite beta was 1.98?mg/m2. Second, two dynamic experiments including co-injection of crude oil and n-heptane (as an asphaltene precipitant) with and without use of zeolite beta nanoparticles in the sand pack was carried out. The results showed that the use of zeolite beta nanoparticles increased the permeability ratio and outlet fluid's asphaltene content about 22% and 40% compared to without use of nanoparticles, respectively. Moreover, a model based on monolayer asphaltene adsorption onto nanoparticles and asphaltene deposition mechanisms including surface deposition, entrainment and pore throat plugging was developed to determine formation damage during co-injection of crude oil and n-heptane into the sand pack. The proposed model presented good prediction of permeability and porosity ratios with AAD% of 1.07 and 0.07, respectively.Kedar, V., Bhagwat, S.S., 2018. Effect of polar head surfactants on the demulsification of crude oil. Petroleum Science and Technology 36, 91-98. can act as demulsifiers to neutralize the stabilizing effect of natural emulsifiers in crude oil. Here, the effect of polar head group of surfactants with identical hydrophobic chain C12 (SLES, SLS, C12E23, BKC, C12E7) on the demulsification of crude oil emulsion and its effect on water separation rate were studied at different temperature. The activation energy for destabilization was calculated. The results indicate that the rate of water separation increases with temperature and surfactant concentration. The emulsion destabilising activation energy decreases as the concentration of the surfactant increases. The Interfacial Tension (IFT) study showed that when the reduction in IFT was the highest, the water separation rate and efficiency achieved was the highest.Kemppinen, K.M.S., Holden, P.B., Edwards, N.R., Ridgwell, A., Friend, A.D., 2018. Coupled climate-carbon cycle simulation of the Last Glacial Maximum atmospheric CO2 decrease using a large ensemble of modern plausible parameter sets. Climate of the Past Discussions 2018, 1-52. the Last Glacial Maximum (LGM), atmospheric CO2 was around 90?ppmv lower than during the preindustrial period. Despite years of research, however, the exact mechanisms leading to the glacial atmospheric CO2 drop are still not entirely understood. Here, a large (471-member) ensemble of GENIE-1 simulations is used to simulate the equilibrium LGM minus preindustrial atmospheric CO2 concentration difference (ΔCO2). The ensemble has previously been weakly constrained with modern observations and was designed to allow for a wide range of large-scale feedback response strengths. Out of the 471 simulations, 315 complete without evidence of numerical instability, and with a ΔCO2 that centres around ?20?ppmv. Roughly a quarter of the 315 runs predict a more significant atmospheric CO2 drop, between ~?30 and 90?ppmv. This range captures the error in the model's process representations and the impact of processes which may be important for ΔCO2 but are not included in the model. These runs jointly constitute what we refer to as the plausible glacial atmospheric CO2 change-filtered (PGACF) ensemble. Our analyses suggest that decreasing LGM atmospheric CO2 tends to be associated with decreasing SSTs, increasing sea ice area, a weakening of the Atlantic Meridional Overturning Circulation (AMOC), a strengthening of the Antarctic Bottom Water (AABW) cell in the Atlantic Ocean, a decreasing ocean biological productivity, an increasing CaCO3 weathering flux, an increasing terrestrial biosphere carbon inventory and an increasing deep-sea CaCO3 burial flux. The increases in terrestrial biosphere carbon are predominantly due to our choice to preserve rather than destroy carbon in ice sheet areas. However, the ensemble soil respiration also tends to decrease significantly more than net photosynthesis, resulting in relatively large increases in non-burial carbon. In a majority of simulations, the terrestrial biosphere carbon increases are also accompanied by decreases in ocean carbon and increases in lithospheric carbon. In total, however, we find there are 5 different ways of achieving a plausible ΔCO2 in terms of the sign of individual carbon reservoir changes. The PGACF ensemble members also predict both positive and negative changes in global particulate organic carbon (POC) flux, AMOC and AABW cell strengths, and global CaCO3 burial flux. Comparison of the PGACF ensemble results against observations suggests that the simulated LGM physical climate and biogeochemical changes are mostly of the right sign and magnitude or within the range of observational error, except for the change in global deep-sea CaCO3 burial flux – which tends to be overestimated. We note that changing CaCO3 weathering flux is a variable parameter (included to account for variation in both the CaCO3 weathering rate and the un-modelled CaCO3 shallow water deposition flux), and this parameter is strongly associated with changes in global CaCO3 burial rate. The increasing terrestrial carbon inventory is also likely to have contributed to the LGM increase in deep-sea CaCO3 burial flux via the process of carbonate compensation. However, we do not yet rule out either of these processes as causes of ΔCO2 since missing processes such as Si fertilisation, Si leakage and the effect of decreasing SSTs on CaCO3 production may have introduced a high LGM global CaCO3 burial rate bias. Including these processes would, all else held constant, lower the rain ratio seen by the sediments and result in a decrease in atmospheric CO2 and increase in ocean carbon. Despite not modelling Δ14C(atm (DIC)) and δ13C(atm (DIC)), we also highlight some ways in which our results may potentially be reconciled with these records.Kendall, C., Eriksen, A.M.H., Kontopoulos, I., Collins, M.J., Turner-Walker, G., 2018. Diagenesis of archaeological bone and tooth. Palaeogeography, Palaeoclimatology, Palaeoecology 491, 21-37. understanding of the structural complexity of mineralised tissues is fundamental for exploration into the field of diagenesis. Here we review aspects of current and past research on bone and tooth diagenesis using the most comprehensive collection of literature on diagenesis to date. Environmental factors such as soil pH, soil hydrology and ambient temperature, which influence the preservation of skeletal tissues are assessed, while the different diagenetic pathways such as microbial degradation, loss of organics, mineral changes, and DNA degradation are surveyed. Fluctuating water levels in and around the bone is the most harmful for preservation and lead to rapid skeletal destruction. Diagenetic mechanisms are found to work in conjunction with each other, altering the biogenic composition of skeletal material. This illustrates that researchers must examine multiple diagenetic pathways to fully understand the post-mortem interactions of archaeological skeletal material and the burial environment.Kenny, R., 2018. A geochemical view into continental palaeotemperatures of the end-Permian using oxygen and hydrogen isotope composition of secondary silica in chert rubble breccia: Kaibab Formation, Grand Canyon (USA). Geochemical Transactions 19, Article 2. upper carbonate member of the Kaibab Formation in northern Arizona (USA) was subaerially exposed during the end Permian and contains fractured and zoned chert rubble lag deposits typical of karst topography. The karst chert rubble has secondary (authigenic) silica precipitates suitable for estimating continental weathering temperatures during the end Permian karst event. New oxygen and hydrogen isotope ratios of secondary silica precipitates in the residual rubble breccia: (1) yield continental palaeotemperature estimates between 17 and 22?°C; and, (2) indicate that meteoric water played a role in the crystallization history of the secondary silica. The continental palaeotemperatures presented herein are broadly consistent with a global mean temperature estimate of 18.2?°C for the latest Permian derived from published climate system models. Few data sets are presently available that allow even approximate quantitative estimates of regional continental palaeotemperatures. These data provide a basis for better understanding the end Permian palaeoclimate at a seasonally-tropical latitude along the western shoreline of Pangaea.Keybondorian, E., Taherpour, A., Bemani, A., Hamule, T., 2018. Application of novel ANFIS-PSO approach to predict asphaltene precipitation. Petroleum Science and Technology 36, 154-159. precipitation is known as one of the challenging problems in petroleum industries which have significant effects on production such as formation damage and wellbore plugging. To solve this problem, calculation of precipitated asphaltene becomes highlighted so in the present study a novel approach is proposed based on ANFIS algorithm to estimate precipitated asphaltene in terms of dilution ration, carbon number of precipitants and temperature. The particle swarm optimization (PSO) method is applied to optimize ANFIS algorithm parameters. The proposed model was evaluated based on statistical parameters and the calculated R2, AARD and RMSE for the total data are 0.90309, 9.4908 and 7.9468. They showed the predicting algorithm performed in acceptable manner so a high accurate and simple tool was proposed to predict the precipitated asphaltene as function of Dilution ration, temperature and carbon number of precipitants.Khalaf, M.H., Mansoori, G.A., 2018. A new insight into asphaltenes aggregation onset at molecular level in crude oil (an MD simulation study). Journal of Petroleum Science and Engineering 162, 244-250. findings reported here is to understand the nature of asphaltenes aggregation behavior at the molecular level in crude oil. Previous studies have been rich with the statistical and macroscopic aspects of heavy organics behavior in petroleum fluids. Molecular dynamics simulations of three different model asphaltene molecules in a "modeled crude oil" composed of n-heptane and o-xylene were conducted. The roles of van der Waals (vdW), hydrogen bond (H-b), and electrostatic (ES) interaction energies on asphaltenes aggregation were investigated. Trends in aggregations, radial distribution functions (RDFs), vdW, H-b, and ES interactions were produced and analyzed. Our studies indicated asphaltenes with different molecular structures behaved differently from one another. At high paraffinic conditions, the preferred stacking of asphaltene molecules was face-to-face. The presence of H-b enhanced the stability of the aggregate. The number of H-bs varied in each model of asphaltene, depending on their detailed structures. The ES interactions between asphaltenes were either attraction or repulsion depending on the molecular structure. Overall, the major factor was the architecture of each asphaltene molecule, such as the number and length of chains, the number and position of heteroatoms, and the number and size of the aromatic cores where they are linked together to represent asphaltene behavior.Khan, M.K., Kwek, W., Kim, J., 2018. Conversion of petroleum emulsion into light fraction-rich upgraded oil in supercritical methanol. Fuel 218, 78-88. crude oil extraction, transportation, and downstream refining have encountered a huge formation of petroleum emulsion (or rag layer), which causes serious problems such as equipment corrosion, loss of crude oil, and catalyst poisoning. In addition, if not treated properly, the rag layer engenders toxic and hazardous effects on the environment and living organisms. In this study, we developed a supercritical methanol (scMeOH) route to convert the petroleum emulsions into light fraction-rich upgraded oil with low impurities. Several process variables were investigated, including temperature (350–400?°C), rag layer concentration (16.7–100?wt%), and reaction time (30–90?min). At 400?°C, 35?MPa, 16.7?wt%, and 90?min, a high recoverable oil yield (76.7?wt%) was achieved. In addition, the naphtha-to-diesel fractions increased significantly from 6.0 (rag layer) to 42.0?wt% (upgraded oil), the acidity in terms of total acid number (TAN) was reduced by up to 91.5% from 58.7 (rag layer) to 5.0?mg-KOH/g-oil (upgraded oil), and the heteroatoms (O, N, S) and metallic impurities (Ca, Ni, V, Fe) were reduced significantly in the upgraded oil. A model compound study revealed that esterification is the major deacidification pathway for TAN reduction. The rag layer conversion in scMeOH was compared with those in subcritical water (without adding additional methanol or water) and in supercritical water (scH2O). Asphaltenes, Ni, and N were completely removed from the toxic rag layer in the presence of scMeOH as compared to scH2O treatment, which makes it more suitable for upgrading.Khan, N., Maezato, Y., McClure, R.S., Brislawn, C.J., Mobberley, J.M., Isern, N., Chrisler, W.B., Markillie, L.M., Barney, B.M., Song, H.-S., Nelson, W.C., Bernstein, H.C., 2018. Phenotypic responses to interspecies competition and commensalism in a naturally-derived microbial co-culture. Scientific Reports 8, Article 297. fundamental question of whether different microbial species will co-exist or compete in a given environment depends on context, composition and environmental constraints. Model microbial systems can yield some general principles related to this question. In this study we employed a naturally occurring co-culture composed of heterotrophic bacteria, Halomonas sp. HL-48 and Marinobacter sp. HL-58, to ask two fundamental scientific questions: 1) how do the phenotypes of two naturally co-existing species respond to partnership as compared to axenic growth? and 2) how do growth and molecular phenotypes of these species change with respect to competitive and commensal interactions? We hypothesized – and confirmed – that co-cultivation under glucose as the sole carbon source would result in competitive interactions. Similarly, when glucose was swapped with xylose, the interactions became commensal because Marinobacter HL-58 was supported by metabolites derived from Halomonas HL-48. Each species responded to partnership by changing both its growth and molecular phenotype as assayed via batch growth kinetics and global transcriptomics. These phenotypic responses depended on nutrient availability and so the environment ultimately controlled how they responded to each other. This simplified model community revealed that microbial interactions are context-specific and different environmental conditions dictate how interspecies partnerships will unfold.Khani, B., Kamali, M., Mirshahani, M., Memariani, M., Bargrizan, M., 2018. Maturity modeling and burial history reconstruction for Garau and Sargelu formations in Lurestan basin, south Iran. Arabian Journal of Geosciences 11, 39. Upper Jurassic Sargelu and the Cretaceous Garau formations are important source rocks in the Lurestan basin, southwest Iran. In this study, the maturity evolution and burial history of these source rocks are investigated using 1D modeling in 15 wells within the Lurestan basin. These models are calibrated using temperature and vitrinite reflectance readings at well locations. Results indicate that thermal maturity of studied source rocks increases towards the northwest of the Lurestan basin and is the lowest over the Anaran High. The present-day level of maturity suggests that these formations are suitable candidates for shale gas resources in the Lurestan basin.Khlebnikov, V.N., Antonov, S.V., Mishin, A.S., Liang, M., Khamidullina, I.V., Zobov, P.M., Likhacheva, N.V., Gushchin, P.A., 2017. Major factors influencing the generation of natural gas hydrate in porous media. Natural Gas Industry B 4, 442-448. researches related to natural gas hydrate mainly focus on its physical and chemical properties, as well as the approaches to the production (decomposition) of hydrate. Physical modeling of the flow process in hydrate deposits is critical to the study on the exploitation or decomposition of hydrate. However, investigation of the dynamic hydrate process by virtue of porous media like sand-packed tubes which are widely used in petroleum production research is rarely reported in literature. In this paper, physical simulation of methane hydrate generation process was conducted using river sand-packed tubes in the core displacement apparatus. During the simulation, the influences of parameters such as reservoir temperature, methane pressure and reservoir model properties on the process of hydrate generation were investigated. The following results are revealed. First, the use of ice-melted water as the immobile water in the reservoir model can significantly enhance the rate of methane hydrate generation. Second, the process driving force in porous media (i.e., extents to which the experimental pressure or temperature deviating those corresponding to the hydrate phase equilibrium) plays a key role in the generation of methane hydrate. Third, the induction period of methane hydrate generation almost does not change with temperature or pressure when the methane pressure is above 1.4 folds of the hydrate phase equilibrium pressure or the laboratory temperature is lower than the phase equilibrium temperature by 3?°C or more. Fourth, the parameters such as permeability, water saturation and wettability don't have much influence on the generation of methane hydrate.Khlebnikov, V.N., Gushchin, P.A., Antonov, S.V., Mishin, A.S., Meng, L., Khamidullina, I.V., Zobov, P.M., Likhacheva, N.V., Semenov, A.P., Vinokurov, V.A., 2017. Simultaneous injection of thermodynamic inhibitors and CO2 to exploit natural gas hydrate: An experimental study Natural Gas Industry 37, 40-46. the CO2 replacement method is used to exploit natural gas hydrate (NGH), the replacement rate and the replacement degree are both low. In view of this, this paper proposed an inhibitor-replacement method, with the technical idea of combining the CO2 replacement method with thermodynamic inhibitor method. The dissociation results of CH4 hydrate, while CO2 and methanol solutions with different concentrations were injected simultaneously, were experimentally measured in a core displacement device by using the sand packed tube model. And the following experimental results were obtained. First, the concentration of methanol solution plays a decisive role in NGH exploitation. The lower the concentration of methanol solution, the weaker the dissociation of CH4 hydrate. And it is dominantly transformed from the dissociation of CH4 hydrate to the generation of CO2 hydrate. Second, when a mixed CO2–methanol solution with a concentration of 20.8% is injected simultaneously, the main process is the dissociation of CH4 hydrate, and CO2 hydrate is hardly generated. Third, during the simultaneous injection of the mixed solution with a concentration of 15%, CH4 hydrate is dissociated and CO2 hydrate is generated. And fourth, When CO2 is injected simultaneously together with the methanol solution with a concentration of 10%, the generation of CO2 hydrate is dominant, and CH4 hydrate is hardly dissociated. It is concluded that the proposed inhibitor-replacement method can promote the dissociation of CO2 hydrate, increasing its exploitation efficiency.Khurshid, I., Al-Attar, H., Alraeesi, A., 2018. Modeling cementation in porous media during waterflooding: Asphaltene deposition, formation dissolution and their cementation. Journal of Petroleum Science and Engineering 161, 359-367. due to water availability, ease and low cost is the most common technique for maintaining reservoir pressure and increasing the recovery of oil. However, the injected water may chemically interact with the reservoir fluids and rock, and it could cause asphaltene deposition and rock dissolution. This paper provides details of the state of the art research performed on characterizing these processes and their effects. It is observed that the dissoluted particles may precipitate on the deposited asphaltene in the porous media leading to cementation. Where this cementation might cause an irreversible and permanent impairment of reservoir porosity and permeability, reducing the productivity of the whole waterflooding operation: decreasing oil productivity and water injectivity.In the development of the proposed model, the radial flow geometry has been adopted and a solution is sought to predict the deposition of asphaltene, rock dissolution and precipitation with respect to time and space. The developed model also predicts the phenomenon of cementation in the porous media and different factors that will enhance cementation. These factors include: asphaltene concentration, water injection rate, injection period, the depth and temperature of the reservoir. It is found from the detailed analysis that the cementation remain very low but it could cause complete pore plugging with time. The derived cementation model assumes that the temperature of reservoir remains constant during waterflooding and the interfacial tensional forces are negligible. But practically the latter may support the cementation process.Kiesenhofer, D.P., Fluch, S., 2018. The promises of microalgae—still a long way to go. FEMS Microbiology Letters 365, Article fnx257. the past decades, interest in microalgae has grown exponentially. Especially industrial applications, such as biodiesel production from microalgae were hyped in the early 2000s. But since the first attempts to commercialise microalgae-derived products for energy applications, only a few developments made it to the market. What is hindering the full exploitation of this valuable resource for food, feed, and energy applications? This opinion paper reflects on the state of the art of industrial microalgae culturing and the knowledge gaps which still need to be filled jointly by academia and industry.Kinsey, J.D., Corradino, G., Ziervogel, K., Schnetzer, A., Osburn, C.L., 2018. Formation of chromophoric dissolved organic matter by bacterial degradation of phytoplankton-derived aggregates. Frontiers in Marine Science 4, 430 doi: 10.3389/fmars.2016.00008. matter produced and released by phytoplankton during growth is processed by heterotrophic bacterial communities that transform dissolved organic matter into biomass and recycle inorganic nutrients, fueling microbial food web interactions. Bacterial transformation of phytoplankton-derived organic matter also plays a poorly known role in the formation of chromophoric dissolved organic matter (CDOM) which is ubiquitous in the ocean. Despite the importance of organic matter cycling, growth of phytoplankton and activities of heterotrophic bacterial communities are rarely measured in concert. To investigate CDOM formation mediated by microbial processing of phytoplankton-derived aggregates, we conducted growth experiments with non-axenic monocultures of three diatoms (Skeletonema grethae, Leptocylindrus hargravesii, Coscinodiscus sp.) and one haptophyte (Phaeocystis globosa). Phytoplankton biomass, carbon concentrations, CDOM and base-extracted particulate organic matter (BEPOM) fluorescence, along with bacterial abundance and hydrolytic enzyme activities (α-glucosidase, β-glucosidase, leucine-aminopeptidase) were measured during exponential growth and stationary phase (~3–6 weeks) and following 6 weeks of degradation. Incubations were performed in rotating glass bottles to keep cells suspended, promoting cell coagulation and, thus, formation of macroscopic aggregates (marine snow), more similar to surface ocean processes. Maximum carbon concentrations, enzyme activities, and BEPOM fluorescence occurred during stationary phase. Net DOC concentrations (0.19–0.46 mg C L?1) increased on the same order as open ocean concentrations. CDOM fluorescence was dominated by protein-like signals that increased throughout growth and degradation becoming increasingly humic-like, implying the production of more complex molecules from planktonic-precursors mediated by microbial processing. Our experimental results suggest that at least a portion of open-ocean CDOM is produced by autochthonous processes and aggregation likely facilitates microbial reprocessing of organic matter into refractory DOM.Kirchman, D.L., 2018. Microbial proteins for organic material degradation in the deep ocean. Proceedings of the National Academy of Sciences 115, 445-447. material is synthesized in the sunlit surface layer of the oceans and that is where most of it is decomposed back to carbon dioxide and other inorganic constituents. However, a small fraction escapes immediate degradation and makes its way into deeper waters, some as far as the bottom thousands of meters below the surface. This sinking organic material contributes to sequestering atmospheric carbon dioxide and to feeding the biota of the deep ocean. Degradation is carried out by a complex microbial community whose taxonomic composition and metabolic potential vary greatly along the kilometer-long trip to the ocean floor. The metabolic potential of microbial communities has been deduced from metagenomics, genomic information gained by sequencing the entire community. In PNAS, Bergauer et al. (1) use metagenomics and another omic approach to explore changes in microbial communities and metabolism from 100-m to over 4,000-m deep in the Atlantic Ocean. They find many changes, but more surprising were the similarities in the cellular proteins used by microbes to degrade organic material along this depth profile and to support microbial life in the deep ocean. In the surface layer, bacteria use dissolved organic material (DOM) from phytoplankton, either produced directly or indirectly via release by grazers and viral lysis. The source for deep oceanic microbes is less obvious. One source is the organisms and particulate organic detritus produced in the surface layer that then sink to deeper waters. Because the biomass production of microbes on particles is much less than that by their free-living counterparts (2, 3), it is thought that sinking particulate organic material is broken up and solubilized to DOM (4) before being taken up by free-living heterotrophic bacteria and archaea (Fig. 1). Another potential source, albeit smaller than sinking particles, is the export of surface-layer DOM to deeper waters … Kittler, F., Heimann, M., Kolle, O., Zimov, N., Zimov, S., G?ckede, M., 2017. Long-term drainage reduces CO2 uptake and CH4 emissions in a Siberian permafrost ecosystem. Global Biogeochemical Cycles 31, 1704-1717. landscapes in northern high latitudes with their massive organic carbon stocks are an important, poorly known, component of the global carbon cycle. However, in light of future Arctic warming, the sustainability of these carbon pools is uncertain. To a large part, this is due to a limited understanding of the carbon cycle processes because of sparse observations in Arctic permafrost ecosystems. Here we present an eddy covariance data set covering more than 3 years of continuous CO2 and CH4 flux observations within a moist tussock tundra ecosystem near Chersky in north-eastern Siberia. Through parallel observations of a disturbed (drained) area and a control area nearby, we aim to evaluate the long-term effects of a persistently lowered water table on the net vertical carbon exchange budgets and the dominating biogeochemical mechanisms. Persistently drier soils trigger systematic shifts in the tundra ecosystem carbon cycle patterns. Both, uptake rates of CO2 and emissions of CH4 decreased. Year-round measurements emphasize the importance of the non-growing season—in particular the “zero-curtain” period in the fall—to the annual budget. Approximately 60% of the CO2 uptake in the growing season is lost during the cold seasons, while CH4 emissions during the non-growing season account for 30% of the annual budget. Year-to-year variability in temperature conditions during the late growing season was identified as the primary control of the interannual variability observed in the CO2 and CH4 fluxes.Korobova, E.M., 2017. Principles of spatial organization and evolution of the biosphere and the noosphere. Geochemistry International 55, 1205-1282. his last lifetime essay, “A Few Words about the Noosphere”, Academician V.I. Vernadsky (1944) wrote that all living organisms on the planet, including man, are integral to the biosphere of the Earth, its material and energy structure and cannot be physically independent of it even for a minute. However, the substrate that generates all living beings and is no less tightly bound to the biosphere has always been characterized by a significant geochemical heterogeneity, traced both in the vertical and in the lateral structure of all geospheres.The present work is devoted to three most important aspects of modern geochemistry and biogeochemistry: ·evolution of the ecological and geochemical state of the environment under conditions of a virgin (anthropogenically untouched) biosphere;·structural features of the geochemical organization of the modern noosphere;·specificity of the interaction of living matter with the environment under increasing anthropogenic load.On the basis of theoretical concepts of biogeochemistry and geochemical ecology, formulated in the works of V.I. Vernadsky, A.P. Vinogradov, A.E. Fersman, B.B. Polynov, A.I. Perel’man, M.A. Glazovskaya, V.V. Kovalsky, E. Odum, B. Commoner, E.I. Kolchinskii and others, the author puts forward a hypothesis that there exist two qualitatively different stages in the evolution of the biosphere.The first stage is recognized as the period of natural evolution of the biosphere during which it evolves successively into a more complex and more biogeochemically specialized object. In the course of the geological time, this constantly results, on the one hand, in an increase in species diversity and the perfection of individual species, and, on the other hand, to directed improvement and a greater differentiation of the geochemical conditions of the environment. At this stage, the evolution of all systems of the biosphere that were controlled by the mechanisms of self-organization and self-regulation resulted in the establishment of a dynamic equilibrium, which was responsible for the cycling of all essential chemical elements and therefore providing ecologically optimal geochemical conditions in all ecological niches and for all species and biocenoses inhabiting the biosphere at any given moment.The beginning of the second stage is related to the appearance of reason and qualitative changes in the biosphere caused by the goal-directed activity of the human mind, as an entirely new geological force that appeared to be able not only to disrupt the functioning of natural mechanisms of self-regulation and selforganization, but also to transform the environment in the intersts of a single biological species, Homo sapiens. A direct consequence of this change was the uncontrolled transformation of the natural environment, during which the primary structure (geochemical background) created in the course of billions of years was eventually superimposed by a qualitatively new layer of anthropogenically-derived chemical elements and compounds, thus building an interference pattern of a new geochemical field with which practically all modern living organisms are now forced to interact.An outstanding feature of the new evolutionary stage of the natural environment, called by Vernadsky the noosphere, is that biogeochemical changes at this stage proceed at a rate which exceeds that required for the living matter to adapt to these changes. The result is the disruption of the existing parameters of the biological cycle, leading to the emergence of a significant number of endemic diseases of geochemical nature.The proposed approach was used to prove the anthropogenic genesis of existing geochemical endemic diseases and explain the mechanisms of their appearance. In addition, this approach allowed us to develop a new methodology for mapping zones of ecological and geochemical risk and noticeably simplify the procedure of monitoring distribution and prevention of all diseases of geochemical nature.Kosaka, Y., 2018. Slow warming and the ocean see-saw. Nature Geoscience 11, 12-13. slowdown in surface warming in the early twenty-first century has been traced to strengthening of the Pacific trade winds. The search for the causes identifies a planetary-scale see-saw of atmosphere and ocean between the Atlantic and Pacific basins.Global mean surface temperatures increased less rapidly between the late 1990s and the early 2010s than in the preceding two decades, despite comparable rates of increase in atmospheric greenhouse gas concentrations1. This decadal slowdown of surface warming has raised a host of scientific questions. For example, it underlines the need to update our records of aerosol concentrations and of solar irradiance in order to quantify the influence of fluctuations in radiative forcing on Earth’s temperature2. The distribution of heat in the ocean has been invoked in order to reconcile the slow global surface warming with an increasing greenhouse effect3. Regional climate events such as droughts in the southwestern US4 and the supertyphoon Haiyan5 are investigated in relation to the global warming slowdown. In terms of the cause of this warming slowdown, natural climate variability in the tropical Pacific Ocean on decadal scales has been identified as a key ingredient. In addition, writing in Nature Climate Change in 2014, McGregor and colleagues6 proposed that an inter-basin see-saw of atmosphere and ocean between the Atlantic and Pacific oceans also contributed significantly.Modelling studies have attributed the warming slowdown to a mode of decadal climate variability inherent in the tropical Pacific that describes the variability of sea surface temperatures in the Pacific Ocean on timescales of several decades, called the Interdecadal Pacific Oscillation7. A negative trend of the Interdecadal Pacific Oscillation features decadal intensification of the Pacific trade winds — that is, prevailing westward surface winds over the tropical Pacific — and surface cooling in the tropical eastern Pacific. Such a pattern of change tends to reduce the global mean surface temperature by cooling the global atmosphere, and thereby counteracts the warming trend that would otherwise occur in response to radiative forcing due to increasing atmospheric greenhouse gas concentrations8,9.However, atmospheric and oceanic conditions in the tropical Pacific are coupled and positively feed back on each other. Stronger trade winds promote upwelling of cool subsurface seawater in the eastern equatorial Pacific while pushing sun-baked warm surface water westward. The resultant east–west contrast of sea surface temperature accelerates the trade winds. Because of this feedback, it is difficult to discern causes and effects of phase transitions in the Interdecadal Pacific Oscillation from observed data alone.McGregor et al.6 therefore performed a suite of numerical experiments that allowed them to investigate an external trigger that set the feedback in motion. They noted that Atlantic warming since the 1990s can potentially trigger transitions in the phase of the Interdecadal Pacific Oscillation from positive to negative. Tropical atmospheric uplift is facilitated by warmer ocean surfaces, and similarly, downward motion is induced over cool waters. The tropical Atlantic warming and eastern Pacific cooling have therefore been changing the pattern of the Walker circulation, a planetary-scale overturning circulation of the tropical atmosphere that extends in the east–west direction. The trade winds at the surface of the Pacific Ocean are part of the Walker circulation, and they affect the heat exchange between ocean and atmosphere. An intensification of the trades therefore further cools the tropical eastern Pacific and leads to an excitation of the negative phase of the Interdecadal Pacific Oscillation6,10.It is thus the inter-basin thermal contrast between the tropical Atlantic and Pacific oceans — rather than solely the Atlantic warming — that drives the circulation changes and initiates an inter-basin see-saw (Fig. 1a). However, ocean–atmosphere interactions in McGregor and colleagues’ simulations are limited to thermodynamic effects, and are missing feedbacks in the dynamics. Follow-up studies have shown that allowing the ocean currents to interact with the atmosphere further amplifies the Pacific anomalies in sea surface temperatures and trade-wind strength10. Indeed, swings of this multidecadal inter-basin see-saw are found throughout the twentieth century11 (Fig. 1b).Moreover, it turns out that the discovery of this Atlantic–Pacific inter-basin see-saw by McGregor and colleagues could help to extend predictability of tropical Pacific climate. Seasonal prediction skill in the tropical Pacific arises from El Ni?o–Southern Oscillation and has been generally limited to a year, the lifetime of a typical El Ni?o or La Ni?a event. By contrast, the predictability associated with the Atlantic Multidecadal Oscillation extends to several years12. The surface signature of the Atlantic Multidecadal Oscillation is most pronounced in the extratropical North Atlantic, but it may be possible to exploit its tropical extension to improve tropical Pacific predictability through the inter-basin influence13.The existence of an inter-basin interaction between the Atlantic and Pacific oceans has raised the question whether the Indian Ocean has a similar remote influence. Indeed, the tropical Indian Ocean warming can also cool the eastern tropical Pacific14, but its role is minor compared to the Atlantic6,10,13. Interestingly, the mutual influence between the tropical Pacific and the other two tropical basins is asymmetric. Tropical Atlantic and Indian Ocean thermal changes enhance the inter-basin temperature contrast with the tropical Pacific, whereas the Pacific variability acts to induce temperature anomalies of the same sign across the entire tropics9,10. Despite this apparent negative feedback from the tropical Pacific, whether and how the inter-basin contrast can sustain itself remains to be addressed.At this point, the most important unresolved question is where the Atlantic–Pacific thermal contrast that triggered the inter-basin see-saw originated from. Radiative forcing by greenhouse gases is highly uniform globally, and cannot explain a strong east–west asymmetry in the tropics, unless oceanic dynamical effects dominate the thermodynamic responses15. Other possibilities include inhomogeneous influences on temperature, for example from aerosols16,17, or the impacts of the Atlantic Multidecadal Oscillation triggered by stochastic fluctuations in the atmosphere18. If we can quantify those influences, along with the natural internal variability in the Pacific19 and other ocean basins, we will be able to fully attribute the warming slowdown event.The decadal timescale is where the spectra of natural climate variability and anthropogenic climate change overlap. Mixture of the two signals in observational records has rendered decadal variability studies difficult. Atmosphere–ocean coupled models such as the one used by McGregor and colleagues6 can break these barriers and help advance our understanding of decadal variability. Coordinated multi-model experiments planned for the Decadal Climate Prediction Project20 under the Coupled Model Intercomparison Project phase 6 will provide an avenue for further understanding global warming modulations and their uncertainties, and they will help with finding the causes of such events in the future.References1. Medhaug, T., Stolpe, M. B., Fischer, E. M. & Knutti, R. Nature 545, 41–47 (2017).2. Schmidt, G. A., Shindell, D. T. & Tsigaridis, K. Nat. Geosci. 7, 158–160 (2014).3. Yan, X.-H. et al. Earth’s Future 4, 472–482 (2016).4. Delworth, T. L., Zeng, F., Rosati, A., Vecchi, G. A. & Wittenberg, A. T. J. Clim. 28, 3834–3845 (2015).5. Lin, I.-I., Pun, I.-F. & Lien, C.-C. Geophys. Res. Lett. 41, 8547–8553 (2014).6. McGregor, S. et al. Nat. Clim. Change 4, 888–892 (2014).7. Power, S., Casey, T., Folland, C., Colman, A. V. & Mehta, V. Clim. Dynam. 15, 319–324 (1999).8. England, M. E. et al. Nat. Clim. Change 4, 222–227 (2014).9. Kosaka, Y. & Xie, S.-P. Nature 501, 403–407 (2013).10. Li, X., Xie, S.-P., Gille, S. T. & Yoo, C. Nat. Clim. Change 6, 275–279 (2016).11. Kucharski, F. et al. Clim. Dynam. 46, 2337–2351 (2016).12. Meehl, G. A. et al. Bull. Am. Meteorol. Soc. 95, 243–267 (2014).13. Chikamoto, Y. et al. Nat. Commun. 6, 6869 (2015).14. Luo, J.-J., Sasaki, W. & Masumoto, Y. Proc. Natl Acad. Sci. USA 109, 18701–18706 (2012).15. Xie, S.-P. et al. J. Clim. 23, 966–986 (2010).16. Booth, B. B., Dunstone, N. J., Halloran, P. R., Andrews, T. & Bellouin, N. Nature 484, 228–232 (2012).17. Takahashi, C. & Watanabe, M. Nat. Clim. Change 6, 768–772 (2016).18. Robson, J., Sutton, R., Lohmann, K., Smith, D. & Palmer, M. D. J. Clim. 25, 4116–4134 (2012).19. Meehl, G. A., Hu, A. & Teng, H. Nat. Commun. 7, 11718 (2016).20. Boer, G. J. et al. Geosci. Model Dev. 9, 3751–3777 (2016).21. Compo, G. P. et al. Q. J. R. Meteorol. Soc. 137, 1–28 (2011).22. Huang, B. et al. J. Clim. 30, 8179–8205 (2017).Koutavas, A., 2018. Temperature correlations between the eastern equatorial Pacific and Antarctica over the past 230,000 years. Earth and Planetary Science Letters 485, 43-54. sea surface temperatures (SSTs) warmed and cooled in step with the Pleistocene ice age cycles, but the mechanisms are not known. It is assumed that the answer must involve radiative forcing by CO2 but SST reconstructions have been too sparse for a conclusive test. Here I present a 230,000-yr tropical SST stack from the eastern equatorial Pacific (EEP) using two new Mg/Ca reconstructions combined with three earlier ones. The EEP stack shows persistent covariation with Antarctic temperature on orbital and millennial timescales indicating tight coupling between the two regions. This coupling however cannot be explained solely by CO2 forcing because in at least one important case, the Marine Isotope Stage (MIS) 5e–5d glacial inception, both regions cooled ～5–6.5 thousand years before CO2 decreased. More likely, their covariation was due to advection of Antarctic climate signals to the EEP by the ocean. To explain the MIS 5e–5d event and glacial inception in general the hypothesis is advanced that the cooling signal spreads globally from the Northern Hemisphere with an active ocean circulation – first from the North Atlantic to the Southern Ocean with a colder North Atlantic Deep Water, and then to the Indian and Pacific Oceans with cooler Antarctic deep and intermediate waters.Kreisserman, Y., Emmanuel, S., 2018. Release of particulate iron sulfide during shale-fluid interaction. Environmental Science & Technology 52, 638-643. hydraulic fracturing, a technique often used to extract hydrocarbons from shales, large volumes of water are injected into the subsurface. Although the injected fluid typically contains various reagents, it can become further contaminated by interaction with minerals present in the rocks. Pyrite, which is common in organic-rich shales, is a potential source of toxic elements, including arsenic and lead, and it is generally thought that for these elements to become mobilized, pyrite must first dissolve. Here, we use atomic force microscopy and environmental scanning electron microscopy to show that during fluid-rock interaction, the dissolution of carbonate minerals in Eagle Ford shale leads to the physical detachment, and mobilization, of embedded pyrite grains. In experiments carried out over a range of pH, salinity, and temperature we found that in all cases pyrite particles became detached from the shale surfaces. On average, the amount of pyrite detached was equivalent to 6.5 × 10–11 mol m–2 s–1, which is over an order of magnitude greater than the rate of pyrite oxidation expected under similar conditions. This result suggests that mechanical detachment of pyrite grains could be an important pathway for the mobilization of arsenic in hydraulic fracturing operations and in groundwater systems containing shales.Kremer, A., Stein, R., Fahl, K., Ji, Z., Yang, Z., Wiers, S., Matthiessen, J., Forwick, M., L?wemark, L., O'Regan, M., Chen, J., Snowball, I., 2018. Changes in sea ice cover and ice sheet extent at the Yermak Plateau during the last 160 ka – Reconstructions from biomarker records. Quaternary Science Reviews 182, 93-108. Yermak Plateau is located north of Svalbard at the entrance to the Arctic Ocean, i.e. in an area highly sensitive to climate change. A multi proxy approach was carried out on Core PS92/039-2 to study glacial-interglacial environmental changes at the northern Barents Sea margin during the last 160 ka. The main emphasis was on the reconstruction of sea ice cover, based on the sea ice proxy IP25 and the related phytoplankton - sea ice index PIP25. Sea ice was present most of the time but showed significant temporal variability decisively affected by movements of the Svalbard Barents Sea Ice Sheet. For the first time, we prove the occurrence of seasonal sea ice at the eastern Yermak Plateau during glacial intervals, probably steered by a major northward advance of the ice sheet and the formation of a coastal polynya in front of it. Maximum accumulation of terrigenous organic carbon, IP25 and the phytoplankton biomarkers (brassicasterol, dinosterol, HBI III) can be correlated to distinct deglaciation events. More severe, but variable sea ice cover prevailed at the Yermak Plateau during interglacials. The general proximity to the sea ice margin is further indicated by biomarker (GDGT) - based sea surface temperatures below 2.5?°C.Kremer, B., Ka?mierczak, J., ?rodoń, J., 2018. Cyanobacterial-algal crusts from Late Ediacaran paleosols of the East European Craton. Precambrian Research 305, 236-246. top surface of the Ediacaran flood basalts of West Ukraine (Volyn), extruded during the break-up of Rodinia supercontinent, is weathered into several meters thick paleosol, covered by late Ediacaran (ca. 550 Ma) sediments. The paleosol grades from unaltered basaltic material into saprock and finally clay-dominated saprolite with a minor content of the organic matter. The upper parts are dominated by kaolinite and hematite. SEM images and SEM-EDS analyses revealed in one of the paleosol profiles a horizon with significant amount of morphologically recognizable organic structures, mineralized by silicates and iron oxides. HF-etching of the bulk rock samples revealed lithic fragments covered irregularly by a biocrust of colonial coccoid cyanobacteria associated with irregularly distributed unicellular algae. The cyanobacteria are preserved as mineralized common mucilage sheaths (glycocalyx), which reproduce the original shape typical of sheaths of modern coccoidal cyanobacterial biofilms, whereas the heavily mineralized algae show features characteristic of modern chlorococcaleans. The preservation of morphologically distinguishable remnants of cyanobacterial biofilms and aggregates of unicellular algae in terrestrial weathering deposits is a rare preservational phenomenon requiring rapid post-mortem permineralization of the dead microbiota. One of the main factors facilitating such a unique fossilization was supposedly a copious excretion of extracellular polymeric substances (EPS) by the biocrust forming biota in which early mineral nucleation occurred. The colonization of the Late Ediacaran land by the presumably desiccation-resistant cyanobacteria-dominated crust communities associated with algae was of importance for creating fertile soils and a soil-forming microbial ecosystem that later allowed a successful land invasion by the ancestors of vascular plants.La Cono, V., Ruggeri, G., Azzaro, M., Crisafi, F., Decembrini, F., Denaro, R., La Spada, G., Maimone, G., Monticelli, L.S., Smedile, F., Giuliano, L., Yakimov, M.M., 2018. Contribution of bicarbonate assimilation to carbon pool dynamics in the deep Mediterranean Sea and cultivation of actively nitrifying and CO2-fixing bathypelagic prokaryotic consortia. Frontiers in Microbiology 9, 3. doi: 10.3389/fmicb.2018.00003. two-thirds of our planet, the global deep ocean plays a central role in supporting life on Earth. Among other processes, this biggest ecosystem buffers the rise of atmospheric CO2. Despite carbon sequestration in the deep ocean has been known for a long time, microbial activity in the meso- and bathypelagic realm via the “assimilation of bicarbonate in the dark” (ABD) has only recently been described in more details. Based on recent findings, this process seems primarily the result of chemosynthetic and anaplerotic reactions driven by different groups of deep-sea prokaryoplankton. We quantified bicarbonate assimilation in relation to total prokaryotic abundance, prokaryotic heterotrophic production and respiration in the meso- and bathypelagic Mediterranean Sea. The measured ABD values, ranging from 133 to 370 μg C m?3 d?1, were among the highest ones reported worldwide for similar depths, likely due to the elevated temperature of the deep Mediterranean Sea (13–14°C also at abyssal depths). Integrated over the dark water column (≥200 m depth), bicarbonate assimilation in the deep-sea ranged from 396 to 873 mg C m?2 d?1. This quantity of produced de novo organic carbon amounts to about 85–424% of the phytoplankton primary production and covers up to 62% of deep-sea prokaryotic total carbon demand. Hence, the ABD process in the meso- and bathypelagic Mediterranean Sea might substantially contribute to the inorganic and organic pool and significantly sustain the deep-sea microbial food web. To elucidate the ABD key-players, we established three actively nitrifying and CO2-fixing prokaryotic enrichments. Consortia were characterized by the co-occurrence of chemolithoautotrophic Thaumarchaeota and chemoheterotrophic proteobacteria. One of the enrichments, originated from Ionian bathypelagic waters (3,000 m depth) and supplemented with low concentrations of ammonia, was dominated by the Thaumarchaeota “low-ammonia-concentration” deep-sea ecotype, an enigmatic and ecologically important group of organisms, uncultured until this study.Laakso, T.A., 2018. Methane multiplication. Nature Geoscience 11, 6-7. combination of two anoxygenic pathways of photosynthesis could have helped to warm early Earth, according to geochemical models. These metabolisms, and attendant biogeochemical feedbacks, could have worked to counter the faint young Sun.Evidence for liquid water on the Earth’s surface dates back to the most ancient rocks of the Archaean eon, rocks that are more than three and a half billion years old (Fig. 1). This apparently temperate past is a surprise1. Stellar physics implies that our sun was substantially less luminous at the time, dim enough to leave the Earth a frozen wasteland. Many solutions have been proposed to this faint young Sun paradox, most of which involve high concentrations of greenhouse gases in the ancient atmosphere. Writing in Nature Geoscience, Ozaki et al.2 implicate an amplified methane cycle in helping maintain a warm Archaean Earth.Carbon dioxide usually tops the list of greenhouse gases that could have countered the faint young Sun. This is because its concentration is believed to adjust in response to changing climatic conditions — a sort of automated thermostat3 that could have kept the Earth warm in those dim days. However, controversial evidence4 from ancient soils suggests that CO2 levels were lower than expected during the Archaean. This has led to debates over the importance of other gases, particularly methane, in warming the planet. Photochemical models have shown that methane would have had a long lifetime in the oxygen-poor atmospheres of the Archaean5, but debate has continued over the rate at which methane would have been produced in the first place.Ozaki and co-workers2 have identified a novel geochemical mechanism that may have sped up the microbial methane pump during the Archaean. Biological production of methane requires a reductant. Today, water is a key reductant, but before the evolution of oxygenic photosynthesis, hydrogen (H2) and ferrous iron (Fe2+) were probably the most abundant options. H2 is used to reduce carbon dioxide directly to methane, whereas Fe2+ is used to fix CO2 into organic carbon, which may undergo subsequent fermentation and disproportionation reactions that ultimately produce methane.Ozaki and co-workers estimate that, even using generous upper bounds, the leak of H2 and Fe2+ from Earth’s mantle would have been too slow to result in large rates of carbon reduction, throttling the source of methane. However, they point out that photochemical reactions — which ultimately remove methane from an anoxic atmosphere — produce H2; this process would lead to secondary cycles of organic carbon fixation and methanogenesis. By including this cycle in a geochemical model, they find that methane fluxes to the atmosphere could have considerably exceeded the limit implied by the supplies of H2 and Fe2+ alone.This is an elegant mechanism for boosting methane production, but was it enough to result in significant warming? As with all models of ancient biogeochemical cycles, the challenge is to constrain the behaviour of long-dead microbial communities living in environments radically different from those found on today’s Earth. Ozaki and colleagues used a Monte Carlo analysis to handle uncertainty in physical parameters, but even the range of possible values is open to debate. For example, methane production in the Archaean depends critically on the fraction of organic carbon that can be processed into methane by the relevant organisms. This fraction is typically assumed to be greater in ancient environments, relative to modern, oxygen- and sulfate-rich conditions. This high value occurred both because methanogenic archaea are obligate anaerobes, and because acetoclastic methanogens would not have been outcompeted for organic substrates by sulfate reducing bacteria as they often are today.However, work in modern anoxic settings6,7 suggests that a large portion of organic matter may not be accessible to methanogens even under ideal conditions. Based on their parameter estimates, Ozaki et al. conclude that there is a strong possibility that methane did provide significant warming to the Archaean Earth. Continued laboratory and fieldwork in Archean-analogue environments8 are needed to more tightly constrain how methanogens behave under relevant conditions.Whether methane or some other warming mechanism ultimately proves to be the solution to the faint young Sun paradox, work of this type is important for exploring the possible ecological, climatic and atmospheric conditions of the Archean9. Ozaki and co-workers include interactions between different communities of primary producers, which are not often included in global biogeochemical models. This raises provocative questions about other interactions that may have been important during the Archaean. For example, how did autotrophs respond to the evolution of biological nitrogen fixation, which may have changed the balance between the demand for nutrients and the need for electron donors? How did non-oxygenic photoautotrophs respond to the evolution of oxygenic competitors?Biogeochemical models such as that of Ozaki et al. can make predictions for how these community changes drive atmospheric chemistry, and whether these changes might be reflected in aspects of the Archaean rock record, such as the mass-independent fractionation of sulfur isotopes. Simulations of successive global communities, guided by our best understanding of metabolic history, may provide insight into how — and when — the Archaean environment evolved in response to the evolution of new biochemical pathways.More generally, this work is part of an exciting struggle to understand the mechanisms of change in remote Earth history. Methane is part of a suite of interlinked chemical cycles that are surely central to understanding the causes and consequences of major events in the later Archaean, such as the Great Oxidation Event and the global glaciations of the earliest Palaeoproterozoic. These events are testing grounds for our understanding of biogeochemical dynamics, challenging any model to fit consistently with the large signals left in the rock record.Ozaki and colleagues2 have demonstrated that the interaction between communities can strongly influence the broader environment. Studies such as this one widen the scope of our imagination regarding the co-evolution of life and environment on Earth…and perhaps on other planets as well.Reference1. Sagan, C. & Mullen, G. Science 177, 52–56 (1972).2. Ozaki, K., Tajika, E., Hong, P., Nakagawa, Y. & Reinhard, C. Nat. Geosci. (2017).3. Walker, J., Hays, P. & Kasting, J. J. Geophys. Res. 86, 9776–9782 (1981).4. Rye, R., Kuo, P. & Holland, H. Nature 378, 603–605 (1995).5. Haqq-Misra, J., Domagal-Goldman, S., Kasting, P. & Kasting, J. Astrobiology 8, 1127–1137 (2008).6. Kuntz, L., Laakso, T., Schrag, D. & Crowe, S. Geobiology 13, 454–461 (2015).7. Shoemaker, J., Varner, R. & Schrag, D. Geochim. Cosmochim. Acta 91, 120–139 (2012).8. Crowe, S. et al. Proc. Natl Acad. Sci. USA 105, 15938–15943 (2008).9. Kharecha, P., Kasting, J. & Siefert, J. Geobiology 3, 53–76 (2005).Labus, M., Lempart, M., 2018. Studies of Polish Paleozoic shale rocks using FTIR and TG/DSC methods. Journal of Petroleum Science and Engineering 161, 311-318. presented investigation is focused on fine-grained Palaeozoic (Silurian and Carboniferous) rocks collected from several wellbores in Poland. The implemented methods are: diffuse reflectance infrared fourier transform spectroscopy (DRIFT) thermal methods (TG/DSC), as well as XRD and Rock-Eval pyrolysis. These methods made it possible to determine the composition of the samples tested, including the presence of minerals and organic matter.The DRIFT technique of FTIR analysis was implemented, because in case of DRIFT technique the high frequency bands are usually more informative with respect to detection of aromatic and aliphatic bands in the examined rocks, compared to other techniques of IR (e.g. ATR). The occurrence of aromatic groups in the samples is the evidence of higher kerogen maturity.Thermal methods (TG/DSC) made it possible to trace the reactions during heating the samples in an oxidizing and inert atmosphere. The pyrolysis peaks in DSC curves indicate kerogen of type II, which agrees with a classification based on Rock-Eval measurement. Basing on the DTG curves the maximum temperature of the pyrolysis peak could be determined, and in a consequence – the thermal maturity of the organic matter in the sample. The enthalpy of organic matter in examined samples, calculated from DSC curves correlates very well with TOC value (Rock Eval), what demonstrates that thermal analysis can be successfully used to determine the content of organic matter in fine grained rocks, such as gas-shales or similar ones.Lai, J., Wang, G., Fan, Z., Zhou, Z., Chen, J., Wang, S., 2018. Fractal analysis of tight shaly sandstones using nuclear magnetic resonance measurements. American Association of Petroleum Geolog Bulletin 102, 175-193. quantitatively the microscopic pore structures of porous rocks, including irregularities of pore shapes and pore size distributions, is becoming one of the most challenging efforts. Nuclear magnetic resonance (NMR) measurements were used to provide insights into the pore geometry (pore size and shape) and pore connectivity of the Chang 7 tight shaly sandstones (in situ permeability <0.1 md) in Ordos basin. The incremental transverse relaxation time (T2) distributions for the 100% brine-saturated samples display unimodal and bimodal behaviors, presenting a geometrical arrangement composed of small to large pore size domains. The NMR parameters such as bulk volume irreducible (BVI) (capillary and clay-bound water), free fluid index (FFI) (movable water), the value of T2 separating the BVI from FFI, the amplitude weighted mean on a logarithmic scale (T2gm), and the value of T2 that shows the highest frequency on the T2 spectrum (T2peak) for each sample were determined. Then the fractal theory was adopted to quantitatively express the complexity and heterogeneity of the sandstones. The results show that only minor primary intergranular porosity remains, and variable amounts of micropores and secondary intragranular porosity with poor connectivity occur in the Chang 7 tight shaly sandstones. Assuming spherical pores, a new model to calculate the fractal dimension of pore structure from the NMR T2 distributions is proposed. The fractal dimensions of all the samples are calculated, and the accuracy of the proposed model is verified by the regression coefficients. The microscopic pore structures are heterogeneous in these tight sandstones according to the high value of fractal dimensions. Micropores are the primary causes of heterogeneity in tight sandstones, and samples with unimodal T2 distribution behaviors and high content of short components have the highest fractal dimension and heterogeneity. The calculated fractal dimension is strongly correlated with T2peak and T2gm; therefore, the fractal model proposed in this study can be used to calculate the fractal dimensions and evaluate the heterogeneities of the porous rocks satisfactorily. The fractal model proposed in this study helps to quantitatively assess the pore structures of tight sandstones using NMR measurements.Lai, J., Wang, G., Wang, Z., Chen, J., Pang, X., Wang, S., Zhou, Z., He, Z., Qin, Z., Fan, X., 2018. A review on pore structure characterization in tight sandstones. Earth-Science Reviews 177, 436-457. sandstone reservoirs typically contain a wide pore throat sizes ranging from the nano-scale to micro-scale, and have complex pore geometry and pore throat structure. Microscopic pore throat structures are the most important factors affecting the macroscopic reservoir quality and fluid flow in tight sandstones. Evaluation and characterization quantitatively the microscopic pore structures, including pore geometry, pore size distribution, and pore connectivity, are of great importance for maintaining and enhancing petroleum recovery. This paper critically reviews the pore throat structures of tight sandstones, as assessed from peer reviewed papers in the literature as well as from the authors' personal experiences, in the particular contexts of comprehensive characterization and description of the entire pore throat structure using various complementary techniques. The depositional controls and diagenetic imprints on reservoir quality and pore structure are firstly discussed. The pore systems including pore throat type, pore geometry, pore size and connectivity, which are related to the depositional attributes and diagenetic modifications, are summarized. Then the theories and procedures of various testing techniques commonly used for pore structure characterization of tight sandstones are reviewed. Additionally, the pore throat structure characteristics in tight sandstones are obtained from various techniques such as MICP, NMR, N2GA and XCT. Pore throat distribution and capillary parameters of tight sandstones are examined, and the relationship between pore throat size distribution and permeability is overviewed. The pore size distribution and 3D pore connectivity are evaluated from NMR and XCT analysis. The NMR spectrum is also linked to the macroscopic performance, and the pore network is determined from N2GA. Then fractal theory is introduced to explain the irregularity and heterogeneity of pore throat structure characteristics, and the models for fractal dimension calculation through various techniques are summarized. Lastly the integration of various techniques is encouraged to fully characterize the entire pore size spectrum in tight sandstones by considering the complex pore structures and limitations of a single experiment in pore throat structure evaluation. This review will provide important insights into the microscopic pore structure characteristics of tight sandstones, and address the gap in comprehensive and quantitative evaluation of the heterogeneity in tight sandstones with complex microscopic pore structures.Lam, M.M., Engwall, M., Denison, M.S., Larsson, M., 2018. Methylated polycyclic aromatic hydrocarbons and/or their metabolites are important contributors to the overall estrogenic activity of polycyclic aromatic hydrocarbon–contaminated soils. Environmental Toxicology and Chemistry 37, 385-397. the present study 42 polycyclic aromatic compounds (PACs) were investigated for their estrogenic potential using the VM7Luc4E2 transactivation assay. Relative potencies were determined for mass-balance analysis. In addition, compounds were tested in combination with the estrogen receptor (ER) antagonist ICI182,780 (ICI) and the aryl hydrocarbon receptor antagonist/CYP1A1 inhibitor α-naphthoflavone. Luciferase induction and CYP1A1-dependent ethoxyresorufin-O-deethylase (EROD) activity were measured to assess whether the estrogenic activity was elicited by the compound itself and/or by its metabolites. Relative potencies ranged between 10?7 and 10?4. The ability of ICI to decrease luciferase activity stimulated by all compounds indicated that the induction responses were ER-dependent. The aryl hydrocarbon receptor antagonist/CYP1A1 inhibitor α-naphthoflavone decreased luciferase induction and EROD activity by several compounds, including the methylated chrysenes, suggesting that metabolites of these chemicals contributed to ER activation. Several PACs, such as acridine and its derivatives, appear to directly activate the ER. Furthermore, extracts of soils from industrial areas were examined using this bioassay, and estrogenic activity was detected in all soil samples. Mass-balance analysis using a combination of relative potencies and chemical analysis of the samples suggested that polycyclic aromatic hydrocarbons (PAHs) and alkylated PAHs, such as 1- and 3-methylchrysene, are important contributors to the overall estrogenic activity. However, these results revealed that a considerable proportion of the estrogenic activity in the soil remained unexplained, indicating the presence of other significant estrogenic compounds. Lane, C.S., Taylor, A.K., Spencer, J., Jones, K.B., 2018. Compound-specific isotope records of late-Quaternary environmental change in southeastern North Carolina. Quaternary Science Reviews 182, 48-64. of late Quaternary paleohydrology are rare from the U.S. Atlantic coastal plain (ACP). Here we present compound-specific hydrogen (δ2Halkane) and carbon (δ13Calkane) isotope analyses of terrestrially-derived n-alkanes from Jones Lake and Singletary Lake in eastern North Carolina spanning the last ～50,000 years. Combined with pollen, charcoal, and bulk geochemical analyses, the δ2Halkane data indicate arid conditions during the late-Pleistocene, but differing edaphic conditions at the sites perhaps related to differing water table depths. The δ13Calkane data indicate a significant C4 plant component during the late Pleistocene, but other proxies indicate a sparsely-vegetated landscape. The Pleistocene-Holocene transition is marked by rapid fluctuations in δ2Halkane values that are similar to the patterns of B?lling Aller?d and Younger Dryas isotope data from Greenland indicating sensitivity of the regional climate to short-lived, high-amplitude climatic events. The δ2Halkane data indicate a mesic early Holocene that supported colonization by Quercus-dominated ecosystems. Evidence of middle Holocene aridity in eastern Tennessee and western North Carolina contrasts with evidence of mesic conditions on the ACP, a geographic pattern similar to modern teleconnected precipitation responses to the Pacific Decadal Oscillation. A transition to Pinus-dominated ecosystems ～5500?cal?yr B.P. is accompanied by a large increase charcoal, but is not coincident with any large changes in δ2Halkane values, indicating that hydrologic change was likely not responsible for sustained late-Holocene dominance of Pinus. The lack of a change in middle Holocene hydrology and the spatiotemporally heterogeneous nature of the Quercus-Pinus transition on the ACP indicate prehistoric anthropogenic land management practices may represent the most parsimonious explanation for the regionally pervasive ecological change.Lang, S.Q., 2018. Hydrothermal stamp on the oceans. Nature Geoscience 11, 10-12. composition of the oceans is altered by hydrothermal circulation. These chemical factories sustain microbial life, which in turn alters the chemistry of the fluids that enter the ocean. A decade of research details this complex interchange.Shortly after the first discovery of seafloor hydrothermal vents, one of the pioneering researchers described the characterization of additional systems as ‘stamp collecting’1. Hydrothermal circulation was seen as the reaction between two relatively uniform materials, hot ocean crust and seawater, and so the range of possible geochemical outcomes seemed limited. Hydrothermal chemistry was thought to be controlled primarily by inorganic reactions1 and of modest importance for ocean chemistry. The past decade has upended these views. Writing in Nature Geoscience in 2010, Tagliabue and coworkers2 demonstrated that Southern Ocean iron concentrations could only be replicated if the input from hydrothermal circulation was included, and in 2011 Wankel and coworkers3 showed that microbial activity can influence hydrothermal fluxes to the deep ocean.Many of the trace metals that are discharged into the deep sea from hydrothermal vents had been seen as only locally important. They were not believed to contribute significantly to the global make-up of the oceans due to rapid local precipitation (Fig. 1). However, some hydrothermal iron escapes precipitation and is transported far from vent sites4,5,. In addition, concentrations of dissolved iron across entire ocean basins correlate with those of the hydrothermal tracer 3He (ref. 6), further suggesting that vents have an influence on ocean chemistry further afield than thought.Upwelling transports this deep hydrothermal source of iron to the surface where iron availability controls primary productivity. This delivery from the deep increases primary productivity in the surface ocean and impacts the global carbon cycle over millennial timescales. Tagliabue and colleagues2 used a compilation of dissolved Fe and 3He ratios and a global ocean model to assess the hydrothermal impact on the dissolved iron in the world’s oceans. They found the response to the hydrothermal input greatest in the Southern Ocean. Here, the hydrothermal input of dissolved iron contributes at least 5–15% of total Southern Ocean carbon exports.The global importance of the hydrothermal iron flux has since been widely confirmed. Dissolved hydrothermal iron has been detected in every ocean basin7, sometimes more than 4,000 km away from the source8. Inorganic pyrite nanoparticles — small enough to stay suspended in the water column9 — and close complexation with organic matter5,9,10 allow metal transport away from spreading centres.Acknowledgement of a potential role for organic-iron complexation highlights a second significant shift in thinking about hydrothermal circulation: it emphasizes the importance of microorganisms in mediating the chemistry of the fluids that exit the seafloor. In the case of iron, organisms that obtain energy via oxidation of inorganic compounds — in a process known as chemolithoautotrophy — may provide the organic matter that helps to stabilize and enable its long-distance transport5. Therefore, these fluids are far from being the sterile output of water–rock reactions. Instead, they show the unmistakable imprint of biological activity. Beyond iron, microorganisms also alter the volatile and carbon content of hydrothermal fluids resulting in compositions that can be unravelled to reveal subsurface reactionsA notable example of the impact of biological activity comes from Wankel and co-workers3, writing in Nature Geoscience in 2011. Making in-situ flow-rate and volatile measurements, they compared fluids from focused, high-temperature vents — that are so hot as to preclude life — with nearby diffuse fluids that have been conductively cooled and mixed with seawater. Although diffuse fluids had been known to host microbial communities11, 12, in this study they were able to quantify that hydrogen from diffuse vents was 50–80% lower than predicted. This loss of hydrogen was attributed to microbial consumption and biological oxidation. Although similar non-conservative behaviour of biologically reactive chemical species had been shown previously13,14, Wankel and colleagues were able to demonstrate that the biological impact on hydrothermal venting was quantitatively important to total fluxes into the oceans.The complexity of these systems is not only in the microbial interactions. Fully integrating the geochemical fluxes associated with hydrothermal circulation into ocean and global elemental cycles has proved difficult because of their heterogeneity in space and time. Early studies showed that episodic events such as fresh magma injections or seismic activity could actually deliver a year’s worth of geochemicals to the ocean in the space of a few months15, 16; systems where seawater circulates through serpentinite rocks instead of basalts and gabbros have fluids with vastly different pHs, temperatures, volatile, metal and carbon content17; and the majority of hydrothermal circulation occurs in older crust, far from the ridge axis, and at lower temperatures that result in fluids that are less drastically altered from seawater signatures18. Chemical signatures and microbial activity will reflect changes in rock type, temperature and extent of mixing with deep seawater but, so far, much of this variability remains unconstrained. No individual vent field is representative of all hydrothermal circulation, and no single cruise can capture the temporal variability of an individual vent field.The challenges of characterizing spatial and temporal variability and the biogeochemical interactions of hydrothermal circulation are being addressed on multiple fronts. The continued development of new in situ chemical sensors holds the promise of capturing the temporal variability of individual systems, particularly when linked to cabled observatories that return data continuously and in real time19 . Devices that incubate microbial cultures at in situ temperatures and pressures may allow better information on the growth rates and metabolisms that alter geochemical fluxes. And the signatures of chemical species in hydrothermal fluids that have received less attention so far — such as organic carbon, nitrogen and phosphorous — will provide additional insights into fundamental relationships.Ultimately, determining how mass and energy are transferred from the mantle to the deep ocean will require a mechanistic understanding of the interactions between water, rocks and microbes. Recognizing and characterizing the temporal and spatial variations in hydrothermal systems is both critical to understanding ocean chemistry and a feasible ambition.References1. Rona, P. A. in Diversity of Hydrothermal Systems on Slow Spreading Ocean Ridges (eds Rona, P. A., Devey, C. W., Dyment, J. & Murton, B. J.) 5–10 (American Geophysical Union, Washington DC, 2010).2. Tagliabue. et al. Nat. Geosci. 3, 252–256 (2010).3. Wankel, S. D. et al. Nat. Geosci. 4, 461–468 (2011).4. Bennett, S. A. et al. Earth Planet. Sci. Lett. 270, 157–167 (2008).5. Toner, B. M. et al. Nat. Geosci. 2, 197–201 (2009).6. Boyle, E. A. et al. Geochim. Cosmochim. Acta 69, 933–952 (2005).7. German, C. R. et al. Phil. Trans. R. Soc. A 374, 20160035 (2016).8. Resing, J. A. et al. Nature 523, 200–206 (2015).9. Yücel, M., Gartman, A., Chan, C. S. & Luther, G. W. III Nat. Geosci. 4, 367–371 (2011).10. Sander, S. G. & Koschinsky, A. Nat. Geosci. 4, 146–150 (2011).11. Holden, J. F., Summit, M. & Baross, J. A. FEMS Microbial Ecol. 25, 33–41 (1998).12. Summit, M. & Baross, J. A. Proc. Natl Acad. Sci. USA 98, 2158–2163 (2001).13. Von Damm, K. L. & Lilley, M. D. in The Subseafloor Biosphere at Mid-Ocean Ridges Vol. 144 (eds Wilcock, W. S. D., Delong, E. F., Kelley, E. S., Baross, J. A. & Cary, C.) 269–289 (Geophysical Monograph Series, American Gephysical Union 2004)14. Butterfield, D. A. et al. in The Subseafloor Biosphere at Mid-Ocean Ridges Vol. 144 (eds Wilcock, W. S. D., Delong, E. F., Kelley, E. S., Baross, J. A. & Cary, C.) 245–268 (Geophysical Monograph Series, American Geophysical Union, Washington DC, 2004).15. Lilley, M. D., Butterfield, D. A., Lupton, J. E. & Olson, E. J. Nature 422, 878–881 (2003).16. Seewald, J., Cruse, A. & Saccocia, P. Earth Planet. Sci. Lett. 216, 575–590 (2003).17. Kelley, D. S. et al. Science 307, 1428–1434 (2005).18. Mottl, M. J. & Wheat, C. G. Geochim. Cosmochim. Acta 58, 1115–1137 (1994).19. Kelley, D. S., Delaney, J. R. & Juniper, S. K. Marine Geol. 352, 426–450 (2014).Lantink, M.L., Oonk, P.B.H., Floor, G.H., Tsikos, H., Mason, P.R.D., 2018. Fe isotopes of a 2.4?Ga hematite-rich IF constrain marine redox conditions around the GOE. Precambrian Research 305, 218-235. hematite- and manganese-rich Hotazel iron formation, Griqualand West basin, South Africa, was deposited at a key moment in time, close to the GOE between 2.4 and 2.3?Ga. It stratigraphically overlies the Ongeluk Formation, comprising thick flood basalts, which in turn interfinger with and cover the Makganyene Formation diamictites, the inferred remnants of the first Paleoproterozoic Snowball Earth interval. No extensive research has been conducted to date on the basal part of the Hotazel Formation due to poor exposure, though it constitutes an important link between a period of large-scale ice cover, extensive volcanism and the onset of atmospheric oxygenation.Here, we present a detailed petrographic, geochemical and Fe isotope study of a roughly 3-metre-long drill-core exposing the Ongeluk to Hotazel contact. Our results show that after the cessation of Ongeluk volcanism, primary precipitation of Fe(III) oxyhydroxides from the photic surface zone of the original basin became the dominant sedimentation mechanism. Negative δ56Fe values (between ?0.26 and ?0.50‰) in micro-drilled hematite-rich chert indicate that surface water δ56Fe compositions at the time of deposition were depleted. Yet, δ56Fe and bulk-rock Fe/Mn values are still substantially higher (1–2‰) than those reported higher up in the Mn-rich layers of the Hotazel sequence, suggesting that redox potentials were still comparatively limited during the earliest stages of the Hotazel depositional environment.The base of the Hotazel Formation thus forms a transitional interval between precipitation from essentially ferruginous seawater, as recorded in the Ghaap Group BIFs, and from isotopically and chemically highly evolved surface waters, as demonstrated by the Hotazel Mn-rich layers. In the absence of Fe(II) as a strong reducing agent, large volumes of photosynthetic oxygen may have eventually escaped into the atmosphere, leading to the onset of atmospheric oxygenation. Our results thus contradict previous models that place the onset of the GOE before the Hotazel Formation, concurrent with and mechanistically linked to the Makganyene and Ongeluk events. Instead, we show that the Hotazel basal sediments are still pre-GOE, consistent with their circa 2.4?Ga age and the continuation of MIF-S higher in the stratigraphic record.Larue, D.K., Smithard, M., Mercer, M., 2018. Three deep resource plays in the San Joaquin Valley compared with the Bakken Formation. American Association of Petroleum Geologists Bulletin 102, 195-243. continuous oil accumulation is one that is pervasive throughout a large area and is not affected by natural hydrodynamic influences. Three source rocks in the San Joaquin Valley of California are actively producing hydrocarbons and represent potential continuous oil accumulations: the Monterey, Kreyenhagen, and Moreno Formations. The Energy Information Administration announced in 2014 that there are potentially 15 billion bbl of recoverable oil in the Monterey Formation in California, spiking huge interest. Such a resource would make the Monterey by far the largest continuous oil accumulation in North America. This number has since been reduced dramatically to 600 million bbl of oil for the state and 21 million bbl of oil within the San Joaquin Valley. In this study, the subsurface character of the Bakken Formation of North Dakota is compared with the three source rocks in the San Joaquin Valley at oil window depths. To characterize these reservoirs, hundreds of well logs, core descriptions, and mud logs were studied. A technique to rank character of oil show data was developed in which interesting, possibly interesting, or not interesting wells were located on thermal maturity maps. Interesting wells have significant oil shows, whereas not interesting wells have minor or no shows. In the Bakken Formation, the character of the oil show correlates with well productivity. Applying this same classification to the San Joaquin Valley source rocks leads to a more disappointing conclusion. Although there are oil shows in the source rocks of the San Joaquin Valley at oil window depths suggesting the presence of a continuous oil accumulation, the distribution of shows is both laterally and vertically heterogeneous and not predictable. Moreover, recent attempts to produce from source rocks at these depths have not been economically successful. We conclude that the three source rocks in the San Joaquin Valley represent heterogeneous and discontinuous oil accumulations at oil window depths in the subsurface. Likely there are billions of barrels of oil in these discontinuous oil accumulations. Source rocks in the Bakken are rated as world class; source rocks in the San Joaquin Valley are good to excellent quality. However, the quality of the oil shows in the San Joaquin Valley appears poorer than the Bakken Formation. It is possible that effective drainage between the source rocks and the up-dip reservoirs has left large volumes of the source rocks at oil window depths with only residual oil saturation. Complex structural and stratigraphic architecture, heterogeneity, and continuity create issues of predictability for optimal areas to target. Rapid rates of subsidence over the past few million years and accompanying thrusting and folding resulted in a complex subsurface pressure regime. The lack of clear hydraulic fracture targets, analogous to the middle Bakken, further complicates drilling decisions and likely deliverability. In addition, the oil windows in the San Joaquin Valley are significantly deeper than the Bakken Formation, which would result in substantially higher well cost. Recent drilling results support this study and suggest that heterogeneous and discontinuous oil accumulations in the San Joaquin are unlikely to become economic without dramatic changes in technology.Lashkarbolooki, M., Ayatollahi, S., 2018. The effects of pH, acidity, asphaltene and resin fraction on crude oil/water interfacial tension. Journal of Petroleum Science and Engineering 162, 341-347. basic understanding of the activities of indigenous surfactants of crude oil at the water/oil interface as a function of aqueous phase pH can give us a better insight into the alkaline enhanced oil recovery processes. The present study aimed to elucidate the effect of salinity and crude oil type, specifically the influence of resin and asphaltene molecules during alkaline flooding through interfacial tension (IFT) measurements via pendant drop and spinning techniques. Several model oils containing asphaltene and resin fractions were prepared and their IFTs were compared with those of the original crude oils. Moreover, the elemental analyses of asphaltene and resin fractions were performed, and the total acid numbers of all oils were measured as well. The IFT results of three studied crude oils and the asphaltenic and resinous model oils with sea water and deionized water underlined the importance of the degree of salinity, and qualitative and quantitative nature of resin and asphaltene fractions. It was also revealed that the amount of asphaltene and resin fractions as well as their structural nitrogen and oxygen contents were the most influential parameters on the IFT of crude oil as a function of pH values. In addition, the variations of IFT crude oils/the ionic solution and deionized water were more noticeable in the basic aqueous solutions.Laskin, J., Laskin, A., Nizkorodov, S.A., 2018. Mass spectrometry analysis in atmospheric chemistry. Analytical Chemistry 90, 166-189. the Earth’s atmosphere, numerous gas-phase species and airborne particles form a complex mixture called atmospheric aerosol. A variety of natural and anthropogenic primary emission sources along with chemical and photochemical transformations of the emitted compounds in the atmosphere contribute to a large diversity of aerosols, which often contain hundreds of individual components existing in different phases in a dynamic gas-particle exchange. Common examples of atmospheric aerosols include sea-salt spray (SSA), biomass burning organic aerosol (BBOA), mineral dust, soot, biological aerosol, and forest haze. Organic aerosol (OA) is commonly categorized either as a primary organic aerosol (POA) or secondary organic aerosol (SOA) depending on how it is produced. However, this distinction is quickly erased by the chemical and physical aging processes in the atmosphere. In the aerosol system, concentrations of individual compounds both in the gas- and condensed phases can differ by orders of magnitude. Chemical properties of these species also are remarkably diverse with respect to their molecular weights, structures, volatility, polarity, light absorption, and reactivity. Furthermore, particles in aerosol mixtures have a distribution of sizes and typically contain several components (internal mixing); mixtures of individual single-component particles (external mixing) are also common. Because of their profound impact on air quality in urban areas, biogeochemical cycling of elements, plant ecology, climate, and human health, atmospheric aerosols have been actively investigated by the scientific community. Assessment and mitigation of aerosols’ impact on the environment require detailed experimental speciation of their chemical composition and physical properties, a challenging task that drives the development and applications of novel mass spectrometry (MS) based analytical techniques for aerosol measurements. In this review, we summarize the most recent developments in MS instrumentation and their applications focused on understanding the formation and transformation of OA, one of the most complex and dynamic atmospheric components, with an emphasis on studies published between 2015 and 2017. The review is by no means comprehensive but rather emphasizes the breadth of analytical developments in both online and offline analysis of volatile organic compounds (VOCs) and condensed-phase aerosol components. In the past 3 decades, MS techniques have been at the forefront of aerosol characterization. MS offers an unmatched potential for both qualitative and quantitative analysis of a broad range of chemical species in OA with high sensitivity and high dynamic range. Inherent versatility in sample introduction, ionization, and mass analysis resulted in numerous innovations in the instrument development and applications. These advances are critical for unraveling the complexity of OA and providing unique information on the aerosol composition and transformations. The broad subject area of MS analysis of atmospheric aerosols, which includes both in situ and offline approaches, has been extensively reviewed. Currently, MS characterization of aerosols is still a rapidly growing area of analytical chemistry that shows no signs of decline. Remarkably, at the time of this manuscript preparation, a search for “Atmospheric Aerosol Mass Spectrometry” on the Web of Science resulted in around 2600 manuscripts in peer-reviewed literature with nearly 800 papers published after 2013. This review is organized into two major sections. In the first section, we present new developments in MS instrumentation and methods that advanced various aspects of gas-phase, cluster, and particle measurements. In the second section, we summarize selected applications of MS-based techniques focused on understanding atmospheric chemistry of OA both in field and laboratory studies. Finally, we discuss several promising future directions in this field.Leclerc, M., Taché, K., Bedford, S., Spriggs, M., Lucquin, A., Craig, O.E., 2018. The use of Lapita pottery: Results from the first analysis of lipid residues. Journal of Archaeological Science: Reports 17, 712-722. and isotopic characterisation of absorbed organic residues have been performed on eight dentate-stamped and two plain Lapita potsherds from the site of Teouma, in Vanuatu. Lipid profiles associated with decorated pots are homogenous, suggesting that similar food types or mixtures of food types were placed in these vessels. This suggests a high degree of consistency in the use of Lapita decorated pots, irrespective of the morphological and stylistic variation of these vessels. Data obtained from single-compound isotope analysis are also not consistent with marine resources as potential food sources for Lapita vessels. The absence of such commonly consumed, ubiquitous and easily accessible resources in Lapita vessels suggests that these pots were not manufactured to be used for ordinary occasions and day-to-day food consumption. This is the first time tangible data related to the use of these vessels are provided to support this claim in addition to contextual inferences.Letham, E.A., Bustin, R.M., 2018. Quantitative validation of pore structure characterization using gas slippage measurements by comparison with predictions from bundle of capillaries models. Marine and Petroleum Geology 91, 363-372. use of gas slippage measurements as a tool for quantitative pore structure geometry characterization was investigated by comparing pore sizes estimated from gas slippage measurements to pore sizes predicted by bundle of capillaries models. A large data set of gas slippage measurements was generated for the study by combining measurements made in our laboratory with measurements from seven previously published studies. Pore size was estimated from the gas slippage measurements using two models, one assuming a circular cross sectional pore geometry and the other slot shaped. When using a porosity function generated for the data set using experimental data and a theoretically derived tortuosity function, pore sizes estimated from bundle of capillaries models yielded a good match to the pore sizes independently estimated from gas slippage data. Better agreement between the models exists when pores in high permeability rocks are modelled as having slot shaped cross sectional geometry and pores in low permeability rocks circular cross sectional geometry, suggesting a systematic shift in pore morphology with changing permeability.Lewis, S.A., Connatser, R.M., Olarte, M.V., Keiser, J.R., 2018. Determining aromatic and aliphatic carboxylic acids in biomass-derived oil samples using 2,4-dinitrophenylhydrazine and liquid chromatography-electrospray injection-mass spectrometry/mass spectrometry. Biomass and Bioenergy 108, 198-206. biomass to a useful fuel commonly incorporates the pyrolysis of the biomass feed stock. The base liquid fraction usually contains high concentrations of ketones, aldehydes and carboxylic acids, of which each can cause detrimental issues related to the storage and upgrading process. Knowing the carbonyl species and the concentration of each will provide value information to the pyrolysis researchers, specifically as that community branches into more targeted end-products such as jet fuel or biogenic-derived oxygenate-containing fuel products. The analysis of aldehydes, ketones and small alkyl carboxylic acids using 2,4-dinitrophenylhydrazine (DNPH) derivation method has been well documented and the method is commonly used the analytical community. By using liquid chromatograph coupled to tandem mass spectrometry, biomass sample analysis can be complete with identification of most carbonyl species. The issue of identifying isobaric ketone and aldehyde compounds can be resolved by utilizing differences in retention time or characteristic fragment ions of ketones and aldehydes. One issue which could not resolved using published methods was identifying aromatic or large non-aromatic carboxylic acids from their corresponding hydroxyl aldehyde or ketone analogs. By modifying the current method for determining carbonyls in biomass samples, carboxylic and hydroxyl-carbonyl can be determined. A careful adjustment of the pH during the extraction procedure and extended heating time of the DNPH solution allowed for the successful derivation of aromatic carboxylic acids. Like other dinitrophenylhydrazones, carboxylic acid derivatives also produce a unique secondary ion pattern, which was useful to distinguish these species from the non-acid analogs.Li, D., Li, R., Zhu, Z., Wu, X., Liu, F., Zhao, B., Cheng, J., Wang, B., 2018. Elemental characteristics and paleoenvironment reconstruction: a case study of the Triassic lacustrine Zhangjiatan oil shale, southern Ordos Basin, China. Acta Geochimica 37, 134-150. trace elements to reconstruct paleoenvironment is a current hot topic in geochemistry. Through analytical tests of oil yield, ash yield, calorific value, total sulfur, major elements, trace elements, and X-ray diffraction, the quality, mineral content, occurrence mode of elements, and paleoenvironment of the Zhangjiatan oil shale of the Triassic Yanchang Formation in the southern Ordos Basin were studied. The analyses revealed relatively high oil yield (average 6.63%) and medium quality. The mineral content in the oil shale was mainly clay minerals, quartz, feldspar, and pyrite; an illite–smectite mixed layer comprised the major proportion of clay minerals. Compared with marine oil shale in China, the Zhangjiatan oil shale had higher contents of quartz, feldspar, and clay minerals, and lower calcite content. Silica was mainly in quartz and Fe was associated with organic matter, which is different from marine oil shale. The form of calcium varied. Cluster analyses indicated that Fe, Cu, U, V, Zn, As, Cs, Cd, Mo, Ga, Pb, Co, Ni, Cr, Sc, P, and Mn are associated with organic matter while Ca, Na, Sr, Ba, Si, Zr, K, Al, B, Mg, and Ti are mostly terrigenous. Sr/Cu, Ba/Al, V/(V?+?Ni), U/Th, AU, and δU of oil shale samples suggest the paleoclimate was warm and humid, paleoproductivity of the lake was relatively high during deposition of the shale—which mainly occurred in fresh water—and the paleo-redox condition was dominated by reducing conditions. Fe/Ti ratios of the oil shale samples suggest clear hydrothermal influence in the eastern portion of the study area and less conspicuous hydrothermal influence in the western portion.Li, D., Li, R., Zhu, Z., Wu, X., Zhao, B., Cheng, J., Liu, F., 2017. Rare earth elements geochemistry characteristics and their geological implications of lacustrine oil shale from Chang 7 oil layer in southern Ordos Basin, China. Geological Journal 52, 119-131. in the middle-western area of China, Ordos Basin is a large continental basin with vast petroleum resources. Oil shale of Chang 7 oil layer from Triassic Yanchang Formation represents the typical lacustrine oil shale in China. Oil shale samples were collected from Chang 7 oil layer to study the characteristics of elements geochemistry. The rare earth elements (REEs) concentration of oil shale samples varies from 138.51 to 206.36 μg/g with an average of 162.64 μg/g, close to the average REEs content of the North American shale Composite and slightly higher than the upper continental crust. The chondrite-normalized and North American shale composite-normalized REEs distribution patterns explain that oil shale samples, together with silty mudstone samples, may have been derived from a similar terrigenous source. The oil shale deposited mainly in early diagenetic stage B period and the paleoclimate condition was warm and humid with moderate chemical weathering. The whole sedimentary rate of oil shale was low. The source rocks of oil shale were mainly from the felsic rocks and deposited in the continental island arc tectonic setting. The total REE of oil shale samples show positive correlations with Al, Si, K, and ash yield concentration and negative correlations with oil yield, Fe, P, and total sulfur concentration, illustrating that REEs concentration in clay minerals is more than that in organic matter. In addition, the light REEs and heavy REEs are both present in clay minerals and controlled by land-derived detritus.Li, G., Li, C., Li, X., Wei, N., 2017. The permeability experiment on the methane hydrate in quartz sands and its model verification. Natural Gas Industry 37, 53-60. permeability of porous media is an important physical parameter that affects the exploitation of natural gas hydrate. At present, however, the measurement methods and porous media used for investigating the permeability are so different that neither well-recognized experiment methods nor measurement results are available yet. In this paper, a one-dimensional test apparatus was developed to measure the permeability of porous media with methane hydrate. By virtue of this apparatus, methane hydrate was generated and the flow rate and pressure difference of inflow liquid water were measured in a stable flow pattern. Then, based on the basic principle of the Darcy's Law, the permeability of 30–40 mesh quartz sands with a methane hydrate system was calculated using steady-state water injection. And the experimental results were obtained. First, this apparatus can provide the flow rates and pressure differences of stable fluid under constant pressures and temperatures, so it satisfies the basic conditions of the Darcy's Law and consequently the permeability is calculated. Second, with this apparatus, the methane hydrate saturation in permeability experiments can be controlled effectively, so that the reliability and repeatability of permeability measurement of methane hydrate bearing quartz sands are ensured. Third, methane hydrate crystals are formed and gradually grow in the pore center, occupying the pore space and blocking the flow channel. And the liquid effective permeability decreases sharply with the increase of methane hydrate saturation. Fourth, the permeability calculated by the Masuda, Dai and Li models is 13.0, 7.0 and 4.0, respectively and the calculated values are in accordance with the experimental results. These research results provide experimental data and a theoretical calculation basis for the quantification of fluid permeability of methane hydrate bearing porous media.Li, H., Dai, S., Ouyang, Z., Xie, X., Guo, H., Gu, C., Xiao, X., Ge, Z., Peng, C., Zhao, B., 2018. Multi-scale temporal variation of methane flux and its controls in a subtropical tidal salt marsh in eastern China. Biogeochemistry 137, 163-179. emissions could vary with biotic and abiotic factors at different time scales. However, little is known about temporal dynamics of CH4 flux and its controls in coastal marshes. In this study, CH4 flux was continuously measured with the eddy covariance technique for 2 years in a subtropical salt marsh in eastern China. Wavelet analysis was applied to explore the multi-scale variations of CH4 flux and its controls. Additionally, partial wavelet coherence was used to disentangle confounding effects of measured variables. No consistent diurnal pattern was found in CH4 fluxes. However, the hot-moments of CH4 flux were observed after nighttime high tide on days near the spring tide. Periodic dynamics were also observed at multi-day, semilunar and seasonal scales. Tide height in summer had a negative effect on CH4 flux at the semilunar scale. Air temperature explained most variations in CH4 fluxes at the multi-day scale but CH4 flux was mainly controlled by PAR and GEP at the seasonal scale. Air temperature explained 48% and 56% of annual variations in CH4 fluxes in 2011 and 2012, respectively. In total, the salt marsh acted as a CH4 source (17.6 ± 3.0 g C–CH4 m?2 year?1), which was higher than most studies report for inland wetlands. Our results show that CH4 fluxes exhibit multiple periodicities and its controls vary with time scale; moreover, CH4 flux is strongly modified by tide. This study emphasizes the importance of ecosystem-specific measurements of CH4 fluxes, and more work is needed to estimate regional CH4 budgets.Li, N., Sun, Z.-F., Sun, C.-Y., Li, P., Chen, G.-J., Ma, Q.-L., Liu, B., 2018. Simulating natural hydrate formation and accumulation in sediments from dissolved methane using a large three-dimensional simulator. Fuel 216, 612-620. slow hydrate formation and accumulation process from dissolved gas in nature was simulated at large-scale in sandy sediments using a three-dimensional hydrate simulator. A low hydrate formation rate (0.37% pore volume per day) was achieved by maintaining the supersaturation of dissolved methane and migration velocity of the pore fluid at very low levels. Electrical and acoustic measurements were performed to track the hydrate formation in the sediments. A dynamic hydrate evolution process was observed: Crystallization – migration – accumulation – recrystallization. This evolution process has a critical effect on the connectivity of the pores and the strength of the sediment frame. After the dynamic evolution process, stiff frame-supporting hydrates and patchy hydrates were observed as the final morphologies in the pores, although the variation in the acoustic velocity indicated that frame supporting was the dominating morphology in the pores. Based on this, hydrate saturation values were inversed from resistivity and acoustic velocity models for frame-supporting hydrates. The calculated results showed that the order of hydrate saturation at different sites from the resistivity model was consistent with that from the acoustic velocity model by overestimating the hydrate saturation obtained from the resistivity inversion. Analysis of the spatial hydrate distribution showed that hydrate distribution in the sediments was discontinuous. The concentration, temperature, and fluid velocity profiles play a key role on this discontinuity, which we propose should be considered in detail in future experimental and numerical studies.Li, T., Xu, J., Zou, R., Feng, H., Li, L., Wang, J., Cohen Stuart, M.A., Guo, X., 2018. Resin from Liaohe heavy oil: Molecular structure, aggregation behavior, and effect on oil viscosity. Energy & Fuels 32, 306-313. accounts for over 30% of the composition of Liaohe heavy crude oil and can result in severe difficulties in oil recovery and transportation. To determine the structure of the resin extracted from Liaohe heavy oil, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, elemental analysis, Fourier-transform IR spectroscopy, and NMR spectroscopy were employed to determine the chemical structure of the resin. The results showed that the resin molecule is composed of anthracene, two cycloalkanes, and six alkyl chains grafted on the cyclic-structure core. UV–visible spectroscopy, turbidity measurements, dynamic light scattering, optical microscopy, and scanning electron microscopy were used to observe the resin aggregation behavior upon addition of a poor solvent. The effect of the resin on the rheology of model oils was investigated systematically. The π–π interactions among resin molecules impose a critical impact on the assembly of the resins. The quantum mechanics calculations revealed that there are two low-well depths of interaction energy when two resin molecules approach, which implies that the bending and branching structure of the resin aggregates may originate from the staggered stacking of the resin molecules. These findings can improve our understanding of the resin aggregation behavior and thus enlighten the solution to the flowing problem during recovery and transportation of heavy oil with a high resin content.Li, X., Guo, Y., Sun, Q., Lan, W., Liu, A., Guo, X., 2018. Experimental study for the impacts of flow rate and concentration of asphaltene precipitant on dynamic asphaltene deposition in microcapillary medium. Journal of Petroleum Science and Engineering 162, 333-340. have been referred to ‘cholesterol of petroleum’ and the heaviest and the most complex components in crude oil. Asphaltene aggregation and deposition have always been a challenging issue on fluid transport in porous media for oil recovery and production processes in industries. Many experimental efforts have been done to study asphaltene aggregation and deposition from crude oil. Most of these works were carried out by coreflood tests or in bulk solution. Only several macroscopic parameters, such as pressure variation and permeability reduction caused by asphlatene deposition, were studied. Few experimental studies have been done to make the direct pore-scale visualization of dynamic asphaltene deposition behavior in capillary flow. In this study, we developed a new experimental approach to directly visualize and measure the dynamic asphaltene deposition process in capillary flow. Effects of concentration of asphaltene precipitant and flowrate were examined. The results indicate that the concentration of precipitant has a significant effect on the dynamic asphaltene deposition in capillary flow. The size of asphaltene deposit increases significantly with elapsed time and size distribution becomes wider at higher precipitant concentration. Higher concentration of asphaltene precipitant could lead to higher deposition rate. The results also indicate that higher flowrate causes faster growth of asphaltene deposits in capillary flow. Larger sizes of asphaltene deposits are formed and number of asphaltene deposits decreases with the elapsed time at higher flowrate. The results produced provide new sights into the dynamic asphaltene deposition in capillary flow at a pore scale. They could contribute to predict the growth rate of arterial asphaltene deposition in porous media and develop accurate numerical simulator for enhanced oil recovery purpose in industries.Li, X., Ma, W., Li, H., Ai, W., Bai, Y., Liu, H., 2018. Sampling and analyte enrichment strategies for ambient mass spectrometry. Analytical and Bioanalytical Chemistry 410, 715-724. mass spectrometry provides great convenience for fast screening, and has showed promising potential in analytical chemistry. However, its relatively low sensitivity seriously restricts its practical utility in trace compound analysis. In this review, we summarize the sampling and analyte enrichment strategies coupled with nine modes of representative ambient mass spectrometry (desorption electrospray ionization, paper vhspray ionization, wooden-tip spray ionization, probe electrospray ionization, coated blade spray ionization, direct analysis in real time, desorption corona beam ionization, dielectric barrier discharge ionization, and atmospheric-pressure solids analysis probe) that have dramatically increased the detection sensitivity. We believe that these advances will promote routine use of ambient mass spectrometry.Li, Y., Dai, C., Zhou, H., Wang, X., Lv, W., Zhao, M., 2018. Investigation of spontaneous imbibition by using a surfactant-free active silica water-based nanofluid for enhanced oil recovery. Energy & Fuels 32, 287-293. in using nanofluids for enhanced oil recovery (EOR) applications has been increasing. Herein, a novel surfactant-free water-based nanofluid for EOR was constructed using active silica nanoparticles. Active silica nanoparticles were synthesized via condensation of hexanedioic acid with the ?OH group of silica. Water-based nanofluid was obtained by transforming carboxyl into carboxylate on the surface of active silica nanoparticles in water. The particle size of the active silica nanoparticles in water ranged from 10 to 20 nm. The interfacial activity of the nanoparticles was endowed through the shape change of the active silica nanoparticle surface groups to minimize their interface energy. The morphology and surface components of the active silica nanoparticles were characterized by transmission electron microscopy and Fourier transform infrared spectroscopy. The interfacial activity of the active silica nanoparticles was proved through interfacial tension and interfacial dilational modulus measurements. Active silica nanoparticles exhibited a stronger ability to reduce interfacial tension and enhance the interfacial film strength than silica nanoparticles. Contact angle measurements showed that this nanofluid exhibited excellent capabilities of oil displacement from a solid surface and wettability alteration. Spontaneous imbibition tests of ultralow permeability cores using different liquid phases (active silica nanofluid, silica nanofluid and brine) were conducted. Oil recovery using active silica nanofluid was higher than that of using silica nanofluid or brine. Active silica nanofluid at a low concentration could display an equal EOR efficiency with highly concentrated silica nanofluid. These results indicated the possible application of the proposed active silica water-based nanofluid in EOR. This preparation method could be used to prepare surfactant-free active nanofluids, and the surfactant-free active nanofluid shows great potential for EOR applications.Li, Y., Xiong, Y., Liang, Q., Fang, C., Chen, Y., Wang, X., Liao, Z., Peng, P.a., 2018. The application of diamondoid indices in the Tarim oils. American Association of Petroleum Geologists Bulletin 102, 267-291. study presents new data for the identification of the source and assessment of the thermal maturity of oils based on the diamondoid indices of oils from the Tazhong and Luntai uplifts in the Tarim Basin in northwest China. The oil samples were divided into three groups according to biomarker characteristics and the abundance and distribution of diamondoids. Group I oils are located along the Tazhong No. 1 fault zone, which contained abundant diamondoids and are of high thermal maturity, suggesting they are late-charged hydrocarbons that were derived from a Middle–Upper Ordovician source. Group II oils are mainly located in blocks close to the Tazhong No. 1 fault zone and are dominated by early formed hydrocarbons from Cambrian–Lower Ordovician source rocks. Group III lacustrine oils comprise relatively low concentrations of diamondoids compared with group I and group II oils. Group III oils were sourced from Jurassic or possibly Triassic units and are hosted by the low-relief Yingmaili section of the Luntai uplift. The thermal maturity of the oils in each group was evaluated using diamondoid parameters; a few group I oils exhibit intense thermal cracking. To estimate the extent of oil cracking using the concentrations of diamondoids in oils, this study proposes a practical approach that facilitates the determination of baseline 4- and 3-methyldiamantane concentrations. Application of this method indicates that the Tarim Basin marine oils contain a baseline concentration of approximately 69 ppm.Liang, C., Jiang, Z., Cao, Y., Wu, J., Wang, Y., Hao, F., 2018. Sedimentary characteristics and origin of lacustrine organic-rich shales in the salinized Eocene Dongying Depression. Geological Society of America Bulletin 130, 154-174. organic-rich shales are well developed within the Eocene Dongying Depression in the Bohai Bay Basin in eastern China and across Southeast Asia. Understanding the sedimentation of these shales is essential to the study of depositional processes, paleoenvironment, and paleoclimate reconstruction. This study investigates the sedimentary characteristics and formation mechanisms of lacustrine shales in the upper fourth member of the Eocene Shahejie Formation (Es4s) within the Dongying Depression based on thin sections and field emission scanning electron microscope (FESEM) observations of well cores combined with X-ray diffraction and geochemical indicators. Six lithofacies were identified: (1) laminated calcareous mudstone, (2) laminated dolomitic mudstone, (3) laminated clay mudstone, (4) laminated gypsum mudstone, (5) massive mudstone, and (6) siltstone. The organic matter in the Es4s shale is mainly type I and type II kerogens, as well as a small proportion of type III kerogen. On the basis of lithofacies associations, paleosalinity values, redox properties, and terrigenous inputs, the lower Es4s shale can be divided into six intervals from bottom to top, numbered I, II, III, IV, V, and VI. The thickness of each interval ranges from several meters to more than 10 m, reflecting high-frequency oscillations in the environment of the lake basin, markedly different from a relatively stable marine environment.The laminated mudstones are characterized by fine grain sizes, scarce large terrigenous debris (quartz and feldspar), and compositions that are rich in pyrite and sapropelic organic matter. These features indicate that these lithofacies were deposited out of suspension in a quiet water body characterized by a relatively low rate of deposition. The characteristic laminae of these lithofacies indicate subtle differences in depositional processes. The laminated gypsum mudstone was likely deposited in an evaporative environment, because its formation would have consumed Ca2+ and SO42–, promoting the deposition of a laminated dolomitic mudstone. In contrast, laminated clay mudstone was deposited in a manner that increased the volume of small terrigenous materials. Deposition of this lithofacies was controlled by the nature of the water body, paleoclimate, and terrigenous inputs. Laminated mudstones are dominant in the lower Es4s shale, suggesting that suspension was the main depositional process leading to formation of the lower Es4s shale. In contrast, the massive mudstones were likely rapidly deposited associated with siltstone as the result of fine-grained turbidites. The lower Es4s shale was formed in a depositional environment composed of a saline, medium-depth lake under anoxic conditions, with limited terrigenous inputs. The depositional process included suspension and turbidity currents. The high salinity is suggested to be related to a marine transgression, which may have been facilitated by a rise in sea level caused by global warming in the early Eocene, together with the large-scale tectonic activity of East Asia. Seawater input affected the lithofacies, influenced lake water body conditions, triggered turbidity currents, and prompted the accumulation of organic matter. The deposition of the Es4s shale in the Dongying Depression may help us to understand the deposition of lacustrine shale, paleoclimate reconstructions for the Eocene, and the tectonic activity of East Asia.Liang, J., Zhang, P., Chen, J., Gong, J., Yuan, Y., 2017. Hydrocarbon preservation conditions in Mesozoic–Paleozoic marine strata in the South Yellow Sea Basin. Natural Gas Industry B 4, 432-441. the South Yellow Sea Basin, Mesozoic–Paleozoic marine strata are generally well developed with large thickness, and they are characterized by multi-source and multi-stage hydrocarbon accumulation, providing a material basis for the formation of large-scale oil and gas fields. However, no substantial breakthrough has been made in this area. Based on previous research results, the complex tectonic pattern of this superimposed basin was formed by multi-stage tectonic movements and the favorable static conditions for hydrocarbon preservation were reworked or destroyed by later superimposition. Therefore, hydrocarbon preservation conditions are the key factors for restricting the breakthrough of marine oil and gas exploration in this area. In this paper, hydrocarbon preservation conditions of marine strata in the South Yellow Sea Basin were comprehensively analyzed from many aspects, such as tectonic movement, source conditions, caprock characteristics, magmatic activities, and hydrogeological and hydrogeochemical characteristics. It is indicated that the complex tectonic pattern of the South Yellow Sea Basin is resulted from tectonic events in multiple stages, and the development and evolution of regional source rocks are mainly controlled by two stages (i.e., the stable evolution stage of Mesozoic–Paleozoic marine basin and the Mesozoic–Cenozoic tectonic pattern transformation and basin formation stage), so the characteristics of differential oil and gas preservation are presented. Besides, better marine hydrocarbon preservation preconditions in this area are weaker tectonic reworking, development of high-quality thick source rocks, good vertical sealing capacity of caprocks, weaker magmatic activity and confined hydrogeological conditions. It is concluded that the Laoshan Uplift in the central part of the South Yellow Sea Basin is structurally stable with weaker faulting and magmatic activities, so it is better in oil and gas preservation conditions. Besides, several large-scale structural traps with good petroleum geological conditions and complete source–reservoir–caprock assemblages are developed in this area. Therefore, this area is the most promising region for Paleozoic marine oil and gas exploration in this basin.Liang, R., Aydin, E., Le Borgne, S., Sunner, J., Duncan, K.E., Suflita, J.M., 2018. Anaerobic biodegradation of biofuels and their impact on the corrosion of a Cu-Ni alloy in marine environments. Chemosphere 195, 427-436. biodegradation linked to sulfate reduction can lead to corrosion of the metallic infrastructure in a variety of marine environments. However, the biological stability of emerging biofuels and their potential impact on copper-nickel alloys commonly used in marine systems has not been well documented. Two potential naval biofuels (Camelina-JP5 and Fisher-Tropsch-F76) and their petroleum-derived counterparts (JP5 and F76) were critically assessed in seawater/sediment incubations containing a metal coupon (70/30 Cu-Ni alloy). Relative to a fuel-unamended control (1.2?±?0.4?μM/d), Camelina-JP5 (86.4?±?1.6?μM/d) and JP5 (77.6?±?8.3?μM/d) stimulated much higher rates of sulfate reduction than either FT-F76 (11.4?±?2.7?μM/d) or F76 (38.4?±?3.7?μM/d). The general corrosion rate (r2?=?0.91) and pitting corrosion (r2?=?0.92) correlated with sulfate loss in these incubations. Despite differences in microbial community structure on the metal or in the aqueous or sediment phases, sulfate reducing bacteria affiliated with Desulfarculaceae and Desulfobacteraceae became predominant upon fuel amendment. The identification of alkylsuccinates and alkylbenzylsuccinates attested to anaerobic metabolism of fuel hydrocarbons. Sequences related to Desulfobulbaceae were highly enriched (34.2–64.8%) on the Cu-Ni metal surface, regardless of whether the incubation received a fuel amendment. These results demonstrate that the anaerobic metabolism of biofuel linked to sulfate reduction can exacerbate the corrosion of Cu-Ni alloys. Given the relative lability of Camelina-JP5, particular precaution should be taken when incorporating this hydroprocessed biofuel into marine environments serviced by a Cu-Ni metallic infrastructure.Lin, D., Qiu, P., Xie, X., Zhao, Y., Chen, G., Zeng, L., 2018. Chemical structure and pyrolysis characteristics of demineralized Zhundong coal. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 40, 282-287. investigate the effects of acid treatments on the chemical structure and pyrolysis behavior of coal, we examined the low-rank Zhundong coal pretreated by four single acids (HCl, HF, H2SO4, HNO3) and a combined acid (HCl-HF-HCl). Our results indicated that the carboxylic and phenolic hydroxyl contents of the coal increased, while the aliphatic and aromatic hydrogen contents decreased after leaching. Nitric acid destroyed long aliphatic chains in coal, which caused the key pyrolysis stage to occur at lower temperature, the number of volatiles increased, and the pyrolysis rate improved.Lin, H., Xia, X., Bi, S., Jiang, X., Wang, H., Zhai, Y., Wen, W., 2018. Quantifying bioavailability of pyrene associated with dissolved organic matter of various molecular weights to Daphnia magna. Environmental Science & Technology 52, 644-653. organic matter (DOM) is a key environmental factor for the bioavailability of hydrophobic organic compounds (HOCs) in natural waters. However, the bioavailability of DOM-associated HOCs is not clear. In this research, pyrene was selected as a model HOC, and its freely dissolved concentration (Cfree) was maintained by passive dosing systems. The immobilization and pyrene content in the tissues excluding gut of Daphnia magna were examined to quantify the bioavailability of DOM-associated pyrene. The results indicated that DOM promoted the bioavailability of pyrene when the Cfree of pyrene was kept constant, and the bioavailability of pyrene associated with DOM of various molecular weights was ordered as middle molecular weight (5?000–10?000 Da) DOM > lower molecular weight (<1?000, 1?000–3?000, and 3?000–5?000 Da) DOM > higher molecular weight (>10?000 Da) DOM. The influencing mechanisms of DOM molecular weight were related with the partition of pyrene between DOM and water, the uptake routes of DOM by D. magna, and the desorption or release of pyrene from DOM in the gut of D. magna. The findings obtained in this research suggest that the bioavailability of DOM-associated HOCs should be taken into account for the eco-environmental risk assessment of HOCs in water systems.Lippens, G., Cahoreau, E., Millard, P., Charlier, C., Lopez, J., Hanoulle, X., Portais, J.C., 2018. In-cell NMR: from metabolites to macromolecules. Analyst 143, 620-629. NMR of macromolecules has gained momentum over the last ten years as an approach that might bridge the branches of cell biology and structural biology. In this review, we put it in the context of earlier efforts that aimed to characterize by NMR the cellular environment of live cells and their intracellular metabolites. Although technical aspects distinguish these earlier in vivo NMR studies and the more recent in cell NMR efforts to characterize macromolecules in a cellular environment, we believe that both share major concerns ranging from sensitivity and line broadening to cell viability. Approaches to overcome the limitations in one subfield thereby can serve the other one and vice versa. The relevance in biomedical sciences might stretch from the direct following of drug metabolism in the cell to the observation of target binding, and thereby encompasses in-cell NMR both of metabolites and macromolecules. We underline the efforts of the field to move to novel biological insights by some selected examples.Liu, B., Yao, S., Hu, W., Cao, J., Xie, D., 2017. Application of nuclear magnetic resonance cryoporometry in unconventional reservoir rocks. Acta Petrolei Sinica 38, 1401-1410., Nuclear magnetic resonance(NMR) cryoporometry is a hotspot technology for studying the pore distribution of unconventional hydrocarbon reservoir. But due to the complex distribution and genesis of such pores, the applicability and accuracy of this method is still uncertain, which is the difficulty in this field study. To deepen this understanding, NMR cryoporometry is used in combination with relatively traditional mercury porosimetry, nitrogen adsorption method and nuclear magnetic resonance method, so as to perform a comparative study on the pore distribution characteristic test of three types of end-member unconventional reservoir samples including shale, coal and tight sandstone. The results show that NMR cryoporometry has good applicability and accuracy in characterizing the nanopore distribution features of unconventional reservoirs, but the test precision, such as sample size, KGibbs-Thomson(KGT) of probe liquid, freezing-thawing damage and metallic mineral (pyrite)content, is also influenced by the samples and experiment conditions to some extent. Thus, in a practical analysis, the samples with suitable grain size should be selected for measurement according to research object. Firstly, it is required to calculate the KGT of the samples to be tested and explore the new probe liquid. However, because of the lower pyrite content (<10%)in most unconventional reservoir samples, the test results can still characterize the pores in a relative complete and quantitative way. NMR cryoporometry has a great potential for characterizing unconventional reservoir pores, and its applicability and accuracy are still to be explored further.Liu, C., Du, Y., Jarochowska, E., Yan, J., Munnecke, A., Lu, G., 2018. A major anomaly in the carbon cycle during the late Cisuralian (Permian): Timing, underlying triggers and implications. Palaeogeography, Palaeoclimatology, Palaeoecology 491, 112-122. Kungurian (late Cisuralian) is associated with elevated atmospheric pCO2 levels and numerous substantial changes in the ocean and terrestrial systems, but carbon cycle perturbations through this time interval are poorly understood. Here, three well-dated organic carbon isotope (δ13Corg) curves from South China, paired with their respective carbonate carbon isotope (δ13Ccarb) data published before, are presented for the first time. Their comparison demonstrates that a prominent, rapid, and synchronous negative excursion in δ13Corg and δ13Ccarb occurred in the early Kungurian (the herein proposed KCIE event dated to ca. 277.9–277.4 Ma). A comparable shift is observed in other deeper-water marine sections in South China and two terrestrial sections in North China and eastern Australia. Based on carbon mass-balance calculations and a review of concurrent geological records, we propose that the KCIE event was driven by an intensive volcanism of a large igneous province in northern Gondwana, dissociation of voluminous methane hydrates induced by this volcanism, and the ensuing worldwide conflagrations. Predicted elevated production of greenhouse gases involved would have warmed the Earth and further resulted in ocean stagnation, anoxia, and acidification, all of which are in conformity with the documented sedimentological, geochemical, and palaeontological data. This major anomaly in the carbon cycle in the late Cisuralian is considered here to play a key role to promote the transition of the Earth to a greenhouse mode.Liu, D., Suo, Y., Zhao, J., Zhu, P., Tan, J., Wang, B., Lu, H., 2018. Effect of demulsification for crude oil-in-water emulsion: Comparing CO2 and organic acids. Energy & Fuels 32, 757-764. substances (naphthenic acids) were found in crude oil, which provides favorable conditions for the formation of surfactants. N,N-Dimethylcyclohexylamine (DMCHA) can activate the naphthenic acid in the crude oil to form the surfactant by noncovalent bonding. This process has an unusual meaning for the crude oil pipelines transportation by the method of forming a low-viscosity oil-in-water emulsion. At the same time, CO2 can be used as a demulsifier to separate crude oil and water at the end of pipeline transportation because the surfactant has a CO2 stimulus response characteristic. In our study, it was found that crude oil-in-water emulsion can be formed and has very good stability. CO2 has a high demulsification efficiency in emulsions with lower crude oil content. For high oil content conditions, the emulsion cannot be demulsified completely by CO2. Since sulfuric acid, hydrochloric acid, and the like are liquid and corrosive, this is not conducive to its application as a demulsifier in crude oil pipeline transportation. Organic acids in this area have a stronger advantage obviously, so citric acid, oxalic acid, acetic acid, and lactic acid were used as demulsifiers in this article; all of them have good demulsification performance in high crude oil content emulsions, especially citric acid. Meanwhile, DMCHA can be recycled and reused by adding NaOH to the lower aqueous solution after demulsification.Liu, H., Cheng, L., Huang, S., Jia, P., Chen, M., 2018. Evolution characteristics of SAGD steam chamber and its impacts on heavy oil production and heat consumption. International Journal of Heat and Mass Transfer 121, 579-596., Steam-Assisted Gravity Drainage (SAGD) is the most successful commercialized method used to produce bitumen from oil sands and heavy oil reservoirs. Precise description of the steam chamber evolution is important for evaluating the economic effectiveness and Greenhouse Gas (GHG) emission of the SAGD process. In this study, the properties of MacKay River Oil Sands were used in laboratory experiments to compare the chamber evolution and production performance of SAGD under different permeability distributions. Then, a mathematical model was established to predict the steam chamber evolution and the closely related oil production and heat consumption in a heterogeneous formation. Next, the calculated production performance and steam chamber evolution were compared with measured experimental data to verify the accuracy of the model. Finally, the chamber evolution characteristics and their impacts on SAGD oil production and heat consumption are discussed in this paper for formations with different permeability distributions. The results indicate that horizontal permeability controls the evolution of steam chamber such that higher horizontal permeability may cause an obvious convex shape of the chamber edge, whereas vertical permeability has little effect on the chamber shape despite significant influence on the oil production in the early stage of SAGD. Moreover, a convex-shaped chamber interface indicates a higher production rate in the spreading stage and a lower rate in the depleting stage. In addition, this study shows that to minimize the heat consumption of the SAGD process, so that GHG emission can be curbed, a concave-like chamber shape is favorable in the early spreading stage, whereas a convex shape is better in the late spreading stage and depleting stage.Liu, H., Zhou, Y., Wang, J., Xiong, C., Xue, J., Zhan, L., Nie, Z., 2018. N-phenyl-2-naphthylamine as a novel MALDI matrix for analysis and in situ imaging of small molecules. Analytical Chemistry 90, 729-736. to its strong ultraviolet absorption, low background interference in the small molecular range, and salt tolerance capacity, N-phenyl-2-naphthylamine (PNA) was developed as a novel matrix in the present study for analysis and imaging of small molecules by matrix-assisted laser desorption/ionization mass spectrometry time-of-fight (MALDI-TOF MS). The newly developed matrix displayed good performance in analysis of a wide range of small-molecule metabolites including free fatty acids, amino acids, peptides, antioxidants, and phospholipids. In addition, PNA-assisted LDI MS imaging of small molecules in brain tissue of rats subjected to middle cerebral artery occlusion (MCAO) revealed unique distributions and changes of 89 small-molecule metabolites including amino acids, antioxidants, free fatty acids, phospholipids, and sphingolipids in brain tissue 24 h postsurgery. Fifty-nine of the altered metabolites were identified, and all the changed metabolites were subject to relative quantitation and statistical analysis. The newly developed matrix has great potential application in the field of biomedical research.Liu, K., Feng, Q., Shen, J., Khan, M., Planavsky, N.J., 2018. Increased productivity as a primary driver of marine anoxia in the Lower Cambrian. Palaeogeography, Palaeoclimatology, Palaeoecology 491, 1-9. relationship between metazoan evolution and ocean-atmosphere oxygen levels has been extensively debated. Similarly, there is no consensus on the factors controlling the evolution of the marine redox landscape. The early Cambrian is a particularly critical time interval to examine, as there is a marked increase in metazoan body plan diversity and increased ecosystem complexity, but few constraints on marine redox conditions during this seminal interval. We present an assessment of early Cambrian marine redox conditions from the Luojiacun section in west Hubei Province (the upper Yangtze platform). There are low trace elements enrichments (U, Mo) in the Yanjiahe Formation followed by an abrupt increase in the overlying Shuijingtuo Formation. U-Mo systematics in the most metal-enriched samples suggest deposition under a weakly restricted offshore basin, which is consistent with previous studies. There is correlation between excess Ba (Baxs) and total organic carbon (TOC), suggesting a strong production control on organic matter concentration. Further, higher Ba excess in the Shuijingtuo Formation than the Yanjiahe Formation indicates dysoxic-oxic conditions in the Yanjiahe Formation is linked to lower productivity, and anoxic conditions in the Shuijingtuo Formation are linked to higher productivity. Although strong productivity controls on Proterozoic and Paleozoic marine redox conditions have been commonly invoked, we provide some of the first empirical evidence for this control on marine redox structure. More broadly, we find that excess barium coupled with redox proxies may provide useful constraints on the interplay between preservation and production controls on organic matter abundances in the Paleozoic successions.Liu, M., Hilty, C., 2018. Metabolic measurements of nonpermeating compounds in live cells using hyperpolarized NMR. Analytical Chemistry 90, 1217-1222. by dissolution dynamic nuclear polarization (D-DNP) has emerged as a technique for enhancing NMR signals by several orders of magnitude, thereby facilitating the characterization of metabolic pathways both in vivo and in vitro. Following the introduction of an externally hyperpolarized compound, real-time NMR enables the measurement of metabolic flux in the corresponding pathway. Spin relaxation however limits the maximum experimental time and prevents the use of this method with compounds exhibiting slow membrane transport rates. Here, we demonstrate that on-line electroporation can serve as a method for membrane permeabilization for use with D-DNP in cell cultures. An electroporation apparatus hyphenated with stopped-flow sample injection permits the introduction of the hyperpolarized metabolite within 3 s after the electrical pulse. In yeast cells that do not readily take up pyruvate, the addition of the electroporation pulse to the D-DNP experiment increases the signals of the downstream metabolic products CO2 and HCO3–, which otherwise are near the detection limit, by 8.2- and 8.6-fold. Modeling of the time dependence of these signals then permits the determination of the respective kinetic rate constants. The observed conversion rate from pyruvate to CO2 normalized for cell density was found to increase by a factor of 12 due to the alleviation of the membrane transport limitation. The use of electroporation therefore extends the applicability of D-DNP to in vitro studies with a wider range of metabolites and at the same time reduces the influence of membrane transport on the observed conversion rates.Liu, S., Wiatrowski, H.A., 2018. Reduction of Hg(II) to Hg(0) by biogenic magnetite from two magnetotactic bacteria. Geomicrobiology Journal 35, 198-208. the biogeochemical cycle of the highly toxic element mercury (Hg) is necessary to predict its fate and transport. In this study, we determined that biogenic magnetite isolated from Magnetospirillum gryphiswaldense MSR-1 and Magnetospirillum magnetotacticum MS-1 was capable of reducing inorganic mercury [Hg(II)] to elemental mercury [Hg(0)]. These two magnetotactic bacteria (MTB) lacked mercuric resistance operons in the genomes. However, they revealed high resistance to Hg(II) under atmospheric conditions and an even higher resistance under microaerobic conditions (1% O2 and 99% N2). Neither strain reduced Hg(II) to Hg(0) under atmospheric conditions. However, a slow rate (0.05–0.21 ?M·d?1) of Hg(II) loss occurred from late log phase to stationary phase in two MTBs' culture media under microaerobic conditions. Increased Hg(II) entered both cells under microaerobic conditions relative to atmospheric conditions. The majority of Hg(II) was still blocked by the cell membrane. Hg(II) reduction was more effective when biogenic magnetite was extracted out, with or without the magnetosome membrane envelope. When magnetosome membrane was present, 8.55–13.53% of 250 nM Hg(II) was reduced to Hg(0) by 250 mg/L biogenic magnetite suspension within 2 hours. This ratio increased to 55.07–64.70% while magnetosome membrane was removed. We concluded that two MTBs contributed to the reduction of Hg(II) to Hg(0) at a slow rate in vivo. Such reduction was more favorable to occur when biogenic magnetite is released from dead cells. It proposed a new biotic pathway for the formation of Hg(0) in aquatic systems.Liu, W., Jiang, H., Yang, J., Wu, G., 2018. Salinity and DOC influence the distribution of free-living and particle-attached aerobic anoxygenic phototrophic bacteria in the Qinghai–Tibetan lakes. Geomicrobiology Journal 35, 247-254. anoxygenic phototrophic bacteria (AAPB) are widespread and play an important role in carbon cycling in the lakes of the Qinghai–Tibetan Plateau. However, little is known about how free-living and particle-attached AAPB distribute with salinity in the Qinghai–Tibetan lakes. In the present study, the abundance and diversity of free-living and particle-attached AAPB were investigated in seven Qinghai–Tibetan lakes with salinity ranging from freshwater to almost saturation (1.2 g L?1 241.1 g L?1). An integrated approach was employed including pufL-M gene (encoding the photosynthetic reaction center of AAPB) based quantitative polymerase chain reaction (qPCR) and PCR-cloning phylogenetic analysis. The qPCR data showed that the ratio between particle-attached and free-living AAPB was positively correlated (R2 = 0.73, p < 0.01) with increasing salinity. The phylogenetic analysis of pufL-M gene showed that the composition of AAPB population varied with salinity in the studied Qinghai–Tibetan lakes. These results suggested that salinity may be the important factor shaping the AAPB distribution in the studied Qinghai–Tibetan lakes, and AAPB may be adapted to the harsh conditions in the Qinghai–Tibetan lakes by attaching to particles.Liu, Y., Ding, J., Han, K.-L., 2018. Molecular dynamics simulation of the high-temperature pyrolysis of methylcyclohexane. Fuel 217, 185-192. better understand the initiation and intermediate reaction mechanisms associated with the high-temperature pyrolysis of methylcyclohexane (MCH), the dissociation of MCH is investigated using reactive molecular dynamics (RMD) and density functional theory (DFT) calculations. It is observed that the pyrolysis of MCH is initiated by four types of reaction channels. The initiation of the decomposition is mainly through the CC bond homolysis of the six-membered ring, leading to ring opening and the formation of C7H14 diradicals. Subsequently, the biradicals undergo successive decomposition by the β-scission of the CC bonds to form ethylene. Furthermore, to provide a detailed description of the pyrolysis behavior of MCH, the distributions of key products, intermediate reactions and corresponding kinetic behavior are systematically analyzed at the atomic level. The apparent activation energy extracted from the RMD simulations is 263.60?kJ/mol at temperatures from 2300?K to 3100?K, which is reasonably consistent with the experimental results.Liu, Y., Li, H.A., Tian, Y., Jin, Z., Deng, H., 2018. Determination of the absolute adsorption/desorption isotherms of CH4 and n-C4H10 on shale from a nano-scale perspective. Fuel 218, 67-77. description of absolute adsorption/desorption behavior for hydrocarbons on shale is of critical importance to the understanding of the fundamental mechanisms governing the storage, transport, and recovery of shale gas or shale gas condensate in shale reservoirs. By applying a thermogravimetric method, we first measure the excess adsorption/desorption isotherms of pure CH4 and n-C4H10 on shale samples over the temperature range of 303.15–393.15?K. The maximum test pressures considered for CH4 and n-C4H10 are 50?bar and 2?bar, respectively. Grand Canonical Monte Carlo (GCMC) simulations are then applied to calculate the density of the adsorption phase by considering the fluid-pore surface interactions. We use such calculated density of the adsorption phase to calibrate the excess adsorption/desorption isotherms, which enables us to eventually obtain the absolute adsorption/desorption isotherms. Such approach for estimating the density of the adsorption phase is essentially different from the commonly used approaches in which the density of the adsorption phase is considered to be independent of temperature, pressure, and pore size.The adsorption/desorption test results show that both CH4 and n-C4H10 exhibit more adsorption as temperature decreases or pressure increases. Their adsorption/desorption isotherms exhibit hysteresis phenomenon and this phenomenon weakens as temperature increases. Comparatively, the hysteresis behavior observed for n-C4H10 is more obvious than that for CH4. Compared with CH4, n-C4H10 has higher adsorption capacity under the same condition, indicating its higher affinity towards the shale with organic matters. As for the conventional approaches, the density calculated from the van der Waals constant b or the liquid hydrocarbon density can be used to reasonably well evaluate the absolute adsorption isotherms of n-C4H10 on shale, but tends to underestimate the absolute adsorption of CH4 on shale. GCMC simulations show that the density of the adsorption phase is strongly correlated with system pressure, temperature, and pore size. Compared to the conventional approaches, GCMC simulations can better capture the in-situ density of adsorption phase; on the basis of the in-situ density of adsorption phase, we can then achieve more accurate determination of the absolute adsorption isotherms of a given hydrocarbon on shale. This study raises the imperativeness of leveraging more sophisticated simulation tools (such as GCMC) for more accurate determination of absolute adsorption isotherms.Liu, Y., Zhang, J., Zhang, P., Liu, Z., Zhao, P., Huang, H., Tang, X., Mo, X., 2018. Origin and enrichment factors of natural gas from the Lower Silurian Songkan Formation in northern Guizhou province, south China. International Journal of Coal Geology 187, 20-29. northern Guizhou area, located near the southwestern margin of the Yangtze Block and south of the Sichuan Basin, is a promising area for shale gas exploration and development. The discovery of a natural gas accumulation in the Lower Silurian Songkan Formation in the study area is the first discovery of natural gas in this stratum in China, marking an exciting breakthrough in natural gas exploration in northern Guizhou area. This paper presents an investigation of this accumulation using gas geochemistry, including gas composition, carbon and hydrogen isotopes, in context with geological information available for the study area.Our results indicate that the natural gas accumulation in Songkan Formation is probably sourced from the Lower Silurian Wufeng-Longmaxi shale. The δ13C(CH4) values range from ? 33.9‰ to ? 33.2‰, the δ13C(C2H6) values range from ? 37.0‰ to ? 36.2‰, and the δ2H(CH4) values range from ? 157‰ to ? 144‰. These results indicate that the gases are of thermogenic origin and are oil-derived. Furthermore, isotopic rollovers seen in the natural gas is similar to that seen in the natural gas from the local Wufeng-Longmaxi shale, which is identified as carbon exchange at high temperature. The δ13C(CO2) values range from ? 20.8 to ? 17.1‰, suggesting that carbon dioxide was mainly generated by thermogenic processes. The fracture investigation indicates that the large development of horizontal fractures in calcareous mudstone is one of the reasons for the high yield of natural gas in Songkan Formation. The petrophysical parameters suggest that limestone with low porosity and permeability effectively prevents natural gas escaping and seals natural gas into calcareous mudstone with horizontal fractures.Liu, Z., Gao, B., Hu, Z., Du, W., Nie, H., Jiang, T., 2017. Reservoir characteristics and pores formation and evolution of high maturated organic rich shale: a case study of Lower Cambrian Jiumenchong Formation, southern Guizhou area. Acta Petrolei Sinica 38, 1381-1389. clarify the pore characteristics and formation mechanism of high-maturity organic rich shale, taking the shale in Lower Cambrian Jiumenchong Formation, the southern of Upper Yangtze Guizhou area as an example, a study is conducted on the pore structures, types and reserving properties of high-maturity organic rich shale with the use of multiple technical methods involving the rock thin section, the total-rock X-ray diffraction, low-temperature nitrogen adsorption, high pressure Hg injection-adsorption simultaneous determination, helium porosity test, argon ion polishing-scanning electron microscope, thermal evolution and pore evolutionary history recovery. Meanwhile, a micro pore formation-evolution model of high-maturity organic rich shale is established based on the diagenesis compaction and thermal evolution process. The research results show that firstly, the average values of total specific surface area and total pore volume in Lower Cambrian high-maturity organic rich shale are 12.66 m2/g and 11.54×10-3cm3/g, respectively, and both possess a favorable positive correlation relationship. Compared with the Lower Silurian shale, the total specific surface area is slightly lower than the total pore volume. The pores are dominated by micro pores and meso pores, while macro pores are basically undeveloped. Secondly, organic rich shale is dominated by organic pore with ultra-small aperture, which is usually less than 30 nm, and the pore boundary configuration is irregular basically without the development of inorganic mineral pores. Thirdly, compared with the Silurian shale, the reserving performance is poorer with an average porosity of only 2.80%, and the horizontal permeability is 1-3 times of vertical permeability and 2 times of average value, reflecting the less development of horizontal laminations. Fourthly, the pore formation and evolution of high-maturity organic rich shale is mainly jointly controlled by the evolutionary process of inorganic mineral intergranular pores under the control of diagenesis compaction, the organic pore formation process in hydrocarbon generation-oil generation-hydrocarbon transformation sequence under the control of thermal evolution, and natural gas dissipation-supply equilibration process under the state of late pore preservation.L?nborg, C., ?lvarez–Salgado, X.A., Letscher, R.T., Hansell, D.A., 2018. Large stimulation of recalcitrant dissolved organic carbon degradation by increasing ocean temperatures. Frontiers in Marine Science 4, 436. doi: 10.3389/fmars.2017.00436. than 96% of organic carbon in the ocean is in the dissolved form, most of it with lifetimes of decades to millennia. Yet, we know very little about the temperature sensitivity of dissolved organic carbon (DOC) degradation in a warming ocean. Combining independent estimates from laboratory experiments, oceanographic cruises and a global ocean DOC cycling model, we assess the relationship between DOC decay constants and seawater temperatures. Our results show that the apparent activation energy of DOC decay (Ea) increases by three-fold from the labile (lifetime of days) and semi-labile (lifetime of months) to the semi-refractory (lifetime of decades) DOC pools, with only minor differences between the world's largest ocean basins. This translates into increasing temperature coefficients (Q10) from 1.7–1.8 to 4–8, showing that the generalized assumption of a constant Q10 of ~2 for biological rates is not universally applicable for the microbial degradation of DOC in the ocean. Therefore, rising ocean temperatures will preferentially impact the microbial degradation of the more recalcitrant and larger of the three studied pools. Assuming a uniform 1°C warming scenario throughout the ocean, our model predicts a global decrease of the DOC reservoir by 7 ± 1 Pg C. This represents a 15% reduction of the semi-labile + semi-refractory DOC pools.López-Ure?a, S., Torres-Lapasió, J.R., Donat, R., García-Alvarez-Coque, M.C., 2018. Gradient design for liquid chromatography using multi-scale optimization. Journal of Chromatography A 1534, 32-42. reversed phase-liquid chromatography, the usual solution to the “general elution problem” is the application of gradient elution with programmed changes of organic solvent (or other properties). A correct quantification of chromatographic peaks in liquid chromatography requires well resolved signals in a proper analysis time. When the complexity of the sample is high, the gradient program should be accommodated to the local resolution needs of each analyte. This makes the optimization of such situations rather troublesome, since enhancing the resolution for a given analyte may imply a collateral worsening of the resolution of other analytes. The aim of this work is to design multi-linear gradients that maximize the resolution, while fulfilling some restrictions: all peaks should be eluted before a given maximal time, the gradient should be flat or increasing, and sudden changes close to eluting peaks are penalized. Consequently, an equilibrated baseline resolution for all compounds is sought. This goal is achieved by splitting the optimization problem in a multi-scale framework. In each scale κ, an optimization problem is solved with Nκ?≈?2κ variables that are used to build the gradients. The Nκ variables define cubic splines written in terms of a B-spline basis. This allows expressing gradients as polygonals of M points approximating the splines. The cubic splines are built using subdivision schemes, a technique of fast generation of smooth curves, compatible with the multi-scale framework. Owing to the nature of the problem and the presence of multiple local maxima, the algorithm used in the optimization problem of each scale κ should be “global”, such as the pattern-search algorithm. The multi-scale optimization approach is successfully applied to find the best multi-linear gradient for resolving a mixture of amino acid derivatives.Lowery, C.M., Cunningham, R., Barrie, C.D., Bralower, T., Snedden, J.W., 2017. The northern Gulf of Mexico during OAE2 and the relationship between water depth and black shale development. Paleoceanography and Paleoclimatology 32, 1316-1335.: Despite their name, Oceanic Anoxic Events (OAEs) are not periods of uniform anoxia and black shale deposition in ancient oceans. Shelf environments account for the majority of productivity and organic carbon burial in the modern ocean, and this was likely true in the Cretaceous as well. However, it is unlikely that the mechanisms for such an increase were uniform across all shelf environments. Some, like the northwest margin of Africa, were characterized by strong upwelling, but what might drive enhanced productivity on shelves not geographically suited for upwelling? To address this, we use micropaleontology, carbon isotopes, and sedimentology to present the first record of Oceanic Anoxic Event 2 (OAE2) from the northern Gulf of Mexico shelf. Here OAE2 occurred during the deposition of the well-oxygenated, inner neritic/lower estuarine Lower Tuscaloosa Sandstone. The overlying organic-rich oxygen-poor Marine Tuscaloosa Shale is entirely Turonian in age. We trace organic matter enrichment from the Spinks Core into the deepwater Gulf of Mexico, where wireline log calculations and public geochemical data indicate organic enrichment and anoxia throughout the Cenomanian-Turonian boundary interval. Redox change and organic matter preservation across the Gulf of Mexico shelf were driven by sea level rise prior to the early Turonian highstand, which caused the advection of nutrient-rich, oxygen-poor waters onto the shelf. This results in organic matter mass accumulation rates 1–2 orders of magnitude lower than upwelling sites like the NW African margin, but it likely occurred over a much larger geographic area, suggesting that sea level rise was an important component of the overall increase in carbon burial during OAE2.Plain Language Summary: The Cretaceous (145-66 million years ago, "Ma") was prone to periods with decreased dissolved oxygen ("anoxia") in large parts of the ocean. These oceanic anoxic events (OAEs) were caused by an increase in nutrients in the oceans, which caused plankton (floating unicellular algae) to increase in number ("increased productivity"); after death, rotting plankton used up all the oxygen in the water. These plankton blooms were not evenly distributed, and parts of the ocean, particularly continental shelves, were much more productive than others. We investigate one possible cause for this on shelf environments by studying fossils and sediments from a core and wells on the northern Gulf of Mexico shelf and deep water during the mid-Cretaceous OAE2, ~94 Ma. We show for the first time that the deepwater Gulf of Mexico was anoxic during OAE2 and that changes in oxygen and productivity on the shelf were driven by sea level rise. As sea level rose, the low-oxygen, nutrient-rich deep waters from the middle of the Gulf climbed onto the shelf, spurring a productivity increase. This is a weaker mechanism for driving productivity than the upwelling that characterizes some shelf sites during OAE2, but it is likely an important process on nonupwelling shelf sites.Lowery, C.M., Leckie, R.M., Bryant, R., Elderbak, K., Parker, A., Polyak, D.E., Schmidt, M., Snoeyenbos-West, O., Sterzinar, E., 2018. The Late Cretaceous Western Interior Seaway as a model for oxygenation change in epicontinental restricted basins. Earth-Science Reviews 177, 545-564. is a critical problem facing the ocean as the world warms, and has the potential to effect coastal upwelling zones, shelf areas influenced by high runoff and nutrification, and restricted and semi-restricted basins. The mechanisms that drive deoxygenation in these diverse environments are still not fully understood, in part because the modern record of redox change is short and anoxia is still relatively rare in the modern ocean. Here, we address this problem of scale by studying deoxygenation in the geologic past. We summarize decades of individual studies of benthic foraminifera to generate a record of bottom water oxygen change in the Cretaceous Western Interior Sea (WIS) of North America over ~ 13 myr (Cenomanian-Campanian), spanning two major sea level cycles. The WIS was prone to major changes in dissolved oxygen content throughout its long history, sometimes directly antiphase to trends in the global ocean.Presented as maps, our data show that bottom water oxygen within the WIS was controlled by a combination of water mass source and mixing moderated by sea level and basin restriction. Areas flooded by cool Boreal (northern-sourced) waters in the northern and western parts of the seaway were better oxygenated than the eastern and southern portions of the seaway, which were flooded by warmer Tethyan (southern-sourced) waters. Beyond east-west differences explained by water mass, the entire seaway was better oxygenated during periods of transgression, and more poorly oxygenated to anoxic during periods of peak transgression/highstand and regression. We suggest that this pattern was due to the formation and downwelling of Western Interior Intermediate Water by the mixing of Tethyan and Boreal waters. During transgressions, an increasing volume of these watermasses entered the seaway, mixed, and downwelled well?oxygenated surface water to the seafloor. During late transgression/highstand, partial stratification and the encroachment of low oxygen waters from the open ocean caused dissolved oxygen levels to drop at the seafloor, but continued downwelling prevented anoxia. During the subsequent regression, a decline in the volume of outside watermasses entering the seaway caused a reduction in mixing and weakened downwelling which led to stratification and seafloor anoxia.As a model for other semi-restricted basins, the trends observed in the WIS show that local changes in relative sea level, mixing, and circulation are critical in controlling oceanic deoxygenation in these environments, in clear contrast to continental margins impinged by oxygen minimum zones, like the contemporaneous Demerara Rise in the southern Caribbean. Although the WIS is larger than most semi-restricted basins, it is characterized by quasi-estuarine circulation driving the interaction of normal marine and brackish watermasses, and thus serves a model for similar shallow epicontinental basins of any size. Understanding how these processes vary in different environments is key to predicting susceptibility of regional water bodies to deoxygenation in the future with a warming world.Lyu, Z., Lu, Y., 2018. Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. The Isme Journal 12, 411-423. have long been considered strictly anaerobic and oxygen-sensitive microorganisms, but their ability to survive oxygen stress has also been documented. Indeed, methanogens have been found in oxidative environments, and antioxidant genes have been detected in their genomes. How methanogens adapt to oxidative environments, however, remain poorly understood. Here, we systematically predicted and annotated antioxidant features from representative genomes across six well-established methanogen orders. Based on functional gene content involved in production of reactive oxygen species, Hierarchical Clustering analyses grouped methanogens into two distinct clusters, corresponding to the Class I and II methanogens, respectively. Comparative genomics suggested a systematic shift in metabolisms across the two classes, resulting in an enrichment of antioxidant features in the Class II. Moreover, meta-analysis of 16?S rRNA gene sequences obtained from EnvDB indicated that members of Class II were more frequently recovered from microaerophilic and even oxic environments than the Class I members. Phylogenomic analysis suggested that the Class I and II methanogens might have evolved before and around the Great Oxygenation Event, respectively. The enrichment of antioxidant features in the Class II methanogens may have played a key role in the adaption of this group to oxidative environments today and historically.Ma, L., Hurtado, A., Eguilior, S., Llamas Borrajo, J.F., 2018. A model for predicting organic compounds concentration change in water associated with horizontal hydraulic fracturing. Science of The Total Environment 625, 1164-1174. drilling and hydraulic fracturing are technologies designed to increase natural gas flow and to improve productivity in low permeability formations. During this drilling operation, tons of flowback and produced water, which contain several organic compounds, return to the surface with a potential risk of influencing the surrounding environment and human health. In order to conduct predictive risk assessments a mathematical model is needed to evaluate organic compound behaviour along the water transportation process as well as concentration changes over time throughout the operational life cycle. A comprehensive model, which fits the experimental data, combining an Organic Matter Transport Dynamic Model with a Two-Compartment First-order Rate Constant (TFRC) Model has been established to quantify the organic compounds concentrations. This algorithm model incorporates two transportation rates, fast and slow. The results show that the higher the value of the organic carbon partition coefficient (koc) in chemicals, the later the maximum concentration in water will be reached. The maximum concentration percentage would reach up to 90% of the available concentration of each compound in shale formation (whose origin may be associated to drilling fluid, connate water and/or rock matrix) over a sufficiently long period of time. This model could serve as a contribution to enhance monitoring strategy, increase benefits out of optimizing health risk assessment for local residents and provide initial baseline data to further operations.Ma, W., Han, Y., Xu, C., Han, H., Ma, W., Zhu, H., Li, K., Wang, D., 2018. Enhanced degradation of phenolic compounds in coal gasification wastewater by a novel integration of micro-electrolysis with biological reactor (MEBR) under the micro-oxygen condition. Bioresource Technology 251, 303-310. aim of this work was to study an integration of micro-electrolysis with biological reactor (MEBR) for strengthening removal of phenolic compounds in coal gasification wastewater (CGW). The results indicated MEBR achieved high efficiencies in removal of COD and phenolic compounds as well as improvement of biodegradability of CGW under the micro-oxygen condition. The integrated MEBR process was more favorable to improvement of the structural stability of activated sludge and biodiversity of specific functional microbial communities. Especially, Shewanella and Pseudomonas were enriched to accelerate the extracellular electron transfer, finally facilitating the degradation of phenolic compounds. Moreover, MEBR process effectively relieved passivation of Fe-C filler surface and prolonged lifespan of Fe-C filler. Accordingly, the synergetic effect between iron-carbon micro-electrolysis (ICME) and biological action played a significant role in performance of the integrated process. Therefore, the integrated MEBR was a promising practical process for enhancing CGW treatment.Ma, Z., Leung, J.Y., Zanon, S., 2018. Integration of artificial intelligence and production data analysis for shale heterogeneity characterization in steam-assisted gravity-drainage reservoirs. Journal of Petroleum Science and Engineering 163, 139-155. Gravity Drainage (SAGD) recovery is strongly impacted by distributions of heterogeneous shale barriers, which impede the vertical growth and lateral spread of a steam chamber and potentially reduce oil production. Conventional reservoir heterogeneities characterization workflows that entail updating static reservoir models with dynamic flow data are quite time-consuming. Furthermore, certain assumptions are often needed to approximate the complex physical processes. This study proposes a workflow integrating artificial intelligence (AI) in a model selection framework that aims to identify associated shale heterogeneities in SAGD reservoir based on extracted features from production time-series data.A series of SAGD models based on typical Athabasca oil reservoir properties and operating conditions is constructed. After constructing the base homogeneous model, the shale barriers are assigned randomly by sampling their location, lateral extent, and thickness from several probability distributions, which are inferred from field data assembled from the public domain. Sensitivity analysis is carried out to identify and analyze features in the production response that are related to shale characteristics: whenever the steam chamber encounters a shale barrier, a drop in the production is observed; this drop continues until the steam chamber has advanced past the shale barrier, and the production would rise again. Several types of input feature extraction methods are introduced in this work: piecewise linear approximation (PLA), cubic spline interpolation (CSI), and discrete wavelet transform (DWT). Next, artificial neural network (ANN) is constructed to calibrate a relationship between the retrieved production pattern parameters (inputs) and the corresponding geologic parameters describing shale heterogeneities (outputs), which include some variables capturing the location, orientation or size of a particular shale barrier encountered by the steam chamber. The final model is implemented in a novel characterization workflow to infer shale heterogeneities from production profiles. A number of realistic applications are presented to illustrate its utility.The ANN models are validated using numerous synthetic models, where the exact shale distributions are known. The trained ANN models can reliably estimate the relevant shale parameters and the associated uncertainties, while accurately predicting the corresponding production responses. It is intended to extend the proposed method to construct the ANN models directly from well logs and production data.This work presents a preliminary attempt in correlating stochastic shale parameters with observable features in production time-series data using AI techniques. The proposed method facilitates the selection of an ensemble of reservoir models that are consistent with the production history; these models can be subjected to further history-matching for a precise final match. The proposed methodology does not intend to replace traditional simulation and history-matching workflows, but it rather offers a complementary tool for extracting additional information from field data and incorporating AI-based models into practical reservoir modeling workflows.Macchi, M., Martinez, M., Tauil, R.M.N., Valacco, M.P., Morelli, I.S., Coppotelli, B.M., 2018. Insights into the genome and proteome of Sphingomonas paucimobilis strain 20006FA involved in the regulation of polycyclic aromatic hydrocarbon degradation. World Journal of Microbiology and Biotechnology 34, Article 7. order to study the mechanisms regulating the phenanthrene degradation pathway and the intermediate-metabolite accumulation in strain S. paucimobilis 20006FA, we sequenced the genome and compared the genome-based predictions to experimental proteomic analyses. Physiological studies indicated that the degradation involved the salicylate and protocatechuate pathways, reaching 56.3% after 15 days. Furthermore, the strain degraded other polycyclic aromatic hydrocarbons (PAH) such as anthracene (13.1%), dibenzothiophene (76.3%), and fluoranthene. The intermediate metabolite 1-hydroxy-2-naphthoic acid (HNA) accumulated during phenanthrene catabolism and inhibited both bacterial growth and phenanthrene degradation, but exogenous-HNA addition did not affect further degradation. Genomic analysis predicted 126 putative genes encoding enzymes for all the steps of phenanthrene degradation, which loci could also participate in the metabolism of other PAH. Proteomic analysis identified enzymes involved in 19 of the 23 steps needed for the transformation of phenanthrene to trichloroacetic-acid intermediates that were upregulated in phenanthrene cultures relative to the levels in glucose cultures. Moreover, the protein-induction pattern was temporal, varying between 24 and 96?h during phenanthrene degradation, with most catabolic proteins being overexpressed at 96 h—e. g., the biphenyl dioxygenase and a multispecies (2Fe–2S)-binding protein. These results provided the first clues about regulation of expression of phenanthrene degradative enzymes in strain 20006FA and enabled an elucidation of the metabolic pathway utilized by the bacterium. To our knowledge the present work represents the first investigation of genomic, proteomic, and physiological studies of a PAH-degrading Sphingomonas strain.Maestrelli, D., Bonini, M., Delle Donne, D., Manga, M., Piccardi, L., Sani, F., 2017. Dynamic triggering of mud volcano eruptions during the 2016–2017 central Italy seismic sequence. Journal of Geophysical Research: Solid Earth 122, 9149-9165. 24 August 2016 a seismic event (Mw 6.0) was the first of the long Central Italy sequence (ongoing at the end of 2017) of medium-to-high magnitude earthquakes, with nine Mw ≥5 up to October 2017, and with about 74.000 seismic events registered after 1?year. The largest was the Mw 6.5 30 October 2016 event near Norcia. After the major seismic events, 17 mud volcanoes erupted around Monteleone di Fermo village (Marche region). Mud volcano eruptions generally occurred a few hours to a few days after the main earthquakes, suggesting a seismic triggering. We analyzed the peak ground velocities and dynamic stresses during the three largest earthquakes. We also evaluated the static stress changes in order to assess the potential influence of normal stress changes on the feeder system of the activated mud volcanoes. We find a correlation with dynamic stresses, whereas static stress changes are negligible or negative (with values reaching ?0.44?bar, clamping feeder dykes). We conclude that seismic shaking (up to ~3.9?bar during Norcia earthquake) is the dominant driver for these eruptions. Finally, we evaluated the response ratio as a function of the dynamic stress. It increases exponentially with peak dynamic stress varying from <10% for peak dynamic stress >0.3?bar to >50% for peak dynamic stress >2?bar, indicating a link between earthquake shaking and mud volcano activity.Magalh?es, V., 2017. Pockmarks and fluid seepage in the Estremadura Spur: implications for regional geology, biology, and petroleum systems. Impact 2017, 25-27. is a process-oriented multidisciplinary project focused on the pockmarks, fluid migration and seepage recently discovered in the Estremadura Spur continental shelf (Portugal), and on their implications to the regional geology, to the evolution of this section of the margin and to their petroleum system, and their significance to the ecosystems. A field with more than 40 individual pockmarks, covering an area of at least 27 km2, was recently discovered and partially surveyed (Kim and shipboard scientific party, 2011? PACEMAKER project funded by the European Research Council). This data set was made available for this project. This field of pockmarks is located at the outer shelf of the Estremadura Spur, between 200 and 350 m water depth, with individual pockmarks up to 120 m in diameter and 10 m depth (Fig. 1). A preliminary processing of the backscatter data indicate that some pockmarks have a high acoustic seafloor reflectivity in their central part, most probably indicating the presence of methane-derived authigenic carbonate hardgrounds. While fluid flow is a widespread process in continental margins and sedimentary basins, this is the first record of fluid escape processes were not previously identified on the W Iberian margin. Gas seepage evidence in the Iberia margin has only been reported in estuarine environments such as the Ria de Vigo (Iglesias and GarciaGil, 2007), the Aveiro Estuary/lagoon (Duarte et al., 2007), and in the Gulf of Cadiz (Magalh?es, 2007? Magalh?es et al., 2012? Pinheiro et al., 2003). This pockmark field and underlying fluid generation and escape processes, which are the focus of this project, are thus the first fluid seepage system identified and reported from the W Portuguese margin, not yet investigated. Fluid seeps are highly dynamic systems characterized by strong coupling processes between the geosphere, biosphere, hydrosphere and atmosphere. As such, PES proposes a comprehensive and transdisciplinary investigation of the Estremadura Spur fluid seepage manifestations with the following main objectives:(1) define the geographical distribution, types, geological setting and activity of the fluid seeps?(2) understand the structural and the stratigraphic control of fluid migration and seepage?(3) determine the composition of the emitted fluids and infer their source (microbial or thermogenic) possible depth of formation and processes occurring during their migration to the seafloor?(4) infer the timing and processes that control the fluid expulsion at the seafloor?(5) understand the controls and mechanisms of geochemical elements transport and breakdown of chemical compounds, diagenetically and by seep biota, to obtain a budget of elements cycling and export at the fluid seeps and better understand the coupling between geosphere and biosphere processes?(6) characterize eventual chemosynthetic benthic ecosystems and evaluate their significance in this intermediate depth and the impact on the non-seepage ecosystem?(7) infer the implications on the structure and petroleum geology of this margin (if the fluids expelled at seeps originated at depth, they may give important information on the underlying petroleum systems)?(8) evaluate the possible impacts of the fluid flow on the chemistry of the ocean and on the atmosphere, and help in assessing impacts of the input of greenhouse gases (e.g. methane) input of into the ocean/atmosphere?(9) assess the potential of these seepage system on the formation of potential gas hydrates (under present day and glacial conditions) and evaluate the regional dynamics of hydrates accumulation and destabilization.The PES research team has a large experience with regards to fluid seepage systems, embracing geology, geophysics, geochemistry, ecosystem characterization and habitat mapping, and includes also key members of the European PEACEMAKER project. The proposed research objectives will be achieved, in a first stage, through the processing of the existing geophysical data where 4 pockmarks will be selected for detailed investigation during one research cruise. Detailed geophysical surveys will be acquired with swath-bathymetry, backscatter, seismics, sidescan sonar and water column acoustics. This will guide the direct seafloor observation with an ROV, capable of seawater analysis and sampling. The geophysical data and ROV observations will allow the characterization of the seepage system, at the seafloor and in depth, at a detailed (at structure) scale. Systematic sampling of sediments, authigenic carbonates, porewater fluids and gas, and macrofauna will follow using gravity, box and multicorer. Sediments and authigenic carbonates will be characterized for their grain size, mineralogy, geochemistry, C and O isotopes, pore water inorganic and organic geochemistry and seepage gas composition, so that the seepage activity will be characterized, allowing to infer the significance of the system to the regional geology and ecology. Mahzari, P., Tsolis, P., Sohrabi, M., Enezi, S., Yousef, A.A., Eidan, A.A., 2018. Carbonated water injection under reservoir conditions; in-situ WAG-type EOR. Fuel 217, 285-296. injection water with CO2 has demonstrated promising results as a method for improving the oil recovery and securely storing CO2 in oil reservoirs. However, mutual interactions taking place between carbonated water and reservoir oil at elevated reservoir conditions are not fully understood. Herein, we present the results of a thorough and direct investigation of the interactions between live-oil/CO2/aqueous-phase leading to additional oil recovery and enhanced CO2 storage in pore-scale and core-scale.CO2 transfer from carbonated water to live oils can trigger liberation of light components in form of a new gaseous phase. This unique phenomenon would bring about higher degrees of oil swelling, and it can also create a three phase flow regime, which leads to effective reduction of residual oil saturation. The observations confirm that the performance of carbonated water injection (CWI) should be investigated under reservoir conditions using multi-components live oil and reservoir cores. From the core displacement tests, it was observed that secondary CWI could recover a significant amount of additional oil, which was 26% compared to conventional seawater injection. When CO2 content of injected CW (carbonated water) was halved, the oil recovery dropped by 1/3 Using live oils, it was found out that CO2 would be trapped in the new phase, which brings about an enhanced CO2 trapping mechanism. Under realistic reservoir conditions where complex mass transfer of CO2 from aqueous phase to oil and gas phases takes place, an “in-situ WAG-type” three-phase flow is generated with more effective sweep efficiency and pore-scale advantages.Maltby, J., Steinle, L., L?scher, C.R., Bange, H.W., Fischer, M.A., Schmidt, M., Treude, T., 2018. Microbial methanogenesis in the sulfate-reducing zone of sediments in the Eckernf?rde Bay, SW Baltic Sea Biogeosciences 15, 137-157. microbial methanogenesis is a known source of methane in marine systems. In most sediments, the majority of methanogenesis is located below the sulfate-reducing zone, as sulfate reducers outcompete methanogens for the major substrates hydrogen and acetate. The coexistence of methanogenesis and sulfate reduction has been shown before and is possible through the usage of noncompetitive substrates by methanogens such as methanol or methylated amines. However, knowledge about the magnitude, seasonality, and environmental controls of this noncompetitive methane production is sparse. In the present study, the presence of methanogenesis within the sulfate reduction zone (SRZ methanogenesis) was investigated in sediments (0–30?cm below seafloor, cm?b.s.f.) of the seasonally hypoxic Eckernf?rde Bay in the southwestern Baltic Sea. Water column parameters such as oxygen, temperature, and salinity together with porewater geochemistry and benthic methanogenesis rates were determined in the sampling area Boknis Eck quarterly from March 2013 to September 2014 to investigate the effect of seasonal environmental changes on the rate and distribution of SRZ methanogenesis, to estimate its potential contribution to benthic methane emissions, and to identify the potential methanogenic groups responsible for SRZ methanogenesis. The metabolic pathway of methanogenesis in the presence or absence of sulfate reducers, which after the addition of a noncompetitive substrate was studied in four experimental setups: (1) unaltered sediment batch incubations (net methanogenesis), (2) 14C-bicarbonate labeling experiments (hydrogenotrophic methanogenesis), (3) manipulated experiments with the addition of either molybdate (sulfate reducer inhibitor), 2-bromoethanesulfonate (methanogen inhibitor), or methanol (noncompetitive substrate, potential methanogenesis), and (4) the addition of 13C-labeled methanol (potential methylotrophic methanogenesis). After incubation with methanol, molecular analyses were conducted to identify key functional methanogenic groups during methylotrophic methanogenesis. To also compare the magnitudes of SRZ methanogenesis with methanogenesis below the sulfate reduction zone (>?30?cm?b.s.f.), hydrogenotrophic methanogenesis was determined by 14C-bicarbonate radiotracer incubation in samples collected in September 2013.Mani-Varnosfaderani, A., Kanginejad, A., Yamini, Y., 2018. Exploring the effects of sparsity constraint on the ranges of feasible solutions for resolution of GC-MS data. Chemometrics and Intelligent Laboratory Systems 173, 30-40. practical pattern recognition problems require non-negativity constraints. For example, pixels in digital images and chemical concentrations are non-negative. Sparse non-negative matrix factorizations (SNMFs) are useful when some degrees of sparseness exist in original data, intrinsically. The present contribution is about the implementation of sparsity constraint in multivariate curve resolution-alternating least square (MCR-ALS) technique for analysis of GC-MS/LC-MS data. The GC-MS and LC-MS data are sparse in mass dimension, and implementation of SNMF techniques would be useful for analyzing such two-way chromatographic data. In this work, L1-regularization paradigm has been implemented in each iteration of the MCR-ALS algorithm in order to force the algorithm to return more sparse mass spectra. L1-regularization has been applied by using the least absolute shrinkage and selection operator (Lasso) instead of the ordinary least square. A comprehensive comparison has been made between MCR-ALS and Lasso-MCR-ALS algorithms for resolution of the simulated and real GC-MS data. The comparison has been made by calculation of the values of sum of square errors (SSE) for 5000 times repetition of both algorithms using the random mass spectra and concentration profiles as initial estimates. The results revealed that regularization of L1-norm in mass dimension prevents occurrence of overfitting in ALS algorithm and this increases the probability of finding “true solution” after the resolution procedure. Moreover, the effect of this “sparsity constraint” has been explored on the area of feasible solutions in MCR methods. The results in this work revealed that implementation of this constraint reduces the extent of rotational ambiguity in MCR solutions and can be helpful for resolution of GC-MS data with high degrees of overlapping in mass spectra and concentration profiles.Mann, A., 2018. Bashing holes in the tale of Earth’s troubled youth. Nature 553, 393-395. analyses undermine a popular theory about an intense asteroid storm 4 billion years ago. Early in Earth’s history, roughly half a billion years after the planet formed, all hell broke loose in the inner Solar System. A barrage of asteroids — some the size of Hong Kong — pummelled the globe intensely enough to melt large parts of its surface. This incendiary spree around 4 billion years ago vaporized most of Earth’s water and perhaps even sterilized its exterior, killing off any life that might have started to emerge. Only after this storm of impacts passed did the planet become safe enough for hardy organisms to take firm root and eventually give rise to all later life.That horrific episode, known as the Late Heavy Bombardment (LHB), has been an integral part of Earth’s origin story for decades, ever since geologists did a systematic study of samples brought back from the Moon by NASA Apollo missions. But now, the once-popular theory has come under attack, and mounting evidence is causing many researchers to abandon it. A growing community of planetary scientists thinks that things quietened down relatively quickly, with a steadily decreasing rain of asteroids that ended a few hundred million years after Earth and the Moon formed.Settling the debate could have major ramifications for some of the biggest questions in geoscience: when did life emerge and what were conditions like on early Earth? But some researchers think that fresh samples will be needed to finally put this conundrum to rest. They are looking with hope at the United States’ recent pledge to send astronauts back to the Moon — although no timeline has yet been set. In the meantime, the community is grappling with the fact that a key chapter of Solar System history might be vanishing before their eyes.“The Late Heavy Bombardment was seen as one of the great triumphs of the Apollo era,” says geochemist Mark Harrison of the University of California, Los Angeles. “There’s no question that something has happened in the past few years that has profoundly upset the apple cart.”The Solar System formed some 4.6 billion years ago, after the centre of a massive cloud of gas and dust collapsed into a dense sphere that became our Sun. Pebbles in a dusty disk orbiting the star continuously collided and sometimes stuck together. After tens of millions of years, these agglomerations had built up into planetesimals — the beginnings of the planets. Other rocky fragments remained, crashing into their larger kin and leaving deep craters. Over time, the Solar System thinned out, leaving something like the configuration we see today.Most of the evidence of this violent history has been erased on Earth by the churning of tectonic plates. But the scarred surface of the Moon, long inert, retains a lengthy record of impacts. Some of that record — roughly 382 kilograms of lunar rock and soil — was collected by Apollo astronauts and carried back to scientists eager to see what the samples might reveal about the Moon’s history. In 1973, the year after the last Apollo landing, a group at Sheffield University, UK, reported a curious pattern in samples from four separate Apollo missions as well as a Soviet Luna mission. Radiometric dating of each one returned the same age: 3.95 billion years1. A team at the California Institute of Technology (Caltech) in Pasadena corroborated the findings the same year2.Curious chronologyThe confluence of ages suggested that a flurry of objects struck the Moon in a narrow 50-million-year window, leaving behind countless impact craters — including as many as a dozen of the Texas-sized basins that scar the surface. Because it seemed to represent a final surge of pandemonium after the Solar System’s chaotic genesis, the Caltech team named the event the terminal lunar cataclysm, although it later became more popularly known as the LHB.The idea was immediately divisive, in large part because of ambiguity in the rock dating. This was done primarily by measuring the rocks’ ratio of argon-40 atoms to radioactive potassium-40. 40K decays into 40Ar with a half-life of 1.25 billion years. At high temperatures, that 40Ar can leak out of minerals. That makes the ratio of these two isotopes a kind of clock: the more time that has elapsed since a rock was hot, the more 40Ar should be present. But making sense of the argon and potassium concentrations can be difficult because the same ratio could have been caused by a concentrated barrage that heated the rocks and released 40Ar some 3.95 billion years ago, or by a long, dwindling asteroid torrent that released it in fits and starts before fizzling out at about the same time.The first really new data arrived in 2000. Planetary scientist David Kring, cosmochemist Timothy Swindle and planetary scientist Barbara Cohen, all then at the University of Arizona in Tucson, collected lunar meteorites that had fallen to Earth after being blasted from the Moon’s surface by asteroid strikes. They hoped such rocks would provide a more random sample of the Moon’s crust than those from Apollo, which represent at most 4% of the lunar surface. But when the results came back, they showed a curious, and familiar, pattern.“Frankly, I thought we’d measure a bunch of these and have ages running back to 4.3 and 4.4 [billion years] and prove once and for all that this whole idea was wrong,” says Swindle. Instead, they found no evidence of impacts before the hypothesized time of the LHB3. “That kind of pushed me to a different side of the fence,” he says.But researchers still wondered how a bombardment could come so long after the Solar System formed. By the half-billion-year mark, most of the leftover debris should either have been cast out or have settled into stable zones such as the main asteroid belt, which sits between Mars and Jupiter, or the Kuiper belt beyond Neptune. Nobody could come up with a physical reason for the unexpected drama at such a late date. “Where did you have the bodies in the Solar System that could hang around for 600 million years and then come screaming in and hit the Moon?” asks Cohen, who is now at NASA’s Goddard Space Flight Center in Greenbelt, Maryland.A potential answer arrived in 2005, with the emergence of what came to be known as the Nice model, after the French city where it was conceived. Originally proposed to explain odd orbital behaviour by distant icy objects in the Kuiper belt, the conjecture asserted that the Solar System’s outer planets had formed much closer to one another than they are now. Computer simulations showed4 how the massive gravitational pull of Jupiter and Saturn could have created an instability that ultimately bumped Uranus and Neptune into more distant orbits, knocked comets out of remote reservoirs and kicked asteroids out of the main belt.The Nice model offered huge support for the LHB. “I think this helped cement this idea,” says physicist Nicolle Zellner of Albion College in Michigan. Geologist Marc Norman of the Australian National University in Canberra agrees. “That was the next real turning point,” he says.Cataclysmic confusionYet just when the idea of the LHB finally seemed unimpeachable, holes began to appear. Apollo data and ‘crater counting’, which estimates the order in which craters were laid down on the basis of how they overlap, had indicated that three of the largest crater basins on the Moon’s near side — Imbrium, Nectaris and Serenitatis — might all be about 3.95 billion years old (see ‘Sampling the Moon’). But high-resolution maps from NASA’s Lunar Reconnaissance Orbiter, which started circling the Moon in 2009, spotted rays of debris extending from Imbrium5. This suggested that the impact that formed the crater might have knocked rocks into nearby Serenitatis, contaminating the Apollo samples picked up there. In 2010, a reanalysis of rocks thought to have been ejected from Nectaris indicated that they were also chemically and geologically similar to Imbrium material6. “We started realizing that maybe we were sampling Imbrium over and over,” says Zellner.The data from lunar meteorites didn’t necessarily help. Although none of the samples seemed to be older than 4 billion years, some were billions of years younger than that3, with no obvious spike around 3.95 billion years. And the Apollo samples held other surprises. Since 2012, detailed study7 of microscopic regions in the rocks has turned up ages of as much as 4.2 billion years, much older than any seen before, suggesting that there had been significant impacts earlier than the proposed spike.Prodded in part by these revelations, some researchers proposed8 a longer-lasting LHB that began around 4.1 billion or 4.2 billion years ago. But that idea had one major strike against it: some of the most ancient crystals on Earth, from the Jack Hills range in Australia, suggest9 that the planet was a fairly clement place then, with relatively low temperatures and ample water.Hot topicOthers are still scrutinizing the original Apollo evidence. To determine the samples’ ages, researchers heated the rocks to release argon, slowly ramping up the temperature. But as far back as 1991, Harrison had pointed out that the process won’t work well for rocks containing multiple minerals. Different minerals will release their argon at different temperatures. A sample heated to 400?°C might provide an age of 2 billion years; to 500?°C, an age of 2.5 billion. Researchers have tried to extrapolate from this behaviour, but Harrison says the complex patterns often lead them to pick essentially arbitrary ages. “This is quackery,” he says. “There’s no physical basis for it.”Swindle says the argon heating situation is not necessarily as bad as Harrison makes it out to be; Apollo samples can be found whose ages don’t change significantly with temperature, and their dates — whether they refer to one or multiple impacts — still cluster around 3.95 billion years. Cohen says that other chronometers, such as those using radioactive isotopes of rubidium and uranium, corroborate the argon ages (although Harrison counters that the dates can differ by as much as 600 million years).Such back and forth underscores how difficult it can be to tease small clues out of extremely ancient rocks. “Sherlock Holmes was good at resolving mysteries that happened last year,” says David Nesvorn?, a planetary scientist at the Southwest Research Institute in Boulder, Colorado. “This all happened 4 billion years ago.”Meanwhile, the Nice model has proved less helpful to the idea of an LHB than it once seemed. More-advanced simulations of the early Solar System’s gravitational interactions indicate that the planetary reshuffling probably happened shortly after formation, not with a delay of hundreds of millions of years10. Nesvorn? likens delaying the reshuffling — and so keeping the Solar System hovering on the edge of instability — to trying to balance a pencil on its tip. “It’s really hard to put the pencil there in such a way that it falls in an hour,” he says.One of the original architects of the Nice model, astronomer Alessandro Morbidelli of the Cote d’Azur Observatory in Nice, admits that the first versions took fine-tuning to get the reshuffling to occur so late. He no longer believes in the LHB, and sees many others in the field trading in the idea of a sudden asteroid deluge for that of a long, declining tail of bombardment. “My prediction is people will abandon the cataclysm,” he says.Even those who remain tied to the LHB have had to modify their ideas. Planetary scientist William Bottke of the Southwest Research Institute agrees that there is no longer much support for a single, short spike. He says the best reading of the evidence, including samples from ancient Earth and radiometric dates in meteorite rocks, is a more drawn-out surge of bombardment that began around 4.1 billion or 4 billion years ago, with a relative lull before that, consistent with the existence of surface water in that period.Astronomer William Hartmann, a visiting scientist at the International Space Science Institute in Bern, thinks the current situation proves that the idea of a cataclysm was never particularly robust. Various research communities “kind of had the impression that the other community had really solved this”, he says. “A paradigm structure was built up from supporting evidence, none of which was actually conclusive in itself.”If an LHB did not happen, that could make it easier to explain how life emerged. Evidence of microbial life has been found in rocks that are around 3.5 billion years old. But those fossils seem quite complex, suggesting that they had been evolving from earlier forms for at least a few hundred million years, during the originally hypothesized time of the LHB. Without the cataclysm, such an ancient genesis might make more sense. Then again, some evidence suggests that the microbes at the base of the tree of life were hyperthermophiles — that is, organisms that thrived in extreme heat. The intense conditions created by a rain of asteroids could have resulted in a number of pockets where life might have emerged.So far, efforts to clinch the LHB debate with evidence from other likely victims — Mercury, Venus, Mars and objects from the asteroid belt — have proved inconclusive. Each camp accuses the other of cherry-picking favourable data and not looking at the total picture. “It’s a Rorschach test,” says Norman. “People see what they want to see and disregard the rest.”The only thing that researchers say will substantially move the needle is new samples from the Moon. Kring, now at the Lunar and Planetary Institute in Houston, Texas, has developed some concepts for sample-return missions, including one that would see astronauts collecting rocks from the South Pole–Aitken basin, the largest and oldest impact crater on the Moon. However, the next human mission to the Moon is still a long way off. The first new lunar rocks to be carried back to Earth may come from China’s Chang’e-5, a robotic mission currently planned for 2019. It aims to collect samples from the volcanic Mons Rümker formation, an area younger than those explored by Apollo astronauts.Although no single exploration effort is likely to end the dispute, researchers’ improved understanding of the Moon and how to determine the ages of samples should provide greater confidence in the results.However things eventually shake out, the new evidence will shift careers and rewrite textbooks. Yet, perhaps because of the long-lived nature of this debate, those trying to make sense of the LHB remain flexible, sceptical and surprisingly lighthearted.“We are close friends and therefore we disagree all the time and then go drink a beer together,” says Bottke. “One should carry models lightly and be prepared to drop them if something better comes along, because it happens all the time.” References1. Turner, G., Cadogan, P. H. & Yonge, C. J. Proc. Lunar Sci. Conf. 4, 1889–1914 (1973).2. Tera, F., Papanastassiou, D. A. & Wasserburg, G. J. Abstr. Lunar Planet. Sci. Conf. 4, 723–725 (1973).3. Cohen, B. A., Swindle, T. D. & Kring, D. A. Science 290, 1754–1756 (2000).4. Gomes, R., Levison, H. F., Tsiganis, K. & Morbidelli, A. Nature 435, 466–469 (2005).5. Spudis, P. et al. J. Geophys. Res. Planets 116, E00H03 (2011).6. Norman, M. D., Duncan, R. A. & Huard, J. J. Geochim. Cosmochim. Acta 74, 763–783 (2010).7. Norman, M. D. & Nemchin, A. A. Early Solar System Impact Bombardment II Conf., Lunar and Planetary Institute (Houston), Abstr. 4013 (2012); available at go.2mbdwvc8. Morbidelli, A., Marchi, S., Bottke, W. F. & Kring, D. A. Earth Planet. Sci. Lett. 355–356, 144–151 (2012).9. Watson, E. B. & Harrison, T. M. Science 308, 841–844 (2005).10. Deienno, R., Morbidelli, A., Gomes, R. S. & Nesvorn?, D. Astron. J. 153, 153 (2017).Mansor, M., Harouaka, K., Gonzales, M.S., Macalady, J.L., Fantle, M.S., 2017. Transport-induced spatial patterns of sulfur isotopes (δ34S) as biosignatures. Astrobiology 18, 59-72. minerals deposited in the presence of microbes may host geochemical biosignatures that can be utilized to detect subsurface life on Earth, Mars, or other habitable worlds. The sulfur isotopic composition of gypsum (CaSO4·2H2O) formed in the presence of sulfur-oxidizing microbes in the Frasassi cave system, Italy, was evaluated as a biosignature. Sulfur isotopic compositions (δ34SV-CDT) of gypsum sampled from cave rooms with sulfidic air varied from ?11 to ?24‰, with minor deposits of elemental sulfur having δ34S values between ?17 and ?19‰. Over centimeter-length scales, the δ34S values of gypsum varied by up to 8.5‰. Complementary laboratory experiments showed negligible fractionation during the oxidation of elemental sulfur to sulfate by Acidithiobacillus thiooxidans isolated from the caves. Additionally, gypsum precipitated in the presence and absence of microbes at acidic pH characteristic of the sulfidic cave walls has δ34S values that are on average 1‰ higher than sulfate. We therefore interpret the 8.5‰ variation in cave gypsum δ34S (toward more negative values) to reflect the isotopic effect of microbial sulfide oxidation directly to sulfate or via elemental sulfur intermediate. This range is similar to that expected by abiotic sulfide oxidation with oxygen, thus complicating the use of sulfur isotopes as a biosignature at centimeter-length scales. However, at the cave room (meter-length) scale, reactive transport modeling suggests that the overall ～13‰ variability in gypsum δ34S reflects isotopic distillation of circulating H2S gas due to microbial sulfide oxidation occurring along the cave wall-atmosphere interface. Systematic variations of gypsum δ34S along gas flow paths can thus be interpreted as biogenic given that slow, abiotic oxidation cannot produce the same spatial patterns over similar length scales. The expression and preservation potential of this biosignature is dependent on gas flow parameters and diagenetic processes that modify gypsum δ34S values over geological timescales.Mardanov, A.V., Gumerov, V.M., Beletsky, A.V., Ravin, N.V., 2018. Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka. Antonie van Leeuwenhoek 111, 35-43. communities of four acidic thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied using amplification and pyrosequencing of 16S rRNA gene fragments. The sites differed in temperature and pH: 1805 (60?°C, pH 3.7), 1810 (90?°C, pH 4.1), 1818 (80?°C, pH 3.5), and 1807 (86?°C, pH 5.6). Archaea of the order Sulfolobales were present among the dominant groups in all four pools. Acidilobales dominated in pool 1818 but were a minor fraction at the higher temperature in pool 1810. Uncultivated Archaea of the Hot Thaumarchaeota-related clade were present in significant quantities in pools 1805 and 1807, but they were not abundant in pools 1810 and 1818, where high temperatures were combined with low pH. Nanoarchaeota were present in all pools, but were more abundant in pools 1810 and 1818. A similar abundance pattern was observed for Halobacteriales. Thermophilic Bacteria were less diverse and were mostly represented by aerobic hydrogen- and sulfur-oxidizers of the phylum Aquificae and sulfur-oxidising Proteobacteria of the genus Acidithiobacillus. Thus we showed that extremely acidic hot pools contain diverse microbial communities comprising different metabolic groups of prokaryotes, including putative lithoautotrophs using energy sources of volcanic origin, and various facultative and obligate heterotrophs.Marozava, S., Mouttaki, H., Müller, H., Laban, N.A., Probst, A.J., Meckenstock, R.U., 2018. Anaerobic degradation of 1-methylnaphthalene by a member of the Thermoanaerobacteraceae contained in an iron-reducing enrichment culture. Biodegradation 29, 23-39. anaerobic culture (1MN) was enriched with 1-methylnaphthalene as sole source of carbon and electrons and Fe(OH)3 as electron acceptor. 1-Naphthoic acid was produced as a metabolite during growth with 1-methylnaphthalene while 2-naphthoic acid was detected with naphthalene and 2-methylnaphthalene. This indicates that the degradation pathway of 1-methylnaphthalene might differ from naphthalene and 2-methylnaphthalene degradation in sulfate reducers. Terminal restriction fragment length polymorphism and pyrosequencing revealed that the culture is mainly composed of two bacteria related to uncultured Gram-positive Thermoanaerobacteraceae and uncultured gram-negative Desulfobulbaceae. Stable isotope probing showed that a 13C-carbon label from 13C10-naphthalene as growth substrate was mostly incorporated by the Thermoanaerobacteraceae. The presence of putative genes involved in naphthalene degradation in the genome of this organism was confirmed via assembly-based metagenomics and supports that it is the naphthalene-degrading bacterium in the culture. Thermoanaerobacteraceae have previously been detected in oil sludge under thermophilic conditions, but have not been shown to degrade hydrocarbons so far. The second member of the community belongs to the Desulfobulbaceae and has high sequence similarity to uncultured bacteria from contaminated sites including recently proposed groundwater cable bacteria. We suggest that the gram-positive Thermoanaerobacteraceae degrade polycyclic aromatic hydrocarbons while the Desulfobacterales are mainly responsible for Fe(III) reduction.Marrone, D.P., Spilker, J.S., Hayward, C.C., Vieira, J.D., Aravena, M., Ashby, M.L.N., Bayliss, M.B., Béthermin, M., Brodwin, M., Bothwell, M.S., Carlstrom, J.E., Chapman, S.C., Chen, C.-C., Crawford, T.M., Cunningham, D.J.M., De Breuck, C., Fassnacht, C.D., Gonzalez, A.H., Greve, T.R., Hezaveh, Y.D., Lacaille, K., Litke, K.C., Lower, S., Ma, J., Malkan, M., Miller, T.B., Morningstar, W.R., Murphy, E.J., Narayanan, D., Phadke, K.A., Rotermund, K.M., Sreevani, J., Stalder, B., Stark, A.A., Strandet, M.L., Tang, M., Wei?, A., 2018. Galaxy growth in a massive halo in the first billion years of cosmic history. Nature 553, 51-54. to the current understanding of cosmic structure formation, the precursors of the most massive structures in the Universe began to form shortly after the Big Bang, in regions corresponding to the largest fluctuations in the cosmic density field. Observing these structures during their period of active growth and assembly—the first few hundred million years of the Universe—is challenging because it requires surveys that are sensitive enough to detect the distant galaxies that act as signposts for these structures and wide enough to capture the rarest objects. As a result, very few such objects have been detected so far. Here we report observations of a far-infrared-luminous object at redshift 6.900 (less than 800 million years after the Big Bang) that was discovered in a wide-field survey. High-resolution imaging shows it to be a pair of extremely massive star-forming galaxies. The larger is forming stars at a rate of 2,900 solar masses per year, contains 270 billion solar masses of gas and 2.5 billion solar masses of dust, and is more massive than any other known object at a redshift of more than 6. Its rapid star formation is probably triggered by its companion galaxy at a projected separation of 8 kiloparsecs. This merging companion hosts 35 billion solar masses of stars and has a star-formation rate of 540 solar masses per year, but has an order of magnitude less gas and dust than its neighbour and physical conditions akin to those observed in lower-metallicity galaxies in the nearby Universe. These objects suggest the presence of a dark-matter halo with a mass of more than 100 billion solar masses, making it among the rarest dark-matter haloes that should exist in the Universe at this epoch.Massei, R., Byers, H., Beckers, L.-M., Prothmann, J., Brack, W., Schulze, T., Krauss, M., 2018. A sediment extraction and cleanup method for wide-scope multitarget screening by liquid chromatography–high-resolution mass spectrometry. Analytical and Bioanalytical Chemistry 410, 177-188. studies on organic sediment contaminants focused mainly on a limited number of highly hydrophobic micropollutants accessible to gas chromatography using nonpolar, aprotic extraction solvents. The development of liquid chromatography–high-resolution mass spectrometry (LC–HRMS) permits the spectrum of analysis to be expanded to a wider range of more polar and ionic compounds present in sediments and allows target, suspect, and nontarget screening to be conducted with high sensitivity and selectivity. In this study, we propose a comprehensive multitarget extraction and sample preparation method for characterization of sediment pollution covering a broad range of physicochemical properties that is suitable for LC–HRMS screening analysis. We optimized pressurized liquid extraction, cleanup, and sample dilution for a target list of 310 compounds. Finally, the method was tested on sediment samples from a small river and its tributaries. The results show that the combination of 100 °C for ethyl acetate–acetone (50:50, neutral extract) followed by 80 °C for acetone–formic acid (100:1, acidic extract) and methanol–10 mM sodium tetraborate in water (90:10, basic extract) offered the best extraction recoveries for 287 of 310 compounds. At a spiking level of 1 μg mL-1, we obtained satisfactory cleanup recoveries for the neutral extract—(93 ± 23)%—and for the combined acidic/basic extracts—(42 ± 16)%—after solvent exchange. Among the 69 compounds detected in environmental samples, we successfully quantified several pharmaceuticals and polar pesticides.Maya, F., Palomino Cabello, C., Ghani, M., Turnes Palomino, G., Cerdà, V., 2018. Emerging materials for sample preparation. Journal of Separation Science 41, 262-287. review provides an update on the implementation of emerging materials as sorbents for sample preparation in combination with chromatographic separation. We have focused on recent applications of metal–organic frameworks, layered double hydroxides, porous carbons obtained from polymers or biomass precursors, and silicates (clays and zeolites). The review is directed toward the strategies followed by the authors to engineer suitable supports enabling the application of materials with unconventional size and shape as high-performance sorbents to explore new boundaries in sample pretreatment in manual or automated modes.Mbah, G.C., Obahiagbon, K.O., 2018. Kinetics of bioremediation of crude oil contaminated soil using organic and inorganic particulates. Petroleum Science and Technology 36, 9-15. potential of organic and inorganic agents for remediating crude oil contaminated soils was investigated in this study. Kinetic models were also developed to predict the bioremediation rates for these agents. The bioremediating agents (organic and inorganic particulates) used in this study were CB-1, PS-1, AL-1, CA-1, SD-1 and OC-1. The percentage (%) degradation of the bioremediating agents calculated from the total hydrocarbon content (THC) obtained over eight weeks were 78.17%, 80.97%, 95.98%, 96.58%, 97.19% and 95.51% for CB-1, PS-1, AL-1, CA-1, SD-1 and OC-1 respectively. The presence of crude oil degrading micro-organisms in these bioremediating agents (particulates) were found to have contributed to the degradation rates obtained. The particulates which are good bulking agents also served as conducive hosts for these micro-organisms. The bioremediation reactions were mostly of the first order and the rate constants (k) obtained were 0.029 day?1, 0.031 day?1, 0.059 day?1, 0.063 day?1, 0.067 day?1 and 0.057 day?1 for CB-1, PS-1, AL-1, CA-1, SD-1 and OC-1 respectively. It was however deduced that plant organics (AL-1, CA-1 and SD-1) were better bioremediating agents compared to animal organics (CB-1 and PS-1) and competed favorably with the synthetic bioremediating agent. (OC-1).McAdams, B.C., Aiken, G.R., McKnight, D.M., Arnold, W.A., Chin, Y.-P., 2018. High pressure size exclusion chromatography (HPSEC) determination of dissolved organic matter molecular weight revisited: Accounting for changes in stationary phases, analytical standards, and isolation methods. Environmental Science & Technology 52, 722-730. reassessed the molecular weight of dissolved organic matter (DOM) determined by high pressure size exclusion chromatography (HPSEC) using measurements made with different columns and various generations of polystyrenesulfonate (PSS) molecular weight standards. Molecular weight measurements made with a newer generation HPSEC column and PSS standards from more recent lots are roughly 200 to 400 Da lower than initial measurements made in the early 1990s. These updated numbers match DOM molecular weights measured by colligative methods and fall within a range of values calculated from hydroxyl radical kinetics. These changes suggest improved accuracy of HPSEC molecular weight measurements that we attribute to improved accuracy of PSS standards and changes in the column packing. We also isolated DOM from wetlands in the Prairie Pothole Region (PPR) using XAD-8, a cation exchange resin, and PPL, a styrene-divinylbenzene media, and observed little difference in molecular weight and specific UV absorbance at 280 nm (SUVA280) between the two solid phase extraction resins, suggesting they capture similar DOM moieties. PPR DOM also showed lower SUVA280 at similar weights compared to DOM isolates from a global range of environments, which we attribute to oxidized sulfur in PPR DOM that would increase molecular weight without affecting SUVA280.McCloskey, T.A., Smith, C.G., Liu, K.-b., Marot, M., Haller, C., 2018. How could a freshwater swamp produce a chemical signature characteristic of a saltmarsh? ACS Earth and Space Chemistry 2, 9–20.–oxidation (redox) reaction conditions, which are of great importance for the soil chemistry of coastal marshes, can be temporally dynamic. We present a transect of cores from northwest Florida wherein radical postdepositional changes in the redox regime has created atypical geochemical profiles at the bottom of the sedimentary column. The stratigraphy is consistent along the transect, consisting of, from the bottom upward, carbonate bedrock, a gray clay, an organic mud section, a dense clay layer, and an upper organic mud unit representing the current saltwater marsh. However, the geochemical signature of the lower organic mud unit suggests pervasive redox reactions, although the interval has been identified as representing a freshwater marsh, an unlikely environment for such conditions. Analyses indicate that this discrepancy results from postdepositional diagenesis driven by millennial-scale environmental parameters. Rising sea level that led to the deposition of the capping clay layer, created anaerobic conditions in the freshwater swamp interval, and isolated it hydrologically from the rest of the sediment column. The subsequent infiltration of marine water into this organic material led to sulfate reduction, the buildup of H2S and FeS, and anoxic conditions. Continued sulfidation eventually resulted in euxinic conditions, as evidenced by elevated levels of Fe, S, and especially Mo, the diagnostic marker of euxinia. Because this chemical transformation occurred long after the original deposition the geochemical signature does not reflect soil chemistry at the time of deposition and cannot be used to infer syn-depositional environmental conditions, emphasizing the importance of recognizing diagenetic processes in paleoenvironmental studies.McConnan Borstad, C., Garvie-Lok, S., Katsonopoulou, D., 2018. Diet at ancient Helike, Achaea, Greece based on stable isotope analysis: From the Hellenistic to the Roman and Byzantine periods. Journal of Archaeological Science: Reports 18, 1-10. and subsidence are common occurrences in the Helike Delta and caused serious destruction in the ancient city of Helike in 373 BCE. Archaeological excavations have uncovered artifacts and inhumation burials in the area, which indicate that resettlement began in the Late Classical/Hellenistic period (late 4th to 2nd centuries BC) and was continuous through to the late Byzantine period (14th to 15th centuries AD). This temporal continuity provides the opportunity to explore dietary resource use in this region of Greece. In addition, it allows for the comparison of dietary resource use between the Byzantine and earlier periods. Meat was prohibited on the numerous Orthodox Christian fasting days but fish and shellfish were acceptable substitutes. If religious practices influenced dietary customs, this may be visible in the stable isotope ratios of Christian era human skeletal remains from Helike.Bone collagen from twenty-four individuals from the Hellenistic, Roman, and Byzantine periods at Helike was analyzed for its stable carbon and nitrogen isotope values. The results suggest that the Hellenistic individuals consumed more marine dietary resources than the later Byzantine individuals, as indicated by higher stable carbon isotope values. The Roman period individuals show values indicative of primarily terrestrial resource use with fewer marine additions. Given the geological history of Helike, the Hellenistic individuals may be distinctive because of access to a temporary lagoon that formed after the earthquake of 373 BCE. This lagoon may have offered a broader spectrum of aquatic resources to Helike's inhabitants, causing dietary differences between the Hellenistic and later periods.Despite the constant availability of terrestrial and marine resources at Helike, lagoon resources appear to have contributed to the diet only at certain times. This study demonstrates the importance of taking into account seismic activity and changing landscapes when reconstructing past diet over a large time span. What may be assumed to be cultural dietary differences may in fact be the result of environmental differences.McGregor, H., 2018. Regional climate goes global. Nature Geoscience 11, 18-19. compilation of hundreds of palaeoclimate records highlighted the extent of regional variability during the past 2,000 years, and therein the uniqueness of recent warming.When it comes to climate change it is most often the global picture that captures the headlines: 2017 shaping up to be one of the warmest years on record; average global temperature rise of almost 1°C since 1880 CE (ref. 1); atmospheric CO2 has reached 403 ppm (ref. 2). But arguably it is how the global changes manifest at the local and regional scale that matters. Different temperatures, synoptic patterns and extremes that occur on the decadal-to-seasonal scale will most affect our day-to-day lives. In this context, the paper from the PAGES 2k Consortium3 published in Nature Geoscience in 2013 represents an important advance in understanding how both regional and global climate has varied over the past 2000 years.Reconstructing regional (and global) climate back in time is a huge undertaking, which relies on climate proxies as diverse as tree rings, ice cores, speleothems and corals, as well as historical records. These proxy records are not evenly distributed, and not all span the full 2,000-year period. In around 2009 the Past Global Changes 2k (PAGES2k) Network formed to draw on the expertise of hundreds of palaeoclimate scientists with in-depth knowledge of the strengths and limitations of the various proxy records. From a total of 511 individual records, seven regional temperature syntheses were published — one for each continent except Africa and one for the Arctic region — and these efforts were assembled in the 2013 paper (Fig. 1). The PAGES 2k Consortium found that the six continents studied, the Arctic region and the majority of individual records cooled over the millennia prior to 1900 CE. However, the rate of cooling varied across the regions and there was considerable variability at the multi-decadal scale. In all regions except Antarctica the cooling trend was reversed by warming over the past from the mid-nineteenth century.These regional differences gave some clues to the drivers of the multi-decadal climate change. Changes in solar irradiance (for example, sunspot cycles); aerosols from volcanic eruptions; land-cover changes; changes in the Earth’s orbit around the sun; and CO2 levels are all known to force climate to change. These factors were all shown to be involved in the global trends. At the regional scale, however, qualitative comparison with climate models suggested that different forcing factors dominate in different places and at different times. For example, the long-term Northern Hemisphere cooling was apparently linked to orbital changes in summer incoming solar radiation4,5, whereas oceans show a more straightforward thermodynamic response to large and frequent volcanic eruptions6,7. Other cooling events were linked to volcanic and or solar forcing3. The regional complexity is perhaps unsurprising given the mixture of climate subsystems and different response rates8, and the role of internal climate oscillations that operate on interannual-to-decadal timescales.Placing present-day temperatures in the context of the past two millennia brought into sharp focus the reversal in temperature trend since the mid-nineteenth century; this reversal corresponds with a rise in atmospheric CO2 concentrations from the burning of fossil fuels. The implications of this work proved controversial: the message that human actions are transforming the planet’s climate is jarring because it says that the energy systems that underpin advancement of present-day society will have unintended consequences for future generations. Studies with such far-reaching implications9,10 should and do attract scrutiny — the paper from the PAGES 2k Consortium is no exception. Methodological improvements were carried out on the Australasia 2k reconstruction11. Errors were found in the Arctic dataset and a Corrigendum12 was published in 2015. The upshot was that the 1971–2000 CE interval in the Arctic was the third rather than second warmest period of the past 2,000 years.The scrutiny and corrections have led to a more robust dataset and more confidence in the paper’s conclusion that the area-weighted global average temperature for 1971–2000 CE is the warmest for 1,400 years. Given the continued march of record warm temperatures we will soon find ourselves outside the temperature envelope of the past 2,000 years at the regional scale too — there are suggestions that the tropical oceans, Arctic, Australasia, Europe and Asia have already exceeded the range of variability back to 1500 CE (ref. 13).Undoubtedly the greatest legacy from the PAGES 2k Consortium paper is that it produced one of the most comprehensive and well-vetted palaeoclimate temperature datasets ever amassed. The original dataset was combined with data compilations from the PAGES Ocean2k working group7,14 and records published after 2013, in a community-wide effort to produce a temperature database that contains an astonishing 692 records, all catalogued into a standard machine-readable database structure15. The open-access database is a tremendous step forward in facilitating wider use of the palaeoclimate data for understanding the role of natural forcing of climate — and the more recent anthropogenic CO2 overprint. Regional climate variability encompasses more than just temperature; variability in hydroclimate, including rainfall, seasonal and multi-year drought, storminess, air pressure and winds are all important for economic and societal wellbeing. Efforts are underway to reconstruct these parameters, for instance refs 16,17,18,19,20.The PAGES 2k Network (<;) has expanded to around 1,000 scientists at last count, and has three main focuses: understanding the mechanisms driving regional climate variability; using palaeoclimate data of the past 2,000 years to improve models of climate dynamics, in complement to the Last Millennium Reanalysis project (<;); and the oft overlooked but fundamentally important need to reduce uncertainties in the palaeoclimate records themselves.Our reconstructions are only as good as the data on which they are built. The work by the PAGES 2k Consortium showed that existing data can be harnessed to provide unprecedented insights in regional differences in climate, and their drivers. Such insights are vital to prepare us for what lies ahead.References1. IPCC Climate Change 2013: The Physical Science Basis (eds Stocker, T. F. et al.) (Cambridge University Press, Cambridge, 2013).2. The State of Greenhouse Gases in the Atmosphere Using Global Observations through 2016 (World Meteorological Organization, 2017).3. PAGES 2k Consortium. Nat. Geosci. 6, 339–346 (2013).4. Kaufman, D. S. et al. Science 325, 1236–1239 (2009).5. Esper, J. et al. Nat. Clim. Change 2, 862 (2012).6. Crowley, T. J. Science 289, 270–277 (2000).7. McGregor, H. V. et al. Nat. Geosci. 8, 671–677 (2015).8. Neukom, R. et al. Nat. Clim. Change 4, 362 (2014).9. Mann, M. E., Bradley, R. S. & Hughes, M. K. Nature 392, 779–787 (1998).10. Mann, M. E., Bradley, R. S. & Hughes, M. K. Geophys. Res. Lett. 26, 759–762 (1999).11. Gergis, J., Neukom, R., Gallant, A. J. E. & Karoly, D. J. J. Clim. 29, 5365–5392 (2016).12. Nat. Geosci. 8, 981 (2015).13. Abram, N. J. et al. Nature 536, 411–418 (2016).14. Tierney, J. E. et al. Paleoceanography 30, 226–252 (2015).15. PAGES2k Consortium. Sci. Data 4, 170088 (2017).16. Goodwin, I. D., Browning, S. A. & Anderson, A. J. Proc. Natl Acad. Sci. USA 111, 14716–14721 (2014).17. Chen, J. et al. Quaternary Sci. Rev. 107, 98–111 (2015).18. Vance, T. R., Roberts, J. L., Plummer, C. T., Kiem, A. S. & van?Ommen, T. D. Geophys. Res. Lett. 42, 129–137 (2015).19. Ljungqvist, F. C., Krusic, P. J., Sundqvist, H. S., Zorita, E., Brattstr?m, G. & Frank, D. Nature 532, 94 (2016).20. Smerdon, J. E. et al. (2017).McGuire, B.A., Burkhardt, A.M., Kalenskii, S., Shingledecker, C.N., Remijan, A.J., Herbst, E., McCarthy, M.C., 2018. Detection of the aromatic molecule benzonitrile (c-C6H5CN) in the interstellar medium. Science 359, 202-205.: Polycyclic aromatic hydrocarbons and polycyclic aromatic nitrogen heterocycles are thought to be widespread throughout the universe, because these classes of molecules are probably responsible for the unidentified infrared bands, a set of emission features seen in numerous Galactic and extragalactic sources. Despite their expected ubiquity, astronomical identification of specific aromatic molecules has proven elusive. We present the discovery of benzonitrile (c-C6H5CN), one of the simplest nitrogen-bearing aromatic molecules, in the interstellar medium. We observed hyperfine-resolved transitions of benzonitrile in emission from the molecular cloud TMC-1. Simple aromatic molecules such as benzonitrile may be precursors for polycyclic aromatic hydrocarbon formation, providing a chemical link to the carriers of the unidentified infrared bands.Editor's summary: A specific interstellar aromatic molecule. Aromatic molecules such as polycyclic aromatic hydrocarbons (PAHs) are known to exist in the interstellar medium owing to their characteristic infrared emission features. However, the infrared emission only indicates the general class of molecule, and identifying which specific molecular species are present is difficult. McGuire et al. used radio astronomy to detect rotational transitions of benzonitrile emitted from a well-known nearby cloud of interstellar gas (see the Perspective by Joblin and Cernicharo). This molecule may be a precursor to more complex PAHs. The identification of benzonitrile sheds light on the composition of aromatic material within the interstellar medium—material that will eventually be incorporated into new stars and planets.Medeiros, J.M., B?ck, D., Pilhofer, M., 2018. Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography. Current Opinion in Microbiology 43, 62-68.–host interactions are important for diverse ecological settings including pathogenicity and symbiosis. Electron cryotomography is a powerful method for studying the macromolecular complexes that mediate such interactions in situ. The main limitation of electron cryotomography is its restriction to relatively thin samples such as individual bacterial cells. Cryo-focused ion beam milling was recently proposed as a solution to the thickness limitation. This approach allows the artifact-free thinning of biological specimens for subsequent imaging in the transmission electron microscope. By enabling near-native imaging of bacteria inside their eukaryotic host, this combination of techniques promotes the integration of data from structural biology and infection biology. Therefore, electron cryotomography associated with cryo-focused ion beam milling holds great potential for establishing multiscale models of cell–cell interactions from the atomic, to the cellular and to the intercellular scale.Meier, T., 2018. At its extremes: NMR at giga-pascal pressures, in: Webb, G.A. (Ed.), Annual Reports on NMR Spectroscopy. Academic Press, pp. 1-74. Implementation of nuclear magnetic resonance in high pressure vessels is among the most demanding technological endeavours of the field, owing to inherently low signal amplitudes, low sensitivities of the resonator set-ups, and samples which are both difficult to handle and to access in the finished experimental set-up. The following chapter presents a review of the basic principles of generating pressures in excess of 1GPa (= 10.000atm), followed by a summary of suitable NMR resonators. Additionally, recent high pressure experiments on correlated and uncorrelated electronic system at pressures as high as 30GPa will be covered.Meng, F., Dai, M., Cao, Z., Wu, K., Zhao, X., Li, X., Chen, J., Gan, J., 2017. Seasonal dynamics of dissolved organic carbon under complex circulation schemes on a large continental shelf: The northern South China Sea. Journal of Geophysical Research: Oceans 122, 9415-9428. examined the distribution and seasonality of dissolved organic carbon (DOC) based on a large data set collected from the northern South China Sea (NSCS) shelf under complex circulation schemes influenced by river plume, coastal upwelling, and downwelling. The highest surface values of ～117 μmol L?1 were observed nearshore in summer suggesting high DOC supplies from the river inputs, whereas the lowest surface values of ～62 μmol L?1 were on the outer shelf in winter due to entrainment of DOC-poor subsurface water under strengthened vertical mixing. While the summer coastal upwelling brought lower DOC from offshore depth to the nearshore surface, the winter coastal downwelling delivered higher surface DOC to the midshelf deep waters from the inner shelf fueled by the China Coastal Current (CCC) transporting relatively high DOC from the East China Sea to the NSCS. The intensified winter downwelling generated a cross-shelf DOC transport of 3.1 × 1012 g C over a large shelf area, which induced a significant depression of the NSCS DOC inventory in winter relative to in autumn. In addition to the variable physical controls, net biological production of DOC was semiquantified in both the river plume (2.8?±?3.0 μmol L?1) and coastal upwelling (3.1?±?1.3 μmol L?1) in summer. We demonstrated that the NSCS shelf had various origins of DOC including riverine inputs, inter-shelf transport and in situ production. Via cross-shelf transport, the accumulated DOC would be exported to and stored in the deep ocean, suggesting that continental shelves are a potentially effective carbon sink.Meng, Q., Su, Y., Jin, Z., Zhu, D., Liu, Q., Xu, B., 2017. External hydrogen index: A new factor for hydrocarbon resource assessment and its calculation method. Acta Geologica Sinica - English Edition 91, 2336-2337. abstractMiao, Y., Li, X., Lee, J., Zhou, Y., Wu, K., Sun, Z., Liu, S., 2018. A new rate-decline analysis of shale gas reservoirs: Coupling the self-diffusion and surface diffusion characteristics. Journal of Petroleum Science and Engineering 163, 166-176. production in shale reservoirs accurately has been of growing interest in the industry in recent years. Until now, various techniques to interpolate production have been developed. Among them, decline curve analysis models have been widely recognized as the most efficient and easiest approach to apply. Unfortunately, each decline curve model has its own limitations and will not allow us to forecast production in shale gas reservoirs with confidence. In this paper, based on the similar characteristics between shale gas production and self-diffusion of dense gas/surface diffusion of adsorbed gas, a new early-late decline model with two fitting parameters were developed by employing general equations of this two behaviors respectively. These flow characteristics cannot be addressed by traditional decline curve models. In addition, a detailed forecasting procedure applying this novel decline model in the whole life of shale gas production was proposed, which is reliable and easy to utilize. Furthermore, this proposed model was validated by numerically simulated cases and field observations. Good matches between forecast rates calculated using this novel method and numerically simulated rates/field rates were obtained. The comparison between this proposed method and traditional methods were further conducted, which indicated that this novel approach leads to more confident forecasts than commonly utilized approaches. This work will provide a theoretical basis for analysts in evaluating hydrocarbon production rapidly and efficiently in shale gas reservoirs.Michalski, J.R., Onstott, T.C., Mojzsis, S.J., Mustard, J., Chan, Q.H.S., Niles, P.B., Johnson, S.S., 2018. The Martian subsurface as a potential window into the origin of life. Nature Geoscience 11, 21-26. traces of Earth’s geologic record are preserved from the time of life’s emergence, over 3,800 million years ago. Consequently, what little we understand about abiogenesis — the origin of life on Earth — is based primarily on laboratory experiments and theory. The best geological lens for understanding early Earth might actually come from Mars, a planet with a crust that’s overall far more ancient than our own. On Earth, surface sedimentary environments are thought to best preserve evidence of ancient life, but this is mostly because our planet has been dominated by high photosynthetic biomass production at the surface for the last ~2,500 million years or more. By the time oxygenic photosynthesis evolved on Earth, Mars had been a hyperarid, frozen desert with a surface bombarded by high-energy solar and cosmic radiation for more than a billion years, and as a result, photosynthetic surface life may never have occurred on Mars. Therefore, one must question whether searching for evidence of life in Martian surface sediments is the best strategy. This Perspective explores the possibility that the abundant hydrothermal environments on Mars might provide more valuable insights into life’s origins.Middelburg, J.J., 2018. Reviews and syntheses: to the bottom of carbon processing at the seafloor. Biogeosciences 15, 413-427. carbon processing at the seafloor is studied by biogeochemists to quantify burial and respiration, by organic geochemists to elucidate compositional changes and by ecologists to follow carbon transfers within food webs. Here I review these disciplinary approaches and discuss where they agree and disagree. It will be shown that the biogeochemical approach (ignoring the identity of organisms) and the ecological approach (focussing on growth and biomass of organisms) are consistent on longer timescales. Secondary production by microbes and animals is identified to potentially impact the composition of sedimentary organic matter. Animals impact sediment organic carbon processing by microbes in multiple ways: by governing organic carbon supply to sediments, by aeration via bio-irrigation and by mixing labile organic matter to deeper layers. I will present an inverted microbial loop in which microbes profit from bioturbation rather than animals profiting from microbial processing of otherwise lost dissolved organic resources. Sediments devoid of fauna therefore function differently and are less efficient in processing organic matter with the consequence that more organic matter is buried and transferred from Vernadsky's biosphere to the geosphere.Middleton, R.S., Yaw, S., 2018. The cost of getting CCS wrong: Uncertainty, infrastructure design, and stranded CO2. International Journal of Greenhouse Gas Control 70, 1-11. capture, and storage (CCS) infrastructure will require industry—such as fossil-fuel power, ethanol production, and oil and gas extraction—to make massive investment in infrastructure. The cost of getting these investments wrong will be substantial and will impact the success of CCS technology. Multiple factors can and will impact the success of commercial-scale CCS, including significant uncertainties regarding capture, transport, and injection-storage decisions. Uncertainties throughout the CCS supply chain include policy, technology, engineering performance, economics, and market forces. In particular, large uncertainties exist for the injection and storage of CO2. Even taking into account upfront investment in site characterization, the final performance of the storage phase is largely unknown until commercial-scale injection has started. We explore and quantify the impact of getting CCS infrastructure decisions wrong based on uncertain injection rates and uncertain CO2 storage capacities using a case study managing CO2 emissions from the Canadian oil sands industry in Alberta. We use SimCCS, a widely used CCS infrastructure design framework, to develop multiple CCS infrastructure scenarios. Each scenario consists of a CCS infrastructure network that connects CO2 sources (oil sands extraction and processing) with CO2 storage reservoirs (acid gas storage reservoirs) using a dedicated CO2 pipeline network. Each scenario is analyzed under a range of uncertain storage estimates and infrastructure performance is assessed and quantified in terms of cost to build additional infrastructure to store all CO2. We also include the role of stranded CO2, CO2 that a source was expecting to but cannot capture due substandard performance in the transport and storage infrastructure. Results show that the cost of getting the original infrastructure design wrong are significant and that comprehensive planning will be required to ensure that CCS becomes a successful climate mitigation technology. In particular, we show that the concept of stranded CO2 can transform a seemingly high-performing infrastructure design into the worst case scenario.Minagawa, H., Ito, T., Kimura, S., Kaneko, H., Noda, S., Tenma, N., 2018. Depressurization and electrical heating of methane hydrate sediment for gas production: Laboratory-scale experiments. Journal of Natural Gas Science and Engineering 50, 147-156. in situ dissociation of methane hydrate is necessary for the commercial recovery of methane gas from sediments. Thermal stimulation and depressurization are both effective dissociation methods. To simulate methane gas production from a methane hydrate (MH) layer, we used laboratory experiments to investigate the use of depressurization with electrical heating on MH sediment. To clarify the effect of temperature around the production well of the MH layer, depressurization experiments were examined at three initial temperatures: 0 °C, 3 °C, and 10 °C. A MH sediment core saturated with NaCl electrolyte solution (3.5 wt.%) was used. After depressurization, the core temperature decreased to between 10 °C and 3 °C below the initial temperature because of the endothermic MH dissociation reaction. When electrical heating was applied during depressurization at the initial temperatures of 3 °C and 10 °C, this decrease in core temperature was suppressed, and the core temperature increased to between 1 °C and 9 °C above the initial temperature. Electrical heating at a current density of 10 A/m2, which corresponds to an electrical power of 1.6–0.8 W/kg, during depressurization was found to dissociate the hydrate effectively. Overall, the findings indicate that depressurization combined with the electrical heating of hydrated sediment saturated with electrolyte solution enables higher gas production compared to depressurization with lower electrical power.Minkkinen, K., Ojanen, P., Penttil?, T., Aurela, M., Laurila, T., Tuovinen, J.-P., Lohila, A., 2018. Carbon accumulation in a drained boreal bog was decreased but not stopped by seasonal drought. Biogeosciences Discussions 2018, 1-35. of peatlands is expected to turn these ecosystems to carbon sources to the atmosphere. We measured carbon dynamics of a drained forested peatland in southern Finland over four years, including one with severe drought during growing season. Net ecosystem exchange (NEE) of carbon dioxide (CO2) was measured with eddy covariance method from a mast above the forest. Soil and forest floor CO2 and methane (CH4) fluxes were measured from the strips and from ditches with closed chambers. Biomasses and litter production were sampled, and soil subsidence was measured by repeated levellings of the soil surface. The drained peatland ecosystem was a strong sink of carbon dioxide in all studied years. Soil CO2 balance was estimated by subtracting the carbon sink of the growing tree stand from NEE, and it showed that also the soil was a sink of carbon. A drought period in one summer significantly decreased the sink through decreased gross primary production. Drought also decreased ecosystem respiration. The site was a small sink for CH4, even when emissions from ditches were taken into account. Despite the continuous carbon sink, peat surface subsided slightly during the 10-year measurement period, which was probably mainly due to compaction of peat. It is concluded that even fifty years after drainage this peatland site acted as a soil C sink due to relatively small changes in water table and in plant community structure compared to similar undrained sites, and the significantly increased tree stand growth and litter production. Although the site is currently a soil C sink, simulation studies with process models are needed to test whether such sites could remain C sinks when managed for forestry over several tree-stand rotations.Mironov, N.A., Abilova, G.R., Sinyashin, K.O., Gryaznov, P.I., Borisova, Y.Y., Milordov, D.V., Tazeeva, E.G., Yakubova, S.G., Borisov, D.N., Yakubov, M.R., 2018. Chromatographic isolation of petroleum vanadyl porphyrins using sulfocationites as sorbents. Energy & Fuels 32, 161-168. comparative analysis of the composition of vanadyl porphyrins isolated from heavy oil using two different sulfocationites has been carried out. As a source of vanadyl porphyrins, heavy oil of Volga-Ural basin characterized by a high vanadium content was used. The N,N-dimethylformamide extract of asphaltenes was derived from this oil and subjected for isolation of primary vanadyl porphyrin concentrate on a SiO2 column, which was then chromatographically purified with sulfocationite by our improved method. Strongly acidic cation-exchange resin and asphaltene sulfocationite recently developed in our laboratory were used as sulfocationites. According to ultraviolet–visible spectroscopy, both sulfocationites showed excellent applicability for purification, providing isolation of a broad (>50%) fraction of vanadyl porphyrins with higher spectral purity compared to results of conventional methods. Results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis showed that composition of isolated vanadyl porphyrins depends upon the chemical nature of sulfocationite. Despite the same range of vanadyl porphyrin homologues (C26–C40, with maximum falling on C32) isolated by both sulfocationites, purification with asphaltene sulfocationite resulted in a 1.4-fold decrease in the content of the most abundant DPEP type of vanadyl porphyrins, with a corresponding 1.1–1.9-fold increase in the content of the rest of the types. It was also established that, when purification is accomplished, a significant part of the same vanadyl porphyrins still remains in the column, which can be explained by their associations with non-porphyrin components of the oil.Mitra, V., Smilde, A.K., Bischoff, R., Horvatovich, P., 2018. Tutorial: Correction of shifts in single-stage LC-MS(/MS) data. Analytica Chimica Acta 999, 37-53. LC-MS(/MS) provides accurate quantitative profiling of proteins and metabolites in complex biological samples such as cell lines, tissues and body fluids. A label-free experiment consists of several LC-MS(/MS) chromatograms> that might be acquired over several days, across multiple laboratories using different instruments. Single-stage part (MS1 map) of the LC-MS(/MS) contains quantitative information on all compounds that can be detected by LC-MS(/MS) and is the data of choice used by quantitative LC-MS(/MS) data pre-processing workflows. Differences in experimental conditions and fluctuation of analytical parameters influence the overall quality of the MS1 maps and are factors hampering comparative statistical analyses and data interpretation. The quality of the obtained MS1 maps can be assessed based on changes in the two separation dimensions (retention time, mass-to-charge ratio) and the readout (ion intensity) of MS1 maps. In this tutorial we discuss two types of changes, monotonic and non-monotonic shifts, which may occur in the two separation dimensions and the readout of MS1 map. Monotonic shifts of MS1 maps can be corrected, while non-monotonic ones can only be assessed but not corrected, since correction would require precise modelling of the underlying physicochemical effects, which would require additional parameters and analysis. We discuss reasons for monotonic and non-monotonic shifts in the two separation dimensions and readout of MS1 maps, as well as algorithms that can be used to correct monotonic or to assess the extent non-monotonic shifts. Relation of non-monotonic shift with peak elution order inversion and orthogonality as defined in analytical chemistry is discussed. We aim this tutorial for data generator and evaluators scientists who aim to known the condition and approaches to produce and pre-processed comparable MS1 maps.Moeini, H., Bonyadi, M., Esmaeilzadeh, F., Rasoolzadeh, A., 2018. Experimental study of sodium chloride aqueous solution effect on the kinetic parameters of carbon dioxide hydrate formation in the presence/absence of magnetic field. Journal of Natural Gas Science and Engineering 50, 231-239. main purpose of this study is to experimentally elucidate the hydrate formation of carbon dioxide in both of deionized water and sodium chloride solution in the presence and absence of the magnetic field with regard to bad and harmful influence of carbon dioxide on the environment and climate. The experimental tests were performed in the equilibrium cell at the initial pressures of 30.5 and 35.5?bar and temperatures of 0, 2 and 4?°C with different concentrations of sodium chloride in water 0–5?wt%. Additionally, the effect of sodium chloride concentration, temperature, pressure and magnetic field on the gas hydrate kinetic parameters including the amount of gas consumption, induction time and pressure drop during the hydrate formation were examined. It is evident from the results that changing the concentration of sodium chloride aqueous solution from 1 to 3?wt%, leads to increase the induction time and hence considerably decreases the gas consumption rate and pressure drop. The results were also shown that changing the sodium chloride aqueous solution from 3 to 5?wt% has a slight effect on the induction time, gas consumption and pressure drop. Moreover, it was observed that the presence of magnetic field with 550 gauss strength has no considerable effect on the kinetic of carbon dioxide hydrate formation.Mohialdeen, I.M.J., Mustafa, K.A., Salih, D.A., Sephton, M.A., Saeed, D.A., 2018. Biomarker analysis of the upper Jurassic Naokelekan and Barsarin formations in the Miran Well-2, Miran oil field, Kurdistan region, Iraq. Arabian Journal of Geosciences 11, Article 51. Miran oilfield is one of the new oil fields in Kurdistan region, northern Iraq, located in the Sulaimani Governorate. Twelve Cuttings samples from the Upper Jurassic Naokelekan and Barsarin formations in well Miran-2 were selected for detailed organic geochemical investigations. All the samples were subjected to bitumen extraction in order to study any biomarkers present using gas chromatography-mass spectrometry. The dominance of low-molecular-weight n-alkanes and other calculated parameters indicate a marine source for the organic matter derived from planktonic algal and bacterial precursors deposited under anoxic conditions. The isoprenoids/n-alkanes ratios indicate type II and mixed II/III kerogen for both formations. The type II/III kerogen is characteristic of transitional environment under anoxic to dysoxic conditions as also indicated by the homohopane index for studied samples. More argillaceous carbonate rocks were deposited when reducing conditions were prevalent. Medium to high gammacerane index values in the rock extracts probably indicate a stratified water column during deposition of both formations. The studied samples from both formations have entered peak oil window maturity as reflected from the biomarker ratios from both aliphatic and aromatic fractions of the extracts.Molnárné Guricza, L., Schrader, W., 2018. Optimized asphaltene separation by online coupling of size exclusion chromatography and ultrahigh resolution mass spectrometry. Fuel 215, 631-637. asphaltene fraction is the heaviest part of a crude oil and is obtained as the fraction which contains compounds that are not soluble in paraffinic solvents such as n-heptane. Due to the limited solubility the use of separation methods is strongly reduced to methods that include solvents that dissolve asphaltenes. Here, the direct coupling of size exclusion chromatography with ultrahigh resolution mass spectrometry to investigate the separation of asphaltenes is accomplished. Different mobile phase systems have been investigated using THF and different mixtures of chloroform and toluene to optimize the separation conditions. Due to the separation the complexity of the asphaltene sample can be reduced, therefore mass spectra with increased information depth can be obtained due to the smaller amount of interacting species. Additionally, correlations can be proposed between molecular mass and structural characteristics of highly condensed aromatic molecules: compounds having both aromatic core and long aliphatic chains with higher masses were detected earlier and the smaller ones containing mostly highly aromatic structures and only a low amount of short alkyl chains (with the same DBE values) have stronger retention. Different experimental conditions such as stationary phase and mobile phase of asphaltene separation with size exclusion chromatography are investigated.Molofsky, L.J., Richardson, S.D., Gorody, A.W., Baldassare, F., Connor, J.A., McHugh, T.E., Smith, A.P., Wylie, A.S., Wagner, T., 2018. Purging and other sampling variables affecting dissolved methane concentration in water supply wells. Science of The Total Environment 618, 998-1007. whether changes in groundwater methane concentration are naturally occurring or related to oil and gas operations can be complicated by numerous sources of variability. This study of 10 residential water supply wells in Northeastern Pennsylvania evaluates how i) sampling from different points within the water well system, ii) purging different water volumes prior to sampling, and ii) natural variation over time, affects concentrations of naturally occurring dissolved methane and other water quality parameters. Among the population of wells, all had dissolved methane concentrations > 1 mg/L. Regardless of the volume of water purged or the timing between events, the maximum change in methane concentration (ratio of maximum to minimum concentration) among samples from a single well was 3.2, with eight out of ten wells exhibiting a maximum change less than a factor of two (i.e., <±100%). Among water wells where methane concentration changed by ± 50% or more, there was a strong correlation with changes in the concentrations of sodium, chloride, and other salinity indicators such as specific conductivity and TDS. This suggests that significant variability in methane concentration is predominantly related to changes in the relative volumes of sodium-rich fluids feeding the wellbore at any given time. Among study well locations with bladder and diaphragm pressure tanks, there was no significant difference in dissolved methane concentrations between samples collected either upstream or downstream of a pressure tank. There appears to be little benefit to purging multiple casing volumes of water from a well prior to sampling because such volumes tend to be much larger than those representative of normal residential use. We recommend purging a volume sufficient to remove standing water in the pressure tank and lines above the pump intake. This article culminates with additional recommendations for improving sample collection methods and interpreting sampling data.Moreno-Mayar, J.V., Potter, B.A., Vinner, L., Steinrücken, M., Rasmussen, S., Terhorst, J., Kamm, J.A., Albrechtsen, A., Malaspinas, A.-S., Sikora, M., Reuther, J.D., Irish, J.D., Malhi, R.S., Orlando, L., Song, Y.S., Nielsen, R., Meltzer, D.J., Willerslev, E., 2018. Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans. Nature 553, 203-207. broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka). Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36?±?1.5?ka, with gene flow persisting until around 25?±?1.1?ka. Gene flow from ancient north Eurasians into all Native Americans took place 25–20?ka, with Ancient Beringians branching off around 22–18.1?ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian ‘standstill model. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5–14.6?ka, and that this probably occurred south of the North American ice sheets. We also show that after 11.5?ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos, Inuits or Kets, and that Native American gene flow into Inuits was through northern and not southern Native American groups. Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.Morrison-Whittle, P., Goddard, M.R., 2018. From vineyard to winery: a source map of microbial diversity driving wine fermentation. Environmental Microbiology 20, 75-84. have been making wine for thousands of years and microorganisms play an integral part in this process as they not only drive fermentation, but also significantly influence the flavour, aroma and quality of finished wines. Since fruits are ephemeral, they cannot comprise a permanent microbial habitat; thus, an age-old unanswered question concerns the origin of fruit and ferment associated microbes. Here we use next-generation sequencing approaches to examine and quantify the roles of native forest, vineyard soil, bark and fruit habitats as sources of fungal diversity in ferments. We show that microbial communities in harvested juice and ferments vary significantly across regions, and that while vineyard fungi account for ～40% of the source of this diversity, uncultivated ecosystems outside of vineyards also prove a significant source. We also show that while communities in harvested juice resemble those found on grapes, these increasingly resemble fungi present on vine bark as the ferment proceeds.Morrissey, A., Scholz, C.A., Russell, J.M., 2018. Late Quaternary TEX86 paleotemperatures from the world’s largest desert lake, Lake Turkana, Kenya. Journal of Paleolimnology 59, 103-117. climatic conditions prevailed across northern and Equatorial Africa during the terminal Pleistocene until the middle Holocene, a climate event known as the “African Humid Period” (AHP). Although hydrologic changes during this period are well-known, very few records of temperature are available for evaluating the mechanisms and dynamics of climate change during the AHP across tropical Africa. To quantify changes in temperature during the onset and termination of the AHP, the TEX86 temperature proxy was used to generate a 14,000 year record of the surface temperature of Lake Turkana. This biomarker and related measures have been used to reconstruct regional and high-latitude paleotemperatures from the oceans and other continental systems, including other large African lakes. Although Lake Turkana’s climate and hydrology are very different from other large African lakes, our reconstruction exhibits a temperature history that shares a number of climatic trends with previous reconstructions. The TEX86 temperatures from Lake Turkana from 14 to 0.4?ka range from 24.3 to 28.6?°C, with a gradual decrease in temperature from early to late Holocene. This cooling roughly follows northern hemisphere summer insolation, similar to the trend observed in Lake Victoria and other regional records. However, the record from Turkana contains many abrupt temperature shifts not seen in other large lakes in the region. Multi-century-scale fluctuations persist through most of the record, and can be attributed to periods of lake mixing. Larger temperature perturbations are likely associated with changes in evaporation and cloud cover.Moutin, T., Wagener, T., Caffin, M., Fumenia, A., Gimenez, A., Baklouti, M., Bouruet-Aubertot, P., Pujo-Pay, M., Leblanc, K., Lefevre, D., Nunige, S.H., Leblond, N., Grosso, O., de Verneil, A., 2018. Nutrient availability and the ultimate control of the biological carbon pump in the Western Tropical South Pacific Ocean. Biogeosciences Discussions 2018, 1-41. waters (0–200?m) of the western tropical South Pacific (WTSP) were sampled along a longitudinal 4000?km transect (OUTPACE cruise, 18 Feb., 3 Apr. 2015) during the stratified period between the Melanesian Archipelago (MA) and the western part of the SP gyre (WGY). Two distinct areas were considered for the MA, the western MA (WMA) and the eastern MA (EMA). The main carbon (C), nitrogen (N), phosphorus (P) pools and fluxes allow for characterization of the expected trend from oligotrophy to ultra-oligotrophy, and to build first-order budgets at the daily and seasonal scales (using climatology). Sea surface chlorophyll a reflected well the expected oligotrophic gradient with higher values obtained at WMA, lower values at WGY and intermediate values at EMA. As expected, the euphotic zone depth, the deep chlorophyll maximum and nitracline depth deepen from west to east. Nevertheless, phosphaclines and nitraclines did not match. The decoupling between phosphacline and nitracline depths in the MA allows excess P to be locally provided in the upper water by winter mixing. We found a significant biological soft tissue carbon pump in the MA sustained almost exclusively by N2 fixation and essentially controlled by phosphate availability in this iron-replete environment. The MA appears to be a net sink for atmospheric CO2 while the WGY is in quasi steady state. We suggest that the necessary excess P, allowing the success of nitrogen fixers and subsequent carbon production and export, is mainly brought to the upper surface by local deep winter convection at an annual scale rather than by surface circulation. We also suggest that mesozooplankton diel vertical migration plays a dominant role in the transfer of carbon from the upper surface to deeper water in the MA. While the origin of the decoupling between phosphacline and nitracline remains uncertain, the direct link between local P upper waters enrichment, N2 fixation, organic carbon production and export, offers a possible shorter time scale than previously thought between N input by N2 fixation and carbon export. The low iron availability in the SP gyre and P availability in the MA during the stratified period may appear as the ultimate control of N input by N2 fixation. Because of the huge volume of water to consider and because the SP Ocean is the place of intense denitrification in the east (N sink) and N2 fixation in the west (N source), precise seasonal C, N, P budgets would be of prime interest to understand the efficiency, at the present time, and in the future, of the oceanic biological carbon pump.Moyen, J.-F., Laurent, O., 2018. Archaean tectonic systems: A view from igneous rocks. Lithos 302–303, 99-125. work examines the global distribution of Archaean and modern igneous rock's compositions, without relying on preconceptions about the link between rock compositions and tectonic sites (in contrast with “geotectonic” diagrams). Rather, Archaean and modern geochemical patterns are interpreted and compared in terms of source and melting conditions.Mafic rocks on the modern Earth show a clear chemical separation between arc and non-arc rocks. This points to the first order difference between wet (arc) and dry (mid-ocean ridges and hotspots) mantle melting. Dry melts are further separated in depleted (MORB) and enriched (OIB) sources. This three-fold pattern is a clear image of the ridge/subduction/plume system that dominates modern tectonics. In contrast, Archaean mafic and ultramafic rocks are clustered in an intermediate position, between the three main modern types. This suggests that the Archaean mantle had lesser amounts of clearly depleted or enriched portions; that true subductions were rare; and that the distinction between oceanic plateaus and ridges may have been less significant.Modern granitic rocks dominantly belong to two groups: arc-related granitoids, petrologically connected to arc basalts; and collision granitoids, related to felsic sources. In contrast, the Archaean record is dominated by the TTG suite that derives from an alkali-rich mafic source (i.e. altered basalt). The geochemical diversity of the TTG suite points to a great range of melting depths, from ca. 5 to > 20 kbar. This reveals the absence of large sedimentary accumulations, again the paucity of modern-like arc situations, and the importance played by reworking of an earlier basaltic shell, in a range of settings (including some proto-subduction mechanisms). Nonetheless, granitoids in each individual region show a progressive transition towards more modern-looking associations of arc-like and peraluminous granites.Collectively, the geochemical evidence suggests an Archaean Earth with somewhat different tectonic systems. In particular, the familiar distinction between collision, arcs, ridges and hotspots seems to blur in the Archaean. Rather, the large-scale geochemical pattern reveals a long-lived, altered and periodically resurfaced basaltic crust. This protocrust is reworked, through a range of processes occurring at various depths that correspond to a progressive stabilization of burial systems and the establishment of true subductions. A punctuated onset of global plate tectonics is unlikely to have occurred, but rather short-term episodes of proto-subduction in the late Archaean evolved over time into longer-term, more stable style of plate tectonics as mantle temperature decayed.Müller, S., Reinhardt, L., Franke, D., Gaedicke, C., Winsemann, J., 2018. Shallow gas accumulations in the German North Sea. Marine and Petroleum Geology 91, 139-151. gas, here defined as free gas that is trapped in unconsolidated, deltaic and shallow marine siliciclastic sediments of Plio-Pleistocene age, is found within the topmost 1000?m of sediment in the southern North Sea. Shallow amplitude anomalies in seismic reflection data are likely due to the presence of gas. The most prominent and easy-to-recognize indicators are high-amplitude anomalies, or “bright spots”, that are widespread within the southern North Sea. Gas from shallow reservoirs is currently produced offshore The Netherlands. In this study, we determine whether there are analogous shallow gas accumulations within the German North Sea. Therefore, we screened 2D and 3D multichannel seismic data for shallow amplitude anomalies. Several clusters of bright spots are identified above salt domes that closely resemble the economic deposits known in the Dutch sector in both size and their characteristic multilayered shape. Three of these potential gas accumulations, occurring in combination with additional hydrocarbon indicators such as seismic attenuation and velocity push-downs, are investigated in detail and compared to shallow gas fields from offshore The Netherlands. Amplitude anomalies indicate gas seepage on the seafloor that may contribute to the atmospheric methane budget and may have an impact on offshore infrastructure.Najoui, Z., Riazanoff, S., Deffontaines, B., Xavier, J.-P., 2018. Estimated location of the seafloor sources of marine natural oil seeps from sea surface outbreaks: A new "source path procedure" applied to the northern Gulf of Mexico. Marine and Petroleum Geology 91, 190-201. oil reservoirs are generally characterized on the sea surface by the presence of natural oil seeps (Sea Surface outbreaks - hereafter SSO). The latter are easily evidenced with Synthetic Aperture Radar (SAR) images because of the dampening effect that oil has on the capillary and associated small gravity waves (Bragg waves). The sea surface outbreaks of oil seeps are offset from their source on the seabed (seafloor sources - SFS) by hundreds meters or even kilometres. This displacement all along the sea water column is a function of the upward velocity of the oil droplet size, and the presence of lateral marine currents. This paper proposes a Vertical Drift Model (VDM) that combines both SAR images to get the SSO and the hydrodynamic model (HYCOM) function of the oil droplet size to estimate the SFS. After oil seeps detection from SAR images, the VDM proceeds to a regression in time and space based on the upward velocity of the oil, based on Stokes law, and the hydrodynamic conditions (HYCOM) to estimate the location of the seep source on the seafloor. The upward velocity depends strongly on the unknown droplet size. We propose herein a new VDM method named "sources paths" that allows to estimate the oil seeps sources on the seafloor without a priori knowledge of the oil droplet size by finding, for each oil seep, the seafloor sources corresponding to different diameters. We call "sources path" the line that joins the seafloor sources for an oil seep. The seafloor sources ought to be at the intersection of the maximum sources paths. The methodology has been applied to the northern Gulf of Mexico where the locations of many prolific oil seep sites are well known. A first validation of the source path procedure is that the obtained SFSs correspond to the seafloor sources of oil droplets having the same diameter and seeped at different times. Another validation has been performed through the comparison of SFS locations and those of the outcropping shallow salt. This comparison shows a good correlation and suggests that the oil seeps may be situated above the allochtonous toward autochthonous salt connections.Nakano, H., Miyazawa, H., Maeno, A., Shiroishi, T., Kakui, K., Koyanagi, R., Kanda, M., Satoh, N., Omori, A., Kohtsuka, H., 2017. A new species of Xenoturbella from the western Pacific Ocean and the evolution of Xenoturbella. BMC Evolutionary Biology 17, Article 245. is a group of marine benthic animals lacking an anus and a centralized nervous system. Molecular phylogenetic analyses group the animal together with the Acoelomorpha, forming the Xenacoelomorpha. This group has been suggested to be either a sister group to the Nephrozoa or a deuterostome, and therefore it may provide important insights into origins of bilaterian traits such as an anus, the nephron, feeding larvae and centralized nervous systems. However, only five Xenoturbella species have been reported and the evolutionary history of xenoturbellids and Xenacoelomorpha remains obscure.Nalin, F., Sander, L.C., Wilson, W.B., Wise, S.A., 2018. Gas chromatographic retention behavior of polycyclic aromatic hydrocarbons (PAHs) and alkyl-substituted PAHs on two stationary phases of different selectivity. Analytical and Bioanalytical Chemistry 410, 1123-1137. indices (I) for 45 polycyclic aromatic hydrocarbons (PAHs) and 63 methyl-substituted PAHs were determined by gas chromatography – mass spectrometry (GC-MS) using two different stationary phases: a Rxi-PAH phase (a “higher phenyl-content stationary phase”) and a 50% (mole fraction) liquid crystalline dimethylpolysiloxane phase. Retention data were obtained for parent PAHs from molecular mass (MM) 128?g/mol (naphthalene) to 328?g/mol (benzo[c]picene) and for 12 sets of methyl-PAHs (methylfluorenes, methylanthracenes, methylphenanthrenes, methylfluoranthenes, methylpyrenes, methylbenz[a]anthracenes, methylbenzo[c]phenanthrenes, methylchrysenes, methyltriphenylenes, methylbenzo[a]pyrenes, methylperylenes, and methylpicenes). Molecular shape descriptors such as length-to-breath ratio (L/B) and thickness (T) were determined for all the PAHs studied. Correlation between I and L/B ratio was evaluated for both stationary phases with a better correlation observed for the 50% liquid crystalline phase (correlation coefficients ranging from 0.22 to 1.00).Nam, I., Nam, H.G., Zare, R.N., 2018. Abiotic synthesis of purine and pyrimidine ribonucleosides in aqueous microdroplets. Proceedings of the National Academy of Sciences 115, 36-40.: Discovery of an improved prebiotic method for the synthesis of ribonucleosides provides support to theories that posit a central role for RNA in the origin of life. It has been assumed that ribonucleosides arose through an abiotic process in which ribose and nucleobases became conjoined, but the direct condensation of nucleobases with ribose to give ribonucleosides in bulk solution is thermodynamically uphill. We show a general synthetic path for ribonucleosides, both purine and pyrimidine bases, using an abiotic salvage pathway in a microdroplet environment with divalent magnesium ion (Mg2+) as a catalyst. Purine and pyrimidine ribonucleosides are formed simultaneously under the same conditions, which suggests a possible scenario for the spontaneous production of random ribonucleosides necessary to generate various types of primitive RNA. Abstract: Aqueous microdroplets (<1.3 ?m in diameter on average) containing 15 mM d-ribose, 15 mM phosphoric acid, and 5 mM of a nucleobase (uracil, adenine, cytosine, or hypoxanthine) are electrosprayed from a capillary at +5 kV into a mass spectrometer at room temperature and 1 atm pressure with 3 mM divalent magnesium ion (Mg2+) as a catalyst. Mass spectra show the formation of ribonucleosides that comprise a four-letter alphabet of RNA with a yield of 2.5% of uridine (U), 2.5% of adenosine (A), 0.7% of cytidine (C), and 1.7% of inosine (I) during the flight time of ～50 ?s. In the case of uridine, no catalyst is required. An aqueous solution containing guanine cannot be generated under the same conditions given the extreme insolubility of guanine in water. However, inosine can base pair with cytidine and thus substitute for guanosine. Thus, a full set of ribonucleosides to generate the purine–pyrimidine base pairs A-U and I-C are spontaneously generated in aqueous microdroplets under similar mild conditions. Ncube, S., Madikizela, L., Cukrowska, E., Chimuka, L., 2018. Recent advances in the adsorbents for isolation of polycyclic aromatic hydrocarbons (PAHs) from environmental sample solutions. TrAC Trends in Analytical Chemistry 99, 101-116. article offers a critical review on the materials that have been applied as adsorbents in the isolation of polycyclic aromatic hydrocarbons from matrix solutions. The review looks at adsorbents that have been used during the clean-up stage to isolate polycyclic aromatic hydrocarbons from aqueous samples and organic solvent extracts from treatment of solid samples. Articles that report the application of adsorbents for solid phase extraction and solid phase microextraction of PAHs in the past decade stretching from 2007 were considered. The review focussed mainly on recent advances that have been done to enhance the applicability of both traditional adsorbents like silica, and modern ones like molecularly imprinted polymers and nanoparticles. The application of adsorbents modified with functional organic groups is critically evaluated with areas for possible improvement suggested. Finally, the authors offer areas of exploration that can allow the analysis of polycyclic aromatic hydrocarbons to reach new heights.Nebel-Jacobsen, Y., Nebel, O., Wille, M., Cawood, P.A., 2018. A non-zircon Hf isotope record in Archean black shales from the Pilbara craton confirms changing crustal dynamics ca. 3 Ga ago. Scientific Reports 8, Article 922. tectonics and associated subduction are unique to the Earth. Studies of Archean rocks show significant changes in composition and structural style around 3.0 to 2.5 Ga that are related to changing tectonic regime, possibly associated with the onset of subduction. Whole rock Hf isotope systematics of black shales from the Australian Pilbara craton, selected to exclude detrital zircon components, are employed to evaluate the evolution of the Archean crust. This approach avoids limitations of Hf-in-zircon analyses, which only provide input from rocks of sufficient Zr-concentration, and therefore usually represent domains that already underwent a degree of differentiation. In this study, we demonstrate the applicability of this method through analysis of shales that range in age from 3.5 to 2.8 Ga, and serve as representatives of their crustal sources through time. Their Hf isotopic compositions show a trend from strongly positive εHfinitial values for the oldest samples, to strongly negative values for the younger samples, indicating a shift from juvenile to differentiated material. These results confirm a significant change in the character of the source region of the black shales by 3 Ga, consistent with models invoking a change in global dynamics from crustal growth towards crustal reworking around this time.Ng, N.-T., Kamaruddin, A.F., Wan Ibrahim, W.A., Sanagi, M.M., Abdul Keyon, A.S., 2018. Advances in organic–inorganic hybrid sorbents for the extraction of organic and inorganic pollutants in different types of food and environmental samples. Journal of Separation Science 41, 195-208. efficiency of the extraction and removal of pollutants from food and the environment has been an important issue in analytical science. By incorporating inorganic species into an organic matrix, a new material known as an organic–inorganic hybrid material is formed. As it possesses high selectivity, permeability, and mechanical and chemical stabilities, organic–inorganic hybrid materials constitute an emerging research field and have become popular to serve as sorbents in various separaton science methods. Here, we review recent significant advances in analytical solid-phase extraction employing organic–inorganic composite/nanocomposite sorbents for the extraction of organic and inorganic pollutants from various types of food and environmental matrices. The physicochemical characteristics, extraction properties, and analytical performances of sorbents are discussed; including morphology and surface characteristics, types of functional groups, interaction mechanism, selectivity and sensitivity, accuracy, and regeneration abilities. Organic–inorganic hybrid sorbents combined with extraction techniques are highly promising for sample preparation of various food and environmental matrixes with analytes at trace levels.Ngo, A.T., Skeini, T., Iancu, V., Redfern, P.C., Curtiss, L.A., Hla, S.W., 2018. Manipulation of origin of life molecules: Recognizing single-molecule conformations in β-carotene and chlorophyll-a/β-carotene clusters. ACS Nano 12, 217-225. and chlorophyll are essential parts of plant leaves and are involved in photosynthesis, a vital biological process responsible for the origin of life on Earth. Here, we investigate how β-carotene and chlorophyll-a form mixed molecular phases on a Au(111) surface using low-temperature scanning tunneling microscopy and molecular manipulation at the single-molecule level supported by density functional theory calculations. By isolating individual molecules from nanoscale molecular clusters with a scanning tunneling microscope tip, we are able to identify five β-carotene conformations including a structure exhibiting a three-dimensional conformation. Furthermore, molecular resolution images enable direct visualization of β-carotene/chlorophyll-a clsuters, with intimate structural details highlighting how they pair: β-carotene preferentially positions next to chlorophyll-a and induces switching of chlorophyll-a from straight to several bent tail conformations in the molecular clusters.Nikitenko, O.A., Ershov, V.V., Levin, B.W., 2017. The first identification of hydrogeochemical indicators of mud volcanic activity. Doklady Earth Sciences 477, 1445-1448. monitoring has been implemented at a mud volcano for the first time in the world. Measurements were carried out during the field season of 2015 at five gryphons of the South Sakhalin mud volcano with various degrees of activity. Statistically significant differences in the chemical compositions of mud-volcano waters from different gryphons are established. These differences are determined by the activity of the gryphons. Original Russian Text ? O.A. Nikitenko, V.V. Ershov, B.W. Levin, 2017, published in Doklady Akademii Nauk, 2017, Vol. 477, No. 5, pp. 586–589.Niu, L., Cai, H., Van Gelder, P.H.A.J.M., Luo, P., Liu, F., Yang, Q., 2018. Dynamics of polycyclic aromatic hydrocarbons (PAHs) in water column of Pearl River estuary (China): Seasonal pattern, environmental fate and source implication. Applied Geochemistry 90, 39-49. on a monthly sampling effort in 2011, >62 polycyclic aromatic hydrocarbons (PAHs) in different environmental phases were detected in the Pearl River estuary, China. The study aimed to investigate seasonal variation in PAH concentration and composition, potential risk source, depth profile and environmental correlation and to provide a non-deterministic insight into the PAH behavior. The total PAHs varied widely throughout the 12 months of the study period, ranging from 25.99?ng/l to 522.26?ng/l in seawater and from 7.37?μg/g to 167.44?μg/g in suspended sediment (SPM). The 16 Environmental Protection Agency (EPA) priority PAHs ranged from 12.70?ng/l to 160.15?ng/l in seawater and from 2.82?μg/g to 112.32?μg/g in SPM. Low molecular weight (LMW) PAHs (2- and 3-ring) were the most abundant, responsible for 81% in seawater and 73% in SPM. Moreover, it appeared that SPM and ambient water temperature were the determining factors controlling the transport and distribution of PAHs in the water column. A higher concentration of SPM contributed to a higher content of PAHs due to adsorption and low solubility. The PAHs were more significantly associated with particles than were dissolved in seawater. In addition, petroleum emissions, vehicle emissions, and wood combustion were considered a potential risk of PAHs via statistically-based methods of principal component analysis (PCA) and diagnostic ratios. The findings are useful for understanding the dynamics of estuarine PAHs, which exert significant influence on coastal ecosystems.Noffke, N., 2018. Comment on the paper by Davies et al. “Resolving MISS conceptions and misconceptions: A geological approach to sedimentary surface textures generated by microbial and abiotic processes” (Earth Science Reviews, 154 (2016), 210–246). Earth-Science Reviews 176, 373-383. article by Davies et al. discusses scientific studies on microbially induced sedimentary structures (MISS). The sedimentary structures are caused by benthic microbes in clastic deposits and have the potential to fossilize. In the opinion of Davies et al., it may be problematic to distinguish MISS-like structures (e.g., ‘wrinkle structures’) from similar, but abiotic structures. Therefore, their article argues, there exists a need for an umbrella classification summarizing both biological and abiotic sedimentary structures. However, Davies et al.'s paper does not reflect a thorough understanding of the formation and preservation of MISS. More so, while the authors appreciate the benefit of geological field work, and petrological as well as geochemical laboratory sample analyses, their article appears to widely disregard that this scientific rigor is presented in studies on MISS. The lack of data make the classification by Davies et al. unsupported and difficult to use. It potentially confuses by producing multiple classification possibilities rather than a pragmatic organization, and it contributes an unnecessary terminological ballast to a research area that has progressed far beyond to the concepts that the paper by Davies et al. presents.Nyadong, L., Lai, J., Thompsen, C., LaFrancois, C.J., Cai, X., Song, C., Wang, J., Wang, W., 2018. High-field Orbitrap mass spectrometry and tandem mass spectrometry for molecular characterization of asphaltenes. Energy & Fuels 32, 294-305. work introduces a novel approach by use of high-energy collision-induced dissociation for fragmenting asphaltenes into their constituent stable aromatic cores as a means for determining the relative proportions of island-to-archipelago structures. This approach is particularly useful for comparing asphaltenes from various crude oils. Ion generation from asphaltenes was performed by use of atmospheric pressure photoionization, which has been demonstrated to provide hydrogen-to-carbon ratios consistent with bulk measurements by combustion analysis with less than 10% relative error. The fragmentation behavior of asphaltenes was first evaluated with model compounds consisting of island and archipelago structures by use of low- and high-energy collision-induced dissociation (CID and HCD). Unlike CID, HCD enables dissociation of model compounds to their stable aromatic cores. This allows facile classification as either island or archipelago on the basis of the discrepancy in the double-bond equivalents between the precursors and stable aromatic cores. Model compound studies also showed that when HCD is utilized for the simultaneous dissociation of multiple precursor ions, efficient fragmentation of all precursors only occurs when ions within a narrow mass window are presented for analysis. The HCD approach was then applied to characterize narrow mass segments of crude oil asphaltenes, including those derived from hydrotreated resids. Observed island-to-archipelago proportions were consistent with the chemical transformations that occur during the hydrotreating process. Importantly, the method also demonstrates that the proportion of island-to-archipelago structures in asphaltenes decreases with increase molecular weight.Ojeda, C.B., Rojas, F.S., 2018. Vortex-assisted liquid–liquid microextraction (VALLME): The latest applications. Chromatographia 81, 89-103. liquid–liquid microextraction employed for the isolation and preconcentration of analytes can be used together with various detection techniques in order to obtain a very versatile tool for the chemical analysis. This allows the analyzing of a great variety of analytes in very diverse concentrations. This review is an update of the manuscript published in 2014 by the same authors.Okoro, C.C., Amund, O.O., 2018. Microbial community structure of a low sulfate oil producing facility indicate dominance of oil degrading/nitrate reducing bacteria and methanogens. Petroleum Science and Technology 36, 293-301. of microbial community structure of a low sulfate oil producing facility in Nigeria using 16S rRNA gene sequencing technique revealed dominance of oil degrading and nitrate reducing bacteria and methanogenic archaea in produced waters and oil samples namely, Marinobacter (37%), Azovibrio (21%), Thauera (10–28%), and Methanolobus (22%). On the contrary, the associated oil pipeline samples revealed massive dominance of potentially corrosive Methanolobus (60%) and Methanobacterium (25-27%). Further experimentation shows that the methanogens implicated in oil pipelines are corrosive moderate halophile that utilizes H2/CO2 and methanol as substrates. More emphasis should therefore be on methanogenic archaea as opposed to sulfate reducing bacteria (SRBs) during mitigation plans for microbially induced corrosion (MIC) in a low sulfate oil producing facility.Olivares, I.R.B., Souza, G.B., Nogueira, A.R.A., Toledo, G.T.K., Marcki, D.C., 2018. Trends in developments of certified reference materials for chemical analysis - Focus on food, water, soil, and sediment matrices. TrAC Trends in Analytical Chemistry 100, 53-64. growing demand for traceable and reliable results in analytical chemistry can be illustrated with the growth in ISO/IEC 17025 accreditation. Among different technical requirements in this quality system, the use of CRMs is highlighted because of its applications in many operations, such as method validation, proficiency tests, estimation of the uncertainties and quality control. Over the past several years, there has been an increased need to use different types of CRMs in chemical analysis, new CRM publications about its developments and certification. This paper proposes to show a detailed review considering the development of certified reference materials (CRM) for chemical analysis, focusing on food, water, soil and sediment matrices. An evaluation of the trends and best-applied practices in its development in the last 2 years was performed, to guide new developments for this material that is increasingly necessary to laboratories.Oren, A., Garrity, G.M., 2018. Uncultivated microbes—in need of their own nomenclature? The Isme Journal 12, 309-311. their paper on ‘Uncultivated microbes in need of their own taxonomy’, Konstantinidis et al. (2017) proposed standards to draw the roadmap for a new genome-based taxonomy aimed at including the great majority of microbial species that are yet uncultivated. According to their proposal, the taxonomy of the uncultivated bacteria and archaea as based on genomic and metagenomic data, would, at least initially, be parallel but highly convergent to the one in existence for isolates. The call to include yet-to-be-cultivated organisms in the taxonomic system of the prokaryotes is not novel; similar proposals have been made for least two decades already. And the rapid development of sequencing technology and of bioinformatic tools to extract relevant information from the sequences obtained has already given us a wealth of information about the uncultivated majority. And there can be no doubt that the field will greatly expand in the years to come.In the last two sections of the Perspectives paper the authors exposed their ideas about nomenclature aspects that must be taken into account when integrating the uncultivated prokaryotic world within the ‘old’ system that is based on isolated strains and especially type strains, representing the ~15?000 species of prokaryotes with names with standing in the nomenclature as regulated by the International Code of Nomenclature of Prokaryotes (the Prokaryotic Code) (Parker et al., 2016), an official publication the International Committee on Nomenclature of Prokaryotes (ICSP). Konstantinidis et al. (2017) called for the establishment of a committee of experts that should be formed to govern and supervise the new classification system, in a similar way to ICSP: ‘We believe it is high time for microbial ecologists to establish their own official committee that will make recommendations on how to classify uncultured taxa with harmonized high standards, supervise and manage an ‘official’ classification and the rules of the nomenclature of uncultured taxa’. This is an intriguing proposal, as also for the cultivated minority such an ‘official’ classification system does not exist. The ICSP does not support any ‘official’ classification of the prokaryotes, and the Prokaryotic Code deals with nomenclature aspects only. Principle 1.4 states: ‘Nothing in this Code may be construed to restrict the freedom of taxonomic thought or action’.Konstantinidis et al. (2017) further recommended ‘the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured bacteria and archaea but with its own list of validly published names. If widely adopted, this system will not only facilitate a comprehensive characterization of the ‘uncultivated majority’ but also provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion’.The Prokaryotic Code does currently not oversee the nomenclature of ‘Candidatus’ taxa, so that the names of ‘Candidatus’ taxa cannot be validly published nor have priority. The authors of the Perspectives paper therefore proposed a new nomenclature system for the uncultivated prokaryotes: ‘We suggest to highlight the names of uncultivated taxa with a simple prefix such as U superscript … which would be omitted once the organism is brought into culture...’. Such a nomenclature system differs in nothing from that for the ‘Candidatus’ taxa proposed in the mid-1990s, a system that also called for omitting the ‘Candidatus’ when a culture becomes available for a previously uncultivated taxon. A formal proposal to incorporate the nomenclature, not only of classical ‘Candidatus’ taxa but also of genome and even of gene sequences to serve as type material for the valid publication of names of prokaryotes is currently pending. The ‘Modest proposals to expand the type material for naming of prokaryotes’ (Whitman, 2016), a document not mentioned by Konstantinidis et al. (2017), prepares the way to unite the nomenclature of the cultivated and the uncultivated prokaryotes into a single system. The proposal is complex, it includes modification of 15 Rules of the Prokaryotic Code, and it is waiting to be discussed first by the Judicial Commission and then by the plenary meeting of the ICSP in accordance with the ICSP statutes. Whether or not Whitman’s ‘Modest proposals’ will be accepted and become part of the Prokaryotic Code cannot be predicted now. But the proposal has at least one great merit: all is done within a single framework: that of the ICSP and the Prokaryotic Code.The idea to establish an alternative or parallel nomenclature system for the uncultivated prokaryotes, to be supervised ‘by a committee of experts, supported by an international microbiological society (no further details provided), in order to govern and supervise the new classification system, in a similar way to ICSP’ was not earlier published as far as we could ascertain. Konstantinidis et al. (2017) further recommended ‘the implementation of an independent nomenclatural system for uncultivated taxa, following the same nomenclature rules as those for cultured bacteria and archaea but with its own list of validly published names. But then follows the contradictory statement that this will ‘provide a unified catalogue of validly published names, thereby avoiding synonyms and confusion’.We are greatly worried about the idea of creating independent nomenclature systems. Konstantinidis et al. (2017) proposed ‘to deviate the least from the current taxonomy (intention is probably nomenclature) of cultivated taxa so that the merging of the two systems will be easy in the future’. When it is possible to remain within a single, well-established framework, that is, the ICSP and the Prokaryotic Code, what can be the advantage of first splitting and then merging? Having two independent systems running in parallel, even for a limited time, is a sure recipe for establishing synonyms and confusion. The authors stated that ‘The merging would mostly depend on the implementation of two straightforward changes to the existing code of nomenclature: (i) priority of the names of uncultivated taxa is recognized by the ICNP; and (ii) DNA genome sequence is accepted as the type material...’. These are exactly the changes proposed by Whitman (2016) </articles/ismej2017188> while remaining within the existing formal framework.As an example that parallel independent nomenclatural systems can work, Konstantinidis et al. (2017) quoted the case of the cyanobacteria/cyanophyta ‘to which some taxonomists apply the International Code of Nomenclature for algae, fungi and plants... while the rest apply the ICNP’. This is not exactly true: most cyanobacterial taxonomists can only apply the rules of the Botanical Code as with very few exceptions only, the generic names of cyanobacteria do not have standing under the Prokaryotic Code. And for the cyanobacteria even two additional nomenclatural systems have been proposed. One is found in the paper by Gaget and co-workers cited by Konstantinidis et al. but without the comments and response published subsequently (Gaget et al., 2015). And yet another, independent, system is that of the ‘Guide to the nomenclature treatment of oxyphototrophic prokaryotes’ (Komárek and Golubic, 1980). Much of the current confusion was caused by a misunderstanding that in 1999 led to an unintended modification of Principle 2 of the Prokaryotic Code. The resulting pluralism, with four different nomenclature systems at the same time, has led to a tremendous confusion; for a comprehensive survey of all issues involved and the historical aspects that led to the current situation see Oren and Ventura (2017). Two opposing proposals to change the ICNP are currently pending: a proposal to largely remove cyanobacterial nomenclature from the Code (Oren and Garrity, 2014) and one to consistently apply the Rules of the Prokaryotic Code for all cyanobacteria (Pinevich, 2015). Whatever the ICSP and its Judicial Commission will decide in the future about these proposals, the single nomenclatural system that hopefully will emerge will be much easier to handle than the current pluralism.Another example where unregulated naming of taxa is increasingly leading to chaos is that of the phyla of prokaryotes. For historical reasons the rank of phylum was never included in the taxonomic ranks covered by the Prokaryotic Code. A proposal to include the rank of phylum in the Code, co-authored by a large number of leading taxonomists (Oren et al., 2015), is waiting to be discussed by the ICSP. That proposal also includes a uniform way in which names of phyla must be formed: by the addition of the suffix -aeota to the stem of the name of one of the contained classes. A look at the many new phylum-level named taxa proposed by Hug et al. (2016), in which not only the suffix -aeota is not used but also the regulations of Appendix 9 to the Prokaryotic Code (Parker et al., 2016) are not followed, shows how independent nomenclatural systems lead to problems that will be difficult to solve when in the future the systems must be merged to result in one coherent nomenclature acceptable to all.For the nomenclature of the prokaryotes, cultivated as well as uncultivated, we must choose between order to be established by the ICSP (without involvement of another ‘international microbiological society’ in charge of the nomenclature of the uncultivated taxa) or pluralism that will inevitably lead to chaos and to the destruction of now well-ordered nomenclature system.ReferencesGaget V, Welker M, Rippka R, Tandeau de Marsac N. (2015). Response to: ‘Comments on: ‘A polyphasic approach leading to the revision of the genus Planktothrix (Cyanobacteria) and its type species, P. agardhii, and proposal for integrating the emended valid botanical taxa, as well as three new species, Planktothrix paucivesiculata sp. nov.ICNPPlanktothrix tepida sp. nov.ICNP, and Planktothrix serta sp. nov.ICNP, as genus and species names with nomenclature standing under the ICNP,’ by V Gaget, M Welker, R Rippka, and N Tandeau de Marsac, Syst. Appl. Microbiol. (2015). ’ <’>, by A Oren [Syst. Appl. Microbiol. (2015), doi:10.1016/j.syapm.2015.03.002]. Syst Appl Microbiol 38: 368–370.Hug LA, Baker BJ, Anantharaman K, Brown CT, Probst AJ, Castelle CJ et al. (2016). A new view of the tree of life. Nat Microbiol 1: 16048.Komárek J, Golubi? S. (1980), Guide to the nomenclature treatment of oxyphototrophic prokaryotes (Cyanoprokarotes and Chloroprokaryotes). Proposal. Available at Konstantinidis KT, Rosselló-Móra R, Amann R. (2017). Uncultivated microbes in need of their own taxonomy. ISME J epub ahead of print 21 July 2017 doi:10.1038/ismej.2017.113.Oren A, Garrity GM. (2014). Proposal to change General Consideration 5 and Principle 2 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 64: 309–310.Oren A, da Costa MS, Garrity GM, Rainey FA, Rosselló-Móra R, Schink B et al. (2015). Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 65: 4284–4287.Parker CT, Tindall BJ, Garrity GM. (2016). International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2008 Revision). Int J Syst Evol Microbiol doi:10.1099/ijsem.0.000778.Pinevich AV. (2015). Proposal to consistently apply the International Code of Nomenclature of Prokaryotes (ICNP) to names of the oxygenic photosynthetic bacteria (cyanobacteria), including those validly published under the International Code of Botanical Nomenclature (ICBN)/International Code of Nomenclature for algae, fungi and plants (ICN), and proposal to change Principle 2 of the ICNP. Int J Syst Evol Microbiol 65: 1070–1074.Whitman WB. (2016). Modest proposals to expand the type material for naming of prokaryotes. Int J Syst Evol Microbiol 66: 2108–2112.Osburn, C.L., Anderson, N.J., Stedmon, C.A., Giles, M.E., Whiteford, E.J., McGenity, T.J., Dumbrell, A.J., Underwood, G.J.C., 2017. Shifts in the source and composition of dissolved organic matter in southwest Greenland lakes along a regional hydro-climatic gradient. Journal of Geophysical Research: Biogeosciences 122, 3431-3445. organic matter (DOM) concentration and quality were examined from Arctic lakes located in three clusters across south-west (SW) Greenland, covering the regional climatic gradient: cool, wet coastal zone; dry inland interior; and cool, dry ice-marginal areas. We hypothesized that differences in mean annual precipitation between sites would result in a reduced hydrological connectivity between lakes and their catchments and that this concentrates degraded DOM. The DOM in the inland lake group was characterized by a lower aromaticity and molecular weight, a low soil-like fluorescence, and carbon stable isotope (δ13C-DOC) values enriched by ~2‰ relative to the coastal group. DOC-specific absorbance (SUVA254) and DOC-specific soil-like fluorescence (SUVFC1) revealed seasonal and climatic gradients across which DOM exhibited a dynamic we term “pulse-process”: Pulses of DOM exported from soils to lakes during snow and ice melt were followed by pulses of autochthonous DOM inputs (possibly from macrophytes), and their subsequent photochemical and microbial processing. These effects regulated the dynamics of DOM in the inland lakes and suggested that if circumpolar lakes currently situated in cool wetter climatic regimes with strong hydrological connectivity have reduced connectivity under a drier future climate, they may evolve toward an end-point of large stocks of highly degraded DOC, equivalent to the inland lakes in the present study. The regional climatic gradient across SW Greenland and its influence on DOM properties in these lakes provide a model of possible future changes to lake C cycling in high-latitude systems where climatic changes are most pronounced.Ossa Ossa, F., Eickmann, B., Hofmann, A., Planavsky, N.J., Asael, D., Pambo, F., Bekker, A., 2018. Two-step deoxygenation at the end of the Paleoproterozoic Lomagundi Event. Earth and Planetary Science Letters 486, 70-83. ca. 2.1 Ga Francevillian Group of Gabon was deposited in the aftermath of the Great Oxidation Event (GOE) and records the Lomagundi Event (LE), which is the most pronounced and long-lived carbon isotope excursion in the geologic record. Moreover, the sedimentary succession contains putative evidence for the earliest appearance of macro-eukaryotes. An emerging paradigm is that the end of the LE was accompanied by a deoxygenation event that preceded the apparent stability of environmental and redox conditions as well as the carbon cycle characteristic of the Mesoproterozoic. However, the processes that led to deoxygenation some 300 to 200 Ma after the beginning of the GOE are not well understood. Here we present a multi-proxy stable isotope (δ34Sδ34S, Δ33SΔ33S, Δ36SΔ36S, δ98Moδ98Mo, δ13Corgδ13Corg, δ13Ccarbδ13Ccarb, and δ18Ocarbδ18Ocarb) study of the Francevillian Group. We suggest that sedimentation of the lower part of the Francevillian Group took place during the LE in oxygenated shallow waters with elevated sulfate concentrations. Two episodes of anoxic water shoaling during deposition of the upper Francevillian Group correspond with broader marine deoxygenation and a contraction of the seawater sulfate reservoir. This shoaling of anoxic conditions may be linked to intense submarine hydrothermal and volcanic activity that led to sedimentary manganese deposits. We propose that increased concentrations of aqueous, hydrothermally sourced reductants drove oxygen consumption during the first deoxygenation event and established a sulfidic oxygen-minimum zone at the margin of the shallow shelf. Carbonates with positive δ13Ccarbδ13Ccarb values characteristic of the LE precipitated during this first stage of deoxygenation. The second deoxygenation, separated from the previous event by a period of well-oxygenated conditions, was marked by a stronger contraction of the seawater sulfate reservoir and coincided with the end of the LE. During this time, widespread euxinic conditions were established in shallow (above storm wave base) marine environments. The presence of a shallow-water redoxcline points to a generally low-oxygen atmosphere–ocean system. Further, the negative co-variation between δ34Sδ34S and δ13Cδ13C values in sediments of the Francevillian Group and other sedimentary successions of similar age worldwide suggests that the inferred two-step deoxygenation corresponding to the end of the LE reflects global rather than local events that likely occurred between ～2.1 and 2.05 Ga ago.Ou, C., Li, C., Zhi, D., Xue, L., Yang, S., 2018. Coupling accumulation model with gas-bearing features to evaluate low-rank coalbed methane resource potential in the southern Junggar Basin, China. American Association of Petroleum Geologists Bulletin 102, 153-174. reveal the resource potential of low-rank coalbed methane (LRCBM) and determine the favorable area from six different zones in the southern Junggar Basin in China, a new LRCBM assessment methodology was developed. This methodology comprises three steps: developing the regional accumulation model, determining the zone with gas-bearing features, and exploring for the favorable targets. First, the coalbed methane (CBM)–generating characteristics, the sealing properties of the over- and underlying rocks in the CBM reservoir, and the hydrogeological characteristics preserved in the reservoir were analyzed. By combining these characteristics with the tectonic burial history, geothermal history, hydrocarbon evolution, and CBM gas-saturation changes, the LRCBM regional accumulation model that illustrates the LRCBM-enrichment characteristics of the Middle–Lower Jurassic series in the southern Junggar Basin was derived. Second, the LRCBM gas-bearing features of each zone were comprehensively analyzed using a large data set acquired from a coalfield; the LRCBM-bearing features and the variation of their related parameters in six different zones of the southern Junggar Basin were presented. These parameters relate to features such as coal-seam distribution, petrology, reservoir property, coal thermal evolution, and coal and gas content characteristics. Third, the favorable targets are explored by calculating the LRCBM resources and intensively evaluating each zone; the favorable targets are candidates for further exploration in the southern Junggar Basin. At depths shallower than 2000 m (～7000 ft), the LRCBM resources in the southern Junggar Basin are 3054.7 × 108 m3 (10.8 × 1012 ft3), with resource abundance of (0.42–11.65) × 108 m3/km2 ([0.06–1.66] × 108 ft3/ac), thereby demonstrating a significantly good exploitation prospect. Moreover, the favorable and relatively favorable areas for further exploration in the southern Junggar Basin are zone 4 and 5, respectively.Oya, M., Suzuki, H., Anas, A.R.J., Oishi, K., Ono, K., Yamaguchi, S., Eguchi, M., Sawada, M., 2018. LC-MS/MS imaging with thermal film-based laser microdissection. Analytical and Bioanalytical Chemistry 410, 491-499. spectrometry (MS) imaging is a useful tool for direct and simultaneous visualization of specific molecules. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used to evaluate the abundance of molecules in tissues using sample homogenates. To date, however, LC-MS/MS has not been utilized as an imaging tool because spatial information is lost during sample preparation. Here we report a new approach for LC-MS/MS imaging using a thermal film-based laser microdissection (LMD) technique. To isolate tissue spots, our LMD system uses a 808-nm near infrared laser, the diameter of which can be freely changed from 2.7 to 500 μm; for imaging purposes in this study, the diameter was fixed at 40 μm, allowing acquisition of LC-MS/MS images at a 40-μm resolution. The isolated spots are arranged on a thermal film at 4.5-mm intervals, corresponding to the well spacing on a 384-well plate. Each tissue spot is handled on the film in such a manner as to maintain its spatial information, allowing it to be extracted separately in its individual well. Using analytical LC-MS/MS in combination with the spatial information of each sample, we can reconstruct LC-MS/MS images. With this imaging technique, we successfully obtained the distributions of pilocarpine, glutamate, γ-aminobutyric acid, acetylcholine, and choline in a cross-section of mouse hippocampus. The protocol we established in this study is applicable to revealing the neurochemistry of pilocarpine model of epilepsy. Our system has a wide range of uses in fields such as biology, pharmacology, pathology, and neuroscience.Ozaki, K., Tajika, E., Hong, P.K., Nakagawa, Y., Reinhard, C.T., 2018. Effects of primitive photosynthesis on Earth’s early climate system. Nature Geoscience 11, 55-59. evolution of different forms of photosynthetic life has profoundly altered the activity level of the biosphere, radically reshaping the composition of Earth’s oceans and atmosphere over time. However, the mechanistic impacts of a primitive photosynthetic biosphere on Earth’s early atmospheric chemistry and climate are poorly understood. Here, we use a global redox balance model to explore the biogeochemical and climatological effects of different forms of primitive photosynthesis. We find that a hybrid ecosystem of H2-based and Fe2+-based anoxygenic photoautotrophs—organisms that perform photosynthesis without producing oxygen—gives rise to a strong nonlinear amplification of Earth’s methane (CH4) cycle, and would thus have represented a critical component of Earth’s early climate system before the advent of oxygenic photosynthesis. Using a Monte Carlo approach, we find that a hybrid photosynthetic biosphere widens the range of geochemical conditions that allow for warm climate states well beyond either of these metabolic processes acting in isolation. Our results imply that the Earth’s early climate was governed by a novel and poorly explored set of regulatory feedbacks linking the anoxic biosphere and the coupled H, C and Fe cycles. We suggest that similar processes should be considered when assessing the potential for sustained habitability on Earth-like planets with reducing atmospheres.Ozbayram, E.G., Kleinsteuber, S., Nikolausz, M., Ince, B., Ince, O., 2018. Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments. Applied Microbiology and Biotechnology 102, 1035-1043. aim of this study was to develop an effective bioaugmentation concept for anaerobic digesters treating lignocellulosic biomass such as straw. For that purpose, lignocellulose-degrading methanogenic communities were enriched on wheat straw from cow and goat rumen fluid as well as from a biogas reactor acclimated to lignocellulosic biomass (sorghum as mono-substrate). The bacterial communities of the enriched cultures and the different inocula were examined by 454 amplicon sequencing of 16S rRNA genes while the methanogenic archaeal communities were analyzed by terminal restriction fragment length polymorphism (T-RFLP) fingerprinting of the mcrA gene. Bacteroidetes was the most abundant phylum in all samples. Within the Bacteroidetes phylum, Bacteroidaceae was the most abundant family in the rumen-derived enrichment cultures, whereas Porphyromonadaceae was the predominant one in the reactor-derived culture. Additionally, the enrichment procedure increased the relative abundance of Ruminococcaceae (phylum: Firmicutes) in all cultures. T-RFLP profiles of the mcrA gene amplicons highlighted that the ruminal methanogenic communities were composed of hydrogenotrophic methanogens dominated by the order Methanobacteriales regardless of the host species. The methanogenic communities changed significantly during the enrichment procedure, but still the strict hydrogenotrophic Methanobacteriales and Methanomicrobiales were the predominant orders in the enrichment cultures. The bioaugmentation potential of the enriched methanogenic cultures will be evaluated in further studies.Pahlevan, K., 2018. Telltale tungsten and the Moon. Nature Geoscience 11, 16-18. in high-precision isotopic analysis have provided key constraints on the origin and early evolution of the Earth and Moon. Measurements of the isotopes of tungsten provide the most stringent constraints on this history.The Earth–Moon system is currently thought to have emerged from the impact of two planet-sized bodies towards the end of planetary accretion1. Although this idea is now more than four decades old2,3, new tools to test, develop and interrogate the giant-impact hypothesis have come of age over the past decade. An isotopic resemblance for lunar and terrestrial rocks was recognized upon initial analysis of the lunar samples returned by the Apollo program, but recent advances in analytical techniques have revealed the scope and magnitude of the isotopic similarities and differences between the Earth and Moon. The flood of new high-precision isotopic data has presented challenges to leading hypotheses of Moon formation and motivated new proposals of processes accompanying lunar origin that can reconcile the observed isotopic signatures. In particular, high-precision measurements of tungsten (W) reported in Nature in 20074> and 20155,6 have stirred the debate over how the Earth–Moon system evolved.When lunar samples were first returned by the Apollo missions and analysed, a general isotopic similarity between Earth’s mantle and the Moon suggested that the two bodies formed from similar material7. It was hypothesized that the similarity could be explained by an off-centre giant impact of a Mars-sized impactor onto the proto-Earth in which the Moon formed from material vaporized from Earth mantle and emplaced into orbit. In such a scenario, the Moon would be expected to be depleted in volatile elements relative to the Earth’s mantle, but similar in isotopic composition for more refractory elements. However, in numerical simulations of this canonical giant-impact scenario, the debris disk is sourced mainly from the impacting body, whereas the Earth’s mantle is sourced mainly from the proto-Earth. Since all planetary bodies from which we have samples show isotopic differences, it is commonly assumed that the proto-Earth and the impactor were isotopically distinct as well. Therefore, it was expected that a difference in the isotopic compositions of the Earth and Moon would ultimately be resolved with improvements in analytical precision.Impressive analytical advances have been achieved, yet for several isotope systems, the Earth and Moon remain apparently identical to a precision difficult to explain by the canonical giant-impact process alone. Oxygen isotopic measurements are extremely similar relative to observed differences between planetary reservoirs. For instance, the difference in oxygen isotopes between Earth and Moon is less than a few percent of the difference between Earth and Mars8.9. Such a high-precision match, like that observed for titanium isotopes10, is suggestive of a common source for terrestrial and lunar mantle material.There is also a match for silicon isotopes. Silicon, however, can be sequestered into planetary cores with lighter isotopes preferentially partitioning into metals11, resulting in isotopically-heavy mantles. Silicon isotope fractionation depends on the pressure and temperature conditions of core formation. Although it is unknown if substantial silicon is sequestered in Earth’s core, the silicon isotopic identity of the Earth and Moon — again offset from Mars – suggests that the Moon formed from the Earth after the Earth’s core had formed. However, despite the high precision of the measurements, the interpretation of the match in O, Ti and Si isotopes is ambiguous: it is also conceivable that the Earth and Moon were built independently, but from the same planetary building blocks.Growing evidence for an apparent genetic link between lunar and terrestrial matter has been accompanied by an evolving and broadening debate about its origin — a debate that has been energized by isotopic measurements of tungsten. Although each element conveys unique information, tungsten yields particularly strict constraints on the events accompanying lunar origin: 182W is a decay product of 182Hf (hafnium), and the tungsten isotopic composition of lunar and terrestrial samples record the relative behaviour of hafnium and tungsten during the first 60 million years of Solar System history — spanning core formation in the Earth and in the putative Moon-forming impactor. Moreover, because tungsten has affinities for metals but hafnium does not, core formation will result in isotopic heterogeneity. Even after 182Hf becomes extinct, tungsten isotopes remain as tracers of geochemical equilibration expected during global differentiation events, such as the Moon-forming event. Unlike oxygen, titanium and silicon isotopes, the isotopes of tungsten would necessarily be affected by these planetary events, so any isotopic similarity between Earth and Moon materials cannot be explained by simply being sourced from the same precursors. Tungsten thus attains special significance in unravelling the lunar origin story.Measurement of indigenous tungsten isotopes in lunar samples is hampered by the exposure to cosmic rays that results in heterogenous compositions. Until recently, tungsten isotopic measurements had been used primarily as chronometers for early lunar differentiation. A decade ago, improved analytical techniques permitted the indigenous tungsten isotopic composition to be extracted from lunar samples4 revealing that diverse lunar rocks have identical indigenous tungsten isotopic compositions. This suggests differentiation of the lunar interior occurred after the 182Hf had been used up, and thus relatively late Moon formation. Moreover, the tungsten isotopic composition of lunar materials is nearly identical that of Earth’s mantle.Like other known isotopes systems, the tungsten similarity supports a terrestrial origin of lunar material. But, since the tungsten isotopic system is so sensitive to core formation conditions and timing, the compositions of proto-Earth mantle and impacting body were probably distinct. Even if they were identical, metal-silicate equilibration in the post-impact Earth and debris disk would be expected to lead to tungsten isotopic heterogeneity in the absence of system-wide mixing. The isotopic similarity in tungsten thus supports equilibration of the terrestrial magma ocean and the proto-lunar disk in the aftermath of the giant impact (Fig. 1), as has also been proposed for oxygen12The Moon-forming impact event is thought to have been a relatively late event that occurred towards the end of Earth formation, but planetary accretion continued after the Moon formed. Indeed, such late accretion has been invoked to explain the abundance of highly siderophile elements in the Earth’s mantle, due to the fact that such elements would have partitioned almost entirely into the core during planetary differentiation. Following the initial measurements of the indigenous tungsten composition of lunar rocks, it was predicted that the delivery of highly siderophile elements, such as tungsten, to the Earth’s mantle by late accretion would have produced an offset between the tungsten isotopic compositions of the silicate Earth and Moon13,14. In 2015, two independent sets of measurements at high precision5,6 found a small offset — only about 25 ppm — between terrestrial and lunar samples, consistent with late accretion to an initially isotopically homogeneous Earth and Moon.The small offset in tungsten’s isotopic composition implies that the composition of the Earth and Moon immediately after Moon formation was incredibly similar: any differences would require even higher precision to observe. Although the isotopic similarity of Earth and Moon is consistent with the giant-impact hypothesis, isotopic equivalence poses problems. If the Moon formed via impact of two planetary bodies, where is the isotopic evidence for the second body? Even if the two impacting bodies were isotopically indistinguishable, an isotopically identical Earth and Moon is not an inevitable or even likely outcome of a single giant impact event: metal–silicate equilibration would be expected to cause observable offsets in the silicate mantles of the Earth and Moon. Efficient mixing of Earth and Moon materials in the aftermath of the impact may be required.The implications of the close, but not perfect, match in tungsten isotopes between the Earth and Moon are inspiring a new generation of models of both Moon formation and late accretion that aim to meet the refined constraints. For example, writing in Nature Geoscience, Marchi and colleagues15 propose that late accretionary impacts of large differentiated bodies — in which highly siderophile elements are sequestered in the planetesimal cores — can explain tungsten isotopic compositions of Earth and Moon materials. A decade of revelations of the isotopic identicality of the Earth and Moon has challenged the canonical giant impact hypothesis of Earth–Moon formation, but has inspired collaborations between isotope geochemists and impact modellers to address the many open questions.References1. Canup, R. M. Philos. Trans. R. Soc A 372, 20130175 (2014).2. Cameron, A. G. W. & Ward, W. R. The origin of the Moon. In 7th Lunar Sci. Conf. abstr. 1041 (1976).3. Hartmann, W. K. & Davis, D. R. Icarus 24, 504–515 (1975).4. Touboul, M., Kleine, T., Bourdon, B., Palme, H. & Wieler, R. Nature 450, 1206–1209 (2007).5. Touboul, M., Puchtel, I. S. & Walker, R. J. Nature 520, 530–533 (2015).6. Kruijer, T. S., Kleine, T., Fischer-Godde, M. & Sprung, P. Nature 520, 534–537 (2015).7. Clayton, R. & Mayeda, T. Genetic relations between the moon and meteorites. In 6th Lunar Planet. Sci. Conf. 1761–1769 (1975)8. Wiechert, U. et al. Science 294, 345–348 (2001).9. Franchi, I. A., Wright, I. P., Sexton, A. S. & Pillinger, C. T. Meteoritics Planet. Sci. 34, 657–661 (1999).10. Zhang, J. J., Dauphas, N., Davis, A. M., Leya, I. & Fedkin, A. Nat. Geosci. 5, 251–255 (2012).11. Georg, R. B., Halliday, A. N., Schauble, E. A. & Reynolds, B. C. Nature 447, 1102–1106 (2007).12. Pahlevan, K. & Stevenson, D. J. Earth Planet. Sci. Lett. 262, 438–449 (2007).13. Halliday, A. N. Philos. Trans. R. Soc. A 366, 4163–4181 (2008).14. Walker, R. J. Philos. Trans. R. Soc A 372, 20130258 (2014).15. Marchi et al. Nat. Geosci. (2017).Pang, H., Pang, X.-q., Dong, L., Zhao, X., 2018. Factors impacting on oil retention in lacustrine shale: Permian Lucaogou Formation in Jimusaer Depression, Junggar Basin. Journal of Petroleum Science and Engineering 163, 79-90. formation developed a set of good quality hydrocarbon source rock in the Jimusaer Depression. Plenty of hydrocarbon shows in shale have been discovered, indicating a good prospect for shale oil exploration. In this paper, the data including Rock-Eval pyrolysis, X-ray diffraction (XRD), lithology, and porosity were used to analyze the impact of oil retention in Lucaogou shale. The results showed that the TOC contents of lacustrine shale have a maximum of 15.51%, averaging 3.49%; the maturity is in the range 0.5%–1.1%; and the organic matters are of type I; the largest net thickness of source rock can reach 194?m, mainly distributed in the centre area rounding J35-J174 well block. Impacts of oil retention in lacustrine shale include TOC, Ro and reservoir physical property. S1 contents increase with growing TOC, and when TOC content is more than 3%, hydrocarbon show thickness ratios (thickness ratio of hydrocarbon show to strata) are over 90%. When Ro reaches 0.8%, OSI (S1/TOC?100) become largest, and hydrocarbon show thickness ratios are over 80%. Good oil saturation relates to high porosity. Argillaceous limestone and argillaceous dolomite primarily develop matrix pores, while mudstone mainly develops organic pores. Since lower content of clay and higher content of brittle minerals in argillaceous limestone and argillaceous dolomite than in mudstone, both of the porosity and oil saturation of argillaceous limestone and argillaceous dolomite are better than that of mudstone. Generally, the areas deeper than hydrocarbon expulsion threshold (3200–4300?m of depth or 0.8%–1.3% of Ro) are most favourable for shale oil accumulation, which matches the actual oil production data. The depths of high production wells are no less than hydrocarbon expulsion threshold, since S1 contents are high enough to satisfy critical residual amount and pores are developed. Meanwhile, good quality of reservoir developed when organic pores and overpressure were formed during hydrocarbon generation and expulsion.Pang, W., Li, H.A., 2018. Application of augmented free-water Rachford-Rice algorithm to water/hydrocarbons mixtures considering the dissolution of methane in the aqueous phase. Fluid Phase Equilibria 460, 75-84. equilibria for water/hydrocarbon mixtures are frequently encountered in hydrocarbon reservoirs. The presence of water in these mixtures can lead to a higher number of equilibrating phases, increasing the complexity of the multiphase split calculations. It is a common approach to treating water as the bulk free phase and performing only two-phase split calculations on the hydrocarbon-rich liquid phase and vapor phase. The free-water flash algorithm uses a different approach; it considers the effect of water presence on the overall phase equilibrium of water/hydrocarbon mixtures, albeit also assuming the aqueous phase to be pure water. The free-water algorithm might be less accurate in some cases where the solubility of methane in the aqueous phase cannot be neglected. In this study, a modified version of the free-water flash method previously developed by the authors, i.e., the so-called augmented free-water flash, is extended to perform three-phase vapor-oleic-aqueous (VOA) flash calculations for water/hydrocarbons mixtures on the basis of the assumption that only the existence of water and methane is considered in the aqueous phase. The flash package incorporating this augmented free-water method can handle the single-phase, two-phase, or three-phase equilibrium calculations. Example calculations made on two water/hydrocarbons mixtures demonstrate that the phase compositions and phase mole fractions calculated by augmented free-water method provide better predictions compared with the traditional free-water method since the solubility of methane is considered in the aqueous phase. Our new algorithm is also shown to be computationally more efficient than the conventional full three-phase flash algorithm. Therefore, the augmented free-water approach strikes a good balance between computational efficiency and prediction accuracy.Panmei, C., Divakar Naidu, P., Mohtadi, M., 2017. Bay of Bengal exhibits warming trend during the Younger Dryas: Implications of AMOC. Geochemistry, Geophysics, Geosystems 18, 4317-4325. sharp decline in temperature during the Younger Dryas (YD) preceding the current warmer Holocene is well documented in climate archives from the Northern Hemisphere high latitudes. Although the magnitude of YD cooling varied spatially, the response of YD cooling was well documented in the Atlantic and Pacific Oceans but not in the Indian Ocean. Here we investigate whether the modern remote forcing of tropical Indian Ocean sea surface temperature (SST) by Northern Hemisphere climate changes holds true for events such as the YD. Our SST reconstruction from the western Bay of Bengal exhibits an overall warming of ～1.8°C during the YD. We further compared our data with other existing Mg/Ca-based SST records from the Northern Indian Ocean and found no significant negative SST anomalies in both the Arabian Sea and the Bay of Bengal compared to pre- and post-YD, suggesting that no apparent cooling occurred during the YD in the Northern Indian Ocean. In contrast, most part of the YD exhibits positive SST anomalies in the Northern Indian Ocean that coincide with the slowdown of the Atlantic Meridional Overturning Circulation during this period.Pant??ek, R., Sedlá?ek, I., Indráková, A., Vrbovská, V., Ma?laňová, I., Kova?ovic, V., ?vec, P., Králová, S., Kri?tofová, L., Kekláková, J., Petrá?, P., Do?ka?, J., 2018. Staphylococcus edaphicus sp. nov., isolated in Antarctica, harbors the mecC gene and genomic islands with a suspected role in adaptation to extreme environments. Applied and Environmental Microbiology 84, Article e01746-17.: Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources comprising stone fragments and sandy soil in James Ross Island, Antarctica. Here, we describe properties of a novel species of the genus Staphylococcus that has a 16S rRNA gene sequence nearly identical to that of Staphylococcus saprophyticus. However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at the whole-genome level, with an average nucleotide identity of <85% and inferred DNA-DNA hybridization of <30%. It forms a separate branch in the S. saprophyticus phylogenetic clade as confirmed by multilocus sequence analysis of six housekeeping genes, rpoB, hsp60, tuf, dnaJ, gap, and sod. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and key biochemical characteristics allowed these bacteria to be distinguished from their nearest phylogenetic neighbors. In contrast to S. saprophyticus subsp. saprophyticus, the novel strains are pyrrolidonyl arylamidase and β-glucuronidase positive and β-galactosidase negative, nitrate is reduced, and acid produced aerobically from d-mannose. Whole-genome sequencing of the 2.69-Mb large chromosome revealed the presence of a number of mobile genetic elements, including the 27-kb pseudo-staphylococcus cassette chromosome mec of strain P5085T (ψSCCmecP5085), harboring the mecC gene, two composite phage-inducible chromosomal islands probably essential to adaptation to extreme environments, and one complete and one defective prophage. Both strains are resistant to penicillin G, ampicillin, ceftazidime, methicillin, cefoxitin, and fosfomycin. We hypothesize that antibiotic resistance might represent an evolutionary advantage against beta-lactam producers, which are common in a polar environment. Based on these results, a novel species of the genus Staphylococcus is described and named Staphylococcus edaphicus sp. nov. The type strain is P5085T (= CCM 8730T = DSM 104441T). Importance: The description of Staphylococcus edaphicus sp. nov. enables the comparison of multidrug-resistant staphylococci from human and veterinary sources evolved in the globalized world to their geographically distant relative from the extreme Antarctic environment. Although this new species was not exposed to the pressure of antibiotic treatment in human or veterinary practice, mobile genetic elements carrying antimicrobial resistance genes were found in the genome. The genomic characteristics presented here elucidate the evolutionary relationships in the Staphylococcus genus with a special focus on antimicrobial resistance, pathogenicity, and survival traits. Genes encoded on mobile genetic elements were arranged in unique combinations but retained conserved locations for the integration of mobile genetic elements. These findings point to enormous plasticity of the staphylococcal pangenome, shaped by horizontal gene transfer. Thus, S. edaphicus can act not only as a reservoir of antibiotic resistance in a natural environment but also as a mediator for the spread and evolution of resistance genes. Paranaíba, J.R., Barros, N., Mendon?a, R., Linkhorst, A., Isidorova, A., Roland, F., Almeida, R.M., Sobek, S., 2018. Spatially resolved measurements of CO2 and CH4 concentration and gas-exchange velocity highly influence carbon-emission estimates of reservoirs. Environmental Science & Technology 52, 607-615. the conclusion of the Cassini mission, we present an updated topographic map of Titan, including all the available altimetry, SARtopo, and stereophotogrammetry topographic data sets available from the mission. We use radial basis functions to interpolate the sparse data set, which covers only ～9% of Titan's global area. The most notable updates to the topography include higher coverage of the poles of Titan, improved fits to the global shape, and a finer resolution of the global interpolation. We also present a statistical analysis of the error in the derived products and perform a global minimization on a profile-by-profile basis to account for observed biases in the input data set. We find a greater flattening of Titan than measured, additional topographic rises in Titan's southern hemisphere and better constrain the possible locations of past and present liquids on Titan's surface.Park, J., Riaz, A., Insyani, R., Kim, J., 2018. Understanding the relationship between the structure and depolymerization behavior of lignin. Fuel 217, 202-210. lignin depolymerization methods have been proposed. Nevertheless, the relationship between the structure of lignin and its depolymerization behavior has not been widely investigated. Herein, six types of lignin samples were produced from oakwood (OW, hardwood) and pinewood (PW, softwood) using three different delignification techniques (ethanolsolv, formasolv, and Klason). The content of ether linkages in the OW-derived lignins was approximately three times higher than that in the PW-derived lignins because of the presence of the sinapyl alcohol unit in the former. The contents of ether linkages in the lignin isolated via the different methods followed the order: formasolv?>?ethanolsolv?>?Klason. The lignin samples were depolymerized in a mixture of supercritical ethanol (scEtOH) and formic acid at temperatures of 250–350?°C. At 350?°C, regardless of the lignin type, high conversion (>95%) and a high bio-oil yield (>81?wt%) could be achieved, demonstrating that the combined use of scEtOH-HCOOH was very effective for the depolymerization of various types of lignin. At the low temperatures of 250–300?°C, the lignin conversion and bio-oil yield were highly dependent on the amount of ether linkages; for example, at 300?°C, the use of OW-derived formasolv lignin resulted in a high bio-oil yield (86.2?wt%), whereas the use of OW-derived Klason lignin resulted in a very low bio-oil yield (27.9?wt%). The properties of the bio-oils produced from the different types of lignin were discussed.Parnell, J., Bowden, S., Mark, D., 2017. Petroleum generation and migration in the Cambro-Ordovician Laurentian margin succession of NW Scotland. Journal of the Geological Society 175, 33-43. inclusion and organic biomarker data show that there was formerly a hydrocarbon system in the Cambro-Ordovician Laurentian margin rocks of NW Scotland. Oil fluid inclusions occur in stylolitized Eriboll Formation sandstone, in K-feldspar cements with an 40Ar/39Ar age of 415?±?5.5/5.8?Ma (2σ, analytical precision/full external precision). Organic extracts from Durness Group black limestones yield biomarker ratios characteristic of high thermal maturity. Organic maturation to yield oil probably occurred during orogenic deformation along the Moine Thrust Zone. The recognition of a hydrocarbon system in Scotland adds to a huge hydrocarbon province in Laurentian rocks including North America and Greenland.Parrott, J.L., Marentette, J.R., Hewitt, L.M., McMaster, M.E., Gillis, P.L., Norwood, W.P., Kirk, J.L., Peru, K.M., Headley, J.V., Wang, Z., Yang, C., Frank, R.A., 2018. Meltwater from snow contaminated by oil sands emissions is toxic to larval fish, but not spring river water. Science of The Total Environment 625, 264-274. assess the toxicity of winter-time atmospheric deposition in the oil sands mining area of Northern Alberta, embryo-larval fathead minnow (Pimephales promelas) were exposed to snowmelt samples. Snow was collected in 2011–2014 near (< 7 km) oil sands open pit mining operations in the Athabasca River watershed and at sites far from (> 25 km) oil sands mining. Snow was shipped frozen back to the laboratory, melted, and amended with essential ions prior to testing. Fertilized fathead minnow eggs were exposed (< 24 h post-fertilization to 7–16 days post-hatch) to a range of 25%–100% snowmelt. Snow samples far from (25–277 km away) surface mining operations and upgrading facilities did not affect larval fathead minnow survival at 100%. Snow samples from sites near surface mining and refining activities (< 7 km) showed reduced larval minnow survival. There was some variability in the potencies of snow year-to-year from 2011 to 2014, and there were increases in deformities in minnows exposed to snow from 1 site on the Steepbank River. Although exposure to snowmelt from sites near oil sands surface mining operations caused effects in larval fish, spring melt water from these same sites in late March–May of 2010, 2013 and 2014 showed no effects on larval survival when tested at 100%. Snow was analyzed for metals, total naphthenic acid concentrations, parent PAHs and alkylated PAHs. Naphthenic acid concentrations in snow were below those known to affect fish larvae. Concentrations of metals in ion-amended snow were below published water quality guideline concentrations. Compared to other sites, the snowmelt samples collected close to mining and upgrading activities had higher concentrations of PAHs and alkylated PAHs associated with airborne deposition of fugitive dusts from mining and coke piles, and in aerosols and particles from stack emissions.Pathak, M., Huang, H., Meakin, P., Deo, M., 2018. Molecular investigation of the interactions of carbon dioxide and methane with kerogen: Application in enhanced shale gas recovery. Journal of Natural Gas Science and Engineering 51, 1-8. with technological advancements such as hydraulic fracturing and horizontal drilling, only 20% of the original gas in shales is recoverable through current industry practices. This low recovery factor is attributed to very low permeability and sorption of much of the gas by solid organic matter. Enhanced gas recovery through carbon dioxide sequestration could be performed either by cyclic injection (huff and puff) of carbon dioxide or fracturing/re-fracturing the formation with a viscosified, foamed or energized carbon dioxide hydraulic fracturing fluid. This work employs molecular modeling to conduct a fundamental investigation of the interactions between carbon dioxide and the solid organic part of the shales, the majority of which is kerogen. In the current work, more realistic molecular models for Type II kerogen in oil-gas window, with active sites were used instead of the graphite based carbon models used in many previously published works. Both adsorption onto kerogen surfaces and absorption within it contribute to its high sorption capacity. Previously, researchers have shown through modeling and experiments that kerogen has a higher affinity and adsorption capacity for carbon dioxide than for methane. The current work studies the sorption of carbon dioxide and methane using quasi equilibrium Molecular Dynamics (MD) simulations. The MD simulations of ternary system of methane, carbon dioxide and kerogen revealed that the carbon dioxide is more strongly retained than methane in the bulk kerogen matrix. The self-diffusion coefficient of carbon dioxide (Dself?=?10-10?m2/s) in the kerogen was found to be an order of magnitude smaller than that of methane (Dself?=?10-9?m2/s) in the kerogen. The MD simulations revealed that in the process of carbon dioxide - methane 1:1 exchange in the kerogen matrix, the kerogen matrix shrinks in volume. This may lead to disturbance in the fluid pathways that contribute to fluid flow in shales. The molecular investigation performed in this fundamental work is relevant to any carbon dioxide enhanced gas production from shale gas resources.Pearce, J.K., Turner, L., Pandey, D., 2018. Experimental and predicted geochemical shale-water reactions: Roseneath and Murteree shales of the Cooper Basin. International Journal of Coal Geology 187, 30-44. back or produced water from shale gas hydraulic stimulation has been reported, most notably in the USA, to contain high concentrations of dissolved metals such as Na, As, Cd, or U which may originate from formation water or fluid-mineral reactions. An understanding of the fluid-mineral geochemical reactions occurring can be gained from constrained experimental studies combined with validated predictive kinetic geochemical modelling. Shales of the Cooper Basin Roseneath-Epsilon-Murteree (REM) sequence are unconventional gas targets in Australia. Two core samples from the Roseneath shale and Murteree shale were geochemically characterised in detail. Both shales contained 55–57% quartz, 14–18% illite/muscovite, 3–5% kaolinite and 15–17% (Mg)-siderite. The Roseneath shale sample from 3266 m contained relatively more sphalerite and pyrite, with a higher V, Cr, Cu, Zn and Pb content. The Murteree shale from 3497 m, contained relatively more siderite and also ankerite, and had a higher Fe, Mn, and Mg content. On experimental reaction with water and traces of air at 75 °C and 200 bar of N2, siderite was dissolved in both cases, and ankerite was dissolved from Murteree shale. Sphalerite, pyrite, and siderite oxidative dissolution reduced the solution pH to ~ 3 during reaction of the Roseneath shale, with open pores and cubic Fe-rich precipitates formed. Higher concentrations of dissolved Cr, Co, Ni, Cu, Zn, Cd, and U were released from the Roseneath shale than the Murteree, though most released concentrations were < 10% of the total amount measured in the core. Ankerite in the Murteree shale initially buffered solution pH to 5.5, but subsequently pH decreased to 4. Spherical Fe-oxides precipitated during reaction of the Murteree Shale ± Cr signatures sequestering metals. Higher concentrations of dissolved Mn, Mg, Ca, Na, Sr, Mo and Hg were initially mobilised from the Murteree shale, with Na, Mo and Hg concentrations subsequently decreasing. Geochemical kinetic modelling of the experiments was performed, using experimental data to estimate mineral reactive surface areas. Mineral reactive surface areas in geochemical models were increased to 1000 cm2/g for clays, and 10–30 cm2/g for carbonates to approximate the experimental water chemistry. Models confirmed the dissolution of siderite, pyrite, sphalerite, and for Murteree shale also ankerite. Fe-oxide, siderite, or sulphide precipitation was predicted.The amount and reactivity of carbonate minerals and the presence of sulphides affect the fluid acidity and dissolved metal content. Metal concentrations in produced water will be site specific partly depending on the mineralogy of the formation and chemistry of injected fluids. Understanding the geochemical evolution of fluids and accurately predicting them via combined experimental and validated model studies could lead to improved upscaled predictions of fluid chemistry or strategies for treatment.The precipitation of Fe-oxides could clog pore throats or fractures, and has the potential to decrease permeability and long-term gas production.Peck, W.D., Azzolina, N.A., Ge, J., Bosshart, N.W., Burton-Kelly, M.E., Gorecki, C.D., Gorz, A.J., Ayash, S.C., Nakles, D.V., Melzer, L.S., 2018. Quantifying CO2 storage efficiency factors in hydrocarbon reservoirs: A detailed look at CO2 enhanced oil recovery. International Journal of Greenhouse Gas Control 69, 41-51. dioxide (CO2) enhanced oil recovery (EOR) will likely be the primary means of geologic CO2 storage during the early stages of commercial-scale carbon capture and storage (CCS) because of the inherent economic incentives as well as the abundant experience and demonstrated success in the United States, where CO2 EOR has been employed since 1974. The work presented here estimates CO2 storage efficiency factors in CO2 EOR operations using a unique industry database of CO2 EOR sites and 12 different reservoir simulation models. The simulation models encompass fluvial clastic and shallow shelf carbonate depositional environments for reservoir depths of 1219 and 2438?m (4000 and 8000 feet) and 7.6-, 20-, and 64-m (25-, 66-, and 209-foot)-thick pay zones. A novel statistical modeling technique incorporating the Michaelis–Menten function is used to generate empirical percentile estimates of CO2 storage efficiency factors.West Texas San Andres dolomite water alternating gas (WAG) CO2 flood performance data were used to derive P10, P50, and P90 CO2 storage efficiency factors of 0.76, 1.28, and 1.74 Mscf/STB (stock tank barrel) of original oil in place. Median CO2 storage efficiency factors from continuous CO2 injection following conventional waterflood varied from 15% to 61% and 8% to 40% for fluvial clastic and shallow shelf carbonate simulation models, respectively, while those from WAG injection varied from 14% to 42% and 8% to 31%, respectively. Variation in the CO2 storage efficiency factors was largely attributable to reservoir depth (a surrogate for reservoir pressure and temperature) and lithology (clastic versus carbonate). The results of this work provide practical information that can be used to quantify CO2 storage resource estimates in oil reservoirs during CO2 EOR operations (as opposed to storage following depletion) and the uncertainty associated with those estimates.Pellegrini, A.F.A., Ahlstr?m, A., Hobbie, S.E., Reich, P.B., Nieradzik, L.P., Staver, A.C., Scharenbroch, B.C., Jumpponen, A., Anderegg, W.R.L., Randerson, J.T., Jackson, R.B., 2018. Fire frequency drives decadal changes in soil carbon and nitrogen and ecosystem productivity. Nature 553, 194-198. frequency is changing globally and is projected to affect the global carbon cycle and climate. However, uncertainty about how ecosystems respond to decadal changes in fire frequency makes it difficult to predict the effects of altered fire regimes on the carbon cycle; for instance, we do not fully understand the long-term effects of fire on soil carbon and nutrient storage, or whether fire-driven nutrient losses limit plant productivity. Here we analyse data from 48 sites in savanna grasslands, broadleaf forests and needleleaf forests spanning up to 65 years, during which time the frequency of fires was altered at each site. We find that frequently burned plots experienced a decline in surface soil carbon and nitrogen that was non-saturating through time, having 36 per cent (±13 per cent) less carbon and 38 per cent (±16 per cent) less nitrogen after 64 years than plots that were protected from fire. Fire-driven carbon and nitrogen losses were substantial in savanna grasslands and broadleaf forests, but not in temperate and boreal needleleaf forests. We also observe comparable soil carbon and nitrogen losses in an independent field dataset and in dynamic model simulations of global vegetation. The model study predicts that the long-term losses of soil nitrogen that result from more frequent burning may in turn decrease the carbon that is sequestered by net primary productivity by about 20 per cent of the total carbon that is emitted from burning biomass over the same period. Furthermore, we estimate that the effects of changes in fire frequency on ecosystem carbon storage may be 30 per cent too low if they do not include multidecadal changes in soil carbon, especially in drier savanna grasslands. Future changes in fire frequency may shift ecosystem carbon storage by changing soil carbon pools and nitrogen limitations on plant growth, altering the carbon sink capacity of frequently burning savanna grasslands and broadleaf forests.Peng, Y., Yue, D., Xiao, L., Qian, X., 2018. Temporal variation and co-occurrence patterns of bacterial communities in eutrophic Lake Taihu, China. Geomicrobiology Journal 35, 186-197. understand the long-term and local variations of bacteria under the influence of annually re-occurred water bloom, bacterial community composition (BCC) was investigated monthly for 3?years (2009?2011) at four different sites located across Lake Taihu. The bacterial community composition was analyzed by 16S rRNA gene clone libraries and terminal restriction fragment length polymorphism. Co-occurrence patterns among bacterial taxa and environmental variables were determined through network analysis. Overall, strong seasonal variation patterns of BCC were observed whilst the spatial variations of BCC were slight in the long-term observation. However, core species bacteria persisted throughout the annual variations. Network analysis showed that the highly connected operational taxonomic units in bacteria-environment network included both the numerically dominant taxa and some functional groups with low abundance, such as Methylophilaceae and Nitrospira. Co-occurrence networks further revealed that the correlations of bacteria-bacteria could be more critical than those between environment and bacteria in structuring microbial communities, and would be a crucial driving factor of BCC in Lake Taihu.Phong, D.D., Hur, J., 2018. Using two-dimensional correlation size exclusion chromatography (2D-CoSEC) and EEM-PARAFAC to explore the heterogeneous adsorption behavior of humic substances on nanoparticles with respect to molecular sizes. Environmental Science & Technology 52, 427-435. adsorption behaviors of different constituents within bulk humic substances (HS) on two nanoparticles, TiO2 and ZnO, were examined by using two-dimensional correlation size exclusion chromatography (2D-CoSEC) and excitation emission matrix–parallel factor analysis (EEM-PARAFAC), which separated bulk HS into different size fractions and fluorescent components, respectively. Subtle changes in the size distributions of HS with increasing adsorbents were successfully identified and tracked via the 2D-CoSEC. From adsorption isotherm experiments, three different HS constituent groups with respect to sizes and fluorescence features were identified by the 2D-CoSEC and EEM-PARAFAC, respectively. The chromatographically separated HS size groups presented dissimilar adsorption behaviors in terms of adsorption affinity and isotherm nonlinearity. The sequence orders of adsorption, interpreted from the 2D-CoSEC, was consistent with those of the isotherm model parameters individually calculated for different HS size subfractions, signifying the promising application of 2D-CoSEC in obtaining an insight into the heterogeneous adsorption of HS in terms of molecular sizes. EEM-PARAFAC results also supported the major finding of the 2D-CoSEC as shown by the preferential adsorption of the fluorescent components associated with large molecular sizes.Pirok, B.W.J., Gargano, A.F.G., Schoenmakers, P.J., 2018. Optimizing separations in online comprehensive two-dimensional liquid chromatography. Journal of Separation Science 41, 68-98. comprehensive two-dimensional liquid chromatography has become an attractive option for the analysis of complex nonvolatile samples found in various fields (e.g. environmental studies, food, life, and polymer sciences). Two-dimensional liquid chromatography complements the highly popular hyphenated systems that combine liquid chromatography with mass spectrometry. Two-dimensional liquid chromatography is also applied to the analysis of samples that are not compatible with mass spectrometry (e.g. high-molecular-weight polymers), providing important information on the distribution of the sample components along chemical dimensions (molecular weight, charge, lipophilicity, stereochemistry, etc.). Also, in comparison with conventional one-dimensional liquid chromatography, two-dimensional liquid chromatography provides a greater separation power (peak capacity). Because of the additional selectivity and higher peak capacity, the combination of two-dimensional liquid chromatography with mass spectrometry allows for simpler mixtures of compounds to be introduced in the ion source at any given time, improving quantitative analysis by reducing matrix effects. In this review, we summarize the rationale and principles of two-dimensional liquid chromatography experiments, describe advantages and disadvantages of combining different selectivities and discuss strategies to improve the quality of two-dimensional liquid chromatography separations.Planavsky, N., 2018. From orogenies to oxygen. Nature Geoscience 11, 9-10. controls on atmospheric oxygenation are frequently invoked — but whether geochemical records support these ties is an unsettled question.The rise of atmospheric oxygen on Earth is a foremost example of life transforming a planet. But the onset of photosynthesis is only part of the tale of oxygen on Earth. Reducing agents, which come largely from Earth’s interior and crust, react with and remove the oxygen from the atmosphere. In this light, tectonic and magmatic processes are as essential as biological processes in controlling atmospheric oxygen levels. In the first volume of Nature Geoscience, published almost a decade ago, Campbell and Allen1 helped trigger a new wave of research investigating such links. By comparing records of past tectonic activity with records of atmospheric oxygen levels, they suggested that intervals of extensive mountain building associated with supercontinent assembly correlate with step increases in atmospheric oxygen levels over time.Oxygenic photosynthesis is an evolutionary singularity and it is the only significant source of free O2 for Earth’s surface. Therefore, our current oxygen-rich atmosphere is a direct result of a discrete evolutionary event. However, O2 is removed from the atmosphere during respiration and decay of organic matter, as well as via the oxidation of pyrite during weathering and of reduced gases produced during volcanism and metamorphism. When organic-matter-rich sediments are buried in sedimentary basins, oxygen accumulates in the atmosphere. Changes in atmospheric oxygen levels through time reflect switches in the balance between the photosynthetic supply of oxygen and its consumption during oxidative reactions, which is controlled in large part by the solid Earth system. For example, today, sedimentation rates play a critical role in controlling burial of organic matter2. Therefore, we might expect that mountain-building events, by mediating increases in sedimentation rates, would favour atmospheric oxygenation.To test this theory, Campbell and Allen1 compiled a global database of the abundance and U–Th–Pb ages of the magmatic mineral zircon and compared this record to independent estimates of surface oxygen levels. Under the assumption that zircon-rich granitic crust forms during mountain-building events while continents collide, the researchers identified peaks in zircon abundance that temporally coincide with assembly of supercontinents or other major orogenic events. Intriguingly, the peaks correlated with previously inferred gradual step increases in atmospheric oxygen through time. To explain this correlation, Campbell and Allen1 proposed that increased erosion during mountain building led to enhanced organic carbon burial. It is reasonable to expect that delivery of large volumes of sediment to the oceans would enhance organic carbon burial, facilitating oxygen accumulation in the atmosphere3.The use of zircon data to reconstruct past tectonic activity has been critiqued4. A fair case can be made that the early generation detrital zircon compilations were not representative of Earth’s surface through time and thus are unlikely to robustly track global-scale processes. However, over the past decade there has been tremendous growth in the amount of detrital zircon data generated (Fig. 1) and new ways of dealing with these vast datasets have also emerged to circumvent biases. For instance, there has been a push to consider the proportion of young detrital zircon grains within given periods of geologic history. This provides a means to quantify the extent of zircon production during a geologic interval, avoiding spatiotemporal biases linked to variable exhumation and erosion histories that commonly mask more ancient mountain-building events5. There has also been a shift to more statistically grounded approaches to address sampling biases. The end result is that detrital zircon records have become established as one of the main tools that we can use to trace the tectonic pulse of the Earth5. Despite these advances, many of the zircon peaks identified by Campbell and Allen1 still stand out in the zircon record. The researchers linked these peaks to the general process of mountain building and supercontinent assembly, but an emerging and more balanced view is probably that peaks in zircon abundance primarily track the production of new granitic crust that largely forms in continental arcs tied to subduction zones5. Importantly, mountains can persist well after arc volcanism wanes, as is the case in several modern mountain chains.Palaeoredox proxy work has also substantially improved over the past decade. Several new proxies that track marine and atmospheric oxygen levels have been developed and the size of palaeoproxy datasets has increased dramatically. With these improvements, our understanding of the structure of Earth’s oxygenation has shifted considerably. Rather than a progressive rise to higher oxygenation levels, similar to that discussed by Campbell and Allen1, an increasingly popular view is one of Earth’s oxygenation as a rollercoaster ride, with large swings in atmospheric O2 levels6. Furthermore, mounting evidence suggests that there were jumps to high atmospheric oxygen levels roughly 2.2 to 2.1 billion years ago, as well as about 850 to 800 million years ago6,7. These transient increases are marked most conspicuously by the appearance of massive sulfate deposits, a direct reflection of a more oxidizing ocean7. Sulfate accumulates and eventually becomes buried as massive evaporates in a well-oxidized ocean–atmosphere system in which pyrite burial is inhibited.These two more recently identified intervals of oxygenation correspond with lulls in zircon production (Fig. 1) — the opposite of the trend predicted by Campbell and Allen1 — and presumably periods of limited arc volcanism5,8. However, this does not mean that there is a total decoupling between mountain building and surface oxygen levels. Following continent–continent collisions, on-going convergence and crustal thickening will lead to sustained intervals of high topography and high rates of erosion and sedimentation, as observed in the Himalayas today5. Additionally, a decrease in volcanism should cause a drop in the amount of reductants being transported from Earth’s interior to the surface. Therefore, the tail end (rather than the peak) of significant pulses in orogenic activity could trigger oxidation events. High sedimentation rates favour increased organic carbon burial, which, coupled with reduced volcanic outgassing of oxygen-consuming compounds, could lead to a spike in surface oxygen levels. Building from this framework, tectonically driven perturbations could have been sufficient to destabilize the Earth from the low-oxygen steady state that appears to have characterized most of Earth’s middle history6.It is difficult to gauge whether these tectonic and atmospheric ties are robust, or whether they will be overturned as proxy records continue to be revised and expanded. There is currently intense debate concerning Proterozoic atmospheric oxygen levels6,9, 10. Nonetheless, few would disagree that we now have a more realistic and refined view of the history of Earth’s oxygenation than we did a decade ago. Similarly, although links between atmospheric and tectonic processes are becoming less tenuous, a clear consensus has not yet emerged.There is, however, agreement that it is a worthwhile endeavour to attempt to disentangle the respective roles that biotic and tectonic evolution played in shaping the history of Earth’s atmosphere — and the work of Campbell and Allen1 played an important role in developing that line of investigation.References1. Campbell, I. H. & Allen, C. M. Nat. Geosci. 1, 554–558 (2008).2. Canfield, D. E. Chem. Geol. 114, 315–329 (1994).3. Galy, V. et al. Nature 450, 407–410 (2007).4. Hawkesworth, C., Cawood, P., Kemp, T., Storey, C. & Dhuime, B. Science 323, 49–50 (2009).5. McKenzie, N. R., Hughes, N. C., Gill, B. C. & Myrow, P. M. Geology 42, 127–130 (2014).6. Lyons, T. W., Reinhard, C. T. & Planavsky, N. J. Nature 506, 307–315 (2014).7. Turner, E. C. & Bekker, A. Geol. Soc. Am. Bull. 128, 203–222 (2016).8. Condie, K. C., Belousova, E., Griffin, W. L. & Sircombe, K. N. Gondwana Res. 15, 228–242 (2009).9. Sperling, E. A., Knoll, A. H. & Girguis, P. R. Annual Rev. Ecol. Evol. System. 46, 215–235 (2015).10. Zhang, S. et al. Proc. Natl Acad. Sci. USA 113, 1731–1736 (2016).11. Lee, C. T. A. et al. Nat. Geosci. 9, 417–420 (2016).Plancq, J., Cavazzin, B., Juggins, S., Haig, H.A., Leavitt, P.R., Toney, J.L., 2018. Assessing environmental controls on the distribution of long-chain alkenones in the Canadian Prairies. Organic Geochemistry 117, 43-55. alkenones (LCAs) have been used for decades to reconstruct quantitative sea-surface temperature records, but they also have a great potential for paleotemperature reconstructions in lacustrine settings. Here, we investigated how the presence and abundance of LCAs in surface sediments from 106 lakes varied with environmental conditions in lakes of the northern Great Plains (Canadian Prairies) in southern Saskatchewan, Canada. Consistent with preliminary research, we found LCAs in 55% of surveyed lakes, with mean concentrations of 143?μg/g dry sediment, but very high concentrations (up to 2.3?mg/g dry sediment) in 7% of lakes. Statistical analyses indicate that salinity and stratification play key roles in determining LCA presence and abundance supporting previous research in Spain and the northern Great Plains, USA. Overall, the alkenone unsaturation index (U37K) was not correlated significantly with average summer water temperature, probably because the timing of maximum LCA production occurs during the spring season. We conclude that improved seasonal sampling is required within the study lakes to better identify the timing and habitat of haptophyte production, and allow development of environmental temperature reconstruction tools.Poad, B.L.J., Zheng, X., Mitchell, T.W., Smith, R.D., Baker, E.S., Blanksby, S.J., 2018. Online ozonolysis combined with ion mobility-mass spectrometry provides a new platform for lipid isomer analyses. Analytical Chemistry 90, 1292-1300. of the most significant challenges in contemporary lipidomics lies in the separation and identification of lipid isomers that differ only in site(s) of unsaturation or geometric configuration of the carbon–carbon double bonds. While analytical separation techniques including ion mobility spectrometry (IMS) and liquid chromatography (LC) can separate isomeric lipids under appropriate conditions, conventional tandem mass spectrometry cannot provide unequivocal identification. To address this challenge, we have implemented ozone-induced dissociation (OzID) in-line with LC, IMS, and high resolution mass spectrometry. Modification of an IMS-capable quadrupole time-of-flight mass spectrometer was undertaken to allow the introduction of ozone into the high-pressure trapping ion funnel region preceding the IMS cell. This enabled the novel LC-OzID-IMS-MS configuration where ozonolysis of ionized lipids occurred rapidly (10 ms) without prior mass-selection. LC-elution time alignment combined with accurate mass and arrival time extraction of ozonolysis products facilitated correlation of precursor and product ions without mass-selection (and associated reductions in duty cycle). Unsaturated lipids across 11 classes were examined using this workflow in both positive and negative ion modalities, and in all cases, the positions of carbon–carbon double bonds were unequivocally assigned based on predictable OzID transitions. Under these conditions, geometric isomers exhibited different IMS arrival time distributions and distinct OzID product ion ratios providing a means for discrimination of cis/trans double bonds in complex lipids. The combination of OzID with multidimensional separations shows significant promise for facile profiling of unsaturation patterns within complex lipidomes including human plasma.Poddar, A., Das, S.K., 2018. Microbiological studies of hot springs in India: a review. Archives of Microbiology 200, 1-18. earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37–99?°C and 6.8–10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.Prebihalo, S.E., Berrier, K.L., Freye, C.E., Bahaghighat, H.D., Moore, N.R., Pinkerton, D.K., Synovec, R.E., 2018. Multidimensional gas chromatography: Advances in instrumentation, chemometrics, and applications. Analytical Chemistry 90, 505-532. of Review: Analysis of volatile and semivolatile analytes by gas chromatography (GC) methods is an indispensable tool in the analytical chemist’s tool box. A myriad of fields of study rely upon the application of GC methods to address an ever growing demand to provide useful chemical information from GC data. As the realm of GC application has expanded, there has been an evolution to develop more powerful instrumental and data analysis approaches to keep pace with the wealth of complex samples that require analysis. To address this challenge, advances in GC instrumentation have evolved from one-dimensional-gas chromatography (1D-GC) and heart cutting approaches such as (GC-GC), to a variety of instrumentation designs referred to broadly as multidimensional gas chromatography (MDGC). The principle form of MDGC that has gained wide implementation is comprehensive two-dimensional (2D) gas chromatography (GC × GC) as shown in Figure 1A, pioneered nearly 26 years ago by Liu and Phillips. When comparing 1D-GC (Figure 1B) relative to GC × GC (Figure 1C), the benefits of a secondary separation become evident. Blumberg and co-workers have theoretically determined that the 2D peak capacity provided by GC × GC compared to the peak capacity of 1D-GC is approximately an order of magnitude higher when the run times are held constant. This benefit is illustrated using a relatively complex sample of coffee. By adding a multivariate detector such as a time-of-flight mass spectrometry (TOFMS), another selective dimension of data is provided which may allow identification of analytes (Figure 1D). This review will focus essentially on GC × GC, with selected developments of other forms of MDGC also covered. In this regard, we focus primarily on research published since the last Fundamental Review published by Seeley and Seeley in 2013, with older publications covered as deemed necessary to provide additional insight into addressing the current challenges, and to put the more recent developments into historical context. This review is organized into the following broad categories: instrumental advances, data analysis, and applications. Within the realm of instrumental advances, there has been significant progress in the areas of modulators and detectors. The modulator is often referred to as the “heart” of the GC × GC instrument (Figure 1A) as it transfers eluate from the primary 1D column to the secondary 2D column facilitating comprehensive separations. Modulators are often classified into three broad categories: (1) thermal, (2) valve-based, and (3) flow. There has also been significant instrumental advances in the area of detectors, such as high-resolution-time-of-flight mass spectrometry (HR-TOFMS), which provides significant gains in chemical selectivity relative to MS with unit mass resolution as well as the vacuum ultraviolet (VUV) absorption detector. As GC × GC instrumentation has evolved to provide superior data, the desire by researchers to study more complex systems (and more samples per study), has led to the need to develop more powerful data analysis approaches while still addressing some of the obstacles of GC × GC, such as random and systemic retention time shifting and variation of peak intensities. Data analysis methods can be broadly divided into four categories: (1) deconvolution, (2) pattern recognition, (3) property prediction, and (4) retention time/index modeling. Advances in these methods have been provided by both commercial sources as well as in-house developed software. Finally, the ultimate goal of applying GC × GC and other MDGC technologies is to provide useful chemical information to address the needs of applications of interest. Several application categories are reviewed in some detail: (1) forensic, (2) environmental, (3) fuels, (4) food, flavors and fragrances, and (5) biological, including metabolomics and biological volatile organic compound (VOC) profiling.Price, M., 2018. Americas peopled in a single wave, ancient genome reveals. Science 359, 14. rare smidgen of ancient DNA has sharpened the picture of one of humanity's greatest migrations. Some 15,000 to 25,000 years ago, people wandered from Asia to North America across a now-submerged land called Beringia, which once connected Siberia and Alaska. But exactly when these ancient settlers crossed and how many migrations occurred are hotly debated. Now, the oldest full genome to be sequenced from the Americas suggests that some settlers stayed in Beringia while another group headed south and formed the population from which all living Native Americans descend.“This is an important study that significantly narrows the subset of possibilities [for how the Americas were peopled],” says David Reich, a geneticist at Harvard Medical School in Boston. “It's very exciting.”The genome comes from an 11,500-year-old infant found in 2013 at the site of Upward Sun River in central Alaska's Tanana River Basin, a part of Beringia that's still above sea level. The infant, one of two from the site, belonged to a population that likely numbered in the low thousands, who hunted Beringia's abundant herds and gathered plants (Science, 28 February 2014, p. 961).A team led by geneticist Eske Willerslev of the University of Copenhagen and the University of Cambridge in the United Kingdom isolated DNA from bone powder taken from the infant's skull. The researchers sequenced the DNA repeatedly to get a virtually complete copy of the genome. They compared it to that of modern Native Americans, as well as to other ancient and living people across Eurasia and the Americas. By looking at genetic similarities and estimating how long it would take for key mutations to pop up, the researchers assembled a family tree with rough dates.The infant's group was most closely related to modern Native Americans—but it wasn't direct ancestor. Instead, it and modern Native Americans shared common ancestors who must have entered Beringia some 25,000 years ago, the researchers report this week in Nature. Perhaps 21,000 years ago, those ancient settlers branched into at least two groups: one that included the infant and another that gave rise to Native Americans.That supports the idea that Asian migrants lingered in Beringia and became genetically isolated—the so-called Beringian standstill model—says anthropologist Connie Mulligan of the University of Florida in Gainesville. “Because they have the whole nuclear genome, you can really tell a lot about when and where this migration happened,” she says. But Reich cautions that date estimates from a single genome are necessarily rough.The researchers also found that the ancient Beringian infant is equally related to both the northern and southern genetic subgroups of Native Americans, implying that both descend from a single migration. The team suggests that a group headed south into North America about 20,000 years ago and only afterward split into distinct subpopulations, perhaps between 14,500 and 17,000 years ago, dates that fit with previous studies.Why did one group linger and thrive in Beringia while another took off to explore the Americas? A search for fresh resources could have spurred the migrants, Willerslev says, but so could sheer curiosity. “There were people who were happy with what they had, and there were others who looked out at the great ice caps and wanted to see what was on the other side,” he says.That's a compelling speculation, Mulligan says. “Once they got into North America, they really high-tailed it through the continent and down into South America within just a few thousand years,” she says. A cultural or genetic penchant for exploration “could help explain why they were in such a hurry.”Probandt, D., Eickhorst, T., Ellrott, A., Amann, R., Knittel, K., 2018. Microbial life on a sand grain: from bulk sediment to single grains. The Isme Journal 12, 623., marine surface sediments constitute a habitat for estimated 1.7 × 1028 prokaryotes. For benthic microbial community analysis, usually, several grams of sediment are processed. In this study, we made the step from bulk sediments to single sand grains to address the microbial community directly in its micro-habitat: the individual bacterial diversity on 17 sand grains was analyzed by 16S ribosomal RNA gene sequencing and visualized on sand grains using catalyzed reporter deposition fluorescence in situ hybridization. In all, 104–105 cells were present on grains from 202 to 635?μm diameter. Colonization was patchy, with exposed areas largely devoid of any epi-growth (mean cell–cell distance 4.5±5.9?μm) and protected areas more densely populated (0.5±0.7?μm). Mean cell–cell distances were 100-fold shorter compared with the water column. In general, growth occurred in monolayers. Each sand grain harbors a highly diverse bacterial community as shown by several thousand species-level operational taxonomic units (OTU)0.97. Only 4–8 single grains are needed to cover 50% of OTU0.97 richness found in bulk sediment. Although bacterial communities differed between sand grains, a core community accounting for >50% of all cells was present on each sand grain. The communities between sediment grains are more similar than between soil macroaggregates.Qin, W., Zhu, Y., Fan, F., Wang, Y., Liu, X., Ding, A., Dou, J., 2017. Biodegradation of benzo(a)pyrene by Microbacterium sp. strain under denitrification: Degradation pathway and effects of limiting electron acceptors or carbon source. Biochemical Engineering Journal 121, 131-138. electron acceptors, the amount of nitrate (nitrite) significantly affect the benzo(a)pyrene (BaP) biodegradation of Microbacterium sp. under denitrifying conditions. In the study, the degradation behavior of Microbacterium sp. and the concentration variations of electron acceptors were investigated at different concentration ratios of BaP/nitrate (nitrite). The results showed that compared with reductions in BaP concentration, the extent of BaP degradation and denitrification was significantly affected by C/N ratios. The Microbacterium sp. strain could use the denitrifying products nitric oxide and nitrous oxide as electron acceptors to degrade BaP and the shortage of electron acceptors did not decrease the BaP removal rates but lead to a decrease in the BaP degradation. The degree of degradation of BaP could be controled by adding appropriate nitrate (nitrite) which calculated based on the fitting equations of the relationship between nitrate (nitrite) consumption and BaP removal amount. The Microbacterium sp. strain performed better under nitrate-reducing condition, and the highest removal rate (84.2%) was obtained at the BaP/nitrate ratio of 1:33 in 10 d. This study will help further mechanism investigation of anaerobic BaP degradation and the conduct of the PAHs bioremediation by adding exogenous electron acceptors.Qu, J., Gerber, A., Mayer, F., Kadic, M., Wegener, M., 2017. Experiments on metamaterials with negative effective static compressibility. Physical Review X 7, Article 041060. volume of ordinary materials decreases in response to a pressure increase exerted by a surrounding gas or liquid, {i.e.}, the material volume compressibility is positive. Recently, poroelastic metamaterial architectures have been suggested theoretically that allow for an unusual negative effective static volume compressibility --- which appears to be forbidden for reasons of energy conservation at first sight. The challenge in the three-dimensional (3D) fabrication of these blueprints lies in the necessary many hollow 3D crosses sealed by thin membranes, which we realize in this work by using 3D laser microlithography combined with a serendipitous mechanism. By using optical-microscopy cross-correlation analysis, we determine an extraordinarily large negative metamaterial effective volume compressibility of keff=-0.8%,bar-1=-80 GPa-1 under pressure control.Popular Summary: Increasing the air pressure exerted on most ordinary materials leads to a decrease in volume—in other words, the object is compressed. Mathematically, physicists describe the object as having “positive volume compressibility.” Common sense suggests that negative compressibility—an object inflating in response to an increase in air pressure—is impossible under static conditions. Such a situation violates both stability and energy conservation. But recent theoretical arguments suggest that certain metamaterials could exhibit this unusual property. In this paper, we report on the fabrication and testing of a three-dimensional (3D) artificial material that exhibits such “forbidden” behavior in an isotropic and stable manner.The challenge in our microfabrication lies in the manufacture of the necessary hollow 3D crosses, containing concealed volumes that are sealed by thin membranes. We demonstrate such concealed microvolumes, which leak only by gas permeation through the bulk of the thin polymer membranes on a time scale of 10 minutes. Using optical imaging, we directly measure an unusually large negative metamaterial effective compressibility equivalent to a relative effective volume increase of about 1% at 1 bar excess air pressure.We demonstrate experimentally, for what we believe is the first time, a metamaterial with a negative effective compressibility under quasistatic conditions. This is a critical step toward some unusual applications, such as in artificial muscles and actuators.Rabett, R.J., 2018. The success of failed Homo sapiens dispersals out of Africa and into Asia. Nature Ecology & Evolution 2, 212-219. evidence for an early dispersal of Homo sapiens from Africa into the Levant during Marine Isotope Stage 5 (MIS-5) 126–74 ka (thousand years ago) was characterized for many years as an ‘abortive’ expansion: a precursor to a sustained dispersal from which all extant human populations can be traced. Recent archaeological and genetic data from both western and eastern parts of Eurasia and from Australia are starting to challenge that interpretation. This Perspective reviews the current evidence for a scenario where the MIS-5 dispersal encompassed a much greater geographic distribution and temporal duration. The implications of this for tracking and understanding early human dispersal in Southeast Asia specifically are considered, and the validity of measuring dispersal success only through genetic continuity into the present is examined.Rafati, R., Smith, S.R., Sharifi Haddad, A., Novara, R., Hamidi, H., 2018. Effect of nanoparticles on the modifications of drilling fluids properties: A review of recent advances. Journal of Petroleum Science and Engineering 161, 61-76. from unconventional hydrocarbon resources, such as shale gas, shale oil, deepwater and arctic reservoirs requires advanced drilling and extraction technologies. Furthermore, minimizing the environmental footprints associated with oil recovery processes are critical. Nanotechnology has been shown promising solutions to overcome such issues in oil and gas industry. Many studies have been conducted to analyse the enhancement of drilling fluids through the use of nanotechnology. In these studies modification of rheological, filtration, and heat transfer properties and friction reduction associated with drilling fluids have been investigated. They also showed that nanoparticles can improve fluid thermal stability, provide better lubricity, hole cleaning and wellbore stability, and mitigate hydrates formation within the fluid circulation system. This manuscript aims to analyse the outcomes of these studies and improvements that were observed for the application of nanoparticles in drilling fluids. This review provides the investigators with a detailed overview and comparison of the recent advancements in the field of drilling fluids and nanotechnology.Rahman, M.M., Jiang, T., Tang, Y., Xu, W., 2018. A simple desorption atmospheric pressure chemical ionization method for enhanced non-volatile sample analysis. Analytica Chimica Acta 1002, 62-69. this work, a simple desorption atmospheric pressure chemical ionization (SDAPCI) source is studied and optimized for analyzing a wide variety of samples such as nonvolatile, volatile and biological samples. In this ion source, the heated mass inlet was used for sample desorption, and a solid needle was used to produce a corona discharge for ionization. The utilization of any additional gas or heater is not required in SDAPCI. Due to its high sensitivity, only a small amount of sample is needed. Sample loading and the consequent mass spectrometry analysis process could be easy and fast, which was demonstrated by the analyses of different types of samples ranging from non-volatile to volatile compounds. High-throughput analysis can be performed by SDAPCI source with minimum or no sample preparation.Rahman, M.W., Rimmer, S.M., Rowe, H.D., 2018. The impact of rapid heating by intrusion on the geochemistry and petrography of coals and organic-rich shales in the Illinois Basin. International Journal of Coal Geology 187, 45-53. intrusion into organic-rich sedimentary rocks and coals has been suggested as a factor in the large-scale release of 13C–depleted thermogenic CH4, which may have led to global warming and mass extinction events in the geologic past. If a significant release of 13C–depleted thermogenic CH4 results from the intrusion of coal or organic-rich rocks, then it should produce 13C–enriched residual coal and dispersed organics in rocks adjacent to the intrusion due to the release of isotopically lighter CH4 gas. A review of the literature suggests only minor changes in the δ13Corg of coals adjacent to intrusions; however, a few studies have shown that changes in δ13Corg in intruded shales may be slightly more pronounced. The current study further evaluates the geochemical, isotopic, and petrographic changes that result from contact metamorphism and specifically compares the intrusion of coal to that of an organic-rich shale collected from the same general vicinity. Data for two different transects of intruded Pennsylvanian coal (Danville (No. 7) Coal) and an intruded organic-rich shale in the southern part of the Illinois Basin are presented.Both transects show similar increases in mean vitrinite reflectance (Rr); reflectance increases from background levels of 0.66% to 4.40% in the Danville (No. 7) Coal and 0.71% to 4.78% in the organic-rich shale. In addition, both transects show the formation of isotropic coke, and even development of fine circular mosaic anisotropic coke structure at and near the contact with the intrusion, along with the visual loss of liptinites at higher reflectances. In the Danville Coal transect, volatile matter, N, H, S, and O decrease whereas fixed carbon, C, and ash increase approaching the intrusion. The coal shows a marked decrease in remaining hydrocarbon potential (S2) and hydrogen index (HI) and an increase in Tmax (°C). Trends in most of the Rock-Eval parameters for the organic-rich shale are less clear due to variations in the amount of organic matter present, but a significant increase in thermal maturity (Tmax, 0C) is observed.No systematic changes in δ13C occur in the No. 7 Coal transect as the intrusion is approached, with δ13C varying between ? 25.4‰ and ? 24.8‰. The organic-rich shale transect shows a minor 1.2‰ enrichment in δ13C (from ? 25.2‰ to ? 24.0‰) within 2 m of the intrusion. These isotopic shifts are not of a magnitude that would be expected if associated with a large-scale release of thermogenic CH4. In addition, no evidence exists in either transect for 13C–depleted condensed gas or pyrolytic carbon at the intrusion contact that could have moderated the isotopic signature. These data agree with those reported previously that indicate no clear isotopic evidence for large-scale CH4 generation due to rapid heating by igneous intrusion into coals or sedimentary rocks.Raine, J.C., Turcotte, D., Romanowski, L., Parrott, J.L., 2018. Oil sands tailings pond sediment toxicity to early life stages of northern pike (Esox lucius). Science of The Total Environment 624, 567-575. Athabasca River in Alberta flows through natural sources of eroding oil sands bitumen and oil sands mining operations that may result in low level contamination of surface waters. Northern pike (Esox lucius) are apex predators and important food and game fish species native to the Athabasca River system. This species has the potential to be exposed to both natural and anthropogenic sources of contamination from oil sands related materials throughout its life cycle. Pike are difficult to rear in the laboratory and little information exists on the toxicity of oil sands related materials to this key indigenous fish species. In this study, the potential effects of two sediment samples collected from different areas of one tailings pond in the Athabasca oil sands area are assessed in a daily renewal bioassay on early life stages of northern pike. Gametes were collected from spawning wild pike captured from a reference site outside of the oil sands area. Fertilized eggs were exposed to control water or increasing concentrations of tailings pond sediments for 21 days, coinciding with initiation of exogenous feeding and completion of yolk absorption. Developing fish were examined for survival and changes in body weight, length, and development. Embryos exhibited increased developmental abnormalities and decreased growth and survival with increasing sediment concentration. Both sediment samples had similar levels of naphthenic acids and similar types of PAHs, with alkylated PAHs dominating. However, concentrations of total and alkylated PAHs differed between sediment samples and were related to increasing developmental abnormalities and decreased growth and survival. This is consistent with developmental changes observed with exposure to PAHs in other fish species. These results provide information on the effects of tailings pond sediments comprising mixtures of PAHs and alkylated PAHs on the development and survival of a key species in the northern aquatic ecosystem.R?tsep, M., Muru, R., Freiberg, A., 2018. High temperature limit of photosynthetic excitons. Nature Communications 9, Article 99. in light-harvesting complexes are known to significantly improve solar-energy harnessing. Here we demonstrate photosynthetic excitons at super-physiological temperatures reaching 60–80?°C in different species of mesophilic photosynthetic bacteria. It is shown that the survival of light-harvesting excitons in the peripheral LH2 antennae is restricted by thermal decomposition of the pigment–protein complex rather than by any intrinsic property of excitons. The regular spatial organization of the bacteriochlorophyll a pigments supporting excitons in this complex is lost upon the temperature-induced breakdown of its tertiary structure. Secondary structures of the complexes survive even higher temperatures. The discovered pivotal role of the protein scaffold in the stabilization of excitons comprises an important aspect of structure–function relationship in biology. These results also intimately entangle the fundamental issues of quantum mechanical concepts in biology and in the folding of proteins.Ravansari, R., Lemke, L.D., 2018. Portable X-ray fluorescence trace metal measurement in organic rich soils: pXRF response as a function of organic matter fraction. Geoderma 319, 175-184. influence of organic matter fraction on portable X-Ray fluorescence (pXRF) trace metal measurements was investigated through the incremental addition of three organic matter surrogates (cellulose, graphite powder, and confectioner's sugar) to a soil matrix. Each surrogate was independently added to and homogenized with samples of Natural Resources Canada Till-1 standard reference material that was initially expunged of organic matter through combustion. Incremental addition was performed 20 times for each surrogate, and concentrations of thirteen elements were measured as a function of varying organic matter fractions using a Thermo Scientific Niton XL3t GOLDD+ 950 XRF analyzer.Results demonstrate attenuation of the pXRF signal with increasing sample organic matter fraction; however, elementally dependent deviations from expected concentrations were also observed. An empirical organic matter fraction-dependent calibration method was developed and its performance was evaluated using four unmodified soil standards with known organic matter content. Estimates incorporating soil organic matter differed from conventional calibration estimates neglecting organic matter content, yet were able to reproduce standard reference material values with similar success.Reddy, P.V., Karegoudar, T.B., Monisha, T.R., Mukram, I., Nayak, A.S., 2018. Biodegradation of fluoranthene by Paenibacillus sp. strain PRNK-6: a pathway for complete mineralization. Archives of Microbiology 200, 171-182. high-efficiency fluoranthene-degrading bacterium Paenibacillus sp. PRNK-6 was isolated from PAH-contaminated soil. The strain degrades 96% (240?mg?l?1) of fluoranthene in 48?h. Various metabolic intermediates of fluoranthene catabolism were identified by gas chromatography (GC) and gas chromatography–high resolution mass spectrometry (GC-HRMS). Metabolite characterization, metabolite-feeding experiments, and appropriate enzyme activities in the cell-free extracts suggest the existence of a bifurcated pathway down the phthalic acid for complete mineralization of fluoranthene in PRNK-6. In this strain, fluoranthene catabolism begins by the attack on the fused aromatic ring portion of fluoranthene. Two terminal aromatic metabolites protocatechuate and catechol undergo ring cleavage by protocatechuate 3,4-dioxygenase and catechol 1,2-dioxygenase, respectively, and enter the central metabolism.Ren, J., Song, C., Hou, A., Song, Y., Zhu, X., Cagle, G.A., 2018. Shifts in soil bacterial and archaeal communities during freeze-thaw cycles in a seasonal frozen marsh, Northeast China. Science of The Total Environment 625, 782-791. freeze-thaw cycles (FTCs) occur in the spring and autumn in boreal wetlands as soil temperatures rise above freezing during the day and fall below freezing at night. A surge in methane emissions from these systems is frequently documented during spring FTCs, accounting for a large portion of annual emissions. In boreal wetlands, methane is produced as a result of syntrophic microbial processes, mediated by a consortium of fermenting bacteria and methanogenic archaea. Further research is needed to determine whether FTCs enhance microbial metabolism related to methane production through the cryogenic decomposition of soil organic matter. Previous studies observed large methane emissions during the spring thawed period in the Sanjiang seasonal frozen marsh of Northeast China. To investigate how FTCs impact the soil microbial community and methanogen abundance and activity, we collected soil cores from the Sanjiang marsh during the FTCs of autumn 2014 and spring 2015. Methanogens were investigated based on expression level of the methyl coenzyme reductase (mcrA) gene, and soil bacterial and archaeal community structures were assessed by 16S rRNA gene sequencing. The results show that a decrease in bacteria and methanogens followed autumns FTCs, whereas an increase in bacteria and methanogens was observed following spring FTCs. The bacterial community structure, including Firmicutes and certain Deltaproteobacteria, was changed following autumn FTCs. Temperature and substrate were the primary factors regulating the abundance and composition of the microbial communities during autumn FTCs, whereas no factors significantly contributing to spring FTCs were identified. Acetoclastic methanogens from order Methanosarcinales were the dominant group at the beginning and end of both the autumn and spring FTCs. Active methanogens were significantly more abundant during the diurnal thawed period, indicating that the increasing number of FTCs predicted to occur with global climate change could potentially promote CH4 emissions in seasonal frozen marshes.Rey, M., Nikitin, A.V., Bézard, B., Rannou, P., Coustenis, A., Tyuterev, V.G., 2018. New accurate theoretical line lists of 12CH4 and 13CH4 in the 0–13400?cm?1 range: Application to the modeling of methane absorption in Titan’s atmosphere. Icarus 303, 114-130. spectrum of methane is very important for the analysis and modeling of Titan’s atmosphere but its insufficient knowledge in the near infrared, with the absence of reliable absorption coefficients, is an important limitation. In order to help the astronomer community for analyzing high-quality spectra, we report in the present work the first accurate theoretical methane line lists (T = 50–350 K) of 12CH4 and 13CH4 up to 13400 cm?1 (?>?0.75 ?m). These lists are built from extensive variational calculations using our recent ab initio potential and dipole moment surfaces and will be freely accessible via the TheoReTS information system (<;, <;). Validation of these lists is presented throughout the present paper. For the sample of lines where upper energies were available from published analyses of experimental laboratory 12CH4 spectra, small empirical corrections in positions were introduced that could be useful for future high-resolution applications. We finally apply the TheoRetS line list to model Titan spectra as observed by VIMS and by DISR, respectively onboard Cassini and Huygens. These data are used to check that the TheoReTS line lists are able to model observations. We also make comparisons with other experimental or theoretical line lists. It appears that TheoRetS gives very reliable results better than ExoMol and even than HITRAN2012, except around 1.6 ?m where it gives very similar results. We conclude that TheoReTS is suitable to be used for the modeling of planetary radiative transfer and photometry. A re-analysis of spectra recorded by the DISR instrument during the descent of the Huygens probe suggests that the CH4 mixing ratio decreases with altitude in Titan’s stratosphere, reaching a value of ～10?2 above the 110 km altitude.Reyes-Garcés, N., Gionfriddo, E., Gómez-Ríos, G.A., Alam, M.N., Boyac?, E., Bojko, B., Singh, V., Grandy, J., Pawliszyn, J., 2018. Advances in solid phase microextraction and perspective on future directions. Analytical Chemistry 90, 302-360. phase microextraction (SPME) is a versatile, nonexhaustive sample preparation tool that has been demonstrated to be well-suited for facile and effective analysis of a broad range of compounds in a plethora of studies. A growing number of reports describing diverse SPME workflows for novel investigations in a variety of fields, such as flavor and fragrance investigations, environmental studies, and diverse bioanalytical applications, among others, corroborate the applicability of this microextraction tool in the analytical sciences. Several reviews compiling the most significant applications of SPME in specific areas, including analysis of wine volatiles, in vivo analysis of pollutants, on-site analysis of soils, analysis of water samples, food analysis, in vitro and in vivo metabolomics studies, pharmaceutical and biomedical analysis, among others, have been recently published by different authors. In addition to the diverse types of applications of SPME, the different features offered by this microextraction technology in comparison to exhaustive extraction techniques have been a matter of consideration in several reviews. Boyaci et al., for instance, discussed the main advantages and limitations of SPME over traditional sample preparation methodologies, while Souza-Silva et al. presented a comprehensive overview of the considerations and challenges associated with the use of SPME for analysis of different complex matrixes. Various publications reviewing the most relevant developments in SPME extraction phases, coating preparation procedures, geometries, and experimental setups have also been recently reported. In addition, novel coupling approaches combining the simplicity of SPME for simple and effective sample cleanup and the capabilities of mass spectrometry (MS) instrumentation standout to showcase the potential of SPME-MS toward the streamlining of analytical workflows in the near future. Undoubtedly, SPME is a constantly evolving analytical technology with great potential to fulfill the needs of novel analytical applications in various fields of study. This review presents the most recent and innovative work published on SPME, mostly focused on original studies reported from 2014 to date. The main sections of this review are comprised of an introduction to the main principles of SPME supported by recent fundamental studies involving computational modeling; an overview of novel developments in SPME coating materials and geometries; a summary of the most significant, recently published applications of SPME in food, environmental, and bioanalytical studies; and finally, a section describing anticipated future research directions and developments in SPME, including current progress on the direct coupling of multiple configurations of SPME to mass spectrometry, which certainly demonstrates the flexibility of SPME for hyphenation with new technologies.Reynolds, D.J., Hall, I.R., Scourse, J.D., Richardson, C.A., Wanamaker, A.D., Butler, P.G., 2017. Biological and climate controls on North Atlantic marine carbon dynamics over the last millennium: insights from an absolutely dated shell-based record from the North Icelandic Shelf. Global Biogeochemical Cycles 31, 1718-1735. the rapid increase in atmospheric carbon dioxide concentrations (pCO2) over the industrial era, there is a pressing need to construct long-term records of natural carbon cycling prior to this perturbation and to develop a more robust understanding of the role the oceans play in the sequestration of atmospheric carbon. Here we reconstruct the past biological and climate controls on the carbon isotopic (δ13Cshell) composition of the North Icelandic shelf waters over the last millennium, derived from the shells of the long-lived marine bivalve mollusk Arctica islandica. Variability in the annually resolved δ13Cshell record is dominated by multidecadal variability with a negative trend (?0.003 ± 0.002‰ yr?1) over the industrial era (1800–2000 Common Era). This trend is consistent with the marine Suess effect brought about by the sequestration of isotopically light carbon (δ13C of CO2) derived from the burning of fossil fuels. Comparison of the δ13Cshell record with Contemporaneous proxy archives, over the last millennium, and instrumental data over the twentieth century, highlights that both biological (primary production) and physical environmental factors, such as relative shifts in the proportion of Subpolar Mode Waters and Arctic Intermediate Waters entrained onto the North Icelandic shelf, atmospheric circulation patterns associated with the winter North Atlantic Oscillation, and sea surface temperature and salinity of the subpolar gyre, are the likely mechanisms that contribute to natural variations in seawater δ13C variability on the North Icelandic shelf. Contrasting δ13C fractionation processes associated with these biological and physical mechanisms likely cause the attenuated marine Suess effect signal at this locality.Rezvani, H., Khalilnezhad, A., Ganji, P., Kazemzadeh, Y., 2018. How ZrO2 nanoparticles improve the oil recovery by affecting the interfacial phenomena in the reservoir conditions? Journal of Molecular Liquids 252, 158-168. nanoparticles (NPs) in certain base fluids is the method that has been recently introduced for enhanced oil recovery (EOR), which seems to be the key solution for rock wettability alteration in carbonate oil reservoirs. This research attempts to offer a better understanding of the ZrO2 NPs' role in the EOR methods, with a special focus on the interfacial tension (IFT) between oil and water, the zeta potential, the contact angle, and the water and oil viscosity measurements. The results of contact angle measurements in different concentrations of NPs illustrate the highest contact angle reduction for 0.008 mol/L of NPs which changed the rock wettability from strongly oil-wet to a moderately water-wet condition by overcoming the available disjoining pressure in the system. In this specific concentration, the zeta potential measurement was the highest (~? 55.4 mV) which agrees well with the contact angle results. In addition, the measurements were all above ? 40 mV which indicates a good stability for NPs in formation water (FW). The IFT measurements indicate that the smallest IFT value for 0.006 mol/L of ZrO2 NPs at 80 °C and 8.273 Mpa. This reduction is due to the adsorption of large oil molecules onto the NPs surface which prevents asphaltene precipitation on the interface between two fluids. Finally, the viscosity measurements at 60 °C show the reduction and increase of oil and FW viscosity with increased concentration, respectively. The oil viscosity reduction results from the breakdown of CC bonds in the large oil molecules by NPs, which is intensified at higher temperatures.Riboulot, V., Ker, S., Sultan, N., Thomas, Y., Marsset, B., Scalabrin, C., Ruffine, L., Boulart, C., Ion, G., 2018. Freshwater lake to salt-water sea causing widespread hydrate dissociation in the Black Sea. Nature Communications 9, Article 117. hydrates, a solid established by water and gas molecules, are widespread along the continental margins of the world. Their dynamics have mainly been regarded through the lens of temperature-pressure conditions. A fluctuation in one of these parameters may cause destabilization of gas hydrate-bearing sediments below the seafloor with implications in ocean acidification and eventually in global warming. Here we show throughout an example of the Black Sea, the world’s most isolated sea, evidence that extensive gas hydrate dissociation may occur in the future due to recent salinity changes of the sea water. Recent and forthcoming salt diffusion within the sediment will destabilize gas hydrates by reducing the extension and thickness of their thermodynamic stability zone in a region covering at least 2800 square kilometers which focus seepages at the observed sites. We suspect this process to occur in other world regions (e.g., Caspian Sea, Sea of Marmara).Richardson, S.D., Ternes, T.A., 2018. Water analysis: Emerging contaminants and current issues. Analytical Chemistry 90, 398-428. biennial Review covers developments in water analysis for emerging environmental contaminants over the period of October 2015–October 2017. Nontarget, unknown analysis continues to be a hot trend, and due to the immense amount of chemical features that can be found using mass spectrometry, detailed workflows are becoming popular to handle all the data, as it can be too time-consuming to manually interpret data for thousands of unknown compounds and spectral features. High resolution (HR)-mass spectrometry (MS) continues to be a cornerstone of unknown identification, as does MS/MS, library database creation and searching, in silico methods, and user-created software. While electron ionization (EI)-MS libraries (such as the NIST and Wiley databases) can have >760?000 compounds, electrospray ionization (ESI)-MS libraries are lagging behind, due in large part to the lack of standardization for MS conditions used to generate mass spectra and to the differences in spectra produced on different brands and types of mass spectrometers. As a result, many separate databases exist, whether created by mass spectrometry companies, the NIST, or individual users. Some research groups are posting these for free online use (see Table 2). Open or semi-open mass spectrometry databases include Metlin, mzCloud, MassBank, European MassBank, MassBank of North America, the Global Natural Products Social Molecular Networking (GNPS), the Human Metabolome Database (HMDB), Stoff-Ident, and ChemSpider. Two commercial MS/MS libraries (NIST and Wiley) are also now available. The NIST2017 library database contains MS/MS spectra for >15?000 compounds, and Wiley’s MSforID database contains MS/MS spectra for >1200 compounds. Workflow tools include Metfrag (a metabolomics MS/MS fragmentation predictor) and Competitive Fragmentation Modeling for Metabolite Identification (CFM-ID), developed by Wishart’s lab at the University of Alberta, which predicts MS/MS spectra for compounds (for input structures) and can rank candidate structures for how well they match the MS/MS spectra. Wishart’s group also recently published a new tool (called CFM-EI) to predict EI mass spectra. This was published in 2016 in Analytical Chemistry(2) and is also freely available at <;. CFM-EI incorporates an artificial neural network and was created using a subset of the NIST library as a training set. It can handle odd-electron ions and isotopes and has shown good prediction capability in cross-validation tests against the NIST database. As such, it can be useful for narrowing the potential chemical structures for unknown identification. Two new analytical techniques also stand out this year. First, ion mobility-MS was recently developed and is beginning to be used for some environmental applications. Ion mobility-MS offers an additional dimension in separation (by cross-section of the molecules), which can aid in identifying compounds in complex environmental mixtures. Examples included in the Review this year include the identification of photolysis transformation products (TPs) from the artificial sweetener acesulfame and the identification of naphthenic acid ozonation products. Another technique recently introduced is a software analysis tool called precursor ion exclusion (PIE). This tool helps to overcome a weakness of data dependent acquisition (DDA), a common method for triggering MS/MS scans for unknowns when doing nontarget analysis using liquid chromatography (LC)-MS/MS. DDA typically generates MS/MS data for only the most abundant chromatographic peaks observed in a LC-MS analysis, such that the smaller peaks typically go unidentified. Using the PIE approach, Li’s group at the University of Alberta was able to exclude those highly abundant peaks in a second analysis, which allowed a more comprehensive determination of unknown peptides and chlorinated peptides in treated drinking water (see Drinking Water DBPs section).Ridley, D.A., Heald, C.L., Ridley, K.J., Kroll, J.H., 2018. Causes and consequences of decreasing atmospheric organic aerosol in the United States. Proceedings of the National Academy of Sciences 115, 290-295.: Ambient particulate matter (PM) was responsible for four million premature deaths globally in 2012. The deleterious health impacts of PM motivated the US Environmental Protection Agency (EPA) to curtail emission of PM and precursor gases. The 2011 EPA report to Congress on the efficacy of the Clean Air Act estimated a dramatic reduction in human mortality resulting from these emissions controls. Surface measurements from 1990 to 2012 indicate a significant US-wide decline in the organic portion of the PM, not accounted for in the EPA report. We show that the decline in organic aerosol is mediated primarily through changes in vehicle and residential fuel-burning emissions, indicating that the Clean Air Act is even more beneficial to US air quality than currently appreciated. Abstract: Exposure to atmospheric particulate matter (PM) exacerbates respiratory and cardiovascular conditions and is a leading source of premature mortality globally. Organic aerosol contributes a significant fraction of PM in the United States. Here, using surface observations between 1990 and 2012, we show that organic carbon has declined dramatically across the entire United States by 25–50%; accounting for more than 30% of the US-wide decline in PM. The decline is in contrast with the increasing organic aerosol due to wildfires and no clear trend in biogenic emissions. By developing a carbonaceous emissions database for the United States, we show that at least two-thirds of the decline in organic aerosol can be explained by changes in anthropogenic emissions, primarily from vehicle emissions and residential fuel burning. We estimate that the decrease in anthropogenic organic aerosol is responsible for averting 180,000 (117,000–389,000) premature deaths between 1990 and 2012. The unexpected decrease in organic aerosol, likely a consequence of the implementation of Clean Air Act Amendments, results in 84,000 (30,000–164,000) more lives saved than anticipated by the EPA between 2000 and 2010. Riley, B.J., Lennard, C., Fuller, S., Spikmans, V., 2018. Pyrolysis-GC-MS analysis of crude and heavy fuel oil asphaltenes for application in oil fingerprinting. Environmental Forensics 19, 14-26. Pyrolysis ? Gas Chromatography ? Mass Spectrometry (Py-GC-MS) method was developed for the analysis and profiling of crude and heavy fuel oil asphaltenes, for application in oil fingerprinting. Asphaltenes were precipitated from ten geographically different oils using n-pentane, and analysed by Py-GC-MS. Alkane profiles and sulphur/aromatic profiles were used to compare the oils, and to correctly differentiate oils from different geographical regions. Py-GC-MS could not differentiate a weathered oil sample and a fresh oil sample from the same source. The results of this study support the findings from a previously developed FTIR method for asphaltene profiling.Rismiller, S.C., Groves, M.M., Meng, M., Dong, Y., Lin, J., 2018. Water assisted liquefaction of lignocellulose biomass by ReaxFF based molecular dynamic simulations. Fuel 215, 835-843. based molecular dynamics (MD) simulation provides opportunities for fundamentally understanding pyrolysis of lignocellulose biomass through precisely controlled reaction conditions and monitoring of reaction evolution processes. Despite demonstration of simulating the pyrolysis process of dry lignocellulose, MD investigation of this process assisted by water is yet to be performed. This is important considering that hydrothermal liquefaction could be promising to concentrate the energy of biocrude yielded from lignocellulose biomass. In this paper, roles of water on the pyrolysis process of the lignocellulose were investigated by ReaxFF MD simulation. In the simulation, both dry cellulose and lignin systems as well as their systems containing 33% and 66% water by weight were studied at a temperature range of 1250–2000?K at a time scale of 6?ns. Products were characterized by studying their phases, H/C, O/C ratios, and their higher heating values (HHV) that are used to evaluate their value as fuels. Time evolutions of water and other chemical products were investigated to determine the role of water in the reactions and to reveal the reaction mechanism. Compared with dry systems, pyrolysis of the cellulose in presence of water shows several interesting trends, including enhanced breakdown of the cellulose polymer, increased oxygenation of the products, and shift of the final products from char to oil. In contrast, lignin remains largely unaffected by water, and simulation has reproduced experimental results of lignin char formation at elevated temperature in liquefaction. Moreover, it is found that the temperature plays an important role in the reactions. As temperature increases the water’s oxygenating effects in the cellulose is decreased. These theoretical results provide solid evidence for unveiling the reaction mechanism of biomass pyrolysis, offering useful guidance for processing wet biomass to liquid fuels.Rognmo, A.U., Heldal, S., Fern?, M.A., 2018. Silica nanoparticles to stabilize CO2-foam for improved CO2 utilization: Enhanced CO2 storage and oil recovery from mature oil reservoirs. Fuel 216, 621-626. we present a comprehensive experimental investigation on the use of nanoparticles as foam stabilizers during co-injection of supercritical CO2 and brine at reservoir conditions. The performance of such particles to stabilize CO2-foam has ramifications on current implementation of oil recovery and CO2 storage for reduced carbon footprint during injection of CO2 in mature oil fields. Quantitative analysis of oil recovery efficiency, pressure gradients, and rate of oil recovery were used to study displacement mechanisms and to evaluate the feasibility of using nanoparticles as CO2 foaming agents. Two main observations were made: 1) silica nanoparticles stabilize CO2-foam in the presence of oil and remain stable during oil displacement: the pressure gradient measured during tertiary co-injections with nanoparticles was between 3 and 5 times higher than without foaming agent. 2) nanoparticle-stabilized CO2-foam increase oil recovery: the incremental oil recovery after waterflooding during tertiary co-injection increased by a factor of two with nanoparticles relative to co-injection with brine.Roostaei, M., Nouri, A., Fattahpour, V., Chan, D., 2018. Numerical simulation of proppant transport in hydraulic fractures. Journal of Petroleum Science and Engineering 163, 119-138. central issue in hydraulic fracturing treatment in petroleum wells is the transport of proppant particles by the injection fluid. In this paper, we present an innovative proppant transport model in a fixed rectangular- and elliptic-shaped slots. The proposed model is an improvement to the current modeling of proppant transport by applying a non-oscillatory numerical scheme which has high accuracy everywhere in solution domain, even close to the steep gradients. In addition, inertia, fracture wall, and concentration effects on proppant settling along with slurry evolution as a function of proppant concentration has been considered.This paper introduces the mathematical equations that govern the proppant transport phenomenon and discusses special front capturing numerical techniques, boundary conditions, coupling between proppant and slurry mass conservation equations and time stepping restrictions required for the solution stability. We incorporated published correlations obtained from proppant transport laboratory experiments in our numerical model to better capture the physics of the problem. 5th- order WENO scheme was used to avoid oscillation and diffusion at the proppant front since traditional finite difference discretization was found to be insufficient in solving the hyperbolic transport partial differential equations. Results show that the technique used in this study can capture the proppant distribution with minimum oscillation and diffusion.A series of sensitivity analysis was conducted to explore the legitimacy of these assumptions and to provide guidelines that allow more accurate predictions of the proppant and fluid transfer. Numerical results are presented to show how proppant distribution is impacted by the injection fluid viscosity, density difference between proppant particles and injection fluid, proppant size, and fluid flow injection rate. Results of the sensitivity analysis illustrate the significance of choosing appropriate viscosity of the injection fluid as small changes in the viscosity may cause noticeable effects on the concentration distribution. In addition, we found that variation of proppant size and density within a reasonable range have a modest effect on proppant concentration distribution.Furthermore, we also investigated the amount of gravity driven vertical motion of proppant which is driven by density differences (convection) and compare it to a second gravity driven motion which is proppant settlement. Both of these two well recognized mechanisms can occur inside a fracture during proppant placement, however, the importance of each mechanism as a function of proppant injection design parameters is not fully understood.Rout, S.K., Friedmann, M.P., Riek, R., Greenwald, J., 2018. A prebiotic template-directed peptide synthesis based on amyloids. Nature Communications 9, Article 234. prebiotic replication of information-coding molecules is a central problem concerning life’s origins. Here, we report that amyloids composed of short peptides can direct the sequence-selective, regioselective and stereoselective condensation of amino acids. The addition of activated DL-arginine and DL-phenylalanine to the peptide RFRFR-NH2 in the presence of the complementary template peptide Ac-FEFEFEFE-NH2 yields the isotactic product FRFRFRFR-NH2, 1 of 64 possible triple addition products, under conditions in which the absence of template yields only single and double additions of mixed stereochemistry. The templating mechanism appears to be general in that a different amyloid formed by (Orn)V(Orn)V(Orn)V(Orn)V-NH2 and Ac-VDVDVDVDV-NH2 is regioselective and stereoselective for N-terminal, L-amino-acid addition while the ornithine-valine peptide alone yields predominantly sidechain condensation products with little stereoselectivity. Furthermore, the templating reaction is stable over a wide range of pH (5.6–8.6), salt concentration (0–4?M NaCl), and temperature (25–90?°C), making the amyloid an attractive model for a prebiotic peptide replicating system.Roy, A., Dutta, A., Pal, S., Gupta, A., Sarkar, J., Chatterjee, A., Saha, A., Sarkar, P., Sar, P., Kazy, S.K., 2018. Biostimulation and bioaugmentation of native microbial community accelerated bioremediation of oil refinery sludge. Bioresource Technology 253, 22-32. for developing an engineered bioremediation strategy for the treatment of hydrocarbon-rich petroleum refinery waste was investigated through biostimulation and bioaugmentation approaches. Enhanced (46–55%) total petroleum hydrocarbon (TPH) attenuation was achieved through phosphate, nitrate or nitrate+phosphate amendment in the sludge with increased (upto 12%) abundance of fermentative, hydrocarbon degrading , sulfate-reducing, CO2-assimilating and methanogenic microorganisms (Bacillus, Coprothermobacter, Rhodobacter, Pseudomonas, Achromobacter, Desulfitobacter, Desulfosporosinus, T78, Methanobacterium, Methanosaeta, etc). Together with nutrients, bioaugmentation with biosurfactant producing and hydrocarbon utilizing indigenous Bacillus strains resulted in 57–75% TPH reduction. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis revealed enhanced gene allocation for transporters (0.45–3.07%), ABC transporters (0.38–2.07%), methane (0.16–1.06%), fatty acid (0.018–0.15%), nitrogen (0.07–0.17%), butanoate (0.06–0.35%), propanoate (0.004–0.26%) metabolism and some xenobiotics (0.007–0.13%) degradation. This study indicated that nutrient-induced community dynamics of native microorganisms and their metabolic interplay within oil refinery sludge could be a driving force behind accelerated bioremediation.Ruhala, S.S., Zarnetske, J.P., Long, D.T., Lee-Cullin, J.A., Plont, S., Wiewiora, E.R., 2018. Exploring dissolved organic carbon cycling at the stream–groundwater interface across a third-order, lowland stream network. Biogeochemistry 137, 105-126. stream–groundwater interface (SGI) is thought to be an important location within stream networks for dissolved organic carbon (DOC) processing (e.g., degradation, removal), since it is considered a hotspot for microbial activity and biogeochemical reactions. This research is one of the first attempts to collect and assess DOC conditions at the SGI across a stream network—an entire third-order, lowland watershed in Michigan, USA. We present an initial exploration of this unique data set and highlight some of the challenges when working at these scales. Overall, our results show that SGI DOC conditions are complex at the network scale and do not conform to predictions based upon previous point- and small-scale studies. We found no strong pattern of DOC removal within the SGI at the network scale even after using chloride and temperature as natural tracers to differentiate between hydrological processes and biogeochemical reactions influencing DOC cycling. Instead, trends in DOC quantity and molecular qualities suggest that potential biotic reactions, including aerobic microbial respiration, had an influence on DOC concentrations at only some of the sites, while physical mixing of ground and stream surface waters appears to explain the majority of the observed changes in DOC concentrations at other sites. In addition, results show that neither SGI sites indicating DOC removal nor DOC molecular quality shifts measured correlated with stream order. It did reveal that DOC variability across surface water, groundwater, and the SGI locations was consistently greatest in the shallow sediments of the SGI, demonstrating that the SGI is a systematically distinct location for DOC conditions in the watershed. Our empirical stream network-scale SGI data are some of the first that are compatible with recently developed process-based, network-scale, SGI models. Our results indicate that these process-based models may not accurately represent SGI exchange of lowland, groundwater discharge-dominated streams like the one in this study. Lastly, this study shows that new methods are needed to achieve the goal of making and linking SGI observations to network-scale biogeochemical processes and theory. To help develop these methods we provide a discussion of the approach we used (i.e., “lessons-learned”) that might become the basis for systematic data analysis of SGI porewaters in future, network-wide biogeochemical studies of the SGI.Russell, J.M., Hopmans, E.C., Loomis, S.E., Liang, J., Sinninghe Damsté, J.S., 2018. Distributions of 5- and 6-methyl branched glycerol dialkyl glycerol tetraethers (brGDGTs) in East African lake sediment: Effects of temperature, pH, and new lacustrine paleotemperature calibrations. Organic Geochemistry 117, 56-69. distribution of branched glycerol dialkyl glycerol tetraethers (brGDGTs) in soils, peats, and lake sediments has been shown to correlate with mean annual air temperature (MAAT) and has provided valuable new climate reconstructions. Here we use an improved chromatographic method to quantify the fractional abundances of 5- and 6-methyl isomers in surface sediments from 65 East African lakes spanning temperatures 1.6–26.8?°C, and investigate the relationships between these fractional abundances and temperature, lake pH, and other environmental variables. We find that temperature exerts a strong control on brGDGT distributions, including the relative abundances of 5- and 6-methyl isomers, whereas other environmental variables, including lake pH, are weakly correlated to the fractional abundances of the brGDGTs. The distributions of brGDGTs in our lake sediments differ from those of soils and peats, leading to temperature offsets if soil- and peat-based brGDGT temperature calibrations are applied. We develop new calibrations for MAAT for use in lake sediment based upon the MBT′5Me and Index 1 ratios, as well as a multivariate regression of brGDGT fractional abundances on temperature using stepwise forward selection. We obtain root mean square errors (RMSE) between ～ 2.1 and 2.5?°C for these calibrations, highlighting the potential for brGDGTs to provide precise temperature reconstructions using lake sediment cores. Calibrations for lake pH perform more poorly, likely due to weak correlations between pH and brGDGT distributions in East African lakes. These results indicate that quantification of 5- and 6-methyl isomers separately in lake sediment can improve paleoclimatic reconstructions.Rustam, Y.H., Reid, G.E., 2018. Analytical challenges and recent advances in mass spectrometry based lipidomics. Analytical Chemistry 90, 374-397. no internationally accepted consensus definition exists, lipids can be broadly defined as “fatty acids and their derivatives and substances related biosynthetically or functionally to these compounds”.Lipids play critical roles as (i) the major structural components of biological membranes and as functional and regulatory components of membrane protein signaling, (ii) bioactive intra- and intercellular signaling molecules, and (iii) energy storage molecules for the maintenance of energy homeostasis. With studies originating almost 1 century ago, significant insights continue to be made toward elucidating the functional role of lipid metabolism in the dynamic regulation of cellular homeostasis and in determining the role of dysregulated lipid metabolism in the onset and progression of a range of human diseases, including diabetes, neurodegeneration, and cancer.These diverse functions are highly dependent on the structures of the lipids, their concentrations, and their inter- and intracellular spatial and temporal distributions. Lipid structures may be divided into eight main categories: fatty acyls (FA), glycerolipids (GL), glycerophospholipids (GP), sphingolipids (SP), sterol lipids (ST), prenol lipids (PR), saccharolipids (SL), and polyketides (PK). with further subclassifications into lipid class and subclass, based on the general structural motifs or physiochemical properties (e.g., polarity, charge, shape, size, and dynamics) of the molecular species within each category or class. The complexity and molecular diversity of the structures of lipids within each category, class, and subclass is apparent from an examination of the LIPID MAPS database, which serves as a compendium of structures and annotations of biologically relevant lipids that currently includes a total of 40?825 (20?512 curated and 20?313 computationally generated) unique lipid structures (October 19, 2017) along with experimental data and useful tools for their analysis.Over the past 3 decades, technical advances in analytical method development have enabled large-scale studies aimed at determining the complete set of lipids that may be present within a cell or organism, along with quantification of their abundances and analysis of their interactions with other lipids, proteins, and metabolites. This has led to the field of “lipidomics”, a term whose formal usage first appeared in the literature in 2001. Importantly, therefore, lipidomic analysis can facilitate not only a comprehensive understanding of the biochemical mechanisms underlying lipid metabolism and lipid-associated diseases but also lead to the discovery of lipid biomarkers for disease diagnosis, prognostic monitoring, and as targets for novel therapeutic interventions. Figure 1 shows the increasing number of scientific publications relating to lipidomics, indexed in PubMed, between 2000 and 2017, indicating that while the field is still growing, it is now approaching maturity. Notably, although only 5.64% of all “lipid”, “lipidome”, “lipidomic”, or “lipidomics” publications in 2017 also contained the term “mass spectrometry” (MS), this has increased >1.8-fold since 2000. Furthermore, 47.0% of all 2017 “lipidome”, “lipidomic”, or “lipidomics” publications also contain the term “mass spectrometry” and has remained relatively constant since 2003. In contrast, the number of publications involving the term nuclear magnetic resonance (NMR) along with “lipidome”, “lipidomic”, or “lipidomics” are significantly lower (only 1.7% in 2017), while overall the use of “NMR” with “lipid”, “lipidome”, “lipidomic”, or “lipidomics” has been steadily decreasing since 2014. This is most likely due to the generally lower sensitivity and higher complexity of NMR data for lipidomic analysis, despite having several potential advantages including nondestructive sample analysis, the ability to perform direct quantification with high analytical reproducibility, and to obtain information regarding molecular dynamics in complex lipid systems. On the other hand, MS methods offer higher sensitivity, a broad range of ex vivo and in vivo applications due to the availability of different ionization methods, mass analyzer types, and compatibility with multiple solution- and/or gas-phase separation techniques, as well as simpler data interpretation.Saiz, G., Goodrick, I., Wurster, C., Nelson, P.N., Wynn, J., Bird, M., 2018. Preferential production and transport of grass-derived pyrogenic carbon in NE-Australian savanna ecosystems. Frontiers in Earth Science 5, 115. doi: 10.3389/feart.2017.00115. the main factors driving fire regimes in grasslands and savannas is critical to better manage their biodiversity and functions. Moreover, improving our knowledge on pyrogenic carbon (PyC) dynamics, including formation, transport and deposition, is fundamental to better understand a significant slow-cycling component of the global carbon cycle, particularly as these ecosystems account for a substantial proportion of the area globally burnt. However, a thorough assessment of past fire regimes in grass-dominated ecosystems is problematic due to challenges in interpreting the charcoal record of sediments. It is therefore critical to adopt appropriate sampling and analytical methods to allow the acquisition of reliable data and information on savanna fire dynamics. This study uses hydrogen pyrolysis (HyPy) to quantify PyC abundance and stable isotope composition (δ13C) in recent sediments across 38 micro-catchments covering a wide range of mixed C3/C4 vegetation in north Queensland, Australia. We exploited the contrasting δ13C values of grasses (i.e., C4; δ13C > ?15‰) and woody vegetation (i.e., C3; δ13C < ?24‰) to assess the preferential production and transport of grass-derived PyC in savanna ecosystems. Analyses were conducted on bulk and size-fractionated samples to determine the fractions into which PyC preferentially accumulates. Our data show that the δ13C value of PyC in the sediments is decoupled from the δ13C value of total organic carbon, which suggests that a significant component of PyC may be derived from incomplete grass combustion, even when the proportion of C4 grass biomass in the catchment was relatively small. Furthermore, we conducted 16 experimental burns that indicate that there is a comminution of PyC produced in-situ to smaller particles, which facilitates the transport of this material, potentially affecting its preservation potential. Savanna fires preferentially burn the grass understory rather than large trees, leading to a bias toward the finer C4-derived PyC in the sedimentary record. This in turn, provides further evidence for the preferential production and transport of C4-derived PyC in mixed ecosystems where grass and woody vegetation coexist. Moreover, our isotopic approach provides independent validation of findings derived from conventional charcoal counting techniques concerning the appropriateness of adopting a relatively small particle size threshold (i.e., ~50 μm) to reconstruct savanna fire regimes using sedimentary records. This work allows for a more nuanced understanding of the savanna isotope disequilibrium effect, which has significant implications for global 13C isotopic disequilibria calculations and for the interpretation of δ13C values of PyC preserved in sedimentary records.Salahshoor, S., Fahes, M., Teodoriu, C., 2018. A review on the effect of confinement on phase behavior in tight formations. Journal of Natural Gas Science and Engineering 51, 89-103. resources, including tight oil and gas formations and shale plays, have become a vital source of energy all over the world. The unique characteristic of these reservoirs, which has made their development challenging, is the low-to ultra-low- permeability due to the abundance of nano-scale pores. In these tiny pores and pore-throats, phase behavior and saturation pressures of the confined fluid are shifted from those of the bulk fluid within larger pores of the conventional medium-to high-permeability reservoirs. During the past few decades, many scholars attempted to compare this alteration in fluid phase behavior inside the tiny pores of tight formations to that of the bulk by studying the fundamentals behind this behavior through mathematical models, simulations, and experimental studies. Reduced pore size and pore structure, mineralogy, adsorption, and capillary condensation phenomena have been addressed in different studies as the source of this deviation in properties. Attempts to model fluid phase behavior in narrow pores started by applying the knowledge of classical thermodynamics in molecular simulations of the confined fluid, which has an inhomogeneous distribution inside the narrow pores. This was followed by modifying different types of equations of state to capture the difference in saturation pressures and temperatures of the confined fluid and that of the bulk. Experimental efforts in this area cover a wide range of non-visual approaches and precise visual approaches using the lab-on-a-chip techniques. However, conducting experiments at the nano-scale, specifically less than 100?nm, is rare due to many experimental limitations. This review provides a comprehensive summary of the theoretical and experimental studies in this area, highlights the advantages and disadvantages of each method, and indicates a lack of data at the challenging range of pore scales, less than 10?nm, for simulation validation purposes.Saliu, F., Della Pergola, R., 2018. Organic bases, carbon dioxide and naphthenic acids interactions. Effect on the stability of petroleum crude oil in water emulsions. Journal of Petroleum Science and Engineering 163, 177-184. the mechanisms that lead to the formation of petroleum crude oil in water emulsion is fundamental for the development of sustainable exploitation procedures and efficient oil spills remediation technologies. In this study we surveyed the effectiveness of different nitrogen-containing organic bases in promoting emulsification through the interaction with the naphthenic acid fraction present in crude oil. It was found that bulky secondary amines were the most effective, able to stabilize the emulsion at 10?wt% of oil content for more than 20?min, and the emulsion at 40?wt% for more than 5?h. Interfacial tension measurements indicated that the interaction was effective even when naphtenic acids were dosed at very low levels (total acid number lass than 0.3). It was also observed that a successive addition of carbon dioxide to the system readily induced the breaking of the emulsion, probably by affecting the equilibrium involved in the formation of the naphthenates stabilizing species. In the light of these findings, we tested polyethylene glycols bearing a terminal amino moiety as a new class of CO2 responsive emulsifiers suitable for the petroleum industry.Sánchez-Espa?a, J., Wang, K., Falagán, C., Yusta, I., Burgos, W.D., 2018. Microbially mediated aluminosilicate formation in acidic anaerobic environments: A cell-scale chemical perspective. Geobiology 16, 88-103. the use of scanning transmission electron microscopy (STEM) combined with other complementary techniques (SEM, cryo-TEM, HRTEM, and EELS), we have studied the interaction of microorganisms inhabiting deep anoxic waters of acidic pit lakes with dissolved aluminum, silica, sulfate, and ferrous iron. These elements were close to saturation (Al, SiO2) or present at very high concentrations (0.12 m Fe(II), 0.12–0.22 m SO42?) in the studied systems. The anaerobic conditions of these environments allowed investigation of geomicrobial interactions that are difficult to see in oxidized, Fe(III)-rich environments. Detailed chemical maps and through-cell line scans suggest both extra- and intracellular accumulation of Al, Si, S, and Fe(II) in rod-like cells and other structures (e.g., spherical particles and bacteriomorphs) of probable microbial origin. The bacterial rods showed external nanometric coatings of adsorbed Fe(II) and Al on the cell surface and cell interiors with significant presence of Al, Si, and S. These microbial cells coexist with spherical particles showing similar configuration (Fe(II) external coatings and [Al, Si, S]-rich cores). The Al:Si and Al:S ratios and the good Al–Si correlation in the cell interiors suggest the concurrent formation of two amorphous phases, namely a proto-aluminosilicate with imogolite-like composition and proto-hydrobasaluminite. In both cases, the mineralization appears to comprise two stages: a first stage of aluminosilicate and Al-hydroxysulfate precipitation within the cell or around cellular exudates, and a second stage of SO42? and Fe(II) adsorption on surface sites existing on the mineral phases in the case of (SO42?) or on presumed organic molecules [in the case of Fe(II)]. These microbially related solids could have been formed by permineralization and mineral replacement of senescent microbial cells. However, these features could also denote biomineralization by active bacterial cells as a detoxification mechanism, a possibility which should be further explored. We discuss the significance of the observed Al/microbe and Si/microbe interactions and the implications for clay mineral formation at low pH.Sangiorgi, F., Bijl, P.K., Passchier, S., Salzmann, U., Schouten, S., McKay, R., Cody, R.D., Pross, J., van de Flierdt, T., Bohaty, S.M., Levy, R., Williams, T., Escutia, C., Brinkhuis, H., 2018. Southern Ocean warming and Wilkes Land ice sheet retreat during the mid-Miocene. Nature Communications 9, Article 317. and model experiments highlight the importance of ocean heat in forcing ice sheet retreat during the present and geological past, but past ocean temperature data are virtually missing in ice sheet proximal locations. Here we document paleoceanographic conditions and the (in)stability of the Wilkes Land subglacial basin (East Antarctica) during the mid-Miocene (~17–13.4 million years ago) by studying sediment cores from offshore Adélie Coast. Inland retreat of the ice sheet, temperate vegetation, and warm oligotrophic waters characterise the mid-Miocene Climatic Optimum (MCO; 17–14.8?Ma). After the MCO, expansion of a marine-based ice sheet occurs, but remains sensitive to melting upon episodic warm water incursions. Our results suggest that the mid-Miocene latitudinal temperature gradient across the Southern Ocean?never resembled that of the present day. We demonstrate that a strong coupling of oceanic climate and Antarctic continental conditions existed and that the East Antarctic subglacial basins were highly sensitive to ocean warming.Sans, M., Feider, C.L., Eberlin, L.S., 2018. Advances in mass spectrometry imaging coupled to ion mobility spectrometry for enhanced imaging of biological tissues. Current Opinion in Chemical Biology 42, 138-146. present complex biochemical and morphological composition associated with their various cell types and physiological functions. Mass spectrometry (MS) imaging technologies are powerful tools to investigate the molecular information from biological tissue samples and visualize their complex spatial distributions. Coupling of gas-phase ion mobility spectrometry (IMS) technologies to MS imaging has been increasingly explored to improve performance for biological tissue imaging. This approach allows improved detection of low abundance ions and separation of isobaric molecular species, thus resulting in more accurate determination of the spatial distribution of molecular ions. In this review, we highlight recent advances in the field focusing on promising applications of these technologies for metabolite, lipid and protein tissue imaging.Santiago, C.J.S., Kantzas, A., 2018. Investigating the effects of gas type and operation mode in enhanced gas recovery in unconventional reservoirs. Journal of Natural Gas Science and Engineering 50, 282-292. model that combines the Dusty-Gas approach and Darcy's Law is used to investigate the dynamics of production enhancement by gas injection in unconventional reservoirs. A comparison between CH4, N2 and CO2 injection in both Huff-n-Puff and Flooding operation modes is performed.The mechanism of production enhancement for each gas is different. CO2 can be injected to preferentially adsorb into the shale matrix, releasing hydrocarbons. In this case, the dominant mechanism is competitive adsorption. Due to stronger affinity with adsorption sites, CO2 injection would suggest high cumulative production. In spite of that, frontal displacement is very slow in this case, resulting in poorer short-term production when compared to N2 and CH4.N2 injection induces the release of hydrocarbons solely by partial pressure reduction. Frontal velocities are fast, resulting in high short-term production. Yet, since N2 is deemed inert, it does not replace components retained in the adsorbed phase.CH4 injection also prompts desorption of heavier hydrocarbons by partial pressure reduction. However, as heavier fractions are desorbed, CH4 molecules occupy the vacant sites. In this case, combined mechanisms of partial pressure reduction and uptake by the adsorption sites results in efficient release of heavier hydrocarbons.In this work, we demonstrate the impact of the presence of heavier hydrocarbon fractions in modeling gas transport during enhanced gas recovery processes. Multicomponent gas flow affects average reservoir pressure, produced gas composition and natural gas liquids (NGLs) yields, which is relevant for development of wet-gas and dry-gas unconventional reservoirs. Moreover, we demonstrate that injection gas composition significantly influences transport behavior of chemical species through the porous medium, and we highlight the relevant transport mechanisms during enhanced gas recovery in tight reservoirs.Santos, N.A., Cacique, A.P., Barbosa, ?.S., Silvério, F.O., Pinho, G.P.d., 2017. Validation of a method for extraction of polycyclic aromatic hydrocarbons from sewage sludge and analysis by GC-MS. International Journal of Environmental Analytical Chemistry 97, 1393-1404. the present study, the solid–liquid extraction with low temperature purification was validated for the determination of 16 polycyclic aromatic hydrocarbons from sewage sludge by gas chromatography-mass spectrometry. Recoveries ranged 70–114% for naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene, anthracene, fluoranthene, pyrene, benzo[a]anthracene and chrysene, while the compounds benzo[b]fluoranthene, benzo[k]fluoranthene, benzo[a]pyrene, indeno[1,2,3-cd]pyrene, dibenzo[a,h]anthracene and benzo[g,h,i]perylene showed recoveries of between 40 and 70%. The relative standard deviation was less than 13% for all of the compounds. Negative matrix effect was observed on the 10 compounds with less retention time in the chromatographic analysis and positive matrix effect noticed on the others. The limits of quantification were from 2 to 20 μg kg?1, about 30 times less than the maximum residue limit allowed in sludge by the European Union. The validated method produced quantification of 11 PAHs in one sludge sample at concentrations ranging 20–2000 μg kg?1.Scaife, J.D., Ruhl, M., Dickson, A.J., Mather, T.A., Jenkyns, H.C., Percival, L.M.E., Hesselbo, S.P., Cartwright, J., Eldrett, J.S., Bergman, S.C., Minisini, D., 2017. Sedimentary mercury enrichments as a marker for submarine large igneous province volcanism? Evidence from the mid-Cenomanian Event and Oceanic Anoxic Event 2 (Late Cretaceous). Geochemistry, Geophysics, Geosystems 18, 4253-4275. Anoxic Event 2 (OAE 2), during the Cenomanian-Turonian transition (～94 Ma), was the largest perturbation of the global carbon cycle in the mid-Cretaceous and can be recognized by a positive carbon-isotope excursion in sedimentary strata. Although OAE 2 has been linked to large-scale volcanism, several large igneous provinces (LIPs) were active at this time (e.g., Caribbean, High Arctic, Madagascan, Ontong-Java) and little clear evidence links OAE 2 to a specific LIP. The Mid-Cenomanian Event (MCE, ～96 Ma), identified by a small, 1‰ positive carbon-isotope excursion, is often referred to as a prelude to OAE 2. However, no underlying cause has yet been demonstrated and its relationship to OAE 2 is poorly constrained. Here we report sedimentary mercury (Hg) concentration data from four sites, three from the southern margin of the Western Interior Seaway and one from Demerara Rise, in the equatorial proto-North Atlantic Ocean. We find that, in both areas, increases in mercury concentrations and Hg/TOC ratios coincide with the MCE and the OAE 2. However, the increases found in these sites are of a lower magnitude than those found in records of many other Mesozoic events, possibly characteristic of a marine rather than atmospheric dispersal of mercury for both events. Combined, the new mercury data presented here are consistent with an initial magmatic pulse at the time of the MCE, with a second, greater pulse at the onset of OAE 2, possibly related to the emplacement of LIPs in the Pacific Ocean and/or the High Arctic.Schaedler, F., Lockwood, C., Lueder, U., Glombitza, C., Kappler, A., Schmidt, C., 2018. Microbially mediated coupling of Fe and N cycles by nitrate-reducing Fe(II)-oxidizing bacteria in littoral freshwater sediments. Applied and Environmental Microbiology 84, Article e02013-17.: Nitrate-reducing iron(II)-oxidizing bacteria have been known for approximately 20 years. There has been much debate as to what extent the reduction of nitrate and the oxidation of ferrous iron are coupled via enzymatic pathways or via abiotic processes induced by nitrite formed by heterotrophic denitrification. The aim of the present study was to assess the coupling of nitrate reduction and iron(II) oxidation by monitoring changes in substrate concentrations, as well as in the activity of nitrate-reducing bacteria in natural littoral freshwater sediment, in response to stimulation with nitrate and iron(II). In substrate-amended microcosms, we found that the biotic oxidation of ferrous iron depended on the simultaneous microbial reduction of nitrate. Additionally, the abiotic oxidation of ferrous iron by nitrite in sterilized sediment was not fast enough to explain the iron oxidation rates observed in microbially active sediment. Furthermore, the expression levels of genes coding for enzymes crucial for nitrate reduction were in some setups stimulated by the presence of ferrous iron. These results indicate that there is a direct influence of ferrous iron on bacterial denitrification and support the hypothesis that microbial nitrate reduction is stimulated by biotic iron(II) oxidation. Importance: The coupling of nitrate reduction and Fe(II) oxidation affects the environment at a local scale, e.g., by changing nutrient or heavy metal mobility in soils due to the formation of Fe(III) minerals, as well as at a global scale, e.g., by the formation of the primary greenhouse gas nitrous oxide. Although the coupling of nitrate reduction and Fe(II) oxidation was reported 20 years ago and has been studied intensively since then, the underlying mechanisms still remain unknown. One of the main knowledge gaps is the extent of enzymatic Fe(II) oxidation coupled to nitrate reduction, which has frequently been questioned in the literature. In the present study, we provide evidence for microbially mediated nitrate-reducing Fe(II) oxidation in freshwater sediments. This evidence is based on the rates of nitrate reduction and Fe(II) oxidation determined in microcosm incubations and on the effect of iron on the expression of genes required for denitrification. Schedl, A., Zweckmair, T., Kikul, F., Bacher, M., Rosenau, T., Potthast, A., 2018. Pushing the limits: Quantification of chromophores in real-world paper samples by GC-ECD and EI-GC-MS. Talanta 179, 693-699. the methodology of chromophore analysis in pulp and paper science, a sensitive gas-chromatographic approach with electron-capture detection is presented and applied to model samples and real-world historic paper material. Trifluoroacetic anhydride was used for derivatization of the chromophore target compounds. The derivative formation was confirmed by NMR and accurate mass analysis. The method successfully detects and quantifies hydroxyquinones which are key chromophores in cellulosic matrices. The analytical figures of merit appeared to be in an acceptable range with an LOD down to approx. 60ng/g for each key chromophore, which allows for their successful detection in historic sample material.Schmidt, D.N., 2018. Determining climate change impacts on ecosystems: the role of palaeontology. Palaeontology 61, 1-12. change is projected to change the ecosystems on land and in the sea at rates that are unprecedented for millions of years. The most commonly used approach to derive projections of how ecosystems will look in the future are experiments on living organisms. By their nature, experiments are unlike the real world and cannot capture the ability of organisms to migrate, select and evolve. They are often limited to a select few species and drivers of environmental change and hence cannot represent the complexity of interactions in ‘real’ ecosystems. The fossil record is an archive of responses to climate change at a global ecosystem scale. If, and only if, fossil assemblage variation is combined with independent information of environmental changes, sensitives of species or higher taxa to a specific magnitude of change of an environmental driver can be determined and used to inform future vulnerabilities of this species to the same driver. While records are often fragmented, there are time intervals which, when thoroughly analysed with quantitative data, can provide valuable insights into the future of biodiversity on this planet. This review provides an overview of projected impacts on marine ecosystems including: (1) the range of neontological methods, observations and their challenges; and (2) the complementary information that palaeontologists can contribution to this global challenge. I advocate that, in collaborations with other disciplines, we should aim for a strong visibility of our field and the knowledge it can provide for policy relevant assessments of the future.Schopf, J.W., Kitajima, K., Spicuzza, M.J., Kudryavtsev, A.B., Valley, J.W., 2018. SIMS analyses of the oldest known assemblage of microfossils document their taxon-correlated carbon isotope compositions. Proceedings of the National Academy of Sciences 115, 53-58.: Although the existence of the Archaea (one of three all-encompassing domains of life) in the Archean Eon (4,000 to 2,500 million years ago) has been inferred from carbon isotopes in bulk samples of ancient rocks, their cellular fossils have been unknown. We here present carbon isotope analyses of 11 microbial fossils from the ～3,465-million-year-old Western Australian Apex chert from which we infer that two of the five species studied were primitive photosynthesizers, one was an Archaeal methane producer, and two others were methane consumers. This discovery of Archaea in the Archean is consistent with the rRNA “tree of life,” confirms the earlier disputed biogenicity of the Apex fossils, and suggests that methane-cycling methanogen?methanotroph communities were a significant component of Earth’s early biosphere. Abstract: Analyses by secondary ion mass spectroscopy (SIMS) of 11 specimens of five taxa of prokaryotic filamentous kerogenous cellular microfossils permineralized in a petrographic thin section of the ～3,465 Ma Apex chert of northwestern Western Australia, prepared from the same rock sample from which this earliest known assemblage of cellular fossils was described more than two decades ago, show their δ13C compositions to vary systematically taxon to taxon from ?31‰ to ?39‰. These morphospecies-correlated carbon isotope compositions confirm the biogenicity of the Apex fossils and validate their morphology-based taxonomic assignments. Perhaps most significantly, the δ13C values of each of the five taxa are lower than those of bulk samples of Apex kerogen (?27‰), those of SIMS-measured fossil-associated dispersed particulate kerogen (?27.6‰), and those typical of modern prokaryotic phototrophs (?25 ± 10‰). The SIMS data for the two highest δ13C Apex taxa are consistent with those of extant phototrophic bacteria; those for a somewhat lower δ13C taxon, with nonbacterial methane-producing Archaea; and those for the two lowest δ13C taxa, with methane-metabolizing γ-proteobacteria. Although the existence of both methanogens and methanotrophs has been inferred from bulk analyses of the carbon isotopic compositions of pre-2,500 Ma kerogens, these in situ SIMS analyses of individual microfossils present data interpretable as evidencing the cellular preservation of such microorganisms and are consistent with the near-basal position of the Archaea in rRNA phylogenies. Schout, G., Hartog, N., Hassanizadeh, S.M., Griffioen, J., 2018. Impact of an historic underground gas well blowout on the current methane chemistry in a shallow groundwater system. Proceedings of the National Academy of Sciences 115, 296-301.: The rapid increase in shale gas production in recent years has led to increased attention to its potential negative environmental effects, including the risks of contaminating groundwater with methane and other substances. In this context, the uncontrolled gas migration that is triggered during well blowouts is an understudied environmental hazard. We show that the methane chemistry in shallow groundwater overlying the site of a catastrophic underground blowout continues to be impacted 50 y later. The occurrence of anaerobic methane oxidation limits the spatial extent to which the dissolved thermogenic methane plume could be observed and discerned from local biogenic methane sources. However, it also highlights the requirement to carry out monitoring in close proximity to potential gas leakage sources. Abstract: Blowouts present a small but genuine risk when drilling into the deep subsurface and can have an immediate and significant impact on the surrounding environment. Nevertheless, studies that document their long-term impact are scarce. In 1965, a catastrophic underground blowout occurred during the drilling of a gas well in The Netherlands, which led to the uncontrolled release of large amounts of natural gas from the reservoir to the surface. In this study, the remaining impact on methane chemistry in the overlying aquifers was investigated. Methane concentrations higher than 10 mg/L (n = 12) were all found to have δ13C-CH4 values larger than ?30‰, typical of a thermogenic origin. Both δ13C-CH4 and δD-CH4 correspond to the isotopic composition of the gas reservoir. Based on analysis of local groundwater flow conditions, this methane is not a remnant but most likely the result of ongoing leakage from the reservoir as a result of the blowout. Progressive enrichment of both δ13C-CH4 and δD-CH4 is observed with increasing distance and decreasing methane concentrations. The calculated isotopic fractionation factors of εC = 3 and εD = 54 suggest anaerobic methane oxidation is partly responsible for the observed decrease in concentrations. Elevated dissolved iron and manganese concentrations at the fringe of the methane plume show that oxidation is primarily mediated by the reduction of iron and manganese oxides. Combined, the data reveal the long-term impact that underground gas well blowouts may have on groundwater chemistry, as well as the important role of anaerobic oxidation in controlling the fate of dissolved methane. Schrimpe-Rutledge, A.C., Sherrod, S.D., McLean, J.A., 2018. Improving the discovery of secondary metabolite natural products using ion mobility–mass spectrometry. Current Opinion in Chemical Biology 42, 160-166. metabolite discovery requires an unbiased, comprehensive workflow to detect unknown unknowns for which little to no molecular knowledge exists. Untargeted mass spectrometry-based metabolomics is a powerful platform, particularly when coupled with ion mobility for high-throughput gas-phase separations to increase peak capacity and obtain gas-phase structural information. Ion mobility data are described by the amount of time an ion spends in the drift cell, which is directly related to an ion's collision cross section (CCS). The CCS parameter describes the size, shape, and charge of a molecule and can be used to characterize unknown metabolomic species. Here, we describe current and emerging applications of ion mobility–mass spectrometry for prioritization, discovery and structure elucidation, and spatial/temporal characterization.Schultz, R., Atkinson, G., Eaton, D.W., Gu, Y.J., Kao, H., 2018. Hydraulic fracturing volume is associated with induced earthquake productivity in the Duvernay play. Science 359, 304-308.: A sharp increase in the frequency of earthquakes near Fox Creek, Alberta, began in December 2013 in response to hydraulic fracturing. Using a hydraulic fracturing database, we explore relationships between injection parameters and seismicity response. We show that induced earthquakes are associated with completions that used larger injection volumes (104 to 105 cubic meters) and that seismic productivity scales linearly with injection volume. Injection pressure and rate have an insignificant association with seismic response. Further findings suggest that geological factors play a prominent role in seismic productivity, as evidenced by spatial correlations. Together, volume and geological factors account for ~96% of the variability in the induced earthquake rate near Fox Creek. This result is quantified by a seismogenic index–modified frequency-magnitude distribution, providing a framework to forecast induced seismicity.Editor's Summary: Seismicity curbed by lowering volume. Determining why hydraulic fracturing (also known as fracking) triggered earthquakes in the Duvernay Formation in Canada is important for future hazard mitigation. Schultz et al. found that injection volume was the key operational parameter correlated with induced earthquakes in the Duvernay. However, geological factors also played a considerable role in determining whether a large injection volume would trigger earthquakes. These findings provide a framework that may lead to better forecasting of induced seismicity.Segschneider, J., Schneider, B., Khon, V., 2018. Climate and marine biogeochemistry during the Holocene from transient model simulations. Biogeosciences Discussions 2018, 1-52. and marine biogeochemistry changes over the Holocene are investigated based on transient global climate and biogeochemistry model simulations over the last 9,500?yr. The simulations are forced by accelerated and non-accelerated orbital parameters, respectively, and atmospheric pCO2. The analysis focusses on key climatic parameters of relevance to the marine biogeochemistry, on the processes that determine the strength of the carbon pumps that drive the ocean–atmosphere carbon flux, and on the oxygen minimum zones (OMZs) in the ocean. The most pronounced changes occur in the eastern equatorial Pacific (EEP) OMZ, and in the North Atlantic. Changes in global mean values of biological production and export of detritus remain modest, with generally lower values in the mid-Holocene. The simulated ocean–atmosphere CO2-flux is of the right order of magnitude to explain the observed atmospheric pCO2 evolution, but with different timing. As the most significant result, we find a substantial increase in volume of the OMZ in the EEP continuing into the late Holocene in the non-accelerated simulation. The concurrent increase of age of the water mass within the EEP OMZ suggests that this growth is driven by a slow down of the circulation in the interior of the deep Pacific. This results in large scale deoxygenation in the deeper Pacific and hence the source regions of the EEP OMZ waters from mid-to-late Holocene. The simulated expansion of the OMZ raises the question whether the currently observed deoxygenation is a continuation of the orbitally driven decline in oxygen, or if it is already a result of the occuring climate change from anthropogenic forcing as widely assumed. An additional explanation would be that the anthropogenic forcing amplifies the natural forcing. The increase in water mass age and EEP OMZ volume can only be simulated with the non-accelerated model simulation. The simulations thus demonstrate that non-accelerated experiments are required for an analysis of the marine biogeochemistry in the Holocene.Shabani, M., Moallemi, S.A., Krooss, B.M., Amann-Hildenbrand, A., Zamani-Pozveh, Z., Ghalavand, H., Littke, R., 2018. Methane sorption and storage characteristics of organic-rich carbonaceous rocks, Lurestan province, southwest Iran. International Journal of Coal Geology 186, 51-64. methane sorption isotherms have been measured on nineteen samples from the Jurassic Sargelu and the Cretaceous Garau formations in Lurestan province, southwest Iran. Measurements were performed on dry and moisture-equilibrated samples. The study aimed at investigating the effects of pressure, temperature, organic matter and water content on sorption and gas storage characteristics.On the dry samples sorption isotherms were measured between 45 and 130 °C at pressures up to 25 MPa. Isotherms for the moisture-equilibrated samples were measured at 45 °C. An excess sorption function based on the Langmuir model was used to fit the experimental data.The total organic carbon (TOC) contents of the Garau samples range between 0.18 and 5.41 wt% and those of the Sargelu samples vary between 0.23 and 15.91 wt%. Carbonate is the dominant mineral in both sample sets, followed by quartz and clay minerals. No clear correlation was found between TOC content and porosity of the samples, indicating multiple factors controlling the abundance and volumes of both organic and inorganic pores.A linear correlation between sorption capacity and TOC value was found for both sample sets. Due to the larger variance in TOC values this relationship was more obvious for the Sargelu samples. Clay minerals constitute only a minor component of these carbonate-rich rocks. Therefore, as expected, no correlation was observed between sorption capacity and clay content. Organic matter content thus is the pivotal factor controlling methane sorption capacity.With increasing temperature the excess sorption capacity decreases while the Langmuir pressure increases, as evidenced by decrease in the initial slope of the isotherms.A negative correlation was observed between water content and sorption capacities and a positive correlation between water content and the Langmuir pressure (PL).The total gas storage capacity of the two sample sets was estimated as a function of depth based on all measured data and representative temperature and pressure gradients. Sorption generally tends to dominate the total storage capacity of shale gas systems in the low-depth/low-pressure range (as high as 90% depending on TOC content and specific pore volume), whereas in the great-depth/high-pressure range the volumetric storage capacity prevails.Shabaninejad, M., Middlelton, J., Fogden, A., 2018. Systematic pore-scale study of low salinity recovery from Berea sandstone analyzed by micro-CT. Journal of Petroleum Science and Engineering 163, 283-294. low salinity effect in clay-rich outcrop sandstones is probed by micro-CT imaging and analysis. A set of eight Berea sandstone mini-plugs underwent primary drainage and aging in crude oil to a mixed-wet state, followed by spontaneous imbibition of high and low salinity brines and imaging of this sequence of prepared starting and endpoint states. Tomogram registration and analysis were used to determine the salinity-induced changes in oil volume, oil/rock and oil/brine interfacial areas, and oil/brine interfacial mean curvature. Pore-scale statistics were extracted to explore any local correlation between the low salinity effect and pore geometry/topology. The qualitative observations and quantitative analyses demonstrated that the small oil recovery by the low salinity effect corresponded to a slight shift towards water-wet.Sharp, M., Tranter, M., 2017. Glacier biogeochemistry. Geochemical Perspectives 6, 173-339. volume charts our interlinked research pathways, which began with an interest in water flow paths at glacier beds and expanded into an exploration of the role of glaciers and ice sheets in local, regional, and global biogeochemical cycles. Along the journey, we discovered that glacier beds are habitats for microbes, and that the microbes are sustained by a variety of rock- and organic carbon-related processes. We were encouraged to write our story in a travelogue style, highlighting the contributions of the great students, post docs and colleagues we have had the pleasure to work with, the sometimes random nature of the factors that led us to explore new systems and processes, and some of the dead ends we ran into. We could have written so much more, but we have covered the state of the science when we were post grads, the things that motivated us to study rock dissolution and water flow paths at glacier beds, what happened when we explored glacier beds for the first time, in terms of biogeochemical weathering reactions, our desire to upscale from small valley glaciers to the larger ice masses of Svalbard and Ellesmere Island and, finally, the opportunities we had to work on the biogeochemistry of the Greenland and Antarctic Ice Sheets. It is with some pride that we note that most of the biogeochemical processes we deduced from our studies of smaller glacier systems also occur beneath the large ice masses, given due regard to differences in spatial scale, the timescales on which processes operate, and the provenance of sediment at the glacier beds. Our students have made huge contributions to the field of glacier biogeochemistry, the role of glaciers in fertilising the oceans, and the role of bedrock abrasion and crushing in subsidising microbial communities beneath ice sheet interiors. We suspect that these are going to be topics they will write about in future volumes of this series, as a minimum.Shay, P.-E., Peter Constabel, C., Trofymow, J.A., 2018. Evidence for the role and fate of water-insoluble condensed tannins in the short-term reduction of carbon loss during litter decay. Biogeochemistry 137, 127-141. temperatures associated with climate change have the potential to accelerate litter decay and subsequently release large amounts of carbon stored in soils. Condensed tannins are widespread secondary metabolites, which accumulate to high concentrations in many woody plants and play key roles in forest soil nutrient cycles. Future elevated atmospheric CO2 concentrations are predicted to reduce nitrogen content and increase tannin concentrations in plant tissues, thus reducing litter quality for microbial communities and slowing decomposition rates. How the distinct condensed tannin fractions (water-soluble, acetone:MeOH-soluble and solvent-insoluble) impact soil processes, has not been investigated. We tested the impact of condensed tannin and nitrogen concentrations on decay rates of poplar and Douglas-fir litter at sites spanning temperature and moisture gradients in coastal rainshadow forests in British Columbia, Canada. The three condensed tannin fractions were quantified using recent improvements on the butanol-HCl assay. Decay was assessed based on carbon remaining, while changes in litter chemistry were primarily observed using two methods for proximate chemical analyses. After 0.6 and 1?year of decay, more carbon remained in poplar litter with high, compared to low, condensed tannin concentrations. By contrast, more carbon remained in Douglas fir litter than poplar litter during this period, despite lower condensed tannin concentrations. Rapid early decay was especially attributed to loss of soluble compounds, including water-soluble condensed tannins. Water-insoluble condensed tannin fractions, which were transformed to acid-unhydrolyzable residues over time, were associated with reduced carbon loss in high condensed tannin litter.Shen, B., Qin, J., Tenger, B., Pan, A., Yang, Y., Bian, L., 2018. Identification of bacterial fossils in marine source rocks in South China. Acta Geochimica 37, 68-79. on the results of conventional geochemistry analysis including thin sections and SEM observations, different shapes of bacterial fossils, with size ranging from dozens of nanometers to several microns, were discovered in the low-mature marine source rocks and coal seams in South China, of which the Permian source rocks were dominated by the bacterial fossils derived from symbiotic sulphur bacteria with gypsum, and the Chengkou section in the Cambrian strata were occupied by abundant nanoscale bacterial fossils with rod and bar shapes. In contrast, a large quantity of possible bacterial fossils found in the high-mature Permian, Silurian, and Cambrian source rocks using SEM need?to be further explored. Despite this, this study has indicated that bacterial fossils were prevalent in the source rocks, such as mudstone, siliceous rock and gypsum-bearing coal seams in South China, which has been ignored before. It also suggests that the bacterial fossils may play an important role in the formation and accumulation of shale gas in the geological history.Shen, L., Liu, Y., Wang, N., Jiao, N., Xu, B., Liu, X., 2018. Variation with depth of the abundance, diversity and pigmentation of culturable bacteria in a deep ice core from the Yuzhufeng Glacier, Tibetan Plateau. Extremophiles 22, 29-38. has been suggested that the cryosphere is a new biome uniquely dominated by microorganisms, although the ecological characteristics of these cold-adapted bacteria are not well understood. We investigated the vertical variation with depth of the proportion of pigmented bacteria recovered from an ice core drilled in the Yuzhufeng Glacier, Tibetan Plateau. A total of 25,449 colonies were obtained from 1250 ice core sections. Colonies grew on only one-third of the inoculated Petri dishes, indicating that although the ice core harbored abundant culturable bacteria, bacteria could not be isolated from every section. Four phyla and 19 genera were obtained; Proteobacteria formed the dominant cluster, followed by Actinobacteria, Bacteroidetes and Firmicutes. The proportion of pigmented bacteria increased with depth from 79 to 95% and yellow-colored colonies predominated throughout the ice core, making up 47% of all the colonies. Pigments including α- and β-carotene, diatoxanthin, peridinin, zea/lutein, butanoyloxy, fucoxanthin and fucoxanthin were detected in representative colonies with α-carotene being the dominant carotenoid. To the best of our knowledge, this is the highest resolution study of culturable bacteria in a deep ice core reported to date.Shi, H., Luo, X., Lei, G., Wei, H., Zhang, L., Zhang, L., Lei, Y., 2018. Effects of early oil emplacement on reservoir quality and gas migration in the Lower Jurassic tight sand reservoirs of Dibei gas field, Kuqa Depression, western China. Journal of Natural Gas Science and Engineering 50, 250-258. is common for many tight gas sandstone reservoirs to have experienced an early oil charge before gas invading. To determine the effects of early oil emplacement on reservoir quality and gas migration has important role in predicting “sweet spots” of gas production in tight sand reservoirs. We investigated the palaeo and current fluids contacts accurately due to parameters from quantitative grain fluorescence in the Lower Jurassic Ahe Formation of Dibei gas field. The porosity and permeability values in palaeo-oil leg are totally higher than in palaeo-water leg, especially there being a wide gap of permeability with an order of magnitude. The variation of reservoir quality derives from the early oil emplacement, which restrained clay conversions from kaolinite or illite-smectite mixed-layer into fibrous illite that dramatically increasing flow-path tortuosity in sandstones, according to core analysis and X-ray diffraction. The early oil preserved penetrating quality of palaeo-oil leg, but the sandstones that never experienced early oil emplacement contains much more fibrous illite. It made most of early oil pathways subsequently act as the migration pathways for late gas and less than 50% of the migration pathways for gas were caused by microfractures due to quantitative grain fluorescence. Only the sandstones with medium early oil saturation did become sweet spots for gas in the tight sand reservoirs. Too much and too little oil once saturated in pores maybe adverse to the late gas migration and accumulation.Shiu, R.-F., Lee, C.-L., Chin, W.-C., 2018. Reduction in the exchange of coastal dissolved organic matter and microgels by inputs of extra riverine organic matter. Water Research 131, 161-166. drive large amounts of terrestrial and riverine organic matter into oceans. These organic materials may alter the self-assembly of marine dissolved organic matter (DOM) polymers into microgels and can even affect the behavior of existing natural microgels. We used Suwannee River humic acid, fulvic acid, and natural organic matter as a model of riverine organic matter (ROM) to investigate the impacts of ROM input on DOM polymer and microgel conversion. Our results indicated that the release of extra ROM, even at low concentrations (0.1–10?mg?L?1), into the marine organic matter pool decreased the size of self-assembled DOM polymers (from 4–5?μm to?<?1?μm) and dispersed the existing natural microgels into smaller particles (from 4–5?μm to 2–3?μm). The particle size of the microgel phase was also less sensitive than that of the DOM polymers to external changes (addition of ROM). This size reduction in DOM aggregation and existing microgels may be closely tied to the surface chemistry of the organic matter, such as negative surface charge stabilization and Ca2+ cross-linking bridges. These findings reveal that ROM inputs may therefore impede the self-assembly of DOM polymers into particulate organic matter and reduce the sedimentation flux of organic carbon and other elements from surface water to the deep ocean, thereby disturbing the biological pump, the downward transportation of nutrients, and the marine organic carbon cycle.Shutkova, S.A., Dolomatov, M.Y., 2017. Study of a supramolecular structure of continental type petroleum asphaltenes. Journal of Structural Chemistry 58, 1270-1274., electronic, and chemical structures of petroleum asphaltene molecules are studied. The investigations are carried out by quantum chemistry and molecular mechanics methods. The quantum chemical calculation of the structure-chemical parameters of dimers and trimers of petroleum asphaltenes is made using DFT/B3LYP. The refined values of the ionization potential and electron affinity of petroleum asphaltene molecules, their dimers and trimers agree well with the electron spectroscopy data. The results of the study of geometric structures of petroleum asphaltene dimers and trimers confirm the non-planar structure of asphaltenes. Original Russian Text ? 2017 S. A. Shutkova, M. Yu. Dolomatov.Shvartsburg, A.A., Haris, A., Andrzejewski, R., Entwistle, A., Giles, R., 2018. Differential ion mobility separations in the low-pressure regime. Analytical Chemistry 90, 936-943. mobility spectrometry (IMS) in conjunction with mass spectrometry (MS) has emerged as a powerful platform for biological and environmental analyses. An inherent advantage of differential or field asymmetric waveform IMS (FAIMS) based on the derivative of mobility vs electric field over linear IMS based on absolute mobility is much greater orthogonality to MS. Effective coupling of linear IMS to MS and diverse IMS/MS arrangements and modalities impossible at ambient buffer gas pressure were enabled at much reduced pressures. In contrast, FAIMS devices operate at or near atmospheric pressure, which complicated integration with MS. Here, we show FAIMS at ～15–30 Torr using a planar-gap stage within the MS instrument envelope. Fields up to ～300 Td permitted by the Paschen law at these pressures greatly raise the separation speed, providing fair resolution in ～10 ms and FAIMS scans in under 5 s. Rapid separation and efficient ion collection at low pressure minimize losses in the FAIMS step. Separations for key analyte classes and their dependences on electric field mirror those at ambient pressure. The potential for proteomics is demonstrated by separations of isomeric peptides with variant localization of post-translational modifications.Sie, C.-Y., Nguyen, B., Verlaan, M., Castellanos-Diaz, O., Adiaheno, K., Nguyen, Q.P., 2018. Viscous oil recovery and in situ deasphalting in fractured reservoirs: Part 1. The effect of solvent injection rate. Energy & Fuels 32, 360-372. EOR methods for viscous oil recovery from fractured reservoirs have significant challenges in both cost and energy efficiency. In response, solvent-based methods have been of interest because of their low energy intensity, low greenhouse gas emissions, and no fresh water consumption. Injection strategies for viscous oil recovery by solvent include liquid extraction and vapor oil gravity drainage. Understanding the mechanisms in each phase is of great value for the successful application and optimization of solvent EOR processes. The work presented here studies the effect of solvent injection rate on viscous oil recovery by liquid extraction with n-butane in vertically placed sandstone cores with an artificial fracture. The oil production rate, ultimate recovery, and in situ deasphalting in different sections of the core are analyzed. The oil production rate increased with solvent injection rate until it leveled off as the injection rate exceeded a critical value. The ultimate recovery factor is nearly the same for all solvent injection rates below the critical value. However, it is significantly reduced at higher injection rates. A conceptual model based on convective mass transfer is proposed and the effect of mechanical dispersion is discussed. In situ deasphalting was observed in all cases. The cause of the unexpected changes in production rate was attributed to severe asphaltene deposition and remobilization in the fractured permeable rock. In such a medium, solvent injection rate seems to show an optimal value for maximizing oil production rate, ultimate recovery factor, and solvent efficiency.Silva, I.S.d.A., de Sousa, A.A.C., de Souza, I.V.A.F., Capilla, R., da Cruz, G.F., Citó, A.M.d.G.L., de Lima, S.G., 2018. Characterization of oils from Fazenda Belém – Potiguar Basin, northeast Brazil. Petroleum Science and Technology 36, 173-178. (isolated by preparative TLC) from Potiguar Basin (Brazil) crude oils were submitted to mild oxidation to disrupt their structure, releasing the occluded oil. The released hydrocarbons were compared with those from the original crude oil, in order to provide an additional insight regarding composition in biomarkers and depositional paleoenvironment. It was possible to suggest that the oil samples present low thermal evolution, marine depositional environment and anoxide. The results showed that the release of these occluded hydrocarbon, which are remnants from the original oil, can be a tool for the geochemical study of highly biodegraded oils, leading to better maturation and origin information.Simonin, K.A., Roddy, A.B., 2018. Genome downsizing, physiological novelty, and the global dominance of flowering plants. PLOS Biology 16, Article e2003706.: The abrupt origin and rapid diversification of the flowering plants during the Cretaceous has long been considered an “abominable mystery.” While the cause of their high diversity has been attributed largely to coevolution with pollinators and herbivores, their ability to outcompete the previously dominant ferns and gymnosperms has been the subject of many hypotheses. Common among these is that the angiosperms alone developed leaves with smaller, more numerous stomata and more highly branching venation networks that enable higher rates of transpiration, photosynthesis, and growth. Yet, how angiosperms pack their leaves with smaller, more abundant stomata and more veins is unknown but linked—we show—to simple biophysical constraints on cell size. Only angiosperm lineages underwent rapid genome downsizing during the early Cretaceous period, which facilitated the reductions in cell size necessary to pack more veins and stomata into their leaves, effectively bringing actual primary productivity closer to its maximum potential. Thus, the angiosperms' heightened competitive abilities are due in no small part to genome downsizing.Author summary: The angiosperms, commonly referred to as the flowering plants, are the dominant plants in most terrestrial ecosystems, but how they came to be so successful is considered one of the most profound mysteries in evolutionary biology. Prevailing hypotheses have suggested that the angiosperms rose to dominance through an increase in their maximum potential photosynthesis and whole-plant carbon gain, allowing them to outcompete the ferns and gymnosperms that had previously dominated terrestrial ecosystems. Using a combination of anatomy, cytology, and modelling of liquid water transport and CO2 exchange between leaves and the atmosphere, we now provide strong evidence that the success and rapid spread of flowering plants around the world was the result of genome downsizing. Smaller genomes permit the construction of smaller cells that allow for greater CO2 uptake and photosynthetic carbon gain. Genome downsizing occurred only among the angiosperms, and we propose that it was a necessary prerequisite for rapid growth rates among land plants.Simpson, A.J., Simpson, M.J., Soong, R., 2018. Environmental nuclear magnetic resonance spectroscopy: An overview and a primer. Analytical Chemistry 90, 628-639. spectroscopy is a versatile tool for the study of structure and interactions in environmental media such as air, soil, and water as well as monitoring the metabolic responses of living organisms to an ever changing environment. Part review, part perspective, and part tutorial, this Feature is aimed at nonspecialists who are interested in learning more about the potential and impact of NMR spectroscopy in environmental research.Nuclear magnetic resonance (NMR) spectroscopy is a widely recognized tool for its unparalleled ability to ascertain the molecular structure of matter in various states (solutions, solids, and gels). NMR spectroscopy is commonly applied in diverse fields due to its versatility in studying structure and interactions across a range of molecular systems. NMR experiments can range from simple one-dimensional (1-D) to more complex multidimensional experiments that identify bond connectivities and spin–spin interactions. Consequently, there are potentially thousands of experiments that can be employed to access specific, molecular-level information often inaccessible by other analytical techniques. In addition, NMR is also highly reproducible even across different laboratories, at difference magnetic field strengths, and with different operators as well as providing accurate quantification without the need for external standards. As such, NMR is a nonselective detector (for example, detects any molecules containing an NMR active nucleus such as 1H or 13C) making it an ideal tool for nontargeted analyses. Using two-dimensional (2-D) NMR experiments, unknowns can be identified without prior knowledge of the compounds present. This is a major benefit given that other analytical techniques, such as mass spectrometry (MS), require some basic prior information about the analytes of interest to optimize the analysis (e.g., chromatographic separation, ionization, etc.). Environmental systems are highly complex and variable. Ecosystems are dynamic and a number of complex biological, chemical, and physical processes occur within them. Furthermore, climate change, urbanization, agriculture, and industrial activity all threaten to change ecosystem function. Therefore, it is imperative to understand molecular-level processes that occur within these ecosystems or environmental compartments (air, soil, and water) to increase the fundamental knowledge of ecosystem processes. Environmental chemists are tasked with trying to resolve these complex processes and NMR spectroscopy is playing a central role in this endeavor. The search for clean energy and understanding the fundamental chemistry of biofuels is another important research area that necessitates the use of advanced analytical techniques such as NMR spectroscopy. In addition, NMR spectroscopy is used for assessing wastewater treatment efficiency.In many ways, understanding larger scale environment phenomena involves working through a continuum of interconnected questions as illustrated in Figure 1. In this case the ultimate question being asked is “how does contaminant X impact aquatic organisms”. The first line of thought may be to expose the organism to a contaminant and using the noninvasive nature of NMR to understand the biological pathways impacted, which helps explain “why” the chemical is toxic. However, related questions such as “Is the chemical bioavailable in sediment?; what transformation products are formed?; does the chemical become sequestered in sediment?”; all complicate the scenario. Again, NMR’s ability to be applied to solution, gel, and solid phases is essential to study processes in situ and help tackle these complex and interconnected questions. Arguably, however, it is nearly impossible to understand how a contaminant binds to sedimentary organic matter without first understanding the structure of the sediment, ideally in its natural fully swollen state. Here NMR’s ability to study both structure and molecular interactions (often determined by mapping spatial proximities) while solving structure and conformation de novo is paramount. In summary, many environmental concerns can be broken down into three basic categories: structure, interactions, and impact. Fundamentally structural information is required to understand interactions with environmentally relevant contaminants and agrochemicals, and these interactions in turn determine bioavailability and toxicity, which then regulate their impact on living organisms. As such, the following feature is organized into three complementary topics, first the role of NMR to study structure in soil, air, and water, followed by molecular interactions and finally the response of living systems to environmental change and stress.Singh, A.K., Jha, M.K., 2018. Hydrocarbon potential of Permian coals of South Karanpura Coalfield, Jharkhand, India. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 40, 163-171. present study investigates the hydrocarbon generative potential of the coal seams of Barka Sayal Area of South Karanpura Coalfield, India, using petrological and geochemical characteristics. These coals are vitrinite rich followed by liptinite and inertinite. Rank wise these are sub-bituminous ‘A’ to high volatile bituminous ‘C’ and fall in the early catagenesis stage of evolution. The presence of Type III kerogen and high hydrogen index value indicates excellent gaseous hydrocarbon generative potential, but low Tmax suggests a characteristic of immature source rock. The calculated high conversion (%) and sufficient oil yield (%) justifies the suitability of these coals for liquefaction processes.Skeff, W., Recknagel, C., Düwel, Y., Schulz-Bull, D.E., 2018. Adsorption behaviors of glyphosate, glufosinate, aminomethylphosphonic acid, and 2-aminoethylphosphonic acid on three typical Baltic Sea sediments. Marine Chemistry 198, 1-9. batch experiment was conducted to study the adsorption behaviors of glyphosate, glufosinate, aminomethylphosphonic acid (AMPA), and 2-aminoethylphosphonic acid (2-AEP) in marine sediments (mud, silt, and sand) from the Baltic Sea. The experiment took into account the influence of pH, salinity, and temperature on the adsorption behaviors of the studied compounds. In contrast to glufosinate, glyphosate exhibited an adsorption affinity for the three types of sediments. AMPA and 2-AEP showed similar adsorption behaviors on mud and silt, while their adsorption on sand was negligible. The equilibrium adsorption data for glyphosate, AMPA, and 2-AEP on mud and silt fit well with the linear partitioning and Freundlich isotherms, whereas the data for glyphosate on sand could only be fitted with the Freundlich isotherm. The Freundlich distribution coefficients (kf) were in the range of 6.1–259.5 L/kg for glyphosate, 9.2–39.5 L/kg for AMPA, and 7.7–38.5 L/kg for 2-AEP under the experimental conditions of pH 8.1, temperature = 21 °C, and a salt concentration of 8 g/L. The adsorption kinetic was better described by the pseudo-second-order than the pseudo-first-order model, suggesting chemisorption as the adsorption mechanism. The order of adsorption of the compounds on the sediments was: glyphosate > AMPA ≥ 2-AEP > glufosinate. The adsorption capacity of sediments followed the sequence: mud > silt > sand. Increasing the pH, salinity, or temperature of the solution significantly reduced the adsorption capacity of the compounds. The data obtained in this study provide valuable information on the fate and distribution of the investigated phosphonates in the Baltic Sea.Snelgrove, P.V.R., Soetaert, K., Solan, M., Thrush, S., Wei, C.-L., Danovaro, R., Fulweiler, R.W., Kitazato, H., Ingole, B., Norkko, A., Parkes, R.J., Volkenborn, N., 2018. Global carbon cycling on a heterogeneous seafloor. Trends in Ecology & Evolution 33, 96-105. biological communities mediate the transformation, transport, and storage of elements fundamental to life on Earth, including carbon, nitrogen, and oxygen. However, global biogeochemical model outcomes can vary by orders of magnitude, compromising capacity to project realistic ecosystem responses to planetary changes, including ocean productivity and climate. Here, we compare global carbon turnover rates estimated using models grounded in biological versus geochemical theory and argue that the turnover estimates based on each perspective yield divergent outcomes. Importantly, empirical studies that include sedimentary biological activity vary less than those that ignore it. Improving the relevance of model projections and reducing uncertainty associated with the anticipated consequences of global change requires reconciliation of these perspectives, enabling better societal decisions on mitigation and adaptation.Soeder, D.J., 2018. The successful development of gas and oil resources from shales in North America. Journal of Petroleum Science and Engineering 163, 399-420. hydrocarbon resources of shale gas and tight oil have made a significant impact on North American energy reserves over the past decade. The production of so-called “unconventional” natural gas from U.S shales like the Barnett, Haynesville, Fayetteville, Marcellus, and Utica, and Canadian shales like the Muskwa, Montney, and Duvernay have saturated North American gas markets, boosted Canada's exports, and turned the U.S. into a net exporter of natural gas. Tight oil production from the Bakken Shale has made important contributions to the economy of the Canadian province of Saskatchewan. North Dakota has become the second largest oil producing state in the U.S. thanks to production from the Bakken. It trails only the state of Texas, which maintains first place because of equally prolific hydrocarbon liquids production from the Eagle Ford Shale and shales in the Permian basin. It is difficult to overstate the importance of these shale gas and oil resources to the U.S., North American, and world energy economies.North American shale development blossomed in the United States between 2005 and 2010, driven by high natural gas and oil prices, the availability of favorable lease positions on shale plays, and the application of drilling and stimulation technology that could successfully produce commercial quantities of hydrocarbons from these formations at economical costs. Development in Canada began a bit later, and some development has also taken place on shales in Mexico. Many people who express surprise at the apparent “overnight” success of shale gas and oil production were simply not paying attention. The truth is that a historic and protracted engineering struggle was required to identify, modify, and apply the right technology for economically-viable production. Modern assessments of the resource potential of these rocks began in the late 1970s, as did the first systematic engineering attempts to drill directional wells and hydraulically fracture shale. Success was elusive for nearly two decades, however, until the right combination of economics and technology came along. The ability of some visionary people to recognize the applications of that technology led directly to the current success of shale gas and tight oil production. Other countries considering development of their own shale resources are looking to the North American example for leadership.The success of shale resource development has not been without controversy. Public fear of the hydraulic fracturing process, or “fracking” has been amplified by shale gas opponents, leading to restrictions against shale development in many areas, and outright bans in some locations like New York and Quebec. The “boomtown” nature of the early development, and the lack of definitive environmental risk data has added to the negative perceptions, resulting in a backlash against some exploration and production ventures. Researchers have been gradually reducing the amount of uncertainty with respect to environmental risks, and as operators have gained more experience, the frequency of incidents has fallen. Many operators now recognize that obtaining a “social license” from the community is a necessary first step for successful shale gas development.Sokol, A.G., Tomilenko, A.A., Bul’bak, T.A., Sobolev, N.V., 2017. Synthesis of hydrocarbons by CO2 fluid conversion with hydrogen: Experimental modeling at 7.8 GPa and 1350°C. Doklady Earth Sciences 477, 1483-1487. of hydrocarbons by the interaction of a CO2 fluid with hydrogen mantle domains has been simulated in an experiment at 7.8 GPa and 1350°C. The synthesized fluid contains mainly aldehydes; lower amounts of ketones, alcohols, esters, and ethers; as well as noticeable amounts of isobutane and butane, alkenes, arenes, and polycyclic aromatic and heterocyclic hydrocarbons. The fluid is compositionally close to volatiles found in inclusions from mantle olivines and picroilmenites. Original Russian Text ? A.G. Sokol, A.A. Tomilenko, T.A. Bul’bak, N.V. Sobolev, 2017, published in Doklady Akademii Nauk, 2017, Vol. 477, No. 6, pp. 699–703.Sommers, P., Darcy, J.L., Gendron, E.M.S., Stanish, L.F., Bagshaw, E.A., Porazinska, D.L., Schmidt, S.K., 2018. Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes. FEMS Microbiology Ecology 94, Article fix167. cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley. We found that eukaryotic alpha and beta diversity were strongly related to those of bacteria across scales ranging from 140 m to 41 km apart. Alpha diversity of both was significantly related to position in the valley and surface area of the cryoconite hole, with pH also significantly correlated with the eukaryotic diversity. Beta diversity for both bacteria and eukaryotes was significantly related to position in the valley, with bacterial beta diversity also related to nitrate. These results are consistent with transport of sediments onto glaciers occurring primarily at local scales relative to the size of the valley, thus creating feedbacks in local chemistry and diversity.Song, D., Li, C., Song, B., Yang, C., Li, Y., 2017. Geochemistry of mercury in the Permian tectonically deformed coals from Peigou Mine, Xinmi Coalfield, China. Acta Geologica Sinica - English Edition 91, 2243-2254. the mercury emitted from coal combustion can lead to serious environmental issues, researchers pay more attention to the content, distribution and occurrence of mercury in coal. In this paper, the content, distribution, and occurrence of mercury in the Permian tectonically deformed coals from Peigou Mine, Xinmi coalfield, Henan Province were investigated. A total of 18 bench samples were taken from No.2-1 coals seam in Peigou Mine, including 15 coal bench samples, two roofs and one floor. The mercury concentration, mineral composition, and main inorganic element content of 18 samples were determined by DMA-80 direct mercury analyzer, XRD, and XRF respectively. The results show that the mercury content ranges from 0.047 ppm to 0.643 ppm, with an average of 0.244 ppm. Though the coal seam has turned into typical tectonically deformed coal by the strong tectonic destruction and plastic deformation, the vertical distribution of mercury has remarkable heterogeneity in coal seam section. By the analysis of correlation between mercury and the main inorganic elements and the mineral composition in coal, we infer that majority of mercury mainly relates to pyrite or kaolinite.Song, W., Yao, J., Ma, J., Couples, G.D., Li, Y., Sun, H., 2018. Pore-scale numerical investigation into the impacts of the spatial and pore-size distributions of organic matter on shale gas flow and their implications on multiscale characterisation. Fuel 216, 707-721. to their differences in surface properties and pore geometry, pores of predominant submicron sizes in organic and inorganic matter of gas shale incur different gas flow and transport behaviours. Those differences can manifest at sample scales differently depending on the spatial distributions of shale organic and inorganic matter, and the pore-size distributions in these types of matter. Therefore, understanding the impacts of variable configurations of them on the gas flow is essential to guide progressive subsampling in multiscale shale characterisation that is required for modelling shale gas flow at the first place. This article reports a pore-scale numerical investigation into the impacts of combinations of three end-member spatial arrangements of the organic matter and two contrasting sets of organic and inorganic pore-size distributions at variable organic fractions on gas flow using pore-network modelling. A unified pore-network flow model for shale gas that captures a comprehensive set of gas flow and transport mechanisms is developed in this work to calculate the effective gas apparent permeability at reservoir conditions. In terms of the mean permeability at each selected organic fraction, the largest differences are found to appear at a high fraction above 25% across all the arrangements, and the upper bound can reach more than two orders of magnitude greater than the lower bound. The results suggest that subsampling ought to focus on subdomains where organic fractions are high, organic and inorganic pores differ in size, and distinct flow-enhancing or baffling arrangements of organic matter are present.Song, X., Li, H., Yin, M., Ma, Y., 2018. Determination of 16 polycyclic aromatic hydrocarbons in marine sediments by gas chromatography-tandem mass spectrometry with accelerated solvent extraction. Chinese Journal of Chromatography 36, 43-50. method based on gas chromatography-tandem mass spectrometry (GC-MS/MS) with accelerated solvent extraction (ASE) was developed for the determination of 16 polycyclic aromatic hydrocarbons (PAHs) in marine sediments. The sediment samples were extracted with hexane-acetone (1:1, v/v). The extracts were dehydrated with anhydrous sodium sulfate, and concentrated with a termovap sample concentrator. The concentrated solutions were further cleaned up with Si SPE columns. The purified solutions were then isolated by HP-5MS column (30 m×0.25 mm×0.25 μm). The analytes were detected using electron impact source under multiple reaction monitoring (MRM) mode. The results showed that the 16 PAHs had good linearities in the range of 0.01-1.00 mg/L with the correlation coefficients (R) greater than 0.997. The spiked recoveries of the 16 PAHs were in the range of 75.8%-97.8%, and the relative standard deviations (RSDs) were less than 10%. The method detection limits (MDLs) of the 16 PAHs ranged from 0.048-0.234 μg/kg with 20.0 g sampling weight. This method is suitable for the determination of trace PAHs in marine sediments.Sosa, O.A., 2018. Phosphorus redox reactions as pinch hitters in microbial metabolism. Proceedings of the National Academy of Sciences 115, 7-8. (P) is required by all living organisms for the synthesis of genetic and cellular components, metabolism, and energy transfer. The phosphate ion (PO43-, P valence +5), also referred to as inorganic phosphate (Pi), is typically the most easily assimilated P species but is also a limiting nutrient in many ecosystems. Microorganisms can also obtain Pi from inorganic and organic forms of reduced P compounds (P valence +1, +2, +3), including phosphonates (organophosphorus compounds with a direct C-P bond), phosphite (HPO32-), and hypophosphite (1). Reduced P compounds have long been known to exist in the environment, although only recently has it become clear that these compounds make up a significant proportion of the P available to microbial organisms (2?–4). DNA sequencing studies have revealed the corresponding enormous diversity of microorganisms that can utilize or synthesize reduced P compounds (5, 6). Therefore, the microbial transformations of reduced P compounds are expected to have previously unrecognized roles in the ecology and biogeochemistry of ecosystems. Figueroa et al. (7) explore how microorganisms in an anoxic environment obtain all of the energy necessary for growth by oxidizing phosphite to Pi, thereby contributing to the production of new biomass and to the P redox cycle. Their findings contribute to emerging evidence that the P redox cycle is an intrinsic part of the microbial cycling of carbon, energy, and other nutrients. In oceanic waters, P redox pathways are an active component of the P cycle (8 … Sousa, D.Z., Visser, M., van Gelder, A.H., Boeren, S., Pieterse, M.M., Pinkse, M.W.H., Verhaert, P.D.E.M., Vogt, C., Franke, S., Kümmel, S., Stams, A.J.M., 2018. The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways. Nature Communications 9, Article 239. is generally metabolized through a pathway initiated by a cobalamine-containing methanol methyltransferase by anaerobic methylotrophs (such as methanogens and acetogens), or through oxidation to formaldehyde using a methanol dehydrogenase by aerobes. Methanol is an important substrate in deep-subsurface environments, where thermophilic sulfate-reducing bacteria of the genus Desulfotomaculum have key roles. Here, we study the methanol metabolism of Desulfotomaculum kuznetsovii strain 17T, isolated from a 3000-m deep geothermal water reservoir. We use proteomics to analyze cells grown with methanol and sulfate in the presence and absence of cobalt and vitamin B12. The results indicate the presence of two methanol-degrading pathways in D. kuznetsovii, a cobalt-dependent methanol methyltransferase and a cobalt-independent methanol dehydrogenase, which is further confirmed by stable isotope fractionation. This is the first report of a microorganism utilizing two distinct methanol conversion pathways. We hypothesize that this gives D. kuznetsovii a competitive advantage in its natural environment.Sousa, F.L., Preiner, M., Martin, W.F., 2018. Native metals, electron bifurcation, and CO2 reduction in early biochemical evolution. Current Opinion in Microbiology 43, 77-83. hydrogen is an ancient source of energy and electrons. Anaerobic autotrophs that harness the H2/CO2 redox couple harbour ancient biochemical traits that trace back to the universal common ancestor. Aspects of their physiology, including the abundance of transition metals, radical reaction mechanisms, and their main exergonic bioenergetic reactions, forge links between ancient microbes and geochemical reactions at hydrothermal vents. The midpoint potential of H2 however requires anaerobes that reduce CO2 with H2 to use flavin based electron bifurcation — a mechanism to conserve energy as low potential reduced ferredoxins via soluble proteins — for CO2 fixation. This presents a paradox. At the onset of biochemical evolution, before there were proteins, how was CO2 reduced using H2? FeS minerals alone are probably not the solution, because biological CO2 reduction is a two electron reaction. Physiology can provide clues. Some acetogens and some methanogens can grow using native iron (Fe0) instead of H2 as the electron donor. In the laboratory, Fe0 efficiently reduces CO2 to acetate and methanol. Hydrothermal vents harbour awaruite, Ni3Fe, a natural compound of native metals. Native metals might have been the precursors of electron bifurcation in biochemical evolution.?pánik, I., Machyňáková, A., 2018. Recent applications of gas chromatography with high-resolution mass spectrometry. Journal of Separation Science 41, 163-179. chromatography coupled to high-resolution mass spectrometry is a powerful analytical method that combines excellent separation power of gas chromatography with improved identification based on an accurate mass measurement. These features designate gas chromatography with high-resolution mass spectrometry as the first choice for identification and structure elucidation of unknown volatile and semi-volatile organic compounds. Gas chromatography with high-resolution mass spectrometry quantitative analyses was previously focused on the determination of dioxins and related compounds using magnetic sector type analyzers, a standing requirement of many international standards. The introduction of a quadrupole high-resolution time-of-flight mass analyzer broadened interest in this method and novel applications were developed, especially for multi-target screening purposes. This review is focused on the development and the most interesting applications of gas chromatography coupled to high-resolution mass spectrometry towards analysis of environmental matrices, biological fluids, and food safety since 2010. The main attention is paid to various approaches and applications of gas chromatography coupled to high-resolution mass spectrometry for non-target screening to identify contaminants and to characterize the chemical composition of environmental, food, and biological samples. The most interesting quantitative applications, where a significant contribution of gas chromatography with high-resolution mass spectrometry over the currently used methods is expected, will be discussed as well.Sparrow, K.J., Kessler, J.D., Southon, J.R., Garcia-Tigreros, F., Schreiner, K.M., Ruppel, C.D., Miller, J.B., Lehman, S.J., Xu, X., 2018. Limited contribution of ancient methane to surface waters of the U.S. Beaufort Sea shelf. Science Advances 4, Article eaao4842. response to warming climate, methane can be released to Arctic Ocean sediment and waters from thawing subsea permafrost and decomposing methane hydrates. However, it is unknown whether methane derived from this sediment storehouse of frozen ancient carbon reaches the atmosphere. We quantified the fraction of methane derived from ancient sources in shelf waters of the U.S. Beaufort Sea, a region that has both permafrost and methane hydrates and is experiencing significant warming. Although the radiocarbon-methane analyses indicate that ancient carbon is being mobilized and emitted as methane into shelf bottom waters, surprisingly, we find that methane in surface waters is principally derived from modern-aged carbon. We report that at and beyond approximately the 30-m isobath, ancient sources that dominate in deep waters contribute, at most, 10 ± 3% of the surface water methane. These results suggest that even if there is a heightened liberation of ancient carbon–sourced methane as climate change proceeds, oceanic oxidation and dispersion processes can strongly limit its emission to the atmosphere.Speranza, E.D., Colombo, M., Skorupka, C.N., Colombo, J.C., 2018. Early diagenetic alterations of sterol biomarkers during particle settling and burial in polluted and pristine areas of the Rio de la Plata Basin. Organic Geochemistry 117, 1-11. and diagenetic alterations of sterol markers were studied in settling material and sediments near the Buenos Aires main sewer (BA), and at a relatively non-polluted northern site at the Uruguay River (N). Vertical particle fluxes were 7-times higher at BA relative to N (34?±?24 vs 4.6?±?3.6?mg/cm2/day; mean?±?standard deviation), increasing during rainy months. Total sterol contents were consistently higher at BA, both in settling material (7140?±?7905 vs 41?±?47?μg/g at N) and sediments (708?±?454 vs 1.9?±?0.18?μg/g). This difference was further amplified in the vertical flux of sterols (116?±?168 vs 0.070?±?0.13?mg/cm2/year). At BA, sterol composition of settling material and sediments was dominated by fecal sterols (75–77%), with extreme coprostanol concentrations (3.6?±?4.8 vs 0.35?±?0.28?mg/g at N) which are similar to sewage sludge. In contrast, at N the sterol profile was dominated by plant sterols (57–64%), mainly sitosterol, stigmasterol and campesterol. At BA the discharge of fresh sewage was confirmed by the high coprostanol/(coprostanol?+?epicoprostanol) ratio. At N, the overwhelming dominance of plant sterols over herbivore fecal sterols was reflected by the high sitosterol/(sitosterol?+?24-ethylcoprostanol) ratio and the low coprostanol/(coprostanol?+?24-ethylcoprostanol) ratio. The coprostanol/(coprostanol?+?epicoprostanol) and cholesterol/(cholesterol?+?cholestanol) ratios were lower in sediments than in settling material, reflecting the sterol degradation at the sediment surface. The accumulation efficiencies, calculated as the difference between trap fluxes and sediment inventories, were 2–7 times higher at BA reflecting strong vertical fluxes and enhanced preservation under anoxic conditions. During diagenetic processes, epicoprostanol (partially produced in situ), cholestanol and plant sterols were the best-preserved sterols, while cholesterol was the most labile during burial.Sperfeld, M., Rauschenbach, C., Diekert, G., Studenik, S., 2018. Microbial community of a gasworks aquifer and identification of nitrate-reducing Azoarcus and Georgfuchsia as key players in BTEX degradation. Water Research 132, 146-157. analyzed a coal tar polluted aquifer of a former gasworks site in Thuringia (Germany) for the presence and function of aromatic compound-degrading bacteria (ACDB) by 16S rRNA Illumina sequencing, bamA clone library sequencing and cultivation attempts. The relative abundance of ACDB was highest close to the source of contamination. Up to 44% of total 16S rRNA sequences were affiliated to ACDB including genera such as Azoarcus, Georgfuchsia, Rhodoferax, Sulfuritalea (all Betaproteobacteria) and Pelotomaculum (Firmicutes). Sequencing of bamA, a functional gene marker for the anaerobic benzoyl-CoA pathway, allowed further insights into electron-accepting processes in the aquifer: bamA sequences of mainly nitrate-reducing Betaproteobacteria were abundant in all groundwater samples, whereas an additional sulfate-reducing and/or fermenting microbial community (Deltaproteobacteria, Firmicutes) was restricted to a highly contaminated, sulfate-depleted groundwater sampling well. By conducting growth experiments with groundwater as inoculum and nitrate as electron acceptor, organisms related to Azoarcus spp. were identified as key players in the degradation of toluene and ethylbenzene. An organism highly related to Georgfuchsia toluolica G5G6 was enriched with p-xylene, a particularly recalcitrant compound. The anaerobic degradation of p-xylene requires a metabolic trait that was not described for members of the genus Georgfuchsia before. In line with this, we were able to identify a putative 4-methylbenzoyl-CoA reductase gene cluster in the respective enrichment culture, which is possibly involved in the anaerobic degradation of p-xylene.Srivastava, K., Wiesenberg, G.L.B., 2018. Severe drought-influenced composition and δ13C of plant and soil n-alkanes in model temperate grassland and heathland ecosystems. Organic Geochemistry 116, 77-89. events are predicted to increase under future climate change. In temperate ecosystems, plants are capable of resisting drought due to their hydrophobic wax layer, in which n-alkanes are important constituents. In soils, plant-derived n-alkanes are comparatively resistant to degradation. To improve understanding of the significance of n-alkanes in plant-soil systems during a severe drought period (104?days), we investigated bulk organic carbon (Corg) concentration, total lipid extract (TLE) concentration, and n-alkane molecular ratios such as average chain length (ACL), carbon preference index (CPI) and chain length ratios of different n-alkane compounds, in addition to the compound-specific isotope composition (δ13C) of n-alkanes in model temperate grassland and heathland plant-soil systems. Although plant communities of two (heathland) and four (grassland) species were available, only one representative species per biome was accessible for the current study.Heathland plants and soil revealed significantly higher concentrations of Corg and TLE compared with grassland. TLE and alkane composition responded quickly during the first drought phase (0–40?days). This indicates that plants were actively utilizing C and produced more n-alkanes in order to withstand drought, which was confirmed by increased (2–3‰) δ13C values for n-alkanes in shoot biomass. However, during later drought phases all the parameters remained constant for plants and soils. This suggests limited change in biosynthesis and cycling of plant lipids such as n-alkanes during intense drought. Surprisingly, during the first drought phase, increased ACL and CPI values in soil demonstrated a rapid input of plant-derived long chain n-alkanes to soil, which was not expected due to the decadal residence time of alkanes in soil. The study enabled tracing of plant metabolic response in terms of alkane biosynthesis under different phases of drought and rapid cycling of alkanes in the plant-soil system.Staudigel, P.T., Murray, S., Dunham, D.P., Frank, T.D., Fielding, C.R., Swart, P.K., 2018. Cryogenic brines as diagenetic fluids: Reconstructing the diagenetic history of the Victoria Land Basin using clumped isotopes. Geochimica et Cosmochimica Acta 224, 154-170. isotopic analyses (δ13C, δ18O, and Δ47) of carbonate phases recovered from a core in McMurdo Sound by ANtarctic geologic DRILLing (ANDRILL-2A) indicate that the majority of secondary carbonate mineral formation occurred at cooler temperatures than the modern burial temperature, and in the presence of fluids with δ18Owater values ranging between ?11 and ?6‰ VSMOW. These fluids are interpreted as being derived from a cryogenic brine formed during the freezing of seawater. The Δ47 values were converted to temperature using an in-house calibration presented in this paper. Measurements of the Δ47 values in the cements indicate increasingly warmer crystallization temperatures with depth and, while roughly parallel to the observed geothermal gradient, consistently translate to temperatures that are cooler than the current burial temperature. The difference in temperature suggests that cements formed when they were ～260?±?100?m shallower than at the present day. This depth range corresponds to a period of minimal sediment accumulation from 3 to 11?Myr; it is therefore interpreted that the majority of cements formed during this time. This behavior is also predicted by time-integrated modeling of cementation at this site. If this cementation had occurred in the presence of these fluids, then the cryogenic brines have been a longstanding feature in the Victoria Land Basin. Brines such as those found at this site have been described in numerous modern high-latitude settings, and analogous fluids could have played a role in the diagenetic history of other ice-proximal sediments and basins during glacial intervals throughout geologic history. The agreement between the calculated δ18Owater value and the measured values in the pore fluids shows how the Δ47 proxy can be used to identify the origin of negative δ18O values in carbonate rocks and that extremely negative values do not necessarily need to be a result of the influence of meteoric fluids or reaction at high temperature.Steinke, M., Hodapp, B., Subhan, R., Bell, T.G., Martin-Creuzburg, D., 2018. Flux of the biogenic volatiles isoprene and dimethyl sulfide from an oligotrophic lake. Scientific Reports 8, Article 630. volatile organic compounds (BVOCs) affect atmospheric chemistry, climate and regional air quality in terrestrial and marine atmospheres. Although isoprene is a major BVOC produced in vascular plants, and marine phototrophs release dimethyl sulfide (DMS), lakes have been widely ignored for their production. Here we demonstrate that oligotrophic Lake Constance, a model for north temperate deep lakes, emits both volatiles to the atmosphere. Depth profiles indicated that highest concentrations of isoprene and DMS were associated with the chlorophyll maximum, suggesting that their production is closely linked to phototrophic processes. Significant correlations of the concentration patterns with taxon-specific fluorescence data, and measurements from algal cultures confirmed the phototrophic production of isoprene and DMS. Diurnal fluctuations in lake isoprene suggested an unrecognised physiological role in environmental acclimation similar to the antioxidant function of isoprene that has been suggested for marine biota. Flux estimations demonstrated that lakes are a currently undocumented source of DMS and isoprene to the atmosphere. Lakes may be of increasing importance for their contribution of isoprene and DMS to the atmosphere in the arctic zone where lake area coverage is high but terrestrial sources of BVOCs are small.Stelmach, K.B., Neveu, M., Vick-Majors, T.J., Mickol, R.L., Chou, L., Webster, K.D., Tilley, M., Zacchei, F., Escudero, C., Flores Martinez, C.L., Labrado, A., Fernández, E.J.G., 2018. Secondary electrons as an energy source for life. Astrobiology 18, 73-85. on Earth is found in a wide range of environments as long as the basic requirements of a liquid solvent, a nutrient source, and free energy are met. Previous hypotheses have speculated how extraterrestrial microbial life may function, among them that particle radiation might power living cells indirectly through radiolytic products. On Earth, so-called electrophilic organisms can harness electron flow from an extracellular cathode to build biomolecules. Here, we describe two hypothetical mechanisms, termed “direct electrophy” and “indirect electrophy” or “fluorosynthesis,” by which organisms could harness extracellular free electrons to synthesize organic matter, thus expanding the ensemble of potential habitats in which extraterrestrial organisms might be found in the Solar System and beyond. The first mechanism involves the direct flow of secondary electrons from particle radiation to a microbial cell to power the organism. The second involves the indirect utilization of impinging secondary electrons and a fluorescing molecule, either biotic or abiotic in origin, to drive photosynthesis. Both mechanisms involve the attenuation of an incoming particle's energy to create low-energy secondary electrons. The validity of the hypotheses is assessed through simple calculations showing the biomass density attainable from the energy supplied. Also discussed are potential survival strategies that could be used by organisms living in possible habitats with a plentiful supply of secondary electrons, such as near the surface of an icy moon. While we acknowledge that the only definitive test for the hypothesis is to collect specimens, we also describe experiments or terrestrial observations that could support or nullify the hypotheses.Strassert, J.F.H., Karnkowska, A., Hehenberger, E., del Campo, J., Kolisko, M., Okamoto, N., Burki, F., Janou?kovec, J., Poirier, C., Leonard, G., Hallam, S.J., Richards, T.A., Worden, A.Z., Santoro, A.E., Keeling, P.J., 2018. Single cell genomics of uncultured marine alveolates shows paraphyly of basal dinoflagellates. The Isme Journal 12, 304-308. alveolates (MALVs) are diverse and widespread early-branching dinoflagellates, but most knowledge of the group comes from a few cultured species that are generally not abundant in natural samples, or from diversity analyses of PCR-based environmental SSU rRNA gene sequences. To more broadly examine MALV genomes, we generated single cell genome sequences from seven individually isolated cells. Genes expected of heterotrophic eukaryotes were found, with interesting exceptions like presence of proteorhodopsin and vacuolar H+-pyrophosphatase. Phylogenetic analysis of concatenated SSU and LSU rRNA gene sequences provided strong support for the paraphyly of MALV lineages. Dinoflagellate viral nucleoproteins were found only in MALV groups that branched as sister to dinokaryotes. Our findings indicate that multiple independent origins of several characteristics early in dinoflagellate evolution, such as a parasitic life style, underlie the environmental diversity of MALVs, and suggest they have more varied trophic modes than previously thought.Stringer, C., Galway-Witham, J., 2018. When did modern humans leave Africa? Science 359, 389-390. skeletal features of our species, Homo sapiens, include a globular braincase, brow ridges that are divided into central and side portions, a flat and retracted midface, a chin on the lower jaw, and a narrow pelvis. Fossils showing many of these characteristics have been excavated from the Ethiopian sites of Omo Kibish and Herto, dated at ～195,000 and ～160,000 years ago, respectively (1). Possible more primitive members of the species are known from Jebel Irhoud (Morocco) and Florisbad (South Africa), dated at ～315,000 and ～259,000 years ago, respectively (1). Yet, the oldest known H. sapiens fossils outside of Africa, from Skhul and Qafzeh in Israel, have been dated to just 90,000 to 120,000 years old. On page 456 of this issue, Hershkovitz et al. (2) provide fossil evidence from Misliya Cave, Israel, suggesting that our species had already left Africa by ～180,000 years ago (see the figure).Misliya Cave lies on Mount Carmel, Israel, and has been excavated over the last century. It shows successive periods of hominin occupation with Lower and Middle Paleolithic tools, the use of fire, and the exploitation of a diverse fauna. Given Misliya's position at a crucial crossroads between Africa and Eurasia, the latest discoveries have enormous potential for understanding early populations of H. sapiens in western Asia.The newly excavated material is represented by a partial upper jaw (Misliya-1), which includes some of the bone surrounding the tooth sockets, part of the cheekbone, the roof of the mouth, the bottom of the nasal cavity, and the complete upper left dentition. The size and shape of the specimen fall within the known range of variation of later H. sapiens fossils. Furthermore, Misliya-1 lacks the unique diagnostic features of Neandertals and earlier hominin species.Hershkovitz et al. note Misliya-1's similarities to the later Skhul and Qafzeh fossils, although the size of one of the tooth cusps in Misliya-1 is reduced relative to the other fossils. Individual traits associated with the morphology exhibited in Misliya-1 are sometimes seen in other hominin taxa, but the combination of traits is characteristically that of H. sapiens.Stone tools excavated from the same stratigraphic layer as that of Misliya-1 show the use of Levallois technology, a complex tool preparation method involving a prepared core. This technology has also been identified in ～190,000- to 260,000-year-old artifacts from nearby Tabun Cave (3), but the material at Misliya represents the earliest known association of this industry with modern human fossils in the region. Levallois tools associated with putative early H. sapiens fossils have also been found at Jebel Irhoud (Morocco) (1), suggesting that the emergence of this tool technology may be linked with the appearance and dispersal of our species in both Africa and western Asia.Hershkovitz et al. dated the fossil and archaeological specimens from Misliya using multiple methods. They used uranium-thorium dating to determine the age of tooth dentine samples; combined uranium series and electron spin resonance techniques to directly date enamel samples; uranium-thorium dating to determine the age of the sediment adhering to the upper jaw; and thermoluminescence to measure the age of the burned tools found close to the fossil. Collectively, the results of these dating methods provide an estimated age of ～177,000 to 194,000 years for Misliya-1 and its associated artifacts.It remains unclear where and when humans lived in western Asia in the period prior to that of the Misliya specimen. Fragmentary fossils are known from the Israeli caves of Qesem and Zuttiyeh, the former consisting of isolated teeth dated to ～400,000 years old, the latter represented by a partial skull, perhaps of similar antiquity. Both show primitive traits, and some that are found in Neandertals or H. sapiens (4, 5). Archaeological evidence for occupation of the region spans the time between these fossils and Misliya, but imprecise dating makes it impossible to tell whether human presence was continuous or episodic.Paleoclimatic reconstructions using speleothems, deep sea cores, and paleoenvironmental data suggest that there were several humid phases between 244,000 and 190,000 years ago, one or more of which could have facilitated the spread of H. sapiens into the region (6). But there were severe periods of aridity before and after this time, meaning that the region was probably more often a “boulevard of broken dreams” than a stable haven for early humans (7). Direct local evolutionary continuity between the population represented by the Misliya fossil and later Skhul and Qafzeh peoples thus seems unlikely.If the Misliya population extended further into Eurasia, encountering Neandertals, this may have led to gene flow between these two lineages of humans. The main phases of genetic introgression from Neandertals into H. sapiens are estimated to have occurred between ～50,000 and 60,000 years ago (8), but genetic analyses of Neandertal fossils from Denisova Cave (Siberia, Russia) and Hohlenstein-Stadel (Germany) indicate at least one earlier phase of introgression, from H. sapiens into Neandertals. This event has been estimated at ～219,000 to 460,000 years ago, suggesting that it predated the Misliya fossil (9). The H. sapiens fossils from Misliya, Skhul, and Qafzeh could therefore represent relatively late excursions of our species from Africa. During earlier humid phases, western Asia could have attracted more primitive members of the H. sapiens and H. neanderthalensis lineages, providing repeated opportunities for exchanges of genes and technologies.Beyond western Asia, evidence for early dispersals of H. sapiens prior to ～120,000 years ago is weak. Age estimates for fragmentary Chinese fossils from Zhiren and Daoxian Caves only range between ～80,000 and 113,000 years ago (10). The Misliya find is important in establishing an earlier dispersal of H. sapiens from Africa into western Asia. It also highlights how little we know about the early occupants of the region, nearly a century after the first discoveries from the caves of Zuttiyeh, Skhul, Qafzeh, and Tabun.References 1. C. B. Stringer, J. Galway-Witham, Nature 546, 212 (2017).2. I. Hershkovitz et al., Science 359, 456 (2018).3. N. Mercier, H. Valladas, J. Hum. Evol. 45, 401 (2003).4. I. Hershkovitz et al., Am. J. Phys. Anthropol. 144, 575 (2011).5. S. E. Freidline et al., J. Hum. Evol. 62, 225 (2012).6. P. S. Breeze et al., Quat. Sci. Rev. 144, 155 (2016).7. J. J. Shea, in Rethinking the Human Revolution, P. Mellars et al., Eds. (McDonald Institute for Archaeological Research Monographs, Cambridge, 2007), chap. 19.8. R. Nielsen et al., Nature 541, 302 (2017).9. C. Posth et al., Nat. Commun. 8, 16046 (2017).10. M. Martinón-Torres et al., Curr. Anthropol. 58, S434 (2017).Struchkov, I.A., Rogachev, M.K., 2018. The challenges of waxy oil production in a Russian oil field and laboratory investigations. Journal of Petroleum Science and Engineering 163, 91-99. objective of this paper is selection the appropriate well operation conditions and effective wax inhibitor to reduce impact of wax in oil on production. The field operation is complicated with formation of wax deposits in flowlines and tubings due to high wax concentration in oil and improper wells operation. Expensive selection of effective wax inhibitor is regularly carried out in the field.The methodology of research used in this paper basically includes theoretical and experimental approaches. Theoretical approach is devoted to studying the thermodynamic functions of state of the system during wax crystallization in oil. This approach allows to explain behavior of wax in oil during crystallization. The authors of this paper calculated thermodynamic state functions of the system during wax precipitation in hydrocarbon solution and in reservoir oil to describe the process of wax crystallization and to explain change of apparent WAT with change of the well operation conditions and dosing of wax inhibitor. Calculations of thermodynamic state functions for model hydrocarbon solutions were carried out for pressure, ranging from 0.1 to 40?MPa, and for wax concentration in solution, ranging from 10 to 60%. Experimental approach was based on studying wax precipitation in reservoir oil by visual method using microscope under high pressure. The study was performed in the pressure range from 5.6 to 18.4?MPa, and wax concentration of 24%. Experimental data of wax precipitation in kerosene and in oil was processed using Vant Hoff's diagrams, Gibbs free energy equation during chemical reaction, and first and second laws of thermodynamic equations.The main result of this paper is examination of impact external factors on wax crystallization in oil, which will assist to select the well operation conditions in the presence of parafinization. Particularly, it was determined that with increase in pressure, apparent wax appearance temperature (WAT) is increasing, however, wax crystallization rate is declining. Additional research showed that apparent WAT is decreasing when oil cooling rate and depressurization rate are rising. Authors explain this phenomenon in reliance on thermodynamic parameters of wax crystallization in oil. Also wax inhibitor is developed for oil field conditions. Experiments demonstrated, that addition of inhibitor to oil leads to decrease in apparent WAT and does not accelerate wax crystallization, which will promote reduction of wax formation in oil wells.The proposed methodology has allowed to evaluate the most dangerous range of flowrates in terms of well parafinization and to propose measures for prevention of well parafinization in the field.Su, L., Zhang, D., Yang, H., Chen, Y., Chen, G., Zheng, J., Xu, Y., 2018. Chemical kinetics evaluation and its application of natural gas generation derived from the Yacheng Formation in the deep-water area of the Qiongdongnan Basin, China. Acta Oceanologica Sinica 37, 50-59. natural gas generation process is simulated by heating source rocks of the Yacheng Formation, including the onshore-offshore mudstone and coal with kerogens of Type II2-III in the Qiongdongnan Basin. The aim is to quantify the natural gas generation from the Yacheng Formation and to evaluate the geological prediction and kinetic parameters using an optimization procedure based on the basin modeling of the shallow-water area. For this, the hydrocarbons produced have been grouped into four classes (C1 C2 C3 and C4-6). The results show that the onset temperature of methane generation is predicted to occur at 110°C during the thermal history of sediments since 5.3 Ma by using data extrapolation. The hydrocarbon potential for ethane, propane and heavy gaseous hydrocarbons (C4-6) is found to be almost exhausted at geological temperature of 200°C when the transformation ratio (TR) is over 0.8, but for which methane is determined to be about 0.5 in the shallow-water area. In contrast, the end temperature of the methane generation in the deep-water area was over 300°C with a TR over 0.8. It plays an important role in the natural gas exploration of the deep-water basin and other basins in the broad ocean areas of China. Therefore, the natural gas exploration for the deep-water area in the Qiongdongnan Basin shall first aim at the structural traps in the Ledong, Lingshui and Beijiao sags, and in the forward direction of the structure around the sags, and then gradually develop toward the non-structural trap in the deep-water area basin of the broad ocean areas of China.Suárez-Domínguez, E.J., Pérez-Sánchez, J.F., Palacio-Pérez, A., Rodríguez-Valdes, A., Izquierdo-Kulich, E., González-Santana, S., 2018. A viscosity bio-reducer for extra-heavy crude oil. Petroleum Science and Technology 36, 166-172. that high viscosity of extra-heavy crudes is related to the formation of a dispersed phase of asphaltenes, a dynamic interaction model is proposed which explains the mechanism to achieve viscosity reduction based on the molecular interacting energies between the ester active principle of a viscosity bio-reducer and the asphaltene fraction of crude oil. A qualitative comparison is made between the theoretical and experimental results observed in relation to the rheological behavior of Mexican extra-heavy crudes in the presence of the enhancer. Both, theoretical and experimental data, described a decrease in the asphaltenes dispersed fraction in relation to the ester concentration mainly because of polarity in asphaltenic crudes.Subha Anand, S., Rengarajan, R., Shenoy, D., Gauns, M., Naqvi, S.W.A., 2018. POC export fluxes in the Arabian Sea and the Bay of Bengal: A simultaneous 234Th/238U and 210Po/210Pb study. Marine Chemistry 198, 70-87. variation in POC export flux, from the upper ocean, was studied during post southwest monsoon (October–November 2013) and spring intermonsoon (May 2014) at selected locations in the central and southern Arabian Sea and during northeast monsoon (January 2014) and spring intermonsoon (March 2014) in the northern Bay of Bengal. POC fluxes estimated from two particle-reactive radionuclide flux proxies (234Th/238U and 210Po/210Pb) were compared. Spatial and temporal variations were observed in the POC/radionuclide ratios, net deficit flux of radionuclides and the estimated POC export fluxes in both the basins. During post southwest monsoon, the 234Th flux (1346 ± 101 dpm m? 2 d? 1), POC/234Th ratio (5.96 ± 0.29 μmol dpm? 1) and associated POC flux (8.0 ± 0.6 mmol m? 2 d? 1) were high in the southern Arabian Sea than those in the central Arabian Sea (450 ± 95 dpm m? 2 d? 1, 1.76 ± 0.07 μmol dpm? 1 and 0.8 ± 0.2 mmol m? 2 d? 1, respectively). However, during spring intermonsoon these trends were similar in both the central and southern Arabian Sea with mean 234Th fluxes, POC/234Th ratios and 234Th based POC export fluxes being 2762 ± 61 dpm m? 2 d? 1, 1.45 ± 0.05 μmol dpm? 1 and 4.0 ± 0.14 mmol m? 2 d? 1, respectively. On the other hand, the 210Po based POC export fluxes in the southern Arabian Sea (3.37 ± 0.32 and 6.73 ± 0.47 mmol m? 2 d? 1) were higher by a factor of 2–3 than those in the central Arabian Sea (2.08 ± 0.16 and 2.12 ± 0.28 mmol m? 2 d? 1) during post southwest monsoon and spring intermonsoon, respectively. In the northern Bay of Bengal, the 234Th based POC export fluxes were similar and low (0.6–1.2 mmol m? 2 d? 1) while the 210Po based POC export fluxes were much higher (3.75–8.48 mmol m? 2 d? 1) during both the northeast monsoon and spring intermonsoon seasons. One reason could be that more production and carbon export occurring in months prior to the period preceding sample collection due to weeks to several months difference in the mean-lives of the isotopes. The computed POC export fluxes and inferred efficiency of the biological carbon pump in the Arabian Sea and the northern Bay of Bengal are differentiated by this different span in half-lives of 234Th and 210Po (weeks to months, respectively). Also these values are distinct due to their biogeochemical behavior and preferred affinity for specific types of particles. This would require more joint application of each tracer in time and space for various biogeochemical regimes.Subraveti, S.G., Nikrityuk, P., Rajendran, A., 2018. Computational fluid dynamics study of viscous fingering in supercritical fluid chromatography. Journal of Chromatography A 1534, 150-160. numerical simulations are carried out to study the dynamics of a plug introduced through a mixed-stream injection in supercritical fluid chromatographic columns. The computational fluid dynamics model developed in this work takes into account both the hydrodynamics and adsorption equilibria to describe the phenomena of viscous fingering and plug effect that contribute to peak distortions in mixed-stream injections. The model was implemented into commercial computational fluid dynamics software using user-defined functions. The simulations describe the propagation of both the solute and modifier highlighting the interplay between the hydrodynamics and plug effect. The simulated peaks showed good agreement with experimental data published in the literature involving different injection volumes (5?μL, 50?μL, 1?mL and 2?mL) of flurbiprofen on Chiralpak AD-H column using a mobile phase of CO2 and methanol. The study demonstrates that while viscous fingering is the main source of peak distortions for large-volume injections (1?mL and 2?mL) it has negligible impact on small-volume injections (5?μL and 50?μL). Band broadening in small-volume injections arise mainly due to the plug effect.Sugiyama, I., Williams-Jones, A.E., 2018. An approach to determining nickel, vanadium and other metal concentrations in crude oil. Analytica Chimica Acta 1002, 18-25. ability to accurately determine the metal content of crude oils is necessary for reasons ranging from the need to identify the source of the oils (Ni and V) to removing components that might inhibit catalysis during refining or impact negatively on the environment during hydrocarbon combustion. Here we show that ashing followed by chemical oxidation and acid digestion, coupled with ICP-MS analysis, provides an accurate method for determining the concentration of metals in crude oil. Nickel and vanadium concentrations were measured in certified Ni and V oil standards and in various light, intermediate and heavy crude oils after application of a single vessel ashing-chemical oxidation-acid digestion sample preparation and storing technique. Prior to the ashing, chemical oxidation and acid digestion, an aliquot of the crude oil was placed in a 10 ml Pyrex? culture tube and capped with quartz wool. The capped culture tubes were then subjected to thermal combustion, followed by chemical oxidation and leaching. The leachates and the aqueous standards were diluted and analyzed for their Ni and V contents using inductively coupled plasma mass spectrometry (ICP-MS).The measured concentrations of Ni in oil standards, reported to contain 1, 100, and 1000 mg kg?1 Ni (±2% error), were 1.1 ± 0.01, 99.8 ± 1.46, and 1025 ± 24 mg kg?1 respectively. The corresponding concentrations of V in these standards, reported to contain 2, 100, and 1000 mg kg?1 V, were measured to be 1.93 ± 0.06, 104 ± 1.3, and 1027 ± 7.5 mg kg?1, respectively. Crude oil samples, A, B, C, D and E, that varied significantly in their composition, and ranged from light to heavy, were determined to contain 5.59 ± 0.32, 4.05 ± 0.03, 6.22 ± 0.22, 33.8 ± 0.7 and 41.6 ± 3.5 mg kg?1 Ni, respectively. Their V contents were determined to be 11.98 ± 0.1, 12.2 ± 0.1, 16.5 ± 0.4, 34.7 ± 0.4, and 104 ± 8.9 mg kg?1, respectively. The results were thus repeatable on average to 4.1% and 2.75% for Ni and V, respectively; the repeatability was worst (～8.5%) for crude oil E, a heavy (viscous) oil with a very high asphaltene content (27.2%).This modified single vessel ashing-digestion technique (combustion, chemical oxidation, acid leaching and storing) minimizes contamination and significantly reduces the loss of ash. Our results are repeatable, comparable to, and in some cases superior to those of other methods. The method is applicable to a wide range of crude oil compositions, is very accessible and robust, easy to use, and does not require costly equipment in preparing the samples for analysis by ICP-MS.Suleymani, M., Bemani, A., 2018. Prediction of the interfacial tension between hydrocarbons and carbon dioxide. Petroleum Science and Technology 36, 227-231. the recent years due to increasing demand for energy and declination of reservoir production, an impressive notice on enhancement of oil recovery has been found. The gas injection especially carbon dioxide injection due to low cost and friendly environmentally of this approach the special attention to CO2 injection increased. The miscibility is known as key factor which effects on enhancement of recovery. The miscibility is controlled by interfacial tension of hydrocarbons and carbon dioxide so the importance of investigation of the interfacial tension becomes highlighted.in this investigation by using radial basis function (RBF) artificial neural network (ANN) as a novel approach the interfacial tension of hydrocarbons and carbon dioxide in terms of pressure, temperature, liquid and gas densities and molecular weight of alkane. The graphical and statistical results illustrated the fact that RBF-ANN algorithm is applicable for estimation of interfacial tension between hydrocarbons and carbon dioxide with great accuracy.Sun, F., Yao, Y., Li, X., Li, G., Miao, Y., Han, S., Chen, Z., 2018. Flow simulation of the mixture system of supercritical CO2 & superheated steam in toe-point injection horizontal wellbores. Journal of Petroleum Science and Engineering 163, 199-210. heavy oil recovery method of saturated steam injection at heel-point of horizontal wellbores is facing comparatively more serious fingering phenomenon. With this, oil companies are now actively developing new recovery method of supercritical CO2 - superheated steam injection in horizontal wellbores with toe-point injection technique.Firstly, considering the heat exchange between the inner tubing (IT) and annuli, a pipe flow model comprised of energy and momentum conservation equations is developed for the mixture flow in both IT and annuli. Then, coupled with the S-R-K real gas model, variable mass flow model and transient heat transfer model in oil layer, a comprehensive mathematical model is established. Numerical solutions of the mixture flow in toe-point injection wellbores are obtained through straight forward numerical method. Finally, model validation and sensitivity analysis are conducted.The results show that: (1). there exists a good agreement between predicted results and field data. The predicted temperature is higher when the heat exchange between IT and annuli is neglected. The predicted temperature is lower when the friction loss item is considered in the energy balance equation. (2). the temperature of the mixture increases when the mixture flows from toe-point to heel-point in annuli due to heat flow from IT to annuli. (3). While the absorption rate of the mixture in formation increases with increasing of the content of supercritical CO2, it can be offset by the decrease of temperature and enthalpy of the mixture. (4). Both of the mixture temperature and formation mixture absorption rate increase with increasing of injection pressure.Sun, K., Zhai, C., Xin, L., Wang, T., 2017. Triaxial loading permeability experiments on hydrate bearing sediments with different saturations. Natural Gas Industry 37, 61-67. permeability of a natural gas hydrate (NGH) bearing sedimentary reservoir is one of the important physical property parameters that affect the NGH exploitation efficiency. The influencing laws of effective volume stress and NGH saturation on the permeability of NGH bearing sedimentary layers in the process of NGH exploitation was studied through triaxial loading permeability experiments which were carried out on hydrate bearing sediments in different saturations with natural silty soil as the sediment skeleton. And the following test results were obtained. First, when the hydrate saturation is constant, the relationship between the permeability of NGH bearing sediments and the effective volume stress follows the change law of negative exponential curves, and the slope of the curve reduces with the increase of effective volume stress. Second, at a fixed effective volume stress, the relationship between the permeability of NGH bearing sediments and the NGH saturation follows the change law of exponential decline. And third, the effects of effective volume stress and NGH saturation on the permeability of NGH bearing sediments are not independent. That is to say, with the increase of effective volume stress (NGH saturation), the effect of NGH saturation (effective volume stress) on the permeability of NGH bearing sediments reduces. It is concluded that the effect of effective volume stress on the permeability is mainly presented as a compression effect on the seepage channels, and the effect of NGH saturation on the permeability is mainly embodied as an NGH blocking effect on the seepage channels.Sun, M., Yu, B., Hu, Q., Yang, R., Zhang, Y., Li, B., Melnichenko, Y.B., Cheng, G., 2018. Pore structure characterization of organic-rich Niutitang shale from China: Small angle neutron scattering (SANS) study. International Journal of Coal Geology 186, 115-125. structure can greatly impact the gas storage and flow mechanisms in shale reservoirs. Pore characteristics, including the pore (body/throat) size distribution (PSD), porosity, specific surface area, tortuosity, and connectivity, from four Niutitang shale samples were investigated with small-angle neutron scattering (SANS), mercury injection capillary pressure (MICP), and helium porosimetry to complement earlier gas (N2, CO2) sorption and petrographic analyses. In particular, the SANS data provides information on the total porosity, including both the closed and open pores. The large-Q (scattering vector) “flat” background of the SANS data was used to estimate the volumes of pores with diameters of < 5 nm. By evaluating the differences between porosity values determined from multiple complementary methods, the closed fraction of the pores in the Niutitang Shale was derived. Combining these pore-size distribution analyses (body/throat) and previous field emission-scanning electron microscopy observations, it was concluded that the closed pores were rarely present in illite but were mainly within organic matter. Moreover, the fraction of closed pores has a negative correlations with the matrix permeability and geometrical tortuosity. Overall, an improved understanding of the fraction of closed pores will lead to a better understanding of gas storage and production.Sun, T., Wang, J., Sun, Y., 2017. Petroleum geochemical characteristics and accumulation in offshore of Senegal Basin. Acta Sedimentologica Sinica 35, 1284-1292. Basin is the largest passive margin basin with salt in western Africa, but it has limited petroleum exploration activities. Only non-commercial petroleum and heavy oil have been discovered before 2010. However, some oil exploration breakthroughs have been made in offshore area in recent five years. The paper analyzed the oils and source biomarkers as well as source rocks rock hydrocarbon potential. The results show that Aptian-Albian and Cenomanian-Turonian source rocks exist in offshore area. The former is characterized by light δ13Corg and lower Sulfur content. The maturity is at oil window or more. The latter is typical of heavy δ13Corg and medium sulfur content. The maturity is at oil window or low. Oil-source correlation indicates that F-1 Albian oil was generated from Aptian-Albian source rocks and F-1 Turonian oil from Cenomanian-Turonian source rocks. While the S-1 Albian oil shows mix sources characteristics.Sun, Y.-H., Su, K., Li, S.-L., Carroll, J.J., Zhu, Y.-H., 2018. Experimental investigation into the dissociation behavior of CH4–C2H6–C3H8 hydrates in sandy sediments by depressurization. Energy & Fuels 32, 204-213. dissociation kinetics of gas hydrate formed from binary CH4–C3H8 and ternary CH4–C2H6–C3H8 gas mixtures were studied by a gas-collection-analysis method at constant back-pressure and different temperatures. During hydrate dissociation, the gas produced was first collected by sample bags consecutively and then analyzed by gas chromatography. It was found that the gas production of the mixed hydrates was quite different from that of methane hydrate. Interestingly, the molar composition of C3H8 in the gas mixture produced changed little as hydrate dissociation proceeded. The retainment of C3H8 in hydrates was confirmed with the calculation results of composition of hydrates remained during gas production. The preferential of CH4 and C2H6 over C3H8 molecules released from hydrate decomposition was attributed to the difference in guest-to-cavity size ratios. The heterogeneous dissociation of the multiple guests complicates the gas production process as the remaining hydrate rich in C3H8 may act as a barrier to gas diffusion. The self-preservation model for CH4 hydrate dissociation below ice point was applied to describe the heterogeneous dissociation of the mixed hydrates, suggesting that the dissociation kinetics of the mixed hydrates containing C3H8 above ice point was similar to that of CH4 hydrate below ice point. These results are of interest for the gas recovery from hydrates, and for natural gas storage and transportation in the hydrate state.Sun, Z., Zhang, H., Wei, Z., Wang, Y., Wu, B., Zhuo, S., Zhao, Z., Li, J., Hao, L., Yang, H., 2018. Effects of slick water fracturing fluid on pore structure and adsorption characteristics of shale reservoir rocks. Journal of Natural Gas Science and Engineering 51, 27-36. shale-fracturing fluid interaction and its effects on the pore structures and adsorption characteristics of shale are the key factors affecting shale gas exploration. To address this problem, the black shale samples obtained from the Lower Silurian Longmaxi Formation in Sichuan Basin, China were exposed to slick water fracturing fluid at the simulation conditions of 100?°C and 50?MPa for 72?h through a fluid-rock interaction simulation instrument. The slick water fracturing fluid contained 0.2?wt.% friction reducer, 1?wt.% clay control agent, 0.15?wt.% cleanup agent and 0.05?wt.% demulsifier. The mineral composition, pore structure and methane adsorption capacity of shale samples before and after slick water fracturing fluid treatment were measured by X-ray diffraction (XRD), field emission scanning electron microscope (FE-SEM), low-pressure nitrogen adsorption and methane isothermal adsorption experiments using the gravimetric method. The results showed that the carbonate minerals were dissolved during treatment, and as a result, the samples developed many dissolution pores measuring 2–5?μm in diameter, while the other minerals remained relatively undisturbed. The specific surface area and total pore volume of shale sample were reduced after the reaction, and the shale-fracturing fluid interaction exhibited a stronger influence on the mesopores. However, the average pore diameter of nanopore was enlarged after the reaction, increasing from 4.29?nm to 4.78?nm. The changes of fractal dimensions suggested an increase in the roughness of pore surfaces, and the pore structure became more regular. The methane adsorption capacity in shale treated with fracturing fluid was reduced from 1.23?mmol/g to 0.95?mmol/g. The changes in the pore structure and adsorption characteristics of shale could affect the gas flow and gas adsorption capacity. These results indicated that the slick water fracturing fluid may play an important role in shale matrix stimulation.Sutter, B., McAdam, A.C., Mahaffy, P.R., Ming, D.W., Edgett, K.S., Rampe, E.B., Eigenbrode, J.L., Franz, H.B., Freissinet, C., Grotzinger, J.P., Steele, A., House, C.H., Archer, P.D., Malespin, C.A., Navarro-González, R., Stern, J.C., Bell, J.F., Calef, F.J., Gellert, R., Glavin, D.P., Thompson, L.M., Yen, A.S., 2017. Evolved gas analyses of sedimentary rocks and eolian sediment in Gale Crater, Mars: Results of the Curiosity rover's sample analysis at Mars instrument from Yellowknife Bay to the Namib Dune. Journal of Geophysical Research: Planets 122, 2574-2609. sample analysis at Mars instrument evolved gas analyzer (SAM-EGA) has detected evolved water, H2, SO2, H2S, NO, CO2, CO, O2, and HCl from two eolian sediments and nine sedimentary rocks from Gale Crater, Mars. These evolved gas detections indicate nitrates, organics, oxychlorine phase, and sulfates are widespread with phyllosilicates and carbonates occurring in select Gale Crater materials. Coevolved CO2 (160 ± 248–2373 ± 820 μgC(CO2)/g) and CO (11 ± 3–320 ± 130 μgC(CO)/g) suggest that organic C is present in Gale Crater materials. Five samples evolved CO2 at temperatures consistent with carbonate (0.32 ± 0.05–0.70 ± 0.1 wt % CO3). Evolved NO amounts to 0.002 ± 0.007–0.06 ± 0.03 wt % NO3. Evolution of O2 suggests that oxychlorine phases (chlorate/perchlorate) (0.05 ± 0.025–1.05 ± 0.44 wt % ClO4) are present, while SO2 evolution indicates the presence of crystalline and/or poorly crystalline Fe and Mg sulfate and possibly sulfide. Evolved H2O (0.9 ± 0.3–2.5 ± 1.6 wt % H2O) is consistent with the presence of adsorbed water, hydrated salts, interlayer/structural water from phyllosilicates, and possible inclusion water in mineral/amorphous phases. Evolved H2 and H2S suggest that reduced phases occur despite the presence of oxidized phases (nitrate, oxychlorine, sulfate, and carbonate). SAM results coupled with CheMin mineralogical and Alpha-Particle X-ray Spectrometer elemental analyses indicate that Gale Crater sedimentary rocks have experienced a complex authigenetic/diagenetic history involving fluids with varying pH, redox, and salt composition. The inferred geochemical conditions were favorable for microbial habitability and if life ever existed, there was likely sufficient organic C to support a small microbial population.Suzuki, S., Endoh, R., Manabe, R.-i., Ohkuma, M., Hirakawa, Y., 2018. Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca. Scientific Reports 8, Article 940. eukaryotes have evolved by the endosymbiotic uptake of photosynthetic organisms. Interestingly, many algae and plants have secondarily lost the photosynthetic activity despite its great advantages. Prototheca and Helicosporidium are non-photosynthetic green algae possessing colourless plastids. The plastid genomes of Prototheca wickerhamii and Helicosporidium sp. are highly reduced owing to the elimination of genes related to photosynthesis. To gain further insight into the reductive genome evolution during the shift from a photosynthetic to a heterotrophic lifestyle, we sequenced the plastid and nuclear genomes of two Prototheca species, P. cutis JCM 15793 and P. stagnora JCM 9641, and performed comparative genome analyses among trebouxiophytes. Our phylogenetic analyses using plastid- and nucleus-encoded proteins strongly suggest that independent losses of photosynthesis have occurred at least three times in the clade of Prototheca and Helicosporidium. Conserved gene content among these non-photosynthetic lineages suggests that the plastid and nuclear genomes have convergently eliminated a similar set of photosynthesis-related genes. Other than the photosynthetic genes, significant gene loss and gain were not observed in Prototheca compared to its closest photosynthetic relative Auxenochlorella. Although it remains unclear why loss of photosynthesis occurred in Prototheca, the mixotrophic capability of trebouxiophytes likely made it possible to eliminate photosynthesis.Svan, A., Hedeland, M., Arvidsson, T., Pettersson, C.E., 2018. The differences in matrix effect between supercritical fluid chromatography and reversed phase liquid chromatography coupled to ESI/MS. Analytica Chimica Acta 1000, 163-171. many sample matrices, matrix effects are a troublesome phenomenon using the electrospray ionization source. The increasing use of supercritical fluid chromatography with CO2 in combination with the electrospray ionization source for MS detection is therefore raising questions: is the matrix effect behaving differently using SFC in comparison with reversed phase LC? This was investigated using urine, plasma, influent- and effluent-wastewater as sample matrices. The matrix effect was evaluated using the post-extraction addition method and through post-column infusions. Matrix effect profiles generated from the post-column infusions in combination with time of flight-MS detection provided the most valuable information for the study. The combination of both qualitative and semi-quantitative information with the ability to use HRMS-data for identifying interfering compounds from the same experiment was very useful, and has to the authors' knowledge not been used this way before. The results showed that both LC and SFC are affected by matrix effects, however differently depending on sample matrix. Generally, both suppressions and enhancements were seen, with a higher amount of enhancements for LC, where 65% of all compounds and all sample matrices were enhanced, compared to only 7% for SFC. Several interferences were tentatively identified, with phospholipids, creatinine, and metal ion clusters as examples of important interferences, with different impact depending on chromatographic technique. SFC needs a different strategy for limiting matrix interferences, owing to its almost reverse retention order compared to RPLC.Taheri-Shakib, J., Shekarifard, A., Naderi, H., 2018. Characterization of the wax precipitation in Iranian crude oil based on Wax Appearance Temperature (WAT): Part 1. The influence of electromagnetic waves. Journal of Petroleum Science and Engineering 161, 530-540. paper investigated the effects of microwaves (MW) on Wax Appearance Temperature (WAT), the shape and morphology of wax crystals, and the content of elements in crude oil. After WAT was determined using cross-polarized microscopy (CPM), the intra-molecular bonds and the structure of the molecules were determined by subjecting crude oil and its wax content to Fourier-transform infrared (FTIR) spectroscopy analysis. Cracking and simultaneous evaporation of crude-oil combinations due to irradiation with MW caused peaks with different intensities in the oils' spectrums to appear. In addition, with irradiation, peaks reappeared that had been hidden in the range of virgin oil samples, and which were more closely related to aromatic compounds. The two processes of cracking and evaporation together resulted in a lighter oil sample with a lower WAT, which is evident in the samples' FTIR spectrum. Analysis of the images from the wax crystals under a polarization light microscope with image processing revealed a close connection between the shape and size of the wax particles and peak intensity of the FTIR spectrum and the crude-oil composition. Oil samples exposed to MW radiation had more rounded crystals and more similar proportions than virgin-oil samples. Radiation of MW waves caused asphaltene cracking to produce saturated, aromatic, and resin compounds. Since asphaltene is the heaviest oil-producing compound, this conversion lightened the oil and reduced the WAT. MW radiation also increased the amount of aromatic compounds derived from the resin in oil. The presence of asphaltene as one of the heavy-oil compounds and its interaction with wax molecules was investigated. It was observed that with respect to the naphthenic/polar of the wax sample, the decrease in the amount of asphaltene in the oil sample after irradiation reduced the interactions between the wax molecules and asphaltenes, and subsequently reduced the WAT. Scanning electron microscopy (SEM) images showed that the MW wax samples were composed of rounded and compacted particles, making it difficult to detect single grains. The size of the grains in the SEM images of MW samples was smaller than in the virgin sample. MW affected the dispersion and the mean size and shape of the wax particles under both the polarized light microscope and SEM; they also affected the bond/molecular structure as determined by FTIR and the amount of resin, asphaltene, saturation, and aromatics of the oil constituents, and decreased the average carbon number of the oil samples, which lowered the WAT.Taherpour, A., Cheshmeh Sefidi, A., Bemani, A., Hamule, T., 2018. Application of Fuzzy c-means algorithm for the estimation of asphaltene precipitation. Petroleum Science and Technology 36, 239-243. of problematic topics in petroleum engineering is Asphaltene precipitation issue which causes problems such as tubing plugging and formation damage due to temperature, pressure and composition changes so the notability of this issue increases. In the present investigation a novel Fuzzy c-means (FCM) algorithm was developed to predict precipitated asphaltene as function of dilution ratio, carbon number of precipitants and temperature for solving the problem. The results showed that this novel approach has great ability to predict precipitated asphaltene in terms of aforementioned parameters. The coefficients of determination (R2) for training and testing steps are calculated as 0.9828 and 0.9387 respectively. This great degree of accuracy expresses that the predicting algorithm has potential to be utilized as software for prediction of asphaltene behavior.Tahmasebi, P., 2018. Nanoscale and multiresolution models for shale samples. Fuel 217, 218-225. of shale systems requires imaging at different scales. One reason can be due to a diverse pore-size distribution. Low-resolution images often cover the large-scale structures and are available for a large region of the sample. On the other hand, fine-scale images usually cover a small region and they are mostly used to discover the complexity within the nano-scale pores in shale samples. Acquiring large image containing both the micro- and the nano-scale feature can be very expensive and time demanding. In this paper, a new method for integrating of such images at different scales is proposed. The aim is to include the nano-scale information within the coarse images. The input of this method is a set of coarse- and fine-scale images. The corresponding regions of each fine-scale image within the coarser image are determined using a similarity map. Then, the coarse image is refined iteratively to include the fine-scale information. The final image contains both the micro and nano-meter images and can readily be used for various purposes.Takahashi, S., Sung, M., Honda, T., Lu, R., Jung, J., Miyakoshi, T., 2018. Analysis of Japanese Jōmon period red lacquerwares by pyrolysis gas chromatography/mass spectrometry. Journal of Archaeological Science: Reports 18, 85-89. lacquerwares excavated from the Minamikonuma ruins located in Saitama City, Saitama Prefecture, Japan, were analyzed by mean of cross-section observation, attenuated total reflection Fourier transform infrared spectroscopy (ATR-FT/IR), energy dispersive X-ray fluorescence (EDXRF), and pyrolysis gas chromatography/mass spectrometry (Py-GC/MS). The results showed that Fe2O3 was used as a red pigment in the relatively cheap lacquerwares or in the under layers, and HgS was used as another red pigment in an advanced stage. The characteristic urushiol products were detected in direct and derivative pyrolysis GC/MS of all sixteen lacquerwares and suggested that these Jōmon period lacquerwares were coated with lacquer sap collected from Toxicodendron vernicifluum lacquer trees.Tan, Q., Shi, Z., Hu, X., Wang, Y., Tian, Y., Wang, C., 2018. Diagenesis of microbialites in the lower Cambrian Qingxudong Formation, South China: Implications for the origin of porosity in deep microbial carbonates. Journal of Natural Gas Science and Engineering 51, 166-182. microbial carbonate is one of the most challenging issues in the field of carbonate sedimentology and reservoir. The biotic and abiotic processes that control microbial carbonate precipitation are becoming more established, but the influence of subsequent diagenesis on microbial carbonate reservoirs has not been adequately studied. Here, we describe microbial carbonate from the lower Cambrian Qingxudong Formation in southeastern Sichuan Basin to assess their formation, textures and subsequent diagenesis. Six stages of calcite cementation (Calcite-1 to Calcite-6) and four stages of dissolution (Dis-1 to Dis-4) were identified in microbialites of the Qingxudong Formation. Stromatolites and thrombolites have a different porosity evolution. Sedimentary processes are the fundamental controlling factors of creating pre-existing pores in stromatolites. For thrombolites, the formation of pre-existing pores is attributed to island dissolution and dolomitization in near-surface processes. Microbial metabolic activities contribute more to the dissolution and dolomitization than mixing water. Meteoric water dissolution (Dis-1) in synsedimentary processes and microbial dissolution (Dis-2) in near-surface processes are the fundamental control factors of porosity creation in microbial carbonate of Qingxudong Formation. Thermochemical sulfate reduction (TSR) is a double-edged sword for the porosity development. The destructive effect of TSR on microbial carbonate reservoirs is greater than the constructive effect. The microbial carbonate reservoirs, especially the fabric-destructive dolomite (Dol-2) evolved by thrombolites, have great potential for gas exploration in the Qingxudong Formation. This study is especially useful for further understanding deeply buried microbialite reservoir formation and development, and deep hydrocarbon exploration in this basin and elsewhere worldwide.Tang, H., Li, S., Zhang, D., 2018. The effect of heterogeneity on hydraulic fracturing in shale. Journal of Petroleum Science and Engineering 162, 292-308. hydraulic fracturing processes in shale oil and gas development remains a major challenge for industrial applications. The omission of heterogeneity inherent in the shale matrix may be one of the causes for the divergence between simulated fractures and those in reality. To elucidate the effects of heterogeneity on hydraulic fracturing, a workflow is developed for generating heterogeneous fields of hydraulic and geomechanical properties based on relatively easily available compressional wave velocity and shear wave velocity. After that, the workflow is implemented in our thermo-hydro-mechanical simulator for hydraulic fracturing. With the integrated simulator, the following are investigated: the effect of heterogeneity and the interactive effects of heterogeneity with other factors, i.e., in-situ stress gradient and stress shadow, the significance of different levels of heterogeneity, and the impact of various injection rates. The simulation results showed that these factors could have either synergetic or competitive effects under different circumstances. Also, different levels of heterogeneity result in different patterns of fractures’ geometry. According to our study, a heterogeneity field with a large coefficient of variation (CV) and medium correlation length (CL) turns out to develop fractures of the most complex patterns. Moreover, the high injection rate leads to neutralization of the influence of heterogeneity through the averaging effect of intense fracturing. The study leads to better understandings in the mechanism of hydraulic fracturing process under complicated factors such as heterogeneity, interactive effects, fracturing strategies, and both modes of rock failure. This study may shed light on future research on hydraulic fracturing and possible applications in practice as well as some improvements in designing hydraulic fracturing simulator.Tang, S., Tang, D., Li, S., Xu, H., Tao, S., Geng, Y., Ma, L., Zhu, X., 2018. Fracture system identification of coal reservoir and the productivity differences of CBM wells with different coal structures: A case in the Yanchuannan Block, Ordos Basin. Journal of Petroleum Science and Engineering 161, 175-189. system identification of coal reservoirs plays a vital role in evaluating favorable zone of coalbed methane (CBM) development and improving CBM well productivity. In order to identify the fracture system of the No. 2 coal reservoir, and to determine the productivity differences of CBM wells with different coal structures in the Yanchuannan (YCN) Block, Ordos Basin, China, a comprehensive analysis method from macroscopy to microscopy and from static to dynamic was provided in this work. Site observations on coal sections and observations under light microscope and scanning electron microscopy (SEM) were combined to understand the fracture characteristics of the coal seam, and the spatial geological model of fracture development was built. The selected logging data was conducted cluster analysis to identify the coal structures of coring wells and to predict the coal structures of non-coring wells. The analysis results show that the No. 2 coal seam has a high fracture development degree, and is dominated by type II coal structure (cataclastic coals). The coals with different structures show evident zonation on the plane, which is largely controlled by faults. The well-developed fracture system and high permeability zone mainly concentrate on the tectonic rolling areas and the areas with small faults. Furthermore, the output data of coal fine and the drainage curves of CBM wells were performed dynamic analysis to indirectly reflect the fracture system difference and the resulting productivity difference. The results indicate that the wells with poor-preserved coals tend to produce more coal fine, and the gas production has a negative correlation with coal fine amount. The productivity pattern of CBM wells can be divided into “high yield—long-term stable yield” and “low yield—decline quickly”. Almost all CBM wells with type I coal structure and most CBM wells with type II coal structure have the first productivity pattern, and part wells with type II coal structure and all wells with type III coal structure present the second productivity pattern.Tao, Y., Yu, J., Liu, X., Xue, B., Wang, S., 2018. Factors affecting annual occurrence, bioaccumulation, and biomagnification of polycyclic aromatic hydrocarbons in plankton food webs of subtropical eutrophic lakes. Water Research 132, 1-11. biological pump plays a critical role in the occurrence and fate of hydrophobic organic contaminants (HOCs) mostly in temperate and frigid oligotrophic waters. However, the factors for the long-term occurrence and fate of HOCs in subtropical eutrophic waters remain largely unknown. This study provides novel insights into biogeochemical and physical factors on the annual occurrence, bioaccumulation, and biomagnification of 16 polycyclic aromatic hydrocarbons (PAHs) in the plankton food webs of four Chinese subtropical eutrophic lakes by one-year simultaneous field observations for five compartments. The annual mean ΣPAH16 in the water columns ranged from 359.69?±?31.52?ng?L?1 to 682.69?±?65.41?ng?L?1, and increased with the annual mean trophic state index, and phytoplankton biomass of these lakes, but was independent on the proximity of the lakes to urban areas. Biodilution effect played an important role in the occurrence of the PAHs in both phytoplankton and zooplankton. In contrast to previous studies in oligotrophic waters, not only the biological pump but also the equilibrium partitioning and the indirect influence of eutrophication (high pH induced by phytoplankton, and phytoplankton life cycling) modulated the annual occurrence of the PAHs in the water columns of these eutrophic lakes. Biphasic correlations were found between the bioaccumulation factors of the PAHs by plankton and the temperature (n?=?97–136, R2?=?0.06–0.24, p?≤?.008), and were related to plankton phenology. Bioaccumulation factors by plankton were dependent on the hydrophobicity of the PAHs (n?=?16, R2?=?0.27–0.31, p?≤?.023), and decreased with plankton biomass (n?=?94–103, R2?=?0.09–0.27, p?≤?.010). Trophic transfer of the PAHs from phytoplankton to zooplankton increased with phytoplankton biomass (n?=?26, R2?=?0.27, p?=?.004), and the temperature (n?=?102–135, R2?=?0.06–0.13, p?≤?.004), but decreased with lake trophic state index. Biomagnification only occurred during phytoplankton bloom periods.Taraji, M., Haddad, P.R., Amos, R.I.J., Talebi, M., Szucs, R., Dolan, J.W., Pohl, C.A., 2018. Chemometric-assisted method development in hydrophilic interaction liquid chromatography: A review. Analytica Chimica Acta 1000, 20-40. an enormous growth in the application of hydrophilic interaction liquid chromatography (HILIC), there has also been significant progress in HILIC method development. HILIC is a chromatographic method that utilises hydro-organic mobile phases with a high organic content, and a hydrophilic stationary phase. It has been applied predominantly in the determination of small polar compounds. Theoretical studies in computer-aided modelling tools, most importantly the predictive, quantitative structure retention relationship (QSRR) modelling methods, have attracted the attention of researchers and these approaches greatly assist the method development process. This review focuses on the application of computer-aided modelling tools in understanding the retention mechanism, the classification of HILIC stationary phases, prediction of retention times in HILIC systems, optimisation of chromatographic conditions, and description of the interaction effects of the chromatographic factors in HILIC separations. Additionally, what has been achieved in the potential application of QSRR methodology in combination with experimental design philosophy in the optimisation of chromatographic separation conditions in the HILIC method development process is communicated. Developing robust predictive QSRR models will undoubtedly facilitate more application of this chromatographic mode in a broader variety of research areas, significantly minimising cost and time of the experimental work.Tarhan, L.G., Planavsky, N.J., Wang, X., Bellefroid, E.J., Droser, M.L., Gehling, J.G., 2018. The late-stage “ferruginization” of the Ediacara Member (Rawnsley Quartzite, South Australia): Insights from uranium isotopes. Geobiology 16, 35-48. paleoenvironmental setting in which the Ediacara Biota lived, died, and was preserved in the eponymous Ediacara Member of the Rawnsley Quartzite of South Australia is an issue of long-standing interest and recent debate. Over the past few decades, interpretations have ranged from deep marine to shallow marine to terrestrial. One of the key features invoked by adherents of the terrestrial paleoenvironment hypothesis is the presence of iron oxide coatings, inferred to represent the upper horizons of paleosols, along fossiliferous sandstone beds of the Ediacara Member. We find that these surficial oxides are characterized by (234U/238U) values which are not in secular equilibrium, indicating extensive fluid-rich alteration of these surfaces within the past approximately 2 million years. Specifically, the oxide coatings are characterized by (234U/238U) values >1, indicating interaction with high-(234U/238U) fluids derived from alpha-recoil discharge. These oxides are also characterized by light “stable” δ238/235U values, consistent with a groundwater U source. These U isotope data thus corroborate sedimentological observations that ferric oxides along fossiliferous surfaces of the Ediacara Member consist of surficial, non-bedform-parallel staining, and sharply irregular patches, strongly reflecting post-depositional, late-stage processes. Therefore, both sedimentological and geochemical evidence indicate that Ediacara iron oxides do not reflect synsedimentary ferruginization and that the presence of iron oxides cannot be used to either invoke a terrestrial paleoenvironmental setting for or reconstruct the taphonomic pathways responsible for preservation of the Ediacara Biota. These findings demonstrate that careful assessment of paleoenvironmental parameters is essential to the reconstruction of the habitat of the Ediacara Biota and the factors that led to the fossilization of these early complex ecosystems.Teehera, K.B., Jungbluth, S.P., Onac, B.P., Acosta-Maeda, T.E., Hellebrand, E., Misra, A.K., Pflitsch, A., Rappé, M.S., Smith, S.M., Telus, M., Schorghofer, N., 2018. Cryogenic minerals in Hawaiian lava tubes: A geochemical and microbiological exploration. Geomicrobiology Journal 35, 227-241. Mauna Loa volcano, on the Island of Hawaii, has numerous young lava tubes. Among them, two at high altitudes are known to contain ice year-round: Mauna Loa Icecave (MLIC) and the Arsia Cave. These unusual caves harbor cold, humid, dark, and biologically restricted environments. Secondary minerals and ice were sampled from both caves to explore their geochemical and microbiological characteristics. The minerals sampled from the deep parts of the caves, where near freezing temperatures prevail, are all multi-phase and consist mainly of secondary amorphous silica SiO2, cryptocrystalline calcite CaCO3, and gypsum CaSO4·2H2O. Based on carbon and oxygen stable isotope ratios, all sampled calcite is cryogenic. The isotopic composition of falls on the global meteoric line, indicating that little evaporation has occurred. The microbial diversity of a silica and calcite deposit in the MLIC and from ice pond water in the Arsia Cave was explored by analysis of ～50,000 small subunit ribosomal RNA gene fragments via amplicon sequencing. Analyses reveal that the Hawaiian ice caves harbor unique microbial diversity distinct from other environments, including cave environments, in Hawaii and worldwide. Actinobacteria and Proteobacteria were the most abundant microbial phyla detected, which is largely consistent with studies of other oligotrophic cave environments. The cold, isolated, oligotrophic basaltic lava cave environment in Hawaii provides a unique opportunity to understand microbial biogeography not only on Earth but also on other planets.Tejero-Andrade, A., Argote-Espino, D.L., Cifuentes-Nava, G., Hernández-Quintero, E., Chávez, R.E., García-Serrano, A., 2018. ‘Illuminating’ the interior of Kukulkan's Pyramid, Chichén Itzá, Mexico, by means of a non-conventional ERT geophysical survey. Journal of Archaeological Science 90, 1-11.én Itzá, located in the north-central portion of the Yucatán Peninsula, is one of the major pre-Hispanic cities established in the southern lowlands of Mexico. The main objective of this investigation was to “unveil” the interior of the pyramid of El Castillo, also known as the Temple of Kukulkan, an emblematic structure in this archaeological site. To that end, 828 flat electrodes were deployed around each of the 9 bodies that compose the pyramid, including the base of the structure. A dataset consisting of 37,548 observations was obtained. A precise topographic control for each electrode was carried out and introduced in the inversion model. The mathematical process to compute a final 3D model was made possible by taking 9 observation levels (33,169 measurements) into account, due to computational limitations. The results showed the existence of two older pyramids within the main Mayan building and provided important information regarding our understanding of this Mayan civilization. Future archaeological studies in the older substructure could reveal information about early settlement on this site, its evolution in time and its cultural influences.Teklu, T.W., Li, X., Zhou, Z., Alharthy, N., Wang, L., Abass, H., 2018. Low-salinity water and surfactants for hydraulic fracturing and EOR of shales. Journal of Petroleum Science and Engineering 162, 367-377. are significant recoverable oil and gas resources stored in shale reservoirs throughout the world. Horizontal well with multistage hydraulic fracturing is an enabling technology for economic production of these shale resources. Recovery factors of liquid rich shale reservoirs is typically less than 10%, hence, there is an incentive for implementing enhanced oil recovery (EOR) technologies to improve oil production from these very tight reservoirs. Brine, chemical (surfactant), gas, or combination of these fluids imbibition or injection in huff-n-puff scenario could improve oil recovery of liquid rich shale reservoirs. In this study, low-salinity water and low-salinity water + surfactant imbibition are assessed as both hydraulic fracturing and EOR fluids in liquid rich shale reservoirs. Osmosis, capillary pressure, wettability alteration, and other effects are among the mechanisms by which these fluids can improve oil recovery from shale reservoirs. These favorable effects were investigated through imbibition experiments. Experiments show: (a) low-salinity water huff-n-puff in tight formations can improve oil production from tight formations. This is because wettability alteration, capillary, and osmotic forces; (b) surfactant + low-salinity-water huff-n-puff can further improve oil production due to additional IFT decrease and wettability alteration by surfactants; hence, improve oil production from stimulated ultra-tight formations. Based on experimental observations and literature reviewed, low-salinity water huff-n-puff (until economical), followed by low-salinity water + surfactant huff-n-puff EOR process is recommended to optimize production from liquid rich shale reservoirs, while minimizing cost. These fluids can be used to reduce matrix-fracture skin damage. The effectiveness of these hydraulic fracturing and EOR fluids in shales is highly dependent on the existence and extent of natural fractures or laminations within the stimulated reservoir volume; this is because osmosis and diffusion are very slow processes.Teng, F., Zhu, Q., Wang, Y., Du, J., Lu, N., 2018. Enhancing reproducibility of SALDI MS detection by concentrating analytes within laser spot. Talanta 179, 583-587. laser desorption/ionization time-of-flight mass spectrometry (SALDI TOF MS) has become one of the most important analytical methods due to its less interference at low molecular weight range. However, it is still a challenge to obtain a good reproducibility of SALDI TOF MS because of the inhomogeneous distribution of analyte molecules induced by coffee ring effect. We propose a universal and reliable method to eliminate the coffee ring effect by concentrating all the analyte molecules within the laser spot. This method exhibits an excellent reproducibility of spot-to-spot and substrate-to-substrate, and the relative standard deviations (RSDs) for different concentrations are lower than 12.6%. It also performs good linear dependency (R2 > 0.98) in the log-log plot with the concentration range of 1 nM to 1 μM, and the limit of detection for R6G is down to 1 fmol.Tian, S., Wang, T., Li, G., Sheng, M., Ren, W., 2017. Molecular simulation of methane adsorption behavior in different shale kerogen types. Natural Gas Industry 37, 18-25. impact of different kerogen types on the methane adsorption behavior is still not clear at present. In view of this, a model was built according to the molecular structures of three kirogen types: TypeⅠ—Sapropel, TypeⅡ—Sapropel–Humic, and Type Ⅲ—Humic), in which the adsorption behaviors of methane were investigated by using the Grand Canonical Monte Carlo (GCMC) and Molecular Dynamic (MD) methods, and this model and results were validated. On this basis, the effects were also discussed of temperature, geothermal gradient, and the molecular composition and the specific surface area of kerogen on the adsorption of a methane–kerogen adsorption system, and the microscopic adsorption mechanism of methane in kerogen was revealed. The following results were obtained. (1) The adsorbed methane amount in Type Ⅰ kerogen was the largest, followed by Type Ⅱ, and Type Ⅲ the smallest. (2) The chemical structure of kerogen significantly influences its adsorption amount of methane: the kerogen with more aromatic hydrocarbons and cyclanes have a stronger affinity for methane, and the carbon and sulfur atoms play an important role in the adsoprtion of kerogen to methane. (3) As temperature increases, the average isosteric adsorption heat of methane decreases, and it is always less than 42 kJ/mol, indicating that this adsorption is a physical adsorption. (4) As the depth of stratum increases, the adsorption amount first increases and then decreases, reaching the maximum at 2000-2500 meters. At the same depth, the smaller the geothermal gradient, the more the methane adsorption amount. (5) The adsorption amount of methane has a linear relationship with the specific surface area of kerogen.Timofeeva, I.I., Vakh, C.S., Bulatov, A.V., Worsfold, P.J., 2018. Flow analysis with chemiluminescence detection: Recent advances and applications. Talanta 179, 246-270. article highlights the most important developments in flow analysis with chemiluminescence (CL) detection, describing different flow systems that are compatible with CL detection, detector designs, commonly applied CL reactions and approaches to sample treatment. Recent applications of flow analysis with CL detection (focusing on outputs published since 2010) are also presented. Applications are classified by sample matrix, covering foods and beverages, environmental matrices, pharmaceuticals and biological fluids. Comprehensive tables are provided for each area, listing the specific sample matrix, CL reaction used, linear range, limit of detection and sample treatment for each analyte. Finally, recent and emerging trends in the field are also discussed.Toth, C.R.A., Gieg, L.M., 2018. Time course-dependent methanogenic crude oil biodegradation: Dynamics of fumarate addition metabolites, biodegradative genes, and microbial community composition. Frontiers in Microbiology 8, 2610. doi: 10.3389/fmicb.2017.02610. of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32) or heavy crude oil (°API = 16). Over the course of 17 months, we conducted routine analytical (GC, GC-MS) and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing) surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella), along with syntrophic bacteria (Syntrophus), methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”). Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems.Tréguer, P., Bowler, C., Moriceau, B., Dutkiewicz, S., Gehlen, M., Aumont, O., Bittner, L., Dugdale, R., Finkel, Z., Iudicone, D., Jahn, O., Guidi, L., Lasbleiz, M., Leblanc, K., Levy, M., Pondaven, P., 2018. Influence of diatom diversity on the ocean biological carbon pump. Nature Geoscience 11, 27-37. sustain the marine food web and contribute to the export of carbon from the surface ocean to depth. They account for about 40% of marine primary productivity and particulate carbon exported to depth as part of the biological pump. Diatoms have long been known to be abundant in turbulent, nutrient-rich waters, but observations and simulations indicate that they are dominant also in meso- and submesoscale structures such as fronts and filaments, and in the deep chlorophyll maximum. Diatoms vary widely in size, morphology and elemental composition, all of which control the quality, quantity and sinking speed of biogenic matter to depth. In particular, their silica shells provide ballast to marine snow and faecal pellets, and can help transport carbon to both the mesopelagic layer and deep ocean. Herein we show that the extent to which diatoms contribute to the export of carbon varies by diatom type, with carbon transfer modulated by the Si/C ratio of diatom cells, the thickness of the shells and their life strategies; for instance, the tendency to form aggregates or resting spores. Model simulations project a decline in the contribution of diatoms to primary production everywhere outside of the Southern Ocean. We argue that we need to understand changes in diatom diversity, life cycle and plankton interactions in a warmer and more acidic ocean in much more detail to fully assess any changes in their contribution to the biological pump.Tribelli, P.M., Rossi, L., Ricardi, M.M., Gomez-Lozano, M., Molin, S., Raiger Iustman, L.J., Lopez, N.I., 2018. Microaerophilic alkane degradation in Pseudomonas extremaustralis: a transcriptomic and physiological approach. Journal of Industrial Microbiology & Biotechnology 45, 15-23. fuel is one of the most important sources of hydrocarbon contamination worldwide. Its composition consists of a complex mixture of n-alkanes, branched alkanes and aromatic compounds. Hydrocarbon degradation in Pseudomonas species has been mostly studied under aerobic conditions; however, a dynamic spectrum of oxygen availability can be found in the environment. Pseudomonas extremaustralis, an Antarctic bacterium isolated from a pristine environment, is able to degrade diesel fuel and presents a wide microaerophilic metabolism. In this work RNA-deep sequence experiments were analyzed comparing the expression profile in aerobic and microaerophilic cultures. Interestingly, genes involved in alkane degradation, including alkB, were over-expressed in micro-aerobiosis in absence of hydrocarbon compounds. In minimal media supplemented with diesel fuel, n-alkanes degradation (C13–C19) after 7?days was observed under low oxygen conditions but not in aerobiosis. In-silico analysis of the alkB promoter zone showed a putative binding sequence for the anaerobic global regulator, Anr. Our results indicate that some diesel fuel components can be utilized as sole carbon source under microaerophilic conditions for cell maintenance or slow growth in a Pseudomonas species and this metabolism could represent an adaptive advantage in polluted environments.Tripathi, B.M., Kim, M., Kim, Y., Byun, E., Yang, J.-W., Ahn, J., Lee, Y.K., 2018. Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores. Scientific Reports 8, Article 504. the microbial communities and ecological processes that influence their structure in permafrost soils is crucial for predicting the consequences of climate change. In this study we investigated the bacterial and archaeal communities along depth profiles of four soil cores collected across Alaska. The bacterial and archaeal diversity (amplicon sequencing) overall decreased along the soil depth but the depth-wise pattern of their abundances (qPCR) varied by sites. The community structure of bacteria and archaea displayed site-specific pattern, with a greater role of soil geochemical characteristics rather than soil depth. In particular, we found significant positive correlations between methane trapped in cores and relative abundance of methanogenic archaeal genera, indicating a strong association between microbial activity and methane production in subsurface soils. We observed that bacterial phylogenetic community assembly tended to be more clustered in surface soils than in deeper soils. Analyses of phylogenetic community turnover among depth profiles across cores indicated that the relative influence of deterministic and stochastic processes was mainly determined by soil properties rather than depth. Overall, our findings emphasize that the vertical distributions of bacterial and archaeal communities in permafrost soils are to a large extent determined by the variation in site-specific soil properties.Tully, B.J., Wheat, C.G., Glazer, B.T., Huber, J.A., 2018. A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. The Isme Journal 12, 1-16. rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.Vacquand, C., Deville, E., Beaumont, V., Guyot, F., Sissmann, O., Pillot, D., Arcilla, C., Prinzhofer, A., 2018. Reduced gas seepages in ophiolitic complexes: Evidences for multiple origins of the H2-CH4-N2 gas mixtures. Geochimica et Cosmochimica Acta 223, 437-461. paper proposes a comparative study of reduced gas seepages occurring in ultrabasic to basic rocks outcropping in ophiolitic complexes based on the study of seepages from Oman, the Philippines, Turkey and New Caledonia. This study is based on analyses of the gas chemical composition, noble gases contents, stable isotopes of carbon, hydrogen and nitrogen. These seepages are mostly made of mixtures of three main components which are H2, CH4 and N2 in various proportions. The relative contents of the three main gas components show 4 distinct types of gas mixtures (H2-rich, N2-rich, N2-H2-CH4 and H2-CH4). These types are interpreted as reflecting different zones of gas generation within or below the ophiolitic complexes. In the H2-rich type, associated noble gases display signatures close to the value of air. In addition to the atmospheric component, mantle and crustal contributions are present in the N2-rich, N2-H2-CH4 and H2-CH4 types. H2-bearing gases are either associated with ultra-basic (pH 10–12) spring waters or they seep directly in fracture systems from the ophiolitic rocks. In ophiolitic contexts, ultrabasic rocks provide an adequate environment with available Fe2+ and alkaline conditions that favor H2 production. CH4 is produced either directly by reaction of dissolved CO2 with basic-ultrabasic rocks during the serpentinization process or in a second step by H2-CO2 interaction. H2 is present in the gas when no more carbon is available in the system to generate CH4. The N2-rich type is notably associated with relatively high contents of crustal 4He and in this gas type N2 is interpreted as issued mainly from sediments located below the ophiolitic units.Valle, J., Gonsior, M., Harir, M., Enrich-Prast, A., Schmitt-Kopplin, P., Bastviken, D., Conrad, R., Hertkorn, N., 2018. Extensive processing of sediment pore water dissolved organic matter during anoxic incubation as observed by high-field mass spectrometry (FTICR-MS). Water Research 129, 252-263. organic matter (DOM) contained in lake sediments is a carbon source for many microbial degradation processes, including aerobic and anaerobic mineralization. During anaerobic degradation, DOM is partially consumed and transformed into new molecules while the greenhouse gases methane (CH4) and carbon dioxide (CO2) are produced. In this study, we used ultrahigh resolution mass spectrometry to trace differences in the composition of solid-phase extractable (PPL resin) pore water DOM (SPE-DOM) isolated from surface sediments of three boreal lakes before and after 40 days of anoxic incubation, with concomitant determination of CH4 and CO2 evolution. CH4 and CO2 production detected by gas chromatography varied considerably among replicates and accounted for fractions of ～2–4 × 10?4 of sedimentary organic carbon for CO2 and ～0.8–2.4 × 10?5 for CH4. In contrast, the relative changes of key bulk parameters during incubation, such as relative proportions of molecular series, elemental ratios, average mass and unsaturation, were regularly in the percent range (1–3% for compounds decreasing and 4–10% for compounds increasing), i.e. several orders of magnitudes higher than mineralization alone. Computation of the average carbon oxidation state in CHO molecules of lake pore water DOM revealed rather non-selective large scale transformations of organic matter during incubation, with depletion of highly oxidized and of highly reduced CHO molecules, and formation of rather non-labile fulvic acid type molecules. In general, proportions of CHO compounds slightly decreased. Nearly saturated CHO and CHOS lipid-like substances declined during incubation: these rather commonplace molecules were less specific indicators of lake sediment alteration than the particular compounds, such as certain oxygenated aromatics and carboxyl-rich alicyclic acids (CRAM) found more abundant after incubation. There was a remarkable general increase in many CHNO compounds during incubation across all lakes. Differences in DOM transformation between lakes corresponded with lake size and water residence time. While in the small lake Svarttj?rn, carboxyl-rich alicyclic molecules (CRAM) increased during incubation, lignin-and tannin-like compounds were enriched in the large lake Bisen, suggesting selective preservation of these rather non-labile aromatic compounds rather than recent synthesis. SPE-DOM after incubation may represent freshly synthesized compounds, leftover bulk DOM which is primarily composed of intrinsically refractory molecules and/or microbial metabolites which were not consumed in our experiments. In spite of a low fraction of the total DOM being mineralized to CO2 and CH4, the more pronounced change in molecular DOM composition during the incubation indicates that diagenetic modification of organic matter can be substantial compared to complete mineralization.Vance, S.D., Kedar, S., Panning, M.P., St?hler, S.C., Bills, B.G., Lorenz, R.D., Huang, H.-H., Pike, W.T., Castillo, J.C., Lognonné, P., Tsai, V.C., Rhoden, A.R., 2018. Vital signs: Seismology of icy ocean worlds. Astrobiology 18, 37-53. ocean worlds possess diverse energy sources and associated mechanisms that are capable of driving significant seismic activity, but to date no measurements of their seismic activity have been obtained. Such investigations could reveal the transport properties and radial structures, with possibilities for locating and characterizing trapped liquids that may host life and yielding critical constraints on redox fluxes and thus on habitability. Modeling efforts have examined seismic sources from tectonic fracturing and impacts. Here, we describe other possible seismic sources, their associations with science questions constraining habitability, and the feasibility of implementing such investigations. We argue, by analogy with the Moon, that detectable seismic activity should occur frequently on tidally flexed ocean worlds. Their ices fracture more easily than rocks and dissipate more tidal energy than the <1 GW of the Moon and Mars. Icy ocean worlds also should create less thermal noise due to their greater distance and consequently smaller diurnal temperature variations. They also lack substantial atmospheres (except in the case of Titan) that would create additional noise. Thus, seismic experiments could be less complex and less susceptible to noise than prior or planned planetary seismology investigations of the Moon or Mars.Vandieken, V., Marshall, I.P.G., Niemann, H., Engelen, B., Cypionka, H., 2018. Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., novel Bacteroidetes isolated from subsurface sediments of the Baltic Sea. Frontiers in Microbiology 8, 2614. doi: 10.3389/fmicb.2017.02614. communities in deep subsurface sediments are challenged by the decrease in amount and quality of organic substrates with depth. In sediments of the Baltic Sea, they might additionally have to cope with an increase in salinity from ions that have diffused downward from the overlying water during the last 9000 years. Here, we report the isolation and characterization of four novel bacteria of the Bacteroidetes from depths of 14–52 m below seafloor (mbsf) of Baltic Sea sediments sampled during International Ocean Discovery Program (IODP) Expedition 347. Based on physiological, chemotaxonomic and genotypic characterization, we propose that the four strains represent two new species within a new genus in the family Marinifilaceae, with the proposed names Labilibaculum manganireducens gen. nov., sp. nov. (type strain 59.10-2MT) and Labilibaculum filiforme sp. nov. (type strains 59.16BT) with additional strains of this species (59.10-1M and 60.6M). The draft genomes of the two type strains had sizes of 5.2 and 5.3 Mb and reflected the major physiological capabilities. The strains showed gliding motility, were psychrotolerant, neutrophilic and halotolerant. Growth by fermentation of mono- and disaccharides as well as pyruvate, lactate and glycerol was observed. During glucose fermentation, small amounts of electron equivalents were transferred to Fe(III) by all strains, while one of the strains also reduced Mn(IV). Thereby, the four strains broaden the phylogenetic range of prokaryotes known to reduce metals to the group of Bacteroidetes. Halotolerance and metal reduction might both be beneficial for survival in deep subsurface sediments of the Baltic Sea.Varma, A.K., Mishra, D.K., Samad, S.K., Prasad, A.K., Panigrahi, D.C., Mendhe, V.A., Singh, B.D., 2018. Geochemical and organo-petrographic characterization for hydrocarbon generation from Barakar Formation in Auranga Basin, India. International Journal of Coal Geology 186, 97-114. in pace with global studies of shale gas/oil, the authors had selected fifty-one (41 shales and 10 coal) core samples of Barakar Formation (lower Sakmarian–Kungurian) from four boreholes of Auranga basin, to understand hydrocarbon generation potential. The Rock-Eval pyrolysis along with total organic carbon content (TOC), organo-petrographic, vitrinite reflectance, Fourier Transform infrared spectroscopy (FTIR), X-ray fluorescence (XRF) analyses were carried. These studies indicate that all the samples (coal and shale) have fair to excellent hydrocarbon generation in respect of TOC and S2 (under Rock-Eval pyrolysis). Further, the thermal maturity (Tmax) of shales and coals are placed in ranges from 409 to 468 and 420–426 °C respectively. However, vitrinite grains having reflectance > 0.60% (↑ Vt60%) may indicate the onset of thermogenic oil generation could possible in the majority of the samples. The presence of alginite, sporinite, resinite, liptodetrinite and suberinite along with perhydrous vitrinite and inertinite macerals is observed. The linear relationship of total maceral content (TMC) with TOC may help in their determination empirically. Multiple regression analysis denote maceral reactivity in the generation of S2. In addition, A-factor (aliphatic/aromatic peak intensity) and C-factor (carbonyl/aromatic peak intensity) under FTIR spectra, suggest dominance of kerogen type III, IV and II/III. The geochemical indices like CIA (chemical index of alteration), CIW (chemical index of weathering) and ICV (index of compositional variation) indicate strong to intermediate weathering, under passive continental margin depositional environment supporting luxurious vegetation and organic matter preservation.Veli?kovi?, D., Chu, R.K., Carrell, A.A., Thomas, M., Pa?a-Toli?, L., Weston, D.J., Anderton, C.R., 2018. Multimodal MSI in conjunction with broad coverage spatially resolved MS2 increases confidence in both molecular identification and localization. Analytical Chemistry 90, 702-707. critical aspect of mass spectrometry imaging (MSI) is the need to confidently identify detected analytes. While orthogonal tandem MS (e.g., LC–MS2) experiments from sample extracts can assist in annotating ions, the spatial information about these molecules is lost. Accordingly, this could cause mislead conclusions, especially in cases where isobaric species exhibit different distributions within a sample. In this Technical Note, we employed a multimodal imaging approach, using matrix assisted laser desorption/ionization (MALDI)-MSI and liquid extraction surface analysis (LESA)-MS2I, to confidently annotate and localize a broad range of metabolites involved in a tripartite symbiosis system of moss, cyanobacteria, and fungus. We found that the combination of these two imaging modalities generated very congruent ion images, providing the link between highly accurate structural information onfered by LESA and high spatial resolution attainable by MALDI. These results demonstrate how this combined methodology could be very useful in differentiating metabolite routes in complex systems.Vogt, J.C., Abed, R.M.M., Albach, D.C., Palinska, K.A., 2018. Bacterial and archaeal diversity in hypersaline cyanobacterial mats along a transect in the intertidal flats of the Sultanate of Oman. Microbial Ecology 75, 331-347. intertidal zones are highly dynamic ecosystems that are exposed to multiple extreme environmental conditions including rapidly and frequently changing parameters (water, nutrients, temperature) as well as highly elevated salinity levels often caused by high temperatures and evaporation rates. Microbial mats in most extreme settings, as found at the coastline of the subtropical-arid Arabian Peninsula, have been relatively less studied compared to their counterparts around the world. We report, here, for the first time on the diversity of the bacterial and archaeal communities of marine microbial mats along an intertidal transect in a wide salt flat with strongly increased salinity employing Illumina MiSeq technology for amplicon sequencing of 16S rRNA gene fragments. Microbial communities were dominated by typical halotolerant to halophilic microorganisms, with clear shifts in community composition, richness, and diversity along the transect. Highly adapted specialists (e.g., Euhalothece, Salinibacter, Nanohaloarchaeota) were mainly found at the most extreme, upper tidal sites and less specialized organisms with wide tolerance ranges (e.g., Lyngbya, Rhodovibrio, Salisaeta, Halobacteria) in intermediate sites of the transect. The dominating taxa in the lower tidal sites were typical members of well-stabilized mats (e.g., Coleofasciculus, Anaerolineaceae, Thaumarchaeota). Up to 40% of the archaeal sequences per sample represented so far unknown phyla. In conclusion, the bacterial richness and diversity increased from upper towards lower tidal sites in line with increasing mat stabilization and functional diversity, opposed to that of cyanobacteria only and archaea, which showed their highest richness and diversity in upper tidal samples.Voosen, P., 2018. Cliffs of ice spied on Mars. Science 359, 145. more than a decade, Colin Dundas, a geologist at the U.S. Geological Survey in Flagstaff, Arizona, has had a daily routine: inspecting a dozen or so high-resolution images beamed back every day from the Mars Reconnaissance Orbiter (MRO). A few years ago, something surprising popped out from the planet's sea of rust: a pale sliver of blue.What Dundas saw that day, and subsequently found at seven other sites, are steep cliffs, up to 100 meters tall, that expose what appears to be nearly pure ice. The discovery points to large stores of underground ice buried only a meter or two below the surface at surprisingly low martian latitudes. “This kind of ice is more widespread than previously thought,” says Dundas, who, with his co-authors, describes the cliffs this week in Science. Each cliff seems to be the naked face of a glacier, tantalizing scientists with the promise of a layer-cake record of past martian climates and space enthusiasts with a potential resource for future human bases.Finding ice on Mars is nothing new. Ice covers the poles, and a radar instrument on the MRO has detected signatures of thick, buried ice across the planet's belly (Science, 26 February 2010, p. 1075 </lookup/doi/10.1126/science.327.5969.1075>). Some researchers suggested these deposits could be the remnants of glaciers that existed millions of years ago when the planet's spin axis and orbit were different. But the depth of the ice and whether it exists as relatively pure sheets or as granules frozen in the pore spaces of martian soil have been uncertain.A decade ago, researchers using the MRO spotted a related clue: pools of seemingly pure ice in the floors of small craters carved out by fresh meteorite impacts. But it was unclear whether these frozen pools were connected to the buried glaciers or were merely isolated patches. At the ice cliffs, Dundas and his team could see the glaciers in cross section, and they patiently revisited the sites to see how they changed over time.They found that the ice persisted through the martian summer, when any ephemeral frost would have vaporized. And last year, the MRO caught several boulders tumbling out of one of the cliff faces, suggesting that gradual erosion had released them from a massive ice deposit. Evidently the near-surface ice and the large subsurface deposits are one and the same, says Ali Bramson, a co-author and graduate student at the University of Arizona in Tucson. “This deep, thick, pure ice extends almost all the way up to the surface.”Banding and subtly varying shades of blue suggest that the slabs of ice are stacked. That implies that the deposits built up over many seasons as layers of snow were compressed in a previous climate cycle, says Susan Conway, a planetary geologist at the University of Nantes in France. Winds then buried the ice sheets in grit. “It's the only reasonable explanation,” she says.Drilling a core from one of these deposits and returning it to Earth would offer a treasure trove of information to geologists about the past martian climate, says G. Scott Hubbard, a space scientist at Stanford University in Palo Alto, California. “That preserved record would be of extreme importance to go back to,” he says.These sites are “very exciting” for potential human bases as well, says Angel Abbud-Madrid, director of the Center for Space Resources at the Colorado School of Mines in Golden, who led a recent NASA study exploring potential landing sites for astronauts. Water is a crucial resource for astronauts, because it could be combined with carbon dioxide, the main ingredient in Mars's atmosphere, to create oxygen to breathe and methane, a rocket propellant. And although researchers suspected the subsurface glaciers existed, they would only be a useful resource if they were no more than a few meters below the surface. The ice cliffs promise abundant, accessible ice, Abbud-Madrid says.The cliffs are all found at latitudes about 55° north or south, however, which grow frigid and dark in the martian winter—unpromising latitudes for a solar-powered human base. For this reason, the NASA study was limited to sites to within 50° of the equator. Now, Hubbard wants NASA's human exploration program to look for similar cliffs closer to the equator. “What's the cutoff point?” he asks. He hopes the next surprise will be ice closer to the martian tropics.Votrubova, J., Emmerova, B., Brzobohata, H., Sumberova, R., Vanek, D., 2017. Comparison of two Neolithic mtDNA haplotypes from a Czech excavation site with the results of mitochondrial DNA studies on European Neolithic and Mesolithic individuals. Forensic Science International: Genetics Supplement Series 6, e125-e128. aim of the present study was to compare the mtDNA haplotypes (haplogroups H and W) obtained from 2 young females buried within a Neolithic circular enclosure (rondel) with the results of the scientific studies on Neolithic and Mesolithic skeletal material. We collected 164 mtDNA literature sequences and data concerning the age of the specimen, location of the excavation site (Denmark, France, Germany, Hungary, Italy, Poland, Spain, and Sweden), D-loop mutations, haplogroups, sequencing primers, and methods used.Walder, R., Van Patten, W.J., Adhikari, A., Perkins, T.T., 2017. Going vertical to improve the accuracy of atomic force microscopy based single-molecule force spectroscopy. ACS Nano 12, 198–207. force spectroscopy (SMFS) is a powerful technique to characterize the energy landscape of individual proteins, the mechanical properties of nucleic acids, and the strength of receptor–ligand interactions. Atomic force microscopy (AFM)-based SMFS benefits from ongoing progress in improving the precision and stability of cantilevers and the AFM itself. Underappreciated is that the accuracy of such AFM studies remains hindered by inadvertently stretching molecules at an angle while measuring only the vertical component of the force and extension, degrading both measurements. This inaccuracy is particularly problematic in AFM studies using double-stranded DNA and RNA due to their large persistence length (p ≈ 50 nm), often limiting such studies to other SMFS platforms (e.g., custom-built optical and magnetic tweezers). Here, we developed an automated algorithm that aligns the AFM tip above the DNA’s attachment point to a coverslip. Importantly, this algorithm was performed at low force (10–20 pN) and relatively fast (15–25 s), preserving the connection between the tip and the target molecule. Our data revealed large uncorrected lateral offsets for 100 and 650 nm DNA molecules [24 ± 18 nm (mean ± standard deviation) and 180 ± 110 nm, respectively]. Correcting this offset yielded a 3-fold improvement in accuracy and precision when characterizing DNA’s overstretching transition. We also demonstrated high throughput by acquiring 88 geometrically corrected force-extension curves of a single individual 100 nm DNA molecule in ～40 min and versatility by aligning polyprotein- and PEG-based protein–ligand assays. Importantly, our software-based algorithm was implemented on a commercial AFM, so it can be broadly adopted. More generally, this work illustrates how to enhance AFM-based SMFS by developing more sophisticated data-acquisition protocols.Walker, D.J.F., Adhikari, R.Y., Holmes, D.E., Ward, J.E., Woodard, T.L., Nevin, K.P., Lovley, D.R., 2018. Electrically conductive pili from pilin genes of phylogenetically diverse microorganisms. The Isme Journal 12, 48-58. possibility that bacteria other than Geobacter species might contain genes for electrically conductive pili (e-pili) was investigated by heterologously expressing pilin genes of interest in Geobacter sulfurreducens. Strains of G. sulfurreducens producing high current densities, which are only possible with e-pili, were obtained with pilin genes from Flexistipes sinusarabici, Calditerrivibrio nitroreducens and Desulfurivibrio alkaliphilus. The conductance of pili from these strains was comparable to native G. sulfurreducens e-pili. The e-pili derived from C. nitroreducens, and D. alkaliphilus pilin genes are the first examples of relatively long (>100 amino acids) pilin monomers assembling into e-pili. The pilin gene from Candidatus Desulfofervidus auxilii did not yield e-pili, suggesting that the hypothesis that this sulfate reducer wires itself with e-pili to methane-oxidizing archaea to enable anaerobic methane oxidation should be reevaluated. A high density of aromatic amino acids and a lack of substantial aromatic-free gaps along the length of long pilins may be important characteristics leading to e-pili. This study demonstrates a simple method to screen pilin genes from difficult-to-culture microorganisms for their potential to yield e-pili; reveals new sources for biologically based electronic materials; and suggests that a wide phylogenetic diversity of microorganisms may use e-pili for extracellular electron exchange.Wallmann, K., Riedel, M., Hong, W.L., Patton, H., Hubbard, A., Pape, T., Hsu, C.W., Schmidt, C., Johnson, J.E., Torres, M.E., Andreassen, K., Berndt, C., Bohrmann, G., 2018. Gas hydrate dissociation off Svalbard induced by isostatic rebound rather than global warming. Nature Communications 9, Article 83. seepage from the upper continental slopes of Western Svalbard has previously been attributed to gas hydrate dissociation induced by anthropogenic warming of ambient bottom waters. Here we show that sediment cores drilled off Prins Karls Foreland contain freshwater from dissociating hydrates. However, our modeling indicates that the observed pore water freshening began around 8 ka BP when the rate of isostatic uplift outpaced eustatic sea-level rise. The resultant local shallowing and lowering of hydrostatic pressure forced gas hydrate dissociation and dissolved chloride depletions consistent with our geochemical analysis. Hence, we propose that hydrate dissociation was triggered by postglacial isostatic rebound rather than anthropogenic warming. Furthermore, we show that methane fluxes from dissociating hydrates were considerably smaller than present methane seepage rates implying that gas hydrates were not a major source of methane to the oceans, but rather acted as a dynamic seal, regulating methane release from deep geological reservoirs.Walters, C.C., 2017. Origin of Petroleum, in: Hsu, C.S., Robinson, P.R. (Eds.), Springer Handbook of Petroleum Technology. Springer International Publishing, pp. 359-379. concerning the origin of oil on Earth fall into two camps: biogenic, where oil is generated by the thermal conversion of sedimentary organic matter derived from living organisms, and abiogenic, where oil is formed from mineral catalyzed reactions of non-biological carbon deep within the Earth. Most geochemists believe that there are multiple and overwhelming lines of evidence supporting biogenic origins for petroleum. While there are known occurrences of abiogenic methane generated by geologic processes, these contribute little to petroleum resources. Economic reserves require all specific elements and processes occur within a sedimentary basin. The Petroleum System must contain: (1) at least one formation of organic-rich sediments (source rock) that has been buried to a sufficient depth by overburden rock such that petroleum is generated and expelled, (2) Pathways (permeable strata and faults) that allow the petroleum to migrate, (3) Reservoir rocks with sufficient porosity and permeability to accumulate economically significant quantities of petroleum, and (4) Seal rock (low permeability) and structures that retain migrated petroleum within the reservoir rock. In the case of many unconventional resources, the source rock itself serves as source, reservoir, and seal. Petroleum, composed of hydrocarbons and heteroatomic molecules, is the most complex mixture occurring in nature. The composition of petroleum generated within its source rock is influenced by the type of organisms that contributed organic matter, the environment of deposition, and thermal exposure. Most of the deposited biomolecules are chemically altered, broken apart, and reassembled into an insoluble carbonaceous material termed kerogen. Upon burial and heating, the kerogen reacts producing mostly compounds that have lost their biochemical signature; however, some of these generated molecules, termed biomarkers, preserve enough of their chemical structure that their original biological precursor can be identified. Expulsion from the source rock chemically fractionates the generated petroleum, with the expelled product enriched in gases and hydrocarbons, and retained bitumen enriched in heteroatomic polar species and asphaltenes. Petroleum composition can be further altered as it migrates and resides in reservoir rocks by physical, chemical and biological processes. Collectively, these processes result in petroleum accumulations with a diverse range of compositions and physical properties.Wang, C., Guo, W., Li, Y., Stubbins, A., Li, Y., Song, G., Wang, L., Cheng, Y., 2017. Hydrological and biogeochemical controls on absorption and fluorescence of dissolved organic matter in the northern South China Sea. Journal of Geophysical Research: Biogeosciences 122, 3405-3418. Kuroshio intrusion from the West Philippine Sea (WPS) and mesoscale eddies are important hydrological features in the northern South China Sea (SCS). In this study, absorption and fluorescence of dissolved organic matter (CDOM and FDOM) were determined to assess the impact of these hydrological features on DOM dynamics in the SCS. DOM in the upper 100?m of the northern SCS had higher absorption, fluorescence, and degree of humification than in the Kuroshio Current of the WPS. The results of an isopycnal mixing model showed that CDOM and humic-like FDOM inventories in the upper 100?m of the SCS were modulated by the Kuroshio intrusion. However, protein-like FDOM was influenced by in situ processes. This basic trend was modified by mesoscale eddies, three of which were encountered during the fieldwork (one warm eddy and two cold eddies). DOM optical properties inside the warm eddy resembled those of DOM in the WPS, indicating that warm eddies could derive from the Kuroshio Current through Luzon Strait. DOM at the center of cold eddies was enriched in humic-like fluorescence and had lower spectral slopes than in eddy-free waters, suggesting inputs of humic-rich DOM from upwelling and enhanced productivity inside the eddy. Excess CDOM and FDOM in northern SCS intermediate water led to export to the Pacific Ocean interior, potentially delivering refractory carbon to the deep ocean. This study demonstrated that DOM optical properties are promising tools to study active marginal sea-open ocean interactions.Wang, E., Ding, J., Qu, Z., Han, K., 2018. Development of a reactive force field for hydrocarbons and application to iso-octane thermal decomposition. Energy & Fuels 32, 901-907. force field (Reaxff) is a powerful method, which employs bond order/bond length formulism to describe bond breaking and bond reformation. In this work, a modification to the bond order formula was made and Reaxff parameters were re-optimized. The underlying idea of these modifications is to improve the energy gradient. Better agreements of the bond dissociation potential curves with the quantum mechanical curves were obtained on the basis of the aforementioned changes. Reaxff simulation was carried out to gain the understandings of the iso-octane pyrolysis. The apparent rate constants obtained using the newly optimized parameters fit well with the experimental results. The simulation results are in agreement with the existing experimental results. A maximum of C2 hydrocarbons were found to have the largest percentage. The distribution of the iso-octane decomposition pathway was illustrated.Wang, F., Liu, X., XiuQin, D., Li, Y., Tian, J., Li, S., You, J., 2017. Geochemical characteristics and environmental implications of trace elements of Zhifang Formation in Ordos Basin. Acta Sedimentologica Sinica 35, 1265-1273. trace elements of sedimentary rocks have a high sensitivity on hydrological changes of sedimentary environment, so the trace elements can be used as an effective method on the study of paleoclimate and paleoenvironment during deposition period. The Zhifang Formation in Ordos Basin is a new series of strata of Triassic with oil & gas seeps, the ancient climate and ancient water environment have great significance in restoring the ancient sedimentary framework and geography of that period and hydrocarbon accumulation. In this paper, the trace element of the profile and 21 shale and siltstone core sample of the middle Triassic Zhifang Formation in Ordos Basin have been determined by means of ICP-MS, and trace elements of strontium (Sr), ba (Ba), thorium (Th), uranium (U), vanadium (V), nickel (Ni), cobalt (Co) were selected as the discriminant mark, and combining sedimentology and sporopollen analysis, the sedimentary environment and ancient climate characteristics of Ordos Basin were discussed. The results show that by Li, Sr, Ni, Ga content and the ratio of Sr/Ba indicating the sedimentary environment was continental fresh-brackish water. The ratio of U/Th is from 0.09 to 0.38, δU is from 0.43 to 1.07, the ratio of V/(V+Ni)is from 0.69 to 0.89, the ratio of V/Cr is from 0.87 to 5.57, the ratio of Ni/Co is from 1.21 to 2.93, which indicate the oxidation-weak reduction environment. Combining sedimentology mark and quantitative calculation of Co elements, the average water depth of Zhifang Formation is less than 30 m, and the large catchment lake has not yet formed. The ratio of Sr/Cu is from 0.85 to 16.7, most Sr/Cu ratio is less than 10, and combining with the sporopollen analysis, which show that the dry climate of Heshanggou Formation was translated into warm climate of Zhifang Formation.Wang, F., Pan, Z., Zhang, S., 2018. Coupled thermo-hydro-chemical modeling of fracturing-fluid leakoff in hydraulically fractured shale gas reservoirs. Journal of Petroleum Science and Engineering 161, 17-28. the low-temperature, high-pressure and low-salinity water contacts the shale matrix through the hydraulic fractures during the treatment of hydraulic fracturing, both mass and energy transfer occur due to the significant temperature, pressure, saturation and salinity gradients. Although, many leakoff models have been published, none of the models coupled the transient fluid flow modeling with heat transfer and chemical-potential equilibrium phenomena. In this paper, a coupled thermo-hydro-chemical (THC) model based on the derivation of non-isothermal chemical-potential equations from Gibbs’ free energy is presented to simulate fluid/heat flow behaviors during the leakoff process of hydraulic fracturing. The THC model takes into account a two-phase flow and a triple-porosity medium, which includes hydraulic fractures, organic and inorganic shale matrix. The simulation of fluid flow and leakoff with the THC model accounts for all the important mass and heat transfer processes occurring in fractured shale system, including fluid transport driven by convection, adsorption and diffusion, and heat transport driven by thermal convection and conductivity. The dynamic temperature, pressure, saturation and salt concentration profiles within fractures and shale matrix are calculated, revealing a multi-field coupled invasion region of fracturing-fluids during the treatment of hydraulic fracturing. In sensitivity analyses, cases with different initial reservoir temperature, pressure, saturation and brine salinity are considered. The impacts of the temperature, pressure, saturation and salinity gradients between the shale formation and the pumped fluids on the well injection and leakoff volumes during the treatment of hydraulic fracturing are investigated. Results show that although hydraulic pressure is the most factor which affects the fracturing-fluid leakoff behavior, the combination of chemical-osmosis, thermal-osmosis and capillarity still has a non-negligible influence on the fracturing-fluid leakoff. This study provides a better understanding of the mass and heat transport mechanism of water-based fracturing-fluids in shale gas reservoirs.Wang, F., Pan, Z., Zhang, Y., Zhang, S., 2018. Simulation of coupled hydro-mechanical-chemical phenomena in hydraulically fractured gas shale during fracturing-fluid flowback. Journal of Petroleum Science and Engineering 163, 16-26. flowback in hydraulically fractured gas shale is a complicated transport behavior involving hydrodynamic (H), mechanical (M) and chemical (C) processes. Although, many flowback models have been published, none of the models flly coupled the transient fluid flow modeling with chemical-potential equilibrium and fracture closure phenomena.In this paper, a coupled hydro-mechanical-chemical (HMC) model based on hydrodynamics, linear-elastic fracture mechanics, and chemical-potential equations is presented to simulate the fracturing-fluid flowback behavior in hydraulically fractured gas shale. The HMC model takes into account a gas-liquid two-phase flow and a triple-porosity medium, which includes primary hydraulic fractures, secondary induced fractures and shale matrix. The flowback simulation with the HMC model accounts for all the important processes in fractured shale system, including (1)water transport driven by hydraulic, capillary and osmotic convections, (2)gas transport induced by both hydraulic pressure driven convection and adsorption, and (3)fracture closure considered as an elastic deformation. The fluid transport, coupled with rock deformation, are described by a set of partial differential equations. The semi-implicit finite-difference method is used to solve these equations.The evolution of pressure, saturation, salinity and aperture profiles of hydraulic fractures, induced fractures and matrix is calculated, revealing the multi-field coupled flowback behavior in fractured gas shale. The sensitivity analysis is also performed to investigate the physiochemical properties of shale on the water load recovery and gas production rate during the fracturing-fluid flowback. The results indicate that the capillarity has the most effect followed by chemical osmosis and induced fracture closure. The sub-irreducible water saturation has the weakest effect. Moreover, the matrix-related physiochemical parameters cause opposite influences on water load recovery and gas production rate. While, the influence of induced fracture-related parameters on both water load recovery and gas production rate is consistent. Results from this study are expected to explain which is the predominant mechanism for fracturing-fluid retention and the inherent relationship between fracturing-fluid flowback and gas production for different initial physiochemical properties of shale.Wang, G., Zhong, L., Zhou, S., Liu, Q., Li, Q., Qiang, F., Wang, L., Huang, R., Wang, G., Li, X., 2017. Jet breaking tools for natural gas hydrate exploitation and their support technologies. Natural Gas Industry 37, 68-74. natural gas hydrate (NGH) reservoirs in China are characterized by shallow burial depth and weak cementing. In view of these characteristics, it is in an urgent need to develop a series of technologies and support tools to ensure safe, economical, green and efficient NGH exploitation. In this paper, a new technical idea of NGH jet breaking and fluidization exploitation without changing the temperature and pressure conditions of NGH reservoirs was proposed, and the support nozzle tools for NGH jet breaking was designed, experimentally tested and optimized. Then, the relationships between the jet breaking parameters of nozzles (e.g. working pressure drop, flow rate, and upward and downward moving velocity and frequency) and the pore diameters and breaking rates of broken NGH were investigated based on laboratory tests, and the field construction engineering charts of NGH jet breaking and fluidization exploitation were established. Finally, this method was practically verified at Well Liwan 3 in the South China Sea. And following research results were obtained. First, the NGH jet breaking and fluidization exploitation technology can increase the production efficiency of NGH exploitation, protect the safety of reservoir bottom and reduce the energy consumption of NGH exploitation. Second, by using the nozzle tools of NGH jet breaking, the generated pore diameters are regular, broken particles can flow back well, and the lowering velocity of jet breaking without pilot holes is less than 7.1 m/h. Third, the engineering charts of NGH jet breaking and fluidization exploitation interpret the influential laws of jet breaking behaviors and construction parameters on the pore diameters and breaking rates of NGH so as to provide a reference for the selection of NGH production test technology parameters. And fourth, the successful implementation of the NGH jet breaking and fluidization technology in the production tests of Well Liwan 3 verifies the feasibility of NGH jet breaking and fluidization exploitation process, and exhibits its promising application prospects in NGH future commercial exploitation.Wang, H., Fei, Z., Li, Z., Xing, R., Liu, Z., Zhang, Y., Ding, H., 2018. Coupling laser desorption with corona beam ionization for ambient mass spectrometric analysis of solution and powder samples. Talanta 179, 364-368. infrared (940nm) laser desorption coupled with corona beam ionization (LD-CBI) technique was developed for expanding the application of the ambient mass spectrometry (AMS). A black ceramic sample plate was employed to facilitate the non-resonance absorption of laser energy. Solution and powder samples were immobilized in the shallow depression on ceramic plate and desorbed precisely since there was not gas disturbing. The dimer ion (m/z 1216.51) of reserpine was detected without any matrix assistance. In comparison with similar APCI-related ambient technique, the upper mass rang of analyte was broadened significantly. The feasibility of LD-CBI approach was demonstrated with 10 model pesticides. Typically, the limit of detection (LOD) of Malathion was as low as 6pg in the selected reaction monitoring (SRM) mode. The value is 166 times lower than the results from preceding technique desorption corona beam ionization (DCBI). As an APCI related ambient desorption ionization approach, LD-CBI technique could be a well complementary tool for direct detection of solution and powder samples.Wang, H., Hu, J., Xu, K., Tang, X., Xu, X., Shen, C., 2018. Biodegradation and chemotaxis of polychlorinated biphenyls, biphenyls, and their metabolites by Rhodococcus spp. Biodegradation 29, 1-10. biphenyl-degrading bacterial strains, SS1 and SS2, were isolated from polychlorinated biphenyl (PCB)-contaminated soil. They were identified as Rhodococcus ruber and Rhodococcus pyridinivorans based on the 16S rRNA gene sequence, as well as morphological, physiological and biochemical characteristics. SS1 and SS2 exhibited tolerance to 2000 and 3000?mg/L of biphenyl. And they could degrade 83.2 and 71.5% of 1300?mg/L biphenyl within 84?h, respectively. In the case of low-chlorinated PCB congeners, benzoate and 3-chlorobenzoate, the degradation activities of SS1 and SS2 were also significant. In addition, these two strains exhibited chemotactic response toward TCA-cycle intermediates, benzoate, biphenyl and 2-chlorobenzoate. This study indicated that, like the flagellated bacteria, non-flagellated Rhodococcus spp. might actively seek substrates through the process of chemotaxis once the substrates are depleted in their surroundings. Together, these data provide supporting evidence that SS1 and SS2 might be good candidates for restoring biphenyl/PCB-polluted environments.Wang, J., Shen, X., Rey, J., Yuan, Q., Yan, Y., 2018. Recent advances in microbial production of aromatic natural products and their derivatives. Applied Microbiology and Biotechnology 102, 47-61. natural products represent a diverse class of chemicals with great industrial significance. Usually, they serve as the building blocks for production of various polymers, esters, fibers, nutraceuticals, and pharmaceuticals. However, industrial synthesis of aromatic natural products still relies heavily on petroleum-based chemical processes, which are not sustainable and eco-friendly. In the past decades, construction of microbial cell factories that are able to efficiently convert renewable carbon sources into value-added products has made significant progress. This review highlights the recent advances in metabolic engineering efforts for biological production of aromatic natural products and their derivatives. Many novel pathways, enzymes, and products were reported in the literatures but have not yet detailed and informative viewed so far. Our goals are to provide a landscape of current works and present guidelines to address future challenges in biosynthesis of aromatic natural products and their derivatives using engineered microorganisms.Wang, J., Wang, C., Han, X., 2018. Enhanced coverage of lipid analysis and imaging by matrix-assisted laser desorption/ionization mass spectrometry via a strategy with an optimized mixture of matrices. Analytica Chimica Acta 1000, 155-162. matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) analysis and imaging of lipids, comprehensive ionization of lipids simultaneously by a universal matrix is a very challenging problem. Ion suppression of readily ionizable lipids to others is common. To overcome this obstacle and enhance the coverage of MALDI MS analysis and imaging of lipids, we developed a novel strategy employing a mixture of matrices, each of which is capable of selective ionization of different lipid classes. Given that MALDI MS with either 9-aminoacridine (9-AA) or N-(1-naphthyl) ethylenediamine dihydrochloride (NEDC) yields weak in-source decay which is critical for analysis of complex biological samples and possesses orthogonal selectivity for ionization of lipid classes, we tested the mixtures of NEDC and 9-AA with different ratios for analysis of standard lipids and mouse brain lipid extracts. We determined 1.35 of NEDC/9-AA as an optimized molar ratio. It was demonstrated that an enhanced coverage with the optimized mixture was obtained, which enabled us to analyze and map all the major classes of phospholipids and sulfatide from either lipid extracts or tissue slides, respectively. We believe that this powerful novel strategy can enhance lipidomics analysis and MALDI MS imaging of lipids in a high-throughput and semi-quantitative fashion.Wang, P., Hu, Y., Liu, L., Jiang, X., Li, C., Bartholomew, C.J., Zhang, G., 2017. Re–Os dating of bitumen from paleo–oil reservoir in the Qinglong Antimony Deposit, Guizhou Province, China and its geological significance. Acta Geologica Sinica - English Edition 91, 2153-2163. organic inclusions are present in the Qinglong antimony deposit. However, the source rocks of these organic matters have not been reliably identified. Recently, a paleo-oil reservoir was found in the Qinglong antimony deposit. In view of similar components of gaseous hydrocarbon, we propose that the organic matters observed in inclusions in Qinglong antimony deposit would come from this paleo-oil reservoir. We used the Re-Os dating method to determine the age of the bitumen from this paleo-oil reservoir, and obtained an isochron age of 254.3±2.8 Ma. The age indicates that the oil-generation from source rock occurred in the early Late Permian, earlier than the Sb mineralization age (～148±8.5 Ma) in the Qinglong antimony deposit area. After oil generation from Devonian source rock, first and secondary migration, the crude oil have probably entered into the fractures and pores of volcanic rocks and limestone and formed a paleo-oil reservoir in the western wing of Dachang anticline. As burial process deepened, the crude oil has turned into natural gas, migrates into the core of Dachang anticline and formed a paleo-gas reservoir. The hydrocarbons (including CH4) in the reservoirs can serve as reducing agent to provide the sulfur required for Sb mineralization through thermal chemical reduction of sulfates. Therefore, the formation of oil-gas in the area is a prerequisite for the Sb mineralization in the Qinglong antimony deposit.Wang, S., Chen, C., Shiau, B., Harwell, J.H., 2018. In-situ CO2 generation for EOR by using urea as a gas generation agent. Fuel 217, 499-507. injection of CO2 has great potential for increasing oil production, this potential is limited by site conditions and operational constraints such as lack of proper infrastructure, limited cheap CO2 sources, viscous fingering, gravity override at the targeted zones, and so forth. To mitigate some of these common limitations, we explore alternative methodologies which can successfully deliver CO2 through gas generation in situ, with superior IOR performance, while offering reasonable chemical cost.A new approach of in situ CO2 generation EOR was proved through a series of high-pressure and high-temperature laboratory scale experiments in this work. Urea was selected as a potential source of generating CO2 in situ because of its remarkable availability at bulk quantity and resistance to divalent cations. Urea is highly soluble in fresh water or brine and can decompose at reservoir conditions spontaneously to release carbon dioxide and ammonia. The tertiary oil recovery performance of the urea solution was evaluated in sand pack flooding at different operational conditions. We studied the flow rate ranging from 13.6?in./day to 36.2?in./day, the urea concentration ranging from 5% to 35%, the pressure ranging from 1500 psi to 4000 psi and the oil API ranging from 27 to 57.3, either with or without the presence of divalent ions. Recovered oil compositional analyses also revealed the additional benefits from the produced ammonia in tertiary recovery.Most importantly, results of injecting urea solution (as low as 5% solution) showed superior tertiary recovery performance (as high as 37.5%) as compared to the most recent efforts at our group (29.5%) as well as similar in situ CO2 generation EOR (2.4%–18.8%) approaches proposed by others. Because of the remarkable reservoir brine compatibility of urea, even under seawater levels of divalent ions, the floods showed no detectible effect of brine composition on the recovery and/or any occurrence of formation damage. Furthermore, the preferable wettability reversal was indicated by recovered oil compositional analyses. The economic feasibility and advantages of the newly proposed technique were demonstrated. The results served as a proof of concept for in situ CO2 generation tertiary oil recovery potential for both onshore and offshore fields.Wang, S., Feng, Q., Zha, M., Javadpour, F., Hu, Q., 2018. Supercritical methane diffusion in shale nanopores: Effects of pressure, mineral types, and moisture content. Energy & Fuels 32, 169-180. molecular dynamics, we simulated the diffusion behavior of supercritical methane in shale nanopores composed of different matrix mineral types (organic matter, clay, and calcite). We studied the effects of pore size, pore pressure, and moisture content on the diffusion process. Our results show that confined methane molecules diffuse more rapidly with increases in pore size and temperature but diffuse slowly with an increase in pressure. Anisotropic diffusion behavior is also observed in directions parallel and perpendicular to the basal surfaces of nanoslits. We also found that mineral types composing the pore walls have a prominent effect on gas diffusion. The perfectly ordered structure and ultrasmooth surface of organic matter facilitate the transport of methane in dry pores, even though its adsorption capability is much stronger than that of inorganic minerals. Moisture inhibits methane diffusion, but this adverse effect is more evident in organic pores because water migrates in the form of cluster, which acts as a piston and severely impedes methane diffusion. However, only an adsorbed water membrane is present at the surfaces of inorganic materials, leading to a weaker impact on methane diffusion. Remarkably, the ratios of the self-diffusion coefficients of the confined fluid and bulk phases at different temperatures collapse onto a master curve dependent solely on the slit aperture. Therefore, we propose a mathematical model to facilitate up-scaling studies from atomistic computations to macroscale measurements. The findings of this study provides a better understanding of hydrocarbon transport through shale formation, which is fundamentally important for reliably predicting production performance and optimizing hydraulic-fracturing design.Wang, T., Tian, S., Li, G., Sheng, M., 2018. Selective adsorption of supercritical carbon dioxide and methane binary mixture in shale kerogen nanopores. Journal of Natural Gas Science and Engineering 50, 181-188. adsorption of carbon dioxide and methane binary mixture in shale kerogen nanopores and the underlying mechanism significantly affect the supercritical carbon dioxide enhanced shale gas development project. In this study, we investigated the adsorption properties of carbon dioxide and methane in shale kerogen using grand canonical Monte Carlo (GCMC) method. Shale kerogen was fabricated based on Ungerer molecular model and its parameters were validated. The effects of temperature, pressure, mole fraction on the adsorption isotherms, average isosteric heat, potential energy distribution, and adsorption selectivity of binary mixture were discussed. The results show that the absolute adsorption capacity of methane in binary mixture decreases as temperature increases, but increases as mole fraction increases. Compared with methane, carbon dioxide is in lower energy absorption sites, which indicates the adsorption capacity of carbon dioxide in shale kerogen is stronger than that of methane. The adsorption selectivity of carbon dioxide over methane first decreases as pressure increases until pressure reaches critical pressure (7.38?MPa for carbon dioxide), and then stays at around 3.8 as pressure continues to rise. Adsorption selectivity and desorption quantity are used to reveal that the optimal injection depth for supercritical carbon dioxide enhanced shale gas development project is 1000–2500?m. This study will reveal the mechanism of the adsorption of methane in kerogen and provide some fundamental data for supercritical carbon dioxide enhanced shale gas development project.Wang, T., Tian, Z., Bengtson, P., Tunlid, A., Persson, P., 2017. Mineral surface-reactive metabolites secreted during fungal decomposition contribute to the formation of soil organic matter. Environmental Microbiology 19, 5117-5129. organic matter (SOM) constitutes the largest terrestrial C pool. An emerging, untested, view is that oxidation and depolymerization of SOM by microorganisms promote the formation of SOM-mineral associations that is critical for SOM stabilization. To test this hypothesis, we performed laboratory-scale experiments involving one ectomycorrhizal and one saprotrophic fungus that represent the two major functional groups of microbial decomposers in the boreal forest soils. Fungal decomposition enhanced the retention of SOM on goethite, partly because of oxidative modifications of organic matter (OM) by the fungi. Moreover, both fungi secreted substantial amounts (>?10% new biomass C) of aromatic metabolites that also contributed to an enhanced mineral retention of OM. Our study demonstrates that soil fungi can form mineral-stabilized SOM not only by oxidative conversion of the SOM but also by synthesizing mineral surface-reactive metabolites. Metabolites produced by fungal decomposers can play a yet overlooked role in the formation and stabilization of SOM.Wang, T., Yu, L., Xiu, J., Ma, Y., Lin, W., Ma, T., Wang, X., Wang, L., 2018. A mathematical model for microbial enhanced oil recovery using biopolymer-producing microorganism. Fuel 216, 589-595. on the analysis of bacterial behavior in different environments, a one-dimensional two-phase, five-component mathematical model was developed to simulate the biopolymer flooding process in porous media. The components of this mathematical model consist of oil, water, microorganisms, nutrients and metabolites, wherein the main metabolite is biopolymer. The equations of this numerical model take into account the decay and growth of microorganisms, nutrient consumption, biopolymer production, chemotaxis, convection–dispersion, water viscosity increment, adsorption, desorption. This newly presented model is validated with a classical simulator and a core flooding experiment. Variable microbial death rate in the presence or absence of nutrients is also considered as a factor, and a model of two death rates is used to modify the reaction kinetics equation accordingly. In this study, the sensitivity of the water viscosity and the death rate were analyzed through a simulator developed according to our mathematical model. We found that: (1) this simulator can simulate the microbial flooding process in reservoirs under different water viscosity functions; (2) microbial flooding has a positive effect on reducing water cut and increasing oil recovery of the reservoir when compared with water flooding; (3) the model of two death rates is better than that of single death rate for simulating the curve of water cut; (4) the higher the microbial death rate in the absence of nutrients, the more realistic the production of the metabolites.Wang, Y.-n., Tsang, Y.F., Wang, L., Fu, X., Hu, J., Li, H., Le, Y., 2018. Inhibitory effect of self-generated extracellular dissolved organic carbon on carbon dioxide fixation in sulfur-oxidizing bacteria during a chemoautotrophic cultivation process and its elimination. Bioresource Technology 252, 44-51. features of extracellular dissolved organic carbon (EDOC) generation in two typical aerobic sulfur-oxidizing bacteria (Thiobacillus thioparus DSM 505 and Halothiobacillus neapolitanus DSM 15147) and its impact on CO2 fixation during chemoautotrophic cultivation process were investigated. The results showed that EDOC accumulated in both strains during CO2 fixation process. Large molecular weight (MW) EDOC derived from cell lysis and decay was dominant during the entire process in DSM 505, whereas small MW EDOC accounted for a large proportion during initial and middle stages of DSM 15147 as its cytoskeleton synthesis rate did not keep up with CO2 assimilation rate. The self-generated EDOC feedback repressed cbb gene transcription and thus decreased total bacterial cell number and CO2 fixation yield in both strains, but DSM 505 was more sensitive to this inhibition effect. Moreover, the membrane bioreactor effectively decreased the EDOC/TOC ratio and improved carbon fixation yield of DSM 505.Wang, Y., Liu, H., Song, G., Hao, X., Zhu, D., Zhu, D., Ding, J., Yang, W., Yin, Y., 2017. Carbonate genesis and geological significance of shale hydrocarbon in lacustrine facies mud shale: a case study of source rocks in the upper submember of Member 4 and lower submember of Member 3 of Shahejie Formation, Dongying sag. Acta Petrolei Sinica 38, 1390-1400. genetic mechanism of carbonate in the deep lacustrine facies source rocks of the upper submember of Member 4 and lower submember of Member 3 of Shahejie Formation, Dongying sag is studied based on data involving cores, thin sections, whole-rock mineral components, elements and isotopes. It is considered that there are four kinds of carbonate developed in the deep lake, i.e., lenticular coarse crystalline, lamellar micro-fine crystalline, lamellar cryptocrystalline and massive cryptocrystalline. Among them, the lenticular coarse crystalline carbonate is the product of diagenetic recrystallization. The lamellar micro-fine crystalline carbonate and lamellar cryptocrystalline are generated by algal photosynthesis, i.e., CO2 is constantly extracted from water, thus leading to that the CO32- is increased in water and then interacts with Ca2+ carried by lake water surface. Saline water environment is favorable to the preservation of carbonate particles, where the carbonates are mostly shown as micro-fine crystalline with the lamellar distribution. In the brackish water environment, the water is deeper, and dissolution usually occurs to the carbonate crystalline beneath the carbonate compensation depth surface, where most lamellar cryptocrystalline are preserved. The massive cryptocrystalline carbonate is the product of the sedimentary carbonate in the shallow water migrating to deep water by gravity flow. The reserving property and compressibility of mud shale in the upper submember of Member 4 and lower submember of Member 3 of Shahejie Formation, Dongying sag are controlled by carbonate, providing important information for the restoration of paleo-lake sedimentary environment.Wang, Y., Rui, M., Lu, G., 2018. Recent applications of metal–organic frameworks in sample pretreatment. Journal of Separation Science 41, 180-194.–organic frameworks are promising materials in diverse analytical applications especially in sample pretreatment by virtue of their diverse structure topology, tunable pore size, permanent nanoscale porosity, high surface area, and good thermostability. According to hydrostability, metal–organic frameworks are divided into moisture-sensitive and water-stable types. In the actual applications, both kinds of metal–organic frameworks are usually engineered into hybrid composites containing magnetite, silicon dioxide, graphene, or directly carbonized to metal–organic frameworks derived carbon. These metal–organic frameworks based materials show good extraction performance to environmental pollutants. This review provides a critical overview of the applications of metal–organic frameworks and their composites in sample pretreatment modes, that is, solid-phase extraction, magnetic solid-phase extraction, micro-solid-phase extraction, solid-phase microextraction, and stir bar solid extraction.Wang, Z., Zheng, Y., Chen, F., Xie, X., Wu, S., Sun, L., 2018. Biomarker geochemistry of Eq34-10 cyclothem shale in Qianjiang Depression of the Jianghan salt lake facies Basin. Petroleum Science and Technology 36, 148-153. objective of this study is to provide biomarker geochemistry information on shale between sheet-like salts from Qianjiang Depression of the Jianghan salt lake facies Basin, and illustrate the depositional conditions, source organic matter input and maturation. 7 shale samples from Eq34-10 rhythmic were analysed with gas chromatography-mass spectrometry. The investigated biomarkers show that the shale oil are charactertized by an apperent odd-even preference of n-alkane, low Pr/Ph values and a high content of gammacerane and C30+ hopanes, maderate C21-/C21+ ratios, the high relative content of C27 5α(H), 14α(H), 17α(H)- steranes (20R), and an anomaly high C29 sterane ββ/(ββ + αα) value. These biomarker geochemistry characterizations suggested that the shale oils were derived from mixed aquatic organisms and land plants, and deposited in an anoxic and saline-hypersaline depositional environment.Watson, B.I., Williams, J.W., Russell, J.M., Jackson, S.T., Shane, L., Lowell, T.V., 2018. Temperature variations in the southern Great Lakes during the last deglaciation: Comparison between pollen and GDGT proxies. Quaternary Science Reviews 182, 78-92. understanding of deglacial climate history in the southern Great Lakes region of the United States is primarily based upon fossil pollen data, with few independent and multi-proxy climate reconstructions. Here we introduce a new, well-dated fossil pollen record from Stotzel-Leis, OH, and a new deglacial temperature record based on branched glycerol dialkyl glycerol tetraethers (brGDGTs) at Silver Lake, OH. We compare these new data to previously published records and to a regional stack of pollen-based temperature reconstructions from Stotzel-Leis, Silver Lake, and three other well-dated sites. The new and previously published pollen records at Stotzel-Leis are similar, but our new age model brings vegetation events into closer alignment with known climatic events such as the Younger Dryas (YD). brGDGT-inferred temperatures correlate strongly with pollen-based regional temperature reconstructions, with the strongest correlation obtained for a global soil-based brGDGT calibration (r2?=?0.88), lending confidence to the deglacial reconstructions and the use of brGDGT and regional pollen stacks as paleotemperature proxies in eastern North America. However, individual pollen records show large differences in timing, rates, and amplitudes of inferred temperature change, indicating caution with paleoclimatic inferences based on single-site pollen records. From 16.0 to 10.0ka, both proxies indicate that regional temperatures rose by ～10?°C, roughly double the ～5?°C estimates for the Northern Hemisphere reported in prior syntheses. Change-point analysis of the pollen stack shows accelerated warming at 14.0?±?1.2ka, cooling at 12.6?±?0.4ka, and warming from 11.6?±?0.5ka into the Holocene. The timing of B?lling-Aller?d (B-A) warming and YD onset in our records lag by ～300–500 years those reported in syntheses of temperature records from the northern mid-latitudes. This discrepancy is too large to be attributed to uncertainties in radiocarbon dating, and correlation between pollen and brGDGT temperature reconstructions rules out vegetation lags as a cause. However, the YD termination appears synchronous among the brGDGT record, regional pollen stack, and Northern Hemisphere stack. The cause of the larger and lagged temperature changes in the southern Great Lakes relative to Northern Hemisphere averages remains unclear, but may be due to the effects of continentality and ice sheet extent on regional climate evolution.Weber, K., Quicker, P., 2018. Properties of biochar. Fuel 217, 240-261. can be used in a large number of applications, ranging from heat and power production to soil amendment. The properties of carbonized biomass depend on the feedstock and the process conditions. Selection of suitable conditions to produce a char with the desired properties therefore requires knowledge of dependencies and influencing factors, both quantitatively and qualitatively. This paper reviews and summarizes the results from a large number of experiments on biochar production in order to give a general overview of the properties that can be achieved by feedstock selection and process design. Production processes include both torrefaction as well as slow pyrolysis at high temperatures. The data evaluation has shown that among all process conditions, the treatment temperature has by far the most dominant influence on all properties. Especially the rather narrow temperature range between 200 and 400?°C causes the most significant changes and is therefore very sensible to influences and possibly difficult to control.Webster, K.D., Drobniak, A., Etiope, G., Mastalerz, M., Sauer, P.E., Schimmelmann, A., 2018. Subterranean karst environments as a global sink for atmospheric methane. Earth and Planetary Science Letters 485, 9-18. air in subterranean karst cavities is often depleted in methane (CH4) relative to the atmosphere. Karst is considered a potential sink for the atmospheric greenhouse gas CH4 because its subsurface drainage networks and solution-enlarged fractures facilitate atmospheric exchange. Karst landscapes cover about 14% of earth's continental surface, but observations of CH4 concentrations in cave air are limited to localized studies in Gibraltar, Spain, Indiana (USA), Vietnam, Australia, and by incomplete isotopic data. To test if karst is acting as a global CH4 sink, we measured the CH4 concentrations, δ1CCH4, and δ2HCH4 values of cave air from 33 caves in the USA and three caves in New Zealand. We also measured CO2 concentrations, δ13CCO2, and radon (Rn) concentrations to support CH4 data interpretation by assessing cave air residence times and mixing processes. Among these caves, 35 exhibited subatmospheric CH4 concentrations in at least one location compared to their local atmospheric backgrounds. CH4 concentrations, δ13CCH4, and δ2HCH4 values suggest that microbial methanotrophy within caves is the primary CH4 consumption mechanism. Only 5 locations from 3 caves showed elevated CH4 concentrations compared to the atmospheric background and could be ascribed to local CH4 sources from sewage and outgassing swamp water. Several associated δ13CCH4 and δ2HCH4 values point to carbonate reduction and acetate fermentation as biochemical pathways of limited methanogenesis in karst environments and suggest that these pathways occur in the environment over large spatial scales. Our data show that karst environments function as a global CH4 sink.Wei, N., Xu, H., Sun, W., Zhao, J., Zhang, L., Fu, Q., Pang, W., Zheng, L., Lü, X., 2017. Migration laws of natural gas hydrate solid particles with different abundance in horizontal wells. Natural Gas Industry 37, 75-80. a horizontal well is drilled through the natural gas hydrate (NGH) strata with different abundance, the NGH bearing solid debris tends to lead to the deposit and adhesion of solid particles in the lateral sections and consequently cuttings carrying is not smooth. In this paper, the critical return rate model of drilling fluid in the case of cutting rolling (normal drilling) and saltation (pump off for sand settling) under NGH adhesion in the laterals was established according to the force and migration laws of cuttings under the condition of multiphase flow in a horizontal well and the particle migration theory. Then, numerical simulation was conducted and the influential factors and migration laws of cuttings starting in the case of normal drilling and pump off were analyzed. And the following results were obtained. First, the critical starting flow rate decreases with the rise of NGH abundance and it is higher when the NGH adhesion is taken into account. Besides, the higher the NGH abundance, the greater the effect of NGH adhesion. Second, the critical starting flow rate increases with the rise of drilling cuttings particle size when the NGH abundance is less than 85%; and it decreases with the rise of drilling cuttings particle size when the NGH abundance is more than 85%. Third, the critical starting flow rate decreases with the rise of drilling fluid density and viscosity. And fourth, under the same conditions, the critical return rate for saltation is about 1.28 times that for rolling. It is suggested that the rolling model should be adopted for the normal drilling while the saltation model for the recycle after pump-off sand settling. The research results are of great significance to the optimization of NGH drilling parameters and the reduction of drilling safety risks.Wei, P., Pu, W., Sun, L., Pu, Y., Wang, S., Fang, Z., 2018. Oil recovery enhancement in low permeable and severe heterogeneous oil reservoirs via gas and foam flooding. Journal of Petroleum Science and Engineering 163, 340-348. view of the co-existence of the low permeability and severe heterogeneity, the effective tertiary technique for the enhanced oil recovery is still in progress. In this study, on the base of the simulation of SH reservoir conditions, we conducted the trinal-core flooding experiments about gas flooding (N2 and CO2), WAG (N2 and CO2) injection and foam flooding (N2 and CO2). Combined with some static investigations, we found that CO2 flooding achieves additional oil recovery due to the development of near-miscibility and CO2 extraction, and the WAG injection can relieve the gas channeling associated with gas flooding. As for the foam flooding, CO2 foam has the advantage of oil displacement in a higher permeability layer and nitrogen foam is capable of diverting the flow to the least permeability zone in the strong heterogeneity formation and sharply increasing the oil recovery. It is also found that, in the pilot test of SH reservoir, nitrogen foam flooding is qualified for flow adjustment, water controlling and oil recovery enhancement in the low permeable and severe heterogeneous reservoir.Wei, Z., Wang, Y., Wang, G., Sun, Z., Zhang, T., Xu, L., Ma, X., He, W., 2018. Paleoenvironmental conditions of organic-rich Upper Permian Dalong Formation shale in the Sichuan Basin, southwestern China. Marine and Petroleum Geology 91, 152-162. geochemical and trace element analysis of a suite of 33 samples collected from the Shangsi section of the Upper Permian Dalong Formation, located near Guangyuan in the northwestern Sichuan Basin, have been used to better understand the marine depositional environment of its shale lithofacies. A 15?m-thick black shale interval near the middle of the formation is enriched in total organic carbon (TOC?=?1.1–14.4%, mean?=?6.4%). The n-alkane, terpane and sterane biomarker distributions of the shale suggest that its organic matter is of predominantly marine algal origin. Pr/Ph, Pr/n-C17, Ph/n-C18 and gammacerane/C30 hopane ratios demonstrate that reducing conditions prevailed during its deposition. This interpretation is supported by the redox-sensitive abundance of Mo and the trace element redox ratios Ni/Co, V/Cr, U/Th and V/(V + Ni), all of which indicate deposition in a euxinic/anoxic setting. The Mo-TOC relationship in the Dalong shales plots mid-way between those of sediments in the present-day Saanich Inlet and Cariaco Basin, suggesting a moderately restricted depocentre. However, the δ13Corg values of these shales reveal that their organic matter is isotopically much lighter than that found in modern euxinic sediments, implying extremely anoxic bottom waters and a slow-down of oceanic circulation during the Late Permian.Wenk, C.B., Wing, B.A., Halevy, I., 2018. Electron carriers in microbial sulfate reduction inferred from experimental and environmental sulfur isotope fractionations. The Isme Journal 12, 495-507. sulfate reduction (DSR) has been a key process influencing the global carbon cycle, atmospheric composition and climate for much of Earth’s history, yet the energy metabolism of sulfate-reducing microbes remains poorly understood. Many organisms, particularly sulfate reducers, live in low-energy environments and metabolize at very low rates, requiring specific physiological adaptations. We identify one such potential adaptation—the electron carriers selected for survival under energy-limited conditions. Employing a quantitative biochemical-isotopic model, we find that the large S isotope fractionations (>55‰) observed in a wide range of natural environments and culture experiments at low respiration rates are only possible when the standard-state Gibbs free energy (ΔG′°) of all steps during DSR is more positive than ?10?kJ?mol?1. This implies that at low respiration rates, only electron carriers with modestly negative reduction potentials are involved, such as menaquinone, rubredoxin, rubrerythrin or some flavodoxins. Furthermore, the constraints from S isotope fractionation imply that ferredoxins with a strongly negative reduction potential cannot be the direct electron donor to S intermediates at low respiration rates. Although most sulfate reducers have the genetic potential to express a variety of electron carriers, our results suggest that a key physiological adaptation of sulfate reducers to low-energy environments is to use electron carriers with modestly negative reduction potentials.White, J.C., Williams, G., Chadwick, A., Furre, A.-K., Ki?r, A., 2018. Sleipner: The ongoing challenge to determine the thickness of a thin CO2 layer. International Journal of Greenhouse Gas Control 69, 81-95. is the world’s longest-running CO2 storage project. Since injection commenced in 1996 almost 1 million tonnes per year have been injected with more than 16 million tonnes successfully stored by 2016. A comprehensive programme of time-lapse 3D seismic monitoring has been carried out, providing unrivalled imaging of the CO2 plume as it has developed and migrated in the storage reservoir. The plume has a tiered structure comprising a number of thin layers of CO2 of the order of a few metres thick. Determination of accurate layer morphology is key to understanding details of fluid flow processes in the plume which is necessary to demonstrate future storage security. Migration of the topmost layer of CO2, trapped directly beneath the reservoir topseal, determines the longer-term storage performance at Sleipner and here we focus on mapping its travel-time (temporal) thickness. Our primary approach is to use spectral analysis to determine tuning frequencies across the layer and from these to derive temporal thickness. These range from zero at the layer edges to around 16?ms in the central parts of the layer and correlate closely with the base topseal topography. Uniquely, results are then compared with those from other published approaches including amplitude analysis, temporal shifts and direct measurement of temporal spacing on the latest high-resolution seismic data. It is clear that the spectral methods provide robust determination of temporal thickness well below the tuning thickness, and, taken in suitable combination with the various other methods, can provide reliable determination of temporal thickness across the range from close to zero to well above the tuning thickness where explicit layer resolution is obtained. Application of an appropriate layer velocity allows true layer thicknesses to be determined and layer volumetrics to be estimated.Wiczling, P., Daghir-Wojtkowiak, E., Yumba Mpanga, A., Szczesny, D., Kaliszan, R., Markuszewski, M.J., 2017. How to model temporal changes in nontargeted metabolomics study? A Bayesian multilevel perspective. Journal of Separation Science 40, 4667-4676. of time series data addresses the question on mechanisms underlying normal physiology and its alteration under pathological conditions. However, adding time variable to high-dimension, collinear, noisy data is a challenge in terms of mining and analysis. Here, we used Bayesian multilevel modeling for time series metabolomics in vivo study to model different levels of random effects occurring as a consequence of hierarchical data structure. A multilevel linear model assuming different treatment effects with double exponential prior, considering major sources of variability and robustness to outliers was proposed and tested in terms of performance. The treatment effect for each metabolite was close to zero suggesting small if any effect of cancer on metabolomics profile change. The average difference in 964 signals for all metabolites varied by a factor ranging from 0.8 to 1.25. The inter-rat variability (expressed as a coefficient of variation) ranged from 3–30% across all metabolites with median around 10%, whereas the inter-occasion variability ranged from 0–30% with a median around 5%. Approximately 36% of metabolites contained outlying data points. The complex correlation structure between metabolite signals was revealed. We conclude that kinetics of metabolites can be modeled using tools accepted in pharmacokinetics type of studies.Wiesheu, A.C., Brejcha, R., Mueller, C.W., K?gel-Knabner, I., Elsner, M., Niessner, R., Ivleva, N.P., 2018. Stable-isotope Raman microspectroscopy for the analysis of soil organic matter. Analytical and Bioanalytical Chemistry 410, 923-931. examined the potential of stable-isotope Raman microspectroscopy (SIRM) for the evaluation of differently enriched 13C-labeled humic acids as model substances for soil organic matter (SOM). The SOM itself can be linked to the soil water holding capacity. Therefore, artificial humic acids (HA) with known isotopic compositions were synthesized and analyzed by means of SIRM. By performing a pregraphitization, a suitable analysis method was developed to cope with the high fluorescence background. Results were verified against isotope ratio mass spectrometry (IRMS). The limit of quantification was 2.1 × 10?1 13C/C tot for the total region and 3.2 × 10?2 13C/C tot for a linear correlation up to 0.25 13C/C tot. Complementary nanoscale secondary ion mass spectrometry (NanoSIMS) analysis indicated small-scale heterogeneity within the dry sample material, even though—owing to sample topography and occurring matrix effects—obtained values deviated in magnitude from those of IRMS and SIRM. Our study shows that SIRM is well-suited for the analysis of stable isotope-labeled HA. This method requires no specific sample preparation and can provide information with a spatial resolution in the micrometer range.Wiest, L.A., Lukens, W.E., Peppe, D.J., Driese, S.G., Tubbs, J., 2018. Terrestrial evidence for the Lilliput effect across the Cretaceous-Paleogene (K-Pg) boundary. Palaeogeography, Palaeoclimatology, Palaeoecology 491, 161-169. research has demonstrated that the Lilliput effect (reduction of body size in biota associated with the aftermath of mass extinctions) affected all trophic levels in the marine realm following the Cretaceous-Paleogene (K-Pg) event. However, it is unclear if this size change was strictly a marine signal, or a global phenomenon that also affected continental ecosystems. Herein we present the results of an ichnological proxy for body size of soil-dwelling insects across the K-Pg boundary in Big Bend National Park, Texas, U.S.A. Quantitative efforts focused on Naktodemasis bowni, which are characterized as unbranching burrows composed of ellipsoidal packets of backfill menisci. These traces were likely produced by beetle larvae or cicada nymphs based on previous comparison with structures generated in modern soils and laboratory experiments. As an approximation for the body size of the subterranean insects, this dataset indicates that a smaller N. bowni diameter (DN) is statistically correlated (α < 0.05) with several edaphic factors including poor soil drainage and weak soil development (Entisols). Additionally, the DN in strata immediately superjacent to the highest Cretaceous-specific taxa is smaller by 23% (5.6 ± 1.8 mm) in comparison to DN within the subjacent Cretaceous interval (7.3 ± 2.7 mm). This abrupt shift occurs in a well-drained Inceptisol, and cannot be attributed to facies changes, drainage, or paleosol maturity. Furthermore, a reduced DN (6.6 ± 2.3 mm) persists above this anomalous shift for at least 20 stratigraphic meters within chron 29r. The cause for this negative response in body size within soil-dwelling biota may be attributed to plant-community shifts in taxonomic composition and ecological strategies, which would have caused fundamental alterations to the diet of the herbivorous, subterranean insects. This study provides empirical evidence that the Lilliput effect was not restricted to marine environments during the aftermath of the K-Pg event.Willis, C.E., Kirk, J.L., St. Louis, V.L., Lehnherr, I., Ariya, P.A., Rangel-Alvarado, R.B., 2018. Sources of methylmercury to snowpacks of the Alberta oil sands region: A study of in situ methylation and particulates. Environmental Science & Technology 52, 531-540. in the Alberta Oil Sands Region (AOSR) of Canada contain elevated loadings of methylmercury (MeHg; a neurotoxin that biomagnifies through foodwebs) due to oil sands related activities. At sites ranging from 0 to 134 km from the major AOSR upgrading facilities, we examined sources of MeHg by quantifying potential rates of MeHg production in snowpacks and melted snow using mercury stable isotope tracer experiments, as well as quantifying concentrations of MeHg on particles in snowpacks (pMeHg). At four sites, methylation rate constants were low in snowpacks (km = 0.001–0.004 d–1) and nondetectable in melted snow, except at one site (km = 0.0007 d–1). The ratio of methylation to demethylation varied between 0.3 and 1.5, suggesting that the two processes are in balance and that in situ production is unlikely an important net source of MeHg to AOSR snowpacks. pMeHg concentrations increased linearly with distance from the upgraders (R2 = 0.71, p < 0.0001); however, snowpack total particle and pMeHg loadings decreased exponentially over this same distance (R2 = 0.49, p = 0.0002; R2 = 0.56, p < 0.0001). Thus, at near-field sites, total MeHg loadings in snowpacks were high due to high particle loadings, even though particles originating from industrial activities were not MeHg rich compared to those at remote sites. More research is required to identify the industrial sources of snowpack particles in the AOSR.Winkler, C.K., Faber, K., Hall, M., 2018. Biocatalytic reduction of activated C=C-bonds and beyond: emerging trends. Current Opinion in Chemical Biology 43, 97-105. biocatalytic reduction of activated C=C-bonds is dominated by ene-reductases from the Old Yellow Enzyme family, which gained broad practical use owing to exquisite stereoselectivity combined with wide substrate scope. Protein diversity is fostered by mining distinct protein classes and by implementing protein engineering techniques. Recent efforts are focusing on expanding the chemical complexity of the product portfolio, either through substrate functionalization or design of multi-step reactions. This review also highlights unusual chemistries catalyzed by ene-reductases and presents emerging methodologies developed to bypass the need of natural nicotinamide cofactors.Worden, R.H., Bukar, M., Shell, P., 2018. The effect of oil emplacement on quartz cementation in a deeply buried sandstone reservoir. American Association of Petroleum Geologists Bulletin 102, 49-75. is an important, porosity-occluding cement in sandstone reservoirs that have been subjected to elevated temperature (>80°C to 100°C) for a substantial period of time. The effect of oil emplacement on quartz cementation in reservoir sandstones is controversial; some studies have concluded that early oil emplacement can inhibit quartz cementation, leading to the preservation of porosity, whereas other studies have concluded that quartz cementation appears largely unaffected by oil emplacement. Here we have studied shallow marine, Upper Jurassic sandstones from Ula field, Norwegian North Sea, with reservoir temperatures of approximately 150°C, to determine whether oil emplacement had a significant impact on diagenesis with particular attention to quartz cementation. Following sedimentological description of cores, samples above and below the oil–water contact have been collected, adjacent to core-analysis plug points. These samples then underwent a series of studies, including petrographic point counting with a transmitted light microscope, scanning electron microscopy (SEM), backscattered electron microscopy, SEM-cathodoluminescence microscopy, and fluid-inclusion studies. These data were integrated with routine core-analysis and petrophysical log data. Density and resistivity log data have been used to determine the precise oil saturation of each sample studied. The distributions of all potential controls on porosity and permeability, such as grain size, sorting, matrix clay content, and degree of bioturbation, the presence of grain coatings and dolomite cement, and the amount of quartz cement, have been assessed. The presence of primary oil inclusions within quartz cement shows that oil ingress into the Ula reservoir commenced prior to the onset of quartz cementation. Very fine–grained, matrix-rich, bioturbated, microquartz-cemented sandstones have uniformly low quartz-cement contents irrespective of oil saturation. Medium-grained, graded, matrix-poor, microquartz-poor sandstones have quartz cement ranging from 1% to greater than 17%, associated with core porosities of approximately 22% and 7%, respectively. Higher oil saturations equate to higher porosities and permeabilities in the medium-grained, graded, matrix-poor, microquartz-poor sandstones, which cannot be explained by any control other than the amount of quartz cement as a function of pore fluid type. Oil emplacement therefore appears to have inhibited quartz cementation at high oil saturations and can be viewed as an important control on reservoir quality. The significance of this study is that the presence of oil in a sandstone reservoir at the time that quartz cement was growing can have a considerable impact on reservoir quality. Models that seek to predict quartz cement and reservoir quality in sandstones need to account for the timing of oil emplacement compared with other diagenetic processes.Wu, X., Liu, Q., Liu, G., Wang, P., Li, H., Meng, Q., Chen, Y., Zeng, H., 2017. Geochemical characteristics and genetic types of natural gas in the Xinchang gas field, Sichuan Basin, SW China. Acta Geologica Sinica - English Edition 91, 2200-2213. molecular compositions and stable carbon and hydrogen isotopic compositions of natural gas from the Xinchang gas field in the Sichuan Basin were investigated to determine the genetic types. The natural gas is mainly composed of methane (88.99%–98.01%), and the dryness coefficient varies between 0.908 and 0.997. The gas generally displays positive alkane carbon and hydrogen isotopic series. The geochemical characteristics and gas-source correlation indicate that the gases stored in the 5th member of the Upper Triassic Xujiahe Formation are coal-type gases which are derived from source rocks in the stratum itself. The gases reservoired in the 4th member of the Xujiahe Formation and Jurassic strata in the Xinchang gas field are also coal-type gases that are derived from source rocks in the 3rd and 4th members of the Xujiahe Formation. The gases reservoired in the 2nd member of the Upper Triassic Xujiahe Formation are mainly coal-type gases with small amounts of oil-type gas that is derived from source rocks in the stratum itself. This is accompanied by a small amount of contribution brought by source rocks in the Upper Triassic Ma'antang and Xiaotangzi formations. The gases reservoired in the 4th member of the Middle Triassic Leikoupo Formation are oil-type gases and are believed to be derived from the secondary cracking of oil which is most likely to be generated from the Upper Permian source rocks.Wu, X., Xing, L., Zhang, T., Xiang, R., 2018. Mid–late Holocene changes in sedimentary organic matter on the inner shelf of the East China Sea. Journal of Asian Earth Sciences 154, 248-254. seas are important transitional zones for the delivery of terrestrial organic matter (TOM) from land to the open sea, and they play an important role in the carbon cycle. Tracing the source of sedimentary organic matter (SOM) deposited in marginal seas is fundamental to our understanding of the dispersal, degradation, migration, and conversion of organic matter. This paper presents high-resolution records of bulk organic matter and biomarker proxies from Core T08 that was recovered from the inner shelf of the East China Sea (ECS), and aims to identify the contributions of marine and terrestrial organic matter over the past 3725?yrs. Total organic carbon (TOC) values were low (0.50%) and showed no significant change between 3725 and 1800?yr BP (Period I), and increased continuously from 0.40% to 0.86% after 1800?yr BP (Period II: 1800–750?yr BP; Period III: 750?yr BP–present). The TMBR′ (ratio of terrestrial to marine biomarkers) and δ13CTOC (δ13C of TOC) values showed steady TOM contribution during Period I and higher TOM contribution driven by the increased Changjiang River (CR)-derived TOM under strong East Asian Summer Monsoon (EASM) and El Ni?o during Period II. During Period III, the increase in marine organic matter (MOM) contribution was indicated by the TMBR′, and this was caused by enhanced marine productivity related to intensified vertical mixture that was driven by the strengthened East Asian Winter Monsoon (EAWM). δ13CTOC shows a contrary trend to the TMBR′ during Period III, probably influenced by variations in the C3 vegetation type during this period. Spectral analysis of the TMBR′ series for the last 1200 yrs shows cycles with periods of 119, 75–85, and 54 yrs, confirming that climate-related events influenced the variation in SOM under the modulation of solar activity and solar irradiance at the centennial scale.Wu, Y., Zhang, Z., Sun, L., Li, Y., He, C., Ji, L., Su, L., Zhang, D., 2018. Hydrocarbon generation and potential in continental organic-rich shales at the highly-mature stage, as determined by hydrous pyrolysis under supercritical conditions. International Journal of Coal Geology 187, 83-93. pyrolysis experiments were conducted to assess hydrocarbon generation and potential in three continental organic-rich shales at the highly-mature stage. The results of this study have important implications for deep petroleum exploration in China. The calcareous shale dominated by type-I kerogen reached its peak oil generation at a vitrinite reflectance (VR) of 1.5 %Ro, and entered the major stage of gas generation at a VR ranging from 1.50 to 2.44 %Ro. The high HI, low S2 and low atomic H/C ratio revealed that the calcareous shale has some potential for hydrocarbon generation at a VR greater than 2.44 %Ro. The mudstone with type-II kerogen reached its peak oil generation at a VR of 2.5 %Ro. The high atomic H/C ratio, but low HI and S2 indicated that mudstone may retain some hydrocarbon potential. The carbonaceous mudstone dominated by type-III kerogen had still not reached its peak of hydrocarbon generation at a VR of 3.12 %Ro. The low dryness of the gaseous hydrocarbon yields shows that the carbonaceous mudstone was still in the primary gas generation stage. The high values of S2 and atomic H/C fraction, but low HI, revealed that the carbonaceous mudstone may retain a large hydrocarbon generation potential at higher maturity stages. Our results suggested that the continental type-I and -II kerogen may have potential for shale gas and deep petroleum generation, while the continental type-III kerogen retained good potential for yielding deep natural gas.Wu, Z., Liu, H., Wang, X., 2018. 3D experimental investigation on enhanced oil recovery by flue gas coupled with steam in thick oil reservoirs. Energy & Fuels 32, 279-286. gas mainly consists of N2 and CO2 and is applied in petroleum industry as a kind of displacement agents. In this paper, flue gas was introduced into the thermal recovery process of thick heavy oil reservoir. First, the PVT experiments under different conditions were carried out to research the dissolution of flue gas in crude oil. Then, a series of 3D physical simulations were performed to study the oil displacement characteristics of flue gas coupled with steam flooding in a thick reservoir with consideration of the important production parameters including oil production, oil-to-steam ratio (OSR), water cut, and oil recovery in both the steam-flooding process and the process of steam flooding coupled with flue gas. Finally, the enhanced oil recovery mechanisms of flue gas coupled with steam flooding for thick heavy oil reservoirs were summarized on the basis of the experimental results. This study provided a reference that the reasonable use of flue gas can improve recovery of thick heavy oil reservoirs while reducing greenhouse gas emissions.Xiao, L., Schultz, Z.D., 2018. Spectroscopic imaging at the nanoscale: Technologies and recent applications. Analytical Chemistry 90, 440-458. in technology now enable infrared and Raman vibrational spectroscopic imaging with resolution on the molecular scale. A number of techniques have emerged that provide spectroscopic imaging with nanometer scale resolution including tip-enhanced Raman scattering (TERS), infrared scattering-type scanning near-field optical microscopy (IR s-SNOM), atomic force microscopy infrared (AFM-IR), and photo-induced force microscopy (PiFM). In this review, we profile recent advances in nanoscale spectroscopic imaging, discussing differences in the methods, highlighting recent technical advances, and reporting applications with each approach. Since the first demonstrations showing that spectroscopy can inform about the chemical composition of images in a microscope, researchers have investigated advances in instrumentation to improve the sensitivity, spatial resolution, and specificity of these spectroscopic imaging techniques. In particular, the chemical rich signals of vibrational spectroscopies, both infrared and Raman, have attracted considerable interest. Applications of infrared and Raman spectroscopic imaging span diverse applications from biomedical diagnostics to forensics, cultural heritage, and materials characterization. There have been a number of recent advances using vibrational signals as markers for selective imaging. For example, a recent study showed the vibrational signal of a triple bond made an effective tag for more sensitive stimulated Raman imaging. Other examples include the development of surface enhanced Raman tags, where a specific enhanced signal marks an analyte of interest. We limit our review to reports that measure a spectrum to discriminate and identify molecular components, or changes in molecular components, using the detected spectroscopic signals. Improvements in hardware have been particularly influential in advancing infrared and Raman imaging. In particular, the past few years have seen the commercialization of a number of techniques, which combine vibrational spectroscopy with scanning probe microscopes to provide spectroscopic imaging on nanometer length scales. These techniques, including TERS, IR s-SNOM, AFM-IR, and PiFM, are providing unprecedented spatial resolution and chemical contrast. In many ways these techniques appear quite similar and the differences between the techniques can be difficult to discern. In all of these methodologies, an optical response (e.g., absorption, scattering, induced dipole) is combined with a scanning probe microscope to provide increased spatial resolution and increased sensitivity. Many of these techniques are enabled by advances in instrumentation and suggest increased facility obtaining experimental results by nonexperts.Xiao, W., Jones, A.M., Li, X., Collins, R.N., Waite, T.D., 2018. Effect of Shewanella oneidensis on the kinetics of Fe(II)-catalyzed transformation of ferrihydrite to crystalline iron oxides. Environmental Science & Technology 52, 114-123. (oxyhydr)oxides are widespread in natural and engineered systems, potent adsorbents of contaminants and a source of energy for iron-reducing bacteria. Microbial reduction of iron (oxyhydr)oxides results in the formation of Fe(II) which can induce the transformation of these iron minerals, typically from less crystalline to more crystalline forms, affecting the biogeochemical cycling of iron and the behavior of any species adsorbed to the iron (oxyhydr)oxides. Factors influencing the transformation rate of the poorly crystalline iron (oxyhydr)oxide, ferrihydrite, to more crystalline forms in the presence of the iron reducing bacterium Shewanella oneidensis MR-1 are investigated under controlled laboratory conditions in this work. In particular, the amount of Fe(II) produced increased the transformation rate while increasing concentrations of the electron donor, lactate, decreased the rate. Using kinetic parameters determined from abiotic controls, the results of transformation experiments in the presence of Shewanella oneidensis were modeled with this exercise revealing that less goethite and more lepidocrocite formed than expected. Conversely, studies using the Shewanella exudate only, containing biogenic Fe(II), displayed rates of transformation that were satisfactorily modeled using these abiotic control kinetic parameters. This result suggests that the physical presence of the microbes is pivotal to the reduction in ferrihydrite transformation rate observed in the biotic experiments relative to the analogous abiotic controls.Xie, J., 2017. Rapid shale gas development accelerated by the progress in key technologies: A case study of the Changning–Weiyuan national shale gas demonstration zone Natural Gas Industry 37, 1-10. gas resources in the Lower Silurian Longmaxi ,southern Sichuan Basin are huge, where, the geological setting, unlike that in North America, is quite complicated and ground surface infrastructure is poor. Therefore, adaptable key technologies will be essential to achieve commercial exploitation of shale gas there. In the case study of the Changning–Weiyuan national shale gas demonstration zone, six series of key techniques were summarized in comprehensive geological evaluation, development optimization, fast and superior drilling of horizontal wells, horizontal-well volumetric fracturing, cluster-well and factory-like operation in well blocks, and highly-efficient and clean exploitation. The above techniques were applied in this field after three rounds of adjustment and optimization, the resulted production rates of shale gas wells were getting higher and higher and the single-well estimated ultimate recovery (EUR) was also rising. Compared with that in the first round, the average EUR of wells in the third round was increased by 128%. In conclusion, the application practices prove that the above series of key techniques with adaptation and flexibility provide a robust technical support for the rapid output of shale gas production in South Sichuan Basin.Xie, Z., Wei, G., Zhang, J., Yang, W., Zhang, L., Wang, Z., Zhao, J., 2017. Characteristics of source rocks of the Datangpo Fm, Nanhua System, at the southeastern margin of Sichuan Basin and their significance to oil and gas exploration. Natural Gas Industry B 4, 405-414. recent years, much attention has been paid to the development environment, biogenetic compositions and hydrocarbon generation characteristics of ancient source rocks in the deep strata of the Sichuan Basin because oil and gas exploration extends continuously to the deep and ultra-deep strata and a giant gas field with the explored reserves of more than 1 × 1012 m3 was discovered in the Middle and Upper Proterozoic–Lower Paleozoic strata in the stable inherited paleo-uplift of the central Sichuan Basin. Based on the previous geological research results, outcrop section of the Datangpo Fm, Nanhua System, at the southeastern margin of the Sichuan Basin was observed and the samples taken from the source rocks were tested and analyzed in terms of their organic geochemistry and organic petrology. It is shown that high-quality black shale source rocks of the Datangpo Fm are developed in the tensional background at the southeastern margin of the Sichuan Basin between two glacial ages, i.e., Gucheng and Nantuo ages in the Nanhua Period. Their thickness is 16–180 m and mineral compositions are mainly clay minerals and clastic quartz. Besides, shale in the Datangpo Fm is of high-quality sapropel type source rock with high abundance at an over-mature stage, and it is characterized by low pristane/phytane ratios (0.32–0.83), low gammacerane abundance, high-abundance tricyclic terpane and higher-content C27 and C29 gonane, indicating that biogenetic compositions are mainly algae and microbes in a strong reducing environment with low salinity. It is concluded that the Datangpo Fm source rocks may be developed in the rift of Nanhua System in central Sichuan Basin. Paleo-uplifts and paleo-slopes before the Caledonian are the favorable locations for the accumulation of dispersed liquid hydrocarbons and paleo-reservoirs derived from the Datangpo Fm source rocks. In addition, scale accumulation zones of dispersed organic matter cracking gas and paleo-reservoirs originated from the Datangpo Fm source rocks may be discovered in the stable area inside the Sichuan Basin.Xiong, B., Miller, Z., Roman-White, S., Tasker, T., Farina, B., Piechowicz, B., Burgos, W.D., Joshi, P., Zhu, L., Gorski, C.A., Zydney, A.L., Kumar, M., 2017. Chemical degradation of polyacrylamide during hydraulic fracturing. Environmental Science & Technology 52, 327-336. (PAM) based friction reducers are a primary ingredient of slickwater hydraulic fracturing fluids. Little is known regarding the fate of these polymers under downhole conditions, which could have important environmental impacts including decisions on strategies for reuse or treatment of flowback water. The objective of this study was to evaluate the chemical degradation of high molecular weight PAM, including the effects of shale, oxygen, temperature, pressure, and salinity. Data were obtained with a slickwater fracturing fluid exposed to both a shale sample collected from a Marcellus outcrop and to Marcellus core samples at high pressures/temperatures (HPT) simulating downhole conditions. Based on size exclusion chromatography analyses, the peak molecular weight of the PAM was reduced by 2 orders of magnitude, from roughly 10 MDa to 200 kDa under typical HPT fracturing conditions. The rate of degradation was independent of pressure and salinity but increased significantly at high temperatures and in the presence of oxygen dissolved in fracturing fluids. Results were consistent with a free radical chain scission mechanism, supported by measurements of sub-μM hydroxyl radical concentrations. The shale sample adsorbed some PAM (～30%), but importantly it catalyzed the chemical degradation of PAM, likely due to dissolution of Fe2+ at low pH. These results provide the first evidence of radical-induced degradation of PAM under HPT hydraulic fracturing conditions without additional oxidative breaker.Xu, C., Wang, B., Pu, Y., Tao, J., Zhang, T., 2018. Techniques for the analysis of pentacyclic triterpenoids in medicinal plants. Journal of Separation Science 41, 6-19. are a major class of chemical compounds found in natural plants and can be categorized into acyclic triterpenoids, monocyclic triterpenoids, tricyclic triterpenoids, tetracyclic triterpenoids, and pentacyclic triterpenoids. Among them, pentacyclic triterpenoids have gained more extensive attention due to their biological activities, including anti-inflammation, antibacterial, antioxidation, antitumor, anti-HIV, hepatoprotection, and immunological adjuvant properties. In this review, we summarize the extraction and analytical methods for pentacyclic triterpenoids, where more than 56 triterpenes from 49 kinds of plants were involved. The analysis methods include gas chromatography, liquid chromatography, capillary electrophoresis, thin-layer chromatography, supercritical fluid chromatography, NMR spectroscopy, and X-ray spectroscopy. This review provides valuable reference for the determination of pentacyclic triterpenoids in medicinal plants.Xu, Q., Ma, Y., Liu, B., Song, X., Li, L., Xu, J., Su, J., Wu, K., Chen, Z., 2018. Fractal characteristics of lacustrine tight carbonate nanoscale reservoirs. Energy & Fuels 32, 107-118. complexity and heterogeneity of pore structure greatly affect gas-liquid accumulation and transport, and the fractal theory has been proven to be an effective approach for studying nanoscale reservoirs in shale, coal, and tight sandstones. However, researches on fractal characteristics and control mechanisms for the lacustrine tight carbonate have received little attention. Lacustrine tight carbonate samples from the Jurassic Da’anzhai Member in the Sichuan Basin in China were systematically investigated focusing on the fractal characteristics and control mechanisms of storage spaces, minerals, diagenesis, and paleoenvironments. The fractal dimensions can be separated into two different and valid parts including D1 (2.515–2.785, average 2.652) and D2 (2.424–2.562, average 2.485), and the correlation between them is negative rather than positive. The average pore diameters exhibit a positive correlation with D1 and a negative correlation with D2, and the storage space is positively correlated with D2 and negatively correlated with D1. Terrigenous minerals (e.g., quartz and clay) exhibit a positive correlation with D2 and a negative correlation with D1, whereas the effects of authigenic CaCO3 minerals (e.g., calcite and aragonite) are exactly opposite to those of terrigenous minerals, which is due to the diagenesis and the own characteristics of minerals. CaCO3 minerals can effectively change pore structures and fill the storage spaces (>5 nm) by cementation, compaction, pressure-solution, recrystallization, and replacement, whereas terrigenous minerals have developed irregular intraparticle pores, interparticle pores, and microcracks. The low salinity and the humid (rainy) paleoclimate are favorable for the formation of terrigenous minerals (elements), whereas they are harmful to the formation of authigenic minerals (elements), which increases D2 and reduces D1. Additionally, paleoredox has a weak influence on the fractal dimensions.Xu, W., Ruhl, M., Jenkyns, H.C., Leng, M.J., Huggett, J.M., Minisini, D., Ullmann, C.V., Riding, J.B., Weijers, J.W.H., Storm, M.S., Percival, L.M.E., Tosca, N.J., Idiz, E.F., Tegelaar, E.W., Hesselbo, S.P., 2018. Evolution of the Toarcian (Early Jurassic) carbon-cycle and global climatic controls on local sedimentary processes (Cardigan Bay Basin, UK). Earth and Planetary Science Letters 484, 396-411. late Early Jurassic Toarcian Stage represents the warmest interval of the Jurassic Period, with an abrupt rise in global temperatures of up to ～7?°C in mid-latitudes at the onset of the early Toarcian Oceanic Anoxic Event (T-OAE; ～183 Ma). The T-OAE, which has been extensively studied in marine and continental successions from both hemispheres, was marked by the widespread expansion of anoxic and euxinic waters, geographically extensive deposition of organic-rich black shales, and climatic and environmental perturbations. Climatic and environmental processes following the T-OAE are, however, poorly known, largely due to a lack of study of stratigraphically well-constrained and complete sedimentary archives. Here, we present integrated geochemical and physical proxy data (high-resolution carbon-isotope data (δ13C), bulk and molecular organic geochemistry, inorganic petrology, mineral characterisation, and major- and trace-element concentrations) from the biostratigraphically complete and expanded entire Toarcian succession in the Llanbedr (Mochras Farm) Borehole, Cardigan Bay Basin, Wales, UK. With these data, we (1) construct the first high-resolution biostratigraphically calibrated chemostratigraphic reference record for nearly the complete Toarcian Stage, (2) establish palaeoceanographic and depositional conditions in the Cardigan Bay Basin, (3) show that the T-OAE in the hemipelagic Cardigan Bay Basin was marked by the occurrence of gravity-flow deposits that were likely linked to globally enhanced sediment fluxes to continental margins and deeper marine (shelf) basins, and (4) explore how early Toarcian (tenuicostatum and serpentinum zones) siderite formation in the Cardigan Bay Basin may have been linked to low global oceanic sulphate concentrations and elevated supply of iron (Fe) from the hinterland, in response to climatically induced changes in hydrological cycling, global weathering rates and large-scale sulphide and evaporite deposition.Yan, G., Wei, C., Song, Y., Luo, J., Zhang, J., 2018. Quantitative description of shale pore structure using image analysis and determination of controls on shape, size and orientation complexity. Arabian Journal of Geosciences Article 11, 11. structure characteristics are important aspects of shale reservoirs. Shale samples were collected from the Taiyuan and Shanxi Formations from the WX-1 well in the Qinshui basin, Shanxi, China. Pore morphology was analyzed using argon ion polishing scanning electron microscopy (Ar-SEM) and focused ion beam scanning electron microscopy (FIB-SEM). Subsequently, the structural pore features in the images were quantitatively characterized using the pores (Particles) and cracks analysis system (PCAS) method. The results show that the sample pores are primarily organic pores, intergranular pores, and intragranular pores, and the pore sizes are concentrated at less than 100?nm. In addition, the following rules are determined: first, with the pixel accuracy (PA) increase on the same pore, the pore edge becomes smooth, the degree of pore orientations (DPO) improves, and the apparent pore structure complexity (APSC) decreases. In addition, when the pore edge roughness increases and the DPO decreases, this effect becomes larger to change PA. Second, when the pore shape tends to be “round,” the edge becomes smooth, and APSC decreases; when the pore tends to be “narrow,” the edge becomes rough, and the APSC increases. Third, with the increase of depth, the pore size and DPO first increase and then decrease, and the APSC decreases gradually; with the increase of maturity, the pore size first decreases and then increases. Conversely, the APSC first increases and then decreases when the turning point occurs in the high-mature to over-mature stages of the transition, and the DPO improves.Yan, J., Kim, M., Haberl, M., Kwok, H., Brunswick, P., MacInnis, C., van Aggelen, G., Shang, D., 2018. Determination of polycyclic aromatic hydrocarbons in surface water using simplified liquid-liquid micro-extraction and pseudo-MRM GC/MS/MS. Analytical Methods 10, 405-416. simplified liquid–liquid micro-extraction (LLME) GC/MS/MS method was developed for the determination of 18 polycyclic aromatic hydrocarbons (PAHs) in surface water. This method utilizes a pseudo multiple reaction monitoring (PMRM) mode, a technique in which the third quadrupole monitors the same m/z as for the first quadrupole precursor ion. The use of helium as the only collision gas improved the sensitivity by significantly reducing both PAH compound fragmentation and baseline noise. For PAH determination, the PMRM approach proved superior to the classical quadrupole MRM technique in terms of enhanced sensitivity. With observed improvements in sensitivity, micro-extraction using only 4 mL of a novel binary solvent became possible, with corresponding reduction in time consuming sample preparation procedures and toxic solvent usage. Quantifying and qualifying ions, in addition to retention times, were used to verify trace level PAHs. During method validation, the limit of quantitation (LOQ) in surface water was observed to be 10 ng L?1 for the target PAHs. The recovery of individual PAHs was in the range of 80 to 114% from a water matrix, with a corresponding precision between 1.4 and 4.8% RSD. The robustness and accuracy of this method was demonstrated by its success in repeated proficiency test studies. The procedure has been successful during routine use in environmental sample testing and analysis of chemically enhanced water accommodated fraction (CEWAF) samples from toxicological LC50 (50% lethal concentration) bioassays, showing its applicability to situations in which both crude oil and oil spill dispersants are present.Yang, B., Zhang, H., Shu, J., Ma, P., Zhang, P., Huang, J., Li, Z., Xu, C., 2018. Vacuum-ultraviolet-excited and CH2Cl2/H2O-amplified ionization-coupled mass spectrometry for oxygenated organics analysis. Analytical Chemistry 90, 1301-1308. mass spectrometry analysis of oxygenated volatile organic compounds (OVOCs) remains challenging due to their limited ionization efficiencies. In this study, we surprisingly found that, under vacuum-UV (VUV) excitation, a gaseous mixture of CH2Cl2/H2O/analyte (OVOCs) in N2 buffer generated large amounts of H3O+ and protonated analyte even when the photon energy was lower than the ionization energy of the neutral species involved. In contrast to those obtained with VUV photoionization alone, the signal intensities of oxygenated organics can be amplified by more than 3 orders of magnitude. The isotope tracing experiment revealed that the proton donor is water, and the dependence of the signal intensities on the VUV photon intensities verified that the reaction was a single-photon process. The observed ionization process is assigned as an undocumented chemi-ionization reaction in which a complex formed from the ion-pair state CH2Cl2*, H2O, and analyte and then autoionized to produce the protonated analyte with the aid of the reorganization energy released from the formation of CH2O and HCl. Essentially, here we present an efficient chemi-ionization method for the direct protonation of oxygenated organics. By the method, the mass spectrometric sensitivities toward acetic acid, ethanol, aldehyde, diethyl ether, and acetone were determined to be 224 ± 17, 245 ± 5, 477 ± 14, 679 ± 11, and 684 ± 6 counts pptv–1, respectively, in 10 s acquisition time. In addition, the present ionization process provides a new method for the generation of a high-intensity H3O+ source (～1011 ions s–1, measured by ion current) by which general organics can be indirectly protonated via a conventional proton-transfer reaction. These results open new aspects of chemi-ionization reactions and offer new technological applications that have the potential to greatly improve mass spectrometry sensitivity for detecting trace gaseous organics.Yang, G., Liu, C., Fan, J., Chen, P., 2017. Burial history and petroleum entrapment in the Yaoyingtai region of the Changling Fault Depression, China. Acta Geologica Sinica - English Edition 91, 2230-2242. work aims to reconstruct the burial history of various kinds of sandstones penetrated by the well YS201 in the Yaoyingtai region of the Changling Fault Depression, southern Songliao Basin, China. Analyses of fluid inclusions in the reservoir rocks, combined with a review of the regional tectonic evolution, revealed the hydrocarbon accumulation stage and accumulation age of the Early Cretaceous Denglouku group and the first member of the Quantou group reservoir, which are the future exploration focus for deep gas reservoirs in this region. Acoustic time data and sedimentary rates calculated for sediments in the YS201 well yielded thicknesses for the Yingcheng, Nenjiang, and Mingshui groups of 506, 539.18, and 144.85 m, respectively, thereby revealing the burial history of the sediments in the well. Fluid inclusions of the Denglouku group reservoir and the first member of the Quantou group reservoir contain oil inclusions and hydro-carbonaceous salt water inclusions. The main peaks of the homogenization temperature and salinity of these saltwater inclusions in the first member of the Quantou group reservoir are generally 110–120°C and 6wt%–8wt%, respectively, and for the Denglouku group are 130–140°C and 4wt%–6wt%. The data for both reservoirs show only one main peak, indicating that they both have experienced single-stage accumulation. Combining the homogenization temperature of the reservoir fluid inclusions with the burial and thermal history of the sediments in the YS201 well, we infer that the hydrocarbon gas in these two intervals accumulated at 79 Ma (middle Late Cretaceous).Yang, J., Verba, C., Torres, M., Hakala, J.A., 2018. Empirically assessing the potential release of rare earth elements from black shale under simulated hydraulic fracturing conditions. Journal of Natural Gas Science and Engineering 50, 259-268. earth elements (REEs) are economically important to modern society and the rapid growth of technologies dependent on REEs has placed considerable economic pressure on their sourcing. This study addresses whether REEs could be released as a byproduct of natural gas extraction from a series of experiments that were designed to simulate hydraulic fracturing of black shale under various pressure (25 and 27.5?MPa) and temperature (50, 90, 130?°C) conditions. The dissolved REEs in the reacted fluids displayed no propensity for the REEs to be released from black shale under high pressure and temperature conditions, a result that is consistent across the different types of fluids investigated. Overall, there was a net loss of REEs from the fluid. These changes in dissolved REEs were greatest at the moment the fluids first contacted the shale and before the high temperature and high pressure conditions were imposed, although the magnitude of these changes (10?4?μg/g) were small compared to the magnitude of the total REE content present in the solid shale samples (102?μg/g). These results highlight the variability and complexity of hydraulic fracturing systems and indicate that REE may not serve as robust tracers for fracturing fluid-shale reactions. Additionally, the results suggest that significant quantities of REEs may not be byproducts of hydraulically fractured shales.Yang, Y., Dou, Y., An, S., 2018. Testing association between soil bacterial diversity and soil carbon storage on the Loess Plateau. Science of The Total Environment 626, 48-58. are widely distributed and play an important role in soil carbon (C) cycling. The impact of soil bacterial diversity on soil C storage has been well established, yet little is known about the underlying mechanisms and the interactions among them. Here, we examined the association between soil bacterial diversity and soil C storage in relation to vegetation restoration on the Loess Plateau. The dominant phyla among land use types (artificial forest, Af; natural shrubland, Ns; artificial grassland, Ag; natural grassland, Ng; slope cropland, Sc) were Acidobacteria, Actinobacteria, Alphaproteobacteria, and Betaproteobacteria, which transited from Acidobacteria-dominant to Actinobacteria-dominant community due to vegetation restoration. Soil C storage and the Shannon diversity index of soil bacterial community (HBacteria) showed the order Ns?>?Ng?>?Af?>?Ag?>?Sc, whereas no significant difference was found in Good's coverage (p?>?.05). Further, a strong relationship was observed between the relative abundance of dominant bacterial groups and soil C storage (p?<?.05). Additionally, soil bacterial diversity was closely related to soil C storage based on the structural equation model (SEM) and generalized additive models (GAMs). Specifically, soil C storage had the largest deterministic effects, explaining >70% of the variation and suggesting a strong association between soil C storage and soil bacterial diversity. Overall, we propose that further studies are necessary with a focus on the soil bacterial groups with specific functions in relation to soil C storage on the Loess Plateau.Yang, Y., Wu, J., Zhao, S., Han, Q., Pan, X., He, F., Chen, C., 2018. Assessment of the responses of soil pore properties to combined soil structure amendments using X-ray computed tomography. Scientific Reports 8, Article 695. amendments, such as straw mulch, organic fertilizers and superabsorbent polymer (SAP), are extensively applied to improve soil structure and porosity, and we reported the functional consequences of the individual application of these amendments in our previous study. However, whether combined amendments are more effective than their individual applications for improving soil pore structure is unknown. Here, we conducted X-ray computed tomography (CT) scanning on undisturbed soil columns to investigate the efficiency of two-amendment application, including straw mulch and organic manure, SAP and organic manure, or SAP and straw mulch, for improving soil pore properties and pore distribution. The X-ray CT technique allows us to accurately determine the number, morphology, and location of macropores (>1?mm in diameter) and smaller pores (0.13–1.0?mm). Compared to the control treatment, which showed the lowest increase in soil porosity, all the combined treatments led to an increase in the numbers of both macropores and smaller soil pores, causing a significant improvement in soil structure and porosity. Among these treatments, the application of both straw mulch and organic manure was the most effective for improving soil porosity and soil physical structure.Yarranton, H.W., Powers, D.P., Okafor, J.C., van den Berg, F.G.A., 2018. Regular solution based approach to modeling asphaltene precipitation from native and reacted oils: Part 2, molecular weight, density, and solubility parameter of saturates, aromatics, and resins. Fuel 215, 766-777. molecular weight, density, and solubility parameter of the crude oil medium are inputs to regular solution based models for asphaltene precipitation. For native oils, these properties can be determined from a SARA (saturate, aromatic, resin, asphaltene) assay and existing correlations for each SARA component. However, thermo- and hydrocracking alter these properties and these changes must be accounted for when modeling the solubility of reacted oils. The effect of cracking on asphaltene properties was considered in a previous study. In the current study, the molecular weight and density for saturate, aromatic, and resin fractions from 15 native and reacted fluid samples are measured. The solubility parameters of saturates and aromatics are determined by fitting asphaltene precipitation yield data in these solvents with a modified regular solution model. The solubility parameter of resins is calculated using correlations previously developed for the asphaltenes. An elemental analysis of each fraction is also performed. The effect of thermo- and hydrocracking on the SAR fraction properties is discussed. Average properties and correlations are developed to predict the SAR fraction properties in the absence of direct measurements. These properties and correlations are a key step in extending regular solution models for asphaltene precipitation to refinery streams.Yin, Q.-J., Zhang, W.-J., Qi, X.-Q., Zhang, S.-D., Jiang, T., Li, X.-G., Chen, Y., Santini, C.-L., Zhou, H., Chou, I.-M., Wu, L.-F., 2018. High hydrostatic pressure inducible trimethylamine N-oxide reductase improves the pressure tolerance of piezosensitive bacteria Vibrio fluvialis. Frontiers in Microbiology 8, 2646. doi: 10.3389/fmicb.2017.02646. hydrostatic pressure (HHP) exerts severe effects on cellular processes including impaired cell division, abolished motility and affected enzymatic activities. Transcriptomic and proteomic analyses showed that bacteria switch the expression of genes involved in multiple energy metabolism pathways to cope with HHP. We sought evidence of a changing bacterial metabolism by supplying appropriate substrates that might have beneficial effects on the bacterial lifestyle at elevated pressure. We isolated a piezosensitive marine bacterium Vibrio fluvialis strain QY27 from the South China Sea. When trimethylamine N-oxide (TMAO) was used as an electron acceptor for energy metabolism, QY27 exhibited a piezophilic-like phenotype with an optimal growth at 30 MPa. Raman spectrometry and biochemistry analyses revealed that both the efficiency of the TMAO metabolism and the activity of the TMAO reductase increased under high pressure conditions. Among the two genes coding for TMAO reductase catalytic subunits, the expression level and enzymatic activity of TorA was up-regulated by elevated pressure. Furthermore, a genetic interference assay with the CRISPR-dCas9 system demonstrated that TorA is essential for underpinning the improved pressure tolerance of QY27. We extended the study to Vibrio fluvialis type strain ATCC33809 and observed the same phenotype of TMAO-metabolism improved the pressure tolerance. These results provide compelling evidence for the determinant role of metabolism in the adaption of bacteria to the deep-sea ecosystems with HHP.Yoshida, K., Orozbaev, R., Hirajima, T., Miyake, A., Tsuchiyama, A., Bakirov, A., Takasu, A., Sakiev, K., 2018. Micro-excavation and direct chemical analysis of individual fluid inclusion by cryo-FIB-SEM-EDS: Application to the UHP talc-garnet-chloritoid schist from the Makbal Metamorphic Complex, Kyrgyz Tian-Shan. Geochemical Journal, 52, 59-67. chemical analysis of a single fluid inclusion was conducted by micro-excavation at cryo-temperatures. A scanning electron microscope (SEM) equipped with a focused ion beam (FIB), an energy dispersive X-ray spectrometer (EDS), and a cold stage, were used to analyze the chemical composition of the sample fluid inclusion, which was trapped in the ultrahigh-pressure (UHP) talc-garnet-chloritoid schist obtained from the Makbal metamorphic complex, Kyrgyz. Conventional techniques such as microthermometry and cryo-temperature and room-temperature Raman spectroscopy enabled the detection of NaCl and CaCl2 as solute species in the fluid inclusions, as well as high salinity of 20.5 mass% CaCl2 and 1.7 mass% NaCl with the assumption of a NaCl-CaCl2-H2O ternary system. However, additional chemical analysis using the present cryo-FIB-SEM-EDS system further revealed the presence of K as a solute element, which is hardly identified by conventional techniques. Petrographic examination of the fluid inclusions indicated that they had been trapped during the exhumation stage of the UHP talc-garnet-chloritoid schist, possibly originating from the decompression breakdown of lawsonite. The data acquired from the present study challenges previous reports of the existence of simple chemical system of aqueous fluids in high-pressure and UHP metamorphic terrane in eastern Asia. This is imperative because misidentification of solute species introduces errors into salinity estimation, resulting in inaccuracy propagation in quantitative analytical processes such as LA-ICP-MS. A detailed fluid inclusion petrography would thus require accurate quantitative analysis involving FIB-based sample-preparation and SEM-EDS analysis. You, L., Kang, Y., Chen, Q., Fang, C., Yang, P., 2017. Prospect of shale gas recovery enhancement by oxidation-induced rock burst. Natural Gas Industry B 4, 449-456. horizontal well multi-staged fracturing technology, shale rocks can be broken to form fracture networks via hydraulic force and increase the production rate of shale gas wells. Nonetheless, the fracturing stimulation effect may be offset by the water phase trapping damage caused by water retention. In this paper, a technique in transferring the negative factor of fracturing fluid retention into a positive factor of changing the gas existence state and facilitating shale cracking was discussed using the easy oxidation characteristics of organic matter, pyrite and other minerals in shale rocks. Furthermore, the prospect of this technique in tackling the challenges of large retention volume of hydraulic fracturing fluid in shale gas reservoirs, high reservoir damage risks, sharp production decline rate of gas wells and low gas recovery, was analyzed. The organic matter and pyrite in shale rocks can produce a large number of dissolved pores and seams to improve the gas deliverability of the matrix pore throats to the fracture systems. Meanwhile, in the oxidation process, released heat and increased pore pressure will make shale rock burst, inducing expansion and extension of shale micro-fractures, increasing the drainage area and shortening the gas flowing path in matrix, and ultimately, removing reservoir damage and improving gas recovery. To sum up, the technique discussed in the paper can be used to “break” shale rocks via hydraulic force and to “burst” shale rocks via chemical oxidation by adding oxidizing fluid to the hydraulic fracturing fluid. It can thus be concluded that this method can be a favorable supplementation for the conventional hydraulic fracturing of shale gas reservoirs. It has a broad application future in terms of reducing costs and increasing profits, maintaining plateau shale gas production and improving shale gas recovery.Yu, J., Jiang, C., Guan, Q., Gu, J., Ning, P., Miao, R., Chen, Q., Zhang, J., 2018. Conversion of low-grade coals in sub-and supercritical water: A review. Fuel 217, 275-284. coals are very abundant in several regions throughout the world. However, it is difficult to use the low-rank coals directly due to their undesirable characteristics such as high moisture, high ash and high oxygen content. The utilization of low-rank coals has received more and more attention with the increase of consumption of other fossil fuels. Besides the pyrolysis and alcoholysis, the conversion of low-lank coals under hydrothermal conditions (including sub-and supercritical water) for high-quality solid fuel, coal liquefied oil and gaseous fuels has also been widely investigated. In this review, the development of low-rank coal hydrothermal upgrading, the liquid fuel production from coal in sub-and supercritical water and supercritical water gasification of coal for hydrogen production, including partial oxidative gasification, homogeneous/heterogeneous catalytic gasification and related kinetic investigations are discussed. In addition, the element transformation such as N, S and metals during the hydrothermal process are also presented.Yu, Q., Ren, Z., Li, R., Wang, B., Qin, X., Tao, N., 2017. Paleogeotemperature and maturity evolutionary history of the source rocks in the Ordos Basin. Geological Journal 52, 97-118. evolution has an important control on maturity and hydrocarbon-generation of source rocks. On the basis of analysis of the present-day geothermal gradient, rock thermophysical parameters and heat flow, the thickness contour and vitrinite reflectance can be identified, and the distribution of thermal anomaly was discussed. The paleogeotemperature and paleogeothermal gradients are calculated after the recovery of the erosional thickness. With the theory of the recovering of the superposed and modified sedimentary basin, the evolutionary history since the end of Triassic, the end of Jurassic, the Late Early Cretaceous is presented for two sets of source rocks recovered in various perspectives of plans, cross-sections, important wells, and typical areas. The impact of tectonothermal evolution on the maturity and hydrocarbon-generation history of the source rocks is discussed. The paleogeothermal gradient (4.0 °C/100 m on average) is higher than the present one (2.9 °C/100 m on average). With the slightly continuous increase since the Late Paleozoic, the paleogeotemperature of the Ordos Basin reached its maximum in Late Early Cretaceous and decreased continuously from then on. The paleogeotemperature and maturity of the source rocks continuously increased before Late Early Cretaceous. The tectonothermal event during Late Jurassic to Early Cretaceous controlled the source rocks with the high temperature and maturity in the Wuqi-Qingyang-Fuxian. The temperature decreased, and the maturity hardly changed after the Late Cretaceous. The source rocks of the Shanxi Formation reached maturity, high maturity and over-maturity at the Late Triassic, the Late Jurassic, and the Early Cretaceous, respectively. The source rocks of the Yanchang Formation reached low maturity and maturity sequentially all in the Early Cretaceous.Yu, X., Granados-Focil, S., Tao, M., Burnham, N.A., 2018. Time- and composition-dependent evolution of distinctive microstructures in bitumen. Energy & Fuels 32, 67-80.’s chemistry often results in complicated intermolecular associations, which are manifested by the diverse microstructures as observed by atomic force microscopy (AFM). These microstructures largely contribute to bitumens’ bulk mechanical properties; therefore, it is essential to understand the chemical–microstructural–mechanical relationships for optimal design of bitumen-related applications. However, the complex nature of bitumen and the various influencing factors often lead to practical challenges in investigation of bitumens’ microstructures and their chemical origins. This study aims at addressing some of the main concerns related to AFM characterization of bitumens’ microstructures, namely the dependence of bitumens’ microstructures on such factors as sample preparation methods, annealing conditions and durations, and chemical composition. Our results suggest that microstructures of bitumen films of a few micrometers or thicker (i.e., the thickness of the asphalt-coating layer over the aggregates in asphalt concrete) were comparable regardless of their sample preparation methods, provided that toluene was likely completely removed. Additionally, bitumens annealed at room temperature for over 2 months showed time-dependent microstructures, which correlate well with bitumens’ room-temperature steric hardening behavior as verified by other researchers using modulated differential scanning calorimetry. Microstructures of the bitumen films stabilized after different annealing durations depending on the dimensions of the molecular structures and the complexity of the molecular interactions among the multiple phases in each bitumen. Distinctive microstructures were observed for remixed bitumens with increasing asphaltene concentrations. Consistency between our observations and other relevant literature suggests that microstructures observed by AFM are probably not just a surface phenomenon. The above findings provide deeper insights into the establishment of the complicated chemical–mechanical relationships for bitumen that pave the path toward tuned bitumen performance.Yu, X., H?rst, S.M., He, C., McGuiggan, P., Bridges, N.T., 2017. Direct measurement of interparticle forces of Titan aerosol analogs (“tholin”) using atomic force microscopy. Journal of Geophysical Research: Planets 122, 2610-2622. understand the origin of the dunes on Titan, it is important to investigate the material properties of Titan's organic sand particles on Titan. The organic sand may behave distinctively compared to the quartz/basaltic sand on terrestrial planets (Earth, Venus, and Mars) due to differences in interparticle forces. We measured the surface energy (through contact angle measurements) and elastic modulus (through Atomic Force Microscopy) of the Titan aerosol analog (tholin). We find that the surface energy of a tholin thin film is about 70.9?mN/m, and its elastic modulus is about 3.0?GPa (similar to hard polymers like PMMA and polystyrene). For two 20?μm diameter particles, the theoretical cohesion force is therefore 3.3?μN. We directly measured interparticle forces for relevant materials: tholin particles are 0.8 ± 0.6?μN, while the interparticle cohesion between walnut shell particles (a typical model materials for the Titan Wind Tunnel, TWT) is only 0.4 ± 0.1?μN. The interparticle cohesion forces are much larger for tholins and presumably Titan sand particles than materials used in the TWT. This suggests that we should increase the interparticle force in both analog experiments (TWT) and threshold models to correctly translate the results to real Titan conditions. The strong cohesion of tholins may also inform us how the small aerosol particles (～1?μm) in Titan's atmosphere are transformed into large sand particles (～200?μm). It may also support the cohesive sand formation mechanism suggested by Rubin and Hesp (2009), where only unidirectional wind is needed to form linear dunes on Titan.Yu, X., Yu, Q., Zhu, M., Tang, M., Li, S., Yang, W., Zhang, Y., Deng, W., Li, G., Yu, Y., Huang, Z., Song, W., Ding, X., Hu, Q., Li, J., Bi, X., Wang, X., 2017. Water soluble organic nitrogen (WSON) in ambient fine particles over a megacity in south China: Spatiotemporal variations and source apportionment. Journal of Geophysical Research: Atmospheres 122, 13,045-13,060. nitrogen aerosols are complex mixtures and important compositions in ambient fine particulate matters (PM2.5), yet their sources and spatiotemporal patterns are not well understood particularly in regions influenced by intensive human activities. In this study, filter-based ambient PM2.5 samples at four stations (one urban, two rural, plus one urban roadside) and PM samples from combustion sources (vehicle exhaust, ship emission, and biomass burning) were collected in the coastal megacity Guangzhou, south China, for determining water soluble organic nitrogen (WSON) along with other organic and inorganic species. The annual average WSON concentrations, as well as the ratios of WSON to water soluble total nitrogen, were all significantly higher at rural sites than urban sites. Average WSON concentrations at the four sites during the wet season were quite near each other, ranging from 0.41 to 0.49 μg/m3; however, they became 2 times higher at the rural sites than at the urban sites during the dry season. Five major sources for WSON were identified through positive matrix factorization analysis. Vehicle emission (29.3%), biomass burning (22.8%), and secondary formation (20.2%) were three dominant sources of WSON at the urban station, while vehicle emission (45.4%) and dust (28.6%) were two dominant sources at the urban roadside station. At the two rural sites biomass burning (51.1% and 34.1%, respectively) and secondary formation (17.8% and 30.5%, respectively) were dominant sources of WSON. Ship emission contributed 8–12% of WSON at the four sites. Natural vegetation seemed to have very minor contribution to WSON.Yuan, D.-X., Zhang, Y.-C., Shen, S.-Z., 2018. Conodont succession and reassessment of major events around the Permian-Triassic boundary at the Selong Xishan section, southern Tibet, China. Global and Planetary Change 161, 194-210. major discrepancy for the age of the Selong Group from middle Cisuralian (Early Permian) to Changhsingian resulted from previous reports of Sakmarian, Kungurian and Guadalupian (Middle Permian) conodonts and Lopingian (Late Permian) brachiopods. Recently, Cisuralian and Guadalupian conodonts were reported again from the Selong Group and the basal part of the Kangshare Formation at the Selong section, but the age discrepancy remains. We present our conodont materials based on large samples collected from the Selong Group and our interpretation based on identifications using a sample population approach. Three conodont zones are recognized in our re-investigation of the upper part of the Selong Group. They include the Vjalovognathus sp., the Mesogondolella hendersoni, and the M. sheni zones, in ascending order. These zones are overlain by the basal Triassic Hindeodus parvus Zone and the Otoceras woodwardi Zone. Our reassessment of conodonts reported by previous studies from Selong and nearby sections suggest that all specimens consistently point to a Lopingian age; the upper part of the Selong Group is latest Changhsingian in age based on the presence of Clarkina orchardi and Mesogondolella sheni. Previously reported early Cisuralian and Guadalupian conodonts are misidentified using a form species concept. A hiatus may be present at the erosional surface between the Selong Group and the Waagenites Bed of the basal part of the Kangshare Formation. However, the hiatus is minimal because conodont and brachiopod assemblages above and below this surface are very similar, and it results from a latest Changhsingian transgression just before the extinction that follows a global latest Changhsingian regression. There is a distinct rapid end-Permian mass extinction at Selong within the Waagenites Bed, as indicated by the disappearances of all benthic brachiopods, rugose corals and Permian bryozoans. The burst of Clarkina species in the Waagenites Bed and throughout the entire Lower Triassic at Selong is interpreted as a southward migration of equatorial conodont animals associated with the rapid global warming beginning at the end of the Permian. The cool- or cold-water species of Mesogondolella, in the upper part of the Selong Group and the basal part of the Kangshare Formation, are representative of the uppermost Permian in the bipolar/bi-temperate cold-water province and are not reworked from the underlying Selong Group or any other unknown Cisuralian or Guadalupian deposits.Yuan, X., Oleschuk, R.D., 2018. Advances in microchip liquid chromatography. Analytical Chemistry 90, 283-301. its most fundamental, liquid chromatography utilizes a column filled with stationary phase materials to either separate/isolate a compound (for purification) or sequentially deliver an analyte to a detector (for analysis). A wide selection of stationary phase materials is available that can provide highly selective separations based upon different chemical properties (i.e., van der Waals, hydrophobic, hydrophilic, hydrodynamic radius (size), electrostatic forces, etc.) As a result, it is the most utilized separation method for compounds of moderate to low volatility, and the global market value for liquid chromatography is in excess of 5.1 billion U.S. dollars per year (2015). The miniaturization of analytical platforms and the development of micro total analysis systems (μTAS)is driven by the idea of reduced sample requirement, reagent use, and improved analysis speed. In particular, miniaturization is being directed at situations where there is a definite sample limitation, where obtaining more sample would be either difficult or impossible. The challenges to miniaturization of liquid chromatography stem from the “plumbing”, where all the fluidic components need to be assembled with ultralow dead volume fittings because imperfections in connections, packing, and injection become exacerbated as column/device dimensions are reduced. Two strategies have emerged for liquid chromatographic miniaturization. The first would be viewed as miniaturization of conventional LC technologies where column, injection volumes, and detection volumes are decreased. Significant research and engineering has been invested in this strategy to reduce sample injection volume, flow/gradient delivery, column manufacture, detection volume, etc. The first commercial capillary LC instrument was introduced in 1998; after which, the market of capillary LC has grown significantly to meet the demands of bioanalysis.Alternatively microchip LC (chipLC) refers to the integration of liquid handling on a planar substrate, “dubbed” a microchip. The same functionality as the conventional miniaturized LC systems is offered; however, the idea is that the microchip is a “modular” device that can simply be “plug and played”. In this way, the more complex instrumental parameters, that those of us who love chromatography like to manipulate/build, are put within a “black box”, with the hope that they can be operated by individuals with less specialized training. Furthermore, once the module has been utilized/spent, the module can be simply discarded and replaced. The advantages of chipLC have prompted the commercialization of various formats of microchip LC columns and interfaces with mass spectrometers in the past decade. Regardless of which miniaturization strategy is employed, there are fundamental reasons to miniaturize liquid chromatographic methods. Specifically, capillary LC excels in sample limited applications (e.g., “omic” studies). When coupled with a detection method favorable for miniaturization (e.g., fluorescence, electrochemical, mass spectrometry), a significant increase in mass sensitivity can be realized due to reduced sample dilution in small i.d. columns. For example, under identical chromatographic and injection conditions, a 235-fold increase in mass sensitivity is expected for a reduction of column i.d. from 4.6 mm to 300 μm. In addition to chromatographic performance improvements, there is a significant reduction in packing material required for column construction. The quantity of stationary phase material needed to pack a 10 cm long, 300 μm i.d. capillary column is less than 10 mg. All conditions being equal, this equates to a material saving of more than 99% compared to a conventional 4.6 mm column, a cost saving the column manufacturers have yet to pass along to capillary LC practitioners. Moving forward, the environmental advantages of miniaturized LC are also becoming more apparent, due to significant reductions in solvent use. Although only a blip, we note the acetonitrile shortage of 2009, increasingly stringent disposal standards, and more significant disposal costs. One need only recount visits to large analytical facilities that employ large numbers of liquid chromatographs operating at mL/min flow rates, to envision how miniaturization could significantly reduce the “footprint” of liquid chromatographic analysis. Merely 200 mL solvent is consumed if a capillary/chip LC column with a flow rate of 400 nL/min is continuously operated for a year. In comparison, a conventional LC operated at 1 mL/min consumes 500 L solvents (24 h operation per day, 360 days in a year). We have so far identified the positive attributes associated with miniaturizing LC. There are significant reasons why the analytical world has yet to completely switch to either capillary LC or chipLC systems. For the most part only those that absolutely require the increased sensitivity have adopted capillary LC and/or microchip LC. The resistance emanates from the less robust nature of capillary and microchip LC and the stresses the reduced dimensions put on analyte detection. Capillary LC is more susceptible to fluidic clogging and more complex connections among microfluidic pump, sampler, capillary column, detector, etc. also present the difficulty of preventing and locating fluid leakage. Solid reviews of the miniaturized liquid chromatographic field have been published in the past. The review by Desmet et al. in particular has pointed out that microchip LC is the most important trend for LC miniaturization.This is not surprising considering the rapid development of μTAS beginning in the early 1990s. The reduced amount of analyte/volume utilized for chipLC necessitates significant enhancements in detector configuration, or the use of only the most sensitive detection methodologies. A decrease in channel volume significantly limits the amount of analyte available to detect. For example, 6 × 1011 molecules (at 1 μM concentration) are present in 1 mm3 volume. Reducing the dimensions to 1 μm3 houses only 600 molecules at the same concentration. Microchip LC inherits the advantages of μTAS with the potential to integrate several functional components of the analytical system on a planar substrate. Development of robust, reliable, and efficient chipLC relies on the cooperation of chemists, material scientists, mechanical and electrical engineers, etc. Since 2010, a few review articles on chipLC were published focusing on different aspects of the development. Different metrics are used to describe chromatographic performance including sensitivity, resolution, reduced plate height (hmin), number of theoretical plates (N), peak capacity, etc. These reviews provide a good introduction to basic chromatographic theory and how it relates to chipLC. The present review highlights important advances in chipLC over the past 2 years, relating material and fabrication, geometry and fluidic design, stationary phase formats, spectroscopic detection, and interfacing with mass spectrometry, etc. Figure 1 shows interesting examples of recent microchip developments from both academic researchers and the commercial sector.Yuan, Z., Liu, P., Zhang, S., Li, X., Shi, L., Jin, R., 2018. Experimental study and numerical simulation of nitrogen-assisted SAGD in developing heavy oil reservoirs. Journal of Petroleum Science and Engineering 162, 325-332. presence of significant amounts of injected steam and heat loss are unavoidable issues occurred that are observed during the steam-assisted gravity drainage (SAGD) process in developing heavy oil reservoirs. Because of these limitations and concerns, non-condensable gas co-injection has become a potential technique to enhancing oil recovery and reducing energy consumption. However, the oil production mechanism is complicated and has not been totally understood, thereby requiring further discussion. In this work, a two-dimensional physical model was designed to investigate the production mechanisms of nitrogen on SAGD. Two comparative injection schemes, specifically the conventional SAGD and nitrogen assisted SAGD (NA-SAGD), were conducted to investigate the effect of nitrogen co-injection with steam on the SAGD performance. Dynamic temperature profile changes during the two experiment processes were monitored and recorded. The observation results indicate that nitrogen accumulation at the upper part of the model resulted in the effective expansion of the NA-SAGD process steam chamber along the horizontal direction. The swept area of steam increased significantly and the residual oil saturation was reduced. The cumulative oil production of NA-SAGD was higher than that of the conventional SAGD. Moreover, the apparent heat loss reduction, which defines the heat utilization efficiency, exhibited an increase following nitrogen injection. In addition, a numerical simulation was generated to compare and verify the results obtained in the two experiments. Nitrogen co-injection with steam effectively enhanced the oil recovery. Studies indicate that NA-SAGD is a feasible method for improving oil production in developing heavy oil reservoirs.Zanbouri, H., Ashtari Larki, S., Bemani, A., Shokrollahzadeh Behbahani, H., 2018. Applying Grid partitioning based Fuzzy inference system as novel algorithm to predict asphaltene precipitation. Petroleum Science and Technology 36, 302-307. precipitation is one of challenging problems in petroleum and chemical engineering so the importance of investigation of Asphaltene precipitation is clear. The asphaltene deposition effects on wellbore plugging, wettability alteration and facility damages. In order to solve these problems, a novel investigation based on Grid partitioning based Fuzzy inference system algorithm to predict precipitated asphaltene in terms of dilution ratio, temperature and carbon number of precipitant was developed. The predicting algorithm performance was evaluated statistically and graphically. The coefficients of determination (R2) for training and testing phases 0.9973 and 0.9900 respectively which confirm the great accuracy and high potential of predicting algorithm for estimation of precipitated asphaltene so this algorithm can be used as high accurate and simple software for prediction of asphaltene behavior in crude oil.Zanganeh, P., Dashti, H., Ayatollahi, S., 2018. Comparing the effects of CH4, CO2, and N2 injection on asphaltene precipitation and deposition at reservoir condition: A visual and modeling study. Fuel 217, 633-641. Oil Recovery (EOR) through various methodologies has been an active research for many years seeking efficient methods to increase the crude oil recovery efficiency from oil reservoirs. Among different gas injection scenarios, carbon dioxide (CO2), natural gas (mainly methane (CH4)) and nitrogen (N2) injection are considered as promising EOR agents. Asphaltene precipitation and deposition during EOR methods cause severe problems, which affect the recovery efficiency and increase the cost of the incremental oil production. This study is aimed to investigate the effects of CH4 and N2 injection compared with CO2 injection on asphaltene precipitation and deposition. The different mole percent of the mentioned gases were introduced into the high-pressure cell, then the amount of precipitated asphaltene was measured at the reservoir condition. The evolution of asphaltene deposition was monitored through a high-resolution microscope. Moreover, Image processing software was utilized to check the amount of deposited asphaltene and its size distribution under different conditions. The most apparent finding to emerge from this study is that both CO2 and natural gas increase the amount of precipitated asphaltene whereas the nitrogen as an inert gas has no considerable effect on the amount of precipitated asphaltene. According to the results, the increment of precipitated asphaltene by CO2 is much higher than natural gas. Further, the thermodynamic solid model used in this study reasonably predicted the trend of asphaltene precipitation process for the mentioned EOR scenarios.Zeng, Z., Tice, M.M., 2017. Electron transfer strategies regulate carbonate mineral and micropore formation. Astrobiology 18, 28-36. microbial carbonates are robust biosignatures due to their distinct morphologies and compositions. However, whether carbonates induced by microbial iron reduction have such features is unknown. Iron-reducing bacteria use various strategies to transfer electrons to iron oxide minerals (e.g., membrane-bound enzymes, soluble electron shuttles, nanowires, as well as different mechanisms for moving over or attaching to mineral surfaces). This diversity has the potential to create mineral biosignatures through manipulating the microenvironments in which carbonate precipitation occurs. We used Shewanella oneidensis MR-1, Geothrix fermentans, and Geobacter metallireducens GS-15, representing three different strategies, to reduce solid ferric hydroxide in order to evaluate their influence on carbonate and micropore formation (micro-size porosity in mineral rocks). Our results indicate that electron transfer strategies determined the morphology (rhombohedral, spherical, or long-chained) of precipitated calcium-rich siderite by controlling the level of carbonate saturation and the location of carbonate formation. Remarkably, electron transfer strategies also produced distinctive cell-shaped micropores in both carbonate and hydroxide minerals, thus producing suites of features that could potentially serve as biosignatures recording information about the sizes, shapes, and physiologies of iron-reducing organisms.Zerfa?, C., Chen, J., Soyer, O.S., 2018. Engineering microbial communities using thermodynamic principles and electrical interfaces. Current Opinion in Biotechnology 50, 121-127. communities present the next research frontier. We argue here that understanding and engineering microbial communities requires a holistic view that considers not only species–species, but also species–environment interactions, and feedbacks between ecological and evolutionary dynamics (eco-evo feedbacks). Due this multi-level nature of interactions, we predict that approaches aimed soley at altering specific species populations in a community (through strain enrichment or inhibition), would only have a transient impact, and species–environment and eco-evo feedbacks would eventually drive the microbial community to its original state. We propose a higher-level engineering approach that is based on thermodynamics of microbial growth, and that considers specifically microbial redox biochemistry. Within this approach, the emphasis is on enforcing specific environmental conditions onto the community. These are expected to generate higher-level thermodynamic bounds onto the system, which the community structure and function can then adapt to. We believe that the resulting end-state can be ecologically and evolutionarily stable, mimicking the natural states of complex communities. Toward designing the exact nature of the environmental enforcement, thermodynamics and redox biochemistry can act as coarse-grained principles, while the use of electrodes — as electron providing or accepting redox agents — can provide implementation with spatiotemporal control.Zhai, L., Wu, C., Ye, Y., Zhang, S., An, Z., 2018. Marine redox variations during the Ediacaran–Cambrian transition on the Yangtze Platform, South China. Geological Journal 53, 58-79. widely developed black shales on the Yangtze Platform recorded palaeoceanographic environment information during the Ediacaran–Cambrian transition. This paper describes an integrated geochemical study of rare earth elements (REEs), redox-sensitive trace elements (RSTEs), and total organic carbon (TOC) contents in Ediacaran–Cambrian black shales at Daotuo, northeastern Guizhou Province, South China. Integrated RSTE data from the Daotuo area, in combination with previously published Fe speciation and Mo-based proxies from another six sections (Shatan, Jiulongwan, Zhongling, Yangjiaping, Longbizui and Wuhe), suggest three major periods of water euxinia during the Ediacaran–Cambrian transition. Under these conditions, organic matter and RSTEs experienced various levels of enrichment in the black shales, especially in the lower Jiumenchong Formation. Given the patterns of Mo-U covariations, metal-oxyhydroxide particulate shuttles may have operated during the black shale deposition of the Doushantuo Formation (Member II) at Daotuo. Conspicuously, the upper slope water was oxic-dysoxic during the earliest Cambrian, as determined by the REE, RSTE data and sedimentological characteristics of the Liuchapo Formation and the basal Jiumenchong Formation. The generally low RSTE concentrations in the Bianmachong Formation black shales (Cambrian Series 2, end of Stage 3) suggest a persistently oxic water column in upper slope settings. The coincidence between the marine oxygenation and the development of the ecosystem likely indicates the galvanizing effects of enhanced oxygen and biological element content on the fauna during the Ediacaran–Cambrian transition. Copyright ? 2016 John Wiley & Sons, Ltd.Zhang, B., Daigle, H., 2018. Oil-soluble contrast agents for NMR. Journal of Petroleum Science and Engineering 162, 180-189. well logging applications, nuclear magnetic resonance (NMR) is recognized as a powerful tool to differentiate various fluids inside porous media. However, it can be challenging to do so in complex situations, e.g. when fluid peaks overlap with each other. Water-soluble contrast agents, such as MnCl2 or Gd-EDTA, have been proposed for use to accelerate the water relaxation, thus separating the water signal from those of other fluids. Together with these contrast agents, the log-inject-log method is used and the difference between the two logs is attributed to the doped water phase. This application only works with water-based mud. To extend its use to oil-based mud (OBM), it is desirable to find alternatives to water-soluble contrast agents that are compatible with OBM.In this work, we introduce a new group of doping agents: oil-soluble contrast agents. We selected several iron-based complex compounds that are oil-soluble, and tested and evaluated their effects on oil signal relaxation using a laboratory NMR apparatus. We also tested hydrophobic iron oxide nanoparticles as a contrast agent. The results showed that both the complex compounds and nanoparticles were able to reduce the transverse relaxation time of oil from longer than 2?s to less than 20 ms. To demonstrate their applicability in porous media, we injected doped oil into gas-saturated Berea sandstone and limestone core plugs. With conventional 1D NMR measurements or the use of water-soluble contrast agents, it is not straightforward to discern the gas signal from the OBM signal. Our experiments showed that the gas signal could be easily identified in the presence of doped oil via simple T2 scans. We also performed experiments to demonstrate that the peaks of water and doped oil could be readily differentiated.The use of oil-soluble doping agents can significantly enhance the contrast of the NMR signals originated from different formation fluids, thus facilitating the fluid typing process. It provides a key alternative to the current water-doping technique. It is particularly advantageous when changing the oil relaxation is desired, such as for eliminating signal interferences from OBM invasion and differentiating heavy oil from clay-bound water. It also provides the possibility of speeding up the logging process by dramatically reducing the oil relaxation time. In addition, they can be employed in the laboratory for various purposes such as water saturation determination and fluid displacement monitoring. These contrast agents can also be of useful when oil-soluble contrast agents are desired in other fields, such as medical imaging applications.Zhang, J., Bi, Z., Liang, Y., 2018. Development of a nutrient recipe for enhancing methane release from coal in the Illinois basin. International Journal of Coal Geology 187, 11-19. literature has shown that in order to enhance methane release from coal through biogasification, suitable nutrient solutions are needed to stimulate microbial activities toward coal depolymerization and conversion to biogas. Specific for bituminous coal in the Illinois basin, a nutrient recipe that can be used to enhance coal biogasification in situ is not available yet. To develop such a recipe, the formation water and the indigenous microbial community were first characterized in detail. Based on these characteristics and our previous experience working with Illinois coal, four parameters, Fe powder, methanol, ethanol, and trace minerals were optimized through using a Box-Behnken design. The optimal condition predicted by the models was: Fe-powder at 74 mM; methanol at 97.9 mM, ethanol at 100 mM, and trace minerals at 100%. Under these conditions, the predicted methane yield and content was 1417.35 ft3/ton and 80.7%, respectively. These results were then validated by experimental studies. In addition, each added component was evaluated in terms of its contribution to methane generated. Specifically, the role of coal in the biogasification process was studied against two other solid materials. Overall, this study demonstrated that coal can be converted to methane and nutrient solution can definitely enhance methane release from coal. The real effect of this recipe in improving methane release from coal in situ needs to be further evaluated in a field scale.Zhang, J., Ding, X., Guan, R., Zhu, C., Xu, C., Zhu, B., Zhang, H., Xiong, Z., Xue, Y., Tu, J., Lu, Z., 2018. Evaluation of different 16S rRNA gene V regions for exploring bacterial diversity in a eutrophic freshwater lake. Science of The Total Environment 618, 1254-1267. partial sequencing of 16S rRNA genes has become the predominant tool used for studying microbial ecology. However, determining which hypervariable regions and primer sets should be used for screening microbial communities requires extensive investigation if controversial results are to be avoided. Here, the performances of different variable regions of the 16S rRNA gene on bacterial diversity studies were evaluated in silico with respect to the SILVA non-redundant reference database (SILVA SSU Ref 123NR), and subsequently verified using samples from Lake Taihu in China, a eutrophic lake. We found that the bacterial community composition results were strongly impacted by the different V regions. The results show that V1–V2 and V1–V3 regions were the most reliable regions in the full-length 16S rRNA sequences, while most V3 to V6 regions (including V3, V4, V3–V4, V5, V4–V5, V6, V3–V6, V4-V6, and V5–V6) were more closely aligned with the SILVA SSU Ref 123NR database. Overall, V4 was the most prominent V region for achieving good domain specificity, higher coverage and a broader spectrum in the Bacteria domain, as confirmed by the validation experiments. S-D-Bact-0564-a-S-15/S-D-Bact-0785-b-A-18 is, therefore, a promising primer set for surveying bacterial diversity in eutrophic lakes.Zhang, J., Wang, M., Liang, P., Cao, Y., Cao, Z., Wong, M.H., Christie, P., Wu, S., 2018. Effects of land use change on soil organic carbon sources and molecular distributions: 6280?years of paddy rice cropping revealed by lipid biomarkers. Journal of Soils and Sediments 18, 12-23.: The sources of and changes in molecular composition of soil organic carbon (SOC) due to land use change in a paddy soil chronosequence ?6000 years old were studied using a lipid biomarker approach.Materials and methods: Lipid biomarkers comprising fatty acids, aliphatic alcohols, and sterols were used to evaluate rice field reclamation and management over 6000 years on sources of and changes in molecular composition of SOC in two soil profiles comprising of the following three soil chronosequence layers (from bottom to top): 6280-year-old BP prehistoric paddy soil/pristine upland, 3320-year-old BP ancient paddy soil, and the present paddy soil. Furthermore, comparison with adjacent abandoned paddy soils was made to indicate the effect of abandoning cultivation due to urbanization on the sources and fluctuations in the molecular composition of SOC.Results and discussion: Fatty acids and aliphatic alcohols represented the most abundant fraction (～80%) of autochthonous organic carbon sources from microbial activity in the prehistoric pristine upland. Reclamation of pristine upland to submerged rice fields led to 44.5 and 41.1% increases in the ratio of long-chain n-fatty acids and n-alcohols (≥C22), respectively, to the total saturated homologs indicating an increased input of allochthonous organic matter sources derived from rice cropping. The evolution of the paddy soil from 6280 to 3320 years BP and then to the present was accompanied by a slight and gradual increase in the proportion of the higher plant-derived organic components. Abandonment of rice cropping led to an apparent decrease in the concentration of the lipid biomarkers suggesting a decline in rice roots and stubble inputs and of microbial activity.Conclusions: Lipid biomarkers can be used to trace the sources and fluctuations in the molecular composition of SOC in paddies owing to land use change. Fatty acids were more suitable as the lipid proxy than aliphatic alcohols or sterols.Zhang, J., Zhou, G., Zhang, G., Li, G., Wang, H., 2018. Geological characteristics and exploration orientation of Mid-Permian natural gas in the Sichuan Basin. Natural Gas Industry 38, 10-20. the Sichuan Basin, the less-proved natural gas resources in the Mid-Permian strata are highly potential for exploration. In this paper, sedimentary and reservoir characteristics of Mid-Permian natural gas in the basin were analyzed. On this basis, researches were conducted on hydrocarbon supply, reservoir and trap types, preservation conditions, structure, and phases and patterns of hydrocarbon accumulation to highlight the controlling factors for the enrichment of Mid-Permian natural gas in the basin and the orientation of future exploration operations. Research results are as follows. First, the Mid-Permian natural gas reservoirs in the Sichuan Basin are characterized by multiple sources from different layers, existence of reservoirs and traps of various types, formation of different reservoirs at different stages and other features. Second, hydrocarbon source rocks are predominantly in the Permian strata. There are also some hydrocarbon source rocks in the Lower Cambrian Qiongzhusi and Lower Silurian Longmaxi Fms. The gas-generation center of Mid-Permian Fms lies in the northwestern and central–southern parts of the Sichuan Basin. With a gas-generation intensity of 26×108～44×108 m3/km2, it has the necessary material basis available for the formation of large- or medium-sized gas fields. Third, the Mid-Permian strata contain dolomite and karst fractured-vuggy limestone reservoirs, with the former distributed predominantly in grain beach or around basement faults, and the latter distributed extensively in middle and upper parts of the Maokou Fm. Fourth, the presence of high-quality hydrocarbon source rocks, and dolomitization and epigenetic karstification of reservoirs are controlling factors for the distribution of large- and medium-sized gas fields. Fifth, the Indosinian paleo-uplifts are favorable zones for the accumulation of hydrocarbons, and the Himalayan is the key period of oil and gas adjustment. In conclusion, in the Mid-Permian Qixia Fm, the favorable exploration zones are represented by platform margin beaches mainly along the Guanyuan–Jiangyou and Dujiangyan areas in the NW Sichuan Basin, followed by platform margins in the SW Sichuan Basin, and intraplatform beaches predominantly in the Gaoshiti–Moxi area in the central and southern Sichuan Basin. Besides, in the Mid-Permian Maokou Fm, the favorable exploration zones are mainly the Luzhou–Neijiang area, followed by the Shuangyushi–Nanchong, Wolonghe–Shizhu, Gaoshiti–Moxi, Dazhou–Kaijiang, Jiulongshan and other areas.Zhang, K., Cheng, Y., Wang, L., 2018. Experimental study on the interactions of supercritical CO2 and H2O with anthracite. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 40, 214-219. better understand the mechanism of interactions of supercritical CO2 (SCCO2) and H2O, untreated, SCCO2 treated and SCCO2-H2O treated anthracites were adopted to analyze changes in pore structure, adsorption capacity. Observations from experimental data reveal that mineral and other substances in the fractures and matrix of coal body are dissolved and mobilized by the carbonic acid formed from the mixture of SCCO2 and H2O, which may contribute to smaller pore development and enhance the adsorption capacity. These findings may provide new insights into effective and safe storage of CO2 in coal reservoir.Zhang, K., Jiang, Z., Xie, X., Gao, Z., Liu, T., Yin, L., Jia, C., Song, Y., Shan, C.a., Wu, Y., Wang, P., 2018. Lateral percolation and its effect on shale gas accumulation on the basis of complex tectonic background. Geofluids 2018, Article 5195469. a result of complex tectonic background, shale gas in China exhibits differential enrichment. Choosing a favorable exploration target accurately is a crucial problem to be solved. In this study, the tests show that there is a superior transportation pathway within shale layer. Gas in the shale layer percolates much more in the direction parallel to the plane. Therefore, the accumulation pattern of shale gas indicates a complex tectonic background. Gas in the lower part of the structure diffuses and percolates in the vertical direction into the surrounding rock. Most gas percolates towards the high part of the structure in the direction parallel to the plane. When the shale was exposed, gas percolated along the parallel direction into the air. In the case of fracture development, if there is a reverse fault, gas would be enriched in the footwall. However, if there is an unsealed fault, it would become a pathway for gas migration. The above accumulation pattern was proved in several Areas. Also, this research presented a basis of evaluation units division. According to the buried depth, fractures, and structural position, Xiuwu Basin was divided into five evaluation units and Unit A3 is the most favorable exploration target.Zhang, L., Liu, C.-W., Zhang, Q., 2018. Online 2D-LC-MS/MS platform for analysis of glycated proteome. Analytical Chemistry 90, 1081–1086. proteins are emerging as good indicators for diabetes and age related diseases. However, the platform for analysis of glycated proteome has been relatively less well established. We here introduce an online 2D-LC-HCD-MS/MS platform for comprehensive glycated peptide quantification. This platform includes a boronate affinity column in the first dimension for enrichment, reversed phase nanoLC column in the second dimension for separation, a benchtop Orbitrap mass spectrometer with HCD-MS/MS for peptide sequencing, and MaxQuant bioinformatics tool for identification and quantification of glycated peptides. This online 2D-LC-HCD-MS/MS platform has high enrichment efficiency with 85% of identified peptides in the enriched fraction as glycated, high sensitivity for detection of glycated peptides with LOD and LOQ at 1.2 and 2.4 pg, respectively, and high reproducibility with interday CVs < 20% for 80% of the glycated peptides. The number of glycated peptides quantified in in vitro glycated human plasma increased more than 3-fold using this platform in comparison to that obtained using 1D-LC-HCD-MS/MS platform without boronate affinity enrichment. Application of this online platform to human plasma identified 376 glycated peptides from 10 μg of protein digests. This highly sensitive and reproducible online 2D platform is promising for glycated protein analysis of complex clinical samples.Zhang, M., Fu, X., Wang, H., 2018. Analysis of physical properties and influencing factors of middle-rank coal reservoirs in China. Journal of Natural Gas Science and Engineering 50, 351-363. coal mainly refers to bituminous coal with the vitrinite maximum reflectance (Ro,max) between 0.65% and 2.0%. Based on the results of a proximate analysis, maceral composition, high-pressure mercury intrusion porosimetry (MIP) experiments and isothermal adsorption experiments, combined with gas content and permeability derived from well test, the pore size distribution (PSD), adsorption characteristics and the evolutionary paths of middle-rank coal were analyzed, and the influencing factors of the gas-bearing property and permeability were discussed. The results indicated that as Ro,max increases, the porosity shows first decreasing and then increasing, with the minimum values reached when Ro,max?=?～1.0%. The volume and specific surface area of the total pores have the same evolutionary paths with each class of pores, first decreasing and then increasing with the increases of Ro,max. The minimum value appears when Ro,max is between 1.2% and 1.3%. As Ro,max increases, VL increases while PL first increases and then decreases, the maximum value is again reached at near Ro,max?=?1.3%. The gas content increases with the increases of Ro,max, first increasing and then decreasing with the increases of buried depth, and the buried depth at 950?m is the critical depth of gas content. There is a positive correlation between gas content and gas saturation; the permeability decreases with the increases of buried depth, and increases with the increases of coal reservoir porosity. Ground stress is the main controlling factor of reservoir permeability.Zhang, S., Huang, Z., Huang, P., Wu, X., Xiong, C., Zhang, C., 2018. Numerical and experimental analysis of hot dry rock fracturing stimulation with high-pressure abrasive liquid nitrogen jet. Journal of Petroleum Science and Engineering 163, 156-165. liquid nitrogen (L-nitrogen) jet fracturing is a novel technology, which is expected to be suitable for hot dry rock (HDR) fracturing. In this paper, numerical simulation has been presented to analyze the fluid flow, heat transfer and thermal stresses distribution in HRD fracturing with abrasive L-nitrogen jet. The simulation is carried out with a three-dimensional model in transient state. The low Reynolds number κ-ε model is employed to accurately predict the near wall flow. The heat transfer between L-nitrogen and hot rock on solid-liquid interface is computed by an inverse method of conjugate heat transfer. The thermo-elastic model is used to calculate the thermal stresses distribution in rock. Numerical results indicate that abrasive L-nitrogen jet has a better performance in perforation than abrasive water and supercritical CO2 jet. Great tensile stress distributes in the region near interface, however, its affected depth is limited. This tensile is expected to be favor for fractures generation and growth along perforation direction. Short perforation length can promote the heat transfer on interface. The initial rock temperature has an important influence on values of thermal stresses. Experiments, in which the hot granite specimens with a small hole in center were impacted by L-nitrogen jet, have been conducted to validate the effect of thermal stresses on fracturing. The fractal method is adopt to quantitatively describe the flow and transport capability in rock masses. Experimental results show that numerous thermal cracks were generated on the interface. Rising rock temperature can significantly increase the number and size of thermal cracks and improve the connectivity of fractured rock, which are benefit to fracture initiation during L-nitrogen jet fracturing. The results in this paper would shed light on L-nitrogen jet fracturing for HDR as well as some high-temperature oil reservoirs.Zhang, S., Liu, J., Wei, M., Elsworth, D., 2018. Coal permeability maps under the influence of multiple coupled processes. International Journal of Coal Geology 187, 71-82. evolution of coal permeability has been studied exhaustively and a broad array of permeability models developed. These models are normally derived under the assumption of fluid pressure equilibrium between matrix and fractures. Under this assumption, these models define coal permeability as a function of either gas pressure or effective stress. However, experimental observations indicate that coal permeability may change significantly under a constant observed gas pressure or assumed effective stress. The goal of this study is to resolve this contradiction. In this study, we hypothesize that coal permeability is closely related to the expansion of gas-invaded area/volume as a concentration front propagates from the fracture wall into the matrix. When this invaded volume/area is localized around the fracture, the gas-induced swelling reduces the coal permeability. When the area spreads throughout the entire matrix, gas-induced swelling may increase coal permeability. This important mechanism of transition from local (to the fracture) swelling to global (into the matrix medium) swelling is incorporated into an overlapping dual permeability approach. In this approach, the coal is characterized by a well-defined macroscopic model consisting of four overlapping/interpenetrating continua comprising: (1) coal matrix system; (2) coal fracture system; (3) gas flow in the matrix system; and (4) gas flow in the fracture system. These four continua are connected through a full set of cross-coupling relations, including (1) local force balance between the matrix and the fracture; (2) local deformation compatibility between the matrix and the fracture; and (3) mass exchange between the matrix and the fracture. We apply this approach to generate coal permeability maps under the influence of multiple coupled processes. For a particular coal sample, the permeability is bounded by the solutions for the free-swelling case (upper bound) and for the constant volume case (lower bound). The variations of permeability between the upper and lower bounds under a constant gas pressure are determined by the dynamics of matrix-fracture interactions. Current experimental measurements are bounded by these limits depending on the state of equilibrium between matrix and fractures. These model results are verified against experimental observations reported in the literature.Zhang, S., Zhang, S., Ge, X., Zhang, Y., 2018. Evaluation of bitumen intervals in the carbonate reservoir, case study in Y oilfield of Iran. Petroleum Science and Technology 36, 115-121. bitumen intervals, which were drilled at Y oilfield of Iran, often reduce drilling efficiency. The characteristics of high natural gamma radioactive(GR), low uranium-free gamma(KTH), and poor GR-KTH relationship have been found to detect the bitumen by logging. Conventional porosity logs, Poisson's ratio, the P & S-wave velocity ratio and the wave impedance, derived from logging, can be used to identify the heavy oil bitumen. The bitumen distribution can be predicted by the log interpretation. Implementation of log evaluation allows better solving the bitumen intervals identify problems, and also to helps in enhancing development efficiency in the similar petroleum reservoirs.Zhang, Y., Bao, Z., Yang, F., Mao, S., Song, J., Jiang, L., 2018. The controls of pore-throat structure on fluid performance in tight clastic rock reservoir: A case from the Upper Triassic of Chang 7 Member, Ordos Basin, China. Geofluids 2018, Article 3403026. characteristics of porosity and permeability in tight clastic rock reservoir have significant difference from those in conventional reservoir. The increased exploitation of tight gas and oil requests further understanding of fluid performance in the nanoscale pore-throat network of the tight reservoir. Typical tight sandstone and siltstone samples from Ordos Basin were investigated, and rate-controlled mercury injection capillary pressure (RMICP) and nuclear magnetic resonance (NMR) were employed in this paper, combined with helium porosity and air permeability data, to analyze the impact of pore-throat structure on the storage and seepage capacity of these tight oil reservoirs, revealing the control factors of economic petroleum production. The researches indicate that, in the tight clastic rock reservoir, largest throat is the key control on the permeability and potentially dominates the movable water saturation in the reservoir. The storage capacity of the reservoir consists of effective throat and pore space. Although it has a relatively steady and significant proportion that resulted from the throats, its variation is still dominated by the effective pores. A combination parameter (ε) that was established to be as an integrated characteristic of pore-throat structure shows effectively prediction of physical capability for hydrocarbon resource of the tight clastic rock reservoir. Zhang, Y., Liu, S., Fan, L., Zhou, N., Mubashar Omar, M., Peng, P., Anderson, E., Addy, M., Cheng, Y., Liu, Y., Li, B., Snyder, J., Chen, P., Ruan, R., 2018. Oil production from microwave-assisted pyrolysis of a low rank American brown coal. Energy Conversion and Management 159, 76-84. energy from brown coal is an everlasting pursuit. This study detailed the oil production from microwave-assisted pyrolysis of a low rank American brown coal. The effects of feedstock load (20, 30, 40, 50, and 60?g), pyrolysis temperature (550, 600, 650, 700, and 750?°C) and heating time (10, 15, 20, 25, and 30?min) on the oil yields and compounds were also investigated. The results showed that the oil yields obtained were 13.17–22.97?wt% of the brown coal on ash free basis, and it increased initially and then decreased with increasing feedstock load, pyrolysis temperature, and heating time. Light oil and heavy oil accounted for 33.49–65.08?wt% and 34.92–61.94?wt% of the oil yields, and the compound weights were 1.21–5.41?wt% and 90.75–98.14?wt%, respectively. The highest oil yield was achieved at the feedstock load of 50?g, pyrolysis temperature of 700?°C and heating time of 20?min, and it was very close to the oil yield at high heating rates of 2000–10,000?°C/s for the electrical heating pyrolysis. The results obtained from this study not only detailed the oil yields and compounds obtained from microwave-assisted pyrolysis of a brown coal but also demonstrated the effects of feedstock load, pyrolysis temperature and heating time on the oil production. The results also indicated that microwave-assisted pyrolysis may be a more suitable technology for obtaining oil from brown coals than electrical heating pyrolysis.Zhang, Y., Yu, W., Li, Z., Sepehrnoori, K., 2018. Simulation study of factors affecting CO2 Huff-n-Puff process in tight oil reservoirs. Journal of Petroleum Science and Engineering 163, 264-269. injection is one of the effective enhanced oil recovery (EOR) methods in conventional oil reservoirs, which has been widely applied in the tight oil reservoirs. Although there are some efforts on the investigation of engineering parameters such as fracture half-length, fracture conductivity, and fracture height, the effects of CO2 molecular diffusion, nanopore confinement, and stress-dependent deformation on CO2-EOR effectiveness are poorly understood. In this paper, we modified the conventional phase-equilibrium model to accurately compute the phase behavior in shale nanopores. Subsequently, we investigated the minimum miscibility pressure (MMP) of CO2-EOR process under different pore sizes. Afterwards, we evaluated the well performance of CO2 Huff-n-Puff process by fully capturing physics of CO2 molecular diffusion and nanopore confinement. The impacts of matrix permeability, CO2 injection rate and stress-dependent deformation mechanisms on the CO2 Huff-n-Puff process are examined in detail. The results show that CO2 diffusion and nanopore confinement play an important role in improving the oil recovery factor, which should be correctly implemented in reservoir simulation model. Additionally, matrix permeability, CO2 injection rate, and stress-dependent deformation mechanisms significantly influence the CO2 Huff-n-Puff process. This work enables operators to optimize the CO2 Huff-n-Puff process to improve the efficiency of CO2-EOR and CO2 storage in tight oil reservoirs.Zhao, F., Li, P., Guo, C., Shi, R.-J., Zhang, Y., 2018. Bioaugmentation of oil reservoir indigenous Pseudomonas aeruginosa to enhance oil recovery through in-situ biosurfactant production without air injection. Bioresource Technology 251, 295-302. the anoxic conditions within oil reservoirs, a new microbial enhanced oil recovery (MEOR) technology through in-situ biosurfactant production without air injection was proposed. High-throughput sequencing data revealed that Pseudomonas was one of dominant genera in Daqing oil reservoirs. Pseudomonas aeruginosa DQ3 which can anaerobically produce biosurfactant at 42?°C was isolated. Strain DQ3 was bioaugmented in an anaerobic bioreactor to approximately simulate MEOR process. During bioaugmentation process, although a new bacterial community was gradually formed, Pseudomonas was still one of dominant genera. Culture-based data showed that hydrocarbon-degrading bacteria and biosurfactant-producing bacteria were activated, while sulfate reducing bacteria were controlled. Biosurfactant was produced at simulated reservoir conditions, decreasing surface tension to 33.8?mN/m and emulsifying crude oil with EI24?=?58%. Core flooding tests revealed that extra 5.22% of oil was displaced by in-situ biosurfactant production. Bioaugmenting indigenous biosurfactant producer P. aeruginosa without air injection is promising for in-situ MEOR applications.Zhao, T., Li, X., Ning, Z., Zhao, H., Li, M., 2018. Molecular simulation of methane adsorption on type II kerogen with the impact of water content. Journal of Petroleum Science and Engineering 161, 302-310. on realistic kerogen model, the effects of water content on methane (CH4) adsorption capacity were studied qualitatively and quantitatively using the molecular dynamics (MD) and Monte Carlo (MC) simulation methods. The methane single component adsorption process under the dry condition, methane and water two components competitive adsorption on dry kerogen, and methane single component adsorption on moist conditions (0.6, 1.2, 1.8, 2.4, and 3.0 wt%) were simulated. Adsorption processes under different temperatures (298, 323, and 348 K) were modeled, and the pressure was up to 20 MPa. Simulation results show that the absolute adsorption capacity of CH4 on the dry kerogen increases with the increasing pressure but decreases with the increasing temperature. The excess adsorption capacity increases up to a specific pressure and then declines with the increasing pressure. The competitive adsorption simulation results indicate that kerogen prefers to adsorb water (H2O) than CH4. At the pressure of 20 MPa and temperature of 298 K, the competitive adsorption capacity of CH4 (0.53 mmol/g) is only a seventh of the single component adsorption capacity of CH4 (3.92 mmol/g) on dry kerogen. The CH4 adsorption capacity on moist kerogen also decreases with the increasing moist content. Compared with the absolute adsorption capacity on the dry kerogen (3.92 mmol/g), the adsorption capacity on the moist kerogen reduces about 16%, 30%, 40%, 47%, and 55% at 20 MPa, respectively. The reduction of the adsorption capacity is attributed to the strong attraction between kerogen and water. At last, the effect of the water content on the shale gas adsorption is discussed under the micro-scale, and the adsorption capacity reduction curves were calculated under the reservoir conditions. The results show that the adsorption capacity of shale gas is significantly affected by water at the economically recoverable depth. The dry condition is considered as the situation of the maximal adsorption capacity of the shale gas reservoir. This study can serve as a reference for better understanding of the transportation and storage mechanism of shale gas under the reservoir conditions.Zhao, Y., Fu, D., Liu, Y., Liang, X., Xue, H., 2018. Separation of chemical compositions in root of Rumex patientia L. with off-line two-dimensional liquid chromatography. Chinese Journal of Chromatography 36, 37-42. innovative analytical method based on the off-line two-dimensional reversed-phase/reversed-phase liquid chromatography (2D-RPLC/RPLC) was established to separate the components of root of Rumex patientia L. The chromatograms of ethyl acetate extract of root of Rumex patientia L. on a phenyl/tetrazolium column (250 mm×4.6 mm, 7 μm) and a Unitary C18 column (250 mm×4.6 mm, 7 μm) were compared, and they showed different separation abilities. A phenyl/tetrazolium column was used for the first dimensional separation with 0.1% (v/v) formic acid aqueous solution and methanol as mobile phases, and 18 fractions was collected. The second dimensional liquid chromatography analysis was carried out on a Unitary C18 column with 0.1% (v/v) formic acid aqueous solution and methanol as mobile phases. Based on the experiment setup and results, it was concluded that off-line 2D-LC can be an effective method for the separation of the trace components and the screening of active compounds of root of Rumex patientia L.Zhao, Z., Li, R., Feng, W., Yu, Q., Yang, H., Zhu, L., 2017. Enrichment conditions and favorable zone prediction of Wufeng–Longmaxi shale gas reservoirs in the northern Yunnan–Guizhou provinces, China Natural Gas Industry 37, 26-34. shale of Upper Ordovician Wufeng–Lower Silurian Longmaxi Fms in the northern Yunnan–Guizhou provinces of China has a good prospect of shale gas resources. At present, however, the enrichment laws of shale gas accumulation under complex geological conditions are not clear. In this paper, the shale gas enrichment conditions (e.g. the depositional environment of Wufeng–Longmaxi Fms, distribution and depth of quality shale, organic geochemical indicators, reservoir parameters and gas bearing property) were analyzed systematically based on the latest drilling data, combined with field outcrop profile observation and sample test results. Then the favorable zones of quality shale were predicted and their exploration potential was evaluated. And the following research results were obtained. First, the Wufeng–Longmaxi shale gas reservoirs in this area are deposited in an environment of shallow–deep water shelf, and the thickness and distribution of quality shale are controlled by the depositional environment. The burial depth of bottom boundary is dominated by a historical depositional pattern and the later tectonic movement reworking and it is in the range of 0–4 000 m. And the depositional thickness of quality shale is between 0 and 60 m. Second, the quality shale in this area is characterized by high TOC content (1.0–4.0%), high thermal evolution degrees (over-mature), stable types of organic matters (TypeⅠ–Ⅱ1), high hydrocarbon generating intensity (1.0×108–4.0×108 m3/km2) and a great hydrocarbon generating potential. Third, the quality shale has a better fracturing potential due to its higher content of brittle mineral, and there are various types of reservoir space with developed micro fractures. And fourth, the preservation condition in this area is locally good and it is geologically favorable for shale gas accumulation. It is concluded that western Yanjin, southern Junlian, Weixin–Xuyong–Gulin and eastern Xishui are the most favorable shale gas exploration zones in the northern Yunnan–Guizhou provinces of China, and they are superior in the shale gas accumulation of Wufeng–Longmaxi Fms, presenting a great potential of shale gas exploration.Zhao, Z., Li, Y., Yu, Q., Zhang, Y., 2018. Ferroferric oxide triggered possible direct interspecies electron transfer between Syntrophomonas and Methanosaeta to enhance waste activated sludge anaerobic digestion. Bioresource Technology 250, 79-85. was reported to enrich H2-utilizing methanogens that enhanced interspecies H2 transfer, while Fe(III) oxide served as a conductive material to promote direct interspecies electron transfer (DIET). However, the interaction of these two modes in anaerobic digestion has not been clarified yet. In this study, when adding Fe3O4 and ZVI simultaneously into an anaerobic digester, the abundance of hydrogenotrophic methanogens decreased drastically compared to ZVI-added digester and Fe-free digester. However, the methane production of ZVI?+?Fe3O4 added digester were 68.9% higher than Fe-free digester and 20.0% higher than ZVI-added digester, respectively. Sludge reduction rate of these three digesters also showed similar results. These indicated that hydrogenotrophic methanogenesis was not the main reason for methanogenesis in Fe3O4-added digester. Instead, Syntrophomonas and Methanosaeta were specially enriched in Fe3O4-added digesters, which implied that the potential DIET between Syntrophomonas and Methanosaeta was likely a crucial reason for accelerating anaerobic digestion of waste sludge.Zheng, M., Wang, W., Hayes, M., Nydell, A., Tarr, M.A., Van Bael, S.A., Papadopoulos, K., 2018. Degradation of Macondo 252 oil by endophytic Pseudomonas putida. Journal of Environmental Chemical Engineering 6, 643-648. endophytic microbes, accustomed to the Macondo oil-spill environment, may be ideal candidates for crude-oil degradation, bioremediation and endophyte-assisted phytoremediation. We tested both single strain and bacteria consortia for their ability to degrade weathered crude oil, over 25?days, and found the single strain Pseudomonas putida (P. putida) exhibited the best performance for degrading all alkanes from C14 to C32 and 61.01% of the Total Petroleum Hydrocarbons (TPHs), but bacterial consortia did not degrade as much of the n-alkanes as the single strain, with TPHs degradation ranging from 28.4% to 51.5%. This is the first time the endophyte P. putida has been shown to improve the degradation of crude oil, demonstrating the potential of this strain to benefit biological remediation. We did not find any correlation between bio-surfactant production and oil degradation.Zheng, W., Qi, Y., Xing, Z., Bai, W., Chen, B., Li, X., 2017. Characteristics and paleoenvironmental significance of microbially induced sedimentary structures (MISSs) in terrestrial P-T boundary in Jiyuan, Western Henan Province. Acta Sedimentologica Sinica 35, 1121-1132. have firstly reported the presence of eight kinds of microbially induced sedimentary structures (MISSs) or sedimentary surface textures, including growth ridges, growth postulas, curved desiccation cracks, spindle-shaped cracks, "Manchuriophycus" structures, dendritic desiccation cracks, polygonal desiccation cracks and desiccation cracks from the terrestrial upper Permian Sunjiagou Formation and lower Triassic Liujiagou Formation in Jiyuan western Henan. Large U ridges, oriented sand quartz, mica grains and thin clayey laminae arranged parallel to bedding plane are the main features visible under the microscope. A series of evidence indicate that the Jiyuan MISSs are of biogenic origin. Compared with MISSs of the Mesoproterozoic Yunmengshan Formation in Lushan, the Mesoproterozoic Changchougou Formation in Licheng, Lower Triassic Liujiagou Formation in Yiyang and Liulin, we concluded that microbially induced sedimentary structures has special taphonomic characteristics and was controlled by the end-Permian mass extinction, sedimentary environments and climate factor in Jiyuan. MISSs of Jiyuan stands for terrestrial ecosystems following the end-Permian mass extinction with rich microbial community, scarce metazoan, poor plant, hot weather and serious soil erosion.Zhou, R., Zhou, Y., Mao, T., Jiang, J., 2018. Determination of fatty acids in natural cream and artificial cream by comprehensive two-dimensional gas chromatography-mass spectrometry Chinese Journal of Chromatography 36, 43-50. method for the determination of 37 fatty acids in natural cream and artificial cream was developed by comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC-MS). The samples were extracted with toluene and acetyl chloride-methanol (1:9,v/v) solution was added to the extract for fat esterification. Finally, the fatty acids were analyzed by GC×GC-MS. The GC conditions were as follows:a DB-5 column (30 m×0.25 mm×0.25 μm) was set as the 1st dimensional column and a BPX-50 column (2.5 m×0.1 mm×0.25 μm) was the 2nd dimensional column. The primary oven temperature was programmed from 50℃ (held for 2 min) to 180℃ at a rate of 20℃/min, followed by an increase to 250℃ at 2.5℃/min, then raised up to 300℃ (held for 5 min) at 3℃/min. The ion source temperature was 200℃ with auxiliary temperature of 300℃ in scan mode. All fatty acids were separated effectively and determined accurately while the modulation period was 5s and the scan range of MS was m/z 40-385. This procedure was applied to analyze the fatty acids in commercial natural cream and artificial cream from Chinese markets, among which we found the characteristic components in different kinds of samples. Compared with gas chromatography-flame ionization detector (GC-FID), GC×GC-MS method was more sensitive and more components of fatty acids were detected. Conclusively, this work suggests a new technical approach in analyzing fatty acids in natural cream and artificial cream, which is meaningful to ensure the quality identification and safety of natural cream.Zhou, X., Yuan, Q., Peng, X., Zeng, F., Zhang, L., 2018. A critical review of the CO2 huff ‘n’ puff process for enhanced heavy oil recovery. Fuel 215, 813-824. oil resources have become increasingly important in recent years due to a reduction in light oil production and an increase in energy consumption. A large number of heavy oil reserves are found all over the world, and traditional production methods, such as solution gas drive, water flooding, etc., cannot gain a high heavy oil recovery factor, because of the high viscosity of the heavy oil. Although the thermal method has proven efficient and economical to produce heavy oil, it cannot be applied in deep reservoirs or reservoirs with thin pay zones due to the huge heat loss in these reservoirs. Thus, in order to enhance heavy oil production, several CO2 injection processes are applied in heavy oil reservoirs. Among them, the CO2 huff ‘n’ puff method has proven the most applicable.In this research, the CO2 huff ‘n’ puff process is reviewed in detail. Among the mechanisms of the CO2 huff ‘n’ puff process in enhancing heavy oil production, the formation of foamy oil, viscosity reduction, and oil swelling are the most important ones, so that effect of foamy oil in the production stage is studied, and the viscosity reduction ratio with CO2 injection and oil swelling factors at different temperatures and pressures are summarized. In addition, the diffusion coefficient, which indicates the mass transfer rate and amount of CO2 dissolved into heavy oil through the two-phase interface of CO2 and heavy oil, is analyzed in various heavy oil reservoirs at different temperatures and pressures.Experimental studies on the CO2 huff ‘n’ puff process indicate that the process applied in the heavy oil reservoir is successful and can be carried out with an oil viscosity up to 28,646?mPa·s and a reservoir permeability up to 24,200?mD. In pilot tests in the field, economical CO2 huff ‘n’ puff processes have been applied in the heavy oil reservoirs with an oil gravity as low as 4 °API, a reservoir depth as high as 1985?m, and a pay zone as low as 12.2?m. Specifically, CO2 utilization can be as low as 4.2 Mscf/Stb. Numerical simulation studies can gain very good simulation results on both experimental and pilot tests studies. However, mathematical models have seldom been published on CO2 huff ‘n’ puff processes in heavy oil reservoirs.Zhu, D., Meng, Q., Liu, Q., Zhou, B., Jin, Z., Hu, W., 2018. Natural enhancement and mobility of oil reservoirs by supercritical CO2 and implication for vertical multi-trap CO2 geological storage. Journal of Petroleum Science and Engineering 161, 77-95. accumulation and production of both deep mantle-derived CO2 and light oil were discovered in the Huangqiao reservoir, which is located in the Subei Basin, East China. The Huangqiao reservoir shows that both CO2 and oil are entrapped in and produced from vertical multi-traps. The effects of deep CO2 on the accumulation and production of oil under natural conditions and the implications for CO2 geological storage are investigated in detail. The fluid inclusions in quartz or calcite veins from the Silurian Fentou Formation (S2-3f), Permian Longtan Formation (P2l) and Triassic Qinglong Formation (T1q) have homogenization temperatures (Ths) that display peak ranges of 180°C–190 °C, 170°C–180 °C and 150°C–160 °C, respectively. The Ths are higher than the formation temperatures. The calcite veins have light carbon and oxygen isotope compositions and have high 87Sr/86Sr ratios and positive Eu anomalies. These characteristics reveal the activities of deep CO2-rich hydrothermal fluids in the basin strata. The feldspar in the S2-3f and P2l sandstone reservoirs underwent significant dissolution because of the presence of CO2-rich fluids, forming of a large amount of secondary pores in the sandstone reservoirs and enhancing the reservoirs’ physical properties. The measured porosity reaches 12.3%. CO2 in a supercritical state extracted or dissolved light petroleum components out of sedimentary rocks and then carried them towards reservoirs. Thus, CO2 and oil co-accumulated in the enhanced reservoirs, e.g. S2-3f, P2l and T1q. During drilling development, this supercritical CO2 naturally increased the mobility of oil, resulting in the co-production of highly pure CO2 and light oil. Based on the unique features of the Huangqiao CO2-oil reservoir, we propose a new CO2 geological storage model, namely, a vertical multi-trap geological storage model, which can either entrap large volumes of CO2 or lower the risk of long-term storage.Zhu, G., Du, D., Chen, W., Sun, Q., Li, T., Zhang, Z., Chen, Z., 2017. The discovery and exploration significance of the old thick black mudstones in the southwest margin of Tarim Basin. Acta Petrolei Sinica 38, 1335-1342. is an important petroliferous strata in the world wide,but no breakthrough has been achieved in exploring the Precambrian strata of Tarim Basin due to huge depth,and the existence of high-quality source rocks remains uncertain. At present,more than thirty exploratory wells have been deployed within the southwest Tarim Basin and the pediment region of Kunlun Mountains with a total area exceeding 100 000 km2. Despite the discoveries of some marine hydrocarbon fields including Hetianhe,Bashituopu,Yubei and Luosi 2,the Cambrian or Ordovician source rocks are never encountered,and there is also a dispute on the hydrocarbon source. Recently,a set of black shales and mudstones with huge thickness has been found with favorable outcrops in the exploration of southwest Tarim Basin. The total thickness of mudstones is measured to be more than 140 m (the top is not seen and penetrated by granite),and the TOC (total organic carbon)mainly varies in a range of 0.6% -1.9%,and an average of 1.0% is obtained based on the results of 83 samples. Tmax (maximum pyrolytic temperature)is mainly distributed within 490℃-520℃,equivalent to the Ro of 1.9%-2.9%. Pyrites are very rich in mudstone beds. According to the contact relationship of different members and isotopic chronology,the age of these strata may be determined greater than 517 Ma,primarily considered as Sinian or Nanhua system and temporarily named the "Western Kunlun black rock series". The plate tectonic analysis results show that this set of thick black mudstones is possibly distributed widely in the southwest Tarim Basin,may be controlled by rifting troughs. Thus,this set of black mudstones may be the significant source rocks in the southwest Tarim Basin,indicating the geological conditions for hydrocarbon accumulations in the Precambrian-Cambrian strata. This discovery will definitely promote the hydrocarbon explorations in the deep and ultra-deep strata of the Tarim Basin.Zhu, X., Hitchcock, A.P., Le Nagard, L., Bazylinski, D.A., Morillo, V., Abreu, F., Le?o, P., Lins, U., 2018. X-ray absorption spectroscopy and magnetism of synthetic greigite and greigite magnetosomes in magnetotactic bacteria. Geomicrobiology Journal 35, 215-226. transmission X-ray microscopy at the Fe 2p (L2,3), O1s, C1s, and S2p edges was used to study greigite magnetosomes and other cellular content of a magnetotactic bacterium known as a multicellular magnetotactic prokaryote (MMP). X-ray absorption spectrum (XAS) and X-ray magnetic circular dichroism (XMCD) spectra of greigite (Fe3S4) nanoparticles, synthesized via a hydrothermal method, were measured. Although XAS of the synthetic greigite nanoparticles and biotic magnetosome crystals in MMPs are slightly different due to partial oxidation of the MMP greigite, the XMCD spectra of the two materials are in good agreement. The Fe 2p XAS and XMCD spectra of Fe3S4 are quite different from those of its oxygen analog, magnetite (Fe3O4), suggesting Fe3S4 has a different electronic and magnetic structure than Fe3O4 despite having the same crystal structure. Sulfate and sulfide species were also identified in MMPs, both of which are likely involved in sulfur metabolism.Zhu, Y., Li, Y., Hao, F., Zou, H., Guo, X., 2017. Compositional variations and geochemical significances of stable carbon isotope for organic matters from marine and terrestrial source rocks in Sichuan Basin. Acta Sedimentologica Sinica 35, 1254-1264. 500 kerogens as well selected saturate and aromatic fractions and n-alkanes from various age source rocks in the Sichuan basin were analyzed using MS and GC-ir-MS for δ13C ratios, to characterize the age-trend in organic carbon isotopic composition in marine and terrestrial sediments and their thermal evolution during over-mature stage. Moreover, different kind of marine and terrestrial source rocks with respect to their biological organic sources were distinguished using carbon isotopes in combination with other analytical data. The results indicate the kerogens from marine sediments in Sinian Dengying to middle Triassic Leikoupo Formations in this basin show a trend toward isotopically heavy values with decreasing age, possibly due to biological evolution. Whereas, a reversal isotopic-age trend for the terrigenous organic carbon is observed in upper Triassic Xujiahe to middle Jurassic Qingfoyan Formations and is considered to be dependent of biological source and sedimentary environment. The organic inputs of marine and terrestrial source rocks cannot be differentiated using the carbon isotopic ratios of kerogen, however, it can be distinguished by δ13C values of saturated and aromatic fractions and CV values. The marine and lacustrine source rocks with different facies are of obviously varying δ13C values of kerogens, thus the isotopic ratio, combined with additional relate-source data, can be acted as an indicator for their organic source. Coal and mudstone in coal-bearing strata is not distinguishable for their kerogen carbon isotopes, but has different profiles of n-alkane isotopes with more negative values in mudstone related to coal. The marine (type-Ⅱ)and terrigenous (type-Ⅲ) kerogens both continuously become isotopically enriched in 13C by 1‰~2‰ with maturation during high-over maturity. The negatively sloping curve of carbon isotope for individual n-alkanes from coaly source rock at mature stage is transferred into a flat one at high maturity. These variations in carbon isotope compositions are helpful for oil & gas-rock correlation and hydrocarbon source identification.Zhu, Z., Chen, H., Ren, J., Lu, J.J., Gu, C., Lynch, K.B., Wu, S., Wang, Z., Cao, C., Liu, S., 2018. Two-dimensional chromatographic analysis using three second-dimension columns for continuous comprehensive analysis of intact proteins. Talanta 179, 588-593. develop a new two-dimensional (2D) high performance liquid chromatography (HPLC) approach for intact protein analysis. Development of 2D HPLC has a bottleneck problem – limited second-dimension (second-D) separation speed. We solve this problem by incorporating multiple second-D columns to allow several second-D separations to be proceeded in parallel. To demonstrate the feasibility of using this approach for comprehensive protein analysis, we select ion-exchange chromatography as the first-dimension and reverse-phase chromatography as the second-D. We incorporate three second-D columns in an innovative way so that three reverse-phase separations can be performed simultaneously. We test this system for separating both standard proteins and E. coli lysates and achieve baseline resolutions for eleven standard proteins and obtain more than 500 peaks for E. coli lysates. This is an indication that the sample complexities are greatly reduced. We see less than 10 bands when each fraction of the second-D effluents are analyzed by sodium dodecyl sulfate – polyacrylamide gel electrophoresis (SDS-PAGE), compared to hundreds of SDS-PAGE bands as the original sample is analyzed. This approach could potentially be an excellent and general tool for protein analysis.Zobel, M., Davison, J., Edwards, M.E., Brochmann, C., Coissac, E., Taberlet, P., Willerslev, E., Moora, M., 2018. Ancient environmental DNA reveals shifts in dominant mutualisms during the late?Quaternary. Nature Communications 9, Article 139. snapshots of ancient vegetation have shown that the composition of high-latitude plant communities changed considerably during the late Quaternary. However, parallel changes in biotic interactions remain largely uninvestigated. Here we show how mutualisms involving plants and heterotrophic organisms varied during the last 50,000 years. During 50–25 ka BP, a cool period featuring stadial-interstadial fluctuations, arbuscular mycorrhizal and non-N-fixing plants predominated. During 25-15 ka BP, a cold, dry interval, the representation of ectomycorrhizal, non-mycorrhizal and facultatively mycorrhizal plants increased, while that of N-fixing plants decreased further. From 15 ka BP, which marks the transition to and establishment of the Holocene interglaciation, representation of arbuscular mycorrhizal plants decreased further, while that of ectomycorrhizal, non-mycorrhizal, N-fixing and wind-pollinated plants increased. These changes in the mutualist trait structure of vegetation may reflect responses to historical environmental conditions that are without current analogue, or biogeographic processes, such as spatial decoupling of mutualist partners. ................
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