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GEOCHEMISTRY ARTICLES – December 2018?Analytical ChemistryKe?ili, R., Büyüktiryaki, S., Hussain, C.M., 2019. Advancement in bioanalytical science through nanotechnology: Past, present and future. TrAC Trends in Analytical Chemistry 110, 259-276.Walker, S.W.C., Anwar, A., Psutka, J.M., Crouse, J., Liu, C., Le Blanc, J.C.Y., Montgomery, J., Goetz, G.H., Janiszewski, J.S., Campbell, J.L., Hopkins, W.S., 2018. Determining molecular properties with differential mobility spectrometry and machine learning. Nature Communications 9, Article 5096.Xia, L., Liu, L., Dou, Y., Guo, L., Li, G., Sun, Z., You, J., 2018. A stable mesoporous metal-organic framework as highly efficient sorbent of dispersive micro solid-phase extraction for the determination of polycyclic aromatic hydrocarbons by HPLC. Journal of Separation Science 41, 4331-4339.Zhang, Y., Li, Z., 2019. Raman spectroscopic study of chemical structure and thermal maturity of vitrinite from a suite of Australia coals. Fuel 241, 188-198.Gas Chromatography/GC×GC/GC-MSBahaghighat, H.D., Freye, C.E., Gough, D.V., Synovec, R.E., 2019. Comprehensive two-dimensional gas chromatography and time-of-flight mass spectrometry detection with a 50 ms modulation period. Journal of Chromatography A 1583, 117-123.Carrero-Carralero, C., Escobar-Arnanz, J., Ros, M., Jiménez-Falcao, S., Sanz, M.L., Ramos, L., 2019. An untargeted evaluation of the volatile and semi-volatile compounds migrating into food simulants from polypropylene food containers by comprehensive two-dimensional gas chromatography?time-of-flight mass spectrometry. Talanta 195, 800-806.Catherin, N., Blanco, E., Piccolo, L., Laurenti, D., Simonet, F., Lorentz, C., Leclerc, E., Calemma, V., Geantet, C., 2019. Selective ring opening of decalin over bifunctional RuS2/zeolite catalysts. Catalysis Today 323, 105-111.Cramer, J.A., Hammond, M.H., Loegel, T.N., Morris, R.E., 2018. Evolving window factor analysis-multivariate curve resolution with automated library matching for enhanced peak deconvolution in gas chromatography-mass spectrometry fuel data. Journal of Chromatography A 1581-1582, 125-134.Gough, D.V., Bahaghighat, H.D., Synovec, R.E., 2019. Column selection approach to achieve a high peak capacity in comprehensive three-dimensional gas chromatography. Talanta 195, 822-829.Jaramillo, R., Dorman, F.L., 2018. Retention time prediction in thermally modulated comprehensive two-dimensional gas chromatography: Correcting second dimension retention time modeling error. Journal of Chromatography A 1581-1582, 116-124.Kondyli, A., Schrader, W., 2018. High-resolution GC/MS studies of a light crude oil fraction. Journal of Mass Spectrometry 54, 47-54.Lazzari, E., Polidoro, A.d.S., Onorevoli, B., Schena, T., Silva, A.N., Scapin, E., Jacques, R.A., Caram?o, E.B., 2019. Production of rice husk bio-oil and comprehensive characterization (qualitative and quantitative) by HPLC/PDA and GC?× GC/qMS. Renewable Energy 135, 554-565.Li, W.-y., Wang, W., Mu, H., Li, W., Ye, C.-p., Feng, J., 2019. Analysis of light weight fractions of coal-based crude oil by gas chromatography combined with mass spectroscopy and flame ionization detection. Fuel 241, 392-401.Park, G., Brunswick, P., Kwok, H., Haberl, M., Yan, J., MacInnis, C., Kim, M., Helbing, C., van Aggelen, G., Shang, D., 2018. A rapid gas chromatography tandem mass spectrometry method for the determination of 50 PAHs for application in a marine environment. Analytical Methods 10, 5559-5570.Savareear, B., Escobar-Arnanz, J., Brokl, M., Saxton, M.J., Wright, C., Liu, C., Focant, J.-F., 2018. Comprehensive comparative compositional study of the vapour phase of cigarette mainstream tobacco smoke and tobacco heating product aerosol. Journal of Chromatography A 1581–1582, 105-115.Xiang, Z., Chen, X., Zhao, Z., Xiao, X., Guo, P., Song, H., Yang, X., Huang, M., 2018. Analysis of volatile components in Dalbergia cochinchinensis Pierre by a comprehensive two-dimensional gas chromatography with mass spectrometry method using a solid-state modulator. Journal of Separation Science 41, 4315-4322.Zhu, H., She, J., Zhou, M., Fan, X., 2019. Rapid and sensitive detection of formaldehyde using portable 2-dimensional gas chromatography equipped with photoionization detectors. Sensors and Actuators B: Chemical 283, 182-187.Zou, Y., Niu, S., Dong, L., Hamada, N., Hashi, Y., Yang, W., Xu, P., Arakawa, K., Nagata, J., 2018. Determination of short-chain chlorinated paraffins using comprehensive two-dimensional gas chromatography coupled with low resolution mass spectrometry. Journal of Chromatography A 1581-1582, 135-143.Imaging: Atomic Force MicroscopyCornelissen, R., B?ggild, A., Thiruvallur Eachambadi, R., Koning, R.I., Kremer, A., Hidalgo-Martinez, S., Zetsche, E.-M., Damgaard, L.R., Bonné, R., Drijkoningen, J., Geelhoed, J.S., Boesen, T., Boschker, H.T.S., Valcke, R., Nielsen, L.P., D'Haen, J., Manca, J.V., Meysman, F.J.R., 2018. The cell envelope structure of cable bacteria. Frontiers in Microbiology 9, 3044. doi: 3010.3389/fmicb.2018.03044.Honda, H., Sasahara, A., Onishi, H., 2019. Porphyrins on mica: Atomic force microscopy imaging in organic solvents. Colloids and Surfaces A: Physicochemical and Engineering Aspects 561, 194-200.Liu, L.-Z., Nie, Z.-Y., Yang, Y., Pan, X., Xia, X., Zhou, Y.-H., Xia, J.-L., Zhang, L.-J., Zhen, X.-J., Yang, H.-Y., 2018. In situ characterization of change in superficial organic components of thermoacidophilic archaeon Acidianus manzaensis YN-25. Research in Microbiology 169, 590-597.Liu, Z.L., Rios-Carvajal, T., Andersson, M.P., Ceccato, M., Stipp, S.L.S., Hassenkam, T., 2018. Insights into the pore-scale mechanism for the low-salinity effect: Implications for enhanced oil recovery. Energy & Fuels 32, 12081-12090.Oliveira, I., Gomes, L., Franceschi, E., Borges, G., de Conto, J.F., Albuquerque, F.C., Dariva, C., 2018. Surface and interface characterization of asphaltenic fractions obtained with different alkanes: A study by atomic force microscopy and pendant drop tensiometry. Energy & Fuels 32, 12174-12186.Imaging: SEM, TEM, HIMContreras Ortiz, S.N., Cabanzo, R., Mejía-Ospino, E., 2019. Crude oil/water emulsion separation using graphene oxide and amine-modified graphene oxide particles. Fuel 240, 162-168.Cornelissen, R., B?ggild, A., Thiruvallur Eachambadi, R., Koning, R.I., Kremer, A., Hidalgo-Martinez, S., Zetsche, E.-M., Damgaard, L.R., Bonné, R., Drijkoningen, J., Geelhoed, J.S., Boesen, T., Boschker, H.T.S., Valcke, R., Nielsen, L.P., D'Haen, J., Manca, J.V., Meysman, F.J.R., 2018. The cell envelope structure of cable bacteria. Frontiers in Microbiology 9, 3044. doi: 3010.3389/fmicb.2018.03044.Couasnon, T., Gélabert, A., Ona-Nguema, G., Zanna, S., Ménez, B., Guyot, F., 2019. Experimental assessment of occurrences and stability of lead-bearing minerals in bacterial biofilms. Chemical Geology 505, 23-35.Ding, J., Li, J., Sun, C., Jiang, F., Ju, P., Qu, L., Zheng, Y., He, C., 2019. Detection of microplastics in local marine organisms using a multi-technology system. Analytical Methods 11, 78-87.Divandari, H., Hemmati-Sarapardeh, A., Schaffie, M., Ranjbar, M., 2019. Integrating synthesized citric acid-coated magnetite nanoparticles with magnetic fields for enhanced oil recovery: Experimental study and mechanistic understanding. Journal of Petroleum Science and Engineering 174, 425-436.Gong, Y., Qiao, C., Yu, X., Wang, J., Gong, D., 2019. Study on the ancient putty from the site of the Ming Dynasty (1368–1644?CE) Baochuanchang Shipyard, Nanjing, China. Journal of Archaeological Science: Reports 23, 189-195.Hosseini-Dastgerdi, Z., Meshkat, S.S., 2019. An experimental and modeling study of asphaltene adsorption by carbon nanotubes from model oil solution. Journal of Petroleum Science and Engineering 174, 1053-1061.Li, G.-X., Zhou, S.-Y.-D., Ren, H.-Y., Xue, X.-M., Xu, Y.-Y., Bao, P., 2018. Extracellular biomineralization of gold by Delftia tsuruhatensis GX-3 isolated from a heavy metal contaminated paddy soil. ACS Earth and Space Chemistry 2, 1294-1300.Li, Y., Wang, Z., Pan, Z., Niu, X., Yu, Y., Meng, S., 2019. Pore structure and its fractal dimensions of transitional shale: A cross-section from east margin of the Ordos Basin, China. Fuel 241, 417-431.Omran, B.A., Nassar, H.N., Younis, S.A., Fatthallah, N.A., Hamdy, A., El-Shatoury, E.H., El-Gendy, N.S., 2019. Physiochemical properties of Trichoderma longibrachiatum DSMZ 16517-synthesized silver nanoparticles for the mitigation of halotolerant sulphate-reducing bacteria. Journal of Applied Microbiology 126, 138-154.Pang, Z., Tao, S., Zhang, Q., Zhang, T., Yang, J., Fan, J., Yuan, M., 2018. Secondary migration mechanism and accumulation controlling factors of Jurassic tight oil in Sichuan Basin. Acta Petrolei Sinica 39, 1211-1222.Pearce, J.K., Dawson, G.K.W., Golab, A., Knuefing, L., Sommacal, S., Rudolph, V., Golding, S.D., 2019. A combined geochemical and μCT study on the CO2 reactivity of Surat Basin reservoir and cap-rock cores: Porosity changes, mineral dissolution and fines migration. International Journal of Greenhouse Gas Control 80, 10-24.Sazali, Y.A., Sazali, W.M.L., Ibrahim, J.M., Dindi, M., Graham, G., G?deke, S., 2019. Investigation of high temperature, high pressure, scaling and dissolution effects for Carbon Capture and Storage at a high CO2 content carbonate gas field offshore Malaysia. Journal of Petroleum Science and Engineering 174, 599-606.Shi, Y., Yassin, M.R., Yuan, L., Dehghanpour, H., 2019. Modelling imbibition data for determining size distribution of organic and inorganic pores in unconventional rocks. International Journal of Coal Geology 201, 26-43.Song, W., Wang, D., Yao, J., Li, Y., Sun, H., Yang, Y., Zhang, L., 2019. Multiscale image-based fractal characteristic of shale pore structure with implication to accurate prediction of gas permeability. Fuel 241, 522-532.Valentine, B.J., Hackley, P.C., Hatcherian, J., Yu, J.-J., 2019. Reflectance increase from broad beam ion milling of coals and organic-rich shales due to increased surface flatness. International Journal of Coal Geology 201, 86-101.Wang, Y., Qin, Y., Zhang, R., He, L., Anovitz, L.M., Bleuel, M., Mildner, D.F.R., Liu, S., Zhu, Y., 2018. Evaluation of nanoscale accessible pore structures for improved prediction of gas production potential in Chinese marine shales. Energy & Fuels 32, 12447-12461.Xu, H., Zhou, W., Zhang, R., Liu, S., Zhou, Q., 2019. Characterizations of pore, mineral and petrographic properties of marine shale using multiple techniques and their implications on gas storage capability for Sichuan Longmaxi gas shale field in China. Fuel 241, 360-371.Zhang, C., Shan, W., Wang, X., 2019. Quantitative evaluation of organic porosity and inorganic porosity in shale gas reservoirs using logging data. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 811-828.Zhang, Y., Gao, M., You, Q., Fan, H., Li, W., Liu, Y., Fang, J., Zhao, G., Jin, Z., Dai, C., 2019. Smart mobility control agent for enhanced oil recovery during CO2 flooding in ultra-low permeability reservoirs. Fuel 241, 442-450.Imaging: Xray CTAlvarez, J.O., Saputra, I.W.R., Schechter, D.S., 2018. The impact of surfactant imbibition and adsorption for improving oil recovery in the Wolfcamp and Eagle Ford reservoirs. SPE Journal 23, 2103-2117, SPE-187176-PA.Berthonneau, J., Obliger, A., Valdenaire, P.-L., Grauby, O., Ferry, D., Chaudanson, D., Levitz, P., Kim, J.J., Ulm, F.-J., Pellenq, R.J.M., 2018. Mesoscale structure, mechanics, and transport properties of source rocks’ organic pore networks. Proceedings of the National Academy of Sciences 115, 12365-12370.Li, J., Liu, Y., Gao, Y., Cheng, B., Meng, F., Xu, H., 2018. Effects of microscopic pore structure heterogeneity on the distribution and morphology of remaining oil. Petroleum Exploration and Development 45, 1112-1122.Pearce, J.K., Dawson, G.K.W., Golab, A., Knuefing, L., Sommacal, S., Rudolph, V., Golding, S.D., 2019. A combined geochemical and μCT study on the CO2 reactivity of Surat Basin reservoir and cap-rock cores: Porosity changes, mineral dissolution and fines migration. International Journal of Greenhouse Gas Control 80, 10-24.Sahoo, S.K., Madhusudhan, B.N., Marín-Moreno, H., North, L.J., Ahmed, S., Falcon-Suarez, I.H., Minshull, T.A., Best, A.I., 2018. Laboratory insights into the effect of sediment-hosted methane hydrate morphology on elastic wave velocity from time-lapse 4-D synchrotron X-ray computed tomography. Geochemistry, Geophysics, Geosystems 19, 4502-4521.Wang, Y., Hou, Z.Q., Hu, Y.Z., 2018. In situ X-ray micro-CT for investigation of damage evolution in black shale under uniaxial compression. Environmental Earth Sciences 77, 717.Zhao, Z., Zhou, X.-P., 2019. An integrated method for 3D reconstruction model of porous geomaterials through 2D CT images. Computers & Geosciences 123, 83-94.Liquid Chromatography/LC-MS/SFCChen, R., Zhou, H., Liu, M., Yan, H., Qiao, X., 2019. Ionic liquids-based monolithic columns: Recent advancements and their applications for high-efficiency separation and enrichment. TrAC Trends in Analytical Chemistry 111, 1-12.Chen, Y., Wu, Y., Liu, X., Li, B., Hu, D., Huang, S., Ma, M., Chen, B., 2019. Pulsed elution modulation for on-line comprehensive two-dimensional liquid chromatography coupling reversed phase liquid chromatography and hydrophilic interaction chromatography. Journal of Chromatography A 1583, 98-107.Marlot, L., Batteau, M., De Beer, D., Faure, K., 2018. In silico screening of comprehensive two-dimensional centrifugal partition chromatography × liquid chromatography for multiple compound isolation. Analytical Chemistry 90, 14279-14286 Pirok, B.W.J., Molenaar, S.R.A., Roca, L.S., Schoenmakers, P.J., 2018. Peak-tracking algorithm for use in automated interpretive method-development tools in liquid chromatography. Analytical Chemistry 90, 14011-14019.Santoro, V., Baiocchi, C., Dal Bello, F., Gastaldi, D., Aigotti, R., Zorzi, M., Pellegrino, A., Forte, E., Romaniello, F., Magni, M., Fontana, M., Somenzi, M., Medana, C., 2018. Formation of by-products during chemical interesterification of lipids. Detection and characterization of dialkyl ketones by non-aqueous reversed-phase liquid chromatography-high resolution mass spectrometry and gas chromatography-mass spectrometry. Journal of Chromatography A 1581-1582, 63-70.Zhang, X., Zhao, Y., Cui, X., Wang, X., Shen, H., Chen, Z., Huang, C., Meruva, N., Zhou, L., Wang, F., Wu, L., Luo, F., 2018. Application and enantiomeric residue determination of diniconazole in tea and grape and apple by supercritical fluid chromatography coupled with quadrupole-time-of-flight mass spectrometry. Journal of Chromatography A 1581-1582, 144-155.Mass Spectroscopy/ICR-FTMS/OrbitrapKondyli, A., Schrader, W., 2018. High-resolution GC/MS studies of a light crude oil fraction. Journal of Mass Spectrometry 54, 47-54.Liu, L., Song, C., Tian, S., Zhang, Q., Cai, X., Liu, Y., Liu, Z., Wang, W., 2019. Structural characterization of sulfur-containing aromatic compounds in heavy oils by FT-ICR mass spectrometry with a narrow isolation window. Fuel 240, 40-48.Putman, J.C., Gutiérrez Sama, S., Barrère-Mangote, C., Rodgers, R.P., Lobinski, R., Marshall, A.G., Bouyssière, B., Giusti, P., 2018. Analysis of petroleum products by gel permeation chromatography coupled online with inductively coupled plasma mass spectrometry and offline with Fourier transform ion cyclotron resonance mass spectrometry. Energy & Fuels 32, 12198-12204.Wang, K., Pang, Y., He, C., Li, P., Xiao, S., Sun, Y., Pan, Q., Zhang, Y., Shi, Q., He, D., 2018. Optical and molecular signatures of dissolved organic matter in Xiangxi Bay and mainstream of Three Gorges Reservoir, China: Spatial variations and environmental implications. Science of The Total Environment 657, 1274-1284.Zhou, C., Liu, Y., Liu, C., Liu, Y., Tfaily, M.M., 2019. Compositional changes of dissolved organic carbon during its dynamic desorption from hyporheic zone sediments. Science of The Total Environment 658, 16-23.Ziegs, V., Poetz, S., Horsfield, B., Rinna, J., Hartwig, A., Skeie, J.E., 2018. Deeper insights into oxygen-containing compounds of the Mandal Formation, Central Graben, Norway. Energy & Fuels 32, 12030-12048.Mass Spectroscopy/OtherAlfken, S., W?rmer, L., Lipp, J.S., Wendt, J., Taubner, H., Schimmelmann, A., Hinrichs, K.-U., 2019. Micrometer scale imaging of sedimentary climate archives – Sample preparation for combined elemental and lipid biomarker analysis. Organic Geochemistry 127, 81-91.Mandal, A., Singha, M., Addy, P.S., Basak, A., 2019. Laser desorption ionization mass spectrometry: Recent progress in matrix-free and label-assisted techniques. Mass Spectrometry Reviews 38, 3-21.Peter, K.T., Herzog, S., Tian, Z., Wu, C., McCray, J.E., Lynch, K., Kolodziej, E.P., 2019. Evaluating emerging organic contaminant removal in an engineered hyporheic zone using high resolution mass spectrometry. Water Research 150, 140-152.Thi?ner, J.B., Richter-Brockmann, S., Achten, C., 2018. Analysis of 6- and 7-ring PAH and other non-EPA PAH by atmospheric pressure laser ionization – mass spectrometry (APLI-MS) in environmental certified reference materials NIST 1941b, NIST 1649b, BAM CC013a and IRMM BCR 535. Journal of Chromatography A 1581-1582, 91-99.Wang, Y., Sun, J., Qiao, J., Ouyang, J., Na, N., 2018. A “soft” and “hard” ionization method for comprehensive studies of molecules. Analytical Chemistry 90, 14095-14099.Wu, W., Zhang, D., Chen, K., Zhou, P., Zhao, M., Qiao, L., Su, B., 2018. Highly efficient desalting by silica isoporous membrane-based microfluidic chip for electrospray ionization mass spectrometry. Analytical Chemistry 90, 14395-14401.Metabolomics/LipidomicsFan, K., Zhang, Q., Liu, M., Ma, L., Shi, Y., Ruan, J., 2019. Metabolomic and transcriptional analyses reveal the mechanism of C, N allocation from source leaf to flower in tea plant (Camellia sinensis. L). Journal of Plant Physiology 232, 200-208.Li, H., Qin, Q., Shi, X., He, J., Xu, G., 2019. Modified metabolites mapping by liquid chromatography-high resolution mass spectrometry using full scan/all ion fragmentation/neutral loss acquisition. Journal of Chromatography A 1583, 80-87.Nichols, C.M., Dodds, J.N., Rose, B.S., Picache, J.A., Morris, C.B., Codreanu, S.G., May, J.C., Sherrod, S.D., McLean, J.A., 2018. Untargeted molecular discovery in primary metabolism: Collision cross section as a molecular descriptor in ion mobility-mass spectrometry. Analytical Chemistry 90, 14484-14492.Olivon, F., Elie, N., Grelier, G., Roussi, F., Litaudon, M., Touboul, D., 2018. MetGem software for the generation of molecular networks based on the t-SNE algorithm. Analytical Chemistry 90, 13900-13908.Schwaiger, M., Schoeny, H., El Abiead, Y., Hermann, G., Rampler, E., Koellensperger, G., 2019. Merging metabolomics and lipidomics into one analytical run. Analyst 144, 220-229.Wang, Y., Ma, L., Zhang, M., Chen, M., Li, P., He, C., Yan, C., Wan, J.-B., 2019. A simple method for peak alignment using relative retention time related to an inherent peak in liquid chromatography-mass spectrometry-based metabolomics. Journal of Chromatographic Science 57, 9-16.Wolfender, J.-L., Nuzillard, J.-M., van der Hooft, J.J.J., Renault, J.-H., Bertrand, S., 2018. Accelerating metabolite identification in natural product research: Toward an ideal combination of liquid chromatography–high-resolution tandem mass spectrometry and NMR profiling, in silico databases, and chemometrics. Analytical Chemistry 90, 14095-14099.Yuan, J., Zhang, B., Wang, C., Brüschweiler, R., 2018. Carbohydrate background removal in metabolomics samples. Analytical Chemistry 90, 14100-14104.Zhang, X., Pandiakumar, A.K., Hamers, R.J., Murphy, C.J., 2018. Quantification of lipid corona formation on colloidal nanoparticles from lipid vesicles. Analytical Chemistry 90, 14387-14394.PuppyomicsBelger, J., Br?uer, J., 2018. Metacognition in dogs: Do dogs know they could be wrong? Learning & Behavior 46, 398–413.Archaeological/Art Organic ChemistryBickle, P., 2018. Stable isotopes and dynamic diets: The Mesolithic-Neolithic dietary transition in terrestrial central Europe. Journal of Archaeological Science: Reports 22, 444-451.Caselli, E., Pancaldi, S., Baldisserotto, C., Petrucci, F., Impallaria, A., Volpe, L., D’Accolti, M., Soffritti, I., Coccagna, M., Sassu, G., Bevilacqua, F., Volta, A., Bisi, M., Lanzoni, L., Mazzacane, S., 2018. Characterization of biodegradation in a 17th century easel painting and potential for a biological approach. PLOS ONE 13, Article e0207630.Doering, B., 2019. Effects of fermentation on the carbon and nitrogen isotopes of Chinook salmon. Journal of Archaeological Science: Reports 23, 626-633.Dotsika, E., Michael, D.E., 2018. Using stable isotope technique in order to assess the dietary habits of a Roman population in Greece. Journal of Archaeological Science: Reports 22, 470-481.Dotsika, E., Michael, D.E., Iliadis, E., Karalis, P., Diamantopoulos, G., 2018. Isotopic reconstruction of diet in Medieval Thebes (Greece). Journal of Archaeological Science: Reports 22, 482-491.Fors, Y., Isaksson, S., 2019. GCMS analyses of direct methylated lipids in binders used in 18th–19th century folk painted interiors in H?lsingland, Sweden. Journal of Archaeological Science: Reports 23, 127-136.Gong, Y., Qiao, C., Yu, X., Wang, J., Gong, D., 2019. Study on the ancient putty from the site of the Ming Dynasty (1368–1644?CE) Baochuanchang Shipyard, Nanjing, China. Journal of Archaeological Science: Reports 23, 189-195.Kriss, D., Howe, E., Levinson, J., Rizzo, A., Carò, F., DeLeonardis, L., 2018. A material and technical study of Paracas painted ceramics. Antiquity 92, 1492-1510.Namouchi, A., Guellil, M., Kersten, O., H?nsch, S., Ottoni, C., Schmid, B.V., Pacciani, E., Quaglia, L., Vermunt, M., Bauer, E.L., Derrick, M., Jensen, A.?., Kacki, S., Cohn, S.K., Stenseth, N.C., Bramanti, B., 2018. Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proceedings of the National Academy of Sciences 115, E11790-E11797.Shevchenko, A., Schuhmann, A., Thomas, H., Wetzel, G., 2018. Fine endmesolithic fish caviar meal discovered by proteomics in foodcrusts from archaeological site Friesack 4 (Brandenburg, Germany). PLOS ONE 13, Article e0206483.BiochemistryBarth, C., Weiss, M.C., Roettger, M., Martin, W.F., Unden, G., 2018. Origin and phylogenetic relationships of [4Fe–4S]-containing O2 sensors of bacteria. Environmental Microbiology 20, 4567-4586.Cornelissen, R., B?ggild, A., Thiruvallur Eachambadi, R., Koning, R.I., Kremer, A., Hidalgo-Martinez, S., Zetsche, E.-M., Damgaard, L.R., Bonné, R., Drijkoningen, J., Geelhoed, J.S., Boesen, T., Boschker, H.T.S., Valcke, R., Nielsen, L.P., D'Haen, J., Manca, J.V., Meysman, F.J.R., 2018. The cell envelope structure of cable bacteria. Frontiers in Microbiology 9, 3044. doi: 3010.3389/fmicb.2018.03044.Diefendorf, A.F., Leslie, A.B., Wing, S.L., 2019. A phylogenetic analysis of conifer diterpenoids and their carbon isotopes for chemotaxonomic applications. Organic Geochemistry 127, 50-58.Hill, R.A., Connolly, J.D., 2018. Triterpenoids. Natural Product Reports 35, 1294-1329.Li, X.-G., Zhang, W.-J., Xiao, X., Jian, H.-H., Jiang, T., Tang, H.-Z., Qi, X.-Q., Wu, L.-F., 2018. Pressure-regulated gene expression and enzymatic activity of the two periplasmic nitrate reductases in the deep-sea bacterium Shewanella piezotolerans WP3. Frontiers in Microbiology 9, 3173. doi: 3110.3389/fmicb.2018.03173.Liu, L.-Z., Nie, Z.-Y., Yang, Y., Pan, X., Xia, X., Zhou, Y.-H., Xia, J.-L., Zhang, L.-J., Zhen, X.-J., Yang, H.-Y., 2018. In situ characterization of change in superficial organic components of thermoacidophilic archaeon Acidianus manzaensis YN-25. Research in Microbiology 169, 590-597.Minami, A., Ozaki, T., Liu, C., Oikawa, H., 2018. Cyclopentane-forming di/sesterterpene synthases: widely distributed enzymes in bacteria, fungi, and plants. Natural Product Reports 35, 1330-1346.Singh, P., Patil, Y., Rale, V., 2019. Biosurfactant production: emerging trends and promising strategies. Journal of Applied Microbiology 126, 2-13.Zeng, Z., Liu, X.-L., Wei, J.H., Summons, R.E., Welander, P.V., 2018. Calditol-linked membrane lipids are required for acid tolerance in Sulfolobus acidocaldarius. Proceedings of the National Academy of Sciences 115, 12932-12937.Zhong, Y., Shi, L., 2018. Genomic analyses of the quinol oxidases and/or quinone reductases involved in bacterial extracellular electron transfer. Frontiers in Microbiology 9, 3029. doi: 3010.3389/fmicb.2018.03029.BiodegradationAtashgahi, S., Liebensteiner, M.G., Janssen, D.B., Smidt, H., Stams, A.J.M., Sipkema, D., 2018. Microbial synthesis and transformation of inorganic and organic chlorine compounds. Frontiers in Microbiology 9, 3079. doi: 3010.3389/fmicb.2018.03079.Hellauer, K., Uhl, J., Lucio, M., Schmitt-Kopplin, P., Wibberg, D., Hübner, U., Drewes, J.E., 2018. Microbiome-triggered transformations of trace organic chemicals in the presence of effluent organic matter in managed aquifer recharge (MAR) systems. Environmental Science & Technology 52, 14342-14351.Jones, J.M., Heath, K.D., Ferrer, A., Brown, S.P., Canam, T., Dalling, J.W., 2019. Wood decomposition in aquatic and terrestrial ecosystems in the tropics: contrasting biotic and abiotic processes. FEMS Microbiology Ecology 95, fiy223-fiy223.Liu, S.-H., Zeng, Z.-T., Niu, Q.-Y., Xiao, R., Zeng, G.-M., Liu, Y., Cheng, M., Hu, K., Jiang, L.-H., Tan, X.-F., Tao, J.-J., 2019. Influence of immobilization on phenanthrene degradation by Bacillus sp. P1 in the presence of Cd(II). Science of The Total Environment 655, 1279-1287.Rostami, S., Abessi, O., Amini-Rad, H., 2019. Assessment of the toxicity, origin, biodegradation and weathering extent of petroleum hydrocarbons in surface sediments of Pars Special Economic Energy Zone, Persian Gulf. Marine Pollution Bulletin 138, 302-311.Teramoto, E.H., Chang, H.K., 2019. Geochemical conceptual model of BTEX biodegradation in an iron-rich aquifer. Applied Geochemistry 100, 293-304.Yu, R., Andrachek, R.G., Lehmicke, L.G., Pierce, A.A., Parker, B.L., Cherry, J.A., Freedman, D.L., 2018. Diffusion-coupled degradation of chlorinated ethenes in sandstone: An intact core microcosm study. Environmental Science & Technology 52, 14321-14330.Zhang, C., Huang, L., Tang, Q., Xu, Y., Lan, X., Li, J., Liu, W., Zhao, H., 2018. Electric field assisted technology for improving the screening and application of a thiophene-biodegrading strain. Energy & Fuels 32, 12495-12500.Biodegradation Pathways/GenomicsGregson, B.H., Metodieva, G., Metodiev, M.V., Golyshin, P.N., McKew, B.A., 2018. Differential protein expression during growth on medium versus long-chain alkanes in the obligate marine hydrocarbon-degrading bacterium Thalassolituus oleivorans MIL-1. 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Marine and Petroleum Geology 101, 132-147.Valentine, B.J., Hackley, P.C., Hatcherian, J., Yu, J.-J., 2019. Reflectance increase from broad beam ion milling of coals and organic-rich shales due to increased surface flatness. International Journal of Coal Geology 201, 86-101.Wu, L., Lu, Y., Jiang, S., Liu, X., Liu, Z., Lu, Y., 2019. Relationship between the origin of organic-rich shale and geological events of the Upper Ordovician-Lower Silurian in the Upper Yangtze area. Marine and Petroleum Geology 102, 74-85.Xu, H., George, S.C., Hou, D., 2019. The occurrence of isorenieratane and 24-n-propylcholestanes in Paleogene lacustrine source rocks from the Dongying Depression, Bohai Bay Basin: Implications for bacterial sulfate reduction, photic zone euxinia and seawater incursions. Organic Geochemistry 127, 59-80.Yang, R., He, S., Hu, Q., Zhai, G., Yi, J., Zhang, L., 2018. Comparative investigations on wettability of typical marine, continental, and transitional shales in the Middle Yangtze Platform (China). Energy & Fuels 32, 12187-12197.Zhang, B., He, Y., Chen, Y., Meng, Q., Huang, J., Yuan, L., 2018. Petrologic and geochemical characteristics of high-quality saline lacustrine source rocks in western Qaidam Basin. Petroleum Research 3, 359-369.Zhang, F., Jiao, Y., Wu, L., Rong, H., Li, J., Wan, D., 2019. Enhancement of organic matter maturation because of radiogenic heat from uranium: A case study from the Ordos Basin in China. AAPG Bulletin 103, 157-176.Zhang, Y., Li, Z., 2019. Raman spectroscopic study of chemical structure and thermal maturity of vitrinite from a suite of Australia coals. Fuel 241, 188-198.Zhao, X., Zhou, L., Pu, X., Jiang, W., Jin, F., Xiao, D., Han, W., Zhang, W., Shi, Z., Li, Y., 2018. Hydrocarbon-generating potential of the Upper Paleozoic section of the Huanghua Depression, Bohai Bay Basin, China. Energy & Fuels 32, 12351–12364.Ziegs, V., Poetz, S., Horsfield, B., Rinna, J., Hartwig, A., Skeie, J.E., 2018. Deeper insights into oxygen-containing compounds of the Mandal Formation, Central Graben, Norway. Energy & Fuels 32, 12030-12048.Unconventional ResourcesAlvarez, J.O., Saputra, I.W.R., Schechter, D.S., 2018. The impact of surfactant imbibition and adsorption for improving oil recovery in the Wolfcamp and Eagle Ford reservoirs. SPE Journal 23, 2103-2117, SPE-187176-PA.Berthonneau, J., Obliger, A., Valdenaire, P.-L., Grauby, O., Ferry, D., Chaudanson, D., Levitz, P., Kim, J.J., Ulm, F.-J., Pellenq, R.J.M., 2018. Mesoscale structure, mechanics, and transport properties of source rocks’ organic pore networks. Proceedings of the National Academy of Sciences 115, 12365-12370.Bhowmik, S., Dutta, P., 2019. A study on the effect of gas shale composition and pore structure on methane sorption. 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Comparison of pore systems of clay-rich and silica-rich gas shales in the lower Silurian Longmaxi formation from the Jiaoshiba area in the eastern Sichuan Basin, China. Marine and Petroleum Geology 101, 265-280.Han, X., Nie, J., Guo, J., Yang, L., Xu, D., 2019. Rock physics modelling of elastic properties of organic shale considering kerogen stress and pore pressure distribution. Journal of Petroleum Science and Engineering 174, 891-902.He, Z., Li, S., Nie, H., Yuan, Y., Wang, H., 2019. The shale gas “sweet window”: “The cracked and unbroken” state of shale and its depth range. Marine and Petroleum Geology 101, 334-342.Li, C., Lin, M., Ji, L., Jiang, W., Cao, G., 2018. Rapid evaluation of the permeability of organic-rich shale using the 3D intermingled-fractal model. SPE Journal 23, 2175-2187, SPE-191358-PA.Li, J., Liu, Y., Gao, Y., Cheng, B., Meng, F., Xu, H., 2018. Effects of microscopic pore structure heterogeneity on the distribution and morphology of remaining oil. 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Experimental measurement and analytical estimation of methane absorption in shale kerogen. Fuel 240, 192-205.Pang, Z., Tao, S., Zhang, Q., Zhang, T., Yang, J., Fan, J., Yuan, M., 2018. Secondary migration mechanism and accumulation controlling factors of Jurassic tight oil in Sichuan Basin. Acta Petrolei Sinica 39, 1211-1222.Panja, P., Pathak, M., Deo, M., 2019. Productions of volatile oil and gas-condensate from liquid rich shales. Advances in Geo-Energy Research 3, 29-42.Peng, X., Wang, Y., Diao, Y., Zhang, L., Yazid, I.M., Ren, S., 2019. Experimental investigation on the operation parameters of carbon dioxide huff-n-puff process in ultra low permeability oil reservoirs. Journal of Petroleum Science and Engineering 174, 903-912.Shi, Y., Yassin, M.R., Yuan, L., Dehghanpour, H., 2019. Modelling imbibition data for determining size distribution of organic and inorganic pores in unconventional rocks. 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Environmental Earth Sciences 77, 717.Wang, Y., Qin, Y., Zhang, R., He, L., Anovitz, L.M., Bleuel, M., Mildner, D.F.R., Liu, S., Zhu, Y., 2018. Evaluation of nanoscale accessible pore structures for improved prediction of gas production potential in Chinese marine shales. Energy & Fuels 32, 12447-12461.Xia, L., Cao, J., Hu, S., Li, S., Shi, C., 2019. Organic geochemistry, petrology, and conventional and unconventional hydrocarbon resource potential of Paleogene saline source rocks in eastern China: The Biyang Sag of the Nanxiang Basin. Marine and Petroleum Geology 101, 343-354.Xu, H., Zhou, W., Zhang, R., Liu, S., Zhou, Q., 2019. Characterizations of pore, mineral and petrographic properties of marine shale using multiple techniques and their implications on gas storage capability for Sichuan Longmaxi gas shale field in China. Fuel 241, 360-371.Yang, Z., Zou, C., Wu, S., Lin, S., Pan, S., Niu, X., Men, G., Tang, Z., Li, G., Zhao, J., Jia, X., 2019. Formation, distribution and resource potential of the "sweet areas (sections)" of continental shale oil in China. Marine and Petroleum Geology 102, 48-60.Yao, Y., Liu, J., Liu, D., Chen, J., Pan, Z., 2019. A new application of NMR in characterization of multiphase methane and adsorption capacity of shale. International Journal of Coal Geology 201, 76-85.Zhang, C., Shan, W., Wang, X., 2019. Quantitative evaluation of organic porosity and inorganic porosity in shale gas reservoirs using logging data. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 811-828.Zhang, Y., Yao, S., Zhang, M., Zhou, X., Mei, H., Zeng, F., 2018. Prediction of adsorption isotherms of multicomponent gas mixtures in tight porous media by the oil–gas-adsorption three-phase vacancy solution model. Energy & Fuels 32, 12166-12173.Zhao, Z., Zhou, X.-P., 2019. An integrated method for 3D reconstruction model of porous geomaterials through 2D CT images. Computers & Geosciences 123, 83-94.AbstractsAgrawal, V., Sharma, S., 2018. Improved kerogen models for determining thermal maturity and hydrocarbon potential of shale. Scientific Reports 8, Article 17465. is the insoluble component of organic-rich shales that controls the type and amount of hydrocarbons generated in conventional and unconventional reservoirs. Significant progress has recently been made in developing structural models of kerogen. However, there is still a large gap in understanding the evolution of the molecular components of kerogen with thermal maturation and their hydrocarbon (HC) generative potential. Here, we determine the variations in different molecular fragments of kerogen from a Marcellus Shale maturity series (with VRo ranging from 0.8 to 3) using quantitative 13C MultiCP/MAS NMR and MultiCP NMR/DD (dipolar dephasing). These molecular variations provide insight into the (1) evolution of the molecular structure of kerogen with increasing thermal maturity and, (2) the primary molecular contributors to HC generation. Our results also indicate that old model equations based on structural parameters of kerogen underestimate the thermal maturity and overestimate the HC generation potential of Marcellus Shale samples. This could primarily be due to the fact that the kerogen samples used to reconstruct old models were mostly derived from immature shales (VRo <1) acquired from different basins with varying depositional environments. We utilized the kerogen molecular parameters determined from the Marcellus maturity series samples to develop improved models for determining thermal maturity and HC potential of Marcellus Shale. The models generated in this study could also potentially be applied to other shales of similar maturity range and paleo-depositional environments.Aldunate, M., De la Iglesia, R., Bertagnolli, A.D., Ulloa, O., 2018. Oxygen modulates bacterial community composition in the coastal upwelling waters off central Chile. Deep Sea Research Part II: Topical Studies in Oceanography 156, 68-79. community composition and its relationship to oxygen were investigated in the non-sulfidic shelf waters exposed to seasonal upwelling and oxygen deficiency off central Chile. Using 16S rRNA gene clone libraries, terminal restriction fragment length polymorphism (T-RFLP) and iTAG sequencing analyses of nearly 4 years of monthly sampling through the water column (5–80?m depth), we found a clear partitioning of community composition that could be attributed to dissolved oxygen (Spearman correlation coefficient = 0.578) in comparison to other environmental variables, such as light, fluorescence, temperature, salinity, microbial abundance or nutrients. Bacteroidetes (orders Sphingobacteriales and Flavobacteriales), SAR11 (subclades Ia - Candidatus Pelagibacter ubique and II), an unclassified group of Alphaproteobacteria, and SAR86 dominated in waters containing dissolved oxygen concentrations ≥70?μM. In contrast, taxonomic groups associated with capabilities of either oxidative or reductive cycling of inorganic sulfur dominated in waters with dissolved oxygen from ~70?μM to undetectable levels. The dominant groups were Arctic96BD-19, SUP05 and SAR324 (sulfur oxidation) and Desulfobacterales (sulfate reduction). Desulfobacterales are known to come primarily from sulfidic, nitrate/nitrite-depleted waters and sediments. Their presence, therefore, provides taxonomic evidence for pelagic dissimilatory sulfate reduction within oxygen-depleted coastal environments.Alfken, S., W?rmer, L., Lipp, J.S., Wendt, J., Taubner, H., Schimmelmann, A., Hinrichs, K.-U., 2019. Micrometer scale imaging of sedimentary climate archives – Sample preparation for combined elemental and lipid biomarker analysis. Organic Geochemistry 127, 81-91. spectrometry imaging (MSI) can be used for the ?m scale mapping of target molecules on intact sample surfaces. Recently we demonstrated that MSI of non-disturbed sediments can be used for paleoenvironmental studies; using matrix-assisted laser desorption/ionization coupled to Fourier transform-ion cyclotron resonance-mass spectrometry we visualized the spatial distributions of archaeal glycerol dibiphytanyl glycerol tetraether (GDGT) lipids. There is a pressing need for implementing sample preparation procedures that allow exploiting the full potential of sediment MSI. Here we present a suite of sample preparation steps, optimized for the analysis of GDGTs in marine sediments. It considers the crucial requirements for successful MSI and optional combination with elemental imaging via micro X-Ray Fluorescence Spectroscopy (?-XRF). Preservation of the sediment’s spatial distribution is achieved with freeze-drying and subsequent embedding in a mixture of gelatin and carboxymethyl cellulose. This enables sectioning the sample into sequential slices from 20 to 500??m in thickness. Thinner sections showed enhanced signal intensity in MSI, but elemental mapping by ?-XRF is more accurate for thicker sections; 100??m thick slices provide satisfactory results for both analyses and are recommended for congruent elemental and biomarker imaging. When applied to the uppermost ～5?cm of marine sediment from a Santa Barbara Basin box core, the optimized sample preparation yields reproducible ultra-high-resolution GDGT records from sequential slices, thus demonstrating the robustness of the method. Congruent ?-XRF results aid the establishment of a contextual framework regarding supply of terrigenous and marine detritus as well as the assignment of molecular data to annual layers.Ali, M.Y., Lee, J., 2019. Petroleum geology of the Nogal Basin and surrounding area, northern Somalia: Part 1, Stratigraphy and tectonic evolution. Journal of Petroleum Geology 42, 91-120. this study, 92 closely‐spaced reflection seismic profiles (～4000 line‐km) were tied to biostratigraphic and lithological data from six deep exploration wells in the poorly‐known Nogal rift basin, northern Somalia, and were integrated with outcrop and aeromagnetic data to investigate the basin stratigraphy and tectonic evolution. Aeromagnetic data show NW‐SE trending magnetic anomalies which are interpreted as plutonic bodies intruded during the Early Cretaceous, probably contemporaneously with a pre‐Cenomanian uplift phase. The aeromagnetic data also suggest a change of basement type from Inda Ad Series metasediments in the SE of the study area to igneous and high‐grade metamorphic basement in the NW. Biostratigraphic data and seismic reflection profiles define the Nogal Basin as a WNW–ESE striking half‐graben, approximately 250 km long and 40 km wide, which formed as a result of mainly Cenomanian–Maastrichtian and Oligocene–Miocene intracontinental rifting. The depocentre contains at least 7000 m of Mesozoic and Cenozoic sediments and is located in the centre of the basin (east of well Nogal‐1), to the south of the Shileh Madu Range. To the north, the basin is bounded by a major border fault along which significant variations in the thickness of sedimentary units are observed, suggesting that the fault controlled basin architecture and patterns of sedimentation. Oligocene–Miocene normal faults which resulted in north‐tilted fault blocks are widespread within the main basin; smaller‐scale sub‐basins oriented NW‐SE to WNW‐ESE are observed to the NW of the basin and probably developed contemporaneously.The Late Jurassic rift phase which has been documented elsewhere in northern Somalia is either missing in the Nogal Basin or is preserved only in localised grabens in the western and central parts of the basin. This is probably due to the pre‐Cenomanian uplift and erosion which removed almost the entire Jurassic and Lower Cretaceous successions over a wide area referred to as the Nogal‐Erigavo Arch. A more pronounced rifting episode followed this erosional event in the Cenomanian–Maastrichtian and resulted in the deposition of well‐sorted fluvio‐deltaic sandstones (Gumburo and Jesomma Formations), more than 2000 m thick. In wells in the Nogal Basin, these formations are between two and three times thicker than in wells drilled in footwall locations, and include excellent reservoir rocks sealed by transgressive mudstones and carbonates. A final rifting event in the Oligocene–Miocene was related to the opening of the Gulf of Aden. A rift sag phase which accommodated the Early Oligocene continental sediments of the Nogal Group initially developed at the centre of the basin. This was followed by a period of strong rotational faulting and tilting, which reactivated the Cenomanian–Maastrichtian structures.Alvarez, J.O., Saputra, I.W.R., Schechter, D.S., 2018. The impact of surfactant imbibition and adsorption for improving oil recovery in the Wolfcamp and Eagle Ford reservoirs. SPE Journal 23, 2103-2117, SPE-187176-PA. oil recovery from unconventional liquid reservoirs (ULRs) is a major challenge, and knowledge of recovery mechanisms and the interaction of completion-fluid additives with the rock is fundamental in tackling the problem. Fracture-treatment performance and consequent oil recovery can be improved by adding surfactants to stimulation fluids to promote imbibition by wettability alteration and moderate interfacial-tension (IFT) reduction. Also, the extent of surfactant adsorption on the ULR surface during the imbibition of completion fluids is a key factor to consider when designing fracture jobs. The experimental and modeling work presented in this paper focuses on the effectiveness of surfactant additives for improving oil recovery in Wolfcamp and Eagle Ford reservoirs, as well as the extent of surfactant loss by adsorption during the imbibition of surfactant-laden completion fluid. Original rock wettability is determined by contact angle (CA) and zeta potential. Then, distinct types of surfactants—anionic, anionic/nonionic, and cationic—are evaluated to gauge their effectiveness in altering wettability and IFT. Moreover, surfactant-adsorption measurements are performed using ultraviolet/visible (UV/Vis) spectroscopy. Next, the potential for improving oil recovery using surfactant additives in ultralow-permeability Wolfcamp and Eagle Ford shale cores is investigated by spontaneous-imbibition experiments, and computed-tomography (CT) methods are used to determine fluid imbibition in real time. Finally, laboratory data are used in numerical simulations to model laboratory results and to upscale these findings to field scale. The results showed that aqueous solutions with surfactants altered rock wettability from oil-wet and intermediate-wet to water-wet and reduced IFT to moderately low values. In addition, cationic surfactant presented the highest adsorption capacity following a Langmuir-type adsorption profile. Spontaneous-imbibition results showed that aqueous solutions with surfactants had higher imbibition, and were better at recovering oil from shale core compared with water without surfactants, which agrees qualitatively with wettability and IFT alteration. However, rock lithology and surfactant type played a key role in adsorption capacity and oil recovery. Our upscaling result showed that, compared with a well that is not treated with surfactant, a 24% increase in the initial peak oil rate and an 8% increase in the 3-year cumulative oil production were observed. For the results obtained, we can conclude that the addition of surfactants to completion fluids can improve oil recovery by wettability alteration and IFT reduction, maximizing well performance after stimulation from Wolfcamp and Eagle Ford unconventional reservoirs.Ameri, A., Esmaeilzadeh, F., Mowla, D., 2018. Effect of brine on asphaltene precipitation at high pressures in oil reservoirs. Petroleum Chemistry 58, 1076-1084. this study, the effect of NaCl, KCl, CaCl2, MgCl2, MgSO4, and CaCl2 salts in brine in the range of low (1000?5000 ppm) and intermediate (5000?40?000 ppm) salinity water on the amount and offset pressure of asphaltene precipitation was investigated. The measurements were performed at reservoir temperature (350.15 K) and high pressures (0?100 bar). The IFT (Interfacial Tension) values increased with pressure and a sudden increase was observed at a specific pressure namely, an offset pressure of asphaltene precipitation in APE (Asphaltene Precipitation Envelope). For all brines, the amount of IFT with increasing concentration was in descending order and after a minimum value it changed to uptrend. Likewise, similar results were obtained for the precipitated asphaltene amount. All the brines intensified the asphaltene precipitation. Monovalent cations like Na+ and K+ showed higher values of IFT and hence more asphaltene precipitation, however, MgCl2 showed the least IFT, offset pressure and the amount of asphaltene precipitation.Amosu, A., Sun, Y., 2019. A quantitative probabilistic framework for estimating the critical moment in a petroleum system. American Association of Petroleum Geologists Bulletin 103, 177-187. petroleum system concept spans the spatial and temporal extent of all elements and processes required for the generation and preservation of petroleum. The critical moment of a petroleum system is the moment with the highest probability for the generation–migration–accumulation of hydrocarbons. It is an important concept in petroleum exploration risk assessment because the stratigraphic and geographic extents of a petroleum system are determined at the critical moment. In petroleum systems, thermal history data, burial history data, and vitrinite reflectance data may be unavailable, unreliable, or incomplete; this introduces significant uncertainty in the choice of the critical moment. We present here a quantitative probabilistic framework for estimating the critical moment and quantifying the associated uncertainty in such cases. We define a probabilistic early bound and late bound for the critical moment (which, combined together, we term the critical range) and then estimate the moment with the highest numerical probability of generation–migration–accumulation. We define the uncertainty associated with the critical moment as half the absolute value of the critical range. In cases with little ambiguity or duplicity in the timing of petroleum system elements and processes, the critical range converges to one point, which is also the critical moment. The probabilistic framework introduces consistency to the critical moment estimation problem and quantifies the level of uncertainty in the estimation. This reduces the risk involved in petroleum exploration assessment.Arroua, B., Grimaud, R., Hirschler-Réa, A., Bouriat, P., Magot, M., Urios, L., Ranchou-Peyruse, A., 2018. Pleomorphochaeta naphthae sp. nov., a new anaerobic fermentative bacterium isolated from an oil field. International Journal of Systematic and Evolutionary Microbiology 68, 3747-3753. novel anaerobic fermentative bacterium, strain SEBR 4209T, was isolated from a water sample of a Congolese oil field. Strain SEBR 4209T is phylogenetically related to the genus Pleomorphochaeta , in the family Spirochaetaceae . Its closest relatives are Pleomorphochaeta caudata SEBR 4223T (94.5?% 16S rRNA gene sequence similarity) and Pleomorphochaeta multiformis MO-SPC2T (94.3?% similarity). Like the other members of this genus, cells have a pleomorphic morphology, in particular an annular shape and long stalks. Optimal growth was observed at 37?°C, at pH between 6.8 and 7.0, and with 40?g l?1 NaCl. This strain was only able to grow by fermentation of carbohydrates. The fermentation products from glucose utilization were acetate, ethanol, CO2 and H2. Predominant fatty acids were C14?:?0, C14?:?0 DMA, C16?:?0 and C16?:?1ω7c. The major polar lipids were phosphoglycolipids, phospholipids and glycolipids. The G+C?content of the DNA was 29.6?mol%. Based on phenotypic characteristics and phylogenetic traits, strain SEBR 4209T is considered to represent a novel species of the genus Pleomorphochaeta, for which the name Pleomorphochaeta naphthae sp. nov. is proposed. The type strain is SEBR 4209T (=DSM 104684T=JCM 31871T). The GenBank/ EMBL/ DDBJ accession number for the 16S rRNA gene sequence of strain SEBR 4209T is KX791435.Asadi, F., Ejtemaei, M., Birkett, G., Searles, D.J., Nguyen, A.V., 2019. The link between the kinetics of gas hydrate formation and surface ion distribution in the low salt concentration regime. Fuel 240, 309-316. salts can thermodynamically inhibit gas hydrate formation. However, some inorganic salts at low concentration can act as a kinetic hydrate promoter. The mechanism of kinetic hydrate promotion in the presence of low concentration of inorganic salts is still unknown. This paper presents an experimental study into methane hydrate formation in an impeller-agitated vessel in the presence of sodium halides and alkali metal chlorides at low concentrations. It is shown that alkali metal chlorides and sodium halides at low concentration can reduce the induction time and kinetically promote gas hydrate formation. It has been proposed that bubbles form inside the agitated vessel as a result of the gas pocket break-up. Simulated gas pocket break-up studies show a smaller gas bubble formation in the salts solution with low concentrations in comparison with in the pure water. The small bubbles formation leads to an increase in the gas-water interface area and gas hold-up of the vessel. Consequently, there will be an increase in the mass transfer for gas hydration formation. In addition, the strength of hydrogen bonds at the gas/water interface affect the gas dissolution rate into the aqueous phase. Ions that have more affinity for the interface order water molecules weakly and improve the gas hydrate formation. Bubbles zeta potential measurements also confirm the ion-specific effect of the applied salts at the gas-water interface. Ultimately, gas-water interfacial area and ion-specific effect play critical roles in the gas hydrate formation.Asmala, E., Haraguchi, L., Markager, S., Massicotte, P., Riemann, B., Staehr, P.A., Carstensen, J., 2018. Eutrophication leads to accumulation of recalcitrant autochthonous organic matter in coastal environment. Global Biogeochemical Cycles 32, 1673-1687. nutrient enrichment is changing the structure and the function of coastal ecosystems. These coastal zones are transitions between freshwater and marine systems where multiple biogeochemical processes remove, produce, and transform organic matter. The extent to which the coastal zone is merely a conduit for terrestrial (allochthonous) organic matter versus a distinct source of autochthonous organic matter fueled by eutrophication is unclear. To address this issue, we characterized the freshwater and marine dissolved organic matter (DOM) pools in a eutrophic estuary with a long water residence time (Roskilde Fjord, Denmark) over an annual cycle. We combined elemental, optical (absorbance and fluorescence), and isotopic analyses to obtain insight about the bulk properties of the DOM pool during this period. We also used sediment traps to analyze the changes related to the exchange of organic matter between the particulate organic matter and DOM fractions. The results showed that labile autochthonous DOM from in situ primary production was rapidly transformed to more recalcitrant DOM that accumulated in the estuary despite continuous exchange with the open sea. Also, parts of the particulate organic matter pool were degraded rapidly (within 24?hr) and transformed into the DOM pool. Accumulated DOM was characterized by relatively low molecular size and stable carbon isotopic value and by high protein-like fluorescence. These results indicate that autotrophic material can be a major source of specific recalcitrant DOM in eutrophic coastal waters, contributing significantly to the flux of organic carbon to the ocean.Atashgahi, S., Liebensteiner, M.G., Janssen, D.B., Smidt, H., Stams, A.J.M., Sipkema, D., 2018. Microbial synthesis and transformation of inorganic and organic chlorine compounds. Frontiers in Microbiology 9, 3079. doi: 10.3389/fmicb.2018.03079. and inorganic chlorine compounds are formed by a broad range of natural geochemical, photochemical and biological processes. In addition, chlorine compounds are produced in large quantities for industrial, agricultural and pharmaceutical purposes, which has led to widespread environmental pollution. Abiotic transformations and microbial metabolism of inorganic and organic chlorine compounds combined with human activities constitute the chlorine cycle on Earth. Naturally occurring organochlorines compounds are synthesized and transformed by diverse groups of (micro)organisms in the presence or absence of oxygen. In turn, anthropogenic chlorine contaminants may be degraded under natural or stimulated conditions. Here, we review phylogeny, biochemistry and ecology of microorganisms mediating chlorination and dechlorination processes. In addition, the co-occurrence and potential interdependency of catabolic and anabolic transformations of natural and synthetic chlorine compounds are discussed for selected microorganisms and particular ecosystems.Azdarpour, A., Afkhami Karaei, M., Hamidi, H., Mohammadian, E., Honarvar, B., 2018. CO2 sequestration through direct aqueous mineral carbonation of red gypsum. Petroleum 4, 398-407. this study, the physical and chemical characteristics and direct aqueous mineral carbonation of red gypsum have been investigated. The characterization studies showed that red gypsum is a very potential feedstock for mineral carbonation. It is mainly consisted of CaO, Fe2O3 and SO3 along with some impurities. On the other hand, the carbonation results showed that direct aqueous carbonation of red gypsum resulted in CaCO3 and FeCO3 production, however, the carbonates purity and carbonation efficiency are still very low.Baba, M.u., Parnell, J., Muirhead, D., Bowden, S., 2019. Oil charge and biodegradation history in an exhumed fractured reservoir, Devonian, UK. Marine and Petroleum Geology 101, 281-289. distribution of oil residues in fractured Upper Devonian reservoir sandstones of Caithness help us to understand relationships between oil charge and episodes of fracturing. The sandstones are cut by an extensive set of tightly cemented deformation bands in the vicinity of the Brough Fault, and calcite-mineralized open fractures. The deformation bands compartmentalized the reservoir, which subsequently was charged by oil to varying extent in different compartments. Petrographic and biomarker data distinguish two charges of oil. The first charge of oil was unaltered. The later mineralized fractures introduced a heavier biodegraded oil that spread into the sandstone pores and displaced/overprinted the earlier oil. Two distinct oil charges are also evident from two generations of oil fluid inclusions, firstly in overgrowths on quartz grains, and secondly in the calcite veins, exhibiting distinct fluorescence characteristics. Migration and trapping of oil depended on the combination of two fracturing episodes of different character, in which the first episode created sealed compartments which were then filled by oil introduced by the second episode.Bahaghighat, H.D., Freye, C.E., Gough, D.V., Synovec, R.E., 2019. Comprehensive two-dimensional gas chromatography and time-of-flight mass spectrometry detection with a 50 ms modulation period. Journal of Chromatography A 1583, 117-123. ultrafast flow modulation period, PM of 50?ms, for comprehensive two-dimensional (2D) gas chromatography (GC?×?GC) with time-of-flight mass spectrometry (TOFMS) detection is demonstrated, producing narrow peak widths, 2W (4σ width-at-base on the 2D dimension), demonstrating the potential for ultrafast (2D) separations with high peak capacity. The modulator is a pulse flow valve that injects a narrow pulse of carrier gas at a user defined PM, at the union between the 1D and 2D columns. The raw data produced combines the properties of vacancy chromatography and frontal analysis. Deconvolution of the raw data using unconstrained multivariate curve resolution alternating least squares (MCR-ALS) analysis facilitates identification and quantification for overlapped analyte peaks. The peak profile loadings obtained from MCR-ALS are converted into traditional appearing GC?×?GC data through a process commonly used with frontal analysis. An 18-component test mixture at seven different injected mass levels was studied. The 2D peaks generated ranged from an 2W of 16 to 36?ms with an average of 26?ms. At an on-column injected mass of 14?ng per analyte, an average mass spectral match value, MV, of 822 was achieved using in-house collected spectra for comparison, with an average match value RSD of 7.1%. Calibration of overlapped test analytes was evaluated using the areas of the MCR-ALS loadings, with excellent quantification demonstrated. The advancement demonstrated in modulation performance for GC?×?GC represents a significant decrease in PM as most commercial modulators have a minimum PM of 1?s, while maintaining the benefits of a duty cycle of essentially 1.0, which promises to enable new chemical analyzer designs, compatible with the vacuum requirements of the TOFMS detector.Bai, C., Zhang, G., Lu, J.a., Liang, J., Yang, Z., Yan, W., Zhu, D., Tian, Y., 2019. Deep-water sediment waves as a special gas hydrate reservoirs in the Northeastern South China Sea. Marine and Petroleum Geology 101, 476-485. gas hydrate is attracting increasing attention in the sedimentary geology as an alternative energy source in the future. Recent exploration efforts have indicated that gas hydrate is commonly associated with sediment waves in slope area of quasi-passive continental margin. Based on the deep-water seismic data and core data of the northeastern part of the South China Sea (SCS), this research describes the seismic and geological characteristics of the sediment waves and gas hydrate reservoirs, and discusses the accumulation model of gas hydrate in sediment waves reservoir. The results demonstrate that: (1) the sediment waves widely appear in study area, and those have a “wave-like” bedform and are formed by deep-water contour or turbid current sedimentation. Meanwhile, the sediment waves are affected by gas leakage, diapirism, and neotectonics. (2) The stable zone of gas hydrate which simulated calculation by theory is consistent with core data. The complete and typical gas hydrate seismic model including a “bottom-simulating reflection (BSR)?+?blank zone (BZ)?+?enhanced reflector body (eHB)” structure can be observed in the sediment waves seismic profile of the study area. (3) The gas hydrates are stored in sediment waves, which are influenced by the original structure of the sediments and have different gas hydrate accumulation dynamics that are driven by diffusion and/or leakage. Thus, the sediment waves as a favorable reservoir of gas hydrate have research significance.Bai, Y., Sui, H., Liu, X., He, L., Li, X., Thormann, E., 2019. Effects of the N, O, and S heteroatoms on the adsorption and desorption of asphaltenes on silica surface: A molecular dynamics simulation. Fuel 240, 252-261. adsorption and desorption of asphaltene on silica surface is highly dependent on the heteroatoms present in its structure. Herein, some model asphaltene molecules with different heteroatoms (i.e., N, O, S) at different positions (in the aromatic cores, in the middle and termination of alkane side chains) are selected as the adsorbates to investigate their adsorption and desorption behaviors on silica surface through molecular dynamics (MD) simulation. Results reveal that the characteristic adsorption configuration of asphaltenes is ascribed to the competition between the asphaltene-silica interaction and π–π stacking interaction among the asphaltene polyaromatic rings. The presence of heteroatoms is found to be able to strengthen the interactions between asphaltenes and silica, depending on their type and location. For example, the terminal polar groups, especially the carboxyl (COOH), exhibit the greatest contribution to the electrostatic interaction (increasing from ?81 to ?727?kJ/mol). The S atoms are also found to increase the van der Waals interaction energies by 25%. According to the equilibrium desorption conformation and density profile, the presence of heteroatoms is found to significantly hinder the desorption of asphaltenes from silica due to the enhanced polar interactions. The impeded desorption is also confirmed by the slower detachment of asphaltenes based on the time-dependent interaction energies and center of mass (COM) distances analysis. Additionally, the terminal polar groups lead to extraordinary desorption properties of asphaltenes. It is observed that the strong asphaltene-silica and asphaltene-water interactions coexist in these systems due to the high polarity and hydrophilicity of the terminal polar groups.Bandekar, M., Ramaiah, N., Jain, A., Meena, R.M., 2018. Seasonal and depth-wise variations in bacterial and archaeal groups in the Arabian Sea oxygen minimum zone. Deep Sea Research Part II: Topical Studies in Oceanography 156, 4-18. variations, as well as depth-wise distribution patterns of bacterial and archaeal communities in the Arabian Sea oxygen minimum zone (AS-OMZ), were analyzed by examining 16S rRNA gene clones and their sequences. Sampling was carried out at the Arabian Sea Time Series (ASTS) location (17°0.126′ N, 67°59.772′ E) from five different depths during three different seasons. A total of 743 and 256 non-chimeric bacterial and archaeal 16S rRNA gene sequences were analyzed. Most of the bacterial 16S rRNA gene sequences were affiliated to Gammaproteobacteria (39.31%), Alphaproteobacteria (23.56%) and Cyanobacteria (20.2%). The archaeal 16S rRNA gene sequences mostly aligned with Marine Group II (MG-II, Euryarchaeota). An explicit vertical partitioning of bacterial communities between the surface (surface and DCM) and OMZ (250?m, 500?m, and 1000?m) was observed. Also evident was an apparent seasonal variation among surface bacterial communities but a minimal variation among OMZ bacterial and archaeal communities. LINKTREE and canonical correspondence analysis (CCA) indicates that differences in the concentrations of dissolved oxygen (DO) and total organic carbon (TOC) seem to cause the vertical separation among bacterial communities in the ASTS station. A higher number of shared OTUs affiliated mainly to Alteromonadales (bacteria) and Methanosarcinales (archaea) contributed towards seasonally stable community structure in the OMZ depths.Bandekar, M., Ramaiah, N., Meena, R.M., 2018. Diversity and abundance of denitrifying and anammox bacteria from the Arabian Sea oxygen minimum zone. Deep Sea Research Part II: Topical Studies in Oceanography 156, 19-26. community involved in nitrogen transformations in the oxygen minimum zones (OMZ) with dissolved oxygen (DO) levels below 0.5?ml?L?1 is ascribed to be responsible for the reported 40% losses of fixed nitrogen. The Arabian Sea (AS) OMZ is among the largest suboxic regions accounting for a substantial loss of fixed nitrogen. Sampling was carried out at the Arabian Sea Time Series (ASTS) location (17°0.126′ N, 67°59.772′E) during three different seasons to document the diversity and abundance of both denitrifying and anammox bacteria, based on their molecular markers. Quantitative PCR (qPCR) was done to assess the abundance and distribution of genes encoding nitrite reductase (nirS) in denitrifying bacteria and hydrazine oxidoreductase (hzo) in anammox bacteria. Copy numbers of these genes had their maxima in the core OMZ depths of 250 and 500?m. The preponderance of nirS to the tune of 0.35?×?106 copy numbers L?1 and hzo, of 1.5?×?106 L?1 is indicative of simultaneous denitrification and anammox processes. The abundance of hzo was higher than nirS during all three seasons implying probable dominance of anammox process at this sampling location. Phylogenetic analysis revealed that nirS gene was present in bacteria belonging to Gammaproteobacteria, Alphaproteobacteria and Deltaproteobacteria. All the hzo sequences obtained in this study apparently imply that Candidatus Scalindua is the dominant anammox bacteria at the ASTS location.Bansal, V.R., Kumar, R., Sastry, M.I.S., Badhe, R.M., Kapur, G.S., Saxena, D., 2019. Direct estimation of shale oil potential by the structural insight of Indian origin kerogen. Fuel 241, 410-416. insight of Indian origin kerogen has been investigated by Solid State 13C Cross Polarization Magic Angle Spinning Nuclear Magnetic Resonance (13C CPMAS NMR) and Infrared (IR) Spectroscopic techniques. Cross Polarization (CP) with decoupling using two pulse phase modulation (TPPM) and Bloch decay experiment with 1H decoupling have been performed on each kerogen sample. Direct estimation of oil potential present in Indian origin kerogen has been done utilizing developed method based on IR and 13C CPMAS NMR techniques. The IR methods have been developed using both transmission and DRIFT reflectance spectra by employing standard blends of oil shale (1–12%) with Vacuum Gas Oil (VGO) range products. Models were developed by correlating the IR intensity in 3000–2700?cm?1 region with the % oil shale in VGO. Validation has been done by estimating aliphatic carbon (Calip) and aromatic carbon (Carom) content obtained by 13C CPMAS NMR method and a comparison has been made between 13CMAS NMR with and without dipolar dephasing, with and without CP. 13C MAS NMR spectra of Indian origin have been compared with Estonia and US Green River origin oil shale, containing high oil potential. Both IR and NMR methods have been applied to number of samples from different Indian sources. Results from these comprehensive studies indicate that both 13C CPMAS NMR and IR techniques are quite useful for structural inputs and direct determination of oil potential from different origin oil shale.Bao, J., Zhu, C., Wang, Z., 2018. Typical end-member oil derived from Cambrian-Lower Ordovician source rocks in the Tarim Basin, NW China. Petroleum Exploration and Development 45, 1177-1188. on GC-MS data of saturate and aromatic hydrocarbon fractions in crude oils from Well TD 2 and the Yingmaili and Tazhong area in the Tarim Basin, the end-member oil derived from Cambrian-Lower Ordovician source rocks was determined. The analytical results show that the crude oil from Well TD2 is rich in 3-6 ring polycyclic aromatic hydrocarbons without alkyl group, suggesting that this oil was altered by an abnormally thermal event. It contains a complete series of normal alkanes and 25-norhopanes, indicating that it is mixed oil of normal oil and biodegraded oil, so it can't be taken as end-member oil derived from Cambrian source rocks. The geochemical characteristics of crude oils from Well TZ11 and TZ30 are completely different from the crude oils from Well YM101 and YM201 generated by Middle–Upper Ordovician source rocks, so it is inferred that they are derived from Cambrian-Lower Ordovician source rocks. In addition, these crude oils don't contain 25-norhopanne series, indicating that they haven't suffered biodegradation and satisfy with geochemical conditions of end-member oil. It is noteworthy that the two kinds of marine oils have similar triaromatic steroids and methyl triaromatic steroids, but very different C27-29 steranes and C28-30 methyl steranes, showing that they are not a good indicator of organic matter input. Triaromatic dinosteroids are a kind of biomarkers most usually used in marine oil-source correlation in the Tarim Basin, but the big differences in their relative abundances between crude oil from Well TD 2 and two kinds of end-member marine oils suggest that they are easily affected by thermal maturity and should be cautiously used in marine oil-source correlation.Baross, J.A., 2018. The rocky road to biomolecules. Nature 564, 42-43. natural chemical reaction that occurs below the sea floor makes the amino acid tryptophan without biological input. This finding reveals a process that might have helped life on Earth to begin. Robert Frost’s poem Fire and Ice ponders which of these two will eventually cause life on Earth to cease. Conversely, scientists have long been interested in whether life on this planet originated in hot or cold conditions. Did life arise in a hot volcanic environment1,2 or, as Charles Darwin suggested in a letter (see go.2q8w3n5), in “some warm little pond”? Might we need to invoke a global setting that includes ice3 or would an ocean-floor setting suffice1–5? Writing in Nature, Ménez et al.6 report an analysis of rocky material below the ocean floor at sites called serpentinizing hydrothermal vents, which are hot springs that discharge alkaline, gas-rich water. The authors provide evidence that a chemical reaction occurs there that could have set the stage for life to begin — the generation of an amino acid by a process that is not biologically mediated. A well-characterized form of hydrothermal vent on the ocean floor, called black-smoker chimneys, occurs in a volcanic, magma-rich setting. These vents emit acidic fluids into the ocean that have high concentrations of gases and also of metals that are in a chemically reduced form. However, in 2000, the serendipitous discovery of a mid-Atlantic ocean-floor site called Lost City revealed another type of hydrothermal-vent environment7. The Lost City vents were found to arise by a process termed serpentinization — a chemical interaction between water and a type of rock called peridotite that contains minerals enriched in magnesium, iron and silica. Serpentinization generates alkaline conditions that aid the formation of majestic carbonate-rich towers (Fig. 1). Serpentinization also produces hydrogen and a variety of organic molecules, including formate, acetate and pyruvate, which might be important in supporting the microbial life at Lost City and could also have been used in the biochemical steps that led to life on Earth8,9. Studies of Lost City have provided a treasure trove of scientific discoveries that have greatly altered our understanding of hydrothermal vents and the geological history of the early Earth10. They have also led to testable hypotheses about possible environmental settings for the origin of life.In laboratory experiments that simulate conditions in magma-hosted hydrothermal vents, amino acids can be synthesized by chemical reactions11 that do not require biological input. However, whether such abiotic generation of amino acids can occur in serpentinizing hydrothermal vents was unknown. Amino acids have been detected12 in fluids emanating from Lost City, but their source was undetermined.To investigate further, Ménez and colleagues analysed material from rock samples retrieved by drilling around 170 metres below the ocean floor at Lost City. The authors present extensive evidence for the presence of the nitrogen-containing amino acid tryptophan in a context in which it was unlikely to have been produced by a biologically mediated process. They report data obtained from three high-resolution techniques that are consistent with the presence of tryptophan. The researchers also found other organic compounds that might be intermediates in the synthesis of tryptophan. Ménez et al. propose that this synthesis could be the result of Friedel–Crafts reactions because they found the molecule indole, which is an intermediate organic compound in the synthesis of tryptophan by this type of reaction. Their case for the abiotic synthesis of tryptophan is strengthened by the absence of other amino acids that would be present if a biological source was there, such as microbial contamination of the rock sample. To extend Ménez and co-workers’ report of the abiotic synthesis of tryptophan, future studies at Lost City should try to collect adequate volumes of fluid to determine a structural property, called chirality, of the tryptophan present. Molecules can exist in two mirror-image chiral forms. Synthesis of a molecule by a non-biological process generally results in equal proportions of these two forms, whereas biologically synthesized amino acids are usually made in predominantly one form or the other. The authors’ work also sheds light on the long-standing mystery of what mechanism reduces nitrogen molecules (N2) to ammonia under hydrothermal-vent conditions. In most of the cases in which ammonia has been detected in hydrothermal-vent environments, it was found to originate from buried sediment sources of organic material and not from abiotic synthesis in the hydrothermal vents13. Ménez and colleagues propose that saponite, an iron-containing clay mineral that they detected, and which is reported14 to be a catalyst for the synthesis of organic compounds and the reduction of N2 to ammonia, might be involved in tryptophan synthesis. Abiotic generation of a source of ammonia, together with saponite’s proposed catalysis of heterocyclic-amine molecules such as tryptophan, also raises the possibility of abiotic synthesis of other heterocyclic amines called pyrimidines and purines, which are components of the nucleic acids DNA and RNA. Moreover, saponite has the potential to promote the formation of organic polymers15,16. Beyond the potential for the synthesis and accumulation of organic compounds that were probably important in the origin of life, serpentinization has two other characteristics that have intriguing implications regarding the origin of life and the establishment of habitable conditions5,8. One characteristic is that serpentinization produces heat. The gradient of temperature can reach more than 200?°C at the site of the serpentinization reaction4. This, in turn, promotes hydration and therefore expansion of rocks, which is the other intriguing characteristic of serpentinization. However, if part of the ocean floor ‘sinks’ (subducts) into Earth’s interior as tectonic plates move, the greater heat and pressure encountered on its descent into the deep subsurface region would reverse such serpentinization, and the water released during this reversal could help to give rise to volcanoes on the ocean floor14. This, in turn, might help to recycle key elements that support life.The geological record at the time of life’s origin, 3.5 billion to 4.4 billion years ago, is enriched in iron- and magnesium-containing minerals (characteristic of the rocks that form Earth’s mafic crust), and in other elements that could have been extracted from rock in a process mediated by high-temperature water, strongly pointing to hydrothermal activity at that time. Yet, during the first billion years of Earth’s history, the heat from the mantle was too great for plate tectonics to occur17,18. Consequently, heat would have been lost from Earth’s interior mainly through volcanoes on the ocean floor. Earth’s crust would have been rich in silicate minerals and iron17,18, allowing high rates of serpentinization and producing high concentrations of hydrogen and organic compounds. Extensive circulation of seawater through volcanic rock during this time might have resulted in heat, fluid and gas ascending from the depths to create convective cells — a phenomenon characterized by currents due to density differences in the liquids or gases present. In the volcanic-rock environment, this could have led to associated gradients of temperature, pressure, chemical composition and wet–dry cycles (hydration–dehydration cycles known to promote chemical reactions that include the polymerization of organic compounds). Regardless of how life originated and in what environmental setting it was first established, serpentinization probably had an important role in facilitating the availability of organic chemicals required for life. Understanding serpentinization at Lost City has wider scientific implications. Saturn’s icy moon Enceladus has many of the chemical properties known to support life19,20 that are seen in serpentinizing environments such as those of Lost City. Whether or not Enceladus, or indeed other icy moons such as Jupiter’s Europa, could or did support life, they nevertheless could provide insight into geochemical processes that might lead to life. Such geochemical analysis seems to support the hypothesis that hydrothermal systems might have had an essential role in the origin of life. A more far-reaching implication of the work by Ménez and colleagues, and of others investigating hydrothermal vents, is that efforts to understand the characteristics of these settings might aid efforts to search for life beyond Earth. A planetary body with evidence of geophysical properties, including plate tectonics and hydrothermal systems, might have a higher probability of acquiring and supporting carbon-based life than planetary bodies lacking such geophysical properties. If true, then targeting such planets might also increase our probability of finding such life.References1. Baross, J. A. & Hoffman, S. E. Orig. Life Evol. Biosph. 15, 327–345 (1985).2. Martin, W. & Russell, M. J. Phil. Trans. R. Soc. Lond. B 362, 1887–1925 (2007).3. Stüeken, E. E. et al. Geobiology 11, 101–136 (2013).4. Martin, W., Baross, J., Kelley, D. & Russell, M. J. Nature Rev. Microbiol. 6, 805–814 (2008).5. Preiner, M. et al. Life 8, 41 (2018).6. Ménez, B. et al. Nature (2018).7. Kelley, D. et al. 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Science 311, 1419–1422 (2006).20. Waite, J. H. et al. Science 356, 155–159 (2017).Barry, P.H., Lawson, M., Meurer, W.P., Cheng, A., Ballentine, C.J., 2018. Noble gases in deepwater oils of the U.S. Gulf of Mexico. Geochemistry, Geophysics, Geosystems 19, 4218-4235. migration and emplacement processes remain underconstrained despite the vast potential economic value associated with oil and gas. Noble gases provide information about hydrocarbon generation, fluid migration pathways, reservoir conditions, and the relative volumes of oil versus water in the subsurface. Produced gas He‐Ne‐Ar‐Kr‐Xe data from two distinct oil fields in the Gulf of Mexico (Genesis and Hoover‐Diana) are used to calibrate a model that takes into account both water‐oil solubility exchange and subsequent gas cap formation. Reconstructed noble gas signatures in oils reflect simple (two‐phase) oil‐water exchange imparted during migration from the source rock to the trap, which are subsequently modified by gas cap formation at current reservoir conditions. Calculated, oil to water volume ratios (Vo/Vw) in Tertiary‐sourced oils from the Hoover‐Diana system are 2–3 times greater on average than those in the Jurassic sourced oils from the Genesis reservoirs. Higher Vo/Vw in Hoover‐Diana versus Genesis can be interpreted in two ways: either (1) the Hoover reservoir interval has 2–3 times more oil than any of the individual Genesis reservoirs, which is consistent with independent estimates of oil in place for the respective reservoirs, or (2) Genesis oils have experienced longer migration pathways than Hoover‐Diana oils and thus have interacted with more water. The ability to determine a robust Vo/Vw, despite gas cap formation and possible gas cap loss, is extremely powerful. For example, when volumetric hydrocarbon ratios are combined with independent estimates of hydrocarbon migration distance and/or formation fluid volumes, this technique has the potential to differentiate between large and small oil accumulations.Barth, C., Weiss, M.C., Roettger, M., Martin, W.F., Unden, G., 2018. Origin and phylogenetic relationships of [4Fe–4S]-containing O2 sensors of bacteria. Environmental Microbiology 20, 4567-4586. advent of environmental O2 about 2.5 billion years ago forced microbes to metabolically adapt and to develop mechanisms for O2 sensing. Sensing of O2 by [4Fe–4S]2+ to [2Fe–2S]2+ cluster conversion represents an ancient mechanism that is used by FNREc (Escherichia coli), FNRBs (Bacillus subtilis), NreBSa (Staphylococcus aureus) and WhiB3Mt (Mycobacterium tuberculosis). The phylogenetic relationship of these sensors was investigated. FNREc homologues are restricted to the proteobacteria and a few representatives from other phyla. Homologues of FNRBs and NreBSa are located within the bacilli, of WhiB3 within the actinobacteria. Archaea contain no homologues. The data reveal no similarity between the FNREc, FNRBs, NreBSa and WhiB3 sensor families on the sequence and structural levels. These O2 sensor families arose independently in phyla that were already present at the time O2 appeared, their members were subsequently distributed by lateral gene transfer. The chemistry of [4Fe–4S] and [2Fe–2S] cluster formation and interconversion appears to be shared by the sensor protein families. The type of signal output is, however, family specific. The homologues of FNREc and NreBSa vary with regard to the number of Cys residues that coordinate the cluster. It is suggested that the variants derive from lateral gene transfer and gained other functions.Bartlett, C.L., Hausrath, E.M., Adcock, C.T., Huang, S., Harrold, Z.R., Udry, A., 2018. Effects of organic compounds on dissolution of the phosphate minerals chlorapatite, whitlockite, merrillite, and fluorapatite: Implications for interpreting past signatures of organic compounds in rocks, soils and sediments. Astrobiology 18, 1543-1558. is an essential nutrient for life on Earth, present in adenosine triphosphate (ATP), deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and phospholipid membranes. Phosphorus does not have a significant volatile phase, and its release from minerals is therefore critical to its bioavailability. Organic ligands can enhance phosphate release from minerals relative to release in inorganic solutions, and phosphorus depletion in paleosols has consequently been used as a signature of the presence of ligands secreted by terrestrial organisms on early Earth. We performed batch dissolution experiments of the Mars-relevant phosphate minerals merrillite, whitlockite, chlorapatite, and fluorapatite in solutions containing organic compounds relevant to Mars. We also analyzed these phosphate minerals using the ChemCam laboratory instrument at Los Alamos, providing spectra of end-member phosphate phases that are likely present on the surface of Mars. Phosphate release rates from chlorapatite, whitlockite, and merrillite were enhanced by mellitic, oxalic, succinic, and acetic acids relative to inorganic controls by as much as >35?×?. The effects of the organic compounds could be explained by the denticity of the ligand, the strength of the complex formed with calcium, and the solution saturation state. Merrillite, whitlockite, and chlorapatite dissolution rates were more strongly enhanced by acetic and succinic acids relative to inorganic controls (as much as >10?×) than were fluorapatite dissolution rates (?2?×). These results suggest that depletion of phosphate in soils, rocks or sediments on Mars could be a sensitive indicator of the presence of organic compounds.Batista, W.R., Fernandes, F.C., Neves, M.H.C.B., Nascimento, T.S., Lopes, R.S.C., Lopes, C.C., Ziegler, G.P., Soler-Figueroa, B.M., Sparks, D., Fontaine, D.N., Carney, K.J., Qui?ones-Oquendo, L.E., Ruiz, G.M., 2018. Synthetic lipids as a biocide candidate for disinfection of ballast water. Marine Pollution Bulletin 137, 702-710. objective of this study is to propose the use of specific synthetic lipid as an active substance (biocide) in the control of harmful aquatic microorganisms, such as pathogens and non-indigenous species, transported in ships' ballast water. The biocide candidate, without metal or halogen components, was produced from a sub-product of the edible oil industry, the lecithin. Laboratory assays were conducted with phytoplankton, zooplankton, and marine bacteria to evaluate the efficiency of the biocide. The study also considers specific biocide's characteristics related to environmental risks, such as chemical composition, persistence, bioaccumulation, and toxicity. Results showed that, in the first 24?h of treatment, the biocide effectively reduced the concentration of the planktonic micro-organisms to very low levels. Additionally, a preliminary risk evaluation pointed that biocide candidate has a low residual toxicity, also a low potential for persistence and bioaccumulation in the environment.Beaudry, P., Longpré, M.-A., Economos, R., Wing, B.A., Bui, T.H., Stix, J., 2018. Degassing-induced fractionation of multiple sulphur isotopes unveils post-Archaean recycled oceanic crust signal in hotspot lava. Nature Communications 9, Articule 5093. source regions feeding hotspot volcanoes likely contain recycled subducted material. Anomalous sulphur (S) isotope signatures in hotspot lavas have tied ancient surface S to this deep geological cycle, but their potential modification by shallow magmatic processes has generally been overlooked. Here we present S isotope measurements in magmatic sulphides, silicate melt inclusions and matrix glasses from the recent eruption of a hotspot volcano at El Hierro, Canary Islands, which show that degassing induces strongly negative δ34S fractionation in both silicate and sulphide melts. Our results reflect the complex interplay among redox conditions, S speciation and degassing. The isotopic fractionation is mass dependent (Δ33S?=?0‰), thus lacking evidence for the recycled Archaean crust signal recently identified at other hotspot volcanoes. However, the source has an enriched signature (δ34S ~?+?3‰), which supports the presence of younger 34S-rich recycled oceanic material in the Canary Island mantle plume.Becker, K.W., Collins, J.R., Durham, B.P., Groussman, R.D., White, A.E., Fredricks, H.F., Ossolinski, J.E., Repeta, D.J., Carini, P., Armbrust, E.V., Van Mooy, B.A.S., 2018. Daily changes in phytoplankton lipidomes reveal mechanisms of energy storage in the open ocean. Nature Communications 9, Article 5179. is the dominant control on phytoplankton biosynthetic activity, and darkness deprives them of their primary external energy source. Changes in the biochemical composition of phytoplankton communities over diel light cycles and attendant consequences for carbon and energy flux in environments remain poorly elucidated. Here we use lipidomic data from the North Pacific subtropical gyre to show that biosynthesis of energy-rich triacylglycerols (TAGs) by eukaryotic nanophytoplankton during the day and their subsequent consumption at night drives a large and previously uncharacterized daily carbon cycle. Diel oscillations in TAG concentration comprise 23?±?11% of primary production by eukaryotic nanophytoplankton representing a global flux of about 2.4 Pg C yr?1. Metatranscriptomic analyses of genes required for TAG biosynthesis indicate that haptophytes and dinoflagellates are active members in TAG production. Estimates suggest that these organisms could contain as much as 40% more calories at sunset than at sunrise due to TAG production.Bejarano, A.C., 2018. Critical review and analysis of aquatic toxicity data on oil spill dispersants. Environmental Toxicology and Chemistry 37, 2989-3001. Oil spill response requires consideration of several countermeasures including chemical dispersants, but their potential toxicity to aquatic species poses a concern. Considerable in vivo aquatic toxicity data from laboratory exposures have been generated since 2010 for current-use dispersants. The objective of the present review is to provide a synthesis of these data to improve dispersant hazard assessments. Data from multiple studies were evaluated based on reliability criteria. Although procedures, standards, endpoints, and statistical approaches were usually described, nearly a quarter of sources did not provide sufficient information to judge study quality but were considered on a case-by-case basis. Data were used to develop dispersant-specific species sensitivity distributions and hazard concentrations protective of 95% of the species (HC5). Given data limitations, post-2010 toxicity data were augmented with pre-2010 data and model predictions. The HC5s calculated for 54 dispersants fell mostly within the moderate to slightly toxic range and were compared to field dispersant-only concentrations estimated from operational application rates under conservative assumptions. Based on available evidence, dispersants may not pose a significant risk under field conditions to most aquatic species, if proper application and dilution are taken into account. Recommendations on improved toxicity testing and reporting as well as research needs are also provided.Belger, J., Br?uer, J., 2018. Metacognition in dogs: Do dogs know they could be wrong? Learning & Behavior 46, 398–413. the current study, we investigated the question of whether dogs were sensitive to the information that they themselves had or had not acquired. For this purpose, we conducted three consecutive experiments in which dogs had to find a reward that was hidden behind one of two V-shaped fences with a gap at the point of the V. This setup allowed us to distinguish between selecting one of the fences by walking around it and seeking additional information by checking through the gap in the fence. We varied whether dogs had visual access to the baiting procedure or not. In addition, we manipulated the type and quality of reward as well as the time delay between baiting and choosing to analyze if the dogs’ searching behavior was affected. Our results were partly consistent with the findings of Call (Animal Cognition, 13 (5), 689–700, 2010) with great apes, on whose findings we based our experiments. We found that dogs checked more often through the corner of the V-shaped fence when they had not seen where the reward was hidden. Interestingly, dogs rewarded with toys selected the correct fence more often than dogs rewarded with food. Even though dogs’ performance was not affected by the food quality condition, dogs were significantly faster in fetching a high-quality food reward as opposed to a low-quality food reward. When testing whether forgetting and checking would increase as a function of delay, we found that although dogs slightly decreased in their success in finding the food when time delays were longer, they were not more likely to check before choosing. We show that – similar to apes – dogs seek additional information in uncertain situations, but their behavior in uncertain situations is less flexible compared to great apes.Belt, S.T., 2019. What do IP25 and related biomarkers really reveal about sea ice change? Quaternary Science Reviews 204, 216-219. changes to Arctic and Antarctic sea ice in recent decades has prompted the development and application of novel approaches to the reconstruction of past sea ice conditions over much longer timeframes. One such approach is based on the variable distribution of certain source-specific highly branched isoprenoid (HBI) lipid biomarkers in well-dated marine sediment records. Thus, IP25 and IPSO25 have emerged as useful proxy measures of seasonal sea ice in the Arctic and Antarctic, respectively. An overview of the salient features of IP25, IPSO25 and related biomarkers is presented, together with aspects that are currently less well understood and potentially provide direction for future research.Benaiges-Fernandez, R., Urmeneta, J., 2018. Use of specific PCR primers for the study of sulfate-reducing bacteria diversity in microbial mats of Ebro Delta, Spain. International Microbiology 21, 231-235. mats are prokaryotic communities that provide model systems to analyze microbial diversity and ecophysiological interactions. Sulfate-reducing bacteria (SRB) play a key role in sulfur and nutrient recycling in these ecosystems. In this work, specific primers for 16S rRNA encoding gene, previously described, were used to study the diversity of SRB in microbial mats of the Ebro Delta. We confirm that this method is reliable to identify the diversity of SRB in these ecosystems. However, some mismatches in obtained sequences had been observed in our system and must be taken under consideration. Various genera of SRB in Ebro Delta microbial mats were identified, such as Desulfonema, Desulfatitalea, Desulfosalsimonas, Desulfoccocus, and Desulfovibrio. The diversity observed in our samples is very similar to previously reported in other microbial mats communities.Bernhardsgrütter, I., V?geli, B., Wagner, T., Peter, D.M., Cortina, N.S., Kahnt, J., Bange, G., Engilberge, S., Girard, E., Riobé, F., Maury, O., Shima, S., Zarzycki, J., Erb, T.J., 2018. The multicatalytic compartment of propionyl-CoA synthase sequesters a toxic metabolite. Nature Chemical Biology 14, 1127-1132. must cope with toxic or reactive intermediates formed during metabolism. One coping strategy is to sequester reactions that produce such intermediates within specialized compartments or tunnels connecting different active sites. Here, we show that propionyl-CoA synthase (PCS), an ～?400-kDa homodimer, three-domain fusion protein and the key enzyme of the 3-hydroxypropionate bi-cycle for CO2 fixation, sequesters its reactive intermediate acrylyl-CoA. Structural analysis showed that PCS forms a multicatalytic reaction chamber. Kinetic analysis suggested that access to the reaction chamber and catalysis are synchronized by interdomain communication. The reaction chamber of PCS features three active sites and has a volume of only 33?nm3. As one of the smallest multireaction chambers described in biology, PCS may inspire the engineering of a new class of dynamically regulated nanoreactors.Berthonneau, J., Obliger, A., Valdenaire, P.-L., Grauby, O., Ferry, D., Chaudanson, D., Levitz, P., Kim, J.J., Ulm, F.-J., Pellenq, R.J.M., 2018. Mesoscale structure, mechanics, and transport properties of source rocks’ organic pore networks. Proceedings of the National Academy of Sciences 115, 12365-12370.: In source rocks, natural hydrocarbons are generated from organic matter dispersed in a fine-grained mineral matrix. The potential recovery of hydrocarbons is therefore influenced by the geometry of the organic hosted porous networks. Here, the three-dimensional structures of such networks are revealed using electron tomography with a subnanometer resolution. The reconstructions are first characterized in terms of morphology and topology and then used to build a multiscale simulation tool to study the mechanics and the transport properties of confined fluids. Our results offer evidence of the prevalent role of connected nanopores, which subsequently constitutes a material limit for long-term hydrocarbon production.Abstract: Organic matter is responsible for the generation of hydrocarbons during the thermal maturation of source rock formation. This geochemical process engenders a network of organic hosted pores that governs the flow of hydrocarbons from the organic matter to fractures created during the stimulation of production wells. Therefore, it can be reasonably assumed that predictions of potentially recoverable confined hydrocarbons depend on the geometry of this pore network. Here, we analyze mesoscale structures of three organic porous networks at different thermal maturities. We use electron tomography with subnanometric resolution to characterize their morphology and topology. Our 3D reconstructions confirm the formation of nanopores and reveal increasingly tortuous and connected pore networks in the process of thermal maturation. We then turn the binarized reconstructions into lattice models including information from atomistic simulations to derive mechanical and confined fluid transport properties. Specifically, we highlight the influence of adsorbed fluids on the elastic response. The resulting elastic energy concentrations are localized at the vicinity of macropores at low maturity whereas these concentrations present more homogeneous distributions at higher thermal maturities, due to pores’ topology. The lattice models finally allow us to capture the effect of sorption on diffusion mechanisms with a sole input of network geometry. Eventually, we corroborate the dominant impact of diffusion occurring within the connected nanopores, which constitute the limiting factor of confined hydrocarbon transport in source rocks.Bertran, E., Leavitt, W.D., Pellerin, A., Zane, G.M., Wall, J.D., Halevy, I., Wing, B.A., Johnston, D.T., 2018. Deconstructing the dissimilatory sulfate reduction pathway: Isotope fractionation of a mutant unable of growth on sulfate. Frontiers in Microbiology 9, 3110. doi: 10.3389/fmicb.2018.03110. sulfur isotope record provides key insight into the history of Earth's redox conditions. A detailed understanding of the metabolisms driving this cycle, and specifically microbial sulfate reduction (MSR), is crucial for accurate paleoenvironmental reconstructions. This includes a precise knowledge of the step-specific sulfur isotope effects during MSR. In this study, we aim at resolving the cellular-level fractionation factor during dissimilatory sulfite reduction to sulfide within MSR, and use this measured isotope effect as a calibration to enhance our understanding of the biochemistry of sulfite reduction. For this, we merge measured isotope effects associated with dissimilatory sulfite reduction with a quantitative model that explicitly links net fractionation, reaction reversibility, and intracellular metabolite levels. The highly targeted experimental aspect of this study was possible by virtue of the availability of a deletion mutant strain of the model sulfate reducer Desulfovibrio vulgaris (strain Hildenborough), in which the sulfite reduction step is isolated from the rest of the metabolic pathway owing to the absence of its QmoABC complex (ΔQmo). This deletion disrupts electron flux and prevents the reduction of adenosine phosphosulfate (APS) to sulfite. When grown in open-system steady-state conditions at 10% maximum growth rate in the presence of sulfite and lactate as electron donor, sulfur isotope fractionation factors averaged ?15.9‰ (1 σ = 0.4), which appeared to be statistically indistinguishable from a pure enzyme study with dissimilatory sulfite reductase. We coupled these measurements with an understanding of step-specific equilibrium and kinetic isotope effects, and furthered our mechanistic understanding of the biochemistry of sulfite uptake and ensuing reduction. Our metabolically informed isotope model identifies flavodoxin as the most likely electron carrier performing the transfer of electrons to dissimilatory sulfite reductase. This is in line with previous work on metabolic strategies adopted by sulfate reducers under different energy regimes, and has implications for our understanding of the plasticity of this metabolic pathway at the center of our interpretation of modern and palaeo-environmental records.Bhowmik, S., Dutta, P., 2019. A study on the effect of gas shale composition and pore structure on methane sorption. Journal of Natural Gas Science and Engineering 62, 144-156. moist, powdered European shale samples were analyzed for their sorption properties by volumetric method. The adsorption capacities were correlated to the shale organic types and maturity. The pore-size distribution obtained from low-pressure CO2 micropore adsorption was also correlated with the porosity and shale organic types. Furthermore, pore volume and average pore width were taken into consideration to determine the dominant parameters controlling adsorption. To identify the discrepancy between available and actual pore space for adsorption, helium and krypton gases were used for void volume estimation. Methane adsorption isotherms follow Langmuir Type I behavior and, in general, showed a positive trend with Total Organic Content (TOC) and Hg-porosity although some deviations were also observed. Low to moderate level of hysteresis between adsorption and desorption isotherms for some samples was visible, which may be attributed to the experimental uncertainty and existence of heterogeneous pores for shale-methane interaction. The low-pressure micropore adsorption analysis indicated dominance of nanopore and very fine micropores in the shale matrix structure along with associated microporosity of the clay materials. The observed “negative” adsortion or “decline” in adsorption isotherm are related to the mismatch of the available pore spaces for helium and methane. In general, He-calibrated isotherms showed higher levels of adsorption than the corresponding Kr-calibrated isotherms although the unit void volume for all samples follow a negative trend with the maximum methane capacity.Bickle, P., 2018. Stable isotopes and dynamic diets: The Mesolithic-Neolithic dietary transition in terrestrial central Europe. Journal of Archaeological Science: Reports 22, 444-451. and nitrogen stable isotopes (δ13C and δ15N) have made a huge contribution to understanding dietary change across the Mesolithic-Neolithic transition. One of the major findings is that marine resources were abandoned with the onset of farming in some coastal regions of Europe. This paper considers the isotopic evidence from terrestrial central Europe, asking whether there was a similar large-scale abandonment of freshwater resources in the early Neolithic. Using isotopic data from the published literature, stable isotope ratios from 66 Mesolithic burials are compared to 274 Neolithic individuals, from France, in-land Belgium and Germany. The results are then modelled via FRUITS (Food Reconstruction Using Isotopic Transferred Signals). The results suggest that despite a drop in fish consumption in the Neolithic, aquatic resources continued to form a small but significant part of the diet (est. 6%). Changes in plant protein consumption are argued to account for a greater proportion of the difference between the Mesolithic and Neolithic δ13C and δ15N isotope ratios. It is concluded that plants should see greater attention from interpretative approaches in the early Neolithic of central Europe to further our understanding of diet both as a social practice and subsistence activity.Bidzhieva, S.K., Sokolova, D.S., Tourova, T.P., Nazina, T.N., 2018. Bacteria of the genus Sphaerochaeta from low-temperature heavy oil reservoirs (Russia). Microbiology 87, 757-765. bacteria are usual components of oilfield microbial communities. Since pure cultures of fermenting bacteria utilize carbohydrates and do not grow on oil, their diversity and relationships in the community are of great interest. In the present work, enrichment and pure cultures of fermenting bacteria obtained from formation water of low-temperature oilfields (Russia) were studied. High-throughput sequencing of the V3–V4 region of the 16S rRNA gene was carried out for an enrichment culture. The library was found to contain the genes of anaerobic bacteria of the genus Halanaerobium, which are capable of growth on polysaccharides with thiosulfate reduction to sulfide, as well as the genes of Abyssivirga alkaniphila, which grows on C5–C25 n-alkanes of oil with thiosulfate as an electron acceptor or in a syntrophic association with hydrogenotrophic methanogens. Members of the genus Sphaerochaeta were minor components of the community. Three strains (4-11, 5-8-5, and 17-50) were isolated from enrichment cultures. The isolates were anaerobic mesophilic slightly halophilic bacteria, which fermented a number of carbohydrates and grew as biofilms. The 16S rRNA gene sequences of the new strains exhibited 99.5–100% similarity between each other and 97.2–98.0% similarity to the sequences of the most closely related species Sphaerochaeta associata and Sphaerochaeta globosa, which indicated their affiliation to a new Sphaerochaeta species. The products of maltose fermentation were acetate, propionate, СО2, Н2, and sometimes iso-propanol. The strains did not grow on crude oil. In oilfields Sphaerochaeta species probably consume the products of oil biodegradation by other microorganisms, are involved in biofilms formation, and provide H2 for methanogens and other components of the community.Bif, M.B., Hansell, D.A., Popendorf, K.J., 2018. Controls on the fate of dissolved organic carbon under contrasting upwelling conditions. Frontiers in Marine Science 5, 463. doi: 10.3389/fmars.2018.00463. understand controls on the production and remineralization of recalcitrant dissolved organic carbon produced in association with positive net community production, we simulated upwelling systems of different intensities by combining and incubating whole seawater collected from different depths in the Florida Strait (27?N, ~79?W). The natural microbial communities in the treatments grew under controlled light and temperature for 15 days (i.e., the autotrophic phase); they were subsequently incubated for 35 days in the dark heterotrophic phase. We analyzed the phytoplankton composition and pigment fluorescence intensity during the light phase, and dissolved organic and inorganic variables during both phases. Initial high or low availability of inorganic nutrients controlled phytoplankton growth and the magnitude of NCP. In the strong upwelling treatment, with higher initial inorganic nutrients, 25% of NCP accumulated as DOC after 15 days; however, this material was in turn fully remineralized during the dark phase. In contrast, low nutrients in the weak upwelling treatment not only limited NCP, but also the fraction of NCP accumulated as DOC (11%). Surprisingly, most of this fraction resisted microbial remineralization in the dark phase, suggesting that upwellings of different intensities affect the quality of dissolved organic matter produced, thereby affecting the timing and location of its remineralization and, hence, its prospects for export to the deep ocean.Bissaro, B., Várnai, A., R?hr, ?.K., Eijsink, V.G.H., 2018. Oxidoreductases and reactive oxygen species in conversion of lignocellulosic biomass. Microbiology and Molecular Biology Reviews 82, Article e00029-18. constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.Black, B.A., Neely, R.R., Lamarque, J.-F., Elkins-Tanton, L.T., Kiehl, J.T., Shields, C.A., Mills, M.J., Bardeen, C., 2018. Systemic swings in end-Permian climate from Siberian Traps carbon and sulfur outgassing. Nature Geoscience 11, 949-954. Traps flood basalt magmatism coincided with the end-Permian mass extinction approximately 252 million years ago. Proposed links between magmatism and ecological catastrophe include global warming, global cooling, ozone depletion and changes in ocean chemistry. However, the critical combinations of environmental changes responsible for global mass extinction are undetermined. In particular, the combined and competing climate effects of sulfur and carbon outgassing remain to be quantified. Here we present results from global climate model simulations of flood basalt outgassing that account for sulfur chemistry and aerosol microphysics with coupled atmosphere and ocean circulation. We consider the effects of sulfur and carbon in isolation and in tandem. We find that coupling with the ocean strongly influences the climate response to prolonged flood basalt-scale outgassing. We suggest that sulfur and carbon emissions from the Siberian Traps combined to generate systemic swings in temperature, ocean circulation and hydrology within a longer-term trend towards a greenhouse world in the early Triassic.Blanco, Y., de Diego-Castilla, G., Viúdez-Moreiras, D., Cavalcante-Silva, E., Rodríguez-Manfredi, J.A., Davila, A.F., McKay, C.P., Parro, V., 2018. Effects of gamma and electron radiation on the structural integrity of organic molecules and macromolecular biomarkers measured by microarray immunoassays and their astrobiological implications. Astrobiology 18, 1497-1516. ionizing radiation in the form of solar energetic particles and galactic cosmic rays is pervasive on the surface of planetary bodies with thin atmospheres or in space facilities for humans, and it may seriously affect the chemistry and the structure of organic and biological material. We used fluorescent microarray immunoassays to assess how different doses of electron and gamma radiations affect the stability of target compounds such as biological polymers and small molecules (haptens) conjugated to large proteins. The radiation effect was monitored by measuring the loss in the immunoidentification of the target due to an impaired ability of the antibodies for binding their corresponding irradiated and damaged epitopes (the part of the target molecule to which antibodies bind). Exposure to electron radiation alone was more damaging at low doses (1?kGy) than exposure to gamma radiation alone, but this effect was reversed at the highest radiation dose (500?kGy). Differences in the dose–effect immunoidentification patterns suggested that the amount (dose) and not the type of radiation was the main factor for the cumulative damage on the majority of the assayed molecules. Molecules irradiated with both types of radiation showed a response similar to that of the individual treatments at increasing radiation doses, although the pattern obtained with electrons only was the most similar. The calculated radiolysis constant did not show a unique pattern; it rather suggested a different behavior perhaps associated with the unique structure of each molecule. Although not strictly comparable with extraterrestrial conditions because the irradiations were performed under air and at room temperature, our results may contribute to understanding the effects of ionizing radiation on complex molecules and the search for biomarkers through bioaffinity-based systems in planetary exploration.Blomenkemper, P., Kerp, H., Abu Hamad, A., DiMichele, W.A., Bomfleur, B., 2018. A hidden cradle of plant evolution in Permian tropical lowlands. Science 362, 1414-1416.: The latitudinal biodiversity gradient today has deep roots in the evolutionary history of Earth’s biota over geologic time. In the marine realm, earliest fossil occurrences at low latitudes reveal a tropical cradle for many animal groups. However, the terrestrial fossil record—especially from drier environments that are thought to drive evolutionary innovation—is sparse. We present mixed plant-fossil assemblages from Permian equatorial lowlands in present-day Jordan that harbor precocious records of three major seed-plant lineages that all became dominant during the Mesozoic, including the oldest representative of any living conifer family. These finds offer a glimpse of the early evolutionary origins of modern plant groups in disturbance-prone tropical habitats that are usually hidden from observation.Editor's Summary, Late Permian seed-plant evolution: The great evolutionary expansion of seed plants took place in the Mesozoic era, which began after the Permian mass extinction 252 million years ago. Blomenkemper et al. report the discovery of seed-plant fossils from Late Permian (252-million- to 260-million-year-old) deposits on the margins of the Dead Sea in Jordan. This area represents an equatorial habitat with pronounced dry seasons. These fossils, which include the earliest records of conifers, push back the ages of several important seed-plant lineages. Some of these lineages appear to span the mass extinction event at the end of the Permian, which suggests that the communities they supported may have been more stable than expected over this transition. Thus, early evolutionary innovations can occur in drought-prone tropical habitats—which rarely offer the conditions needed for fossil preservation.Boag, T.H., Stockey, R.G., Elder, L.E., Hull, P.M., Sperling, E.A., 2018. Oxygen, temperature and the deep-marine stenothermal cradle of Ediacaran evolution. Proceedings of the Royal Society B: Biological Sciences 285, Article 20181724. fossils document the early evolution of complex megascopic life, contemporaneous with geochemical evidence for widespread marine anoxia. These data suggest early animals experienced frequent hypoxia. Research has thus focused on the concentration of molecular oxygen (O2) required by early animals, while also considering the impacts of climate. One model, the Cold Cradle hypothesis, proposed the Ediacaran biota originated in cold, shallow-water environments owing to increased O2 solubility. First, we demonstrate using principles of gas exchange that temperature does have a critical role in governing the bioavailability of O2—but in cooler water the supply of O2 is actually lower. Second, the fossil record suggests the Ediacara biota initially occur approximately 571 Ma in deep-water facies, before appearing in shelf environments approximately 555 Ma. We propose an ecophysiological underpinning for this pattern. By combining oceanographic data with new respirometry experiments we show that in the shallow mixed layer where seasonal temperatures fluctuate widely, thermal and partial pressure (pO2) effects are highly synergistic. The result is that temperature change away from species-specific optima impairs tolerance to low pO2. We hypothesize that deep and particularly stenothermal (narrow temperature range) environments in the Ediacaran ocean were a physiological refuge from the synergistic effects of temperature and low pO2.Bonneville, A., Kouzes, R., Yamaoka, J., Lintereur, A., Flygare, J., Varner Gary, S., Mostafanezhad, I., Guardincerri, E., Rowe, C., Mellors, R., 2019. Borehole muography of subsurface reservoirs. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 377, 20180060. subsurface rock formations or geological objects like oil and gas reservoirs, mineral deposits, cavities or even magmatic plumbing systems under active volcanoes has been for many years a major quest of geoscientists. Since these subsurface objects cannot be observed directly, different indirect methods have been developed. These methods are all based on variations of certain physical properties of the subsurface materials that can be detected from the ground surface or from boreholes. To determine the density distribution, a new imaging technique using cosmic-ray muon detectors deployed in a borehole has been developed and a first prototype of a borehole muon detector successfully tested. In addition to providing a static image of the subsurface density in three dimensions (or three-dimensional tomography), borehole muography can also inform on the variations of density with time, which recently became of major importance with the injection of large volumes of fluids, mainly water and CO2, in porous subsurface reservoirs (e.g. aquifer storage and recovery, wastewater disposal, enhanced oil recovery and carbon sequestration). This raises several concerns about the risk of leakage and the mechanical integrity of the reservoirs. Determining the field scale induced displacement of fluids by geophysical methods like muography is thus a priority.Borilova, S., Mandl, M., Zeman, J., Kucera, J., Pakostova, E., Janiczek, O., Tuovinen, O.H., 2018. Can sulfate be the first dominant aqueous sulfur species formed in the oxidation of pyrite by Acidithiobacillus ferrooxidans? Frontiers in Microbiology 9, 3134. doi: 10.3389/fmicb.2018.03134. to the literature, pyrite (FeS2) oxidation has been previously determined to involve thiosulfate as the first aqueous intermediate sulfur product, which is further oxidized to sulfate. In the present study, pyrite oxidation by Acidithiobacillus ferrooxidans was studied using electrochemical and metabolic approaches in an effort to extend existing knowledge on the oxidation mechanism. Due to the small surface area, the reaction rate of a compact pyrite electrode in the form of polycrystalline pyrite aggregate in A. ferrooxidans suspension was very slow at a spontaneously formed high redox potential. The slow rate made it possible to investigate the oxidation process in detail over a term of 100 days. Using electrochemical parameters from polarization curves and levels of released iron, the number of exchanged electrons per pyrite molecule was estimated. The values close to 14 and 2 electrons were determined for the oxidation with and without bacteria, respectively. These results indicated that sulfate was the dominant first aqueous sulfur species formed in the presence of bacteria and elemental sulfur was predominantly formed without bacteria. The stoichiometric calculations are consistent with high iron-oxidizing activities of bacteria that continually keep the released iron in the ferric form, resulting in a high redox potential. The sulfur entity of pyrite was oxidized to sulfate by Fe3+ without intermediate thiosulfate under these conditions. Cell attachment on the corroded pyrite electrode surface was documented although pyrite surface corrosion by Fe3+ was evident without bacterial participation. Attached cells may be important in initiating the oxidation of the pyrite surface to release iron from the mineral. During the active phase of oxidation of a pyrite concentrate sample, the ATP levels in attached and planktonic bacteria were consistent with previously established ATP content of iron-oxidizing cells. No significant upregulation of three essential genes involved in energy metabolism of sulfur compounds was observed in the planktonic cells, which represented the dominant biomass in the pyrite culture. The study demonstrated the formation of sulfate as the first dissolved sulfur species with iron-oxidizing bacteria under high redox potential conditions. Minor aqueous sulfur intermediates may be formed but as a result of side reactions.Borton, M.A., Daly, R.A., O'Banion, B., Hoyt, D.W., Marcus, D.N., Welch, S., Hastings, S.S., Meulia, T., Wolfe, R.A., Booker, A.E., Sharma, S., Cole, D.R., Wunch, K., Moore, J.D., Darrah, T.H., Wilkins, M.J., Wrighton, K.C., 2018. Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale. Environmental Microbiology 20, 4596-4611. 60% of natural gas production in the United States comes from hydraulic fracturing of unconventional reservoirs, such as shales or organic‐rich micrites. This process inoculates and enriches for halotolerant microorganisms in these reservoirs over time, resulting in a saline ecosystem that includes methane producing archaea. Here, we survey the biogeography of methanogens across unconventional reservoirs, and report that members of genus Methanohalophilus are recovered from every hydraulically fractured unconventional reservoir sampled by metagenomics. We provide the first genomic sequencing of three isolate genomes, as well as two metagenome assembled genomes (MAGs). Utilizing six other previously sequenced isolate genomes and MAGs, we perform comparative analysis of the 11 genomes representing this genus. This genomic investigation revealed distinctions between surface and subsurface derived genomes that are consistent with constraints encountered in each environment. Genotypic differences were also uncovered between isolate genomes recovered from the same well, suggesting niche partitioning among closely related strains. These genomic substrate utilization predictions were then confirmed by physiological investigation. Fine‐scale microdiversity was observed in CRISPR‐Cas systems of Methanohalophilus, with genomes from geographically distinct unconventional reservoirs sharing spacers targeting the same viral population. These findings have implications for augmentation strategies resulting in enhanced biogenic methane production in hydraulically fractured unconventional reservoirs.Boudreau, B.P., Middelburg, J.J., Luo, Y., 2018. The role of calcification in carbonate compensation. Nature Geoscience 11, 894-900. long-term recovery of the oceans from present and past acidification is possible due to neutralization by the dissolution of biogenic CaCO3 in bottom sediments, that is, carbonate compensation. However, such chemical compensation is unable to account for all features of past acidification events, such as the enhanced accumulation of CaCO3 at deeper depths after acidification. This overdeepening of CaCO3 accumulation led to the idea that an increased supply of alkalinity to the oceans, via amplified weathering of continental rocks, must accompany chemical compensation. Here we discuss an alternative: that changes to calcification, a biological process dependent on environmental conditions, can enhance and modify chemical compensation and account for overdeepening. Using a simplified ocean box model with both constant and variable calcification, we show that even modest drops in calcification can lead to appreciable long-term alkalinity build-up in the oceans and, thus, create overdeepening; we term this latter effect biological compensation. The chemical and biological manifestations of compensation differ in terms of controls, timing and effects, which we illustrate with model results. To better predict oceanic evolution during the Anthropocene and improve the interpretation of the palaeoceanographic record, it is necessary to better understand biological compensation.Bova, S.C., Herbert, T.D., Altabet, M.A., 2018. Ventilation of northern and southern sources of aged carbon in the eastern Equatorial Pacific during the Younger Dryas rise in atmospheric CO2. Paleoceanography and Paleoclimatology 33, 1151-1168.: Atmospheric carbon dioxide (CO2) levels rose by ~90 ppmv during the last deglaciation, but the source of this carbon remains unknown. One popular hypothesis suggests carbon accumulated in the deep Southern Ocean, becoming increasingly radiocarbon (14C) depleted during the last glacial period, and was released into Antarctic Intermediate Water (AAIW) and, subsequently, the atmosphere during deglaciation. Detection of extremely 14C depleted carbon in the intermediate‐depth tropical oceans during periods of atmospheric CO2 rise was initially considered the smoking gun for the hypothesis, but attempts to reproduce the anomalies closer to the Southern Ocean source have largely failed. Here we present new 14C records from four cores recovered at intermediate depths in the eastern equatorial Pacific (EEP). In the context of additional geochemical records, including benthic foraminiferal stable isotopes and sedimentary nitrogen isotopes, we demonstrate that the extreme 14C anomalies observed during the last deglaciation do not reflect the radiocarbon content of AAIW. We show that although AAIW likely transported modestly 14C depleted carbon to the EEP subsurface, the extreme 14C signatures might reflect a distinct source of aged carbon arriving from the north, suggesting the North Pacific helped transport deep ocean carbon to the atmosphere during the last deglaciation. In the EEP, additional local hydrothermal inputs of 14C‐free carbon near the Galapagos Islands magnified the already low‐14C signatures. Finally, regardless of arrival route (North/South Pacific or hydrothermal), 14C‐depleted carbon was released from the EEP subsurface during a late deglacial pulse of renewed upwelling, likely contributing to the Younger Dryas rise in atmospheric CO2. Plain Language Summary: Atmospheric carbon dioxide (CO2) is an important greenhouse gas that helps propagate major changes in Earth's climate. The last deglaciation (11,000–18,000 years BP) is the most recent natural example of rapid CO2 rise comparable in magnitude, though not in duration, to the human perturbation. Thus, understanding what drove atmospheric CO2 rise during this transition period may help us better understand the carbon system and predict its response to future change. It has been previously hypothesized that the deep ocean stores carbon away from the atmosphere during glacial intervals, thereby cooling global climate, but it is not yet clear what drives its release or by what pathway it returns to the atmosphere during deglaciation. In this paper, we use radiocarbon measurements on the shells of deep‐dwelling foraminifera (single‐celled protists with shells) to detect the release of glacially stored deep ocean carbon, which should have an aged or low radiocarbon signature, in the eastern equatorial Pacific. The data presented here provide evidence for the release of this aged deep ocean carbon in the eastern equatorial Pacific during the last deglaciation and also reveal an influx of radiocarbon‐free geologic carbon to the study site, likely sourced from nearby hydrothermal systems. Bowman, J.S., 2018. Identification of microbial dark matter in Antarctic environments. Frontiers in Microbiology 9, 3165. doi: 10.3389/fmicb.2018.03165. studies have applied molecular techniques to understand the diversity, evolution, and ecological function of Antarctic bacteria and archaea. One common technique is sequencing of the 16S rRNA gene, which produces a nearly-quantitative profile of community membership. However, the utility of this and similar approaches is limited by what is known about the evolution, physiology, and ecology of surveyed taxa. When representative genomes are available in public databases some of this information can be gleaned from genomic studies, and automated pipelines exist to carry out this task. Here the paprica metabolic inference pipeline was used to assess how well Antarctic microbial communities are represented by the available completed genomes. The NCBI’s Sequence Read Archive (SRA) was searched for Antarctic datasets that used one of the Illumina platforms to sequence the 16S rRNA gene. These data were quality controlled and denoised to identify unique reads, then analyzed with paprica to determine the degree of overlap with the closest phylogenetic neighbor with a completely sequenced genome. While some unique reads had perfect mapping to 16S rRNA genes from completed genomes, the mean percent overlap for all mapped reads was 86.6 %. When samples were grouped by environment, some environments appeared more or less well represented by the available genomes. For the domain Bacteria, seawater was particularly poorly represented with a mean overlap of 80.2 %, while for the domain Archaea glacial ice was particularly poorly represented with an overlap of only 48.0 % for a single sample. These findings suggest that a considerable effort is needed to improve the representation of Antarctic microbes in genome sequence databases.Boyle, R., 2018. These dusty young stars are changing the rules of planet-building. Nature 564, 20-23. peer inside planetary nurseries for clues about how our Solar System and others came to be.Some 100,000 years ago, when Neanderthals still occupied the caves of southern Europe, a star was born. It appeared when a ball of gas collapsed and ignited within a stellar factory known as the Taurus Molecular Cloud. Then, leftover material began to cool and coalesce around it, forming dust grains and a hazy envelope of gas.In September 2014, some of the light from that hot young star and its surroundings landed inside 66 silvery parabolas perched on a plateau in Chile’s Atacama desert — the driest on Earth. The photons had taken 450 years to make the journey. Astronomers were waiting. They were conducting a test of the Atacama Large Millimeter/submillimeter Array (ALMA), which features radio antennas separated by distances of up to 15 kilometres. With such long spans between them, the antennas work as a high-resolution receiver that can discern cool objects less than a millimetre across.When the telescope team trained ALMA on the young star, named HL Tauri, they expected to see a bright smear of dust and gas. Instead, when ALMA’s supercomputer stitched together those photons, the image resolved into a disk with a well-defined ring structure, with gaps seemingly etched by small, infant planets orbiting a central star. It looked like a furry, orange Saturn1. It looked like nothing astronomers had ever seen.“I kept flipping through their paper, and I was like, ‘Where is the real image? This is obviously a model’,” says Kate Follette, an astronomer at Amherst College in Massachusetts.What the researchers had captured was a picture of a planetary nursery — where baby planets were forming in a disk of gas and dust around HL Tauri. This observation marked the start of a revolution in the burgeoning field of planetary-disk imaging. In the four years since, astronomers have captured ‘baby pictures’ of numerous other systems. These planet-forming regions exhibit a wide variety of patterns. Some are neat ovals, with lanes as clearly defined as those of a race track. Others look like galaxies in miniature, with swirling arms that branch off into open arcs.The latest observations, including results announced in April and July, have revealed planets in the process of being sculpted, with dust and gas flowing onto bulbous, red-hot infant worlds2,3.But as the menagerie of young planetary systems grows, researchers are struggling to square their observations with current theories on how our Solar System and others formed. Such ideas have been in turmoil ever since astronomers started discovering planets around distant stars — a list that now numbers in the thousands. The Solar System has rocky planets near the Sun and giant gas balls farther out, but the panoply of exoplanets obeys no tidy patterns. And the rule book for world-building is getting more complicated as researchers find evidence of planets in the process of being born. Still, astronomers hope that witnessing such birth pangs will shed light on how all planetary systems, including our own, came to be. “We see all kinds of structure in these disks, even at very young ages,” says Follette. “Even younger than we classically thought planets should form.”Collisions and curdling: The prevailing theory of how the Solar System formed goes back to the German philosopher Immanuel Kant. In 1755, he imagined the Sun and planets arising from a nebulous cloud of gas and dust that slowly collapsed and flattened. Today, the widely accepted general model for how the process unfolded holds that the Sun collapsed inside a molecular cloud, a star factory full of gas molecules. A ring of gas and dust would have remained after the star formed, cooling and progressively condensing into bigger grains, then into larger, asteroid-sized bodies called planetesimals, and ultimately into planets.Theorists have been refining the particulars of the process since the 1970s, taking into account the distribution of planets in the Solar System and the chemical components of meteorites — crumbs from the Solar System’s formation. By the early 2000s, they had settled on two distinct scenarios for making rocky planets and gas giants (see ‘Attractive scenarios’).In one theory, called core accretion, rocky material violently smacks together, melts, coagulates and forms larger bodies, gradually creating protoplanets — compact embryonic worlds several thousand kilometres across. With their gravitational heft, proto-planets can attract a huge envelope of gas as they orbit through the planetary disk. This could enable them to metamorphose into the core of a giant planet, such as Jupiter; alternatively, their growth might ultimately stall at the rock-ball stage, as happened with Earth, Mars and the other terrestrial planets.Others theorized that the Solar System was forged not through violent collisions, but instead by a kind of curdling. In this scenario, called the streaming instability, gas and dust surrounding a star cool off quickly and begin drifting, becoming concentrated and collapsing under their own gravity. The centimetre-scale dust and ice in the disk forms agglomerations that grow into larger, denser bodies between 1 and 100 kilometres across. Then, through other processes, these grow into larger planetary embryos and, eventually, planets.But neither of these ideas can quite explain the Universe we see. Take Jupiter, which contains the vast majority of the material left behind from the Sun’s birth. Among the biggest questions is how the planet could have quickly grown a core big enough to hoover up the bulk of its mass; collisions between planetesimals would take many millions of years. But theorists reckon that the ‘natal disk’ of dust and gas that surrounded the young Sun would have disappeared 1 million to 10 million years after it formed, as gas dissipated and dust spiralled onto the star. (Compounding the problem, NASA’s Juno probe recently revealed that Jupiter’s core is even bigger than expected, meaning that the formation process must have been extremely fast.) Jupiter’s location is also hard to explain. Theorists have speculated since the 1970s that planets might migrate from one orbit to another as they form or jostle with other burgeoning planets.The cracks in planet-formation theories only got worse in the mid-2000s, as discoveries of other planetary systems began rolling in. Some stars have large planets that complete their orbits in just a few days. Other planets circle their hosts at distances that make Jupiter seem like the Sun’s next-door neighbour. Although simulations are growing more complex as hardware and software improve, neither core-accretion nor streaming-instability models do a good job of explaining how such huge worlds are formed, and at such disparate distances from their stars. One scenario that could account for far-out planets emerged in 2012. Astronomers Anders Johansen and Michiel Lambrechts at Lund University, Sweden, devised a variation on the core-accretion and streaming-instability scenarios. In their theory, dubbed pebble accretion, leftover star-forming material assembles as loose collections of dust and pebbles. Already-formed planetesimals swim among them, and then grow quickly by accumulating more pebbles, much as a snowball gets bigger as it rolls downhill. In this scenario, Johansen says, a planet would start out at the edges of a star’s natal disk and gather up pebbles as it migrates inwards. Depending on gravitational interactions between worlds, it could end up either very close to its host star, or far removed from it. Astronomers think that Jupiter and Saturn might have undergone such a migration early in the life of the Solar System.Pebble accretion has quickly gained popularity as a way of explaining systems such as HL Tauri, whose dark rings, etched in luminous dust, seem to harbour planets less than 100,000 years old. “These dark rings probably have young planets” in them, says Matthew Clement, an astronomer at the University of Oklahoma in Norman. “This has been really inspirational for us. It’s confirmation, in a way, that planets grow really fast.”Tallying it up: Although pebble accretion could explain how planets get big fast, it doesn’t provide as much insight into how the seed of a planet — the start of the snowball — forms in the first place.The challenge is bridging the gap between centimetre-scale bits of dust and Moon-sized objects. Older simulations assumed that dust and gas moved together. “When people did this problem historically, they always assumed the dust and gas were perfectly locked to each other,” says Philip Hopkins, an astronomer at the California Institute of Technology in Pasadena.He and Jono Squire, a postdoctoral researcher in his lab, have been revising models to separate the two, exploring complex inter-actions in a protoplanetary disk that can cause gas to swirl around dust grains in the same way as water eddies around sticks floating in a stream4. These redirected gas flows quickly become turbulent and unstable, forcing dust to clump together like flood debris. Such modelling could help to shed light on the fundamentals of planetesimal clumping, Hopkins says. “This could really change the story.”But as theorists tinker with accreting pebbles and swirling gas, another problem is lurking in the background. In 2013, astrophysicist Subhanjoy Mohanty of Imperial College London and astronomer Jane Greaves, now at Cardiff University, UK, published an initial survey of protoplanetary disks in the Taurus Molecular Cloud5. The observatories they used were not powerful enough to clearly resolve grooves in disks like those that ALMA saw around HL Tauri, but when the researchers tallied up how much gas and dust seemed to be present, they found that intermediate-sized stars had disks that packed much less mass than expected.This summer, astronomer Carlo Manara at the European Southern Observatory (ESO) in Garching, Germany, took another look, and found this to be true throughout the Milky Way6. Protoplanetary disks have just a fraction — sometimes as little as 1% — of the combined mass of exoplanets orbiting similar stars, he found. This would mean that planetary systems are bigger than the stuff used to make them.Whatever the explanation for this seemingly impossible scenario, theorists will have to grapple with the implications. To account for exoplanet observations, they have generally started with vast quantities of material. “You need a huge amount of mass in the disk [for it] to exert gravity on itself to act like a seed, and collapse on itself,” Greaves says.It is possible that there is more here than meets the eyepiece. There could, for example, be material in the disk that is difficult for telescopes to catch. Or, as Manara and his colleague Alessandro Morbidelli, a dynamicist at the C?te d’Azur Observatory in Nice, France, suggest, astronomers might be seeing only a snapshot; stars might be accreting new material from outside the protoplanetary disk, from the molecular clouds that forged them.This theft could be hard to spot. But in research published in 2017, astrophysicist Hsi-Wei Yen at the ESO and his colleagues described two gas streams that seem to be connected to HL Tauri’s disk — although they couldn’t tell whether the gas was flowing towards or away from the star7. If it were heading towards the star, Morbidelli says, the inflowing gas would have wide impacts, because it would also affect factors such as the disk’s temperature, density and magnetism. Finding evidence of such flows suggests that stars and planets are not isolated from the larger cosmos as they form and grow. “The disk is not in a box,” he says, “and this is also a revolution in our thinking about disks.”Planetary menagerie: As if theorists did not already have enough to grapple with, observations of planetary nurseries continue to pile up. The latest findings lend weight to the idea that planets are forming early in the lives of their stars, and at distances from them that vary widely.And it’s not just ALMA that’s been supplying images. Astronomers have also turned to the SPHERE instrument mounted on the ESO’s Very Large Telescope. This, too, is in the Atacama desert, about a six-hour drive south of ALMA. SPHERE has a system that can cancel out the blurring effects of the atmosphere and a filter that blocks starlight. In April, astronomers announced that they had used it to capture a diverse array of disks around eight young Sun-like stars2. Some resembled wide platters, some had distinct racetrack-like ovals, and one resembled a galaxy with jets streaming from its centre. Such diversity suggests that planet-forming is a complex process yielding many possible outcomes.Just two months later, news came that ALMA had been used to snap what might be the youngest exoplanets ever seen, orbiting a 4-million-year-old star about 100 parsecs (330 light years) from Earth8,9. ALMA, which is at its most sensitive when viewing small, cool objects, cannot see starlight reflecting off the planets directly. But the swirl of carbon monoxide gas in the disk of the star suggests that three planets — each roughly the mass of Jupiter — are in orbit, forcing gas to flow around them, as rocks control the flow of a stream.Not to be outdone, astronomers who had turned SPHERE towards another young star, called PDS 70, managed to nab a direct image of a gas giant. The planet orbits its star about four times farther than Jupiter does from the Sun, and is still gobbling up material from its natal disk of dust and gas3. The observation confirms the prediction that gas planets such as Jupiter form at vast separations from their stars.Another instrument, the Gemini Planet Imager (GPI), which is mounted on the Gemini South Telescope in Chile’s Andean foothills, has also been capturing disks with planets embedded in them, including a large gas giant that seems to support the core-accretion scenario of planet formation10. As more observations roll in, lingering doubts about whether these young nurseries are really cradling planets — and not, say, displaying instabilities in their disks — are being put to rest. “Almost all of the features that we see can be explained most easily by planets,” says Follette, who works on the GPI.But the latest findings are also showing astronomers that the Universe is much more complex and richly detailed than even our most advanced theories can predict. Several astronomers are realizing that the theoretical work they were doing a decade ago is no longer valid, but they are still not sure how to fix it.“There’s always that aspect; I’m sad that the stuff I did in the past isn’t right any more. But the truth is, it was never right,” says Sean Raymond, an astronomer at the Bordeaux Astrophysics Laboratory in France. “It was hopefully a step forward.”Observations might be of limited use in resolving the picture. ALMA and other radio observatories can see the dust and gas surrounding young stars, and optical instruments such as SPHERE and the GPI can see the disks and planets embedded in them, lit up with reflected starlight. But the range between tiny debris and 1,000-kilometre worlds will remain invisible.Still, current and future telescopes could help to fill in some gaps. Astronomers could reach beyond ALMA’s millimetre-scale vision to the centimetre range, Greaves says, with higher-resolution radio observations from telescopes such as the United Kingdom’s Merlin array — as well as from the forthcoming Square Kilometre Array, due to be hosted in South Africa and western Australia. Such observations could partly bridge the span between dust and protoplanet. Greaves eagerly anticipates the possibility of finding centimetre-scale material swirling around what could be future rocky planets. “Seeing a spot in a disk that indicated an Earth forming at an Earth-like distance from its star — that’s the new holy grail, at least for me.”With the observation of protoplanetary disks still in its infancy, the full story of planet-making will probably be more complicated than anyone expects, and ideas could well be overturned and then overturned again. “Case in point, it looks like the Solar System isn’t even the most common-looking system out there. We’re a little weird,” says Clement. “It turns out there is a lot of complexity out there.”References1. ALMA Partnership Astrophys. J. Lett. 808, L3 (2015).2. Avenhaus, H. et al. Astrophys. J. 863, 44 (2018).3. Keppler, M. et al. Astron. Astrophys. 617, A44 (2018).4. Hopkins, P. & Squire, J. Mon. Not. R. Astron. Soc. 479, 4681–4719 (2018).5. Mohanty, S. et al. Astrophys. J. 773, 168 (2013).6. Manara, C. F., Morbidelli, A. & Guillot, T. Astron. Astrophys. 618, L3 (2018).7. Yen, H-W. et al. Astron. Astrophys. 608, A134 (2017).8. Pinte, C. et al. Astrophys. J. 860, L13 (2018).9. Teague, R. et al. Astrophys. J. 860, L12 (2018).10. Macintosh, B. et al. Science 350, 64–67 (2015).Brandvik, P.J., Storey, C., Davies, E.J., Leirvik, F., 2019. Quantification of oil droplets under high pressure laboratory experiments simulating deep water oil releases and subsea dispersants injection (SSDI). Marine Pollution Bulletin 138, 520-525. experimental and field data are available describing oil droplet formation from subsea releases at high pressure. There are also analytical challenges quantifying oil droplets over a wide size and concentrations range at high pressure. This study quantified oil droplets released from an orifice in seawater at low and high pressure (5?m and 1750?m depth). Oil droplet sizes were quantified using a newly developed sensor (Silhouette camera or SilCam). The droplet sizes measured during experiments at low and high pressure, using the same release conditions, showed no significant difference as a function of pressure. This lack of a pressure effect on oil droplet sizes was observed for both untreated oil and for droplet formation during subsea dispersant injection or SSDI. This strongly indicates that the effectiveness of SSDI is not influenced by water depth or pressure, at least for simulated subsea releases of oil alone (no gas).Bubnova, E.N., Georgieva, M.L., Grum-Grzhimailo, O.A., 2018. Method for isolation and enumeration of fungi developing in marine sediments. Microbiology 87, 777-782. new design for a small growth container which was used for investigation of the microbiota of the White Sea littoral and sublittoral sediments is presented. These chambers made it possible to observe development of fungal mycelium under conditions of a natural ecotope (marine sediments) and to isolate this mycelium as pure cultures. The mycobiota isolated from the containers was compared to that obtained by standard plating method of the same sediments. The mycelium developed in 10% of the containers installed. Intensity of growth was found to be lower in the sublittoral than in the littoral. Most fungi isolated from the containers did not produce spores in pure cultures. Apart from non-sporulating cultures, colonies of marine species Paradendryphiellasalina and Acremoniumfuci were obtained. Standard plating of the sediments often resulted in isolation of Penicillium and Tolypocladium species, while the share of sterile isolates was considerably lower than in the case of isolation using growth containers.Buchwald, C., Homola, K., Spivack, A.J., Estes, E.R., Murray, R.W., Wankel, S.D., 2018. Isotopic constraints on nitrogen transformation rates in the deep sedimentary marine biosphere. Global Biogeochemical Cycles 32, 1688-1702. is known about the nature of microbial community activity contributing to the cycling of nitrogen in organic‐poor sediments underlying the expansive oligotrophic ocean gyres. Here we use pore water concentrations and stable N and O isotope measurements of nitrate and nitrite to constrain rates of nitrogen cycling processes over a 34‐m profile from the deep North Atlantic spanning fully oxic to anoxic conditions. Using a 1‐D reaction‐diffusion model to predict the distribution of nitrogen cycling rates, results converge on two distinct scenarios: (1) an exceptionally high degree of coupling between nitrite oxidation and nitrate reduction near the top of the anoxic zone or (2) an unusually large N isotope effect (~60‰) for nitrate reduction that is decoupled from the corresponding O isotope effect, which is possibly explained by enzyme‐level interconversion between nitrite and nitrate. Burgener, L., Hyland, E., Huntington, K.W., Kelson, J.R., Sewall, J.O., 2019. Revisiting the equable climate problem during the Late Cretaceous greenhouse using paleosol carbonate clumped isotope temperatures from the Campanian of the Western Interior Basin, USA. Palaeogeography, Palaeoclimatology, Palaeoecology 516, 244-267. climates such as the Late Cretaceous period provide important reference frames for understanding modern anthropogenic climate change. Upper Cretaceous terrestrial climate proxies have been interpreted as evidence for “equable” climates with reduced seasonal variations in temperature. However, climate models have largely failed to reproduce these reconstructions unless parameters such as atmospheric CO2 concentrations are set to unreasonable values. To help resolve such model-proxy disagreements, we reconstruct mean annual range in temperature (MART) for the Campanian (~75?Ma) Kaiparowits (south-central Utah) and Two Medicine (northwest Montana) Formations using warmest mean monthly temperature reconstructions from the clumped isotope composition of paleosol carbonate nodules, and reconstructions of local mean annual air temperatures from other methods. An evaluation of the applicability of bulk elemental soil geochemistry temperature proxies in these deposits supports the use of previous leaf physiognomy-based estimates of mean annual temperature for our MART reconstructions. We test the validity of several common assumptions made in reconstructing MART in two novel ways. First, MART is commonly calculated as twice the difference between local mean annual air temperature and warmest mean monthly temperature, and we validate this method by estimating modern MART for a range of environments using climate reanalysis data. Second, we constrain the effect of radiative soil heating on our soil carbonate temperature estimates by showing that for most environments likely to be preserved in the geologic record, summer soil temperatures are <3?°C higher than air temperatures. Our findings suggest that warmest mean monthly temperatures were 30 to 35?±?4?°C at the two study sites, and that MART was 21 to 29?°C for the Kaiparowits Formation, and 21 to 27?°C for the Two Medicine Formation. Mid-latitude Late Cretaceous MARTs were similar to modern ranges in mid-latitude seasonal temperature, and much (>9?°C) larger than previous proxy reconstructions of Late Cretaceous MART. These results add to a growing body of literature showing that terrestrial MART during ancient greenhouse periods was not significantly different from modern seasonal temperature variations. Finally, the similarity in MART between the Kaiparowits and Two Medicine formations suggests that latitudinal changes in MART did not contribute to the faunal provincialism that has been proposed by some paleontologists.Burgos-Hernández, M., Pozo, C., González, D., 2019. Evolutionary history of Musaceae: ancient distribution and the rise of modern lineages. Botanical Journal of the Linnean Society 189, 23-35. conducted a biogeographic analysis of Musaceae, emphasizing the importance of the fossil record to understand the early evolutionary history of the family. Plastid and nuclear DNA sequences were used to estimate divergence times with a Bayesian uncorrelated, lognormal relaxed-clock approach. Ancestral areas were reconstructed using the statistical dispersal-extinction-cladogenesis method under two models: one including and one excluding the fossil distribution. Molecular dating and integration of biogeographic reconstructions suggest a boreotropical origin for Musaceae across the landmasses of North America+Europe+Asia, with its diversification occurring through the Cretaceous / Palaeogene (K/Pg) (45.9–80.1 Mya; 95% HPD) and subsequent diversification occurring in southern South-east Asia. Comparison of the two models showed that biogeographic analysis based only on living species does not provide a complete reconstruction of the evolutionary history. We hypothesize that North America and Europe may be considered the grave of the more ancient lineages of Musaceae and tropical Asia as the cradle of more recent lineages of the family. The incorporation of fossil information in ancestral reconstructions improves the biogeographical history and expands hypotheses about the early evolution of Musaceae.Cabrerizo, A., Muir, D.C.G., De Silva, A.O., Wang, X., Lamoureux, S.F., Lafrenière, M.J., 2018. Legacy and emerging persistent organic pollutants (POPs) in terrestrial compartments in the High Arctic: Sorption and secondary sources. Environmental Science & Technology 52, 14187-14197. persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs), organochlorine pesticides (OCPs), and emerging perfluoroalkyl substances (PFASs) were measured in vegetation and soil samples collected at remote lakes in the Canadian High Arctic. Field studies were carried out in 2015 and 2016 to assess concentrations of POPs, study the relevant sorbing phases, and determine whether Arctic soils were sinks or sources of legacy POPs to the atmosphere and to neighboring lakes. The patterns of legacy POPs in vegetation and soils were dominated by low molecular weight PCB congeners along with OCPs, confirming the importance of long-range atmospheric transport. Lipid and non-lipid organic matter was a key determinant of legacy POPs in Arctic vegetation. Soil organic matter was the main descriptor of hydrophobic PCBs and OCPs in soils, while soil inorganic carbon content, was an important driver of the sorption of PFASs in soils. While contaminant concentrations were low in soil and vegetation, higher PCBs and PFOS organic and inorganic carbon-normalized concentrations were found at Resolute Lake indicating the presence of local sources of contamination. Comparison of fugacities of PCBs in soil and air from Resolute Lake indicated soils as net sources of PCBs to the atmosphere.Cai, L., Xiao, G., Guo, X., Wang, J., Wu, Z., Li, B., 2019. Assessment of Mesozoic and Upper Paleozoic source rocks in the South Yellow Sea Basin based on the continuous borehole CSDP-2. Marine and Petroleum Geology 101, 30-42. lack of core data and measured data, although the marine oil & gas exploration in the South Yellow Sea Basin has been going on for 57 years, no commercial hydrocarbon reservoirs have been found so far. The quantitative source rocks evaluation based on geochemical data and fluid inclusions containing hydrocarbon benefits from the completion of borehole CSDP-2 in 2016, a continuous coring well of the Chinese Continental Shelf Drilling Program (CSDP), which indicates that the marine origin oil-gas exploration in the South Yellow Sea Basin enters into a new stage. As revealed by the well CSDP-2, three sets of effective hydrocarbon source rocks in the Mesozoic and Upper Paleozoic have been identified, which are distributed in the Lower Triassic Qinglong Formation (T1q), Upper Permian Longtan-Dalong Formation (P3l-d) and Middle Permian Gufeng-Qixia Formation (P2g-q) respectively. Among them, organic-rich source rocks mainly concentrate in the lower part of the P3l-d and the middle & upper part of the P2g-q, and the P3d mudstone also works as good source rock. The P3l-d mudstone with high organic abundance is the chief source rock in the South Yellow Sea Basin, whose maximum hydrocarbon-generating intensity may reaches up to 795.09?×?104?t/km2 and hydrocarbon-expulsing intensity remains at the level of 165.03?×?104?t/km2. A noteworthy feature of the P2g-q source rocks is the strong vertical heterogeneity, with the hydrocarbon-expulsing intensity of the upper part being 34.14?×?104?t/km2 while that of the lower part being 18.07?×?104?t/km2. In contrast, the organic abundance of argillaceous limestone in the T1q is mainly poor to medium and its hydrocarbon-expulsing intensity is the weakest one in the three sets of hydrocarbon source rocks, only about 12.7?×?104?t/km2. Taking into consideration the joint influence of depositional, organic matter parent source and biological productivity, the overall quality of source rocks in the South Yellow Sea Basin is at the similar level to the Lower Yangtze Subei Basin, but lower than that of the Upper Yangtze Sichuan Basin. The most significant oil & gas information is that multiple direct oil indications and high value abnormalities of gas logging have been discovered in the well CSDP-2. Moreover, the Mesozoic and Upper Paleozoic marine strata in the South Yellow Sea Basin have experienced three hydrocarbon charging stages, indicating a broad prospect of marine oil & gas exploration.Cao, J., Lai, Q., Liu, P., Wei, Y., Wang, L., Liu, R., Fang, J., 2018. Salinimonas sediminis sp. nov., a piezophilic bacterium isolated from a deep-sea sediment sample from the New Britain Trench. International Journal of Systematic and Evolutionary Microbiology 68, 3766-3771. cold-adapted, piezophilic, slightly halophilic bacterium, designated as N102T, was isolated from a deep-sea (4700?m) sediment sample collected from the New Britain Trench. Strain N102T was Gram-stain-negative, rod-shaped, oxidase- and catalase-positive, and grew optimally at 28?°C (range, 4–40?°C), pH 7.0–7.5 (range, 6.0–9.0) and 3–4?%(w/v) NaCl (range, 2–15?%). The optimum pressure for growth was 10?MPa with tolerance up to 70?MPa. 16S rRNA gene sequence analysis showed that strain N102T was most closely related to Alteromonas addita R10SW13T (97.2?%), Alteromonas stellipolaris LMG 21861T (97.1?%), Alteromonas gracilis 9a2T (97.1?%), Salinimonas lutimaris DPSR-4T (96.1?%) and Salinimonas chungwhensis BH030046T (95.4?%). Phylogenetic analyses based on 16S rRNA gene, gyrB gene and whole-genome sequences placed strain N102T within the genus Salinimonas. Genomic comparisons based on average nucleotide identity and tetranucleotide signature frequencies corroborated the results of the phylogenetic analyses. The principal fatty acids were summed feature 3 (C16?:?1 ω7c/C16?:?1ω6c), C16?:?0 and summed feature 8 (C18?:?1 ω7c/C18?:?1ω6c). The major respiratory quinone was ubiquinone 8. The predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and an unidentified phospholipid. The G+C?content of the genomic DNA was 48.2?mol%. On the basis of phenotypic, chemotaxonomic and molecular data, we conclude that strain N102T represents a novel species of the genus Salinimonas, for which the name Salinimonas sediminis sp. nov. is proposed (type strain N102T=MCCC 1K03497T=KCTC 62440T). The GenBank [/EMBL/DDBJ] accession numbers for the nucleotide sequence reported in this study MH816968 (Salinimonas lutimaris KCTC 23464T, gyrB gene), MG745360 (Salinimonas sediminis N102T, 16SrRNA gene) and CP031769 (Salinimonas sediminis N102T, complete genome).Carmi, I., Kronfeld, J., Moinester, M., 2019. Sequestration of atmospheric carbon dioxide as inorganic carbon in the unsaturated zone under semi-arid forests. CATENA 173, 93-98. carbon, as allogenic and pedogenic carbonates mixtures, can be a significant component of arid and semi-arid zone soils. It has been claimed, that the formation of pedogenic carbonates does not sequester atmospheric carbon dioxide, when formed from the preexisting limestone: Ca+2?+?2HCO3??→?CaCO3 ↓?+?CO2 ↑?+?H2O. But if the cation is derived from a non?carbonate source sequestration can occur. Among the unconsidered sources in nature are the contribution of Ca+2, released from adsorption sites on the clay surfaces. Analysis of DIC, δ13C and Δ14C data show in the present study that sequestration does occur within the unsaturated zones (USZ) in a semiarid region: 1) the DIC is depleted as carbonate precipitates into the USZ, 2) the released CO2, does not immediately return to the atmosphere (except for the samples nearest to the surface) but recycles to the soil-gas of high CO2 partial pressure, and 3) that radiocarbon, which is generated only in the overlying atmosphere, and exhaled into the USZ by roots and the decay of soil organic matter, is incorporated within the calcite mineral. Thus, a net sequestration of atmospheric CO2 does occur.Carrero-Carralero, C., Escobar-Arnanz, J., Ros, M., Jiménez-Falcao, S., Sanz, M.L., Ramos, L., 2019. An untargeted evaluation of the volatile and semi-volatile compounds migrating into food simulants from polypropylene food containers by comprehensive two-dimensional gas chromatography?time-of-flight mass spectrometry. Talanta 195, 800-806. study reports on the potential of comprehensive two-dimensional gas chromatography combined with time-of-flight mass spectrometry (GC×GC?ToF MS) for the exhaustive untargeted characterization of the volatile and semi-volatile analytes migrating from four commercial polypropylene food containers into four simulants (water, 3% acetic acid, 10% ethanol, and isooctane) according to European Regulation 10/2011. Collected extracts were concentrated and directly subjected to GC×GC?ToF MS analysis without any further treatment to preserve migrants integrity. As expected, the nature and total number of compounds detected in the migrates depended on both the brand (i.e., manufacture and/or sterilization procedure) and the simulant applied. In total, 107 analytes, including some less volatile compounds, were either positively or tentatively identified in the investigated simulants, a number of these compounds being reported for the first time as migrants from this type of material. A database containing chromatographic, mass spectral and partition information concerning these compounds, plus 23 remaining unidentified, is provided.Casciotti, K.L., Forbes, M., Vedamati, J., Peters, B.D., Martin, T.S., Mordy, C.W., 2018. Nitrous oxide cycling in the Eastern Tropical South Pacific as inferred from isotopic and isotopomeric data. Deep Sea Research Part II: Topical Studies in Oceanography 156, 155-167. ocean accounts for up to 25% of global emissions of nitrous oxide (N2O), a potent greenhouse gas. Much of this N2O flux occurs in upwelling regions near the ocean's oxygen deficient zones (ODZs), areas known for intense N2O cycling. The Eastern Tropical South Pacific (ETSP) ODZ is one such area, and large uncertainties surround the balance of processes regulating N2O production and emission in this region. Here we examined the distributions of dissolved N2O concentration and stable isotopic composition, in concert with nitrate (NO3-) and nitrite (NO2-) isotopic ratios, to understand the mechanisms that drive N2O production, consumption, and emission from the ETSP ODZ. Keeling plot analysis identified N2O production from both nitrification and denitrification (or nitrifier-denitrification) in the near-surface and in the oxycline, where the largest accumulations of N2O were found. In the N2O concentration maximum that occurs below the ODZ, a higher 15N site preference (SP) indicated nitrification was more prominent. Within the ODZ, significant enrichments were apparent in δ15Nbulk (14–22‰), δ18ON2O (68–100‰) and SP (39–60‰), implying active N2O consumption. Further scrutiny of N2O isotope data in the ODZ highlights a deviation from the relative increases in δ18ON2O and SP expected for bacterial denitrification. At high levels of N2O consumption, SP increased more than expected for the increase in δ18ON2O. This appeared to be due, at least in part, to a decrease in δ15Nβ driven by N2O production in the ODZ, rather than further increases in δ15Nα. Isotopic analysis of co-occurring NO3- and NO2- suggests that NO3- may be the dominant source of N2O in the offshore ETSP ODZ.Caselli, E., Pancaldi, S., Baldisserotto, C., Petrucci, F., Impallaria, A., Volpe, L., D’Accolti, M., Soffritti, I., Coccagna, M., Sassu, G., Bevilacqua, F., Volta, A., Bisi, M., Lanzoni, L., Mazzacane, S., 2018. Characterization of biodegradation in a 17th century easel painting and potential for a biological approach. PLOS ONE 13, Article e0207630. is important to characterize the microorganisms involved in biodeterioration processes to understand their effects on cultural assets and to define an efficient strategy for protecting artworks, monuments, and buildings from microbiological recolonization. In this study, we analyzed the microbial communities dwelling on the verso (front) and recto (back) sides of a 17th century easel painting attributed to Carlo Bononi, an Italian artist of the first Baroque period. Cultivable bacteria and fungi colonizing the painting were isolated and identified in order to characterize the microbial community possibly involved in deteriorating the pictorial layer of the painting. The isolated bacterial strains belonged to the Staphylococcus and Bacillus genera. Furthermore, culture-dependent techniques and SEM/EDS analyses revealed the presence of filamentous fungi of the genera Aspergillus, Penicillium, Cladosporium, and Alternaria. The chemical compositions of pigments were consistent with typical 17th century paintings, and some of the identified pigments, namely red lac and red and yellow earths, could be exploited as nutrient sources by painting-associated microorganisms. The study also evaluated, in vitro, the potential decontaminating activity of a biocompound, containing spores of Bacillus subtilis, Bacillus pumilus, and Bacillus megaterium. The results indicated the ability of this biocompound to counteract the growth of contaminating microorganisms that are potentially dangerous to the painting, suggesting the potential use of these microorganisms to prevent biodeterioration of artworks.Catherin, N., Blanco, E., Piccolo, L., Laurenti, D., Simonet, F., Lorentz, C., Leclerc, E., Calemma, V., Geantet, C., 2019. Selective ring opening of decalin over bifunctional RuS2/zeolite catalysts. Catalysis Today 323, 105-111. discovery of sulfur-resistant catalysts for selective ring opening (SRO) is an important challenge for refiners, considering the future legislation on cetane index of diesel fuels. In the present work, we studied the properties of RuS2 supported on several zeolites in gas-phase decalin hydroconversion at high hydrogen pressure (5?MPa) in the presence of 0.8% H2S concentration. Catalytic bifunctionality was investigated by changing the Ru loading or support acidity. The addition of RuS2 strongly improved catalytic activity of an HY zeolite, decreased coke deposition and dehydrogenation and increased selectivity towards RO products. The mechanism mainly proceeds from skeletal isomerization induced by the acidity of the zeolite but the hydrogen activation properties of RuS2 are beneficial to the activity and stability of the catalyst.Chang, J., Zhang, E., Liu, E., Liu, H., Yang, X., 2018. A 60-year historical record of polycyclic aromatic hydrocarbons (PAHs) pollution in lake sediment from Guangxi Province, Southern China. Anthropocene 24, 51-60. aromatic hydrocarbons (PAHs) are toxic organic pollutants which present and persist ubiquitously in the natural environment. We present a sedimentary record of the 16 priority PAHs pollutants from Lake Baxian, a small freshwater lake in a remote area of southern China, spanning the last ca. 60 years. The concentration of PAHs in the sediment (ranging from 1639 to 8766?ng/g) was much higher than the lakes from the remote plateau, western and northwestern China, and of a similarly high level to the lowland urban sites. The sources of PAHs compounds recorded in the sediment were generally derived from petroleum, biomass burning (grass, wood) and high temperature industrial combustion processes. The PAHs were mainly transported to the site from the surrounding regions by atmospheric deposition instead of direct discharge. There were two periods represented by high levels of PAHs: we linked the 1950s peak to the beginning of regional industrial development under the first ‘Five-Year-Plan (1951–1955)’ policy followed by the founding of the People’s Republic of China, while the 1980–1990?s PAHs peak were primarily related to the industrial reboot under the ‘Reform and Opening-up’ policy (since 1978). Until recently, the ecosystem biodiversity risks imposed by the high level of atmospheric deposited PAHs into remote lowland aquatic systems have been poorly assessed and understood. Our study highlights the importance of investigating the historical total PAHs concentration changes, sources and deposition processes from such systems. Results of this study will provide baseline information to frame management strategies for similar lake systems worldwide.Chase, Z., Ellwood, M.J., van de Flierdt, T., 2018. Discovering the ocean’s past through geochemistry. Elements 14, 397-402. elements and isotopes underlie many of the proxies used to reconstruct past ocean conditions. These proxies, recorded in diverse archives, are used to reconstruct seawater properties such as temperature, pH, and oxygen, or oceanic processes such as circulation, nutrient uptake, and biological productivity. Proxy calibration and validation requires a combination of ocean sediment core-top measurements, sediment trap studies, and laboratory- or field-based observations. New measurements of proxies in the modern ocean are rapidly illuminating the scope and limitations of each proxy while also helping to identify and evaluate new geochemical proxies that are based on trace elements and their isotopes.Chen, F., Zhao, H., Lu, S., Ding, X., Ju, Y., 2019. The effects of composition, laminar structure and burial depth on connected pore characteristics in a shale oil reservoir, the Raoyang Sag of the Bohai Bay Basin, China. Marine and Petroleum Geology 101, 290-302. evaluate the effects of the composition, laminar structure and burial depth on pore volumes connected by pore-throats of different sizes in a shale oil reservoir, the Es1x formation in the Raoyang Sag of the Bohai Bay Basin was selected as an example. The effects of component contents, laminar structure and burial depth on pore volumes connected by pore-throats with widths of <100?nm, 100–1000?nm and 1000–10000?nm were discussed based on total organic carbon (TOC), X-ray diffraction, low-temperature N2 adsorption and mercury intrusion porosimetry methods. The results show that pore volumes connected by pore-throats with widths of <100?nm decrease with increasing contents of TOC and carbonate and increase with increasing clay content. The pore volumes connected by pore-throats with widths of 100–1000?nm initially decrease with increasing quartz?+?feldspar content and then increase when the content exceeds 20%. The pore volumes connected by pore-throats with widths of 1000–10000?nm increase with increasing TOC content, and then decrease when TOC content exceeds 2.5%. They also exhibit a negative relationship with clay content. The pore volumes connected by pore-throats with widths of <100?nm are initially similar in nonlaminated and laminated samples with equivalent burial depths and decrease with increasing burial depth. However, at depths in excess of 3100?m, the connected pore volumes in the nonlaminated samples increase with increasing burial depth and become larger than those of the laminated samples. The pore volumes connected by pore-throats with widths of 100–1000?nm in the nonlaminated and laminated samples are similar, and there are no obvious changes with increasing burial depth. The pore volumes connected by pore-throats with widths of 1000–10000?nm in the nonlaminated and laminated samples are also similar and decrease with increasing burial depth at burial depths less than 3100?m, and then connected pore volumes in the laminated samples increase with increasing burial depth at burial depths exceeding 3100?m. The connected pore volumes in the laminated samples are larger than those in the nonlaminated samples at burial depths exceeding 3400?m.Chen, H., Chow, A.T., Li, X.-W., Ni, H.-G., Dahlgren, R.A., Zeng, H., Wang, J.-J., 2018. Wildfire burn intensity affects the quantity and speciation of polycyclic aromatic hydrocarbons in soils. ACS Earth and Space Chemistry 2, 1262–1270. soil may be an important source of polycyclic aromatic hydrocarbons (PAHs) in the environment. With projected increase of wildfire frequency and intensity due to changing global climate, understanding the quantity and speciation of PAHs, including halogenated PAHs (XPAHs), resulting from different burn intensities has important ramifications for environmental quality concerns and global soil carbon dynamics. Here, we quantified levels of 16 U.S. Environmental Protection Agency regulated PAHs, 3 chlorinated PAHs, and 6 brominated PAHs in nonburned forest soils and burned ash/soil samples covered with black ash (B-Ash; moderate burn intensity) or white ash (W-Ash; severe burn intensity) from the 2013 Rim Fire (1,041 km2) in California. The ∑16PAH concentrations follow (mean ± standard deviation; μg/kg) B-Ash (893 ± 285) > W-Ash (515 ± 333) ≈ nonburned soils (247 ± 58). Moreover, the ∑16PAH profiles were altered by both moderate and severe burn conditions with the size of aromatic structures following B-Ash > W-Ash > nonburned soils. Neither chlorinated nor brominated PAH concentration was significantly elevated by moderate or severe wildfire. Overall, fire intensity is critical in regulating soil PAH concentrations and profiles. Given the high erodibility of wildfire ash, these PAHs can be easily transported to rivers and reservoirs where they could impact the aquatic food web and drinking source water.Chen, J., Kipping, D., 2018. On the rate of abiogenesis from a Bayesian informatics perspective. Astrobiology 18, 1574-1584. appears to have emerged relatively quickly on the Earth, a fact sometimes used to justify a high rate of spontaneous abiogenesis (λ) among Earth-like worlds. Conditioned upon a single datum—the time of earliest evidence for life (tobs)—previous Bayesian formalisms for the posterior distribution of λ have demonstrated how inferences are highly sensitive to the priors. Rather than attempt to infer the true λ posterior, we here compute the relative change to λ when new experimental/observational evidence is introduced. By simulating posterior distributions and resulting entropic information gains, we compare three experimental pressures on λ: (1) evidence for an earlier start to life, tobs, (2) constraints on spontaneous abiogenesis from the laboratory, and (3) an exoplanet survey for biosignatures. First, we find that experiments 1 and 2 can only yield lower limits on λ, unlike 3. Second, evidence for an earlier start to life can yield negligible information on λ if . Vice versa, experiment 2 is uninformative when . While experiment 3 appears the most direct means of measuring λ, we highlight that early starts inform us of the conditions of abiogenesis and that laboratory experiments could succeed in building new life. Altogether, the three experiments are complementary, and we encourage activity in all to solve this grand challenge.Chen, J., Wei, J., Ni, Y., Chen, J., Deng, C., Tian, D., Hu, J., Huang, Z., Zhang, D., Yongke, H., 2018. Determination of main source rocks in the Jiuxi depression of Jiuquan Basin and its implications for oil and gas exploration. Acta Petrolei Sinica 39, 1223-1240. Jiuxi depression in the Jiuquan Basin is a typical well-explored petroliferous depression, in which the Qingnan sag is the main petroleum generation sag. With the increase of the number of exploration wells and the depth of exploration in recent 10 years, more and more source rocks in the lower part of the Xiagou Formation and the Chijinpu Formation have been exposed, which provides valuable information for re-understanding the main source rock and its hydrocarbon generation potential in this sag. A detailed geochemical study on a large number of source rocks from more than 30 wells in the Qingnan sag has been carried out and the results indicate that the abundance of organic matter in the Lower Cretaceous source rocks increases from top to bottom, in which the source rocks in the Zhonggou Formation and the Upper Member of the Xiagou Formation are only fair source rock, while the source rocks in the Middle and Lower members of the Xiagou Formation and the Chijinpu Formation are good or very good source rocks with high content of organic matter dominated by Type Ⅱ kerogen. The organic matter abundance of the source rocks is generally the highest in the central region and slightly lower in the south and north, and the high potential source rocks are mainly distributed in the central-northeastern parts where the Middle and Lower members of the Xiagou Formation and the Chijinpu Formation are all main source rocks, while only the Lower Member of the Xiagou Formation and the Chijinpu Formation are good and main source rocks in the southern part. The Middle and the Lower members of the Xiagou Formation are at the stages of thermally mature and peak oil respectively, and the Chijinpu Formation is at the stage of late oil window to highly mature condensate. These source rocks are the main source rocks in the Qingnan sag, and have generated and expelled a large amount of crude oil. There is still good oil exploration potential in the central and northern parts of the Qingnan sag. These understandings have an important guiding role for the fine exploration of oil and gas in the Jiuxi depression. The example of the Jiuxi depression has an important enlightenment to the fine exploration and research of other well-explorated basins in China.Chen, L., Chen, W.-F., Xu, Z.-L., Li, W., Zhang, X.-Y., Li, W.-J., Wang, L., 2018. Sphingomonas oleivorans sp. nov., isolated from oil-contaminated soil. International Journal of Systematic and Evolutionary Microbiology 68, 3720-3725. FW-11T was isolated from oil-contaminated soil from Panjin in Liaoning, China. It was a Gram-stain-negative, aerobic and rod-shaped bacterium. The strain was confirmed to be a member of the genus Sphingomonas based on phylogenetic inference and phenotypic characteristics. The best growth of strain FW-11T occurred at 30?°C and pH 6.0–7.0. The strain was non-spore-forming, catalase-negative and oxidase-negative. The main polar lipids were sphingoglycolipid, phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and unidentified lipids. The cell-wall peptidoglycan of strain FW-11T included alanine, glycine, glutamic acid, aspartic acid and meso-diaminopimelate. The predominant isoprenoid quinones were ubiquinone Q-10 (93.2?%) and Q-9 (6.8?%). The fatty acid profile (>5?%) included C18?:?1ω6c (43.1?%), C16?:?0 (14.6?%), C17?:?1ω6c (14.0?%) and C14?:?0 2-OH (11.1?%). The most similar neighbours of FW-11T were Sphingomonas fennica K101T (97.4?%) and Sphingomonas haloaromaticamans A175T (97.0?%). The average nucleotide identity relatedness values between strain FW-11T and the two type strains ( S. fennica K101T and S. haloaromaticamans A175T) were 73.2 and 75.3?%, respectively. The genome size of FW-11T was 3.8 Mbp, comprising 3735 predicted genes with a DNA G+C?content of 64.0?mol%. Based on phenotypic, chemotaxonomic and phylogenetic data, strain FW-11T represents a novel species of the genus Sphingomonas , for which the name Sphingomonas oleivorans sp. nov. is proposed. The type strain is FW-11T (=LMG 29274T=HAMBI 3659T). The GenBank accession number for the 16S rRNA gene sequence of Sphingomonas oleivorans sp. nov LMG 29274T is KT855088.Chen, R., Zhou, H., Liu, M., Yan, H., Qiao, X., 2019. Ionic liquids-based monolithic columns: Recent advancements and their applications for high-efficiency separation and enrichment. TrAC Trends in Analytical Chemistry 111, 1-12. of their excellent physicochemical characteristics, ionic liquids (ILs) have been widely reported as new monomers to fabricate versatile monolithic columns with improved separation efficiency and excellent selectivity. In this study, a systematic summary of the recently reported ILs-based monolithic columns was performed. We paid much attention to the characteristics of the introduced ILs as well as the fabrication methods for the monolithic columns. Furthermore, the ILs-based monolithic columns were respectively discussed based on their applications in high performance liquid chromatography, capillary electrochromatography and solid phase extraction. Moreover, ILs as the porogenic solution for fabrication of monolithic columns were also included.Chen, S., Zhao, W., Ge, X., Zeng, Q., Yang, Q., Gai, S., 2019. Predicting gas content in high-maturity marine shales using artificial intelligence based seismic multiple-attributes analysis: A case study from the lower Silurian Longmaxi Formation, Sichuan Basin, China. Marine and Petroleum Geology 101, 180-194. content is the most important index used to evaluate shale gas reservoirs. Compared to the North American marine shales, the marine shales of China are older, characterized by high thermal maturity, and have experienced multiple stages of tectonism. There is no clear positive correlation between the gas content and TOC content for marine shales in China; therefore, it is not feasible to indirectly predict the gas content by predicting TOC content, as has been extensively done for the North American shales. In this study, the geophysical responses of reservoirs with high gas contents, the factors that influence the gas content have been determined based on well log interpretation and seismic rock physics analysis. The seismic attributes and elastic parameters that are sensitive to the gas content have also been investigated. Additionally, a pre-stack seismic inversion has been carried out through a combination of well log and 3D seismic data to obtain the data volumes of the seismic elastic parameters, which are highly sensitive to variations in gas content. A seismic multiple-attribute analysis based on neural networks of AI (artificial intelligence) technology has been applied to determine the type and the combination of elastic parameters for computing the gas content data volume. This kind of analysis has been carried out based on pre-stack inversion of seismic data. The results suggest that the lower Silurian Longmaxi Formation, a high-quality gas-rich reservoir, is characterized by its low density, low Poisson's ratio and low velocity. A combination of six parameters or attributes optimally predicts gas content. The studied block, W202, generally has a high gas content. Two classes of sweet spots have been predicted in the study area based on these results. The application of neural networks has provided a precise prediction for the spatial distribution of gas saturation in the shale reservoir, serving as a basis for locating and designing horizontal wells for shale gas development.Chen, W., Vashistha, P., Yen, A., Joshi, N., Kapoor, Y., Hartman, R.L., 2018. Asphaltenes dissolution mechanism study by in situ Raman characterization of a packed-bed microreactor with HZSM-5 aluminosilicates. Energy & Fuels 32, 12205-12217., which are the most aromatic component of heavy oil, are responsible for the fouling and impairment in flow lines, wellbores, and other production facilities in the petroleum industry. Aromatic solvents such as xylenes are commonly used for the asphaltenes’ cleaning process. Understanding the mechanism of asphaltenes’ dissolution in aromatic solvents is significant for the development of a remediation strategy. The reduction of a reactor’s characteristic length scale leads to the decrease in experimental period while providing high-throughput information. Microfluidic systems with in situ spectroscopy is an excellent platform for time-effective studies of the molecular behavior of asphaltenes in simulated sandstone reservoirs. Here, we injected the HZSM-5 zeolite nanoparticles (707 nm aggregate–1 in isopropanol solution) with varying Al2O3/SiO2 ratios (from 0 to 1/26) into the quartz porous media to represent reservoirs with different characteristic acidity. In-line ultraviolet–visible light (UV-vis) spectroscopy enabled the direct measurement of the dissolution percentage, while in situ Raman spectroscopy revealed where the dissolution occurred within the porous media. In addition to bed occupancy, sheet sizes of asphaltenes molecules can also be determined by in situ Raman spectroscopy. Our results show that the average sheet size of deposited asphaltenes molecules decreased from 2.97 ± 0.25 nm to 2.74 ± 0.26 nm after cleaning the porous media with xylenes. This trend is confirmed with the fluorescence emission spectra of dissolved asphaltenes molecules, where a 10–30 nm red-shift is present, when referenced to asphaltenes source samples. These results provide an explanation to why the dissolution percentage of asphaltenes in aromatic solvents increases from 20.15 wt?% to 51.00 wt?% as the Al2O3 content increases. We can speculate that this increase in weight percentage is attributed to the differences in deposited asphaltenes molecules’ sheet size. These results reveal the importance of π–π interactions during asphaltenes dissolution process in the aromatic solvent. Our results provide the fundamental understanding of asphaltenes dissolution, which otherwise would be challenging to observe using any other analytical methods.Chen, Y.-f., Pu, W.-f., Li, Y.-b., Liu, X.-l., Jin, F.-y., Hui, J., Gong, X.-l., Guo, C., 2018. Novel insight into the viscosity-temperature characteristic by the comparison of Tahe ordinary- and ultra- heavy oils. Energy & Fuels 32, 12308-12318. attention is being paid to the exploitation of unconventional oils, mainly heavy and ultra-heavy oils. Thereinto, the high viscosity nature of heavy and ultra-heavy oils is a major obstruction and challenge to the recovery of the heavy oil reservoir and the selection of the enhanced oil recovery methods. In order to investigate the characteristic of the viscosity variation in sequence temperature regions and the internal mechanism of the shear thinning property, the ordinary heavy and ultra-heavy oils were employed and studied. On the basis of the fundamental physic-chemical analyses, the viscosity-temperature and viscosity-shear rate characteristics in sequence temperature regions were evaluated comparatively for both heavy oils. In addition, the free volume theory was involved to clarify the mechanism of the shear thinning property and viscosity variation. Then the viscous activation energy variation in sequence temperature regions was validated and analyzed with the negative linear relationship between the viscous activation energy and the frequency factor (compensation effect). Satisfying viscosity prediction curves were obtained for both heavy oils with high regression precision (R2 > 0.99). A further understanding of the compensation effect existence and thermal oxidation characteristic comparison for the ultra-heavy oil and its components were obtained. From this study, a novel insight into the characteristic and prediction of viscosity-temperature relationship can be brought based on the viscous activation energy variation in sequence temperature regions.Chen, Y., Gao, Y., Chen, L., Wang, X., Liu, K., Sun, B., 2019. Experimental investigation of the behavior of methane gas hydrates during depressurization-assisted CO2 replacement. Journal of Natural Gas Science and Engineering 61, 284-292. replacement with depressurization assistance is a crossover concept that has been proposed in recent years for natural gas hydrate development. It combines the merits of two traditional methods to improve production and reduce risks. To verify the feasibility of this new method and evaluate the corresponding efficiency, experimental apparatus has been designed to simulate the horizontal interface between a CO2 injection well and a CH4 production well based on the independent extraction mechanism and well structure design. To prepare natural gas hydrate-bearing samples under conditions that conform to actual field conditions, silica sand is packed into a core-holding tube with methane gas and distilled water at appropriate pressures and temperatures. Then a horizontal extraction process with an injection well and a production well are simulated, and the parameters influencing the pressure system, such as inlet pressure (pressure of injection well), outlet pressure (pressure of production well), and confining pressure (pressure of the overburden layer), are controlled as variables and analyzed. The ratio of generated methane and injected CO2 is used to evaluate the corresponding utilization efficiency (UE) in this work. Results indicate that all these pressure parameters have certain effects on CO2 replacement behavior. Generally, the fluid flow driven by pressure differences, and the special phase equilibria properties are the essence of their influence. The feasibility of enhancing CO2 utilization efficiency with depressurization assistance is verified based on experimental data. In consideration of time and cost, the relative pressure parameters should be optimized comprehensively to maximize commercial efficiency before field application.Chen, Y., Wu, Y., Liu, X., Li, B., Hu, D., Huang, S., Ma, M., Chen, B., 2019. Pulsed elution modulation for on-line comprehensive two-dimensional liquid chromatography coupling reversed phase liquid chromatography and hydrophilic interaction chromatography. Journal of Chromatography A 1583, 98-107. this work, a reversed phase liquid chromatography (RPLC) coupling to hydrophilic interaction chromatography (HILIC) system has been constructed, combining with pulsed elution reversed phase liquid chromatography (PE-RPLC) and HILIC to comprehensively analyze P. ginseng root extract, which is rich in saponins. By the application of pulsed elution (PE) modulation technique, the proposed RPLC?×?HILIC system allows the chromatographic separation to be optimized independently in both dimensions. In the first dimension (1D), PE modulation is achieved by the separation of a complex mixture, such as P. ginseng root extract, with a PE gradient. This PE gradient contains a set of pulses where the solvent strength increases gradually. Thus, the modulation of 1D eluent is realized by stepwise-pulse fractionation, rather than by a traditional two-dimensional interface. Furthermore, the number of fractions and the fractionated period can be regulated independently, which leads to independent adjustment of the separation cycle in the second dimension (2D) separation without the loss of D1 separation efficiency. To overcome the inherent solvent incompatibility of RPLC?×?HILIC, we introduced a newly developed trapping interface, equipped with bypass. The result indicates excellent separation of saponins in P. ginseng root extract. Compared with the traditional modulation method, the proposed RPLC?×?HILIC system has extreme flexibility, those modulation time could be regulated in a large range without re-optimizing the 1D PE gradient. Worthily mentioned, the proposed RPLC?×?HILIC system shows excellent orthogonality, and 20% more peaks could be obtained with current method compared to the traditional value based modulation method. Independent regulation of both dimensions could enable the proposed modulation method to be widely applied for complex samples analysis in ordinary laboratory.Chen, Z., Liu, X., Osadetz, K.G., 2019. Petroleum generation kinetic models for Late Ordovician kukersite Yeoman Formation source rocks, Williston Basin (southern Saskatchewan), Canada. Fuel 241, 234-246. Yeoman Fm. kukersite source rocks from Canadian Williston Basin are composed almost exclusively of Gloeocapsomorpha prisca (G. prisca) alginite. Thermocatalytic petroleum generation from G. prisca alginite differs significantly from that of amorphous bituminite typical of marine Type II source rocks. Commonly used petroleum generation kinetic parameter optimization procedures that assume nth order chemical reactions fail to reproduce sample Flame Ionization Detector (FID) pyrograms using expected chemical bond activation energies. A parallel nucleation-growth reaction model (PN-GRM) successfully addresses these deficiencies for this specific kerogen type. Programed pyrolysis of seventeen kukersite sample FID pyrograms as well as two additional kukersite Rock-Eval datasets reveal the kinetic characteristics of this globally significant, but stratigraphically restricted marine Type I source rock. The results show that the PN-GRM closely approximates the chemical reactions as demonstrated by reproduction of kukersite FID pyrograms, that kukersite source rocks are thermally more stable as indicated by elevated petroleum generation onset temperatures, and that compositionally simple and homogeneous source rocks, such as kukersites, typically exhibit a sharply increasing petroleum generation rate and a narrow oil window both in nature and in pyrolysis experiments.Cheng, B., Liang, Y., Xu, J., Deng, Q., Wei, Z., Faboya, O.L., Liao, Z., 2018. Remarkable fractionation of the hydrogen isotope (δD) of hydrocarbon during the fast aromatization process: Insights from the pyrolysis experiments of n-butylcyclohexane. ACS Earth and Space Chemistry 2, 1240–1248. aromatization involves the cleavage of multiple C–H bonds and the dehydrogenation of aliphatic rings, with a resultant fractionation of stable hydrogen between aromatic hydrocarbons and their counterpart precursors. Despite this understanding, there is still the paucity of studies on the hydrogen isotope (δD) fractionation of aromatic compounds and the δD fractionation characteristics during the aromatization process of hydrocarbons. In the present study, n-butylcyclohexane (BCH) was thermally pyrolyzed in a closed gold tube system at different time intervals to investigate the aromatization process of the monoaliphatic ring hydrocarbon. The δD evolutions of toluene (Tol) and methylcyclohexane (MCH) from the BCH pyrolysates were also examined, with the aim of studying the cleavage behavior of the C–H bond at the aliphatic ring. The results of the 24 h BCH pyrolysates showed that toluene was strongly enriched with 2H, whereas MCH was heavily depleted, with ΔδDTol–MCH (δDTol – δDMCH) being 162.3‰ [Vienna Standard Mean Ocean Water (VSMOW)]. In comparison to the initial hydrogen isotope of BCH, ΔδDMCH–BCH and ΔδDTol–BCH were ?46.5 and 115.8‰, respectively. With an increasing pyrolysis time, the degree of δD fractionation between Tol and MCH gradually mitigated. It is speculated that the dehydrogenation of the aliphatic ring started with more possibility of cracking the C–1H bond and then having more C–2H being retained in the aromatic ring at the initial stage of hydrocarbon aromatization, leading to the strong δD fractionation of the aromatic hydrocarbon. This observation is quite instructive, in that fast aromatization of the hydrocarbon caused a remarkable hydrogen isotope fractionation, which may play a significant role in the strong 2H enrichment of aromatic hydrocarbons generated from a fast and high-temperature thermal event, such as a meteorite when passes through the atmosphere.Cheng, Y., Wu, Y., Wen, H., Hubbard, C.G., Engelbrektson, A.L., Tom, L., Li, L., Piceno, Y., Bill, M., Andersen, G., Coates, J.D., Conrad, M.E., Ajo-Franklin, J.B., 2018. Microbial sulfate reduction and perchlorate inhibition in a novel mesoscale tank experiment. Energy & Fuels 32, 12049-12065. sulfate reduction occurs ubiquitously in natural environments. In oil and gas reservoirs, the generation of sulfide (also known as souring) can result in the corrosion of steel infrastructure and downgrading of oil quality, among other environmental and health-related concerns. The complex interplay between hydrological, geochemical, and biological processes during souring is poorly understood, preventing effective treatment and mitigation especially in naturally heterogeneous subsurfaces. In this work, three-dimensional flow tank experiments are utilized as a mesoscale experiment that links well-constrained batch and column experiments to field measurements. The mesoscale tank experiment investigating perchlorate treatment of souring is coupled with reactive transport modeling to understand the effects of heterogeneity on souring and effectiveness of perchlorate treatment. Tracer experiments were conducted at the start and end of the experiment to constrain flow pathways and heterogeneities. Isotopic, geochemical, and microbial data revealed that perchlorate effectively inhibited sulfidogenesis and the growth of dominant sulfate reducing Desulfobacteraceae. Perchlorate treatment enriched Desulfobulbaceae, a sulfur-oxidizing group of bacteria, and Sulfurimonas, a potential perchlorate reducer. More organisms, including sulfate reducing bacteria, were observed closer to the influent. Results from the three-dimensional reactive transport model indicate horizontal preferential flows, as a result of the permeability contrast, led to faster bacteria growth (sulfate reducing bacteria) and sulfate reduction in fast flow regions. This work highlights the control that spatial distributions of hydrologic characteristics exert over reservoir souring and treatment.Chiu, M.-H., Vazquez, C.I., Shiu, R.-F., Le, C., Sanchez, N.R., Kagiri, A., Garcia, C.A., Nguyen, C.H., Tsai, S.-M., Zhang, S., Xu, C., Santschi, P.H., Quigg, A., Chin, W.-C., 2019. Impact of exposure of crude oil and dispersant (Corexit) on aggregation of extracellular polymeric substances. Science of The Total Environment 657, 1535-1542. oil treated with Corexit dispersant can cause unintended impacts on marine environment systems including altering marine organic matter dynamics; however, impacts on microgels and marine oil snow (MOS) formation are still debated and remain to be fully understood. Extracellular polymeric substances (EPS) are a major source of marine organic carbon for MOS and microgel formation. EPS initial aggregation plays key roles in the oil degrading process and various biogeochemical reactions. Here we used four types of EPS with water accommodated fraction (WAF), chemically-enhanced WAF (CEWAF) and Corexit, to represent potential situations during oil spills and post-application of Corexit. We found that Corexit alone can inhibit EPS aggregation and disperse pre-existing microgels. CEWAF can enhance EPS aggregation with efficiency by up to 80%–100% and more aggregates accumulated within the air-water interface. Additionally, more hydrophobic EPS aggregates showed high resistance to Corexit dispersion while hydrophilic EPS were more sensitive. Effects of oil spills on marine gel particle formation are primarily determined by chemical characteristics (hydrophobicity and protein content) of the constituent EPS. This study offers unique insights for organic particle dynamics and identifies controlling factors for MOS or gel particles associated with oil spills and Corexit dispersant used.Choi, J.W., Jeon, E.J., Jeong, K.J., 2019. Recent advances in engineering Corynebacterium glutamicum for utilization of hemicellulosic biomass. Current Opinion in Biotechnology 57, 17-24. glutamicum has been mainly used for industrial production of amino acids, and in recent years, it has also been successfully engineered to broaden its range of substrate and product profiles. In particular, C. glutamicum has been engineered to use non-natural sugar substrates (mainly pentoses) derived from hemicellulosic feedstock, which is the second abundant component of lignocellulosic biomass. Engineering of the host in this context can greatly contribute to the development of an economic and sustainable bioprocess. The present review focuses on the recent progress in engineering C. glutamicum towards efficient utilization of pentose sugars derived in hemicellulose and for direct utilization of hemicellulose. In addition, use of C. glutamicum as a biocatalyst for bioconversion of low-value sugars derived from hemicellulose to high-value product has been reviewed.Christel, S., Herold, M., Bellenberg, S., Buetti-Dinh, A., El Hajjami, M., Pivkin, I.V., Sand, W., Wilmes, P., Poetsch, A., Vera, M., Dopson, M., 2018. Weak iron oxidation by Sulfobacillus thermosulfidooxidans maintains a favorable redox potential for chalcopyrite bioleaching. Frontiers in Microbiology 9, 3059. doi: 10.3389/fmicb.2018.03059. is an emerging technology, describing the microbially assisted dissolution of sulfidic ores that provides a more environmentally friendly alternative to many traditional metal extraction methods, such as roasting or smelting. Industrial interest is steadily increasing and today, circa 15–20% of the world’s copper production can be traced back to this method. However, bioleaching of the world’s most abundant copper mineral chalcopyrite suffers from low dissolution rates, often attributed to passivating layers, which need to be overcome to use this technology to its full potential. To prevent these passivating layers from forming, leaching needs to occur at a low oxidation/reduction potential (ORP), but chemical redox control in bioleaching heaps is difficult and costly. As an alternative, selected weak iron-oxidizers could be employed that are incapable of scavenging exceedingly low concentrations of iron and therefore, raise the ORP just above the onset of bioleaching, but not high enough to allow for the occurrence of passivation. In this study, we report that microbial iron oxidation by Sulfobacillus thermosulfidooxidans meets these specifications. Chalcopyrite concentrate bioleaching experiments with S. thermosulfidooxidans as the sole iron oxidizer exhibited significantly lower redox potentials and higher release of copper compared to communities containing the strong iron oxidizer Leptospirillum ferriphilum. Transcriptomic response to single and co-culture of these two iron oxidizers was studied and revealed a greatly decreased number of mRNA transcripts ascribed to iron oxidation in S. thermosulfidooxidans when cultured in the presence of L. ferriphilum. This allowed for the identification of genes potentially responsible for S. thermosulfidooxidans’ weaker iron oxidation to be studied in the future, as well as underlined the need for new mechanisms to control the microbial population in bioleaching heaps.Chuang, P.-C., Yang, T.F., Wallmann, K., Matsumoto, R., Hu, C.-Y., Chen, H.-W., Lin, S., Sun, C.-H., Li, H.-C., Wang, Y., Dale, A.W., 2019. Carbon isotope exchange during anaerobic oxidation of methane (AOM) in sediments of the northeastern South China Sea. Geochimica et Cosmochimica Acta 246, 138-155. major processes that determine the distribution of methane (CH4) in anoxic marine sediments are methanogenesis and the anaerobic oxidation of methane (AOM), with organoclastic sulfate reduction exerting an important secondary control. However, the factors leading to the distribution of stable carbon isotopes (δ13C) of CH4 are currently poorly understood, in particular the commonly-observed minimum in δ13C-CH4 at the sulfate-methane transition (SMT) where AOM rates reach maximum values. Conventional isotope systematics predict 13C-enrichment of CH4 in the SMT due to preferential 12CH4 consumption by AOM. Two hypotheses put forward to explain this discrepancy are the addition of 12C-enriched CH4 to porewaters by methanogenesis in close proximity to AOM, and enzymatically-mediated carbon isotope equilibrium between forward and backward AOM at low concentrations of sulfate. To examine this in more detail, field data including δ13C of CH4 and dissolved inorganic carbon (DIC) from the continental margin offshore southwestern Taiwan were simulated with a reaction-transport model. Model simulations showed that the minima in δ13C-CH4 and δ13C-DIC in the SMT could only be simulated with carbon isotope equilibrium during AOM. The potential for carbon cycling between methanogenesis and AOM in and just below the SMT was insignificant due to very low rates of methanogenesis. Backward AOM also gives rise to a pronounced kink in the δ13C-DIC profile several meters below the SMT that has been observed in previous studies. We suggest that this kink marks the true base of the SMT where forward and backward AOM are operating at very low rates, possibly sustained by cryptic sulfur cycling or barite dissolution.Connell, L.D., Pan, Z., Camilleri, M., 2019. The variation in produced gas composition from mixed gas coal seam reservoirs. International Journal of Coal Geology 201, 62-75. paper investigates predictive modelling of gas production from coal seam reservoirs that contain mixtures of CO2 and CH4. A series of laboratory experiments are presented that are analogues of the gas production process where gas is drained at a controlled rate from a coal core sample with a known initial gas content and composition. The experiments were performed at two initial gas compositions and for two outflow rates. There was excellent agreement in the mass balance of the experiments with the difference between the initial gas volume and cumulative outflow ranging between 0.8 and 1.8% of the initial volume. During the early stages of gas desorption the CO2 concentration of the outflow gas was significantly lower than that in the adsorbed gas but increased significantly at low pore pressures. Thus, the CH4 was preferentially desorbed relative to CO2. For example, in an experiment in which the initial gas content of the coal was ~30% CO2, the CO2 concentration of the produced gas was only ~13% and did not increase significantly until the pore pressure fell below 0.8?MPa, ultimately increasing to ~95%. A reservoir simulator was used to match the desorption observations, and the results indicate, in a finding consistent with previous work, that the extended Langmuir adsorption model based on pure gas isotherms does not provide accurate predictions. A modified extended Langmuir approach was developed, based on using measurements of the initial gas content and its composition, provided a more accurate fit to the experimental observations of gas desorption. A fully predictive procedure using the 2D Equation of State adsorption model with the pure gas adsorption isotherms provided good agreement with gas desorption observations. A series of hypothetical reservoir simulation case studies are presented that illustrate changes of CO2 concentration with time for a variety of initial compositions.Contreras Ortiz, S.N., Cabanzo, R., Mejía-Ospino, E., 2019. Crude oil/water emulsion separation using graphene oxide and amine-modified graphene oxide particles. Fuel 240, 162-168. oxide (GO) nanosheets have been experimentally proved to be a highly efficiency, rapid and universal demulsifier to break up the crude-in-water emulsion. The alkylamine functionalization of graphene oxide is well known as a way to turn graphene oxide highly affine with organic solvents. In the present work an amphiphilic material, graphene oxide functionalized by amino groups were prepared by Hummer’s modified method. We introduced it as a versatile demulsifier to break up crude-in-water emulsions. The amphiphilic material was characterized by Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, X-ray diffraction (XRD) and emission scanning electron microscope (SEM). The efficient demulsifier to break up crude-in-water emulsion was proved in synthetic emulsion using Colombian crude oil with different concentration. Demulsification tests indicated that graphene oxide amine-modified (GO-A) could separate the crude-in-water emulsion in a short time. Demulsification performance of amphiphilic material was made using the bottle test and evaluated by UV–Vis absorption spectroscopy to measure the final grease concentration after GO-A treatment.Cornelissen, R., B?ggild, A., Thiruvallur Eachambadi, R., Koning, R.I., Kremer, A., Hidalgo-Martinez, S., Zetsche, E.-M., Damgaard, L.R., Bonné, R., Drijkoningen, J., Geelhoed, J.S., Boesen, T., Boschker, H.T.S., Valcke, R., Nielsen, L.P., D'Haen, J., Manca, J.V., Meysman, F.J.R., 2018. The cell envelope structure of cable bacteria. Frontiers in Microbiology 9, 3044. doi: 10.3389/fmicb.2018.03044. bacteria are long, multicellular micro-organisms that are capable of transporting electrons from cell to cell along the longitudinal axis of their centimeter-long filaments. The conductive structures that mediate this long-distance electron transport are thought to be located in the cell envelope. Therefore, this study examines in detail the architecture of the cell envelope of cable bacterium filaments through a combination of classical electron microscopy, cryo-based electron microscopy and tomography, focused ion beam-scanning electron microscopy and atomic force microscopy. We systematically imaged intact filaments with varying diameters. In addition, we investigated the periplasmic fiber sheath that remains after the cytoplasm and membranes have been removed by chemical extraction. Based on these investigations, we present a quantitative structural model of a cable bacterium. Cable bacteria build their cell envelope by a parallel concatenation of ridge compartments that have a standard size. Larger diameter filaments simply incorporate more parallel ridge compartments. Each ridge compartment contains a ~50 nm diameter fiber in the periplasmic space. These fibers are continuous across cell-to-cell junctions, which display a conspicuous cartwheel structure that is likely made by invaginations of the outer cell membrane around the periplasmic fibers. The continuity of the periplasmic fibers across cells makes them a prime candidate for the sought-after electron conducting structure in cable bacteria.Couasnon, T., Gélabert, A., Ona-Nguema, G., Zanna, S., Ménez, B., Guyot, F., 2019. Experimental assessment of occurrences and stability of lead-bearing minerals in bacterial biofilms. Chemical Geology 505, 23-35. precipitation of lead-bearing minerals is investigated in bacterial biofilms grown by Shewanella oneidensis MR-1 under aerobic conditions. Under the different conditions investigated, thermodynamic calculations establish that the stable mineral phases expected to precipitate are either wulfenite PbMoO4 or cerussite PbCO3. However, observations by electron microscopy show that the first solids precipitated within hours at the experimental solution/biofilm interface are crystals of about 20?nm in diameter of pyromorphite Pb5(PO4)3Cl). In Mo-bearing systems, the precipitation of the thermodynamically-predicted wulfenite phase is delayed compared to the abiotic experiment and is observed only after seven?days of lead exposure. The initial lead phosphate crystals observed on the extracellular polymeric substances are assumed to result from concurrent local abundances of adsorbed Pb2+ ions and phosphate groups released by metabolically active cells. Scanning electron microscopy observations of samples milled by focused ion beam reveal effective diffusion-limited precipitation of pyromorphite within the well-preserved biofilm porosity.Cramer, J.A., Hammond, M.H., Loegel, T.N., Morris, R.E., 2018. Evolving window factor analysis-multivariate curve resolution with automated library matching for enhanced peak deconvolution in gas chromatography-mass spectrometry fuel data. Journal of Chromatography A 1581-1582, 125-134. chromatography is inherently limited by the high complexity of petroleum fuel compositions. In practice, almost no fuel components are fully resolved in gas chromatography. This is due to both insufficient peak capacity for the large number of individual components within time and chromatographic efficiency constraints, and insufficient resolving power of the stationary phase in the gas chromatography column relative to the many structurally similar isomers or homologs present in petrochemical fuels. Multidimensional approaches, longer columns and slower heating rates can offer some benefits but will not necessarily fully resolve co-eluting fuel compounds, especially within reasonable analysis times. The following work details how deconvolved mass spectral loadings, combined with library matching, provide a quality metric against which to automatically evaluate results obtained from an experimental evolving window factor analysis-multivariate curve resolution deconvolution algorithm applied to gas chromatography-mass spectrometry data. This algorithm was evaluated in the context of trace component detection in synthetic fuel data sets, dodecane and tetradecane detection in petrochemical fuels, and the detection of natural products unlikely to be present in petrochemical fuels. In the case of the trace component detection challenge, the experimental algorithm outperformed a control algorithm that utilized a singular value-based quality metric. Meanwhile, when detecting dodecane, tetradecane, and natural products in petrochemical fuels, the experimental algorithm allowed for higher-quality compound identification results than could be obtained without peak deconvolution, thus reliably improving fuel component resolution in an automated fashion.Crombie, A.T., Larke-Mejia, N.L., Emery, H., Dawson, R., Pratscher, J., Murphy, G.P., McGenity, T.J., Murrell, J.C., 2018. Poplar phyllosphere harbors disparate isoprene-degrading bacteria. Proceedings of the National Academy of Sciences 115, 13081-13086.: Isoprene is a climate-active gas, produced in huge amounts by trees, yet we know little about its biogeochemical cycle. Bacteria able to grow on isoprene have been isolated from soils and sediments, but the phyllosphere, the principal isoprene source, has remained unexplored. Using targeted cultivation-independent techniques, we show that the phyllosphere of an isoprene-emitting tree contains a diverse and active isoprene-degrading population. We reconstruct the genome of an isoprene-degrading Variovorax strain and show that it contains a functional isoprene monooxygenase. This detailed study targets isoprene degraders from the phyllosphere, applies metaomics to isoprene degradation, and isolates and sequences an isoprene-degrading member of the Proteobacteria.Abstract: The climate-active gas isoprene (2-methyl-1,3-butadiene) is released to the atmosphere in huge quantities, almost equaling that of methane, yet we know little about the biological cycling of isoprene in the environment. Although bacteria capable of growth on isoprene as the sole source of carbon and energy have previously been isolated from soils and sediments, no microbiological studies have targeted the major source of isoprene and examined the phyllosphere of isoprene-emitting trees for the presence of degraders of this abundant carbon source. Here, we identified isoprene-degrading bacteria in poplar tree-derived microcosms by DNA stable isotope probing. The genomes of isoprene-degrading taxa were reconstructed, putative isoprene metabolic genes were identified, and isoprene-related gene transcription was analyzed by shotgun metagenomics and metatranscriptomics. Gram-positive bacteria of the genus Rhodococcus proved to be the dominant isoprene degraders, as previously found in soil. However, a wider diversity of isoprene utilizers was also revealed, notably Variovorax, a genus not previously associated with this trait. This finding was confirmed by expression of the isoprene monooxygenase from Variovorax in a heterologous host. A Variovorax strain that could grow on isoprene as the sole carbon and energy source was isolated. Analysis of its genome confirmed that it contained isoprene metabolic genes with an identical layout and high similarity to those identified by DNA-stable isotope probing and metagenomics. This study provides evidence of a wide diversity of isoprene-degrading bacteria in the isoprene-emitting tree phyllosphere and greatly enhances our understanding of the biodegradation of this important metabolite and climate-active gas.Cui, Y., 2018. Climate swings in extinction. Nature Geoscience 11, 889-890. temperature swings and deteriorating environments are perhaps what killed most life in the end-Permian extinction, suggest climate model simulations. Siberian Traps volcanism probably triggered the events.The Earth, to date, has experienced five mass extinction events, which have been caused by volcanism, meteorite impacts and climate change. The most devastating of these events is the end-Permian mass extinction (252 million years ago). At this time, more than 90% of marine species and over 70% of land species were wiped out1. Siberian Traps volcanism has been identified as the trigger for the end-Permian mass extinction: thousands of kilometres of lava was erupted (Fig. 1), and the levels of volcanic gases, such as carbon dioxide and sulfur dioxide, in the atmosphere increased dramatically. The volcanic eruptions initiated a series of changes in the Earth’s environment. Excess gases led to climate warming, climate cooling, ozone depletion and changes in ocean chemistry. These environmental changes have all been blamed for the extreme loss of life. Writing in Nature Geoscience, Black and colleagues2 present climate model simulations that examine the effects of extremely high sulfur and carbon emissions from the Siberian Traps volcanism and find that systemic swings in temperature and ocean circulation could potentially explain mass loss of life in the ocean and on land.Sulfur dioxide and carbon dioxide are both gaseous products of volcanic eruptions, but have opposing climatic effects. Sulfur dioxide can easily dissolve in water and form sulfuric acid, which can subsequently enter the troposphere and form sulfur aerosols or droplets to cool the climate. Carbon dioxide, on the other hand, is a greenhouse gas, and excess amounts of it in the atmosphere may lead to climate warming. The general effects of SO2 and CO2 acting separately are understood, but the impact when both are emitted together during large volcanic eruptions acting on different timescales is unclear.Black and colleagues2 have analysed how the climatic effects of CO2 and SO2 interact, using the National Climate and Atmospheric Research’s climate model, taking advantage of advances made in computing power. The model not only couples atmosphere and ocean circulation, but also accounts for sulfur chemistry and aerosol microphysics. The team identified and considered the combined effects of the two gases. They find that the residence time of sulfur is short-lived in the atmosphere, but continental flood basalt eruptions, such as the Siberian Traps volcanism, could emit enough sulfur aerosols to reduce temperatures by 10–15 °C in the northern hemisphere on land for 10 years2.The background climate 252 million years ago was very different from today. At a CO2 level of about 2,800 ppm at the time, compared to about 400 ppm in the present atmosphere, Black et al.2 estimate that annual average tropical surface air temperature on land reached 38 °C, about 10 °C warmer than today. They also found that carbon dioxide has a much longer atmospheric residence time than sulfur dioxide. Doubling the CO2 level could result in annual average tropical land surface air temperature of 45 °C. Such an extreme heat would be devastating for plants and animals on land and in the ocean. Sluggish ocean circulation and/or increased primary productivity from extra nutrients weathered on land could lead to oxygen deficiency. Black and colleagues predict that devastating swings driven by the oscillating tempo of the volcanism resulted in a cooler sulfur-climate mode during intervals of intense Siberian Traps volcanism and a warmer carbon-climate mode on longer timescales2.The findings of Black et al. are intriguing, but need to be confirmed using geological data, especially by proxies for temperature, CO2 and SO2. Work is underway to extract magmatic sulfur concentrations from melt inclusions3, but not atmospheric SO2 gas concentrations. Currently, viable proxies for temperature, marine redox conditions and CO2 have a maximum temporal resolution of 10,000 years, three orders of magnitude longer than the swings predicted by Black et al.2. Even though it may be challenging to develop very high-resolution proxy records, they are needed to reconstruct rapid environmental changes that cause mass extinctions4. This will help confirm that flood basalt emissions of SO2 and CO2 are the main causes of the extreme temperature swings during the end-Permian extinction event.Today, we are changing our environment, in particular the carbon cycle at a speed that is probably unprecedented in the past 252 million years5. The consequence could be devastating if the trend continues unabated. The total amount of CO2 added during the end-Permian extinction is estimated at about 20,000 × 1015 g C (ref. 6), but was released at a rate that is likely slower than today5. Better quantification of uncertainties of the rates of carbon and sulfur emissions during the end-Permian extinction could offer valuable lessons for today’s changing climate.Black and colleagues2 suggest that extreme swings in climate resulted from the different timescales of cooling from volcanic sulfur dioxide and the warming from volcanic carbon dioxide during the eruption of the Siberian Traps, and led to the end-Permian mass extinction. However, we need to continue to develop new high-resolution proxies for atmospheric CO2 and SO2 concentrations, precipitation, weathering and ocean circulation to understand devastating environmental changes that cause mass extinctions.References1. Erwin, D. H. The Great Paleozoic Crisis: Life and Death in the Permian (Columbia Univ. Press, New York, 1993).2. Black, B. A. et al. Nat. Geosci. (2018).3. Black, B. A., Hauri, E. H., Elkins-Tanton, L. T. & Brown, S. M. Earth Planet. Sci. Lett. 394, 58–69 (2014).4. Bürger, R. & Lynch, M. Evolution 49, 151–163 (1995).5. Le Quéré, C. et al. Earth Syst. Sci. Data 8, 605 (2016).6. Cui, Y., Kump, L. R. & Ridgwell, A. Palaeogr. Palaoclim. Palaecol 387, 176–184 (2013).Czajka, J.J., Abernathy, M.H., Benites, V.T., Baidoo, E.E.K., Deming, J.W., Tang, Y.J., 2018. Model metabolic strategy for heterotrophic bacteria in the cold ocean based on Colwellia psychrerythraea 34H. Proceedings of the National Academy of Sciences 115, 12507-12512.: Colwellia psychrerythraea 34H is a cold-adapted marine bacterium that represents a genus and species cosmopolitan to the cold ocean. To our knowledge, metabolic flux studies of an obligate psychrophile like 34H are not available. We characterized the physiology and metabolism of 34H, at normal-growth temperature of 4 °C and upper-stress condition of room temperature (23 °C), by integrating metabolic flux studies (tracking 13C-labeled compounds) and genetic analyses (transcriptomics). Results from these system-level analyses reveal unique metabolic features under cold salty conditions, which broaden our understanding of microbial ecology in the cold ocean, currently vulnerable to global warming. Specific findings have relevance to bioremediation of pollutants from the petroleum industry, increasingly active in polar seas, and to biomanufacturing of cold-adapted enzymes.Abstract: Colwellia psychrerythraea 34H is a model psychrophilic bacterium found in the cold ocean—polar sediments, sea ice, and the deep sea. Although the genomes of such psychrophiles have been sequenced, their metabolic strategies at low temperature have not been quantified. We measured the metabolic fluxes and gene expression of 34H at 4 °C (the mean global-ocean temperature and a normal-growth temperature for 34H), making comparative analyses at room temperature (above its upper-growth temperature of 18 °C) and with mesophilic Escherichia coli. When grown at 4 °C, 34H utilized multiple carbon substrates without catabolite repression or overflow byproducts; its anaplerotic pathways increased flux network flexibility and enabled CO2 fixation. In glucose-only medium, the Entner–Doudoroff (ED) pathway was the primary glycolytic route; in lactate-only medium, gluconeogenesis and the glyoxylate shunt became active. In comparison, E. coli, cold stressed at 4 °C, had rapid glycolytic fluxes but no biomass synthesis. At their respective normal-growth temperatures, intracellular concentrations of TCA cycle metabolites (α-ketoglutarate, succinate, malate) were 4–17 times higher in 34H than in E. coli, while levels of energy molecules (ATP, NADH, NADPH) were 10- to 100-fold lower. Experiments with E. coli mutants supported the thermodynamic advantage of the ED pathway at cold temperature. Heat-stressed 34H at room temperature (2 hours) revealed significant down-regulation of genes associated with glycolytic enzymes and flagella, while 24 hours at room temperature caused irreversible cellular damage. We suggest that marine heterotrophic bacteria in general may rely upon simplified metabolic strategies to overcome thermodynamic constraints and thrive in the cold ocean.Di Giulio, M., 2018. A non-neutral origin for error minimization in the origin of the genetic code. Journal of Molecular Evolution 86, 593-597. (J Mol Evol 67:510–516, 2008; J Theor Biol 408:237–242, 2016; Nat Comput. , 2018) claims that the error minimization of the genetic code is derived by means of a neutral process and was not due to the action of natural selection. Here, I argue that this neutralist hypothesis of the origin of error minimization is not based directly on any neutral process but it could be only indirectly. On the contrary, it has been natural selection that has acted during the origin of the genetic code determining the property that similar amino acids are coded by similar codons within the genetic code table.Diefendorf, A.F., Leslie, A.B., Wing, S.L., 2019. A phylogenetic analysis of conifer diterpenoids and their carbon isotopes for chemotaxonomic applications. Organic Geochemistry 127, 50-58. diterpenoids are commonly used as conifer-specific biomarkers and for chemotaxonomic assignment or confirmation. Numerous studies have reported on the utility of diterpenoids as chemotaxonomic indicators, but few have quantitatively analyzed diterpenoid concentrations, especially with respect to conifer phylogeny. In addition, the carbon isotope values (δ13C) of diterpenoids provide a means to track conifer-specific δ13C values, which is useful for tracking water availability and the carbon cycle. To expand on previous work, we measured diterpenoid concentrations and carbon isotopes of 43 conifer species, and Ginkgo biloba, collected at the University of California Botanical Garden at Berkeley. In this collection, all extant conifer families and almost two-thirds of extant genera are present, including many subtropical and Southern Hemisphere groups that were once common and widespread components of fossil assemblages. Overall, we found diterpenoid concentrations were highly variable among species and families. Despite this variability, there is coarse family-level phylogenetic structuring with the lowest concentrations in Pinaceae. When diterpenoid concentrations are fitted to a model of trait evolution (Brownian motion), we however find that there is no phylogenetic signal. In contrast, when terpenoids are analyzed by the proportion of diterpenoid compound structure classes (abietanes, labdanes, pimaranes, tetracyclics, and totarols/sempervirol), there was significant phylogenic signal for the abietane and tetracyclic structures. Diterpenoid biosynthetic carbon isotope fractionation, as expressed between diterpenoids and leaf tissue (εditerpenoid), also contained a phylogenetic signal, as well as the broad phylogenetic structuring observed in total diterpenoid concentrations. Overall, these results indicate that the Pinaceae is unique among conifer clades with respect to terpenoid structure classes, concentrations and εditerpenoid. When diterpenoids are applied to taxonomic assignment of fossils, it would be useful to combine several traits (concentration, proportion, and εditerpenoid). In this context, it should be possible to broadly distinguish three major conifer groups: Cupressaceae, Podocarpaceae and Pinaceae. However, based on these results, we recommend against assuming that closely related species have similar diterpenoid compositions.Ding, J., Li, J., Sun, C., Jiang, F., Ju, P., Qu, L., Zheng, Y., He, C., 2019. Detection of microplastics in local marine organisms using a multi-technology system. Analytical Methods 11, 78-87. with complex polymer compositions are present in a lot of marine organisms. In this study, successive stereo microscopy and micro-Fourier transform infrared spectroscopy equipped with attenuated total reflection (μ-ATR-FTIR) in combination with scanning electron microscopy-energy dispersive spectroscopy (SEM-EDS) were implemented to establish a highly accurate microplastics detection system. The method was applied to analyze microplastics in both the soft tissue and the digestive tract of bivalves and fish collected from the markets in Qingdao and Dongying. The results showed that the individual detection rate of microplastics was higher in the fish than that in the bivalves and that the abundance of microplastics measured in items per individual was significantly higher in the fish than that in the bivalves. Four shapes of microplastics, including fibers, fragments, granules and films, were separated from the organisms above. Fibrous microplastics, being the most dominant ones, accounted for over 70% in different organisms. The average size of the fibrous microplastics was smaller than that of the other three shapes of microplastics. The number of microplastics decreased with increasing microplastics sizes. Microplastics of less than 1 mm obtained from different organisms were in the range of 43% to 78%. Rayon (a semi-synthetic polymer) was the most predominant polymer type of microplastics found, accounting for 48.92%. The demersal fish contained relatively more rayon compared with the pelagic fish samples. Surface chemical components of the microplastics were altered possibly owing to the abiotic oxidation. Large variations of the weathering morphologies were observed in the surface of the differently shaped microplastics originating from the organisms. Some microplastics exhibited a rough surface, broken margins, and pronounced pores. SEM-EDS, as an auxiliary technology, would provide a way for data calibration in microplastics investigation. The combination method can provide complementary data and therefore can be successfully applied to accurately identify microplastics.Dionnet, Z., Aleon-Toppani, A., Baklouti, D., Borondics, F., Brisset, F., Djouadi, Z., Sandt, C., Brunetto, R., 2018. Organic and mineralogic heterogeneity of the Paris meteorite followed by FTIR hyperspectral imaging. Meteoritics & Planetary Science 53, 2608-2623. compositional and structural heterogeneity at nm to mm scales is an important characteristic of primitive extraterrestrial materials. Here, we report the analysis of high‐resolution Fourier transform IR hyperspectral imaging analytical measurements at the micron scale on a fragment of the Paris carbonaceous chondrite, supported by Raman and SEM‐EDS measurements. The fragment is crushed in a diamond compression cell. The micro‐FTIR analyses are performed in transmission with two setups, an imaging microscope with a matrix detector using a thermal source and a system using a single point detector coupled with the synchrotron source at the SOLEIL synchrotron facility. We obtain the spatial distribution of chemical/mineralogical components. We confirm at a larger scale (10 μm) the presence of hydrated amorphous silicates observed at a smaller scale (1 μm). Based on the relative abundance of different minerals (hydrated amorphous silicate, olivine, diopside, and serpentine), we propose a sequence of aqueous alteration. Considering the spatial correlation of minerals with organic matter, we discuss the effects of aqueous alteration on the organic matter in bulk. In particular, we detect an increase in the CH2/CH3 ratio in the altered zone and present the possible scenarios that led to the observed chain length shortening/cracking of hydrocarbons. Divandari, H., Hemmati-Sarapardeh, A., Schaffie, M., Ranjbar, M., 2019. Integrating synthesized citric acid-coated magnetite nanoparticles with magnetic fields for enhanced oil recovery: Experimental study and mechanistic understanding. Journal of Petroleum Science and Engineering 174, 425-436. injection has emerged as an attractive enhanced oil recovery (EOR) process in the past decade. These fluids improve oil recovery by reducing interfacial tension (IFT), modifying wettability, and reducing mobility ratio. In this communication, magnetite citric acid-coated nanoparticles (NPs) were synthesized by an affordable, facile and one step method and then characterized using Field emission scanning electron microscopy (FE-SEM), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), and Dynamic light scattering (DLS). Afterward, the microscopic and macroscopic efficiencies of oil recovery in heterogeneous and homogeneous 2D micromodels were investigated in the presence of magnetic field. Citric acid-coated magnetite NPs started to respond to the magnetic field around the intensity of 800 Gauss and also showed the maximum ultimate recovery factor at the intensity of 2750 Gauss. In addition, citric acid coated magnetite NPs provided more enhanced oil recovery factor compared to hematite NPs, because of reducing interfacial tension (IFT) between the oil and injection fluid, altering surface wettability from oil-wet to water-wet, promoting the NPs distribution in porous media, and generating column-like structure in the presence of magnetic field. In fact, magnetite NPs act as piston toward the magnetic field by creating a column which sweeps the oil and increases production. Furthermore, citric acid-coated magnetite NPs flooding increased ultimate recovery factor more than polymer and hematite NPs flooding.Doering, B., 2019. Effects of fermentation on the carbon and nitrogen isotopes of Chinook salmon. Journal of Archaeological Science: Reports 23, 626-633. is seldom considered in paleodietary analyses of Arctic and Subarctic peoples despite its ubiquitous traditional use as a cooking technique in high latitudes. Further, chemists have yet to assess the potential isotopic effects of fermentation on animal tissues, though isotopic research has documented measurable isotopic effects associated with other cooking techniques such as stewing and boiling. To measure the effects of fermentation on stable carbon and nitrogen isotopes, muscle tissues from 11 central Alaskan Chinook salmon (Oncorhynchus tshawytscha) were fermented following ethnographic methods. The results of this experiment demonstrate statistically significant isotopic differences in both carbon (?1.5‰) and nitrogen (+1.3‰) values taken from fermented muscle tissues compared to raw muscle tissues. Additionally, this study found a significant physiological fractionation effect between bone collagen and raw muscle (+3.3‰) consistent with previous research on Pacific salmon. In contrast to previous research, however, these tissues' nitrogen values show no significant fractionation. These findings have implications for central Alaskan dietary reconstructions, residue analyses, and our understanding of past subsistence practices in the Arctic and Subarctic.Dotsika, E., Michael, D.E., 2018. Using stable isotope technique in order to assess the dietary habits of a Roman population in Greece. Journal of Archaeological Science: Reports 22, 470-481. present isotopic study is the first to assess the dietary habits of a Roman population from Northern Greece. A multi-stable isotope analysis was conducted in 22 individuals deriving from Edessa, a town in Greek Macedonia dated at 2nd–4th c.?CE. The basic aims of the present study are to reconstruct the diet of this population, to explore possible dietary variations in relation to sex and age and to detect possible differentiations between the adult and the childhood/juvenile diet. The results of this study revealed that residents of Edessa probably consumed C3 and C4 items as their primary protein source. In addition, the collagen results along with the collagen-apatite spacing possibly indicated a detectable consumption of freshwater sources, for three singular cases. There were no significant isotopic differences between males and females, or between younger and middle aged adults, whereas indications of a possible differentiation among the juvenile and the adult diet were noted. This study offers new information regarding an underrepresented period in Greek history and hopes to encourage the inclusion of multiple isotopic proxies for dietary reconstruction of ancient populations in Greece.Dotsika, E., Michael, D.E., Iliadis, E., Karalis, P., Diamantopoulos, G., 2018. Isotopic reconstruction of diet in Medieval Thebes (Greece). Journal of Archaeological Science: Reports 22, 482-491. the present isotopic study we assess the dietary patterns of a medieval population in Greece. Three isotopes were measured (δ13Ccoll, δ13Cap, δ15Ν) in a skeletal sample from Thebes, consisting of 16 adult individuals (7 males, 9 females) dated at 13th–14th c. CE. According to historical sources many different ethnicities co-existed in Thebes during the stated period, as Greece was under the Crusader's occupation. Thus, a possible dietary diversity could be expected. The basic aims of the present study are to reconstruct the dietary habits of the stated population by quantifying the individual human diet, to detect possible dietary differentiations in relation to sex and age and to compare our results with the ones of other medieval sites primarily in Greece and secondly in the Mediterranean. According to the isotopic and statistical analysis the population studied showed a significant diversity, as half of the sample assessed seemed to have been reliant on a typical C3 terrestrial diet, whereas the other half consumed both C3 and C4 sources. In particular, C4 items (i.e. millet) seem to have been a major staple for a singular female adult (Th22; δ13Ccoll: ?11‰; δ15N: 10‰; δ13Cap: ?5.5‰). In addition, based on the Δ13Cap-coll values, it seems possible that aquatic sources constituted a food source for three specific adults. Therefore, this study sheds light to the importance of identifying singular cases in generic isotopic patterns, and encourages the inclusion of apatite's signature in palaeodietary reconstructions of populations from Greece.Droser, M.L., Gehling, J.G., Tarhan, L.G., Evans, S.D., Hall, C.M.S., Hughes, I.V., Hughes, E.B., Dzaugis, M.E., Dzaugis, M.P., Dzaugis, P.W., Rice, D., 2019. Piecing together the puzzle of the Ediacara Biota: Excavation and reconstruction at the Ediacara National Heritage site Nilpena (South Australia). Palaeogeography, Palaeoclimatology, Palaeoecology 513, 132-145. of origination and evolution of early complex life on this planet are interpreted largely from the fossils of the Precambrian soft-bodied Ediacara Biota. Excavation and reconstruction of beds of the Ediacara Member of the Rawnsley Quartzite at the National Heritage Ediacara fossil site Nilpena, in the Flinders Ranges of South Australia has exposed nearly 300 square meters of fossiliferous bedding planes. As a result, the taphonomy and sedimentology of the succession are well-constrained, rendering it possible to disentangle ecological from environmental and taphonomic signals. The fossil record that is preserved on these beds is a function of a number of factors including 1) sedimentary environment; 2) initial colonization; 3) nature of textured organic surfaces; 4) duration of time between episodes of disturbance; and 5) biostratinomic processes. The excavation and reconstruction of beds at Nilpena yield an exceptional and unique opportunity to examine not only the taxonomic composition of Ediacara communities but also their ecological character at various stages of development. Preserved ecological ‘snapshots’ of fossil assemblages range from immature communities of small-bodied individuals, associated with poorly developed organic mats to communities characterized by a high diversity of macrofaunal taxa, wide range of body sizes and the presence of dense textured organic surfaces.Drozdowska, V., Kowalczuk, P., Konik, M., Dzierzbicka-Glowacka, L., 2018. Study on different fractions of organic molecules in the Baltic Sea surface microlayer by spectrophoto- and spectrofluorimetric methods. Frontiers in Marine Science 5, 456. doi: 10.3389/fmars.2018.00456. sea surface microlayer (SML), created by surface active organic molecules (called: surfactants), is a highly active interface between the sea and the atmosphere. In this study we used the absorption and fluorescence analysis of organic matter collected in the SML and in subsurface layer, of 1 m depth, to describe the changes in molecular size and weight and the composition of surfactants. Data were collected during three research cruises in coastal zone and open waters of the Baltic Sea. The values of the CDOM absorption coefficient were higher in the SML about 29% (in the UV light) to 17% (in a blue spectral range), that reveal dominance of low molecular weighted CDOM molecules, absorbing in the UV light, in the SML. The spectral slope coefficients at different spectral ranges, SΔλ increased with salinity, while the slope coefficient for 350–400 nm reach lower values by 10.5% in SML compared to SS, caused by an effect of irradiation on the SML. The fluorescence intensities of the main peaks at Excitation Emission Matrix spectra belonging to the main fluorescing components of marine organic matter, called: A, C, M, T, were higher in SML by 41, 43, 41, and 14% compared to SS. The ratio of fluorescence intensities, (M + T)/(A + C) and humification index, HIX, in the SML were, respectively, higher by 17.9% and lower by 10.7% compared to SS. These relationships reveal more intensive process of in situ produced components in the SML as well as faster removal of humic components of high MW in the SML. We have observed an increase of spectral slope ratio, SR, (S275–295 > S350–400) with increasing salinity (from 4.5 to 7.94 of practical salinity), being proof that the samples acquire more marine in character. The SR increased with salinity 33.5 and 23.6% in the SML and SS, respectively, and their maximal values in open water were still maintained. The fluorescence intensity of all FDOM peaks decreased in the same salinity gradient. The decrease rate was higher in SML for the fluorescing peaks by 34, 36, and 26% for A, C, and M, respectively than in the SS. Decrease rate indicated the susceptibility to photochemical degradation of respective peaks. This effect was strongest for C, while T peak was almost unbleached. The fluorescence intensity decrease rate was smaller in SS what indicated shielding effect of the SML.Du, A., Robinson, J.R., Rowan, J., Lazagabaster, I.A., Behrensmeyer, A.K., 2019. Stable carbon isotopes from paleosol carbonate and herbivore enamel document differing paleovegetation signals in the eastern African Plio-Pleistocene. Review of Palaeobotany and Palynology 261, 41-52. of stable carbon isotopes (δ13C) from herbivore dental enamel and paleosol carbonates are important tools for Plio-Pleistocene paleovegetation reconstructions. A single herbivore tooth documents an isotopic record of vegetation on the order of 10–1–1 years and in proportion to that individual's foraging range. Paleosol carbonates, conversely, record environmental information on longer time scales (102–3 years) but smaller spatial scales (101?m2). Given that these two proxies document paleoenvironments at different spatiotemporal scales, it is worth comparing them to see if they offer redundant or complementary paleovegetation information. Here, we compare δ13C patterns from herbivore enamel and paleosol carbonates from geological (sub)members in the Awash Valley, Ethiopia, and Turkana Basin, Kenya, from ~ 4.4–1 million years ago. We find that median herbivore enamel δ13C is typically ~ 5–7 per mil (‰) higher than that from paleosol carbonates within a given (sub)member. The distributions of paleosol carbonate δ13C values usually have less spread (variation) than herbivore enamel. The bias in median and spread between these two data types likely reflects the different spatial and temporal scales at which these proxies record paleoenvironmental information. Most Plio-Pleistocene fossiliferous deposits are formed in fluvial settings in which paleosol carbonates sample the immediate habitat of floodplain woodlands and shrubs, resulting in a lower δ13C (i.e., more C3) signal. On the other hand, fossil teeth of wide-ranging herbivores could generate a higher (i.e., more C4) and more variable δ13C signal if some taxa fed in floodplain woodlands while others fed on open grasslands distal to the floodplain. We conclude that δ13C values from herbivore enamel and paleosol carbonates offer paleovegetation data at different spatiotemporal scales, both of which are informative for hominin habitat reconstructions. Careful consideration of the spatial and temporal signals inherent in these and other proxies should be applied in future studies.Du, H.Y., Yu, G.H., Sun, F.S., Usman, M., Goodman, B.A., Ran, W., Shen, Q.R., 2018. Iron minerals inhibit the growth of bacteria via a free-radical mechanism: Implications for soil carbon storage. Biogeosciences Discussions 2018, 1-39. minerals in soil can inhibit the growth of bacteria that protect organic carbon from decay. However, the mechanism inhibiting the bacterial growth remains poorly understood. Here, using a series of cultivation experiments and biological, chemical and synchrotron-based spectral analyses, we showed that kaolinite, hematite, goethite and ferrihydrite had a significant inhibitory effect on the growth of Pseudomonas J12, which was more prominent with a concentration of 25mgmL?1 than it was with either 10mgmL?1 or 5mgmL?1. In contrast, montmorillonite promoted the growth of Pseudomonas J12. Compared to Al-containing minerals, Fe(III)-containing minerals produced more hydroxyl radical (HO?) that have high efficiency for the inhibition of bacteria. Moreover, a significant positive correlation between HO? radical and Fe(II) was found, suggesting that Fe(II) contributes to the generation of HO?. Furthermore, both micro X-ray fluorescence and X-ray photoelectron spectroscopies indicated that surface Fe(III) was reduced to Fe(II) which can produce HO? through the well-known Fenton reaction series. Together, these findings indicate that the reduced surface Fe(II) derived from Fe(III)-containing minerals inhibit bacteria via a free-radical mechanism, which may further contribute to soil carbon storage.Duncan, B., McKay, R., Bendle, J., Naish, T., Inglis, G.N., Moossen, H., Levy, R., Ventura, G.T., Lewis, A., Chamberlain, B., Walker, C., 2019. Lipid biomarker distributions in Oligocene and Miocene sediments from the Ross Sea region, Antarctica: Implications for use of biomarker proxies in glacially-influenced settings. Palaeogeography, Palaeoclimatology, Palaeoecology 516, 71-89. climate proxies enable climate and environmental reconstructions for regions where other paleoclimatic approaches are unsuitable. The Antarctic Cenozoic record consists of widely varying lithologies, deposited in rapidly changing depositional settings, with large lateral variations. Previous sedimentological and microfossil studies indicate that the incorporation of reworked older material frequently occurs in these sediments, highlighting the need for an assessment of biomarker distribution across a range of depositional settings and ages to assess the role reworking may have on biomarker-based reconstructions. Here, we compare sedimentary facies with the distribution of n-alkanes and hopanoids within a terrestrial outcrop, two glaciomarine cores and a deep sea core, spanning the Late Oligocene to Miocene in the Ross Sea. Comparisons are also made with n-alkane distributions in Eocene glacial erratics and Mesozoic Beacon Supergroup sediments, which are both potential sources of reworked material. The dominant n-alkane chain length shifts from n-C29 to n-C27 between the Late Eocene and the Oligocene. This shift is likely due to changing plant community composition and the plastic response of n-alkanes to climate cooling. Samples from glaciofluvial environments onshore, and subglacial and ice-proximal environments offshore are more likely to display reworked n-alkane distributions, whereas, samples from lower-energy, lacustrine and ice-distal marine environments predominantly yield immature/contemporaneous n-alkanes. These findings emphasise that careful comparisons with sedimentological and paleontological indicators are essential when applying and interpreting n-alkane-based and other biomarker-based proxies in glacially-influenced settings.Dyez, K.A., H?nisch, B., Schmidt, G.A., 2018. Early Pleistocene obliquity-scale pCO2 variability at ~1.5 million years ago. Paleoceanography and Paleoclimatology 33, 1270-1291. the early Pleistocene, global temperature cycles predominantly varied with ~41‐kyr (obliquity‐scale) periodicity. Atmospheric greenhouse gas concentrations likely played a role in these climate cycles; marine sediments provide an indirect geochemical means to estimate early Pleistocene CO2. Here we present a boron isotope‐based record of continuous high‐resolution surface ocean pH and inferred atmospheric CO2 changes. Our results show that, within a window of time in the early Pleistocene (1.38–1.54 Ma), pCO2 varied with obliquity, confirming that, analogous to late Pleistocene conditions, the carbon cycle and climate covaried at ~1.5 Ma. Pairing the reconstructed early Pleistocene pCO2 amplitude (92 ± 13 μatm) with a comparably smaller global surface temperature glacial/interglacial amplitude (3.0 ± 0.5 K) yields a surface temperature change to CO2 radiative forcing ratio of S[CO2]~0.75 (±0.5) °C?1·W?1·m?2, as compared to the late Pleistocene S[CO2] value of ~1.75 (±0.6) °C?1·W?1·m?2. This direct comparison of pCO2 and temperature implicitly incorporates the large ice sheet forcing as an internal feedback and is not directly applicable to future warming. We evaluate this result with a simple climate model and show that the presumably thinner, though extensive, northern hemisphere ice sheets would increase surface temperature sensitivity to radiative forcing. Thus, the mechanism to dampen actual temperature variability in the early Pleistocene more likely lies with Southern Ocean circulation dynamics or antiphase hemispheric forcing. We also compile this new carbon dioxide record with published Plio‐Pleistocene δ11B records using consistent boundary conditions and explore potential reasons for the discrepancy between Pliocene pCO2 based on different planktic foraminifera. Dyksma, S., Lenk, S., Sawicka, J.E., Mu?mann, M., 2018. Uncultured Gammaproteobacteria and Desulfobacteraceae account for major acetate assimilation in a coastal marine sediment. Frontiers in Microbiology 9, 3124. doi: 10.3389/fmicb.2018.03124. is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Its turnover is central to carbon cycling, however, the relative contribution of different microbial populations to acetate assimilation in marine sediments is unknown. To quantify acetate assimilation by in situ abundant bacterial populations, we incubated coastal marine sediments with 14C-labeled acetate and flow-sorted cells that had been labeled and identified by fluorescence in situ hybridization. Subsequently, scintillography determined the amount of 14C-acetate assimilated by distinct populations. This approach fostered a high-throughput quantification of acetate assimilation by phylogenetically identified populations. Acetate uptake was highest in the oxic-suboxic surface layer for all sorted bacterial populations, including deltaproteobacterial sulfate-reducing bacteria (SRB), which accounted for up to 32% of total bacterial acetate assimilation. We show that the family Desulfobulbaceae also assimilates acetate in marine sediments, while the more abundant Desulfobacteraceae dominated acetate assimilation despite lower uptake rates. Unexpectedly, members of Gammaproteobacteria accounted for the highest relative acetate assimilation in all sediment layers with up to 31–62% of total bacterial acetate uptake. We also show that acetate is used to build up storage compounds such as polyalkanoates. Together, our findings demonstrate that not only the usual suspects SRB but a diverse bacterial community may substantially contribute to acetate assimilation in marine sediments. This study highlights the importance of quantitative approaches to reveal the roles of distinct microbial populations in acetate turnover.Elenius, M., Skurtveit, E., Yarushina, V., Baig, I., Sundal, A., Wangen, M., Landschulze, K., Kaufmann, R., Choi, J.C., Hellevang, H., Podladchikov, Y., Aavatsmark, I., Gasda, S.E., 2018. Assessment of CO2 storage capacity based on sparse data: Skade Formation. International Journal of Greenhouse Gas Control 79, 252-271. North Sea aquifers of high quality are the likely major target for 12 Gt of European CO2 emissions that should be stored in the subsurface by 2050. This involves an upscaling of the present combined injection rate from all European projects, which requires careful examination of the storage feasibility. Many aquifers are closed or semi-closed, with storage capacity mainly constrained by consideration of caprock failure criteria. Because the induced overpressure can propagate to sensitive regions far from the injector, the risk of caprock failure must be examined in terms of large volumes and for long times. This poses challenges with respect to fluid-flow simulation in the presence of highly uncertain aquifer properties. In this work, experts on geology, geophysics, geomechanics and simulation technique collaborate to optimize the use of existing data in an efficient simulation framework. The workflow is applied to the large North Sea Skade Formation, with potential for secondary storage and pressure dissipation in the overlying Utsira Formation. Injection at three locations in Skade gives an overall practical capacity of 1–6 Gt CO2 injected over a 50-year period, depending on the reservoir permeability and compressibility. The capacity is limited by local pressure buildup around wells for the lowest estimated reservoir permeability, and otherwise by regional pressure buildup in shallow zones far from the injection sites. Local deformation of clay due to viscoelastoplastic effects do not have an impact on leakage from the aquifer, but these effects may modify the properties of clay layers within the aquifer, which reduces the risk of lateral compartmentalization. Uplift of the seafloor does not impose constraints on the capacity beyond those set by pressure buildup.Erkoyun, H., Kadir, S., Huggett, J., 2019. Occurrence and genesis of tonsteins in the Miocene lignite, Tun?bilek Basin, Kütahya, western Turkey. International Journal of Coal Geology 202, 46-68. beige and white kaolinite claystone layers, 2–50?cm thick from the Tun?bilek basin have the characteristics of tonsteins. The aim of this study was to determine the mode of formation of the tonsteins, together with their mineralogical and geochemical characteristics, in order to identify their environment of deposition. The Miocene lacustrine units in the Tun?bilek lignite deposit associated with tuff and tuffite are comprised of organic-rich shale, organic-rich marl, marl, claystone, silty claystone, siltstone, sandstone, coal seam, and conglomerate deposited in a fluvial and lacustrine environment. Sanidine, plagioclase, biotite and chlorite are partly to completely argillized and enclosed in an authigenic clay matrix in the rhyolitic to rhyodacitic tuff/tuffite, sandstone, organic-rich shale, and serpentinite host rocks of the clay deposit. Abundant kaolinite and quartz are associated with smectite, illite, feldspar, calcite, dolomite, siderite, pyrite, barite, and gypsum. Development of oriented 7?? halloysite tubes on/in altered volcanogenic materials associated with kaolinite, and the occurrence of vermiform kaolinite edging disordered kaolinite, locally siderite and pyrite crystals may suggest formation of halloysite following kaolinite. The reaction pathway is: volcanic glass + feldspar + muscovite/biotite → 7?? halloysite → kaolinite. The slight enrichment of light rare earth elements (LREE) compared to heavy rare earth elements (HREE) with positive Eu anomalies (based on Upper Continental Crust (UCC) normalized values) reflects fractional crystallization of feldspar and amphibole in the parent volcanic rocks and organic-rich shale. Alteration of feldspar, biotite and volcanic glass resulted in the concentration of Al, Si, Fe, Mg, and K and precipitation of kaolinite in an acidic open hydrological system, while in a stagnant and alkaline environment smectite and illite are the alteration products. The Al2O3/TiO2 and low Cr/Ni ratios suggest felsic parent rocks. The trace elements ratios such as Ni/Co, V/Cr, Cu/Zn and U/Th among the basement complex source rocks units also suggest oxic, suboxic, and anoxic conditions. The occurrence of Pinus, Alnus, Quercus, Alnus, Carya, Taxodiaceae and Myrica palymorphs reflect a subtropical to warm temperature, humid climate, low elevations and swamp vegetation condition during the Early–Middle Miocene period in the study area. Association of argillization and silicification with coal, pyrite, and gypsum indicates a swampy environment and hydrothermal processes. This interpretation is corroborated by the calculated formation temperatures from stable isotope analysis of 148.8–168?°C for kaolinite and 145–169.2?°C for smectite. The low δS isotope values of pyrite (?19 to 2.9‰) and high positive values of gypsum (11.5–21.7‰) indicate a mixed diagenetic and hydrothermal origin for the sulfide and sulfate mineral.Evans, K., McCauley, R.D., Eveson, P., Patterson, T., 2018. A summary of oil and gas exploration in the Great Australian Bight with particular reference to southern bluefin tuna. Deep Sea Research Part II: Topical Studies in Oceanography 157-158, 190-202. numbers of juvenile southern bluefin tuna (SBT; Thunnus maccoyii) migrate into the warm shelf waters of the Great Australian Bight (GAB) each austral summer. Whilst in the GAB, they are the focus of a commercially important Australian fishery. Recent expansion of activities associated with oil and gas exploration in the GAB over the last five years has raised concerns that noise associated with geophysical surveys and exploratory drilling activities may impact on the migration and behaviour of SBT, with potential flow-on effects on the commercial fishery and current monitoring of the population for management purposes.As a first step in identifying the potential impacts of expansion of oil and gas exploration activities in the GAB on SBT, we establish the historical extent of these activities in the GAB with a primary focus on geophysical surveys. Potential overlap with the distribution of juvenile SBT in the GAB determined from an archival tag dataset (1998–2011) was then explored. Geophysical surveys have occurred throughout the vast majority of the region since 1960, with the size of energy sources used in surveys and the extent of areas surveyed increasing through time. The use of more complex, higher density 3D surveys has increased gradually since 2000. The timing and distribution of exploration activity has had varying degrees of overlap with SBT occurrence and distribution as described by tagged fish.Determining robust measures of the responses to surveys however, is difficult due to a paucity of data on the hearing capabilities of SBT, uncertainties in the true extent of spatial overlap of activities and tagged fish resulting from geolocation methods used for position estimation from archival tag data, complexities in the drivers of behaviour in SBT, and limitations with using observational data to determine cause-and-effect relationships. These difficulties are typical not just of SBT and the GAB region, but apply to investigations of the responses of marine animals to geophysical surveys more broadly. The data presented in this study, however, represent a first step towards understanding oil and gas exploration within a defined region of the Australian marine environment, and provide important context for exploring the potential impact of such activities on a commercially important top order predator of the GAB ecosystem.Fan, K., Zhang, Q., Liu, M., Ma, L., Shi, Y., Ruan, J., 2019. Metabolomic and transcriptional analyses reveal the mechanism of C, N allocation from source leaf to flower in tea plant (Camellia sinensis. L). Journal of Plant Physiology 232, 200-208. flowering in late autumn competes for a large amount of nitrogen and carbohydrates, potentially undermines the storage of these resources in vegetative organs, and negatively influences the subsequent spring tea yield and quality. The mechanism underlying the re-allocation N and carbohydrate from source leaf to flower in tea plant has not been clearly understood. In this study, 15N allocation, changes in metabolomics, and gene expression in flower buds, flowers, and adjacent leaves were characterized. Total N content of the adjacent leaves significantly decreased during flowering while such a decrease could be reversed by flower bud removal. Foliar-applied 15N in the adjacent leaves markedly decreased and was readily allocated to flowers. Metabolomic analysis revealed that most sugars and benzoic acid increased by more than two-fold whereas theanine, Gln, Arg, Asp, and Asn decreased when flower buds fully opened to become flowers. In this process, Gly, Pro, and cellobiose in the adjacent leaves increased considerably whereas sucrose, galactose, benzoic acid, and many fatty acids decreased. Removal of flower buds reversed or alleviated the above decreases and led to an increase of Asn in the leaves. The expression of genes associated with autophagy (ATG5, ATG9, ATG12, ATG18), sucrose transporters (SUT1, SUT2, SUT4), amino acids permease (AAP6, AAP7, AAP8), glutamine synthetase (GS1;1, GS1;2, GS1;3), and asparagine synthetase (ASN1, ASN2) was significantly up-regulated in leaves during the flowering process and was strongly modulated by the removal of flower buds. The overall results demonstrated that leaves are the ready source providing N and carbohydrates in flowering and a series of genes related to autophagy, protein degradation, turn-over of amino acids, and phloem loading for transport are involved.Fernandez-Cortes, A., Perez-Lopez, R., Cuezva, S., Calaforra, J.M., Ca?averas, J.C., Sanchez-Moral, S., 2018. Geochemical fingerprinting of rising deep endogenous gases in an active hypogenic karst system. Geofluids 2018, Article 4934520. hydrothermal caves linked to active faulting can potentially harbour subterranean atmospheres with a distinctive gaseous composition with deep endogenous gases, such as carbon dioxide (CO2) and methane (CH4). In this study, we provide insight into the sourcing, mixing, and biogeochemical processes involved in the dynamic of deep endogenous gas formation in an exceptionally dynamic hypogenic karst system (Vapour Cave, southern Spain) associated with active faulting. The cave environment is characterized by a prevailing combination of rising warm air with large CO2 outgassing (>1%) and highly diluted CH4 with an endogenous origin. The δ13CCO2 data, which ranges from ?4.5 to ?7.5‰, point to a mantle-rooted CO2 that is likely generated by the thermal decarbonation of underlying marine carbonates, combined with degassing from CO2-rich groundwater. A pooled analysis of δ13CCO2 data from exterior, cave, and soil indicates that the upwelling of geogenic CO2 has a clear influence on soil air, which further suggests a potential for the release of CO2 along fractured carbonates. CH4 molar fractions and their δD and δ13C values (ranging from ?77 to ?48‰ and from ?52 to ?30‰, respectively) suggest that the methane reaching Vapour Cave is the remnant of a larger source of CH4, which was likely generated by microbial reduction of carbonates. This CH4 has been affected by a postgenetic microbial oxidation, such that the gas samples have changed in both molecular and isotopic composition after formation and during migration through the cave environment. Yet, in the deepest cave locations (i.e., 30?m below the surface), measured concentration values of deep endogenous CH4 are higher than in atmospheric with lighter δ13C values with respect to those found in the local atmosphere, which indicates that Vapour Cave may occasionally act as a net source of CH4 to the open atmosphere.Fernández, S., Mercado, A., Cuara, E., Yeverino-Miranda, C., Sierra, U., 2019. Asphalt as raw material of graphene-like resources. Fuel 241, 297-303. search of alternate procedures and raw materials to manufacture graphene oxide and graphene derivatives that could be scaled up to be industrially implemented, we have developed a simple thermal treatment of petroleum asphalt that gives rise to graphite oxide-like materials in high yield. Subsequent treatment of the oxide at higher temperature gives rise to graphene-like products similar to those obtained by conventional top-down methods based on graphite. The method offers economy in manufacturing time and energy spent, allowing the valorization of a waste material.Fiers, G., Bertrand, S., Van Daele, M., Granon, E., Reid, B., Vandoorne, W., De Batist, M., 2019. Hydroclimate variability of northern Chilean Patagonia during the last 20 kyr inferred from the bulk organic geochemistry of Lago Castor sediments (45°S). Quaternary Science Reviews 204, 105-118. Castor (45°S) contains a continuous sediment record of Patagonian climate and environmental change during the last 20 kyr. Here, we use the bulk elemental and isotopic composition of the organic matter preserved in Lago Castor sediments to reconstruct changes in the supply of organic carbon of terrestrial and aquatic origin to the lake through time. Results show that the lake sedimentary organic matter is composed of variable proportions of lake plankton, terrestrial vegetation, and aquatic macrophytes. Before 17.8?cal?kyr BP, aquatic macrophytes were abundant, likely due to the low but rising postglacial lake level. After 17.8?cal?kyr BP, accumulation rates of organic carbon of aquatic macrophyte origin became negligible, whereas those of terrestrial origin increased, reflecting weak westerlies and terrestrial vegetation development under a milder climate, respectively. From 9.3?cal?kyr BP onwards, accumulation rates of organic carbon from both aquatic macrophytes and terrestrial vegetation increased and peaked between 7.5 and 2.0?cal?kyr BP. The latter is interpreted as a period of increased wind strength and precipitation, and is in excellent agreement with the grain-size results previously obtained on the same sediment core. All proxies show a secondary increase in wind strength and precipitation during the last millennium, in agreement with regional high-resolution records of the last 2000 years. These results, which are broadly compatible with regional pollen records during the Holocene, suggest that, at 45°S, the westerlies reached their maximum intensity between 7.5 and 2.0?cal?kyr BP and increased again during the last millennium.Fisher, A., Wangpraseurt, D., Larkum, A.W.D., Johnson, M., Kühl, M., Chen, M., Wong, H.L., Burns, B.P., 2019. Correlation of bio-optical properties with photosynthetic pigment and microorganism distribution in microbial mats from Hamelin Pool, Australia. FEMS Microbiology Ecology 95, fiy219-fiy219. mats and stromatolites are widespread in Hamelin Pool, Shark Bay, however the phototrophic capacity of these systems is unknown. This study has determined the optical properties and light-harvesting potential of these mats with light microsensors. These characteristics were linked via a combination of 16S rDNA sequencing, pigment analyses and hyperspectral imaging. Local scalar irradiance was elevated over the incident downwelling irradiance by 1.5-fold, suggesting light trapping and strong scattering by the mats. Visible light (400–700 nm) penetrated to a depth of 2 mm, whereas near-infrared light (700–800 nm) penetrated to at least 6 mm. Chlorophyll a and bacteriochlorophyll a (Bchl a) were found to be the dominant photosynthetic pigments present, with BChl a peaking at the subsurface (2–4 mm). Detailed 16S rDNA analyses revealed the presence of putative Chl f-containing Halomicronema sp. and photosynthetic members primarily decreased from the mat surface down to a depth of 6 mm. Data indicated high abundances of some pigments and phototrophic organisms in deeper layers of the mats (6–16 mm). It is proposed that the photosynthetic bacteria present in this system undergo unique adaptations to lower light conditions below the mat surface, and that phototrophic metabolisms are major contributors to ecosystem function.Fleming, J.F., Kristensen, R.M., S?rensen, M.V., Park, T.-Y.S., Arakawa, K., Blaxter, M., Rebecchi, L., Guidetti, R., Williams, T.A., Roberts, N.W., Vinther, J., Pisani, D., 2018. Molecular palaeontology illuminates the evolution of ecdysozoan vision. Proceedings of the Royal Society B: Biological Sciences 285. vision is known to have arisen only twice—once in Vertebrata and once within the Ecdysozoa, in Arthropoda. However, the evolutionary history of ecdysozoan vision is unclear. At the molecular level, visual pigments, composed of a chromophore and a protein belonging to the opsin family, have different spectral sensitivities and these mediate colour vision. At the morphological level, ecdysozoan vision is conveyed by eyes of variable levels of complexity; from the simple ocelli observed in the velvet worms (phylum Onychophora) to the marvellously complex eyes of insects, spiders, and crustaceans. Here, we explore the evolution of ecdysozoan vision at both the molecular and morphological level; combining analysis of a large-scale opsin dataset that includes previously unknown ecdysozoan opsins with morphological analyses of key Cambrian fossils with preserved eye structures. We found that while several non-arthropod ecdysozoan lineages have multiple opsins, arthropod multi-opsin vision evolved through a series of gene duplications that were fixed in a period of 35–71 million years (Ma) along the stem arthropod lineage. Our integrative study of the fossil and molecular record of vision indicates that fossils with more complex eyes were likely to have possessed a larger complement of opsin genes.Fleury, B., Gudipati, M.S., Couturier-Tamburelli, I., Carrasco, N., 2019. Photoreactivity of condensed acetylene on Titan aerosols analogues. Icarus 321, 358-366. organic molecules formed by photochemistry in the upper atmosphere of Titan can undergo condensation as pure ices in the stratosphere and the troposphere as well as condense as ice layers onto the organic aerosols that are visible as the haze layers of Titan. As solar photons penetrate through Titan's atmosphere, shorter-wavelength photons are attenuated and longer-wavelength photons make it into the lower altitudes, where aerosols become abundant. We conducted an experimental study to evaluate the long wavelength (λ?>?300?nm) photoreactivity of these ices accreted on the Titan aerosol-analogs (also known as tholins) made in the laboratory. We have focused on acetylene, the third most abundant hydrocarbon in Titan's atmosphere (after CH4 and C2H6). Further, acetylene is the most abundant unsaturated hydrocarbon in Titan's atmosphere. Our results indicate that the aerosols can act as activation centers to drive the photoreactivity of acetylene with the aerosols at the accretion interface at wavelengths where acetylene-ice alone does not show photoreactivity. We found that along with photochemistry, photodesorption plays an important role. We observed that about 15% of the initial acetylene is photodesorbed, with a photodesorption rate of (2.1?±?0.2)?×?10?6 molecules?photon?1 at 355?nm. This photodesorption is wavelength-dependent, confirming that it is mediated by the UV absorption of the aerosol analogues, similar to photochemistry. We conclude that the UV–Vis properties of aerosols would determine how they evolve further in Titan's atmosphere and on the surface through photochemical alterations involving longer-wavelength photons. Stronger extinction coefficients in the longer wavelength UV–Vis regions (>?300?nm) of the aerosol give higher efficiencies of photodesorption of accreted volatiles as well as photochemical incorporation of unsaturated condensates (such as acetylene) into the aerosols.Fors, Y., Isaksson, S., 2019. GCMS analyses of direct methylated lipids in binders used in 18th–19th century folk painted interiors in H?lsingland, Sweden. Journal of Archaeological Science: Reports 23, 127-136. fragments were collected from painted 18th and 19th century interiors from traditional buildings in H?lsingland, Sweden. The aim was to identify binders used by the artists by direct-methylation and GCMS analyses of the lipid fraction in the samples. The lipid content was categorized as mainly animal, plant-based or mixed. The study indicates that used colour tone and possibly also underlying foundation (wood, paper or textile) is essential for the artists? choice of binder components. Animal-lipid based compounds were found to be used for a wide variety of colours, including mixed colour and several light colour tones. Animal and sometimes mixed lipids seem also to be characteristic for colour fragments from paper and textiles. Red, black and blue colours are quite common among the mixed-lipid category. However, half of blue, green and black colours were found in the vegetable lipid group. A tendency towards the plant-lipids was also indicated in colour samples painted on wood. Many different forms of terpenoids were found among the wood samples, suggesting that its origin can be traced mainly to wood composites, such as extractives.Fortenberry, R.C., Lee, T.J., Inostroza-Pino, N., 2019. The possibility of :CNH2+ within Titan’s atmosphere: Rovibrational analysis of :CNH2+ and :CCH2. Icarus 321, 260-265. highest peak in Cassini’s INMS data for stratospheric flybys of Titan’s atmosphere is m/z=28. While this has mostly been attributed to HCNH+, minor contributions from N2+ and C2H2+ are also likely. However, this work shows that :CNH2+ may also be present in a kinetically-favorable potential well based on high-level quantum chemical computations. The ionization energy of N2 is much higher than the isomerization barrier between HCNH+ and :CNH2+. As such, we present computations that provide vibrational and rotational spectroscopic data for the possible remote sensing of this molecule in Titan’s atmosphere. Such data are also computed for the isoelectronic :CCH2 molecule, and comparison to previous laboratory experiments and quantum chemical computations, where available for the hydrocarbon, is excellent. Consequently, the data provided in this work should allow for initial searches for :CNH2+ as well as refinements of data for :CCH2 both in the laboratory and even in Titan’s atmosphere.Fri?ták, V., Laughinghouse, H.D., Packová, A., Graser, M., Soja, G., 2019. Monitoring of methylated naphthalenes in sludge-derived pyrogenic carbonaceous materials. Chemosphere 217, 456-462. analogues of polycyclic aromatic hydrocarbons (PAHs) represent important environmental contaminants produced often at process of feedstock thermochemical conversion. In the present study, we determined and compared levels of 1-methylnaphtalene and 2-methylnaphtalene in municipal sewage sludge (MSS), sludge-derived pyrogenic carbonaceous materials produced at 350?°C (PCM350) and 500?°C (PCM500) in process of slow pyrolysis. The highest extraction efficiency of both aromatic structures from MSS, PCM350 and PCM500 for toluene as extraction agent and 36?h of extraction time was revealed. The total concentrations of 1-methylnaphtalene reached values 8.7?mg/kg for MSS, 14.6?mg/kg for PCM350 and 18.1?mg/kg for PCM500.2-methylnaphtalene was quantified in concentrations 12.5?mg/kg for MSS, 19.3?mg/kg for PCM350 and 23?mg/kg for PCM500. Available levels of 1-methylnaphtalene and 2-methylnaphtalene determined by Tenax resin desorption test during 36 days showed decreasing trend in order PCM500?>?PCM350?>?MSS. In summary, pyrolysis treatment of sewage sludge can increase total amount of methylated PAHs in produced carbonaceous materials but decrease their available forms. This fact can contribute to global ecotoxicological assessment of organic pollutants in biochars and pyrogenic carbonaceous materials applied in agronomy as soil amendments.Fu, H., Tang, D., Pan, Z., Yan, D., Yang, S., Zhuang, X., Li, G., Chen, X., Wang, G., 2019. A study of hydrogeology and its effect on coalbed methane enrichment in the southern Junggar Basin, China. American Association of Petroleum Geologists Bulletin 103, 189-213. paper analyzes regional hydrogeological conditions and divides the study area into three hydrogeological types and seven hydrogeological units, to investigate hydrogeology and its effect on coalbed methane (CBM) enrichment in the southern Junggar Basin, China. From this work, it is found that the groundwater flow paths in the study area are the joint effects of south-to-north and west-to-east flows. This study also shows that microbial gases are widely developed, although the depth limit of microbial gas occurrence is still unclear in the study area. Microbial CO2 reduction is the leading formation path in the study area, except for the Houxia region, where fermentation is the formation mechanism. The abnormally high CO2 in stagnant zones (i.e., water flow is slow and stagnant) is mainly associated with methanogenesis, whereas relatively low CO2 (microbial or thermogenic) is present where water flow is active. The average CBM content within the Xishanyao Formation changes within various hydrogeological units; moreover, the average CBM content within the Badaowan Formation of the same hydrogeological unit (e.g., Fukang) suggests that the hydrogeological and CBM enrichment conditions are different within various structural types. Overall, the hydrogeological conditions exert control on the gas content in the study area; that is, the gas content is high in stagnant zones. Finally, influenced by supplemental microbial gases, changes in the CBM oxidation zone are relatively complex in the study area, the depth of which has no obvious correlation with hydrogeological conditions and changes significantly from west to east.Fu, J., Li, S., Xu, L., Niu, X., 2018. Paleo-sedimentary environmental restoration and its significance of Chang 7 Member of Triassic Yanchang Formation in Ordos Basin, NW China. Petroleum Exploration and Development 45, 998-1008. environment of Chang 7 Member of Upper Triassic Yanchang Formation in Ordos Basin, including the paleoclimate, paleo-salinity and paleo-redox conditions were restored through geochemical elements analysis of 289 samples collected from the outcrop sections around and wells drilled in the basin and using a series of identification indexes of paleo-climate, paleo-salinity and paleo-redox conditions, such as CaO/MgO·Al2O3, Sr/Cu, Rb/Sr, Rb/K2O, Th/U, V/(V+Ni), the content of element B tested from the mudstone. Comprehensive analysis shows that in sedimentary period of the Chang 7, the paleo-climate was warm temperate to subtropical climate with temperature higher than 15 °C, the water body was continental brackish water to freshwater, and the sediments were deposited under strong reduction conditions. Suitable temperature, extensively deep lake basin and strongly reductive paleo-sedimentary environment led to the blooming, enrichment and preservation of organic matter in the submember Chang 73. As a result, a set of high-quality source rock was formed, laying material foundation for large-scale accumulation of shale oil.Ga, J.-K., Kim, J.-H., Kim, D., Kang, S., Shin, K.-H., 2018. Assessing the saponification effect on the quantification of long chain alkenones and the U37K′ paleothermometer. Geochemical Journal 52, 497-507. this study, we evaluated the saponification effect on alkenone quantification and the U37K′ paleothermometer using two internal standards (2-nonadecanone and squalane) by analyzing in-house reference sediment and eleven surface sediments taken from the Yellow Sea. The C37:3 and C37:2 alkenone concentrations of the in-house reference sediment showed significant differences between before and after the saponification (ΔC37:3 and ΔC37:2) depending on the internal standards used. However, the differences in the U37K′ and the estimated sea surface temperatures were insignificant. The ΔC37:3 and ΔC37:2 concentrations were larger when calculating based on 2-nonadecanone (46 ± 26 and 136 ± 67 ng/g, respectively) than those based on squalane (?7 ± 4 and ?12 ± 10 ng/g, respectively) in the surface sediments. Interestingly, the ΔC37:3 and ΔC37:2 concentrations based on 2-nonadecanone showed a strong correlation with the loss of 2-nonadecanone that occurred during saponification. Accordingly, our study indicated that preferential loss of internal standards (e.g., 2-nonadecanone) can occur during saponification, which affects alkenone quantification and, thus, attention should be paid when choosing an internal standard. Gai, H., Tian, H., Cheng, P., Zhou, Q., Li, T., Wang, X., Xiao, X., 2019. Influence of retained bitumen in oil-prone shales on the chemical and carbon isotopic compositions of natural gases: Implications from pyrolysis experiments. Marine and Petroleum Geology 101, 148-161. bitumen in oil-prone source rocks has a significant impact on late gas generation but such influence is still poorly quantified because it is quite difficult to restore the bitumen content retained in a mature source rock. In this study, a suite of artificially-matured samples were prepared from a moderate maturity shale sample to represent shales with different amount of retained bitumen. These samples were then pyrolyzed in sealed gold tubes to investigate how the amount of retained bitumen affects the changes in chemical and carbon isotopic compositions of generated gases, and the uncertainty of the evaluation of gas maturity and source identification. The results indicate that the decrease in yields of hydrocarbon gases is proportional to the reduction of retained bitumen content, however, a progressive enrichment in heavier carbon isotope (13C) of gaseous hydrocarbons occurs while less amount of bitumen is retained in shales. This experimental observation partly explains the heterogeneity of methane carbon isotopes for shale gases that have identical thermal maturity levels. Although the amount of retained bitumen can significantly change the carbon isotopic ratios of individual gas (δ13C1, δ13C2, and δ13C3), the difference in carbon isotopic composition between gaseous components such as ethane and methane (δ13C2 ?δ13C1) or propane and ethane (δ13C3 ?δ13C2) are not significantly affected, and therefore these differential values can be potentially used as maturity indicators for overmature natural gases exhibiting no carbon isotopic reversals. Geochemical and carbon isotopic diagrams that are widely used for the identification of oil- and kerogen-cracking gases are also found to be affected by the retained bitumen content. These results illustrate that it is necessary to take into account the retained bitumen content of shales when thermal maturity and genetic origin of natural gases derived from oil-prone source rocks are being evaluated.Ganeeva, Y.M., Barskaya, E.E., Okhotnikova, E.S., Yusupova, T.N., Davletshina, L.F., Gus’kova, I.A., 2018. Distribution of paraffin hydrocarbons and asphaltenes in acidic water-oil emulsion. Petroleum Chemistry 58, 1099-1106. and solid paraffins isolated from various layers of acidic water-oil emulsions obtained by mixing an oilfield emulsion with 15% solutions of hydrochloric and sulfamic acids with or without addition of Fe(III) have been studied by elemental analysis, IR and EPR spectroscopy, gas–liquid chromatography, and calorimetry. In acidic water-oil emulsions, the high-molecular-weight petroleum components have not been found to concentrate at the oil/water interface; however, a change in their composition has been revealed, which is more pronounced in the presence of Fe(III). The formation of diamagnetic complexes of the paramagnetic centers of asphaltenes with Fe(III) has been detected.Gao, C., Sander, M., Agethen, S., Knorr, K.-H., 2019. Electron accepting capacity of dissolved and particulate organic matter control CO2 and CH4 formation in peat soils. Geochimica et Cosmochimica Acta 245, 266-277. are a major source of atmospheric CH4. The availability of terminal electron acceptors largely affects the ratio of CO2 to CH4 formation under water-logged anoxic conditions in these systems. Although the importance of peat organic matter as an electron acceptor is increasingly recognized, the actual budgets of electron accepting capacities of dissolved and particulate organic matter remain poorly characterized. To address this research need, we incubated three different peat materials and linked changes in the electron accepting capacities (EAC) of peat organic matter (OM), including dissolved and particulate organic matter, to the observed CO2 and CH4 formation. Under anaerobic conditions, EACOM decreased inverse to non-methanogenic CO2 formation. Only after utilizable EACOM was depleted did strictly methanogenic conditions evolve with equimolar CH4 and CO2 formation rates, as theoretically expected. The reduction of OM and the resultant decrease in EACOM explained between 26 and 56% of the non-methanogenic CO2, which was between 5 and 39% of total CO2 produced. Compared to EACPOM, EACDOM remained constant and may have served as a mediator in electron transfer to the POM. In summary, our study quantitatively demonstrated the important role of peat OM as terminal electron acceptor for anaerobic respiration in organic soils.Geibert, W., 2018. Processes that regulate trace element distribution in the ocean. Elements 14, 391-396. elements are powerful tracers – and in some instances drivers – of ocean interactions with the atmosphere, the hydrological cycle, the geology of the seafloor, and life on Earth. The concentration and the isotopic composition of trace elements are, therefore, diagnostic tools for the state of the ocean and its role as part of Earth’s dynamic system. Dissolved and particulate transport mechanisms determine how fast the ocean responds to change. The new wealth of data from the international GEOTRACES programme reveals new sources and sinks at all ocean boundaries, highlighting a much more dynamic equilibrium between the seafloor and the ocean than previously thought.Gibbons, A., 2018. Why modern humans have round heads. Science 362, 1229. since researchers first got a good look at a Neanderthal skull in the 1860s, they were struck by its strange shape: stretched from front to back like a football rather than round like a basketball, as in living people. But why our heads and those of our ice age cousins looked different remained a mystery.Now, researchers have found an ingenious way to identify genes that help explain the contrast. By analyzing traces of Neanderthal DNA that linger in Europeans from their ancestors' trysts, researchers have identified two Neanderthal gene variants linked to slightly less globular head shape in living people, the team reports this week in Current Biology. The genes also influence brain organization, offering a clue to how evolution acting on the brain might have reshaped the skull. This “very important study” pinpoints genes that have a “direct effect on brain shape and, presumably, brain function in humans today,” says paleoanthropologist Chris Stringer of the Natural History Museum in London, who was not a part of the work.Cradle a newborn and you'll see that infants start life with elongated skulls, somewhat like Neanderthals. It's only when the modern human brain nearly doubles in size in the first year of life that the skull becomes globular, says paleoanthropologist Philipp Gunz of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. He and his colleagues analyzed computerized tomography scans of modern human and Neanderthal skulls to develop a “globularity index” of human brains.To explore the underlying differences in brain tissue, they applied that index to MRI scans from 4468 people of European ancestry whose DNA had been genotyped. The team identified two Neanderthal DNA fragments that were correlated with slightly less globular heads. These DNA fragments affect the expression of two genes: UBR4, which regulates the development of neurons, and PHLPP1, which affects the development of myelin sheaths that insulate axons, or projections of neurons.The Neanderthal variants may lower URB4 expression in the basal ganglia and also lead to less myelination of axons in the cerebellum, a structure at the back of the brain. This could contribute to subtle differences in neuronal connectivity and how the cerebellum regulates motor skills and speech, says senior author Simon Fisher of the Max Planck Institute for Psycholinguistics in Nijmegen, the Netherlands. But any effects of the Neanderthal genes in living people would be slight because so many genes shape the brain.Tying Neanderthal DNA to brain scans in living people is an “innovative and exciting approach” because “soft tissue in the brain is impossible to access from the fossil record,” says anthropologist Katerina Harvati of the University of Tübingen in Germany. She'd like to see the findings confirmed in more people.Indeed, Gunz and Fisher plan to delve into the UK Biobank, a giant database of British people's health records and DNA. They hope to use Biobank brain scans to find more genes and to explore how Neanderthal brains would have functioned. “The Neanderthal DNA that remains in us can help us think about what their brains were like,” says geneticist Tony Capra of Vanderbilt University in Nashville.Giunta, T., Young, E.D., Warr, O., Kohl, I., Ash, J.L., Martini, A., Mundle, S.O.C., Rumble, D., Pérez-Rodríguez, I., Wasley, M., LaRowe, D.E., Gilbert, A., Sherwood Lollar, B., 2019. Methane sources and sinks in continental sedimentary systems: New insights from paired clumped isotopologues 13CH3D and 12CH2D2. Geochimica et Cosmochimica Acta 245, 327-351. isotope compositions of methane (δ13C and δD) and of short-chain alkanes are commonly used to trace the origin and fate of carbon in the continental crust. In continental sedimentary systems, methane is typically produced through thermogenic cracking of organic matter and/or through microbial methanogenesis. However, secondary processes such as mixing, migration or biodegradation can alter the original isotopic and composition of the gas, making the identification and the quantification of primary sources challenging. The recently resolved methane ‘clumped’ isotopologues Δ13CH3D and Δ12CH2D2 are unique indicators of whether methane is at thermodynamic isotopic equilibrium or not, thereby providing insights into formation temperatures and/or into kinetic processes controlling methane generation processes, including microbial methanogenesis.In this study, we report the first systematic use of methane Δ13CH3D and Δ12CH2D2 in the context of continental sedimentary basins. We investigated sedimentary formations from the Southwest Ontario and Michigan Basins, where the presence of both microbial and thermogenic methane was previously proposed. Methane from the Silurian strata coexist with highly saline brines, and clumped isotopologues exhibit large offsets from thermodynamic equilibrium, with Δ12CH2D2 values as low as ?23‰. Together with conventional δ13C and δD values, the variability in Δ13CH3D and Δ12CH2D2 to first order reflects a mixing relationship between near-equilibrated thermogenic methane similar to gases from deeper Cambrian and Middle Ordovician units, and a source characterized by a substantial departure from equilibrium that could be associated with microbial methanogenesis. In contrast, methane from the Devonian-age Antrim Shale, associated with less saline porewaters , reveals Δ13CH3D and Δ12CH2D2 values that are approaching low temperature thermodynamic equilibrium. While microbial methanogenesis remains an important contributor to the methane budget in the Antrim Shale, it is suggested that Anaerobic Oxidation of Methane (AOM) could contribute to reprocessing methane isotopologues, yielding Δ13CH3D and Δ12CH2D2 signatures approaching thermodynamic equilibrium.Glenfield, C., McLysaght, A., 2018. Pseudogenes provide evolutionary evidence for the competitive endogenous RNA hypothesis. Molecular Biology and Evolution 35, 2886-2899. competitive endogenous RNA (ceRNA) hypothesis is an attractively simple model to explain the biological role of many putatively functionless noncoding RNAs. Under this model, there exist transcripts in the cell whose role is to titrate out microRNAs such that the expression level of another target sequence is altered. That it is logistically possible for expression of one microRNA recognition element (MRE)-containing transcript to affect another is seen in the multiple examples of pathogenic effects of inappropriate expression of MRE-containing RNAs. However, the role, if any, of ceRNAs in normal biological processes and at physiological levels is disputed. By comparison of parent genes and pseudogenes we show, both for a specific example and genome-wide, that the pseudo-3′ untranslated regions (3′UTRs) of expressed pseudogenes are frequently retained and are under selective constraint in mammalian genomes. We found that the pseudo-3′UTR of BRAFP1, a previously described oncogenic ceRNA, has reduced substitutions relative to its pseudo-coding sequence, and we show sequence constraint on MREs shared between the parent gene, BRAF, and the pseudogene. Investigation of RNA-seq data reveals expression of BRAFP1 in normal somatic tissues in human and in other primates, consistent with biological ceRNA functionality of this pseudogene in nonpathogenic cellular contexts. Furthermore, we find that on a genome-wide scale pseudo-3′UTRs of mammalian pseudogenes (n?=?1,629) are under stronger selective constraint than their pseudo-coding sequence counterparts, and are more often retained and expressed. Our results suggest that many human pseudogenes, often considered nonfunctional, may have an evolutionarily constrained role, consistent with the ceRNA hypothesis.Gnos, E., Hofmann, B.A., Al-Wagdani, K., Mahjub, A., Al-Solami, A.A., Habibullah, S.N., Matter, A., Halawani, M.A., 2018. Sandstone sample analysis and additional structural data from Jabal Rayah, a possible impact structure in Saudi Arabia. Meteoritics & Planetary Science 53, 2652-2660. ~5.5 km sized Jabal Rayah ring structure located at 28°39′N/37°12′E in Saudi Arabia has been classified as a possible complex impact structure located in flat‐lying Paleozoic clastic sediments. Previous, detailed mapping showed that erosional processes led to a relief inversion, with displaced, folded, and faulted blocks of Silurian to Early Devonian strata, interpreted to form a ring syncline, now forming a topographically outstanding, 150 m high ring crest. The drainage toward the center of the structure seems controlled by a set of radial faults. This central part is eroded to the level of the surrounding plateau and partially covered with gravel. Analysis of 28 Qusaiba Formation sandstones showed that at the present outcrop level, the sediments seem devoid of shock features. Measurement of fold axes in the central part of the structure shows radially outward plunging fold axes, becoming steeper toward the center, and also fold axes of other orientation, and folded folds. This fold axis pattern is interpreted as an upward‐pointing, kilometer‐sized sheath fold. Assuming an impact scenario and using the present size of the structure, the minimum central structural uplift is estimated at ~500 m, which is consistent with Qusaiba Formation occupying the center of the ring structure.Gold, D.A., Katsuki, T., Li, Y., Yan, X., Regulski, M., Ibberson, D., Holstein, T., Steele, R.E., Jacobs, D.K., Greenspan, R.J., 2019. The genome of the jellyfish Aurelia and the evolution of animal complexity. Nature Ecology & Evolution 3, 96-104. present the genome of the moon jellyfish Aurelia, a genome from a cnidarian with a medusa life stage. Our analyses suggest that gene gain and loss in Aurelia is comparable to what has been found in its morphologically simpler relatives—the anthozoan corals and sea anemones. RNA sequencing analysis does not support the hypothesis that taxonomically restricted (orphan) genes play an oversized role in the development of the medusa stage. Instead, genes broadly conserved across animals and eukaryotes play comparable roles throughout the life cycle. All life stages of Aurelia are significantly enriched in the expression of genes that are hypothesized to interact in protein networks found in bilaterian animals. Collectively, our results suggest that increased life cycle complexity in Aurelia does not correlate with an increased number of genes. This leads to two possible evolutionary scenarios: either medusozoans evolved their complex medusa life stage (with concomitant shifts into new ecological niches) primarily by re-working genetic pathways already present in the last common ancestor of cnidarians, or the earliest cnidarians had a medusa life stage, which was subsequently lost in the anthozoans. While we favour the earlier hypothesis, the latter is consistent with growing evidence that many of the earliest animals were more physically complex than previously hypothesized.Gomes, J., Khandeparker, R., Bandekar, M., Meena, R.M., Ramaiah, N., 2018. Quantitative analyses of denitrifying bacterial diversity from a seasonally hypoxic monsoon governed tropical coastal region. Deep Sea Research Part II: Topical Studies in Oceanography 156, 34-43. community mediated denitrification leads to nitrate reduction and, its eventual removal from marine ecosystems. Therefore, it is necessary to understand the functional diversity in terms of the abundance and types of nitrate reductases in the microbial communities extant in the hypoxic/suboxic waters where organic matter oxidation is predominantly nitrate- reduction mediated. For this study, water samples from the surface, mid-depth and close to bottom were collected from three coastal locations along the west coast of India during Summer monsoon (SuM), Fall intermonsoon (FIM) and, Spring intermonsoon (SIM). The abundance of nitrate (narG), nitrite (nirS) and nitrous oxide (nosZ) reductase genes from these water samples were quantified by qPCR method. Besides the distinct spatio-temporal differences, the overall ranges of these three functional genes across the sampling sites ranged from 1.9 x 107 to 7.9 x 107 copies L-1 (narG), from 0.001 x 106 to 0.30 x 106 copies L-1 (nirS) and from 0.30 x 106 to 2.9 x 106 copies L-1 (nosZ). Functional gene sequencing of bacterial communities possessing these reductases were diverse and, dominated by members of Alpha-, Beta- and Gamma-proteobacteria, including taxonomic groups containing well known denitrifiers such as Pseudogulbenkiania, Kocuria, Pseudomonas, Herbaspirillum, Achromobacter, Rhodoferax, Mesorhizobium, Sinorhizobium, Shinella, Bradyrhizobiaceae, Rhodopseudomonas, Dinoroseobacter, Paracoccus, Rhodobacter, Ruegeria and Azospirillum sp. Assemblages of bacteria possessing narG, nirS, and nosZ indicated that complete denitrification could occur, particularly in the samples collected close to the bottom.Gong, Y., Qiao, C., Yu, X., Wang, J., Gong, D., 2019. Study on the ancient putty from the site of the Ming Dynasty (1368–1644?CE) Baochuanchang Shipyard, Nanjing, China. Journal of Archaeological Science: Reports 23, 189-195. 2003, the excavation of the ancient site Baochuanchang Shipyard was carried out in Nanjing, China and this shipyard was believed to have been the workshop where the huge vessels of Zheng He's fleet were built and maintained. Several pieces of ancient putty were found here, and a small piece was sampled and analyzed in this paper to study its components and structure. The results of X-ray diffraction (XRD) showed that the putty was mainly composed of calcite (CaCO3), while pyrolysis-gas chromatography–mass spectrometry (Py-GC–MS) analysis indicated that tung oil was used in making the putty. In addition, plant fibers inside the putty were identified as jute by the means of polarizing microscope and scanning electron microscope (SEM) analysis. These findings confirmed the putty as the so-called chu-nam putty, which was a traditional sealing material used in ancient shipbuilding. Moreover, the surface morphology of the putty was obtained by SEM, and pore size distribution was measured by gas adsorption-desorption analysis. The analytical results suggested that the putty was quite compact, which could perform well in sealing huge wooden ships. This research revealed the shipbuilding skills of the Baochuanchang Shipyard. It may provide reference for studying Zheng He's vessels and make further a contribution to the conservation and restoration of ancient wooden ships of the Ming Dynasty.González, H.E., Nimptsch, J., Giesecke, R., Silva, N., 2019. Organic matter distribution, composition and its possible fate in the Chilean North-Patagonian estuarine system. Science of The Total Environment 657, 1419-1431. distribution, composition, and transport of both dissolved and particulate organic carbon (DOC and POC) were studied across a terrestrial - marine transition system in the Chilean North-Patagonia (41°S). At the land-fjord boundary we reported: (i) high concentrations of both silicic acid (up to 100?μM) and integrated chlorophyll a (62?mg?m?2), (ii) dominance of nanophytoplankton (63%), humic-, terrigenous-derived, and protein-like DOC (19 and 36%, respectively), and (iii) a shallow photic zone (12?m depth). In contrast, the estuarine-ocean boundary was characterized by (i) high concentrations of nitrate and phosphate (20 and 2?μM respectively) and low chlorophyll a concentration (11?mg?m?2), (ii) dominance of microphytoplankton (59%) and tyrosine-like C3 autochthonous DOC (34%), and (iii) a deep photic zone (29?m depth).Allochthonous DOC input at the fjord head and the ocean accounted for 60% and 10% of total DOC, respectively. The input of humic-like substances was enhanced by intense forestry and agriculture activity around the Puelo River watershed, contributing from 50% to 14% of total DOC along the fjord - ocean transect. In contrast, autochthonous tyrosine-like substances increased from 25% to 41% of total DOC, highlighting the role of bacterial metabolism in regulating DOM composition. The high correlation (R2?=?0.7) between the UVC-humic:UVA-humic ratio and salinity suggest that processes associated to freshwater input impinged on the DOC chemical characteristics and origins. Overall, our observations support the view that climate warming (freshwater input) and anthropogenic practices (aquaculture) boost the mobilization of terrestrial carbon pools and their intrusion into coastal ocean areas, a process that should be given more attention in climate prediction models.Good, B.H., Hallatschek, O., 2018. Effective models and the search for quantitative principles in microbial evolution. Current Opinion in Microbiology 45, 203-212. evolve rapidly. Yet they do so in idiosyncratic ways, which depend on the specific mutations that are beneficial or deleterious in a given situation. At the same time, some population-level patterns of adaptation are strikingly similar across different microbial systems, suggesting that there may also be simple, quantitative principles that unite these diverse scenarios. We review the search for simple principles in microbial evolution, ranging from the biophysical level to emergent evolutionary dynamics. A key theme has been the use of effective models, which coarse-grain over molecular and cellular details to obtain a simpler description in terms of a few effective parameters. Collectively, these theoretical approaches provide a set of quantitative principles that facilitate understanding, prediction, and potentially control of evolutionary phenomena, though formidable challenges remain due to the ecological complexity of natural populations.Gordadze, G.N., Poshibaeva, A.R., Giruts, M.V., Gayanova, A.A., Semenova, E.M., Koshelev, V.N., 2018. Formation of petroleum hydrocarbons from prokaryote biomass: 2. Formation of petroleum hydrocarbon biomarkers from biomass of Geobacillus jurassicus bacteria isolated from crude oil. Petroleum Chemistry 58, 1005-1012. participation of the Geobacillus jurassicus DS1T bacteria, isolated from the Dagang oilfield (PRC), in the formation of hydrocarbons of the Dagang oil has been shown. Saturated hydrocarbon biomarkers (n-alkanes, isoprenanes, steranes, and terpanes) have been identified by capillary gas-liquid chromatography and gas chromatography–mass spectrometry in the soluble part and products of thermolysis of the insoluble part (kerogen) of the Geobacillus jurassicus bacteria biomass, with the distribution of biomarkers corresponding to weakly transformed marine organic matter and being close to that in the initial oil. Squalene has been found in all samples, including the source oil.Gore, J., 2018. Simple organizing principles in microbial communities. Current Opinion in Microbiology 45, 195-202. is a great deal of interest in discovering the principles that organize microbial communities, to better understand the structure and diversity of these communities in the natural world. Recent conceptual and technical advances have shown how simple organizing principles can give rise to surprising diversity and complex patterns in these consortia. Understanding competition, cooperation, and communication among microbes has provided novel insights into the structure and behavior of microbial collectives, and the use of simple animal models has advanced our understanding of microbial ecology in the host. These multidisciplinary efforts to understand and predict the properties of microbial communities will be critical in the development of microbial ecology as an applied science.Gou, Q., Xu, S., Hao, F., Lu, Y., Zhang, A., Wang, Y., Cheng, X., Qing, J., 2018. Characterization method of shale pore structure based on nano-CT: a case study of Well JY-1 Acta Petrolei Sinica 39, 1253-1261. analysis on nanoporous structure of organic-rich shale is the basis for evaluating the reserving properties of shale reservoirs and the exploration and development potential of shale gas resources. In this study, the nano-CT and 3D reconstruction technique is used to evaluate the shale pore characteristics and connectivity of the Lower Silurian Longmaxi Formation in the Jiaoshiba area of Sichuan Basin. The experimental results show that:(1)nano-CT can display the three-dimensional spatial structure of shale pores, and will be more conducive to characterize the shale pore characteristics in combination with other experimental methods; (2)based on nano-CT, four components including matrix minerals, organic matter, pores, and high-density minerals (such as pyrite)can be distinguished in shale samples with the volume ratio of 89.20%, 6.22%, 2.71% and 1.87% respectively; (3)the pore sizes evaluated by nano-CT range from 79 nm to 4.7 μm, dominated by 100~500 nm, mainly including organic pores and inorganic pores; (4)strong heterogeneity exists in shale pore, generally with better connectivity, dominated by grade Ⅲ connectivity domains.Goudarzi, A., Meckel, T.A., Hosseini, S.A., Trevi?o, R.H., 2019. Statistical analysis of historic hydrocarbon production data from Gulf of Mexico oil and gas fields and application to dynamic capacity assessment in CO2 storage. International Journal of Greenhouse Gas Control 80, 96-102. modeling of CO2 injection and reservoir flow is typically performed to forecast the number of wells, sustainable injection rates, and total storage volume (or mass). A critical determination for CO2 storage in depleted oil and gas reservoirs is characterization of reservoir compartmentalization which informs boundary conditions in simulating injection scenarios. Constraining boundary conditions during CO2 injection into geological formations is a key factor for feasible deployment project. Production history data from 616 wells in 100 oil and gas fields from Gulf of Mexico (GOM) offshore basin can be used to evaluate boundary conditions and total production (oil and gas) and therefor constrain the capacity for potential carbon storage. In general, the combination of decline curve analysis and statistical analysis (to specify constraining boundary conditions) allows the determination of the range of reservoir performance if existing inactive production wells in GOM area of study are used reversibly for CO2 injection. To constrain the mass of CO2 which can be injected, it is useful to consider estimates of cumulative bulk (hydrocarbon?+?brine) production (CBP), which can be converted to equivalent CO2 mass considering reservoir conditions. Summary CBP statistics are presented as a probability of non-exceedance (PNE), providing a forecast of likely injection rates and masses for other located CO2 storage projects with similar geology and boundary conditions in the future. The 50% PNE for Equivalent CO2 is a novel quantitative approach to investigate the possible injection capacity in CO2 storage projects. The PNE sensitivity analysis shows that reservoir age, drive mechanism, reservoir trap, and reservoir porosity are the key controlling parameters for productivity and consequently optimum CO2 storage capacity. Another key finding is the negligible correlation between CBP with reservoir transmissivity and porosity, which implies that other factors than just petrophysical parameters should be studied as constraining factors for CO2 storage statistical analysis.Gough, D.V., Bahaghighat, H.D., Synovec, R.E., 2019. Column selection approach to achieve a high peak capacity in comprehensive three-dimensional gas chromatography. Talanta 195, 822-829. separation power of comprehensive three-dimensional gas chromatography (GC3) is substantially enhanced through proper selection of the phase volume ratio, β, of each column relative to each other on successive dimensions. Consideration and application of the ratio of phase volume ratios, βr, or β ratio, between successive dimensions has been a relatively un-studied approach to maximize separating power in comprehensive multidimensional GC instrument design. Herein, proper selection of βr in multidimensional GC is shown to control the elution temperature, Te, of analytes throughout a 40min primary (1D) column separation, and thus better control width-at-base, W, on all three dimensions. Specifically, between the 1D and secondary (2D) columns, a βr of 0.45 was applied, and between the 2D and tertiary (3D) columns a βr of 1.0 was applied. A total ideal peak capacity of 30,600, or a peak capacity production of ~770 peaks/min, was accomplished with the GC3 instrument with the reconfigured parameters. Additionally, due to the complex nature of this three-dimensional data, a novel approach to “slicing” the chromatographic run into user-defined time intervals is shown. This novel way to view the data still elicits a traditional GC×GC chromatograms, but with the focus on 2D × 3D separations. Moreover, due to proper βr selection, every 2s window (i.e. every 1D modulation period) is shown to have a peak capacity of ~50–100 for each 2D × 3D separation. This high overall peak capacity (30,600) and peak capacity per 1D modulation (~50–100), courtesy of proper column selection, is demonstrated to hold great promise to physically separate truly complex mixtures.Gregson, B.H., Metodieva, G., Metodiev, M.V., Golyshin, P.N., McKew, B.A., 2018. Differential protein expression during growth on medium versus long-chain alkanes in the obligate marine hydrocarbon-degrading bacterium Thalassolituus oleivorans MIL-1. Frontiers in Microbiology 9, 3130. doi: 10.3389/fmicb.2018.03130. marine obligate hydrocarbonoclastic bacterium Thalassolituus oleivorans MIL-1 metabolizes a broad range of aliphatic hydrocarbons almost exclusively as carbon and energy sources. We used LC-MS/MS shotgun proteomics to identify proteins involved in aerobic alkane degradation during growth on medium- (n-C14) or long-chain (n-C28) alkanes. During growth on n-C14, T. oleivorans expresses an alkane monooxygenase system involved in terminal oxidation including two alkane 1-monooxygenases, a ferredoxin, a ferredoxin reductase and an aldehyde dehydrogenase. In contrast, during growth on long-chain alkanes (n-C28), T. oleivorans may switch to a subterminal alkane oxidation pathway evidenced by significant upregulation of Baeyer-Villiger monooxygenase and an esterase, proteins catalyzing ketone and ester metabolism, respectively. The metabolite (primary alcohol) generated from terminal oxidation of an alkane was detected during growth on n-C14 but not on n-C28 also suggesting alternative metabolic pathways. Expression of both active and passive transport systems involved in uptake of long-chain alkanes was higher when compared to the non-hydrocarbon control, including a TonB-dependent receptor, a FadL homolog and a specialized porin. Also, an inner membrane transport protein involved in the export of an outer membrane protein was expressed. This study has demonstrated the substrate range of T. oleivorans is larger than previously reported with growth from n-C10 up to n-C32. It has also greatly enhanced our understanding of the fundamental physiology of T. oleivorans, a key bacterium that plays a significant role in natural attenuation of marine oil pollution, by identifying key enzymes expressed during the catabolism of n-alkanes.Guan, H., Feng, D., Birgel, D., Peckmann, J., Roberts, H.H., Wu, N., Chen, D., 2019. Lipid biomarker patterns reflect different formation environments of mussel- and tubeworm-dominated seep carbonates from the Gulf of Mexico (Atwater Valley and Green Canyon). Chemical Geology 505, 36-47. and tubeworms thriving at many methane seeps typically live in symbiosis with chemosynthetic, chiefly methanotrophic or thiotrophic bacteria. It has been shown that the activities of chemosymbiotic animals can result in large differences in the sedimentary environments of their habitats. Here, we put forward the concept that such environmental variability can be archived in the lipid biomarker inventories of authigenic carbonates forming in different, locally confined environments at seeps, mussel beds and tubeworm bushes in this case. To test this hypothesis, lipid biomarker patterns of carbonates from mussel and tubeworm environments from two seep sites (Atwater Valley 340 and Green Canyon 852) of the Gulf of Mexico were analyzed. Previous work revealed stronger carbon isotope fractionation between the methane source and biomarkers of anaerobic methane oxidizing archaea-2 (ANME-2)/sulfate-reducing Desulfosarcina/Desulfococcus (DSS) consortia than for ANME-1/DSS consortia, both performing anaerobic oxidation of methane (AOM). Similar δ13Cmethane values were found at the mussel and tubeworm sites from the same seeps and the local microbial consortia also appear to be largely similar based on the observed AOM biomarker inventories. Yet, a large average offset of 32‰ between the δ13C values of molecular fossils of sulfate-reducing bacteria (SRB) involved in AOM was observed, with lower values typifying tubeworm carbonates than mussel carbonates. This pattern is interpreted to reflect local effects on isotope fractionation caused by the chemosymbiotic metazoans at mussel- and tubeworm-dominated sites. At tubeworm-dominated sites, the excess sulfate produced by thiotrophic symbionts of tubeworms and pumped down into the sediment results in persistent production of AOM-derived bicarbonate and the enrichment of 12C in sub-surface sediments. Interestingly, tubeworm carbonates also contain high amounts of non-isoprenoidal dialkyl glycerol diethers (DAGEs) with extreme 13C depletions, representing compounds that derived from non-DSS cluster SRB. Most likely, 13C-depleted AOM-derived organic intermediates were used as carbon sources by the DAGE-producing non-DSS cluster SRB, possibly performing organoclastic sulfate reduction. Our study identifies significant variation in biomarker patterns between mussel and tubeworm carbonates at two seep sites in the Gulf of Mexico. Such variation allows to characterize different habitats at seeps, which are shaped by the interaction of chemosymbiotic seep metazoans and their symbionts with the local environment. Metazoan community composition apparently controls geobiological interaction in seep ecosystems to a large degree, which may allow tracing of the effects of chemosymbiosis into the rock record.Guan, H., Sun, Z., Mao, S., Xu, L., Cao, H., Geng, W., Xu, C., Zhang, X., Wu, N., 2019. Authigenic carbonate formation revealed by lipid biomarker inventory at hydrocarbon seeps: A case study from the Okinawa Trough. Marine and Petroleum Geology 101, 502-511. carbonates were recovered from the northern Okinawa Trough at 540–700?m water depth. Development of microbial communities and seepage dynamics driving the precipitation of authigenic carbonates remains poorly constrained, even though the source of methane-rich fluids, formation of Fe-rich carbonates, and the potential driving forces were previously reported. Here, petrologic observations, stable carbon and oxygen isotopic compositions, mineralogy, and lipid inventories of authigenic carbonates from the northern Okinawa Trough were analyzed. The carbonate minerals were comprised predominantly of aragonite, high-magnesium calcite, and siderite. The presence of molecular fossils diagnostic for anaerobic methane oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB) with pronounced 13C depletions (as low as ?134‰), together with highly negative δ13Ccarb values (as low as ?55.8‰), suggest that the carbonates precipitated from anaerobic oxidation of methane (AOM) with microbial methane as the predominant carbon source. The difference between measured and calculated δ18Ocarb values (based on 0‰ of sea water δ18O vs V-SMOW) was higher than +3‰ in one of the carbonates (GGD16), reflecting an origin from gas hydrate dissociation. Most of the carbonates revealed δ18O offsets between measured and calculated values within +3‰, or a lower measured δ18O than calculated value, suggesting a mixture of methane-derived carbonates (low δ13C/high δ18O) and detrital origin carbonates (high δ13C/low δ18O). Biomarker patterns varied significantly among samples. A suite of 13C-depleted biomarkers indicated the predominance of an ANME-1 assemblage for all samples, suggesting carbonates formed at low to medium methane flux. The predominance of ANME-1, abundant detrital minerals, and allochthonous biomarkers, as well as low carbonate contents indicate that most samples formed at greater depth within the sediment column. Only one carbonate sample in this study is interpreted to have precipitated at relatively shallower depth, as indicated by the occurrence of crocetane, dominance of aragonite, and higher overall carbonate content.Gülay, A., ?eki?, Y., Musovic, S., Albrechtsen, H.-J., Smets, B.F., 2018. Diversity of iron oxidizers in groundwater-fed rapid sand filters: Evidence of Fe(II)-dependent growth by Curvibacter and Undibacterium spp. Frontiers in Microbiology 9, 2808. doi: 10.3389/fmicb.2018.02808. earlier circumstantial observations have suggested the presence of iron oxidizing bacteria (IOB) in groundwater-fed rapid sand filters (RSF), ferrous iron (Fe(II)) oxidation in this environment is often considered a chemical process due to the highly oxic and circumneutral pH conditions. The low water temperature (5–10°C), typical of groundwaters, on the other hand, may reduce the rates of chemical Fe(II) oxidation, which may allow IOB to grow and compete with chemical Fe(II) oxidation. Hence, we hypothesized that IOB are active and abundant in groundwater-fed RSFs. Here, we applied a combination of cultivation and molecular approaches to isolate, quantify, and confirm the growth of IOB from groundwater-fed RSFs, operated at different influent Fe(II) concentrations. Isolates related to Undibacterium and Curvibacter were identified as novel IOB lineages. Gallionella spp. were dominant in all waterworks, whereas Ferriphaselus and Undibacterium were dominant at pre-filters of waterworks receiving groundwaters with high (>2 mg/l) Fe(II) concentrations. The high density and diversity of IOB in groundwater-fed RSFs suggest that neutrophilic IOB may not be limited to oxic/anoxic interfaces.Guo, Q., Liu, J., Chen, N., Wu, X., Ren, H., Wei, Y., Chen, G., Gong, D., Yuan, X., 2018. Mesh model building and migration and accumulation simulation of 3D hydrocarbon carrier system. Petroleum Exploration and Development 45, 1009-1022. and accumulation simulation of oil and gas in carrier systems has always been a difficult subject in the quantitative study of petroleum geology. In view of the fact that the traditional geological modeling technology can not establish the interrelation of carriers in three dimensional space, we have proposed a hybrid-dimensional mesh modeling technology consisting of body (stratum), surfaces (faults and unconformities), lines and points, which provides an important research method for the description of geometry of sand bodies, faults and unconformities, the 3D geological modeling of complex tectonic areas, and the simulation of hydrocarbon migration and accumulation. Furthermore, we have advanced a 3D hydrocarbon migration pathway tracking method based on the hybrid-dimensional mesh of the carrier system. The application of this technology in western Luliang Uplift of Junggar Basin shows that the technology can effectively characterize the transport effect of fault planes, unconformities and sand bodies, indicate the hydrocarbon migration pathways, simulate the process of oil accumulation, reservoir adjustment and secondary reservoir formation, predict the hydrocarbon distribution. It is found through the simulation that the areas around the paleo-oil reservoir and covered by migration pathways are favorable sites for oil and gas distribution.Guo, T., 2018. Hydrocarbon accumulation conditions and key technologies for exploration and development of Yuanba Gas Field. Petroleum Research 3, 293-305. paper discusses the exploration and development history and lessons of the large ultra-deep biogenic reef gas field in Yuanba area, where the previous “Kaijiang-Liangping shelf” model provides an insight for the discovery of the biological reef and bank on the platform margin. Systematic analysis of key geological conditions for hydrocarbon accumulation shows that the reef and bank reservoirs in Yuanba area arecharacterized by row and zonal distribution along “Kaijiang-Liangping shelf”, the bank in early and the reef in late , the reef in the frontand the bank in the back, and dominated by lateral accretion and progradation. The major exploration target of high-quality reef-bank reservoirs are developed in Changxing Formation instead of in Feixianguan Formation, Three stages of fractures and dissolution, and dolomitization control the development of the high-quality reservoirs. Two sets of effective source rocks (Permian Dalong Formation and Wujiaping Formation) provide sufficient gas source for the large gas field. Three dimensional migration pathway system composed of micro-faults, micro-fractures and interlayer fissures facilitates the hydrocarbon migration and accumulation. The accumulation model of Yuanba gas field is characterized by the near-sourceaccumulation, three -micro migration pathway system, lithological-stratigraphic reservoirs and tectonics controlling enrichment. According to the complex geological conditions such as ultra-deep reservoirs and multiple pressure systems inYuanba gas field, several key technologies are developed during hydrocarbon exploration and development, including fine prediction of ultra-deep reef-bank reservoirs and identification of gas and water, fine-scale reservoir description and characterization of complex thin and small reef gas reservoirs, optimal & fast drilling of ultra-deep horizontal well, geo-steering of ultra-deep horizontal well for complex reef and bank. All these technologies resulted in the efficient exploration and development of Yuanba gas field and accelerated the innovation of theoretical technology and methods for ultra-deep reservoirs.Guo, X., Qin, Z., Yang, R., Dong, T., He, S., Hao, F., Yi, J., Shu, Z., Bao, H., Liu, K., 2019. Comparison of pore systems of clay-rich and silica-rich gas shales in the lower Silurian Longmaxi formation from the Jiaoshiba area in the eastern Sichuan Basin, China. Marine and Petroleum Geology 101, 265-280. Jiaoshiba area in the eastern Sichuan Basin hosts the largest commercial shale gas field in China with an annual production of 1.7 BCF. The gases are primarily produced from the clay-rich siliceous marine shales in the Wufeng and Longmaxi formations. In this paper, sixteen organic-rich shale samples from a variety of lithofacies from the Longmaxi Formation in the Jiaoshiba area were studied to evaluate the pore systems of clay-rich shales by comparison with the silica-rich gas shales. The investigation includes the assessment of porosity and pore size distribution by means of shale bulk and skeletal density measurements, low-pressure N2/CO2 gas adsorption and mercury intrusion. The shale samples with different lithofacies have porosity values ranging from 3.25% to 5.65% and display similar fractional volumes of micropores, mesopores and macropores, and corresponding specific surface areas. All three pore fractions contribute to the shales’ total pore volumes, while the total specific surface areas are mainly contributed to by micropores and mesopores. There is a positive correlation between pore volumes and TOC contents, indicating that the porosities in the shales are dominated by organic matter pores with TOC content being the main parameter controlling pore development. TOC-normalized pore volumes decrease with a further increase in the TOC content from 1.6% to 4.2%. This may be related to the fact that the TOC-rich shales are more susceptive to mechanical compaction. Clay mineral content appears to have little effect on the pore volume or specific surface area development in the shales. Shale samples with clay-rich siliceous shale lithofacies display similar TOC contents, porosities, and fractional volumes of all pore sizes and specific surface areas with those of the silica-rich argillaceous and argillaceous/siliceous mixed lithofacies. This suggests that the marine shales with silica-rich argillaceous and argillaceous/siliceous mixed lithofacies from the Longmaxi Formation in the Jiaoshiba area are capable of generating significant amount of pore spaces for shale gas storage.Gupta, S., Kumar, K., 2019. Precursors of the Paleocene–Eocene Thermal Maximum (PETM) in the Subathu Group, NW sub-Himalaya, India. Journal of Asian Earth Sciences 169, 21-46. Paleocene–Eocene Thermal Maximum (PETM) is one of the most pronounced and widely documented global warming events in the geological history that occurred at the beginning of the Eocene (～56?Ma) causing substantial changes in biota and geochemistry. It is marked worldwide by a negative isotopic excursion of δ13C. The biotic changes associated with the PETM in marine realm include bloom of the dinoflagellate Apectodinium, turnover of larger foraminiferids, diversification of planktic foraminiferids, and carbonate dissolution of calcareous test shells, etc. while the geochemical changes include decrease in carbonates and increase in abundance of silicates and phyllosilicates, etc.Conspicuously, there has been no attempt to identify the PETM in the Himalaya even though some Himalayan sections are known to have Paleocene–Eocene transition beds. To fill this lacuna, we investigated the basal part of the late Paleocene–middle Eocene Subathu Group exposed at the village Kurla near Subathu in Himachal Pradesh (NW sub-Himalaya) for biotic, mineralogical, and geochemical signatures of this abrupt warming event. The significant results of this study include carbon isotope excursion (CIE) of 3.4‰, occurrence of index dinoflagellate genus Apectodinium, and carbonate dissolution of the larger benthic foraminiferids. The mineralogical changes noted across the Paleocene???Eocene transition include increase in quartz and phyllosilicates and decrease in carbonates. The geochemical changes include (i) increase in SiO2, Al2O3, K2O, and Fe2O3, (ii) decrease in CaCO3, (iii) decreasing trend of Si/Al, Fe/Al, and Mg/Al ratios, (iv) increasing trend of K/Al, Ti/Al, and Zr/Al ratios, (v) changes in trace element abundance, (vi) maximum chemical index of alteration (CIA) of 85–89%, and (vii) increase in abundance of rare earth elements. The aforementioned dataset is clearly very close to the PETM and even reflects its probable onset and peak phases, however, it is insufficient to definitively identify the PETM in the studied section. Nevertheless, since this study is the first from a Himalayan section and brings out considerable new information, all results and interpretations are presented and discussed here.Hall, L.S., Palu, T.J., Murray, A.P., Boreham, C.J., Edwards, D.S., Hill, A.J., Troup, A., 2019. Hydrocarbon prospectivity of the Cooper Basin, Australia. American Association of Petroleum Geologists Bulletin 103, 31-63. Pennsylvanian–Middle Triassic Cooper Basin is Australia’s premier conventional onshore hydrocarbon-producing province. The basin also hosts a range of unconventional gas play types, including basin-centered gas and tight gas accumulations, deep dry coal gas associated with the Patchawarra and Toolachee Formations, and the Murteree and Roseneath shale gas plays.This study used petroleum systems analysis to investigate the maturity and generation potential of 10 Permian source rocks in the Cooper Basin. A deterministic petroleum systems model was used to quantify the volume of expelled and retained hydrocarbons, estimated at 1272 billion BOE (512 billion bbl and 760 billion BOE) and 977 billion BOE (362 billion bbl and 615 billion BOE), respectively. Monte Carlo simulations were used to quantify the uncertainty in volumes generated and to demonstrate the sensitivity of these results to variations in source-rock characteristics.The large total generation potential of the Cooper Basin and the broad distribution of the Permian source kitchen highlight the basin’s significance as a world-class hydrocarbon province. The large disparity between the calculated volume of hydrocarbons generated and the volume so far found in reservoirs indicates the potential for large volumes to remain within the basin, despite significant losses from leakage and water washing. The hydrocarbons expelled have provided abundant charge to both conventional accumulations and to the tight and basin-centered gas plays, and the broad spatial distribution of hydrocarbons remaining within the source rocks, especially those within the Toolachee and Patchawarra Formations, suggests the potential for widespread shale and deep dry coal plays.Hamasaki, K., Shishikura, R., Suzuki, S., Shiozaki, T., Ogawa, H., Nakamura, T., Suwa, Y., 2018. Distribution and phylogeny of anaerobic ammonium-oxidizing (anammox) bacteria in the water column of the central Pacific Ocean. Deep Sea Research Part II: Topical Studies in Oceanography 156, 60-67. ammonium-oxidizing (anammox) bacteria produce dinitrogen gas from nitrite and ammonium under anoxic conditions and significantly contribute nitrogen removal processes in marine environments. Distribution and activity of anammox bacteria in a marine water column have been well studied in some oxygen deficient waters such as Black Sea, Arabian Sea, Namibian upwelling and Peruvian upwelling systems. However, the habitable area of anammox bacteria in the Pacific Ocean is still an open question. Here, we report distribution, abundance and phylogeny of anammox bacteria in the water column along the north-south transect (40?S to 55?N, 170?W) of the Pacific Ocean in order to determine their habitable area in the open ocean. Anammox bacteria-specific 16S rRNA gene was detected at 10 locations mostly from oxygen minimum depths (OMD) where dissolved oxygen (DO) concentration ranged from 10.9 to 46.2??mol?Kg-1. Their abundance measured by qPCR ranged from 3.69 ± 1.35 × 102 copies L-1 to 474 ± 15 × 102 copies L-1. The phylogenetic analysis showed that anammox bacteria detected in this study were all related to Candidatus Scalindua species and clustered into three subgroups: the Scalindua brodae/sorokinii cluster, the sediment cluster and the Arabian Sea cluster. Relationship between the abundance of anammox bacteria and DO concentration varied among these 3 clusters, suggesting their difference in oxygen sensitivity. Although rate measurement of anammox reaction using 15N-labeled substrates failed for all OMD samples tested during the cruise, this study unveiled the distribution of anammox bacteria in the open ocean oxygen minimum zone (OMZ) where oxygen deficiency is not extreme but moderate, which provides an insight into the potential distribution of anammox bacteria in marine environments.Han, X., Nie, J., Guo, J., Yang, L., Xu, D., 2019. Rock physics modelling of elastic properties of organic shale considering kerogen stress and pore pressure distribution. Journal of Petroleum Science and Engineering 174, 891-902. physics model for the elastic properties of organic shale is important for shale oil/gas exploration and production. Up until now, little work has been done to investigate the influence of the distributions of the stress in kerogen (kerogen stress) and the pore pressure on the elastic properties of organic shale. In this work, we used the Kuster- Toks?z (KT) model and Gassmann equation to study such effects. The Gassmann equation was applied for the homogeneous kerogen stress or pore pressure case whereas KT model was suitable for the inhomogeneous case. Four cases with different combinations of kerogen stress and pore pressure distributions, for the elastic properties of organic shale, were analysed and the corresponding models were given. Based on these models, a numerical example was studied. The results showed that the distributions of kerogen stress and pore pressure significantly affect the elastic properties of organic shale. The elastic moduli under the inhomogeneous kerogen stress or pore pressure distributions are larger than the homogeneous case, whose magnitude depends on porosity and kerogen content. Furthermore, the joint effects of kerogen stress and pore pressure distributions are similar to those of kerogen stress due to the much smaller effects of pore pressure. Hence, it is essential to consider the effects of the distributions of kerogen stress and pore pressure when building the rock physics model for the elastic properties of organic shale. This work revealed the importance of kerogen stress and pore pressure distributions on the elastic properties of organic shale and hence is helpful for the shale oil/gas exploration and production.Hansen, B.H., Olsen, A.J., Salaberria, I., Altin, D., ?verjordet, I.B., Gardinali, P., Booth, A., Nordtug, T., 2018. Partitioning of PAHs between crude oil microdroplets, water, and copepod biomass in oil-in-seawater dispersions of different crude oils. Environmental Science & Technology 52, 14436-14444. impact of oil microdroplets on the partitioning of polycyclic aromatic hydrocarbons (PAHs) between water and marine zooplankton was evaluated. The experimental approach allowed direct comparison of crude oil dispersions (containing both micro-oil droplets and water-soluble fraction; WSF) with the corresponding WSF (without oil droplets). Dispersion concentration and oil type have an impact on the PAH composition of WSFs and therefore affect dispersion bioavailability. Higher T-PAH body residues were observed in copepods treated with dispersions compared to the corresponding WSFs. PAHs with log Kow 3–4.5 displayed comparable accumulation factors between treatments; however, accumulation factors for less soluble PAHs (log Kow = 4.5–6) were higher for the WSF than for the dispersions, suggesting low bioavailability for components contained in oil droplets. The higher PAH body residue in dispersion exposures is assumed to result mainly from copepods grazing on oil droplets, which offers an alternative uptake route to passive diffusion. To a large degree this route is controlled by the filtration rates of the copepods, which may be inversely related to droplet concentration.Hansen, B.H., Parkerton, T., Nordtug, T., St?rseth, T.R., Redman, A., 2019. Modeling the toxicity of dissolved crude oil exposures to characterize the sensitivity of cod (Gadus morhua) larvae and role of individual and unresolved hydrocarbons. Marine Pollution Bulletin 138, 286-294. of weathered oil was investigated using Atlantic cod (Gadus morhua) larvae. A novel exposure system was applied to differentiate effects associated with dissolved and droplet oil with and without dispersant. After a 4-day exposure and subsequent 4-day recovery period, survival and growth were determined. Analytical data characterizing test oil composition included polyaromatic hydrocarbons (PAH) based on GC/MS and unresolved hydrocarbon classes obtained by two-dimensional chromatography coupled with flame ionization detection was used as input to an oil solubility model to calculate toxic units (TUs) of dissolved PAHs and whole oil, respectively. Critical target lipid body burdens derived from modeling characterizing the sensitivity of effect endpoints investigated were consistent across treatments and within the range previously reported for pelagic species. Individually measured PAHs captured only 3–11% of the TUs associated with the whole oil highlighting the limitations of traditional total PAH exposure metrics for expressing oil toxicity data.Hassan, A.M., Mahmoud, M.A., Al-Majed, A.A., Elkatatny, S., Al-Nakhli, A.R., Bataweel, M.A., 2018. Novel technique to eliminate gas condensation in gas condensate reservoirs using thermochemical fluids. Energy & Fuels 32, 12843-12850. situ heat generation is one of the promising techniques to enhance hydrocarbon production, by removing the condensate damage from the near-wellbore region, and improve gas mobility. This technology is performed by injecting two thermochemical solutions that will react at reservoir conditions and generate heat and pressure. The use of thermochemical fluids will reduce the injection cost to within 60% compared to the solvent injection. During thermochemical treatment, a considerable alteration in the fluid phase behavior will take place. This paper presents a novel technique and the first application of using thermochemicals to eliminate gas condensation. Experimental measurements and computer modeling group (CMG) modeling were performed to investigate the effect of injecting thermochemical fluids on the gas condensate behavior. A new reactor was fabricated to study the reaction kinetics of thermochemical materials. Thereafter, the influence of thermochemical treatments on removing the condensate, reducing the capillary forces, and improving the gas production was studied. Also, the impact of energizing the condensate region with nitrogen that was generated by thermochemical reaction was emphasized. Finally, the propagation depth of the generated heat from thermochemical reaction was determined as a function of injection time. The obtained results showed that injecting thermochemical fluids will increase the reservoir temperature and pressure beyond the dew point curve. At reservoir conditions, a pressure of 1300 psi could be achieved from the thermochemical reaction. The generated pressure is higher than the dew point pressure; therefore, the condensate liquid will be converted into the gaseous phase. Calculations of capillary forces revealed that thermochemical treatment reduced capillary forces by 25–36%. An exponential relationship was observed between the injection time and the radius of heat propagation. Increasing the injection time will increase the radius of the heated area exponentially. The heat propagation model can be used to determine the injection time required to heat the condensate region inside the reservoir.Hatje, V., Lamborg, C.H., Boyle, E.A., 2018. Trace-metal contaminants: Human footprint on the ocean. Elements 14, 403-408. activities have increased the fluxes of many trace metals into the oceans, changing their concentrations and distribution patterns. Despite their low dissolved concentrations, a number of these metals can still pose human and ecological risks. Some of these metals are well known (e.g. Pb, Hg), while others, such as the rare earth elements, represent emerging problems that impose new analytical challenges and environmental concerns. Defining the baselines of trace contaminants, identifying and quantifying the processes that control their transport, fate, and cycling are important issues to protect the ocean environment, safeguard human health, and support national and international marine decision-making.He, Z., Li, S., Nie, H., Yuan, Y., Wang, H., 2019. The shale gas “sweet window”: “The cracked and unbroken” state of shale and its depth range. Marine and Petroleum Geology 101, 334-342. assist in the progression of shale gas exploration in southern China, we aimed to clarify the burial depth of the “sweet window” of shale gas reservoirs. In this study, we statistically explored the relationship between burial depths and shale gas production of the Wufeng-Longmaxi Formations in the Sichuan Basin, Southwest China, analyzed the development morphology of fractures under different stress fields and fracturing effects of high-yield strata, conducted a series of triaxial mechanical experiments on shales under the formation conditions, and summarized the characteristics of the shale gas “sweet window” as well as its main affecting factors. The results show some interesting conclusions. First, a “sweet window” of shale gas reservoir burial depths does exist. Second, it is found that the bedding cracks and artificial fracture network formations are affected by burial depth. Third, shale mechanical properties in the “sweet windows” generally have the characteristics of transitioning from brittleness to ductility. Based on the above results, a method for determining the top and bottom depth of the shale gas “sweet window” is proposed. The top boundary of the “sweet window”, i.e., the depth at which shale suffers from brittle fractures, can be determined using the shale's over consolidation ratio (OCR). The bottom boundary of the “sweet window”, i.e., the depth at which shale transitions to a ductile state, can be estimated using triaxial stress experiments. The depth range of the “sweet window” top boundary is 2000–2700?m for the Longmaxi shale in the Sichuan Basin, and the depth range of the bottom boundary is 4200–4400?m. In areas with tectonic stability and low geo-stress differences, the top boundary of the “sweet window” can be shallower than the brittle boundary depth as determined by OCR, and the shale gas buried shallower than 2000 m may be preserved effectively and allow for higher production capacity. In areas with higher brittle mineral content and greater geo-stress differences, the bottom boundary of the “sweet window” may reach 4500–5000?m. The area of the Wufeng-Longmaxi shale burial depth between 3500?m and 4500?m is up to 5.5?×?104?km2 in the Sichuan Basin, which is a potential area for shale gas exploration and development in the future.Hellauer, K., Uhl, J., Lucio, M., Schmitt-Kopplin, P., Wibberg, D., Hübner, U., Drewes, J.E., 2018. Microbiome-triggered transformations of trace organic chemicals in the presence of effluent organic matter in managed aquifer recharge (MAR) systems. Environmental Science & Technology 52, 14342-14351. is widely assumed that biodegradation of trace organic chemicals (TOrCs) in managed aquifer recharge (MAR) systems occurs via a cometabolic transformation with dissolved organic carbon serving as primary substrate. Hence, the composition facilitating bioavailability of the organic matter seems to have a great impact on TOrCs transformation in MAR systems. The aim of this study was to elucidate the character of effluent organic matter present in the feedwater of a simulated sequential MAR system throughout the infiltration by use of FT-ICR-MS analyses as well as spectroscopic methods. Furthermore, compositional changes were correlated with TOrCs targeted throughout the system as well as the abundance of different microbial phyla. On the basis of their behavior throughout the infiltration system in which different redox and substrate conditions prevailed, TOrCs were classified in four groups: easily degradable, redox insensitive, redox sensitive, and persistent. Masses correlating with persistent TOrCs were mainly comprised of CHNO-containing molecules but also of CHO which are known as carboxyl-rich alicyclic molecules, while CHOS and CHNOS can be neglected. Easily degradable TOrCs could be associated with CHNO-, CHO-, and CHOS-containing compounds. However, a shift of molecular compounds to mostly CHOS was observed for redox-insensitive TOrCs. Three hundred thirty eight masses correlated with removal of redox-sensitive TOrCs, but no distinct clustering was identified.Henderson, G.M., Achterberg, E.P., Bopp, L., 2018. Changing trace element cycles in the 21st century ocean. Elements 14, 409-413. activity is altering the ocean. This is happening through climate change, the release of pollutants, and direct exploitation of the marine environment. Recent advances in understanding the chemical cycling of trace elements within the global ocean comes at a critical time. Society is now increasingly viewing the ocean as a resource while also recognising that ocean systems are vulnerable to change.Hill, R.A., Connolly, J.D., 2018. Triterpenoids. Natural Product Reports 35, 1294-1329. 2014. Previous review: Nat. Prod. Rep., 2017, 34, 90–122 This review covers the isolation and structure determination of triterpenoids reported during 2014 including squalene derivatives, lanostanes, holostanes, cycloartanes, cucurbitanes, dammaranes, euphanes, tirucallanes, tetranortriterpenoids, quassinoids, lupanes, oleananes, friedelanes, ursanes, hopanes, serratanes, isomalabaricanes and saponins; 374 references are cited.Honda, H., Sasahara, A., Onishi, H., 2019. Porphyrins on mica: Atomic force microscopy imaging in organic solvents. Colloids and Surfaces A: Physicochemical and Engineering Aspects 561, 194-200. of 5,10,15,20-tetraphenyl-21H,23H-porphyrin cobalt (CoTPP) on mica immersed in organic solvents of 1-hexanol, 1-chlorohexane, and 1-phenyloctane was examined. Flat-lying CoTPP molecules were recognized in topographic images observed by atomic force microscopy. The topographic height of individual porphyrins fluctuated by 0.2?nm in a time scale of 10?s. The height fluctuation was ascribed to two states with and without a solvent molecule trapped in the axial ligand position of the CoTPP. In imaging in phenyloctane, adsorbed CoTPPs were removed by adding 1-hexylamine to the imaging solution. Hexylamine ligands would have occupied the axial position of CoTPP to hinder adsorption. In addition, two-dimensional distribution of force pushing the tip was observed in hexanol to show a layered liquid structure parallel to the mica surface.Hong, Y.-d., Lin, B.-q., Xiang, H., Zhu, C.-j., Wang, Z., Nie, W., 2018. Variable pore structure and gas permeability of coal cores after microwave irradiation. Geofluids 2018, Article 9240206. experimental work in this paper investigated the effect of microwave energy on pore structure and gas permeability of coal cores. Fifteen coal samples were irradiated under the condition of 2.45?GHz with 6?kW. The effect of microwave irradiation on the pore structure of coal samples was evaluated by nuclear magnetic resonance (NMR). The water saturation degree has little influence on transverse relaxation time () distribution before the microwave treatment. By contrast, water saturation degree obviously affects the distribution after the microwave energy treatment. Coal permeability increased after microwave energy treatment. But fractal dimension decreased after microwave energy treatment. The results show that microwave energy has a potential for degassing coal seams.Hook, S.E., Revill, A.T., Mondon, J., Corbett, P., Armstrong, E.K., Song, J., Tanner, J.E., Stalvies, C., Ross, A.S., Williams, A., 2018. Naturally occurring hydrocarbon content and baseline condition of deep-sea benthic fauna from the Great Australian Bight. Deep Sea Research Part II: Topical Studies in Oceanography 157-158, 106-120. deep sea (> 500?m) of the Great Australian Bight (GAB) has not been well studied even though it is believed to have high conservation values as evidenced by large marine reserves, and where adjacent (continental shelf) waters support important commercial fisheries and large populations of marine mammals. Recent interest in developing the region's deep-sea hydrocarbon resources has drawn attention to this sparsity of data and the need to characterise the region's benthic ecology in order to detect and understand any potential impacts linked to a developing oil and gas industry. To that end, we measured the naturally occurring hydrocarbon content and baseline condition of a variety of benthic fishes and invertebrates collected during two surveys of the continental slope and seabed geological features. A total of 225 individuals, representing 15 species (7 invertebrates and 8 fishes) were analysed for (i) polycyclic aromatic hydrocarbons (PAH) body burdens or biliary PAH metabolites; (ii) 7-Ethoxyresorufin O-deethylase (EROD), a commonly used oil exposure biomarker; and (iii) lipid profiles and histology. Hydrocarbon concentrations, although measurable at some sites, did not indicate any anthropogenic contamination or unequivocal hydrocarbon seepage. PAH body burdens in the invertebrate species were below the levels of detection, and phenanthrene metabolites showed differences between species of fish surveyed, but were consistently low relative to oil exposed fish. EROD levels varied between species but also did not indicate exposure to oil. Lipid levels were highly variable between individuals and sites, suggesting that a lipid-related metric would not be suitable for monitoring organism health. Histological analysis indicated no gross deformity or infection in either the liver, gill, kidney or spleen. Pathologies identified were of minimal pathological important and likely to be recoverable. Liver exhibited varying levels of lipid accumulation across all fish species. These results, obtained before the commencement of oil and gas industry activity, can be used as a part of a baseline benthic ecosystem characterisation to guide future ecological monitoring programs.Hopkins, M.J., Bapst, D.W., Simpson, C., Warnock, R.C.M., 2018. The inseparability of sampling and time and its influence on attempts to unify the molecular and fossil records. Paleobiology 44, 561-574. two major approaches to studying macroevolution in deep time are the fossil record and reconstructed relationships among extant taxa from molecular data. Results based on one approach sometimes conflict with those based on the other, with inconsistencies often attributed to inherent flaws of one (or the other) data source. Any contradiction between the molecular and fossil records represents a failure of our ability to understand the imperfections of our data, as both are limited reflections of the same evolutionary history. We therefore need to develop conceptual and mathematical models that jointly explain our observations in both records. Fortunately, the different limitations of each record provide an opportunity to test or calibrate the other, and new methodological developments leverage both records simultaneously. However, we must reckon with the distinct relationships between sampling and time in the fossil record and molecular phylogenies. These differences impact our recognition of baselines and the analytical incorporation of age estimate uncertainty.Hoshino, T., Inagaki, F., 2019. Abundance and distribution of Archaea in the subseafloor sedimentary biosphere. ISME Journal 13, 227-231. sedimentary environments harbor a remarkable number of microorganisms that constitute anaerobic and aerobic microbial ecosystems beneath the ocean margins and open-ocean gyres, respectively. Microbial biomass and diversity richness generally decrease with increasing sediment depth and burial time. However, there has been a long-standing debate over the contribution and distribution of Archaea in the subseafloor sedimentary biosphere. Here we show the global quantification of archaeal and bacterial 16S rRNA genes in 221 sediment core samples obtained from diverse oceanographic settings through scientific ocean drilling using microfluidic digital PCR. We estimated that archaeal cells constitute 37.3% of the total microbial cells (40.0% and 12.8% in the ocean margin and open-ocean sites, respectively), corresponding to 1.1?×?1029 cells on Earth. In addition, the relative abundance of archaeal 16S rRNA genes generally decreased with the depth of water in the overlying sedimentary habitat, suggesting that Archaea may be more sensitive to nutrient quality and quantity supplied from the overlying ocean.Hosseini-Dastgerdi, Z., Meshkat, S.S., 2019. An experimental and modeling study of asphaltene adsorption by carbon nanotubes from model oil solution. Journal of Petroleum Science and Engineering 174, 1053-1061. adsorption of asphaltene on the surface of nanoparticles in the crude oil industry is a significant issue. In this regard, carbon nanostructures can be applied as an adsorbent for the removal of asphaltene from crude oil. In this paper, carbon nanotubes (CNTs) were used for the adsorption of three different asphaltenes from toluene solutions. The CNTs were synthesized by Chemical Vapor Deposition (CVD) method. The synthesized CNTs were characterized by Brunauer–Emmett–Teller (BET), Field Emission Scanning Electron Microscopy (FESEM) and Transmission Electron Microscopy (TEM). The asphaltenes were analyzed by X-ray Diffraction (XRD) and elemental analysis techniques. In addition, asphaltene adsorption isotherms and kinetics were offered. The adsorption of asphaltene was fast since equilibrium was reached in 1?h. The kinetic data were fitted well to the pseudo-second-order kinetic model. The equilibrium data of asphaltene A and B was fitted well to the Freundlich model. However, for asphaltene C, Temkin model was consistent with the experimental data due to the strong interactions between asphaltene C and surface arising from pyridinic, pyrrolic, sulfide and disulfide functional groups which existed on the surface of asphaltene C. The results indicated that the capacity and affinity depend on the molecular structure of the asphaltenes. The high adsorption capacity of asphaltene A was attributed to its high aromaticity. An increase in the aromatic nature of asphaltenes increases the self-association of asphaltenes and π?π interactions between asphaltenes and CNTs, which increases the asphaltene adsorption. The thermodynamic parameters indicated that the adsorption of asphaltenes on CNTs is exothermic and spontaneous. According to the results, CNTs showed high adsorption capacity and can be considered as an appropriate choice for asphaltene removal from crude oil.Hou, B., Jia, R., Fu, M., Wang, Y., Bai, Y., Huang, Y., 2018. Wettability alteration of an oil-wet sandstone surface by synergistic adsorption/desorption of cationic/nonionic surfactant mixtures. Energy & Fuels 32, 12462-12468. experimental methods including atomic force microscopy, scanning electron microscopy, zeta potential measurement, and contact angle measurement were used to analyze the mechanisms of wettability alteration of an oil-wet sandstone surface by cationic/nonionic surfactant mixtures in this work. Due to the synergies between cationic surfactants and nonionic surfactants, head groups of CTAB and TX-100 interact with each other, making the cmc of the cationic/nonionic surfactant mixtures lower compared to the single surfactant CTAB or TX-100. Ion pairs are produced by the carboxylic substances and the aggregates formed by CTAB and TX-100, which are irreversibly desorbed from the quartz surface and are solubilized into the mixed micelles formed by the CTAB/TX-100 mixture. The CTAB molecules are preadsorbed on the oil-wet sandstone surface by electrostatic attraction, acting as anchor particles, and the aggregates are formed by TX-100 and CTAB through hydrophobic interaction, thereby increasing the adsorption amount of CTAB on the oil-wet sandstone surface. The ability to form ion pairs for CTAB and the carboxylic substances in the presence of TX-100 and the solubilization ability of the mixed micelles are all enhanced, making the desorption capacity of ion pairs stronger. Thus, the CTAB/TX-100 mixture is more effective than the single surfactant CTAB in altering wettability of the oil-wet sandstone surface toward a more water-wet condition.Hu, B., Wang, P., Wang, C., Qian, J., Bao, T., Shi, Y., 2019. Investigating spectroscopic and copper-binding characteristics of organic matter derived from sediments and suspended particles using EEM-PARAFAC combined with two-dimensional fluorescence/FTIR correlation analyses. Chemosphere 219, 45-53. environmental dynamics of sediment organic matter (SOM) and suspended particulate organic matter (SPOM) result in great disparities in characteristics and subsequent interactions with heavy metals. In this study, sediments and suspended particles were collected from two large and shallow lakes (Taihu and Hongze Lake) to study the difference in the characteristics and copper binding properties between SOM and SPOM through spectroscopy method. Our results showed that SPOM in Taihu Lake was dominated by autochthonous tyrosine-like substance and SOM was dominated by terrestrial humic-like substance, whereas SPOM in Hongze Lake was dominated by terrestrial humic-like substances. Furthermore, dissolved organic matter (DOM) in Taihu and Hongze Lake was controlled by autochthonous protein and terrestrial humic substances, respectively. Comparison of SPOM between these two lakes indicated that various organic matter sources could be responsible for the organic matter characteristics in suspended particles. Meanwhile, relatively higher binding affinities and more binding sites were observed for SPOM in both two lakes compared to SOM through two-dimensional correlation spectroscopy (2D-COS) analysis of synchronous fluorescence spectra. Moreover, 2D-COS analysis of FTIR spectra revealed that hydrophobic groups (i.e., phenolic groups) had higher binding affinity than hydrophilic groups (i.e., polysaccharide groups) for both SOM and SPOM. Our results provide a new angle for understanding the suspended particles in shallow lakes, which might play a more important role in the environmental behaviors of heavy metals, than has been previously thought.Hu, W.-X., Kang, X., Cao, J., Wang, X.-L., Fu, B., Wu, H.-G., 2018. Thermochemical oxidation of methane induced by high-valence?metal oxides in a sedimentary basin. Nature Communications 9, Article 5131. oxidation of methane (TOM) by high-valence metal oxides in geological systems and its potential role as a methane sink remain poorly understood. Here we present evidence of TOM induced by high-valence metal oxides in the Junggar Basin, located in northwestern China. During diagenesis, methane from deeper source strata is abiotically oxidized by high-valence Mn(Fe) oxides at 90 to 135?°C, releasing 13C-depleted CO2, soluble Mn2+ and Fe2+. Mn generally plays the dominant role compared to Fe, due to its lower Gibbs free energy increment during oxidation. Both CO2 and metal ions are then incorporated into authigenic calcites, which are characterized by extremely negative δ13C values (?70 to ?22.5‰) and high Mn content (average MnO?=?5 wt.%). We estimate that as much as 1224 Tg of methane could be oxidized in the study area. TOM is unfavorable for gas accumulation but may act as a major methane sink in the deep crustal carbon cycle.Huang, J., Liu, S., Zhang, C., Wang, X., Pu, J., Ba, F., Xue, S., Ye, H., Zhao, T., Li, K., Wang, Y., Zhang, J., Wang, L., Fan, C., Lu, T.K., Zhong, C., 2019. Programmable and printable Bacillus subtilis biofilms as engineered living materials. Nature Chemical Biology 15, 34-41. biofilms can be programmed to produce living materials with self-healing and evolvable functionalities. However, the wider use of artificial biofilms has been hindered by limitations on processability and functional protein secretion capacity. We describe a highly flexible and tunable living functional materials platform based on the TasA amyloid machinery of the bacterium Bacillus subtilis. We demonstrate that genetically programmable TasA fusion proteins harboring diverse functional proteins or domains can be secreted and can assemble into diverse extracellular nano-architectures with tunable physicochemical properties. Our engineered biofilms have the viscoelastic behaviors of hydrogels and can be precisely fabricated into microstructures having a diversity of three-dimensional (3D) shapes using 3D printing and microencapsulation techniques. Notably, these long-lasting and environmentally responsive fabricated living materials remain alive, self-regenerative, and functional. This new tunable platform offers previously unattainable properties for a variety of living functional materials having potential applications in biomaterials, biotechnology, and biomedicine.Huang, R., Qin, R., Chelme-Ayala, P., Wang, C., Gamal El-Din, M., 2019. Assessment of ozonation reactivity of aromatic and oxidized naphthenic acids species separated using a silver-ion solid phase extraction method. Chemosphere 219, 313-320. to the complexity of naphthenic acids (NAs) in oil sands process water (OSPW), previous ozone-treatment studies mainly investigated the removal of classical NAs (aliphatic O2?NAs) and the understanding of ozonation reactivity of other NA species has been limited. This work utilized a silver-ion solid phase extraction (SPE) approach to separate individual NA species into 20 fractions before subsequent ozone treatment. The ozonation reactivity of aromatic and oxidized NA species in isolated fractions was studied for the first time. Untreated and ozone-treated SPE fractions were characterized using ultra performance liquid chromatography ion mobility time-of-flight mass spectrometry. The removals of aliphatic O2?NAs (Fraction 3), aromatic O2?NAs (Fraction 8), O3?NAs (Fraction 11), and O4?NAs (Fraction 17) with an applied ozone dosage of 16.8?mg?L?1 were 97.2%, 94.7%, 59.4% and 44.7%, respectively. The results showed that aromatic and oxidized NAs with larger carbon number were favorably removed during ozonation treatment. Comparison of the ozone utilization efficiency for different NA species indicated that the degradation of oxidized NAs consumed more ozone in molar ratio than the degradation of classical and aromatic NAs. The reactivity of oxidized NAs was lower than that of classical NAs because the former consumed more ozone in molar ratio during reactions. Knowing the reactivity of different NA species is crucial for the design of ozonation systems targeting species with high toxicity. Moreover, the utilization of silver-ion SPE pre-separation approach has been demonstrated for future studies investigating the degradation mechanism of distinct NA species under other treatment conditions.Illing, C.J., Hallmann, C., Scott, A.C., Collinson, M.E., Briggs, D.E.G., Strauss, H., Summons, R.E., 2019. Heterogeneity of free and occluded bitumen in a natural maturity sequence from Oligocene Lake Enspel. Geochimica et Cosmochimica Acta 245, 240-265. in Oligocene Lake Enspel was rapidly terminated by a basaltic lava flow. This introduced a preservational barrier while imparting a ‘natural flash pyrolysis’, during which the organic matter in underlying stratigraphic units was subjected to rapid thermal maturation resulting in hydrocarbon generation. Samples from these strata exhibit a steep maturity gradient (0.25–1.07% optical vitrinite reflectance, or RO) over uniform organofacies. This offers the opportunity to investigate bitumen generation during rapid thermal maturation mechanistically, in particular the nature of Bitumen 2—occluded bitumen, which is only recoverable after the digestion of the mineral matrix and was frequently dismissed as an artifact of incomplete extraction. Elaborate sequential extraction of the contact metamorphic sequence of oil shales at Enspel revealed systematic changes in bitumen composition. These trend progressively towards those of occluded bitumen, which exhibits a systematically elevated thermal maturity, a higher degree of catalytic biomarker-rearrangement and the conspicuous absence of molecular signatures from vascular plants that are present in the free bitumen. One plausible explanation involves a contribution of allochthonous clay-adsorbed organic matter to Bitumen 2. This could represent a mixture of older reworked bitumen and an early-diagenetic snapshot of clay adsorbed organic matter. Alternatively, a close association of early-generated bitumen with clay minerals may have led to enhanced isomerization and catalytically influenced ‘uniformization’ of alkane signatures. Deviations from the expected relationships between various thermal maturity parameters suggest variable dependence on the time-pressure-temperature pathway (i.e. metamorphic facies). The maturation of organic matter likely behaves differently under a contact metamorphic regime or during rapid subsidence and exhumation, as compared to slow maturation during regional subsidence. Our data also suggest that geologically brief shallow intrusive or extrusive magmatism might not be as destructive to the sedimentary hydrocarbon inventory as hitherto thought. This study draws attention to the small-scale compositional heterogeneity of bitumen that can be studied using sequential extraction methods. More importantly, it suggests that occluded bitumen could potentially harbor information on organic matter that pre-dates in situ primary productivity and may be derived from allochthonous biomass and detrital input.Inglez, L., Warren, L.V., Okubo, J., Sim?es, M.G., Quaglio, F., Arrouy, M.J., Netto, R.G., 2019. Discs and discord: The paleontological record of Ediacaran discoidal structures in the South American continent. Journal of South American Earth Sciences 89, 319-336. sedimentary structures are commonly described in Proterozoic strata, and even more common in Ediacaran to lower Cambrian sedimentary successions. Many abiotic processes are able to produce such circular or discoidal structures in bedding planes, however, their abundance in Ediacaran strata suggests a possible correlation with the evolution and preservation of epibenthic metazoans that emerged at the end of this period. In the South American paleontological record, studies regarding the Ediacaran soft-bodied organisms are meager and restricted to few reports in Brazil, Paraguay, and Argentina. In many cases, such “fossils” were only tentatively characterized in terms of their general morphology and putative taxonomic affinity. Thus, considering the almost absence of work on these enigmatic structures in South America, this paper aims to make a critical analysis on the main occurrences of Ediacaran-Cambrian discoidal structures described in this continent. Based on a detailed review and unpublished data, it was possible to provide a general picture concerning the main paleoenvironmental and sedimentary significance of this structures, as well as on the most promising prospects in terms of the paleontological record of Ediacaran soft-bodied metazoans in South American. In this sense, it was settled that occurrences such as those in the Jaibaras and Itajaí basins should be reassessed in order to establish reliable criteria of biogenicity. In the case of the material from the Sete Lagoas and Tagatiya Guazu formations, it is considered more parsimonious to interpret the discoidal features as resulting from microbial processes. Similarly, the discoidal structures of the Cerro Negro Formation presents a series of internal laminations and textures that resembles those developed by processes of microbial grain binding and trapping suggesting that, at least part of this material, can be related to microbially induced sedimentary structures. Finally, for the ichnologically diversified Puncoviscana and Camaqu? basins, two different scenarios were identified. The first presents an ichnological assemblage strongly indicative of lower Paleozoic, and possibly Cambrian affinity. Thus, the discs in association with these traces, should be viewed with caution and interpretations made in light of a Paleozoic context. The second possesses an ichnological association typical of that expected for the Ediacaran-Cambrian transition, and the diversity of discoidal forms can potentially represent imprints of macroorganisms on a microbially bounded substrate, thus deserving a more detailed approach.Jabir, T., Jesmi, Y., Vipindas, P.V., Mohamed Hatha, A., 2018. Diversity of nitrogen fixing bacterial communities in the coastal sediments of southeastern Arabian Sea (SEAS). Deep Sea Research Part II: Topical Studies in Oceanography 156, 51-59. present study depicts diversity, abundance and activity of nitrogen (N2) fixing bacterial communities in the coastal sediments of southeastern Arabian Sea (SEAS). The diversity of N2 fixing bacterial community was determined by clone library analysis of nifH gene, the culturable N2 fixing bacteria was determined by 16s rRNA and nifH gene analysis. The nitrogen fixation rate in the sediments was also estimated by acetylene reduction assay method. The N2 clone library analysis revealed that fifteen putative diazotrophs, belonging to alpha-, beta-, gamma-, delta-, epsilon- Proteobacteria and Firmicutes. The predominant operational taxonomic units (OTUs) among these were related to α-Proteobacteria (with 16% of total sequences); β-Proteobacteria (10% sequences); γ-Proteobacteria (29% sequences); δ-Proteobacteria (11% sequences); ε-Proteobacteria (21% sequences); Firmicutes (3% of sequences) and percent of some sequences remained unknown. The 16s rRNA gene based identification of culturable N2 fixing bacteria revealed the presence of seven nitrogen fixing bacterial species namely Acinetobacter johnsonii, Rhizobium rosettiformans, Bacillus megaterium, B. circulans, B. flexus, B. oceanisediminis and B. subtilis. The observed N2 fixation rate in the sediments ranged from 0.12 to 0.36?nmol?N?g?1 h?1. Canonical correspondence analysis (CCA) revealed significant influence of the environmental variables such as sediment type, total nitrogen (TN), total organic matter (TOM), total organic carbon (TOC), iron (Fe), manganese (Mn), total sulfur (TS), nitrite (NO2) and nitrate (NO3) on the diversity of N2 fixing bacteria and N2 fixation rate. The observations of the current study provide a better understanding of N2 cycling in coastal sediments of the SEAS and sources of fixed nitrogen.Janjic, A., 2018. The need for including virus detection methods in future Mars missions. Astrobiology 18, 1611-1614. growing scientific interest in the “virus first hypothesis” (VFH) as an early step in the origin of life has practical implications for searches and life detection on future Mars missions. The suite of life-detection methods on future missions could miss important biosignatures because instrument designs currently follow a biased definition of life. There is growing support for the possibility that viruses represent the oldest branch of life on Earth and are precursors of microbial cells. Therefore, future and already existing concepts for Mars sample return missions should be coordinated across disciplines to include hypotheses of virologists and evolutionary ecologists. In addition to ensuring a broader search for life on Mars, it may be the only potential way to falsify competing hypotheses of evolutionary virology.Jaramillo, R., Dorman, F.L., 2018. Retention time prediction in thermally modulated comprehensive two-dimensional gas chromatography: Correcting second dimension retention time modeling error. Journal of Chromatography A 1581-1582, 116-124. retention modeling to a thermally modulated comprehensive two-dimensional gas chromatography (GC?×?GC) system run under constant flow is performed. Significant errors in modeled second dimension retention time (tr,2) were observed, in line with past work on thermally modulated GC?×?GC modeling. A comprehensive study of tr,2 modeling error for alkane separations across a wide range of heating ramp rates and carrier gas flow rates was performed. Modeling errors were found to be systematic and a function of analyte elution temperature and mobile phase velocity. A model to account for these systematic errors was generated, and associated coefficients were determined which reduced average tr,2 retention time error in 144 hydrocarbon separations by an order of magnitude resulting in significant improvement in prediction accuracy. The model was used to correct the separation of 139 Grob mix analyte separations, providing an average tr,2 modeling error of 0.030?±?0.022?s. The model successfully predicted the separation of n-alkanes on a longer second dimension column configuration.Jayakumar, A., Balachandran, D., Rees, A.P., Kearns, P.J., Bowen, J.L., Ward, B.B., 2018. Community composition of nitrous oxide reducing bacteria investigated using a functional gene microarray. Deep Sea Research Part II: Topical Studies in Oceanography 156, 44-50. diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation. Communities from surface ocean waters and agricultural soils differed significantly from each other and from those in oceanic oxygen minimum zones. Atypical nosZ genes, usually associated with incomplete denitrification pathways, were detected in all the environments, including surface ocean waters. The abundance of nosZ genes, as estimated by quantitative PCR, was highest in agricultural soils and lowest in surface ocean waters.Jeandel, C., Derek, V., 2018. New tools, new discoveries in marine geochemistry. Elements 14, 379-384. in the development of seawater sampling systems, analytical procedures and mass spectrometry have allowed measurements of trace elements and their isotopes in the ocean at spatial resolutions and at concentrations never achieved before. Marine geochemists are now exploiting these new developments to measure, for the first time, the stable isotopes of trace metals that are essential for marine life (e.g. Fe, Cu, Ni, Mo, Zn). The new data have already produced new insights into the interaction between ocean life and dissolved trace constituents and into the sources and sinks of those trace elements.Jeltsch-Th?mmes, A., Battaglia, G., Cartapanis, O., Jaccard, S.L., Joos, F., 2018. A large increase in the carbon inventory of the land biosphere since the Last Glacial Maximum: constraints from multi-proxy data. Climate of the Past Discussions 2018, 1-48. CO2 increased by about 90ppm across the transition from the Last Glacial Maximum (LGM) to the end of the preindustrial (PI) period. The contribution of changes in land carbon stocks to this increase remains uncertain. Estimates of the PI-LGM difference in land biosphere carbon inventory (?land) range from ?400 to +1,500GtC, based on upscaling of scarce paleo soil carbon or pollen data. A perhaps more reliable approach infers ?land from reconstructions of the stable carbon isotope ratio in the ocean and atmosphere assuming isotopic mass balance with recent studies yielding ?land values of about 300–400GtC. Surprisingly, however, earlier studies considered a mass balance for the ocean–atmosphere–land biosphere system only. Thereby, these studies neglect carbon exchange with sediments, weathering-burial flux imbalances, and the influence of the deglacial reorganization on the isotopic budgets. We show this neglect to significantly bias low deglacial ?land in simulations using the Bern3D Earth System Model of Intermediate Complexity v.2.0s. We constrain ?land to ～850GtC (median estimate; 450 to 1250GtC 1σ range) by using reconstructed changes in atmospheric δ13C, marine δ13C, deep Pacific carbonate ion concentration, and atmospheric CO2 as observational targets in a Monte Carlo ensemble with half a million members. Sensitivities of the target variables to changes in individual deglacial carbon cycle processes are established from factorial simulations over the past 21,000 years with the Bern3D model. These are used in the Monte Carlo ensemble and provide forcing–response relationships for future model–model and model–data comparisons. Uncertainties in the estimate of ?land remain considerable due to model and proxy data uncertainties. Yet, it is likely that ?land is larger than 450GtC and highly unlikely that the carbon inventory in the land biosphere was larger for the LGM than during the recent preindustrial period.Jia, Z., Hou, D., Sun, D., Jiang, Y., Zhang, Z., Hong, M., 2018. Geochemical characteristics of source rocks in the Lower Cambrian Niutitang Formation in Guizhou Province, China. Journal of Natural Gas Geoscience 3, 263-272. source rock was closely related to the development of hydrothermal sedimentation in geochemistry and others. By studying the characteristics of the source rocks of Lower Cambrian Niutitang Formation in Guizhou Province of China, it was found that the strata affected by both terrigenous inputs and hydrothermal sediments. There were a few samples with a low gross amount of REEs, which widely varied in others. The influence of the hydrothermal sedimentation was stronger in Yangtiao and Jiumen sections, while relatively weaker in Lianxing and Wenshui sections. The content of As and Sb enriched in Niutitang Formation, which indicated the existence of the hydrothermal activity. The δEu/Al ratio can be used to distinguish and indicate the intensity of the hydrothermal sedimentation.Jiang, L.-q., Zheng, A.-q., Meng, J.-g., Wang, X.-b., Zhao, Z.-l., Li, H.-b., 2019. A comparative investigation of fast pyrolysis with enzymatic hydrolysis for fermentable sugars production from cellulose. Bioresource Technology 274, 281-286. this study, ball milling and ionic liquid pretreatments were utilized to alter cellulose structure prior to fast pyrolysis and enzymatic hydrolysis. The variations in the products distribution of cellulose fast pyrolysis, and their dependence on the structure of cellulose, and the temperature of fast pyrolysis were illustrated. Fast pyrolysis of pretreated cellulose yielded more levoglucosan than crystalline cellulose (14.7%) at 300?°C. Nevertheless, the levoglucosan achieved higher yield (64.3%) from crystalline cellulose at 400?°C. At last, a comparison between fast pyrolysis and enzymatic hydrolysis for cellulose saccharifaction was made. Fast pyrolysis was a promising alternative to liberate levoglucosan from cellulose. Further investigation and development were required to maximize the levoglucosan production.Jiang, R., Yu, H., 2019. Interaction between sequestered supercritical CO2 and minerals in deep coal seams. International Journal of Coal Geology 202, 1-13. study investigates the interaction between supercritical CO2 (ScCO2) and minerals in coal that may occur during CO2 sequestration into deep coal seams. Two low-rank coals with low-ash content, one low-rank coal with high-ash content and one high-rank coal with low-ash content were used to study the interactions. A coal-CO2 geochemical interaction experiment with a typical high-ash coal was conducted to investigate change of the water-soluble elements after ScCO2 interaction. X-ray powder diffraction (XRD) was used to determine the effects of ScCO2–H2O on the minerals in the four coals. In addition, the influence of ScCO2 on pore structure of four coals was studied based on liquid nitrogen adsorption experiment. The results suggest that ScCO2 can effectively enhance the solubility of all elements from coal in water because of ScCO2 interaction. ScCO2 can significantly improve the solubility of trace elements than that of major elements. Because of the relatively low mineral content in coals and the short experimental period, secondary minerals formed by ScCO2-mineral-water interaction were not determined with XRD. However, the content of primary minerals changed; the apparent content of quartz increased and the content of kaolinite, carbonate minerals and pyrite decreased. For the experimental coals in this study, ScCO2 can enlarge the pore size of the micropores for low-ash coal and mesopores for low-rank coal, but shrinks that of micropores for high-ash coal and mesopores for high-rank coal.Johnson, K.P., Dietrich, C.H., Friedrich, F., Beutel, R.G., Wipfler, B., Peters, R.S., Allen, J.M., Petersen, M., Donath, A., Walden, K.K.O., Kozlov, A.M., Podsiadlowski, L., Mayer, C., Meusemann, K., Vasilikopoulos, A., Waterhouse, R.M., Cameron, S.L., Weirauch, C., Swanson, D.R., Percy, D.M., Hardy, N.B., Terry, I., Liu, S., Zhou, X., Misof, B., Robertson, H.M., Yoshizawa, K., 2018. Phylogenomics and the evolution of hemipteroid insects. Proceedings of the National Academy of Sciences 115, 12775-12780.: Hemipteroid insects constitute a major fraction of insect diversity, comprising three orders and over 120,000 described species. We used a comprehensive sample of the diversity of this group involving 193 genome-scale datasets and sequences from 2,395 genes to uncover the evolutionary tree for these insects and provide a timescale for their diversification. Our results indicated that thrips (Thysanoptera) are the closest living relatives of true bugs and allies (Hemiptera) and that these insects started diversifying before the Carboniferous period, over 365 million years ago. The evolutionary tree from this research provides a backbone framework for future studies of this important group of insects.Abstract: Hemipteroid insects (Paraneoptera), with over 10% of all known insect diversity, are a major component of terrestrial and aquatic ecosystems. Previous phylogenetic analyses have not consistently resolved the relationships among major hemipteroid lineages. We provide maximum likelihood-based phylogenomic analyses of a taxonomically comprehensive dataset comprising sequences of 2,395 single-copy, protein-coding genes for 193 samples of hemipteroid insects and outgroups. These analyses yield a well-supported phylogeny for hemipteroid insects. Monophyly of each of the three hemipteroid orders (Psocodea, Thysanoptera, and Hemiptera) is strongly supported, as are most relationships among suborders and families. Thysanoptera (thrips) is strongly supported as sister to Hemiptera. However, as in a recent large-scale analysis sampling all insect orders, trees from our data matrices support Psocodea (bark lice and parasitic lice) as the sister group to the holometabolous insects (those with complete metamorphosis). In contrast, four-cluster likelihood mapping of these data does not support this result. A molecular dating analysis using 23 fossil calibration points suggests hemipteroid insects began diversifying before the Carboniferous, over 365 million years ago. We also explore implications for understanding the timing of diversification, the evolution of morphological traits, and the evolution of mitochondrial genome organization. These results provide a phylogenetic framework for future studies of the group.Jones, J.M., Heath, K.D., Ferrer, A., Brown, S.P., Canam, T., Dalling, J.W., 2019. Wood decomposition in aquatic and terrestrial ecosystems in the tropics: contrasting biotic and abiotic processes. FEMS Microbiology Ecology 95, fiy223-fiy223. decomposition, a critical process in carbon and nutrient cycles, is influenced by environmental conditions, decomposer communities and substrate composition. While these factors differ between land and stream habitats, across-habitat comparisons of wood decay processes are rare, limiting our ability to evaluate the context- dependency of the drivers of decay. Here we tracked wood decomposition of three tree species placed in stream and terrestrial habitats in a lowland tropical forest in Panama. At 3 and 11 months we measured mass loss, wood nitrogen and wood polymer concentrations, and sampled wood-associated fungal and bacterial communities. After 11 months of decay we found that mass loss occurred 9% faster in streams than on land, but loss of cellulose, hemicellulose and lignin did not differ between habitats. We also observed large differences in microbial decomposer communities between habitats. Overall, we found faster mass loss of wood in water, but no differences in biotic decay processes between habitats despite distinct microbial communities in streams and on land. Our research challenges the assumption that wood decays relatively slowly in water reflecting unfavorable environmental conditions and a limited capacity of aquatic microbial communities to effectively degrade wood polymers.Kaiser, J., Wang, K.J., Rott, D., Li, G., Zheng, Y., Amaral-Zettler, L., Arz, H.W., Huang, Y., 2019. Changes in long chain alkenone distributions and Isochrysidales groups along the Baltic Sea salinity gradient. Organic Geochemistry 127, 92-103. species of the phylum Haptophyta are the exclusive producers of C37 to C42 long chain alkyl ketones, also called long chain alkenones (LCAs). While LCA distributions are known to vary with temperature and salinity, it is difficult to tease apart the direct effects of environmental parameters vs changes in the LCA-producing organisms. The Baltic Sea surface salinity gradient, which ranges from oligohaline (0.5–5?g/kg) to polyhaline (18–30?g/kg), represents a unique opportunity to study the relationships between salinity changes, species distribution and LCA biomarkers in a single ecosystem. LCA biomarkers revealed the presence of the three known Isochrysidales groups (Groups I, II and III) in Baltic Sea surface sediments, and the presence of Groups I and II were further confirmed with DNA sequencing. Group III Isochrysidales were present in the mixoeuhaline Skagerrak based on LCA signature alone. Groups I and II Isochrysidales were found for the first time in the Baltic Sea using a combination of LCAs and DNA biomarkers, solving an eighteen-year long mystery of Baltic Sea LCA-producing haptophyte identity. Group II Isochrysidales, which have a large salinity tolerance range, were spread over the Skagerrak and the complete Baltic Sea, but were characteristic for the central Baltic Sea. Oligohaline Group I Isochrysidales were representative for the northern Baltic Sea. However, evidence of Group I Isochrysidales in the central and southern Baltic Sea suggests a possible transport by surface currents since this group is typically confined to oligohaline conditions. Testing the recently developed ratio of isomeric C37 ketones (RIK37) against the Baltic Sea surface salinity gradient revealed a significant positive correlation. This may represent a salinity proxy reflecting the amount of Group I Isochrysidales relative to Group II Isochrysidales in oligohaline environments. The present study elucidates for the first time the identity and the spatial distribution of LCA producers thriving in a large and stable brackish environment.Kamimura, N., Sakamoto, S., Mitsuda, N., Masai, E., Kajita, S., 2019. Advances in microbial lignin degradation and its applications. Current Opinion in Biotechnology 56, 179-186. biomass represents a crucial resource for achieving sustainable development by replacing petroleum-based production systems. Lignin, a major component of plant cell walls, has significant potential as a bioresource; however, it is an obstacle in lignocellulosic biomass utilization due to its recalcitrance. Consequently, decomposition or removal of lignin is a crucial step to utilize cell wall components. In nature, lignin may be degraded via two stages: depolymerization and the mineralization of the resulting heterogeneous low-molecular-weight aromatic species. Microbial enzymes responsible for the former could be attractive tools for lignin decomposition during biomass pretreatment, and enzymes involved in the latter are useful for lignin valorization through the production of value-added chemicals. Moreover, specific microbial enzymes could reduce the recalcitrance of lignocellulosic biomass via plant cell wall bioengineering. This review focuses on microbial enzymes that are responsible for lignin degradation and on their applications to biological lignocellulosics pretreatment and biotechnological lignin engineering.Karakas, A., 2018. An abundance of rare isotopes in a planetary nebula. Nature 564, 353-354. reveal that a particular planetary nebula — the ejected envelope of an old star — is unusually enriched in rare carbon, nitrogen and oxygen isotopes. The finding could help to explain the origins of these isotopes. The origin of the chemical elements in the Universe is one of the most fascinating and enduring mysteries in astronomy. Progress so far has come from studies of stars, but here only elemental abundances can be determined reliably. Isotopic ratios are more difficult to obtain. Writing in Nature, Schmidt et al.1 study the composition of the young planetary nebula K4-47 — a glowing shell of gas and dust that formed from the outer layer of a Sun-like star and that was thrown off during the final stages of the star’s evolution. The authors find that the nebula is unusually enriched in rare isotopes of carbon (13C), nitrogen (15N) and oxygen (17O). The measured composition of K4-47 shows that this object is more enriched in these isotopes than is almost any other nebula or star examined so far.Why is Schmidt and colleagues’ finding such a big deal? For one thing, it seems to suggest that stars similar to the Sun can make these rare isotopes — a result that was not expected. Computer simulations2 of Sun-like stars have shown that they can be factories for carbon and nitrogen, but only in the form of the dominant isotopes 12C and 14N. Furthermore, theory2 predicts that the rarer isotopes are not made inside stars that become planetary nebulae. What about direct observations of ageing Sun-like stars, as opposed to planetary nebulae? Such observations are difficult, but the available data3,4 mostly agree with theory, making K4-47 a particularly unusual object.The only instance in which the isotopes 13C, 15N and 17O are synthesized at the same time is in explosions. CNO cycles are a collection of thermonuclear reactions that involve the capture of protons by isotopes of carbon, nitrogen and oxygen. These reactions are the workhorse of stellar energy production but do not make much 13C, 15N and 17O. Generating these isotopes requires conditions of high temperature and density, as well as plenty of protons. Such a mechanism is known as the hot CNO cycle. So far, the products of the hot CNO cycle have been found only in classical novae5 — nuclear explosions that occur in certain binary star systems.So how can the presence of the rare isotopes in K4-47 be explained? One mechanism proposed by Schmidt et al. is that the progenitor of K4-47 underwent an explosive event called a helium-shell flash immediately before it became a planetary nebula. This is, in essence, a mixing event that causes hot material from the core of a star, rich in 12C, to be moved to a cooler region, where hydrogen-fusion reactions are occurring. The mixing elevates the temperature of the cooler region, enabling reactions of the hot CNO cycle to proceed before the material is expelled to space.Although the explosive nature of this scenario is unusual, similar mixing has previously been proposed to explain the composition of other chemically peculiar stars, such as Sakurai’s object6 (also known as V4334 Sagittarii). Detailed computer simulations are needed to test this mechanism. If it can be verified, it will be evidence of previously unknown stellar behaviour that provides insight into how rare isotopes of common elements are generated.But there are other possible explanations. The isotopic composition of K4-47 is similar to that of J-type carbon stars4, which have ratios of 12C to 13C of less than 15. The sequence of events that lead to a J-type star is unknown, and their existence is not predicted by the theory that describes the evolution of single stars. It has been suggested that J-type stars instead result from binary evolution7, in which two stars orbit each other and interact.Such interactions have been proposed for all planetary nebulae that, like K4-47, have an hourglass (bipolar) shape and highly collimated outflows of material8,9 (Fig. 1). Observations show that the central stars of planetary nebulae are more likely to be binary stars than was previously thought, giving further credence to this idea. K4-47 could therefore be the product of an interaction or merger between two stars.Alternatively, K4-47 might not be a planetary nebula at all. It has been speculated that it could be a planetary-nebula mimic, in which the extended nebula was ejected by a pair of interacting binary stars during an explosion10. The isotopic composition of K4-47 could be explained if the interaction of these stars resulted in an explosion akin to a classical nova that would allow for the hot CNO cycle. One prediction of this scenario is that gas would be ejected at high velocities. Has such ejection been observed?Schmidt and colleagues say they have not seen these high-velocity outflows of material, so they rule out a nova-like explosion as an explanation. But this finding is in contrast to previous studies that have observed high-velocity bullets of material ploughing through the surrounding medium11,12. So who is right? Answering this question will require follow-up observations of K4-47 using astronomical instruments that can extract high-resolution spatial, dynamical and chemical information about the object.Either way, K4-47, which is rich in the products normally associated with a nova but is embedded in something that looks like a planetary nebula, is one of the most isotopically unusual astronomical objects studied so far (along with CK Vulpeculae13). Detailed computer modelling and follow-up observations are required to tease out the true nature of the progenitor of K4-47. Such work could tell us something about how the rare isotopes of carbon, nitrogen and oxygen are made in stars.References1. Schmidt, D. R., Woolf, N. J., Zega, T. J. & Ziurys, L. M. Nature 564, 378–381 (2018).2. Karakas, A. I. & Lattanzio, J. C. Publ. Astron. Soc. Aust. 31, e030 (2014).3. Lambert, D. L., Gustafsson, B., Eriksson, K. & Hinkle, K. H. Astrophys. J. Suppl. Ser. 62, 373–425 (1986).4. Abia, C. & Isern, J. Mon. Not. R. Astron. Soc. 289, L11–L15 (1997).5. Gehrz, R. D., Truran, J. W., Williams, R. E. & Starrfield, S. Publ. Astron. Soc. Pacif. 110, 3–26 (1998).6. Herwig, F. et al. Astrophys. J. 727, 89 (2011).7. Zhang, X. & Jeffery, C. S. Mon. Not. R. Astron. Soc. 430, 2113–2120 (2013).8. De Marco, O. Publ. Astron. Soc. Pacif. 121, 316–342 (2009).9. Jones, D. & Boffin, H. M. J. Nature Astron. 1, 0117 (2017).10. Corradi, R. L. M. et al. Astrophys. J. 535, 823–832 (2000).11. Gon?alves, D. R. et al. Mon. Not. R. Astron. Soc. 355, 37–43 (2004).12. Akras, S., Gon?alves, D. R. & Ramos-Larios, G. Mon. Not. R. Astron. Soc. 465, 1289–1296 (2017).13. Kamiński, T. et al. Astron. Astrophys. 607, A78 (2017).Kawai, J., Kebukawa, Y., McKay, C.P., Kobayashi, K., 2019. Nucleic acid bases in Titan tholins and possible genetic systems in the Titan liquidosphere. Life Sciences in Space Research 20, 20-29. is the largest moon of Saturn and possesses a dense atmosphere composed of nitrogen and methane. Various types of organic compounds (hydrocarbons, nitriles, etc.) have been found on Titan, which were generated by reactions taking place in its atmosphere. These reactions are considered to provide crucial evidence for chemical reactions which may have occurred in the atmosphere of primitive Earth. Cassini discovered several lakes of liquid methane and ethane on Titan's surface; in addition, the presence of ammonia water in its sub-surface was implied. In order to simulate the chemical reactions in Titan's atmosphere, gas mixtures of nitrogen and methane have been exposed to plasma discharges to synthesize complex organic matters. In this study, we focused on the formation of nucleic acid bases and related compounds recovered from synthesized Titan tholins. The five nucleic acid bases that terrestrial life uses (adenine, cytosine, thymine, guanine, and uracil) have already been reported to be present in synthesized Titan tholins. Purines and pyrimidines, including the five aforementioned nucleic acid bases, were extracted from synthesized Titan tholins and analyzed by HPLC and LC/MS. As a result, the pyrimidine bases of isocytosine and 2, 4-diaminopyrimidine were detected together with the terrestrial nucleic acid bases of adenine, uracil, and cytosine. The results obtained in conjunction with those from previous studies show that some nucleic acid bases and related pyrimidine bases are found in synthesized Titan tholins, suggesting that chemical evolutions toward xenogenetic systems could occur in Titan's environment.Ke, W., Svartaas, T.M., Chen, D., 2019. A review of gas hydrate nucleation theories and growth models. Journal of Natural Gas Science and Engineering 61, 169-196. this Review, we present a comprehensive overview of fundamental gas hydrate properties and formation theories. Key terminologies, theories and hypotheses for hydrate nucleation process were elucidated as bulletin points, while proposed hydrate growth models were categorized into groups based on variously proposed controlling mechanisms and compared in depth. Understanding and mastering these is instrumental to engineering the formation and dissociation of gas hydrates for beneficial applications. We conclude with an outlook on future research opportunities within this rapidly developing field, to facilitate future endeavors in the realm of gas hydrates.Ke?ili, R., Büyüktiryaki, S., Hussain, C.M., 2019. Advancement in bioanalytical science through nanotechnology: Past, present and future. TrAC Trends in Analytical Chemistry 110, 259-276. the last decade, nanotechnology has inspired in an extraordinary manner to the world and established an interdisciplinary trend between almost all branches of science and technology. It is expected that within no time this technological development will become an integral component of real-world design and innovations. This incorporation of nanotechnology has also impacted BioAnalytical sciences through the development of novel nano devices, nanotools, nanosensors and nanosorbents in analytical processes. As a result, bioanalytical science has played a very crucial rule in order to explore the nanoglobe. In general nanomaterials are nano-sized structures, with extraordinary physical and chemical properties, and exceptional large specific surface areas which have improved the detection sensitivity and miniaturize the devices in bioanalytical procedures. Also, these nanomaterials of various compositions, morphologies and functionalization have provided powerful tools for the bioanalysis systems. In this review, we have summarized recent progresses, prevailing techniques, applied formats, and future trends due to nanotechnology in BioAnalytical arena.Kelson, J.R., Watford, D., Bataille, C., Huntington, K.W., Hyland, E., Bowen, G.J., 2018. Warm terrestrial subtropics during the Paleocene and Eocene: Carbonate clumped isotope (Δ47) evidence from the Tornillo Basin, Texas (USA). Paleoceanography and Paleoclimatology 33, 1230-1249. of subtropical climate on land from the early Paleogene offer insights into how the Earth system responds to greenhouse climate conditions. Fluvial and floodplain deposits of the Tornillo Basin (Big Bend National Park, Texas, USA) preserve a record of environmental and climatic change of the Paleocene and the early Eocene. We report carbon, oxygen, and clumped isotopic compositions (δ13C, δ18O, and Δ47) of paleosol carbonate nodules from this basin. Mineralogical, geochemical, and thermal modeling evidence suggests that the measured isotopic values preserve primary environmental signals with a summer bias with the exception of data from two nodules reset by local igneous intrusions. The unaltered nodules record Δ47 temperatures of 25 ± 4 and 32 ± 2 °C for the Paleocene and early Eocene nodules, respectively, showing an increase in average summer temperatures of 7 ± 3 °C. Calculations of δ18O of soil water are ?2.8 ± 0.7‰ and ?0.8 ± 0.4‰ (standard mean ocean water) for the early‐mid‐Paleocene and late Paleocene‐early Eocene, showing an increase of 2.0 ± 0.9‰. The increase in temperature and δ18O values likely relates to a rise in atmospheric pCO2, although we cannot rule out that changes in paleosol texture and regional precipitation patterns also influence the record. Comparison with Δ47 estimates of summer temperature from the Green River and Bighorn Basins (WY) highlights that terrestrial surface temperatures are heterogeneous, and latitudinal temperature gradients on land remain undetermined. Previously published paleoclimate models predict summer temperatures that are 2 to 6 °C higher than our estimate; discrepancies between climate models and proxy data persist at lower latitudes. Kender, S., Ravelo, A.C., Worne, S., Swann, G.E.A., Leng, M.J., Asahi, H., Becker, J., Detlef, H., Aiello, I.W., Andreasen, D., Hall, I.R., 2018. Closure of the Bering Strait caused Mid-Pleistocene Transition cooling. Nature Communications 9, Article 5386. Mid-Pleistocene Transition (MPT) is characterised by cooling and lengthening glacial cycles from 600–1200 ka, thought to be driven by reductions in glacial CO2 in particular from ~900 ka onwards. Reduced high latitude upwelling, a process that retains CO2 within the deep ocean over glacials, could have aided drawdown but has so far not been constrained in either hemisphere over the MPT. Here, we find that reduced nutrient upwelling in the Bering Sea, and North Pacific Intermediate Water expansion, coincided with the MPT and became more persistent at ~900 ka. We propose reduced upwelling was controlled by expanding sea ice and North Pacific Intermediate Water formation, which may have been enhanced by closure of the Bering Strait. The regional extent of North Pacific Intermediate Water across the subarctic northwest Pacific would have contributed to lower atmospheric CO2 and global cooling during the MPT.Kerimov, V.Y., Mustaev, R.N., Osipov, A.V., 2018. Peculiarities of hydrocarbon generation at great depths in the crust. Doklady Earth Sciences 483, 1413-1417. article describes the peculiarities of hydrocarbon generation at great depths in the Earth’s crust. It is shown that all the conditions necessary for generation of oil and gas are kept at great depths in the crust in the zones of high pressures and temperatures. However, generation of hydrocarbons in such settings significantly differs from the processes of oil and gas formation at shallow depths. A complex system of mutual thermobaric factors and distribution of the oil and gas potential at great depths was revealed: the start of generation and the phase distribution of hydrocarbons in the section are largely affected by settling of abnormally high pore pressure, as well as by paleotemperatures that could differ considerably from the present-day ones depending on the age of deposits. It is shown that different thicknesses of catagenetic zones are related to the kinetic rate of oil and gas generation, which depends on the type of kerogen, the gradient of temperature change, pressure, lithology, and hydrogeological conditions of the host rocks, the sedimentation rate, and other factors.Kessler, A., Galaasen, E.V., Ninnemann, U.S., Tjiputra, J., 2018. Ocean carbon inventory under warmer climate conditions – the case of the Last Interglacial. Climate of the Past 14, 1961-1976. the Last Interglacial period (LIG), the transition from 125 to 115?ka provides a case study for assessing the response of the carbon system to different levels of high-latitude warmth. Elucidating the mechanisms responsible for interglacial changes in the ocean carbon inventory provides constraints on natural carbon sources and sinks and their climate sensitivity, which are essential for assessing potential future changes. However, the mechanisms leading to modifications of the ocean's carbon budget during this period remain poorly documented and not well understood. Using a state-of-the-art Earth system model, we analyze the changes in oceanic carbon dynamics by comparing two quasi-equilibrium states: the early, warm Eemian (125?ka) versus the cooler, late Eemian (115?ka). We find considerably reduced ocean dissolved inorganic carbon (DIC; ?314.1?PgC) storage in the warm climate state at 125?ka as compared to 115?ka, mainly attributed to changes in the biological pump and ocean DIC disequilibrium components. The biological pump is mainly driven by changes in interior ocean ventilation timescales, but the processes controlling the changes in ocean DIC disequilibrium remain difficult to assess and seem more regionally affected. While the Atlantic bottom-water disequilibrium is affected by the organization of sea-ice-induced southern-sourced water (SSW) and northern-sourced water (NSW), the upper-layer changes remain unexplained. Due to its large size, the Pacific accounts for the largest DIC loss, approximately 57?% of the global decrease. This is largely associated with better ventilation of the interior Pacific water mass. However, the largest simulated DIC differences per unit volume are found in the SSWs of the Atlantic. Our study shows that the deep-water geometry and ventilation in the South Atlantic are altered between the two climate states where warmer climatic conditions cause SSWs to retreat southward and NSWs to extent further south. This process is mainly responsible for the simulated DIC reduction by restricting the extent of DIC-rich SSW, thereby reducing the storage of biological remineralized carbon at depth.Kim, A.R., Kim, J.T., Cho, G.C., Lee, J.Y., 2018. Methane production from marine gas hydrate deposits in Korea: Thermal-hydraulic-mechanical simulation on production wellbore stability. Journal of Geophysical Research: Solid Earth 123, 9555-9569. During methane production induced by depressurization, significant mechanical responses of hydrate-bearing sediment (HBS) such as large volume contraction and subsidence can possibly be generated. Moreover, this phenomenon is further exacerbated by strength and stiffness reduction in the HBSs as hydrate dissociation advances. As a result, the highest compressive strength is concentrated in the vicinity of the production wellbore. Therefore, it is essential to address and evaluate the mechanical responses of HBSs and conduct a stability analysis of the production well during depressurization and hydrate dissociation to prevent the destruction of production facilities and consequent leakage of methane gas. In this study, a reservoir-scale thermal-hydraulic-mechanical coupled simulation using FLAC3D (Fast Lagrangian Analysis of Continua in 3 Dimensions) was conducted to evaluate the mechanical responses of HBSs and the stability of a wellbore during methane production by depressurization at the Ulleung Basin. The structural design and mechanical properties including the dimensions of wellbore components and interface properties related to the interaction behavior between the sediment and wellbore were considered in the three-dimensional model.Kim, J.-Y., Choi, J.W., 2019. Effect of molecular size of lignin on the formation of aromatic hydrocarbon during zeolite catalyzed pyrolysis. Fuel 240, 92-100. lignin fractions with different molecular size (Fraction 3?>?Fraction 2?>?Fraction 1) were prepared by sequential solvent fractionation of soda lignin. These were structurally investigated by several analytical techniques, such as GPC, 31P-NMR, 2D-HSQC-NMR, and TGA. They revealed that F1 was the smallest and the most thermally labile lignin fraction. Pyrolyzing lignin fractions at 600?°C with zeolite Y produced aromatic hydrocarbons (benzene, toluene, xylenes, and naphthalenes) with several types of monomeric phenols. Total pyrolysis product yields were the highest for F1, followed by F2 and F3. Additionally, aromatic hydrocarbons formation was inversely proportional to molecular size and abundantly produced with F1 (35.0?mg/g). They gradually increased in all fractions as the pyrolysis temperature increased (up to 800?°C). The transformation behaviors of functional groups were also investigated by using lignin model compounds. Lignin fractions prepared in this study had not only molecular size but also different phenolic hydroxyl (Phe-OH) content which would play a deleterious role in aromatic hydrocarbon formation during zeolite-catalyzed pyrolysis. Therefore, we prepared methylated lignin from each fraction (Methylated fraction 1, 2, and 3) and these were also pyrolyzed under same condition to investigate the independent effect of molecular size.Kim, T., Obata, H., Takeda, S., Wong, K.H., Mashio, A.S., Gamo, T., 2018. Organic complexation of zinc in a coastal hydrothermal area, Tachibana Bay, Nagasaki, Japan. Geochemical Journal 52, e29-e38. of trace metals (Mn, Fe, Cu, and Zn) and Zn chemical speciation were determined in Tachibana Bay to investigate the role of organic complexing ligands and sulfide on Zn in a coastal hydrothermal system. At the coastal area near Obama Hot Springs, dissolved sulfide was only detected in two bottom water samples in Stn. 6 (29.2 and 59.4 nM). At this coastal area, dissolved Mn and Fe concentrations were high and increased toward the bottom, whereas dissolved Cu and Zn concentrations generally decreased toward the bottom. The Zn complexing organic ligands (CL) and conditional stability constants (log K′ZnL,Zn2+) in Tachibana Bay ranged from 0.9 nM to 1.6 nM and from 9.9 to 10.3, respectively. The free sulfide concentration calculated from Zn chemical speciation was much lower than the measured dissolved sulfide concentrations. Although dissolved Zn mainly precipitate as sulfide in shallow hydrothermally active area, the organic complexation of Zn is important in the remaining dissolved Zn. Kondyli, A., Schrader, W., 2018. High-resolution GC/MS studies of a light crude oil fraction. Journal of Mass Spectrometry 54, 47-54. continuous development in analytical instrumentation has brought the newly developed Orbitrap based GC‐MS instrument into the forefront for the analysis of complex mixtures such as crude oil. Traditional instrumentation usually requires a choice to be made between mass resolving power or an efficient chromatographic separation which ideally enables the distinction of structural isomers which is not possible by mass spectrometry alone. Now, these features can be combined, thus enabling a deeper understanding of the constituents of volatile samples on a molecular level. Although electron ionization is the most popular ionization method employed in GC/MS analysis, the need for softer ionization methods has led to the utilization of atmospheric pressure ionization sources. The last arrival to this family is the atmospheric pressure photoionization (APPI), which was originally developed for (LC)MS. With a newly developed commercial GC‐APPI interface it is possible to extend the characterization of unknown compounds. Here, first results about the capabilities of the GC/MS instrument under high or low energy EI or APPI are reported on a volatile gas condensate. The use of different ionization energies helps matching the low abundant molecular ions to the structurally important fragment ions. A broad range of compounds from polar to medium polar were successfully detected and complementary information regarding the analyte was obtained.Kong, F.-x., Lin, X.-f., Sun, G.-d., Chen, J.-f., Guo, C.-m., Xie, Y.F., 2019. Enhanced organic removal for shale gas fracturing flowback water by electrocoagulation and simultaneous electro-peroxone process. Chemosphere 218, 252-258. and organics in shale gas fracturing flowback water (SGFFW) during shale gas extraction are of primary concerns. Coagulation combined with oxidation might be a promising process for SGFFW treatment. In this study, a novel electrocoagulation-peroxone (ECP) process was developed for SGFFW treatment by simultaneous coagulation and oxidation process with a Al plate as the anode and a carbon-PTFE gas diffusion electrode as the cathode, realizing the simultaneous processes of coagulation, H2O2 generation and activation by O3 at the cathode. Compared with electrocoagulation (EC) and peroxi-electrocoagulation (PEC), COD removal efficiency mainly followed the declining order of ECP, PEC and EC under the optimal current density of 50?mA?cm?2. The appearance of medium MW fraction (1919?Da) during ozonation and PEC but disappearance in ECP indicated that these intermediate products couldn't be degraded by ozonation and PEC but could be further oxidized and mineralized by the hydroxyl radical produced by the cathode in ECP, demonstrating the hydroxyl radical might be responsible for the significant enhancement of COD removal. The pseudo-first order kinetic model can well fit ozonation and EC process but not the PEC and ECP process due to the synthetic effect of coagulation and oxidation. However, the proposed mechanism based model can generally fit ECP satisfactorily. The average current efficiency for PEC was 35.4% and 12% higher than that of ozonation and EC, respectively. This study demonstrated the feasibility of establishing a high efficiency and space-saving electrochemical system with integrated anodic coagulation and cathodic electro-peroxone for SGFFW treatment.Kong, X.-Z., Deuber, C.A., Kittil?, A., Somogyvári, M., Mikutis, G., Bayer, P., Stark, W.J., Saar, M.O., 2018. Tomographic reservoir imaging with DNA-labeled silica nanotracers: The first field validation. Environmental Science & Technology 52, 13681-13689. study presents the first field validation of using DNA-labeled silica nanoparticles as tracers to image subsurface reservoirs by travel time based tomography. During a field campaign in Switzerland, we performed short-pulse tracer tests under a forced hydraulic head gradient to conduct a multisource–multireceiver tracer test and tomographic inversion, determining the two-dimensional hydraulic conductivity field between two vertical wells. Together with three traditional solute dye tracers, we injected spherical silica nanotracers, encoded with synthetic DNA molecules, which are protected by a silica layer against damage due to chemicals, microorganisms, and enzymes. Temporal moment analyses of the recorded tracer concentration breakthrough curves (BTCs) indicate higher mass recovery, less mean residence time, and smaller dispersion of the DNA-labeled nanotracers, compared to solute dye tracers. Importantly, travel time based tomography, using nanotracer BTCs, yields a satisfactory hydraulic conductivity tomogram, validated by the dye tracer results and previous field investigations. These advantages of DNA-labeled nanotracers, in comparison to traditional solute dye tracers, make them well-suited for tomographic reservoir characterizations in fields such as hydrogeology, petroleum engineering, and geothermal energy, particularly with respect to resolving preferential flow paths or the heterogeneity of contact surfaces or by enabling source zone characterizations of dense nonaqueous phase liquids.Kosintsev, P., Mitchell, K.J., Devièse, T., van der Plicht, J., Kuitems, M., Petrova, E., Tikhonov, A., Higham, T., Comeskey, D., Turney, C., Cooper, A., van Kolfschoten, T., Stuart, A.J., Lister, A.M., 2019. Evolution and extinction of the giant rhinoceros Elasmotherium sibiricum sheds light on late Quaternary megafaunal extinctions. Nature Ecology & Evolution 3, 31-38. extinction events requires an unbiased record of the chronology and ecology of victims and survivors. The rhinoceros Elasmotherium sibiricum, known as the ‘Siberian unicorn’, was believed to have gone extinct around 200,000?years ago—well before the late Quaternary megafaunal extinction event. However, no absolute dating, genetic analysis or quantitative ecological assessment of this species has been undertaken. Here, we show, by accelerator mass spectrometry radiocarbon dating of 23 individuals, including cross-validation by compound-specific analysis, that E. sibiricum survived in Eastern Europe and Central Asia until at least 39,000?years ago, corroborating a wave of megafaunal turnover before the Last Glacial Maximum in Eurasia, in addition to the better-known late-glacial event. Stable isotope data indicate a dry steppe niche for E. sibiricum and, together with morphology, a highly specialized diet that probably contributed to its extinction. We further demonstrate, with DNA sequencing data, a very deep phylogenetic split between the subfamilies Elasmotheriinae and Rhinocerotinae that includes all the living rhinoceroses, settling a debate based on fossil evidence and confirming that the two lineages had diverged by the Eocene. As the last surviving member of the Elasmotheriinae, the demise of the ‘Siberian unicorn’ marked the extinction of this subfamily.Kriss, D., Howe, E., Levinson, J., Rizzo, A., Carò, F., DeLeonardis, L., 2018. A material and technical study of Paracas painted ceramics. Antiquity 92, 1492-1510. Paracas culture of Late Formative Period south coastal Peru (c. 900–100 BC) is renowned for its elaborate and colourful ceramics—particularly those decorated using the post-fire painting technique. The materials and the methods used to achieve post-fire painting, however, remain elusive. To investigate the evolution of, and regional variation in, this technology, the authors deploy a range of techniques to analyse a sample of Paracas ceramics curated in museum collections. The results indicate diachronic and regional variations in the paint binders and colourants used by the Paracas potters, which correlate with changes in vessel form and iconography over time.Kuang, J., Tavakkoli, M., Yarbrough, J., Wang, J., Jain, S., Ashtekar, S., Abdallah, D.S., Punnapala, S., Vargas, F.M., 2018. Investigation of asphaltene deposition at high temperature and under dynamic conditions. Energy & Fuels 32, 12405-12415. deposition is one of the major flow assurance problems that can potentially deteriorate due to the current tendencies to produce from the deep-water environment or as a result of enhanced oil recovery operations based on miscible gas injection. The deposited asphaltenes in the wellbores and on the surface of the oilfield pipelines can impede the productivity of the wells significantly. The comprehensive understanding of the mechanisms and the techniques to control asphaltene deposition at high temperature and under dynamic conditions can help resolve this critical issue. Thus, it is imperative to develop reliable, straightforward, and inexpensive tools to investigate the asphaltene deposition tendency and the performance of asphaltene inhibitors in the laboratory. In this work, a new stainless steel packed bed column deposition system that was inspired by the work of Vilas B?as Fávero et al. was successfully developed. The packed bed design allows the feasibility of investigating a variety of factors affecting the deposition process under a wide range of temperature (20–300 °C) and gauge pressure (0–3000 psi). The impacts of operating temperature, type of precipitant, degree of asphaltene stability, and chemical additives on the deposition tendency of asphaltenes were investigated. It was found that the solubility of asphaltenes, the diffusion of precipitated asphaltenes, and the formation of aged asphaltene aggregates were competing factors controlling the deposition of asphaltenes under different operating temperatures. Additionally, asphaltenes precipitated by n-pentane induced more deposition than those destabilized by n-heptane. The liquid-like deposits collected from the experiment with n-butanol provided evidence that stronger ability to retain the softness reduced their tendency to build up aged asphaltene deposition on the metallic surface. Variation of the precipitant-to-oil ratio showed that the rate of asphaltene deposition increased linearly with the driving force toward asphaltene precipitation. Furthermore, a comparison between the capillary flow loop and the packed bed column on the assessment of asphaltene inhibitors was conducted. It was found that higher dosage of the asphaltene inhibitor seemed to delay the onset of deposition but did not further reduce the amount of deposition. With this packed bed column operating at high-pressure and high-temperature conditions, advanced simulation tools to predict asphaltene deposition under more realistic production conditions can be developed. Also, it can be used to assess asphaltene deposition inhibitors and solvents to prevent and remediate the asphaltene deposition problems.Kump, L., 2018. Climate change and marine mass extinction. Science 362, 1113-1114. emissions of carbon dioxide to the atmosphere, rapid global warming, and a decline in biodiversity—the storyline is modern, but the setting is ancient: The end of the Permian Period, some 252 million years ago. For the end-Permian, the result was catastrophic: the greatest loss of plant and animal life in Earth history (1). Understanding the details of how this mass extinction played out is thus crucial to its use as an analog for our future. On page 1130 of this issue, Penn et al. (2) add an intriguing clue: The extinction was most severe at high latitudes. Using a state-of-the-art climate model that was interpreted in terms of physiological stress, the authors further identify the killer as hypoxia, which was brought on by warm temperatures and ocean deoxygenation.A number of kill mechanisms for end-Permian extinction have been proposed, most triggered by the tremendous volcanic activity associated with the emplacement of the vast lava flows of the Siberian Traps, the eruption of which was coincident with the mass extinction (3). The Siberian Traps are estimated to have released tens of thousands of petagrams of carbon as carbon dioxide and methane (4), explaining the 10° to 15°C tropical warming revealed by oxygen isotope compositions of marine fossils (5). On land, unbearably hot temperatures and hypoxia likely were the main cause of mass extinction of plants and animals (6), although ultraviolet radiation exposure from a collapsed ozone shield contributed as well (7). Rapid warming also likely led to the loss of oxygen from the ocean's interior, extending up onto the continental shelves—a conclusion supported both by the widespread distribution of indicators for marine anoxia in sedimentary rocks (8) and by numerical modeling of the Permian ocean-atmosphere system (9).Once considered nonselective, mass extinctions are increasingly revealing patterns of differential impact across species, lifestyles, and geographic locations through their fossil records (10). A geographic pattern to Permian extinction, however, has remained elusive. Benefiting from the paleontological community's creation of the expansive Paleobiology Database (11), Penn et al. discovered a meridional gradient to extinction intensity: Groups of organisms that were restricted to higher latitudes prior to the extinction suffered higher proportions of extinction than those established at low latitudes. What was it about living at high latitudes that predisposed marine organisms to extinction?Penn et al. took an innovative approach to answering this question by coupling state-of-the-art computer simulations of end-Permian environmental change to a quantitative estimate of habitat loss for presumed Permian ecotypes. To establish the environmental (temperature and oxygen) tolerance of Permian ecotypes, Penn et al. used studies of modern organisms, grouped into ecotypes that they argue should be representative of the oxygen demands of Permian organisms. From these studies, a metabolic index was assigned to each ecotype, reflecting the critical balance between oxygen supply and demand. Model temperature and oxygen distributions before and during the end-Permian event were then used to map regions of the ocean where the metabolic index fell below the critical value (hypoxic threshold) at which oxygen supply (fundamentally related to the oxygen concentration of the water in which the organism lived, itself a function of ocean circulation, temperature, and rates of aerobic decomposition) could not support the physiological demands of daily life (feeding, reproduction, and defense). The authors found that ecotypes that favored high latitudes before the event preferentially suffered extinction because of their relatively high hypoxic threshold. In other words, as the waters in which they had lived warmed and lost oxygen, they had nowhere to go to avoid hypoxic stress. Tropical ecotypes were preadapted to low oxygen and higher temperatures, and thus were better able to survive global warming (see the figure).Paleoenvironmental reconstruction is challenging enough, but paleophysiological studies like that of Penn et al. are particularly vexing because the organisms whose traits one would like to understand and incorporate into a model are gone. Instead, studies of living organisms must be used. Penn et al. are aware of this limitation of their study and they go to great lengths to show that taxonomic biases, including a bias in the data on living organisms toward more active lifestyles relative to that which predominated in the Permian, have no substantial impact on their general conclusions. Other limitations of their study include both potential biases in the fossil record and required assumptions concerning the nutrient inventory of the Permian ocean and the oxygen concentration of the atmosphere at that time. Nutrients and atmospheric oxygen are important determinants of the oceanic pattern and severity of anoxia at a given climate state of the past, yet there are limited data on these factors. Another factor not considered in this study is the rate of climate change during the end-Permian event. If warming and oxygen loss were imposed slowly, perhaps high-latitude organisms could have adapted to warming and oxygen loss, whereas if these changes happened quickly, massive die-off was destined to occur. Existing geochronological constraints on the fossil record (3) suggest that the rates of these changes were rapid.Voluminous emissions of carbon dioxide to the atmosphere, rapid global warming, and a decline in biodiversity—the storyline is modern, but the setting is ancient: The end of the Permian Period, some 252 million years ago. For the end-Permian, the result was catastrophic: the greatest loss of plant and animal life in Earth history (1). Understanding the details of how this mass extinction played out is thus crucial to its use as an analog for our future. On page 1130 of this issue, Penn et al. (2) add an intriguing clue: The extinction was most severe at high latitudes. Using a state-of-the-art climate model that was interpreted in terms of physiological stress, the authors further identify the killer as hypoxia, which was brought on by warm temperatures and ocean deoxygenation.A number of kill mechanisms for end-Permian extinction have been proposed, most triggered by the tremendous volcanic activity associated with the emplacement of the vast lava flows of the Siberian Traps, the eruption of which was coincident with the mass extinction (3). The Siberian Traps are estimated to have released tens of thousands of petagrams of carbon as carbon dioxide and methane (4), explaining the 10° to 15°C tropical warming revealed by oxygen isotope compositions of marine fossils (5). On land, unbearably hot temperatures and hypoxia likely were the main cause of mass extinction of plants and animals (6), although ultraviolet radiation exposure from a collapsed ozone shield contributed as well (7). Rapid warming also likely led to the loss of oxygen from the ocean's interior, extending up onto the continental shelves—a conclusion supported both by the widespread distribution of indicators for marine anoxia in sedimentary rocks (8) and by numerical modeling of the Permian ocean-atmosphere system (9).Once considered nonselective, mass extinctions are increasingly revealing patterns of differential impact across species, lifestyles, and geographic locations through their fossil records (10). A geographic pattern to Permian extinction, however, has remained elusive. Benefiting from the paleontological community's creation of the expansive Paleobiology Database (11), Penn et al. discovered a meridional gradient to extinction intensity: Groups of organisms that were restricted to higher latitudes prior to the extinction suffered higher proportions of extinction than those established at low latitudes. What was it about living at high latitudes that predisposed marine organisms to extinction?Penn et al. took an innovative approach to answering this question by coupling state-of-the-art computer simulations of end-Permian environmental change to a quantitative estimate of habitat loss for presumed Permian ecotypes. To establish the environmental (temperature and oxygen) tolerance of Permian ecotypes, Penn et al. used studies of modern organisms, grouped into ecotypes that they argue should be representative of the oxygen demands of Permian organisms. From these studies, a metabolic index was assigned to each ecotype, reflecting the critical balance between oxygen supply and demand. Model temperature and oxygen distributions before and during the end-Permian event were then used to map regions of the ocean where the metabolic index fell below the critical value (hypoxic threshold) at which oxygen supply (fundamentally related to the oxygen concentration of the water in which the organism lived, itself a function of ocean circulation, temperature, and rates of aerobic decomposition) could not support the physiological demands of daily life (feeding, reproduction, and defense). The authors found that ecotypes that favored high latitudes before the event preferentially suffered extinction because of their relatively high hypoxic threshold. In other words, as the waters in which they had lived warmed and lost oxygen, they had nowhere to go to avoid hypoxic stress. Tropical ecotypes were preadapted to low oxygen and higher temperatures, and thus were better able to survive global warming (see the figure).Paleoenvironmental reconstruction is challenging enough, but paleophysiological studies like that of Penn et al. are particularly vexing because the organisms whose traits one would like to understand and incorporate into a model are gone. Instead, studies of living organisms must be used. Penn et al. are aware of this limitation of their study and they go to great lengths to show that taxonomic biases, including a bias in the data on living organisms toward more active lifestyles relative to that which predominated in the Permian, have no substantial impact on their general conclusions. Other limitations of their study include both potential biases in the fossil record and required assumptions concerning the nutrient inventory of the Permian ocean and the oxygen concentration of the atmosphere at that time. Nutrients and atmospheric oxygen are important determinants of the oceanic pattern and severity of anoxia at a given climate state of the past, yet there are limited data on these factors. Another factor not considered in this study is the rate of climate change during the end-Permian event. If warming and oxygen loss were imposed slowly, perhaps high-latitude organisms could have adapted to warming and oxygen loss, whereas if these changes happened quickly, massive die-off was destined to occur. Existing geochronological constraints on the fossil record (3) suggest that the rates of these changes were rapid.As our understanding of the drivers and consequences of end-Permian climate change and mass extinction improves, the lessons for the future become clear. Our modern-day “Siberian Trap” is fossil fuel burning, which is driving up atmospheric carbon dioxide to concentrations that Earth has not witnessed for millions of years. The planet is warming and the oceanic response of deoxygenation is already being detected in coastal zones and the open ocean (12). The Permian world may have been more susceptible to rapid climate change and its attendant environmental and biotic effects; carbon cycle–stabilizing calcareous plankton hadn't yet evolved (13), and the supercontinent of Pangaea's arid interiors and sluggish tectonics lowered the threshold for abrupt climate change (14). But even if it represents an extreme case, the lesson is clear: Continued or accelerated fossil fuel burning presents a risk that must be reversed or mitigated so that we can avoid a fate anything like that of the end-Permian.References1. D. Erwin, Extinction: How Life on Earth Nearly Ended 250 Million Years Ago (Princeton Univ. Press, 2015).2. J. Penn et al., Science 362, eaat1327 (2018).3. S. D. Burgess, S. A. Bowring, S.-Z. Shen, Proc. Natl. Acad. Sci. U.S.A. 111, 3316 (2014).4. H. Svensen et al., Nature 429, 542 (2004).5. Y. Sun et al., Science 338, 366 (2012).6. R. B. Huey, P. D. Ward, Science 308, 398 (2005).7. H. Visscher et al., Proc. Natl. Acad. Sci. U.S.A. 101, 12952 (2004).8. P. B. Wignall, R. J. Twitchett, Science 272, 1155 (1996).9. Y. Cui, L. R. Kump, Earth Sci. Rev. 149, 5 (2015).10. J. L. Payne, A. M. Bush, N. A. Heim, M. L. Knope, D. J. McCauley, Science 353, 1284 (2016).11. Scholar12. A. Oschlies, P. Brandt, L. Stramma, S. Schmidtko, Nat. Geosci. 11, 467 (2018).13. A. J. Ridgwell, M. J. Kennedy, K. Caldeira, Science 302, 859 (2003).14. L. R. Kump, Philos. Trans. R. Soc. A 376, 20170078 (2018).Kutterolf, S., Schindlbeck, J.C., Jegen, M., Freundt, A., Straub, S.M., 2019. Milankovitch frequencies in tephra records at volcanic arcs: The relation of kyr-scale cyclic variations in volcanism to global climate changes. Quaternary Science Reviews 204, 1-16. increase in volcanic activity after the last glacial maximum observed on Iceland has led to one of the most fascinating hypothesis in science in the last decades: that deglaciation may force volcanism. Consequently, tephrostratigraphic records of sufficient length that cover multiple glacial cycles have been used to test whether such relationships hold systematically through the Quaternary. Here we review such tephra records that have been linked with climate proxy records such as δ18O in marine sediments, which is a measure of sea-level change and which is thought to be orbitally forced, as it exhibits the characteristic Milankovitch periodicities of precession (～23 kyr), obliquity (～41 kyr) and eccentricity (～100 kyr). Statistical analyses have identified these periodicities also in long tephra records from different latitudes and geotectonic settings, as well as in compiled semi-global records. These studies detect Milankovitch periods in their tephra record, and also a phase shift relative to the δ18O record in such that periods of increased eruption frequencies coincide with the deglaciation period at the glacial/interglacial transition when ice and water loads on the lithosphere change most rapidly. However, there are also disparities in results and interpretations, which may be attributable to the different methods of analysis applied by the studies. We have therefore re-analyzed the four best-characterized tephra records by the same methods. We distinguish between analysis in the frequency domain, a novel approach, and analysis in the time domain, which has been used in previous studies. Analysis in the frequency domain identifies harmonic frequencies that arise from the binary nature of the tephra records and complicate the identification of primary frequencies. However, we show that all four records show spectral density peaks near the main Milankovitch periodicities of 41 and 100 kyr, and that they produce meaningful and significant statistical correlations with each other and the global δ18O record but not with random time series. Although the time-domain correlations with δ18O roughly confirm phase shifts implying peak volcanism during deglaciation, correlation coefficients arising from very noisy records are generally too low for precise constraints on the relative timing. These deficiencies presently hamper the recognition of the physical mechanisms through which global climate changes affect volcanism at both, high-latitude glaciated regions and low-latitude non-glaciated regions.Lam, P.J., Anderson, R.F., 2018. GEOTRACES: The marine biogeochemical cycle of trace elements and their isotopes. Elements 14, 377-378. is an international programme that was created to accelerate research on the global marine biogeochemical cycles of trace elements and their isotopes. Research encompasses four principle themes: 1) micronutrient elements (e.g. Fe, Co, Zn, Mn, Cu), which are essential for life; 2) tracers of processes that supply elements to the ocean; 3) anthropogenic contaminants (e.g. Hg, Pb); 4) geochemical proxies used in paleoceanography (e.g. trace-metal stable isotopes, naturally occurring radionuclides). The strategies adopted by GEOTRACES provide a template that can be adopted by other programmes in emerging fields of geochemistry.Lamolle, G., Musto, H., 2018. Why prokaryotes genomes lack genes with introns processed by spliceosomes? Journal of Molecular Evolution 86, 611-612. 1977, we thought that eukaryotic genes were like those of prokaryotes, that is, continuous sequences beginning with an initiation codon (ATG), followed by an open reading frame, always multiple of three bases (codons), and the message (mRNA) stopped when a stop codon (TAA, TAG or TGA) was reached. This paradigm, which historically seemed completely logical, changed dramatically when two groups, leaded by Sharp and Roberts (Berget et al. 1977; Chow et al. 1977), discovered that (at least some) eukaryotic protein coding genes were interrupted by non-coding sequences and eliminated from the mature (translated) mRNA before translation. Then, Gilbert (1978) coined the concept of exons (regions of the coding DNA that remained in the mRNA) and introns (the regions that are eliminated from the mature mRNA, and therefore are not present in the encoded proteins).Today, there are no doubts that this discovery was a revolution in genetics. It not only challenged our previous definition of what a “gene” is, but led to discoveries and concepts such as splicing (that is, how introns are eliminated and exons are put together to make the mature mRNA), alternative splicing (how different exons from the same “gene” can be combined to make different proteins), or to the great discovery that some RNAs, once transcribed, can eliminate by themselves introns, a mechanism known as autosplicing (see, for instance, Bass and Cech 1986; Cech and Bass 1986; Guerrier-Takada and Altman 1986). In turn, the discovery of autosplicing not only reinforced the idea of the “RNA world” (for a review see Lehman 2015) but eliminated, forever, the time unanimous idea that proteins were the only catalytic molecules.Therefore, the presence of introns in the majority of eukaryotic genes has challenged most of our concepts about genes, their regulation, their evolution, what is an enzyme… and last, but not least, why there are only probably fewer than 20,000 genes in the human genome while a “simple” organism like Escherichia coli has only around 4000. In other words, introns and how they are eliminated from the mature mRNAs has changed our concepts about molecular biology and evolution.But given what we have said in the above lines (which of course do not pretend to be a review about the subject), there is a problem that, in our opinion, deserves some attention. As known, prokaryotes display an enormous divergence and different metabolic routes and lifestyles and occupy all known environments. Then, why did they never develop introns processed by spliceosomes? In the next few lines we shall propose an explanation.Of course, the simplest one is that given that in prokaryotes transcription and translation are coupled, such a system should be a disadvantage from an evolutionary point of view. Furthermore, introns should be present. But there is no evidence that this was the case. Until now, nothing new. But there is a point that, in our opinion, seems very important.As is known, the modern spliceosome, in its simplest form, is a complex of not less than ten different proteins and several RNAs. Let us imagine that this complex, or one even simplest, evolved in a prokaryote. And for some reason, which might be due to combine different genes in new, longest ones, it became fixed (or the existence or primitive introns). It is difficult to imagine such scenario, but let assume that it indeed happened, for example, “putting together” different pieces of genes from the same operon. This could be an advantage, because different pieces from different mRNAs could combine to produce new proteins with different, but related, functions. There is no biological constraint that can prevent this. Even more, it should be a new way to create new genes and, as a consequence, new functions. We stress that this scenario is hard to imagine just because (as far as we know) it did not happen. But if there was an example, it should not be a big surprise.However in our opinion it did not happen because of another reason: one of the main forces in the evolution of prokaryotes is horizontal gene transfer (see, for example, Puigbò et al. 2010). As is known, for a gene (or group of genes) to be fixed several biochemical and evolutionary “steps” must be fulfilled, among them are: (a) to be transferred as a unit, (b) to carry (or to be integrated near) a promoter, (c) to not disturb the normal functions of the receptor, and (d) to confer a selective advantage.Very probably, a putative “primitive spliceosome” (PS) was not as complex as the modern one. But in any case, it should be a rather complex particle, composed by several proteins and RNAs. For it to be transferred successfully, several conditions are needed: (a) All the components of the PS should be transferred simultaneously, which is hard to imagine, because we need to postulate a large “PS operon”, which probably did not existed as such, and therefore, multiple events need to be invoked, which is very unlikely. (b) Introns cannot be possible in the receptor (otherwise, it should had a PS), and if they did not exist, a PS machinery very probably should be extremely harmful for the receptor and eliminated from the population, because of the non-adaptation of genes to the action of the xeno-PS. (c) Even if a and b were disregarded (which of course is more than unlikely), new genes acquired by HGT by the receptor of PS should be negatively affected by the PS acquired. Hence, new events of HGT should be eliminated by the receptor, eliminating, as a consequence, one the major forces in evolution.Hence, we conclude that in the same manner that HGT was one of the main factors that contributed to fix the universal genetic code; as postulated by Vetsigian et al. (2006), it could be a major force inhibiting the appearance (and fixation) of introns processed by spliceosomes among prokaryotes.Lassalle, G., Fabre, S., Credoz, A., Hédacq, R., Borderies, P., Bertoni, G., Erudel, T., Buffan-Dubau, E., Dubucq, D., Elger, A., 2019. Detection and discrimination of various oil-contaminated soils using vegetation reflectance. Science of The Total Environment 655, 1113-1124. use of hyperspectral spectroscopy for oil detection recently sparked a growing interest for risk assessment over vegetated areas. In a perspective of image applications, we conducted a greenhouse experiment on a brownfield-established species, Rubus fruticosus L. (bramble), to evaluate the potential of vegetation reflectance to detect and discriminate among various oil-contaminated soils. The species was grown for 32?days on four different soils with mixtures of petroleum hydrocarbons and heavy metals. Additional plants were grown on either uncontaminated control or water-deficient soils for comparison. Repeated reflectance measurements indicated modified spectral signatures under both oil and water-deficit exposure, from leaf to multi-plant scales. The amplitude of the response varied with mixture composition, exposure time, acquisition scale and spectrum region. Reflectance changes were linked to alterations in chlorophyll, carotenoid and water contents using vegetation indices. These indices were used to catch spectral similarities among acquisition scales and to discriminate among treatments using Kendall's coefficient of concordance (W) and regularized logistic regression. Of the 33 vegetation indices tested, 14 were concordant from leaf to multi-plant scales (W?>?0.75, p?<?0.05) and strongly related to leaf biochemistry (R2?>?0.7). The 14 indices allowed discriminating between each mixture and the control treatment with no or minor confusions (≤5%) at all acquisition scales, depending on exposure time. Some of the mixtures remained difficult to discriminate among them and from the water-deficit treatment. The approach was tested at the canopy scale under natural conditions and performed well for identifying bramble exposed to either one of the experimentally-tested mixtures (90% accuracy) or to uncontaminated soil (83% accuracy). This study provided better understanding of vegetation spectral response to oil mixtures and opens up promising perspectives for future applications.Lax, G., Eglit, Y., Eme, L., Bertrand, E.M., Roger, A.J., Simpson, A.G.B., 2018. Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes. Nature 564, 410–414. all eukaryote life forms have now been placed within one of five to eight supra-kingdom-level groups using molecular phylogenetics. The ‘phylum’ Hemimastigophora is probably the most distinctive morphologically defined lineage that still awaits such a phylogenetic assignment. First observed in the nineteenth century, hemimastigotes are free-living predatory protists with two rows of flagella and a unique cell architecture; to our knowledge, no molecular sequence data or cultures are currently available for this group. Here we report phylogenomic analyses based on high-coverage, cultivation-independent transcriptomics that place Hemimastigophora outside of all established eukaryote supergroups. They instead comprise an independent supra-kingdom-level lineage that most likely forms a sister clade to the ‘Diaphoretickes’ half of eukaryote diversity (that is, the ‘stramenopiles, alveolates and Rhizaria’ supergroup (Sar), Archaeplastida and Cryptista, as well as other major groups). The previous ranking of Hemimastigophora as a phylum understates the evolutionary distinctiveness of this group, which has considerable importance for investigations into the deep-level evolutionary history of eukaryotic life—ranging from understanding the origins of fundamental cell systems to placing the root of the tree. We have also established the first culture of a hemimastigote (Hemimastix kukwesjijk sp. nov.), which will facilitate future genomic and cell-biological investigations into eukaryote evolution and the last eukaryotic common ancestor.Lazzari, E., Polidoro, A.d.S., Onorevoli, B., Schena, T., Silva, A.N., Scapin, E., Jacques, R.A., Caram?o, E.B., 2019. Production of rice husk bio-oil and comprehensive characterization (qualitative and quantitative) by HPLC/PDA and GC?× GC/qMS. Renewable Energy 135, 554-565. of rice husk (RH) is an efficient process for the transformation of biomass to bio-oil (high-added value product). Bio-oil consists of two immiscible phases (organic and aqueous) both with potential for the generation of important chemicals for the industry. The aim of this study was to produce bio-oil by pyrolysis of RH and elucidate its chemical composition. Response surface methodology (RSM) was successfully used to determine the optimal pyrolysis conditions for the RH dry bio-oil production using central composite design (CCD). Temperature and flow rate significantly affected the bio-oil production and higher dry bio-oil yield was achieved at 650?°C and N2 flow rate of 100?mL?min?1 (predicted values of 16.9%). High performance liquid chromatography with photodiode array detection (HPLC/PDA) and comprehensive two-dimensional gas chromatography with quadrupole mass spectrometry detection (GC?×?GC/qMS) were used to provide a comprehensive characterization (qualitative and quantitative) of both phases from RH bio-oil. Through GC?×?GC/qMS analysis a total number of 98 compounds were found in organic phase; from these, 62 were quantified using a developed quantitative method by relative response factors (RRFs). Phenols and ketones (cyclic ketones) were majority in the organic phase, 8.21 and 5.90?wt%, respectively, and the benzofuran (1.37?wt%) corresponds to the major identified compound. HPLC/PDA analysis evidenced a high concentration of benzenediols and furfurals in the aqueous phase. Catechol was the major compound (2063?mg?L?1) followed by furfural (997?mg?L?1) and hydroquinone (899?mg?L?1). This is the first time that GC?×?GC/qMS and HPLC/PDA has been used to characterize (qualitatively and quantitatively) both phases from RH bio-oil which showed potential use as a source of high-added value chemicals.Lee, D.H., Kim, J.H., Lee, Y.M., Stadnitskaia, A., Jin, Y.K., Niemann, H., Kim, Y.G., Shin, K.H., 2018. Biogeochemical evidence of anaerobic methane oxidation on active submarine mud volcanoes on the continental slope of the Canadian Beaufort Sea. Biogeosciences 15, 7419-7433. this study, we report lipid biomarker patterns and phylogenetic identities of key microbial communities mediating anaerobic oxidation of methane (AOM) in active mud volcanoes (MVs) on the continental slope of the Canadian Beaufort Sea. The carbon isotopic compositions (δ13C) of sn-2- and sn-3-hydroxyarchaeol showed the highly 13C-depleted values (?114?‰ to ?82?‰) associated with a steep depletion in sulfate concentrations within 0.7?m of sediment depths. This suggested the presence of methanotrophic archaea involved in sulfate-dependent AOM, albeit in a small amount. The ratio of sn-2-hydroxyarchaeol to archaeol (>?1) and operational taxonomic units (OTUs) indicated that the anaerobic methanotrophic archaea (ANME) clades ANME-2c and ANME-3 were involved in AOM. Higher δ13C values of archaeol and biphytanes (BPs; ?55.2±10.0 ?‰ and ?39.3±13.0 ?‰, respectively) suggested that archaeal communities were also assimilating AOM-derived inorganic carbon. Furthermore, the distinct distribution patterns of methanotrophs in the three MVs appears to be associated with varying intensities of ascending gas fluids. Consequently, our results suggest that the niche diversification of active mud volcanoes has shaped distinct archaeal communities that play important roles in AOM in the Beaufort Sea.Lee, G., Sherer, N.A., Kim, N.H., Rajic, E., Kaur, D., Urriola, N., Martini, K.M., Xue, C., Goldenfeld, N., Kuhlman, T.E., 2018. Testing the retroelement invasion hypothesis for the emergence of the ancestral eukaryotic cell. Proceedings of the National Academy of Sciences 115, 12465-12470.: Phylogenetic evidence suggests that a factor in the emergence of the ancestral eukaryotic cell may have been selection pressure resulting from invasion and proliferation of retroelements. Here we experimentally determine the effects of a retroelement invasion on genetically simple host organisms, and we demonstrate theoretically that the observed effects are sufficient to explain their observed rarity in bacteria. We also show that nonhomologous end-joining (NHEJ), a mechanism of DNA repair found in all extant eukaryotes, but only some bacteria, significantly enhances the efficiency of retrotransposition and the effects of retroelements on the host. We hypothesize that the interplay of NHEJ and retroelements may have played a previously unappreciated role in the evolution of advanced life.Abstract: Phylogenetic evidence suggests that the invasion and proliferation of retroelements, selfish mobile genetic elements that copy and paste themselves within a host genome, was one of the early evolutionary events in the emergence of eukaryotes. Here we test the effects of this event by determining the pressures retroelements exert on simple genomes. We transferred two retroelements, human LINE-1 and the bacterial group II intron Ll.LtrB, into bacteria, and find that both are functional and detrimental to growth. We find, surprisingly, that retroelement lethality and proliferation are enhanced by the ability to perform eukaryotic-like nonhomologous end-joining (NHEJ) DNA repair. We show that the only stable evolutionary consequence in simple cells is maintenance of retroelements in low numbers, suggesting how retrotransposition rates and costs in early eukaryotes could have been constrained to allow proliferation. Our results suggest that the interplay between NHEJ and retroelements may have played a fundamental and previously unappreciated role in facilitating the proliferation of retroelements, elements of which became the ancestors of the spliceosome components in eukaryotes.Lee, L.S., Goh, K.M., Chan, C.S., Tan, G.Y.A., Yin, W.-F., Chong, C.S., Chan, K.-G., 2018. Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring. MicrobiologyOpen 7, Article e00615. ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y‐shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y‐shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.Lenz, O.K., Wilde, V., 2018. Changes in Eocene plant diversity and composition of vegetation: the lacustrine archive of Messel (Germany). Paleobiology 44, 709-735. on high-resolution palynological analysis of 680 samples from a core, short-term changes in plant diversity and floristic composition within the Paleogene greenhouse were detected in the lacustrine succession of a lower to middle Eocene maar lake at Messel (Federal State of Hesse, Germany). The microfloristic data show that taxonomic diversity increased rapidly within some decades during recolonization of a volcanically devastated area around the lake. With the establishment of a climax vegetation at the end of recolonization, the maximum in palynological diversity was reached within the crater area. During the following 640 Kyr the composition of the palynospectrum changed only gradually. However, different richness and evenness estimations show that alpha and gamma diversity decreased up to 35%, which can be related to the establishment of an equilibrium stage within the climax vegetation that led to the dominance of an assemblage of self-replacing species. Nevertheless, time-series analysis of alpha-diversity changes within the climax vegetation reveals that orbitally controlled climate change of Milankovitch and sub-Milankovitch order influenced the diversity of the vegetation, resulting in a rise of beta diversity. Based on the composition of the vegetation and comparison to modern analogues, our analysis proves that Eocene paratropical plant diversity increased during periods of slightly higher temperature and precipitation. Therefore, both composition and diversity of the vegetation was highly susceptible to minor-scale, short-term changes in climate, even during equable greenhouse conditions.Leonte, M., Wang, B., Socolofsky, S.A., Mau, S., Breier, J.A., Kessler, J.D., 2018. Using carbon isotope fractionation to constrain the extent of methane dissolution into the water column surrounding a natural hydrocarbon gas seep in the northern Gulf of Mexico. Geochemistry, Geophysics, Geosystems 19, 4459-4475. gas bubble seep located in the northern Gulf of Mexico was investigated over several days to determine whether changes in the stable carbon isotopic ratio of methane can be used as a tracer for methane dissolution through the water column. Gas bubble and water samples were collected at the seafloor and throughout the water column for isotopic ratio analysis of methane. Our results show that changes in methane isotopic ratios are consistent with laboratory experiments that measured the isotopic fractionation from methane dissolution. A Rayleigh isotope model was applied to the isotope data to determine the fraction of methane dissolved at each depth. On average, the fraction of methane dissolved surpasses 90% past an altitude of 400?m above the seafloor. Methane dissolution was also investigated using a modified version of the Texas A&M Oil spill (Outfall) Calculator (TAMOC) where changes in methane isotopic ratios could be calculated. The TAMOC model results show that dissolution depends on depth and bubble size, explaining the spread in measured isotopic ratios during our investigations. Both the Rayleigh and TAMOC models show that methane bubbles quickly dissolve following emission from the seafloor. Together, these results show that it is possible to use measurements of natural methane isotopes to constrain the extent of methane dissolution following seafloor emission.Leporini, M., Terenzi, A., Marchetti, B., Giacchetta, G., Corvaro, F., 2019. Experiences in numerical simulation of wax deposition in oil and multiphase pipelines: Theory versus reality. Journal of Petroleum Science and Engineering 174, 997-1008. deposition in pipelines transporting waxy oils and multiphase fluids is a significant flow assurance issue. The main problems caused by wax deposition include dramatic viscosity increase or complete “gelling” of crude oil. The present study shows a review of existing literature references concerning the problem of wax deposition, the main driving forces behind the phenomenon and the relative mathematical models developed. In addition, the application of the main mathematical models to real field data is presented in order to compare the numerical results with measured field values. In fact, wax deposition models, generally, are validated using experimental data, obtained from laboratory deposition tests; anyway, since the scale-up of the data to the real field cases is a problem, it is more advisable to compare models’ predictions to real field data. Four sets of field data have been simulated, two involving one phase wax deposition and two related to wax deposition from multiphase flow.Letsch, D., Large, S.J.E., Bernasconi, S.M., Klug, C., Blattmann, T.M., Winkler, W., von Quadt, A., 2019. Northwest Africa’s Ediacaran to early Cambrian fossil record, its oldest metazoans and age constraints for the basal Taroudant Group (Morocco). Precambrian Research 320, 438-453. Anti-Atlas area in southern Morocco preserves one of the most complete latest Ediacaran to Cambrian shallow-marine carbonate records in the world and serves as a standard for global chemostratigraphic δ13Ccarb curves. Contrary to the excellent chemostratigraphic coverage, neither metazoan fossils (only stromatolites and calcified algae) nor radiometric age constraints were hitherto available for the basal part of this carbonate record, the Tifnout Member of the Adoudou Formation of the Taroudant Group. We report an Ediacara-type fauna from shallow-marine sandstones from the basal Tabia Member and microfossils from dolostones from both the Tabia and the Tifnout members of the Adoudou Formation. The former are discoidal fossils and share many characteristics with the form genus Aspidella and exhibit a peculiar style of preservation, pointing towards an early diagenetic two-stage (carbonate followed by silica) cementation history, leading to good preservation of these supposedly once soft-bodied organisms. The dolostone-hosted microfossils are preserved as sparite-filled molds enclosed by a thin opaque envelope. Despite their small size, they resemble late Ediacaran calcifying metazoans such as Namacalathus and tubular small shelly fossils. Together, these fossils constitute the oldest known direct evidence for presumably metazoan life from Northwest Africa. We also report new time constraints for the Adoudou Formation and fossils enclosed therein based on combined LA-ICP-MS and high-precision CA-ID-TIMS U-Pb zircon geochronology of detrital and volcanic zircons. Together with new chemostratigraphic (δ13Ccarb) and literature data, these new age constraints suggest a late Ediacaran age (time span between ca. 561 and 542?Ma) for the discoidal Ediacara-type fossils from the basal Tabia Member, and a latest Ediacaran to earliest Cambrian (time span between ca. 544 and 540?Ma) and an early Cambrian age (time span between ca. 528 and 523?Ma) for the two microfossil faunas from the Tifnout Member.Levresse, G., Tritlla, J., Rosique, A.R., Cardellach, E., Rollion-Bard, C., Pironon, J., Sandoval, S.J., 2019. Hydrocarbons in silica: PVTX properties of fluids and the genesis of diamond quartz from Caravia-Berbes Fluorite district (Asturias, Spain). Marine and Petroleum Geology 102, 1-15. fluid history of “diamond” quartz crystals from Caravia-Berbes Fluorite district is intimately related with episodes of maturation and migration of hydrocarbons within the Asturian basin, probably linked to the structural activation of a Mesozoic rift system. These “diamond” quartz record the migration of hydrothermal silica-rich brines and associated hydrocarbons that recorded a temperature increase (outlined by fluid inclusion studies) from ～90 to ～140?°C. This gradient is also recorded by a change in the organic matter species trapped in quartz, from bitumen located in the inner quartz growth zones to liquid hydrocarbons trapped within the outer quartz overgrowths. Secondary ion mass spectrometer (SIMS) oxygen isotope microanalyses allowed to differentiate two δ18OH2O values corresponding to the oil-dominated zone (core) and the water-dominated zone (outer growth zone). The heavier δ18OH2O values in the water-dominated zone do not only record a higher temperature of formation, but also an increase in the δ18OH2O of the parental fluid. Isotopic compositions of diamond quartz suggest a heterogeneous source of surficial fluids and formation-waters expelled from claystones. Within the basin history, the diamond quartz precipitation took place during early Jurassic to Eocene subsidence periods. Pressure Temperature and composition (PTX) and δ18OH2O characteristics point out a probable relationship with Albian diagenetic events reported in Cantabrian and north Pyrenean basins.Li, C., Lin, M., Ji, L., Jiang, W., Cao, G., 2018. Rapid evaluation of the permeability of organic-rich shale using the 3D intermingled-fractal model. SPE Journal 23, 2175-2187, SPE-191358-PA. Shale possesses abundant micro/nanopores. Most micro/nanopores that exist in organic-rich shale are organic pores and mainly developed in organic matter. The pore distribution in matrix space significantly affects gas percolation and diffusion. Pore-size distribution possesses a self-similar, or fractal, property. The pore space and gas permeability of shale can be easily rebuilt and evaluated, respectively, using fractal theory. In this work, a 3D intermingled-fractal model (3D-IFM) is successfully built using scalable scanning-electron-microscopy (SEM) images of shale samples. 3D-IFM is made up of several components, including organic pores in organic matter and in pyrites, inorganic pores, slits, and matrix. An improved pore-connective-calculation method is also introduced to evaluate the apparent gas permeability of the shale model. The proposed 3D-IFM rapid-permeability-evaluation method for organic-rich shale is valid and useful and considers the main components of shale. This method can rapidly evaluate apparent gas permeability and simplify the apparent-gas-permeability-calculation process. Thus, the method provides a promising means of rapidly evaluating apparent gas permeability.Li, C., Zhu, L., Pan, D., Li, S., Xiao, H., Zhang, Z., Shen, X., Wang, Y., Long, M., 2019. Siderophore-mediated iron acquisition enhances resistance to oxidative and aromatic compound stress in Cupriavidus necator JMP134. Applied and Environmental Microbiology 85, e01938-18.: Many bacteria secrete siderophores to enhance iron uptake under iron-restricted conditions. In this study, we found that Cupriavidus necator JMP134, a well-known aromatic pollutant-degrading bacterium, produces an unknown carboxylate-type siderophore named cupriabactin to overcome iron limitation. Using genome mining, targeted mutagenesis, and biochemical analysis, we discovered an operon containing six open reading frames (cubA–F) in the C. necator JMP134 genome that encodes proteins required for the biosynthesis and uptake of cupriabactin. As the dominant siderophore of C. necator JMP134, cupriabactin promotes the growth of C. necator JMP134 under iron-limited conditions via enhanced ferric iron uptake. Furthermore, we demonstrated that the iron concentration-dependent expression of the cub operon is mediated by the ferric uptake regulator (Fur). Physiological analyses revealed that the cupriabactin-mediated iron acquisition system influences swimming motility, biofilm formation, and resistance to oxidative and aromatic compound stress in C. necator JMP134. In conclusion, we identified a carboxylate-type siderophore named cupriabactin, which plays important roles in iron scavenging, bacterial motility, biofilm formation, and stress resistance.Importance: Since siderophores have been widely exploited for agricultural, environmental, and medical applications, the identification and characterization of new siderophores from different habitats and organisms will have great beneficial applications. Here, we identified a novel siderophore-producing gene cluster in C. necator JMP134. This gene cluster produces a previously unknown carboxylate siderophore, cupriabactin. Physiological analyses revealed that the cupriabactin-mediated iron acquisition system influences swimming motility, biofilm formation, and oxidative stress resistance. Most notably, this system also plays important roles in increasing the resistance of C. necator JMP134 to stress caused by aromatic compounds, which provide a promising strategy to engineer more efficient approaches to degrade aromatic pollutants.Li, G.-X., Zhou, S.-Y.-D., Ren, H.-Y., Xue, X.-M., Xu, Y.-Y., Bao, P., 2018. Extracellular biomineralization of gold by Delftia tsuruhatensis GX-3 isolated from a heavy metal contaminated paddy soil. ACS Earth and Space Chemistry 2, 1294-1300. use of microorganisms in geochemical gold recycling was considered recently. To explore the feasibility of gold biomineralization in this study, bacteria GX-3 were isolated from a heavy metal contaminated paddy soil in Guangxi province, China. This sulfur-reducing bacteria, Delftia tsuruhatensis, can survive in toxic Au3+ solution. Alkaline conditions (pH 8.0) and 35 °C were optimal for GX-3 cultivation. Nanoparticle formation was promoted by the coexistence of Fe3+. Field-emission scanning electron microscopy and transmission electron microscopy (TEM) images of GX-3 showed the presence of spherical particles, ranging from 50 to 100 and 200 to 500 nm in diameter, respectively, that stuck together and distributed around the surface of the bacteria as well as outside the cell. These nanoparticles were identified as gold according to the TEM–energy dispersive X-ray spectroscopy analysis. Here, bacterial extracellular solute-binding protein and/or porin should account for the gold nanoparticle formation and the detoxification in aqueous system as it transports electrons to Au3+ for nanoparticle precipitation. The ubiquitous nature of bacteria in near-surface environments and the rapid precipitation of gold by the sulfur-reducing bacterium suggest that these bacteria could be responsible for the wide bioaccumulation of gold in natural systems.Li, H., Qin, Q., Shi, X., He, J., Xu, G., 2019. Modified metabolites mapping by liquid chromatography-high resolution mass spectrometry using full scan/all ion fragmentation/neutral loss acquisition. Journal of Chromatography A 1583, 80-87. metabolites play important roles in diagnostic monitoring, oxidative response and physiological regulation. Comprehensive analytical methods are greatly needed for improving the coverage of modified metabolites and studying their physiological function. Here, a novel nontargeted profiling method for mapping modified metabolites was developed by liquid chromatography-high resolution mass spectrometry with full scan/all ion fragmentation/neutral loss (FS/AIF/NL) data acquisition. Modified metabolites were unbiasedly defined with less false positive results by mixed standards verification. Thirteen types of modified metabolites in urine were analyzed at the same time, and 198 of 307 modified metabolites at positive mode and 166 of 366 modified metabolites at negative mode were putatively identified. The modified metabolites profiling method was applied for investigating the metabolic differences between the patients with breast cancer and health controls. As a result, many modified metabolites with glucuronidation, ribosylation and indole acetylation modification were significantly up-regulated in breast cancer and four modified metabolites including 7-methylguanosine, N4-acetylcytidine, dihyroxy-1H-indole glucuronide I and indole-3-acetic acid-O-glucuronide were identified as potential biomarkers for the diagnose of breast cancer.Li, J., Brown, E.T., Crowe, S.A., Katsev, S., 2018. Sediment geochemistry and contributions to carbon and nutrient cycling in a deep meromictic tropical lake: Lake Malawi (East Africa). Journal of Great Lakes Research 44, 1221-1234. biogeochemical functioning of large tropical lakes differs substantially from temperate lakes, yet remains poorly understood. We characterized the carbon, nitrogen, and phosphorus cycling in the water column and sediments of a deep meromictic tropical Lake Malawi (East Africa) by measuring geochemical distributions and compiling whole-lake geochemical budgets. Four locations (100 to 650 m water depth) were characterized. The results reveal that sediments contribute significantly to lake-wide biogeochemical budgets. Sedimentation rates have significantly increased in recent decades. While the export efficiency of organic matter from photic zone to deep sediments is low (14%), organic carbon is buried in the anoxic sediments with high efficiency (27–46%). Area-specific rates of carbon mineralization (4.1 mmol m? 2 d? 1) are similar to those in temperate well-oxygenated large lakes and marine sediments in similar water depths. Ammonium effluxes from sediments (0.44 mmol m? 2 d? 1) contribute 29% to the total nitrogen inputs into the water column, while sediment denitrification (0.035 mmol m? 2 d? 1) and burial of organic nitrogen (0.27 mmol m? 2 d? 1) remove 28% of total inputs in the lake. The recycling efficiency of phosphorus in anoxic sediments is high (73%). P effluxes average 0.037 mmol m? 2 d? 1, suggesting a large and previously unquantified contribution (42%) to water column P inputs. The results underscore the importance of sediments in the geochemical budgets of even large lakes and suggest trends in lacustrine carbon cycling that hold across a wide range of environments.Li, J., Liu, Y., Gao, Y., Cheng, B., Meng, F., Xu, H., 2018. Effects of microscopic pore structure heterogeneity on the distribution and morphology of remaining oil. Petroleum Exploration and Development 45, 1112-1122. experiments were performed using Micro-CT on four cores of different pore structures from Donghe sandstone reservoirs in the Tarim Basin. The water, oil and grains were accurately separated by the advanced image processing technology, the pore network model was established, and parameters such as the number of throats and the throat size distribution were calculated to characterize the microscopic heterogeneity of pore structure, the flow of oil phase during displacement, and the morphology and distribution of remaining oil after displacement. The cores with the same macroscopic porosity-permeability have great differences in microscopic heterogeneity of pore structure. Both macro porosity-permeability and micro heterogeneity of pore structure have an influence on the migration of oil phase and the morphology and distribution of remaining oil. When the heterogeneity is strong, the water phase will preferentially flow through the dominant paths and the remaining oil clusters will be formed in the small pores. The more the number of oil clusters (droplets) formed during displacement process, the smaller the average volume of cluster is, and the remaining oil is dominated by the cluster continuous phase with high saturation. The weaker the heterogeneity, the higher the pore sweep efficiency is, and the remaining oil clusters are mainly trapped in the form of non-continuous phase. The distribution and morphology of micro remaining oil are related to the absolute permeability, capillary number and micro-heterogeneity. So, the identification plate of microscopic residual oil continuity distribution established on this basis can describe the relationship between these three factors and distribution of remaining oil and identify the continuity of the remaining oil distribution accurately.Li, J., Lu, J.a., Kang, D., Ning, F., Lu, H., Kuang, Z., Wang, D., Liu, C., Hu, G., Wang, J., Liang, J., 2019. Lithological characteristics and hydrocarbon gas sources of gas hydrate-bearing sediments in the Shenhu area, South China Sea: Implications from the W01B and W02B sites. Marine Geology 408, 36-47. Shenhu area, located in the Pearl River Mouth Basin, South China Sea (SCS), is currently one of the most promising exploration areas for gas hydrates. In this study, the lithological characteristics, as well as the molecular and isotopic composition of hydrocarbon gases are systematically reported for the first time for core sediments obtained from two new drilling sites (referred to as W01B and W02B) in the southeast Shenhu area. Both gas hydrate-bearing and gas hydrate-free samples are characterized by fine-grained sediments (dominantly coarse silt and to a lesser extent, fine and medium silt) and similar median grain-sizes (5.94Φ to 6.49Φ), sorting (2.32 to 2.59), kurtosis (0.82 to 0.97), skewness (?0.12 to 0.03) and mineral compositions. Abundant authigenic pyrites (including euhedral and framboidal pyrites) also occur in these sediments. All these characteristics collectively indicate that the core sediments from the southeast Shenhu area formed in a relatively stable, low-energy and anoxic sedimentary environment. Nevertheless, the hydrate-bearing layers in this study are characterized by lower sand contents and more foraminifera than gas hydrate-free layers. The molecular and isotopic composition of hydrocarbon gases hosted by secondary minerals in the studied sediments indicates that they are of thermogenic origin. Combined with previously published data, we suggest that the abundant foraminifera within the sediments of the Shenhu area play a significant role in controlling the formation of gas hydrates by increasing the porosities of sediments, and that the thermogenic gas is an important source for the hydrocarbon gases of hydrates in the SCS.Li, J., Lu, S., Cai, J., Zhang, P., Xue, H., Zhao, X., 2018. Adsorbed and free oil in lacustrine nanoporous shale: A theoretical model and a case study. Energy & Fuels 32, 12247-12258. oil, rather than adsorbed oil, is potentially the most producible component of tight nanoporous shale reservoirs using existing technologies. To date, a variety of geochemical parameters, mainly related to the retention, migration, and expulsion of generated oil, have been developed to estimate the free oil in shale. However, there is still a lack of theoretical models accounting for the mechanism of oil accumulation in nanoporous shale, which would help evaluate adsorbed and free oil. In this paper, models were developed to estimate the amount of oil confined in nanoporous shale and that is mainly in adsorbed and free states to describe the characteristics of oil accumulation. The models were established for an adsorption saturation situation, and simultaneously considered the multilayer adsorption of an oil mixture and the microstructure of the shale pore system (including pore-throat-fracture). As a case study, adsorbed and free oil in lacustrine shales with different lithofacies, obtained from the Dongying sag of the southeastern Bohai Bay Basin of China, were evaluated using the models. Amounts of adsorbed and free oil obtained from the models agree well with those obtained from the previously established oil saturation index method. Microscopically, the amounts of adsorbed and free oil accumulating in slit-shaped pores were comprehensively impacted by the microstructure (size and volume) of pores and the state of the oil (densities and adsorption thickness). The models may be appropriate for single or mixed liquids confined in nanoporous shales, which develop a large number of slit-shaped pores (i.e., fracture) and few spherical pores with small dimension (such as < about 10 nm in this study), and can help target areas favorable for shale oil exploitation. This study provides significant insight into the microscopic mechanism of oil accumulation in nanoporous shale.Li, K., George, S.C., Cai, C., Gong, S., Sestak, S., Armand, S., Zhang, X., 2019. Fluid inclusion and stable isotopic studies of thermochemical sulfate reduction: Upper Permian and Lower Triassic gasfields, northeast Sichuan Basin, China. Geochimica et Cosmochimica Acta 246, 86-108. inclusions hosted in different stages of TSR-derived diagenetic minerals are expected to record compositions and isotopes of paleo-fluids at the time of trapping during different TSR extents. Here we report the first set of data on carbon isotopes of CH4 and CO2 and hydrogen isotopes of H2O trapped in fluid inclusions in TSR calcites. We find that the NE Sichuan sour dolostones have initially experienced oil- and wet gas-dominated TSR, as recorded in H2S-bearing oil inclusions with lower homogenization temperatures (Th) values (e.g., ≤137?°C) and the coexistence of C2+ hydrocarbon gas and H2S in fluid inclusions. The subsequent dry gas-dominated TSR occurred in higher reservoir temperatures (> about 161.5?°C) when most C2+ hydrocarbons were exhausted. The three-stage TSR resulted in CH4 δ13C values becoming progressively heavier from ?46.7‰ to ?29.6‰, H2O δ2H values shifting negatively from ?36.4‰ to ?67.8‰ and salinities decreasing to as low as 0.9?wt% NaCl. The dry gas-dominated TSR reaction seems to be the most efficient at water production, which, however, was limited by available reactive sulfate, and shows significant differences within the reef and shoal reservoirs along the platform margin, and the anhydrite-bearing reservoirs in the paleo-lagoon area. The TSR reaction within the porous shelf-margin reservoirs is capable of causing carbonate dissolution owing to high porosity and good connectivity of the micropore network and the resulting mass transport away from TSR sites. This resulted in CO2 δ13C positive shift from ?9.3‰ to +6.3‰, and a positive correlation of this parameter with Th. In contrast, in the tight anhydrite-bearing reservoirs, slow mass transport and quick saturation of calcium and dissolved CO2 in the pore waters is expected to precipitate TSR calcite near the anhydrite crystals, resulting in calcite crystals having more depleted δ13C values (?1.4‰ to ?18.9‰). This study shows that there are essential differences in the process and effects of TSR reaction due to geological differences in the settings of TSR sites.Li, M., Song, H., Algeo, T.J., Wignall, P.B., Dai, X., Woods, A.D., 2018. A dolomitization event at the oceanic chemocline during the Permian-Triassic transition. Geology 46, 1043-1046. Permian-Triassic boundary (PTB) crisis caused major short-term perturbations in ocean chemistry, as recorded by the precipitation of anachronistic carbonates. Here, we document for the first time a global dolomitization event during the Permian-Triassic transition based on Mg/(Mg + Ca) data from 22 sections with a global distribution representing shallow- to deep-marine environments. Ten of these sections show high Mg/(Mg + Ca) ratios bracketing the PTB, recording a short-term spike in dolomite formation. The dolomite consists mainly of micron-scale anhedral to subhedral crystals that are associated with abundant fossilized bacterial bodies and extracellular polymeric substances, suggesting that dolomite precipitation was induced by microbial metabolic activity. Sections showing a dolomite spike at the PTB are widely distributed geographically, but mostly encountered in mid-shelf to upper-slope settings. Because the dolomitization event coincided with a rapid expansion of oceanic anoxia and high rates of sulfate reduction, we hypothesize that it was triggered by enhanced microbial sulfate reduction within the oceanic chemocline.Li, W.-y., Wang, W., Mu, H., Li, W., Ye, C.-p., Feng, J., 2019. Analysis of light weight fractions of coal-based crude oil by gas chromatography combined with mass spectroscopy and flame ionization detection. Fuel 241, 392-401. realize the fast and accurate determination of coal-based crude oils, gas chromatography combined with mass spectrometry and flame ionization detection is employed to assist in qualitative and quantitative analysis. In addition, material balance is introduced into the analysis at the same time as a constraint. A new equation is deduced and verified, which can predict flame ionization detection relative response factors mainly by the molecular formula of the compounds. Meanwhile, the formula is integrated with the area normalization method. The standard compound addition method is employed to test the reliability as well, and the recovery experiments show that the designed system is simple, fast, accurate and effective. Finally, the analytical method system is applied to characterize the light weight fractions of coal-based crude oil, and the results show that approximately 70–80?wt% of the components can be balanced.Li, X.-G., Zhang, W.-J., Xiao, X., Jian, H.-H., Jiang, T., Tang, H.-Z., Qi, X.-Q., Wu, L.-F., 2018. Pressure-regulated gene expression and enzymatic activity of the two periplasmic nitrate reductases in the deep-sea bacterium Shewanella piezotolerans WP3. Frontiers in Microbiology 9, 3173. doi: 10.3389/fmicb.2018.03173. species are widely distributed in marine environments, from the shallow coasts to the deepest sea bottom. Most Shewanella species possess two isoforms of periplasmic nitrate reductases (NAP-α and NAP-β) and are able to generate energy through nitrate reduction. However, the contributions of the two NAP systems to bacterial deep-sea adaptation remain unclear. In this study, we found that the deep-sea denitrifier Shewanella piezotolerans WP3 was capable of performing nitrate respiration under high hydrostatic pressure (HHP) conditions. In the wild-type strain, NAP-β played a dominant role and was induced by both the substrate and an elevated pressure, whereas NAP-α was constitutively expressed at a relatively lower level. Genetic studies showed that each NAP system alone was sufficient to fully sustain nitrate-dependent growth and that both NAP systems exhibited substrate and pressure inducible expression patterns when the other set was absent. Biochemical assays further demonstrated that NAP-α had a higher tolerance to elevated pressure. Collectively, we report for the first time the distinct properties and contributions of the two NAP systems to nitrate reduction under different pressure conditions. The results will shed light on the mechanisms of bacterial HHP adaptation and nitrogen cycling in the deep-sea environment.Li, Y., Wang, Z., Pan, Z., Niu, X., Yu, Y., Meng, S., 2019. Pore structure and its fractal dimensions of transitional shale: A cross-section from east margin of the Ordos Basin, China. Fuel 241, 417-431. deposited in marine – continental transitional environments are well developed in the Upper Paleozoic in China with abundant gas resources. The pore structure and its controlling factors of the transitional shales may differ compared to marine and continental shales. Therefore, understanding them is of importance to the gas production behavior from transitional shales. In this work, a detailed experimental program combining rock composition analyses of X-ray diffraction (XRD), total organic carbon (TOC) analysis and Rock-Eval pyrolysis, and pore structure characterization by field emission scanning electron microscopy (FE-SEM), and low temperature nitrogen and carbon dioxide adsorption/desorption analysis were conducted on 16 continuously sampled shale cores from the east margin of the Ordos Basin, China. The results show that these transitional shales are rich in clay minerals with an average value of 58.2% (ranging from 47.7% to 85.0%), which is much higher than that in marine and lacustrine shales. The TOC contents are averaged at 1.3?wt%, and the shales are generally in mature to high mature stage (vitrinite reflectance (Ro) between 1.26% and 1.43%). Unlike the marine and lacustrine shales, the pores in the transitional shale are mainly occurred in clay minerals, and the organic matter pores are relatively poor and isolated. The pore shapes are dominantly intra-particle and inter-particle pores of slit-shaped as identified from the FE-SEM observations and the nitrogen adsorption/desorption curves. The meso (2–50?nm) and macro pore (generally of 50–300?nm) size distributions are unimodal to bimodal, and micropores (<2?nm) vary between 0.4 and 0.85?nm. The micropores and mesopores are abundant for all the shale samples, accounting for more than 90% of the total pore volume and specific surface area. The surface fractal dimension D1 and space structure fractal dimension D2 were obtained from the nitrogen adsorption data. The D1 values show no obvious relationship with clay minerals, TOC and quartz contents, which means that the pore surface irregularity is similar for all the samples. The D2 values show a positive relationship with clay mineral content, showing the clay minerals directly influencing the pore structure and pore diameters heterogeneity. For successful development of transitional shales gas, a further investigation on the clay mineral composition are necessary, with an emphasis on its influence on well drilling and hydraulic fracturing.Liang, Y., Ding, Y., Wang, P., Lu, G., Dang, Z., Shi, Z., 2019. Molecular characteristics, proton dissociation properties, and metal binding properties of soil organic matter: A theoretical study. Science of The Total Environment 656, 521-530. organic matter (SOM) is a key soil sorbent with a large number of reactive binding sites that may complex with metals, controlling their fate, transport, and bioavailability in soil. However, due to the complex and heterogeneous nature of SOM, it is not easy to probe its physical and chemical properties at the molecular level. In this study, an a priori method was developed to predict the molecular properties of SOM, which incorporated computational molecular modeling, SPARC Performs Automated Reasoning in Chemistry's (SPARC's) chemical reactivity models, and linear free energy relationships (LFERs). Specifically, the method uses SOM models simulated by molecular dynamics modeling based on the experimental elemental composition and functional group information of SOM. For the molecular characteristics, the molecular H/C and O/C ratios, molecular weight, aromatic index, and double bond equivalence of the SOM molecules were calculated. For the proton binding constants, the SPARC was used to calculate the microscopic pKa values of every binding sites of individual molecules of the SOM model. Based on the pKa values, the metal binding constants for individual monodentate binding sites were calculated using the Irving-Rossotti LFERs for different heavy metals. The results agreed reasonably with the default values used in the Windermere Humic Aqueous Model (WHAM) (VI) for the investigated metals. The theoretical SOM models, to some extent, represented the average properties of the investigated SOM. Overall, this study gives new quantitative and molecular insight into the structure and chemical properties of SOM. Detailed deprotonation and metal-SOM complexation information was gained for individual SOM binding sites. Such feasible and straightforward predictive scheme is useful to assess the risk of heavy metals in various aquatic and terrestrial environment involving heterogeneous natural organic matter.Lim, G.Q., Matin, M., John, K., 2019. Spatial and temporal characteristics of ambient atmospheric hydrocarbons in an active shale gas region in North Texas. Science of The Total Environment 656, 347-363. the past decade, significant development in shale gas extraction technologies has led to a massive increase in oil and gas production within the Barnett Shale region in North Texas. This region abuts a fast-growing Dallas-Fort Worth urban area with increasing air quality concerns. Air quality information for 2011–2015 from two urban and three non-urban monitoring sites within the Barnett Shale region were analyzed to identify the spatial and temporal trends of volatile organic compounds (VOC) concentrations. The non-urban sites had higher mean concentrations of total non-methane organic compounds (TNMOC) at 123.6 ppb-C than 77.06 ppb-C at the urban sites. Alkanes, which includes ethane, propane and n-butane, were the dominant VOC group at all five monitoring sites, with 88% of TNMOC at urban sites and 95% at the non-urban sites. Alkenes, alkynes and aromatics composition at urban sites accounted for 3.96%, 0.72% and 4.72% of TNMOC, and at the non-urban sites these were 1.55%, 0.43% and 1.94%, respectively. Seasonal variations were noted in the VOC profiles with high concentrations during the winter months and low during summer months. The alkane/TNMOC ratio also showed a similar seasonal pattern, with a median value of 0.8 at the urban sites and 0.9 at non-urban sites. Alkene/TNMOC ratios were highest during the summer months, while alkyne/TNMOC ratios were highest during spring and low in winter, due to the influence of localized urban emissions. Higher concentrations of isoprene were measured at one of the urban sites as a result of biogenic emissions from nearby urban forests. Spatial and temporal analysis of measured VOC concentrations at ambient air monitoring stations in North Texas revealed strong influence of source regions with high oil and gas activities in close proximity.Lin, H., Lian, J., Liu, Y., Xue, Y., Yan, S., Han, S., Wei, W., 2019. Comprehensive study of structure model, pyrolysis and liquefaction behaviour of Heidaigou lignite and its liquefied oil. Fuel 240, 84-91. integrated study involving structure model, pyrolysis and liquefaction behaviour of Heidaigou lignite (HL) and its liquefied oil was carried out to have an in-depth and comprehensive understanding of lignite and its direct liquefaction behaviour. Detailed information on HL was obtained using a molecular structural model constructed on the basis of ultimate analysis combined with solid-state 13C nuclear magnetic resonance (NMR), X-ray photoelectron spectrometer (XPS) and X-ray diffraction (XRD) studies. The HL model has few aromatic ring structures, which are composed of naphthalene, benzene, pyridine and pyrrole. The aromatic structures are linked by the aliphatic chains, and the carbon content in each chain is not less than three. Pyrolysis is the basis of liquefaction; as such, the pyrolysis behaviour of HL was investigated by TG/DTG. Results show that the maximum weight loss rate is about 425?°C. At below 500?°C, some Cal–Cal and Cal–Car broke, but Car–Car did not. The effects of time and temperature on the liquefaction behaviour of HL were investigated in a PARR-stirred high-pressure reactor. The liquefaction took a certain amount of time. With increasing temperature, the coal conversion rate and oil yield remained stable or increased slowly. The optimal time and temperature for liquefaction of HL are 40?min and 440?°C, and the maximum oil yield and HL conversion rate reach 56.68% and 89.79%, respectively. In addition, the optimal temperature of liquefaction (440?°C) is slightly higher than that of the maximum weight loss rate (425?°C). The composition of aromatics in the liquefied oil was determined using column chromatography and GC–MS. Most of the aromatics are tetraline, naphthalene and its derivatives and monocyclic benzenes. Agreements and consistency exist between the HL model, pyrolysis and aromatics in the liquefied oil.Lindgren, J., Sj?vall, P., Thiel, V., Zheng, W., Ito, S., Wakamatsu, K., Hauff, R., Kear, B.P., Engdahl, A., Alwmark, C., Eriksson, M.E., Jarenmark, M., Sachs, S., Ahlberg, P.E., Marone, F., Kuriyama, T., Gustafsson, O., Malmberg, P., Thomen, A., Rodríguez-Meizoso, I., Uvdal, P., Ojika, M., Schweitzer, M.H., 2018. Soft-tissue evidence for homeothermy and crypsis in a Jurassic ichthyosaur. Nature 564, 359–365. are extinct marine reptiles that display a notable external similarity to modern toothed whales. Here we show that this resemblance is more than skin deep. We apply a multidisciplinary experimental approach to characterize the cellular and molecular composition of integumental tissues in an exceptionally preserved specimen of the Early Jurassic ichthyosaur Stenopterygius. Our analyses recovered still-flexible remnants of the original scaleless skin, which comprises morphologically distinct epidermal and dermal layers. These are underlain by insulating blubber that would have augmented streamlining, buoyancy and homeothermy. Additionally, we identify endogenous proteinaceous and lipid constituents, together with keratinocytes and branched melanophores that contain eumelanin pigment. Distributional variation of melanophores across the body suggests countershading, possibly enhanced by physiological adjustments of colour to enable photoprotection, concealment and/or thermoregulation. Convergence of ichthyosaurs with extant marine amniotes thus extends to the ultrastructural and molecular levels, reflecting the omnipresent constraints of their shared adaptation to pelagic life.Liu, L.-Z., Nie, Z.-Y., Yang, Y., Pan, X., Xia, X., Zhou, Y.-H., Xia, J.-L., Zhang, L.-J., Zhen, X.-J., Yang, H.-Y., 2018. In situ characterization of change in superficial organic components of thermoacidophilic archaeon Acidianus manzaensis YN-25. Research in Microbiology 169, 590-597. the first time, synchrotron radiation (SR) -based carbon K-edge X-ray absorption near edge structure (XANES) spectroscopy in-situ characterization was conducted to evaluate the evolution of superficial (about 10 nm) organic components of extracellular polymeric substances (EPS) of thermoacidophilic archaeon Acidianus manzaensis YN-25 acclimated with different energy substrates (FeS2, CuFeS2, S0, FeSO4). The atomic force microscopy (AFM) morphology scanning showed that the strain acclimated with different energy substrates varied a lot in EPS amount. XANES results showed clear associations between the energy substrates and the changes in organic composition in terms of typical function groups (CO, CO and CN). The chalcopyrite- and pyrite-acclimated cells contained higher proportion of proteins but less proportion of polysaccharides than the S0-acclimated cells. The FeSO4-acclimated cells contained the highest proportion of proteins, while the S0-acclimated cells contained more lipids and polysaccharides. The results of linear-combination and peak fitting of the K-edge XANES for the extracellular superficial organic component C is consistent with the trend in comparison with the results of FTIR and spectrophotometric determination, but there are significant differences in the values. These differences are caused by the inconsistencies of measurement depth between XANES and the latter two characterization methods.Liu, L., Song, C., Tian, S., Zhang, Q., Cai, X., Liu, Y., Liu, Z., Wang, W., 2019. Structural characterization of sulfur-containing aromatic compounds in heavy oils by FT-ICR mass spectrometry with a narrow isolation window. Fuel 240, 40-48. structural information on sulfur-containing aromatic compounds in heavy oils is valuable for the petroleum industry. In this work, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with collision-induced dissociation (CID) was applied to study the structures of sulfur-containing aromatic compounds in vacuum gas oil (VGO) and vacuum residue (VR). The parent ions of the sulfur-containing model compounds and high-sulfur heavy oils were isolated by the quadrupole in FT-ICR MS with a narrow isolation window of 1?Da. For most of the sulfur-containing model compounds, removal of S atoms was achieved in the collision voltage range 10–30?V. On the other hand, the removal of S atoms from the sulfur-containing compounds in heavy oils was restrained by optimization of the collision voltage. The structures of VGO and VR were also studied by CID FT-ICR MS with a narrow isolation window at the optimal collision voltages. The results suggested that naphtheno-aromatic sulfur-containing compounds were components of heavy oils and that the structural diversity of the heavy oils increased significantly with an increase in molecular weight.Liu, M., Xie, R., Guo, J., Jin, G., 2018. Characterization of pore structures of tight sandstone reservoirs by multifractal analysis of the NMR T2 distribution. Energy & Fuels 32, 12218-12230. of the pore structure of tight sandstone reservoirs carries great significance for the evaluation of the reservoir storage and transport properties, “sweet spots” prediction, and reservoir development. In this paper, the pore structures of tight sandstone reservoirs are characterized on the basis of the multifractal analysis of nuclear magnetic resonance (NMR) transverse relaxation time (T2) distributions. For the T2 distribution models established using the mixed Gaussian distribution function, the characteristic parameters of the high probability measure areas (the right branch of the generalized fractal dimension spectrum and the left branch of the singularity spectrum) are closely related to the model parameters (weight coefficients and standard deviations of the short relaxation component). For the T2 distributions of the tight sandstone samples, the results of the relationships between the multifractal characteristic parameters of the T2 distributions and the petrophysical parameters of the samples indicate that the characteristic parameters of the high probability measure areas (αmax, α0 – αmax, Dmax, and D0 – Dmax) are closely related to the permeability, T2 geometric mean (T2lm), and T35 (the T2 value at 35% saturation in the normalized reverse accumulated T2 distribution curve) values, which can be used to quantitatively evaluate the pore structure heterogeneity of tight sandstones. These samples can be classified into four types on the basis of the shape of the T2 distribution and the petrophysical parameters. Substantial differences exist among the multifractal characteristics of the different sample types, and several parameters (αmax, α0 – αmax, Dmax, and D0 – Dmax) can be used to classify the sample types. The multifractal characteristic parameters are closely related to the clay mineral content. As the clay mineral content increases, the heterogeneity of the high probability measure areas of the T2 distribution increases. The results of the multifractal analysis of the NMR logging data further demonstrate the effectiveness of evaluating the pore structure of tight sandstone reservoirs based on the multifractal characteristics of the NMR T2 distribution.Liu, R., Du, D.-j., Pu, W.-f., Zhang, J., Fan, X.-b., 2018. Enhanced oil recovery potential of alkyl alcohol polyoxyethylene ether sulfonate surfactants in high-temperature and high-salinity reservoirs. Energy & Fuels 32, 12128-12140. flooding has been widely applied in high-temperature and high-salinity reservoirs. In this paper, the enhanced oil recovery potential of alkyl alcohol polyoxyethylene ether sulfonate (CEOS) was investigated in a combined study of surface activity, crude oil–water interfacial tension (IFT) reduction, emulsifying property, wettability improvement, and macroscopic oil displacement efficiency. The results illustrated that CEOS had high surface activity and IFT could be reduced to an ultralow level (10–3 mN/m) at high-temperature and high-salinity conditions. When salinity ranged from 15 × 104 to 22.5 × 104 mg/L and reservoir permeability was ～10 mD, linear CEOS solution could effectively displace crude oil for its favorable IFT reduction ability. Linear CEOS or CEOS with a benzene ring was optimized for their favorable IFT reduction ability or emulsifying ability when reservoir permeability was ～50 mD or non-homogeneous. A 0.5 pore volume surfactant flooding and subsequent water flooding could remarkably enhance oil recovery to 16.19–19.38%. All of the results indicated that CEOS has great potential for improving oil recovery in high-temperature and high-salinity oil reservoirs.Liu, S.-H., Zeng, Z.-T., Niu, Q.-Y., Xiao, R., Zeng, G.-M., Liu, Y., Cheng, M., Hu, K., Jiang, L.-H., Tan, X.-F., Tao, J.-J., 2019. Influence of immobilization on phenanthrene degradation by Bacillus sp. P1 in the presence of Cd(II). Science of The Total Environment 655, 1279-1287. microbes gradually lost advantages in practical applications of PAHs and heavy metals bioremediation. Therefore this study investigated the effect of immobilization on phenanthrene degradation by Bacillus sp. P1 in the presence of different Cd(II) concentrations. Condensed Bacillus sp. P1 was immobilized with polyvinyl alcohol and sodium alginate and PVA-SA-cell cryogel beads were prepared. The results indicated that the use of gel beads increased the number of adsorption sites thus accelerating phenanthrene degradation. In addition, changes in detoxification indices, including superoxide dismutase (SOD), catalase (CAT) and glutathione (GSH), were determined to elucidate the immobilization mechanisms related to cells protection from Cd(II) when degrading phenanthrene. By protecting the gel membrane, oxidative damage was minimized, while SOD activity increased from 55.72 to 81.33?U/mgprot as Cd(II) increased from 0 to 200?mg/L but later dropped to 44.29?U/mgprot as Cd(II) increased to 300?mg/L for the non-immobilized system. On the other hand, the SOD activity kept increasing from 52.23 to 473.35?U/mgprot for the immobilized system exposed to Cd(II) concentration between 0 and 300?mg/L. For CAT and GSH, immobilization only slowed down the depletion process without any change on the variation trends. The changes in surface properties and physiological responses of microbes caused the differences of immobilization effect on phenanthrene biodegradation in the presence of Cd(II), which is a novel finding.Liu, W., Yao, J., Tong, J., Qiao, Y., Chen, Y., 2019. Organic matter accumulation on the Dalong Formation (Upper Permian) in western Hubei, South China: Constraints from multiple geochemical proxies and pyrite morphology. Palaeogeography, Palaeoclimatology, Palaeoecology 514, 677-689. black shales in the Upper Permian Dalong Formation are considered excellent source rocks in the western Hubei Basin, South China. However, the mechanisms of organic matter (OM) accumulation remain controversial. Furthermore, the evolution of primary productivity and ocean hypoxia during the Late Permian in the western Hubei Basin is unclear. In this study, we discuss the paleoclimate, paleoceanography, paleoenvironment and the mechanisms of OM accumulation based on geochemical characteristics and pyrite framboid data from drillcore H 1 in Ensi, western Hubei Province. Black shales from the Dalong Formation have high total organic carbon (TOC) contents (2.8–9.3%), while the mudstone samples contain low TOC contents (0.48–1.96%). The weak chemical weathering indicates paleoclimate conditions were relatively cold during black shale deposition, whereas rapid warming occurred during gray mudstone deposition, which may be connected with the Late Permian Changhsingian global climate event. Redox indices, namely, V, U, and Mo concentrations, and the relationship of UEF and MoEF combined with pyrite framboid data suggest that an anoxic to euxinic environment predominated during black shale accumulation. In contrast, oxic to hypoxic marine conditions pervaded the western Hubei Basin during the deposition of mudstone. The primary productivity indices (Cu/Al and Nixs) suggest that high paleoproductivity occurred in the Late Permian, especially during periods of transgression. However, declining primary productivity with enhanced intensity of chemical weathering may indicate that biological extinction was associated with a rapid increase in temperature during the Late Permian. Negative/positive relationships between the TOC contents and Baxs and Nixs values demonstrate that sulfate was consumed by a higher OM input and OM accumulation was mainly controlled by high primary productivity. The study implies that ocean hypoxia and high primary productivity played important roles in OM accumulation. The depositional model shows that high primary productivity possibly resulted from weathering of volcanic ash from land during transgressions and that intense degradation of OM resulted in an euxinic environment.Liu, X., Wen, Z., Wang, Z., Song, C., He, Z., 2018. Structural characteristics and main controlling factors on petroleum accumulation in Zagros Basin, Middle East. Journal of Natural Gas Geoscience. Basin is one of the essential basins in the Middle East with the giant oil and gas reserves. It is indicated by regional tectonic and sedimentary evolution, basin structural division, petroleum distribution characteristics and main controlling factors of petroleum accumulation. It has experienced four significant phases which are early Paleozoic intra-Cratonic pull apart basin and platform margin basin, late Paleozoic platform margin basin, Mesozoic passive continental margin basin, and Cenozoic foreland basin. The Zagros Mountain Front Fault and High Zagros Fault divided the basin into foredeep zone, simply folded zone, and Zagros thrust fault zone from southwest to northeast. The oil fields are mainly located in the foredeep zone, while the gas fields are mostly in the simply folded zone and few fields are in the Zagros thrust fault zone. The Lower Cretaceous Kazhdumi Formation mudstone is the main source rock for the Mesozoic, and Cenozoic reservoirs and the Silurian Gahkum Formation mudstone is the main source rock for the Paleozoic reservoirs. The Cenozoic carbonate is main reservoir followed by the Cretaceous Sarvak and upper Permian Dalan carbonate. The evaporite and mudstone are the main seal in the foredeep zone, while the mudstone in the simple anticline zone. The anticline structure and the seal type is the main controlling factor for the petroleum accumulation.Liu, Z.L., Rios-Carvajal, T., Andersson, M.P., Ceccato, M., Stipp, S.L.S., Hassenkam, T., 2018. Insights into the pore-scale mechanism for the low-salinity effect: Implications for enhanced oil recovery. Energy & Fuels 32, 12081-12090. properties and behavior of the interface between mineral surfaces, adsorbed organic compounds, and water are important for oil recovery. Low-salinity (LS) water flooding releases more oil from sandstone reservoirs than conventional flooding with seawater or formation water. However, the role of strongly adsorbed organic material, as an anchor for oil molecules, is not yet completely understood. Here, we mimic reservoir pore surfaces using graphene oxide sheets deposited on flat silicon wafers. The LS response was quantified using atomic force microscopy (AFM) in chemical force mapping mode to directly measure the adhesion force. AFM tips were functionalized to serve as models for hydrophobic and polar oil molecules, i.e., with alkyl, ?CH3, and carboxyl, ?COO(H). Adhesion force, measured with ?CH3 tips, was 18% lower in LS (～1500 ppm) than high-salinity (HS, ～35?600 ppm) solutions, while for ?COO(H) tips, adhesion force was 13% lower in LS than HS solutions. The Dejarguin–Landau–Verwey–Overbeek theory predicts that the difference in response to the salinity-dependent force with the ?CH3 tips results from electric double layer (EDL) repulsion. The response to ?COO(H) tips can be explained by combined EDL repulsion and cation bridging, which is consistent with density functional theory calculations. The absolute adhesion and the level of response agree with observations on sand grains from oil reservoirs, where other studies have demonstrated strongly bound organic compounds. Important implications of our study are that (i) oxidized graphene provides a convincing model for reservoir pore surfaces that is robust and reproducible and can be used for systematic testing for developing more effective enhanced oil recovery strategies and (ii) the new fundamental understanding about pore surfaces can also be applied over a range of disciplines, including improved remediation strategies for contaminated soil and groundwater.Livsey, C.M., Babila, T.L., Robinson, M.M., Bralower, T.J., 2019. The planktonic foraminiferal response to the Paleocene-Eocene thermal maximum on the Atlantic coastal plain. Marine Micropaleontology 146, 39-50. foraminiferal assemblages in two cores from Maryland and New Jersey show evidence for significant changes in surface ocean habitats on the continental shelf during the Paleocene-Eocene Thermal Maximum (PETM). At both sites, significant assemblage shifts occur immediately before the onset of the event. These changes include the appearance of abundant triserial/biserial species as well as rare excursion taxa, which are limited to the interval of the carbon isotope excursion at deep-sea sites. The assemblage shifts signal the development of new habitats immediately prior to the onset of the PETM, likely involving warming, surface ocean acidification, increased stratification and oligotrophy. A sharp increase in diversity at the onset of the event is interpreted as a further increase in stratification and warming, as well as increased water depth and more eutrophic conditions. Finally, we observe variant morphologies of several planktonic foraminifera, which may also signal the response of the assemblage to environmental perturbation.Loh, A., Yim, U.H., Ha, S.Y., An, J.G., Shankar, R., 2019. Fate of residual oils during remediation activities after the Wu Yi San oil spill. Marine Pollution Bulletin 138, 328-332. this study, the fate of residual oils was investigated during remediation activities for a year after the Wu Yi San oil spill. Microscope observations showed that relatively large amounts of oil-suspended particulate matter aggregate (OSA) were formed. Negatively buoyant OSA was the dominant form (>95%), followed by neutrally (~5%) and positively buoyant (<1%) forms. To elucidate the dominance of negative buoyancy OSA, physicochemical properties of the mineral and residual oils were identified. Chemical analysis showed that the weathering percentage of residual oils was 43.7?±?2.59%, which was the driving factor for sedimentation of OSA. As the density of oil increased with weathering stages, the density of OSA also increased simultaneously. These results showed that, during mechanical remediation activities, resurfaced residual oils can form negative buoyancy OSA which tends to sink and transfers oil contaminants from intertidal to benthic environments.Lohan, M.C., Tagliabue, A., 2018. Oceanic micronutrients: Trace metals that are essential for marine life. Elements 14, 385-390. metals are essential for life in the oceans but are present in extremely low concentrations. The availability of trace elements in surface waters frequently regulates the growth of microscopic marine plants called phytoplankton. As phytoplankton are responsible for taking up atmospheric carbon dioxide and exporting this to the deep ocean, trace elements are key components regulating the carbon cycle. New observations of the distribution of trace metals across all ocean basins from the GEOTRACES program have revealed a fascinating story of how the combination of trace metals interact with the ocean to regulate biological activity in new and surprising ways.López-Rodríguez, C., De Lange, G.J., Comas, M., Martínez-Ruiz, F., Nieto, F., Sapart, C.J., Mogollón, J.M., 2019. Recent, deep-sourced methane/mud discharge at the most active mud volcano in the western Mediterranean. Marine Geology 408, 1-17. mobilized, overpressurized shales and shale-diapirism. This appears to control mud expulsion at Carmen mud volcano, a cone-shaped structure 65?m high and 1?km in basal diameter.The presence of gas-rich mud breccia, living chemosynthetic fauna, the absence of hemipelagic draping and the abrupt transition that occurs between high dissolved sulfate in the uppermost interval and low sulfate together with high methane concentrations in the lowermost sediment interval all point to a recent expulsion of mud breccia at the summit of Carmen MV.For the lowermost interval, the depletion of major elements (i.e., Ca2+ and Mg2+) and the enrichment of trace species (i.e., Li and B) in the pore water all indicate a deep fluid source. The δ18Opw (5.7‰ VSMOW) and δDpw (?10‰ VSMOW) of pore water in the lowermost interval correspond with smectite dehydration as the main pore-water freshening mechanism. Water-formation temperatures calculated with empirical geo-thermometers (K-Na, K-Mg; δ18Opw, δDpw, and dissolved B) reveal that fluids were generated at temperatures of ~140?±?20?°C. Taking a regional geothermal gradient </topics/earth-and-planetary-sciences/geothermal-gradient> for the WAB of 25–27?°C/km, this points to a fluid source from ~5?±?1?km sediment depth. This is not only consistent with the depth of overpressurized shales and megabreccia of Lower to Middle Miocene age, but it also fits nicely with the Upper/Middle-Miocene seawater value for the porewater 87Sr/86Sr derived from dissolving carbonates. The stable carbon and hydrogen isotopic composition of methane (δ13Cmethane?~??59.4‰ VPDB and δDmethane ?184‰ VSMOW) for the deepest samples of summit-core GP05PC is consistent with the mentioned deep origin.Mud breccia expulsion of overpressurized deep sedimentary units would be accompanied by rigorous degassing, leading to rapid, ‘instantaneous’ replacement of pore fluid by bottom water in the upper sediments. The absence of oxidized sediment draping, the seawater-like pore-water composition in the uppermost part of the mud breccia interval, and the abrupt methane to sulfate transition all provide evidence for a very recent mud expulsion.The distinctively kink-shaped pore-water Cl? profile in core GP05PC has been used in a numerical transport-reaction model to derive the timing for this event. This eruptive event appears to have taken place very recently, namely 12?±?5?yrs prior to the 2012 coring, thus in the year 2000?CE.Lukoczki, G., Haas, J., Gregg, J.M., Machel, H.G., Kele, S., John, C.M., 2019. Multi-phase dolomitization and recrystallization of Middle Triassic shallow marine–peritidal carbonates from the Mecsek Mts. (SW Hungary), as inferred from petrography, carbon, oxygen, strontium and clumped isotope data. Marine and Petroleum Geology 101, 440-458. marine to peritidal carbonates of the Triassic Csukma Formation in the Mecsek Mts. of SW Hungary are made up of dolomites, limestones and dolomitic limestones that show evidence of a complex diagenetic history. Integration of petrographic, conventional stable oxygen and carbon isotope, clumped isotope, and strontium isotope data with the paleogeography, paleoclimate, and burial history of the region revealed four major diagenetic stages. Stage 1: The peritidal carbonates were dolomitized penecontemporaneously during the Middle Triassic by refluxing evaporatively concentrated brines. Stage 2: Increasing burial during the Late Triassic–Jurassic resulted in recrystallization of the Kán Dolomite Member in an intermediate burial setting. Stage 3: During the Early Cretaceous seawater was drawn down and circulated through rift-related faults, causing renewed recrystallization of the Kán Dolomite Member as well as dolomitization of the Kozár Limestone Member and the underlying limestones in a deep burial setting, but only in the vicinity of the faults. Stage 4: During the Late Cretaceous and Cenozoic thrusting resulted in tectonic expulsion of basinal fluids and precipitation of multiple saddle dolomite cement phases near the faults. The results of this study imply that the clumped isotope method integrated with other geochemical data can successfully be applied to identify the nature and potential sources of extra-formational diagenetic fluids responsible for dolomitization and recrystallization. This study provides conclusive evidence for multi-phase dolomitization and dolomite recrystallization over several millions of years (Middle Triassic through Early Cretaceous) and several thousands of meters of burial in the Csukma Formation in SW Hungary. Furthermore, this study is the first to identify fault-controlled dolomitization by circulating Cretaceous seawater within Triassic carbonates of central Europe, further supporting the viability of the interpretation of dolomitization by seawater initially drawn down and then geothermally circulated through faults in extensional basins.Lupien, R.L., Russell, J.M., Feibel, C., Beck, C., Cast?neda, I., Deino, A., Cohen, A.S., 2018. Reply to comments by Nutz and Schuster (2018) on “A leaf wax biomarker record of early Pleistocene hydroclimate from West Turkana, Kenya”. Quaternary Science Reviews 201, 508-510. to Comments on: “A leaf wax biomarker record of early Pleistocene hydroclimate from West Turkana, Kenya” by Lupien et al. [Quat. Sci. Rev. 186 (2018), 225–235]. Quaternary Science Reviews, Volume 201, 1 December 2018, Pages 505-507Original Article: R.L. Lupien, J.M. Russell, C. Feibel, C. Beck, I. Casta?eda, A. Deino, A.S. Cohen. A leaf wax biomarker record of early Pleistocene hydroclimate from West Turkana, Kenya. Quaternary Science Reviews, Volume 186, 15 April 2018, Pages 225-235We thank Nutz and Schuster (2018) for their constructive comments on our publication, Lupien et al. (2018), and for pointing out their 2017 paper, Orbitally-driven evolution of Lake Turkana (Turkana Depression, Kenya, EARS) between 1.95 and 1.72 Ma: A sequence stratigraphy perspective (Nutz et al., 2017), of which we were not aware at the time of our publication. We fully agree with the authors that comparisons between outcrops and drill cores provide valuable insight into paleohydroclimatic conditions and paleoenvironments. We note that the two records exhibit substantial agreement (Nutz et al., 2017), but also disagreement, and at times Nutz and Schuster (2018) misinterpret our interpretations of paleoclimate in the Turkana Basin.Nutz et al. (2017) present sedimentary facies and sequence stratigraphic reconstructions of Turkana water levels between 1.95 and 1.72 Ma from outcrops. Much of their record overlaps with our paleoclimate reconstruction based upon δDwax measurements from a drill core from West Turkana (WTK13) spanning ～1.87 to ～1.4 Ma. In comparing these records one must remember that each proxy senses different aspects of hydroclimate: δDwax is generally interpreted to reflect variations in precipitation amount in East Africa (Caley et al., 2018; Feakins, 2013; Levin et al., 2009; Liddy et al., 2016; Schefu? et al., 2005, 2011; Tierney & deMenocal, 2013, Tierney et al., 2017; Tierney et al., 2008), and records a variety of atmospheric processes associated with rainfall and the water cycle (Dansgaard, 1964; Rozanski et al., 1993; Tierney et al., 2008; Vuille et al., 2005b). Lake levels are also sensitive to precipitation amount, and can additionally reflect tectonically-driven changes in basin configuration, subsidence, sill depth, and other processes that can modify the relationship between lake levels and rainfall. Modern observations indicate that changes in the δD of precipitation, which is the principal control on δDwax, exhibit a fairly linear relationship with precipitation amount over relatively large precipitation gradients (Rozanski et al., 1993; Vuille et al., 2005a), whereas lake levels and sedimentary facies often do not (Lepre, 2014). For instance, lake levels cannot rise above basin sill depth despite increasing precipitation amount. Additionally, lake level can be controlled by upstream (and downstream) complexities in hydrology (i.e. drainage diversions), which may or may not be in synchrony with local precipitation (e.g. Felton et al., 2007). Because Lake Lorenyang, which occupied the Turkana Basin from ～2.1 to 1.4 Ma, was fundamentally different from modern Lake Turkana (Feibel, 2011), it is not an exact analog for characteristics such as bathymetry, hydrology, or sedimentary facies.Despite these differences in the potential influences on our records, both exhibit a strong signal of orbital precession (～21 kyr periodicity). We observe strong precession-scale variability throughout our ～500-kyr record; the sediments analyzed by Nutz et al. (2017) record precession-scale lake level changes between 1.87 and 1.76 Ma. Nutz et al. (2017) hypothesize precession-scale lake level variations existed at other time intervals, which they term “non-observed second-order periodicity”; our record strongly supports this hypothesis.In other aspects, the two records disagree and the controls on each must be interrogated to provide further insight into Turkana's Pleistocene history. Nutz et al. (2017, 2018) infer that the amplitude of precessionally-forced early Pleistocene lake level variations were less than 25?m, much lower than the amplitude of Holocene lake level change (～100?m; Garcin et al., 2012), and conclude that the early Pleistocene is not a time period of marked climate variability. In contrast, δDwax variations during the early Pleistocene equal, and at times exceed, those experienced during the termination of the African Humid Period (Morrissey, 2014). Our estimates of the amplitude of early Pleistocene hydroclimate change are based on this comparison, not the results of spectral analyses as implied by Nutz and Schuster (2018). It is possible that changes in atmospheric circulation or other factors could have changed the sensitivity of δDwax to changes in precipitation. However, we are not aware of any mechanism that might cause such a shift, and Nutz and Schuster (2018) suggest no mechanism in their comment. Moreover, although Nutz et al. (2017) do not discuss the climate dynamical implications of their work, reduced amplitudes of lake level variations would imply the presence of processes or forcings that operated during the early Pleistocene that counteracted insolation forcing by orbital precession. It is not clear whether such forcings or processes exist. In contrast, our δDwax record suggests changes in the amplitude of East African rainfall tracked changes in the amplitude of precessional insolation forcing through time, in keeping with other records from East Africa (Rose et al., 2016; Rossignol-Strick, 1985). Thus, we suggest that changes in basin physiography between the early Pleistocene, when Lake Lorenyang flowed out to the Indian Ocean, and the closed-basin configuration of Lake Turkana today, altered the relationship between changes in precipitation and lake level changes recorded by the sediments analyzed by Nutz et al. (2017).Nutz et al. (2017) also document a ～200-kyr trend in sedimentary facies that they attribute to a long-term lake level transgression and regression, forced by the 400-kyr eccentricity cycle. In contrast, our δDwax record suggests no long-term shift in mean precipitation over the length of our ～500 kyr record. Much of the change in sedimentary facies documented by Nutz et al. (2017) occurs prior to 1.87 Ma (the KBS Tuff) and thus predates our record, precluding any comparison. The remainder of their record, deposited between the KBS Tuff (1.87 Ma) and ～1.72 Ma, documents a lower-amplitude transgression and regression. Direct comparison of the two records is difficult due to chronologic uncertainty; however, Nutz et al. (2017) observe a significant transgression between the C2N magnetic reversal (1.78 Ma) and the top of their record, 1.72 Ma. The top of C2N is also present in our record, but we do not observe a subsequent ～60-kyr shift in δDwax that signals a wetter climate.The upper sections of WTK13 are comprised of a prolonged regressive sequence associated with the end of Lake Lorenyang (Feibel, 2011). Although this sedimentological change could be interpreted to reflect strong drying, we observe no long-term shift in δDwax within these sediments, similar to the contrast between δDwax and the sediments analyzed by Nutz et al. (2017). Nutz and Schuster (2018) quote our abstract, in which we summarize our interpretations and suggest lake level may be responding mainly to deltaic progradation or tectonic changes, but as discussed later in the paper (Section 5.2), we interpret these differences to indicate that “sedimentary facies… are controlled by delta progradation, fault motion, subsidence, outlet level, or similar processes” that caused water level and sedimentary facies to fluctuate independently of precipitation. Indeed, as discussed by Feibel (2011) over time-scales longer than 105 years, the Turkana Basin's sedimentary record can be interpreted as a long sequence of episodes of basin opening, infilling, and closure controlled by tectonic and other crustal processes. We fully agree with Nutz and Schuster (2018) that such processes should not affect sedimentary records of lake level on shorter (104–105 year, i.e. precessional) time-scales, but on longer time-scales (105 years and greater) these processes cannot be rejected and may be an important, if not dominant control. δDwax is relatively insensitive to these processes and might thus preserve a signal more directly reflective of precipitation amount. Thus, although Nutz et al. (2017) interpret their ～200-kyr transgression and regression to be somehow related to a 400 kyr eccentricity cycle, it is also possible that the sedimentary changes they observe relate to the geomorphic evolution of the basin. That said, our δDwax record does suggest that eccentricity affected the basin's hydroclimate through 100-kyr cycles that modulated the amplitude of insolation-forced variability at the precessional time-scale, as Nutz et al. (2017) hypothesized.Indeed, as suggested by Nutz and Schuster (2018), comparison of sedimentary lake level records against independent climate records can provide considerable insight into the impacts of climate processes on paleoenvironments. We further suggest such comparisons can reveal not only the impacts of climate, but the Earth surface processes that shaped paleo-basins and paleo-landscapes in East Africa, the timing and nature of which represent a major uncertainty in paleoclimatology </topics/earth-and-planetary-sciences/paleoclimatology> and paleoanthropology (c.f. Maslin et al., 2014).Lastly, we agree that the WTK13 core location in our Fig. 1 was misplaced and include a revised figure in this reply. The outline of Lake Lorenyang is based upon data presented in Brown and Feibel (1991).Lyons, S.L., Baczynski, A.A., Babila, T.L., Bralower, T.J., Hajek, E.A., Kump, L.R., Polites, E.G., Self-Trail, J.M., Trampush, S.M., Vornlocher, J.R., Zachos, J.C., Freeman, K.H., 2019. Palaeocene–Eocene Thermal Maximum prolonged by fossil carbon oxidation. Nature Geoscience 12, 54-60. hallmark of the rapid and massive release of carbon during the Palaeocene–Eocene Thermal Maximum is the global negative carbon isotope excursion. The delayed recovery of the carbon isotope excursion, however, indicates that CO2 inputs continued well after the initial rapid onset, although there is no consensus about the source of this secondary carbon. Here we suggest this secondary input might have derived partly from the oxidation of remobilized sedimentary fossil carbon. We measured the biomarker indicators of thermal maturation in shelf records from the US Mid-Atlantic coast, constructed biomarker mixing models to constrain the amount of fossil carbon in US Mid-Atlantic and Tanzania coastal records, estimated the fossil carbon accumulation rate in coastal sediments and determined the range of global CO2 release from fossil carbon reservoirs. This work provides evidence for an order of magnitude increase in fossil carbon delivery to the oceans that began ~10–20?kyr after the event onset and demonstrates that the oxidation of remobilized fossil carbon released between 102 and 104 PgC as CO2 during the body of the Palaeocene–Eocene Thermal Maximum. The estimated mass is sufficient to have sustained the elevated atmospheric CO2 levels required by the prolonged global carbon isotope excursion. Even after considering uncertainties in the sedimentation rates, these results indicate that the enhanced erosion, mobilization and oxidation of ancient sedimentary carbon contributed to the delayed recovery of the climate system for many thousands of years.Lyulin, S.V., Glova, A.D., Falkovich, S.G., Ivanov, V.A., Nazarychev, V.M., Lyulin, A.V., Larin, S.V., Antonov, S.V., Ganan, P., Kenny, J.M., 2018. Computer simulation of asphaltenes. Petroleum Chemistry 58, 983-1004. review describes theoretical approaches based on computer simulations at various levels of details (from quantum chemical calculations to atomistic and coarse-grained models) to study asphaltenes and systems containing asphaltenes. The used methods are described, their advantages and disadvantages are discussed in terms of computational costs and time- and spatial-scales available for simulations. The results of studies of the asphaltenes interactions with each other and their aggregation behavior in low-molecular solvents are presented. The most promising approaches of computer simulations of asphaltenes-based systems are determined.MacGabhann, B.A., Schiffbauer, J.D., Hagadorn, J.W., Van Roy, P., Lynch, E.P., Morrison, L., Murray, J., 2019. Resolution of the earliest metazoan record: Differential taphonomy of Ediacaran and Paleozoic fossil molds and casts. Palaeogeography, Palaeoclimatology, Palaeoecology 513, 146-165. of our knowledge of early metazoan evolution is derived from unmineralized death mask or endorelief mold and cast fossils in Ediacaran clastic sedimentary rocks. This record is often regarded as a unique ‘Ediacaran taphonomic window’; however, the prevalence of soft-bodied molds and casts in Paleozoic clastic rocks has been increasing, begging an extension, or modification, to our understanding of this preservational motif. Chief amongst such fossils are eldonids, a non-biomineralized group of stem deuterostomes. Because eldonids are also preserved as compressed or flattened fossils from deposits like the Burgess Shale, Chengjiang and Kaili, they offer a comparative case study for evaluating the taphonomic fidelity of mold/cast-style preservation during this interval. EDS and Raman microspectroscopic analysis of Ordovician and Devonian eldonid molds and casts, and comparison with Burgess Shale eldonids, suggests the mold/cast taphonomic style produces significantly lower fidelity of fossil preservation. We propose that eldonid mold/cast fossils are preserved by the adsorption of reduced iron ions onto tissues composed primarily of high molecular weight (HMW) biopolymers which require enzymatic degradation prior to decay. Nucleation and growth of aluminosilicates and/or sulfides around these adsorbed ions forms a fossilizable surface veneer, preserving a death mask mold. More labile tissues could not be fossilized in this mold and cast style. Ediacaran mold and cast fossils from South Australia, the White Sea region of Russia, Namibia, and Newfoundland exhibit preservational characteristics consistent with this new proposed model. Analysis of their preservational mode suggests that the first metazoans, which would have lacked HMW biopolymeric tissues, could not have been fossilized in this particular style. Thus, understanding the origin and earliest evolution of the Metazoa requires a focus on alternative modes of fossilization.Madden, J.H., Kaltenegger, L., 2018. A catalog of spectra, albedos, and colors of solar system bodies for exoplanet comparison. Astrobiology 18, 1559-1573. present a catalog of spectra and geometric albedos, representative of the different types of solar system bodies, from 0.45 to 2.5?μm. We analyzed published calibrated, uncalibrated spectra, and albedos for solar system objects and derived a set of reference spectra and reference albedos for 19 objects that are representative of the diversity of bodies in our solar system. We also identified previously published data that appear contaminated. Our catalog provides a baseline for comparison of exoplanet observations to 19 bodies in our own solar system, which can assist in the prioritization of exoplanets for time intensive follow-up with next-generation extremely large telescopes and space-based direct observation missions. Using high- and low-resolution spectra of these solar system objects, we also derive colors for these bodies and explore how a color–color diagram could be used to initially distinguish between rocky, icy, and gaseous exoplanets. We explore how the colors of solar system analog bodies would change when orbiting different host stars. This catalog of solar system reference spectra and albedos is available for download through the Carl Sagan Institute.Mader, M.M., Osinski, G.R., 2018. Impactites of the Mistastin Lake impact structure: Insights into impact ejecta emplacement. Meteoritics & Planetary Science 53, 2492-2518. Mistastin Lake impact structure is an intermediate‐size (~28 km apparent crater diameter), complex crater formed ~36 Myr. The original crater has been differentially eroded; however, a subdued terraced rim and distinct central uplift are still observed and impactites are well exposed in three dimensions. The inner portion of the structure is covered by Mistastin Lake and the surrounding area is locally covered by soil/glacial deposits and vegetation. The crystalline target rocks of the Mistastin Lake region are dominated by anorthosite, granodiorite, and quartz monzonite. Previous studies of the Mistastin Lake impactites have primarily focussed on the impact melt rocks. This study further evaluates the entire suite of impactite rocks in terms of their location within the crater structure and emplacement mechanisms. Locally, allochthonous impactite units including impact melt and various types of breccias are distributed around the lake in the terraced rim and are interpreted as proximal ejecta deposits. A multistage model for the origin and emplacement of impact melt rocks and the formation of impact ejecta is proposed for the Mistastin Lake impact structure based on a synthesis of the field and petrographic observations. This model involves the generation of a continuous ballistic ejecta blanket during the excavation stage, followed by the emplacement of melt‐rich, ground‐hugging flows during the terminal stages of crater excavation and the modification stage of crater formation. Impact melt‐bearing breccias—also termed “suevite” at other sites—are present in several distinct settings within the Mistastin Lake structure and likely have more than one formation mechanism.Mahabadi, N., Dai, S., Seol, Y., Jang, J., 2019. Impact of hydrate saturation on water permeability in hydrate-bearing sediments. Journal of Petroleum Science and Engineering 174, 696-703. of the hydrate-bearing sediments critically affects the hydrate dissociation process as well as the rate and efficiency of gas production. Reported permeability values are observed to be widely are very scattered owing to the dependence on multiple factors such as experimental conditions and test procedures. It is critical that the permeability is measured accurately to enable prediction of long-term gas production using numerical simulation for an economic development of hydrate-bearing reservoirs. In this study, the tetrahydrofuran (THF) hydrates that exhibit pore habits of the pore-filling pattern are formed in sediments, and the water permeability is quantified as a function of hydrate saturation. The results show that a decrease in the permeability for an increase in the hydrate saturation. Based on the measured values that are bounded by Kozeny grain-coating and pore-filling models, the fitting parameters of the empirical permeability models are suggested for use in numerical simulation of long-term hydrate dissociation. Wave velocity measurements reveal pore habits of pore-filling pattern of THF hydrates in the sediments with Sh?<?0.5, and a gradual transition to patchy and load-bearing pore-habits when Sh?>?0.6. The numerical simulation results obtained using the complementary pore-network model suggest that the THF hydrates in the sediments may form in small clusters with an average patch size of ～4 pores.Majumdar, U., Cook, A.E., 2018. The volume of gas hydrate-bound gas in the northern Gulf of Mexico. Geochemistry, Geophysics, Geosystems 19, 4313-4328. northern Gulf of Mexico is known to host gas hydrate in submarine sediments. Estimating the amount of gas hydrate for both carbon cycle and resource interest has been ongoing for more than three decades. A large range of estimates (from 0.2 to 680 trillion cubic meters (TCM)) for hydrate-bound natural gas at standard temperature and pressure exists. We bring a new perspective to resource estimates by using ~800 publicly available petroleum industry well logs assessed for natural gas hydrate. Our resulting probabilistic range of the gas hydrate-bound natural gas in the northern Gulf of Mexico ranges from 37 TCM (10th percentile estimate) to 78 TCM (90th percentile estimate) of gas hydrate-bound natural gas, with a mean estimate of 56?TCM. This suggests that the gas hydrate resource density of the northern Gulf of Mexico is 4 times lower than that previously estimated by the Bureau of Ocean Energy Management. Our results also indicate that over half of the gas hydrate in the area is strategically hosted in sand reservoirs, which is significantly higher than that previously estimated.Makhin, M.N., Zanaveskin, K.L., Zanaveskin, L.N., Khadzhiev, S.N., 2018. Recovery of rare metals from high-boiling petroleum fractions. Petroleum Chemistry 58, 1085-1090. possibility of recovering compounds of rare and other valuable metals from bottom ash from the combustion of high-boiling petroleum fractions (HBF BA) by chlorination in a fluidized bed reactor has?been shown. The reactivity of the main HBF BA components has been found to decrease in the order: MoO3 > V2O5 > NiO > Fe2O3.The conditions for running the process to enable a high rate of recovery of rare and other valuable metals have been determined.Mallick, S., 2019. Biodegradation of acenaphthene by Sphingobacterium sp. strain RTSB involving trans-3-carboxy-2-hydroxybenzylidenepyruvic acid as a metabolite. Chemosphere 219, 748-755. gram-negative bacterium designated as RTSB was isolated from a petroleum-contaminated soil competent of utilizing acenaphthene as the solitary source of carbon and energy. The strain RTSB was identified as a Sphingobacterium species based on the morphological, nutritional and biochemical features of the organism as well as 16S rRNA sequence analysis. By a combination of chromatographic and spectrometric techniques, different metabolites of the acenaphthene degradation pathway by the strain RTSB were isolated and identified, which indicate a novel acenaphthene degradation pathway involving 1-naphthoic acid. Characterization of different metabolites suggested transformation of acenaphthene to 1-naphthoic acid through 1-acenaphthenol, acenaphthenequinone and naphthalene-1,8-dicarboxylic acid in the upper pathway of degradation; while in the later, 1-naphthoic acid was processed via a novel meta-cleavage pathway, leading to the formation of trans-3-carboxy-2-hydroxybenzylidenepyruvic acid, and then to salicylic acid and catechol entering into the TCA cycle intermediates. This detailed study of acenaphthene degradation by a Sphingobacterium species describes a distinct pathway of acenaphthene degradation involving the novel metabolite trans-3-carboxy-2-hydroxybenzylidenepyruvic acid.Mandal, A., Singha, M., Addy, P.S., Basak, A., 2019. Laser desorption ionization mass spectrometry: Recent progress in matrix-free and label-assisted techniques. Mass Spectrometry Reviews 38, 3-21. MALDI-based mass spectrometry, over the last three decades, has become an important analytical tool. It is a gentle ionization technique, usually applicable to detect and characterize analytes with high molecular weights like proteins and other macromolecules. The earlier difficulty of detection of analytes with low molecular weights like small organic molecules and metal ion complexes with this technique arose due to the cluster of peaks in the low molecular weight region generated from the matrix. To detect such molecules and metal ion complexes, a four-prong strategy has been developed. These include use of alternate matrix materials, employment of new surface materials that require no matrix, use of metabolites that directly absorb the laser light, and the laser-absorbing label-assisted LDI-MS (popularly known as LALDI-MS). This review will highlight the developments with all these strategies with a special emphasis on LALDI-MS.Mangenot, X., Gasparrini, M., Gerdes, A., Bonifacie, M., Rouchon, V., 2018. An emerging thermochronometer for carbonate-bearing rocks: ?47 /(U-Pb). Geology 46, 1067-1070. the thermal evolution of sedimentary basins is critical for understanding the origin of natural resources (including ores, geothermal fluids, or hydrocarbons) and for deciphering larger-scale tectonic and geodynamic evolutions. Modern reconstructions of past subsurface temperatures mostly rely on thermochronometers that are not applicable to carbonate rocks [e.g., fission-track and (U-Th)/He analyses]. Here, by coupling carbonate clumped isotope (?47) thermometry and laser ablation U-Pb geochronology on a complete paragenetic sequence, we demonstrate the applicability of an emerging thermochronometer for carbonate bearing-rocks. Paired ?47 and U-Pb data were obtained for calcite and dolomite phases precipitated in a Middle Jurassic carbonate hydrocarbon reservoir of the Paris Basin depocenter (France). The absolute thermochronological data allow the precise reconstruction of the thermal history of these rocks: from shallow burial temperatures (～40 °C), occurring in the Late Jurassic, toward a progressive burial and heating stage (up to 87 °C) during the Cretaceous, followed by a cooling stage (down to 69 °C) during the Tertiary uplift of the basin. The inferred time-temperature path based on Δ47/(U-Pb) data is mostly consistent with the thermal scenario independently deduced from organic maturity indicators from the underlying Lower Jurassic shales. The Δ47/(U-Pb) thermochronological data also highlight a thermal anomaly during Aptian–Albian time that requires revisiting the accepted timing for hydrocarbon migration in the Middle Jurassic reservoir carbonates.Mangerud, G., Paterson, N.W., Riding, J.B., 2019. The temporal and spatial distribution of Triassic dinoflagellate cysts. Review of Palaeobotany and Palynology 261, 53-66. records of fossil dinoflagellate cysts from the Late Triassic, the time during which they first appear abundantly in the geological record, are reviewed. Most of the Triassic palynological literature pertains to terrestrial palynomorphs, thus it is challenging to establish a global picture of the temporal and spatial distribution of Late Triassic dinoflagellate cyst around the Pangea supercontinent. Moreover, data on Late Triassic dinoflagellate cysts are dispersed, and there are currently no records of dinoflagellate cysts from many marine successions. With the exception of an Australian record of the dinoflagellate cyst Sahulidinium ottii from the upper Mid Triassic, and a possible early Carnian occurrence of, among others, Rhaetogonyaulax in the Swiss Alps, cyst-forming dinoflagellates first appeared relatively synchronously around Pangea from the late Carnian. There are 3–6 species of pre-Norian species globally, whereas species richness exceeded 25 by the end of the Norian. During the Rhaetian, marine seaways had gradually opened due to sustained continental breakup, allowing the expansion of dinoflagellates into many European basins. New species are present, some known only from restricted areas, whereas others like Dapcodinium appear to have a global distribution. The majority of Triassic dinoflagellate cyst taxa do not extend into the Jurassic.Marcé, R., Obrador, B., Gómez-Gener, L., Catalán, N., Koschorreck, M., Arce, M.I., Singer, G., von Schiller, D., 2019. Emissions from dry inland waters are a blind spot in the global carbon cycle. Earth-Science Reviews 188, 240-248. large part of the world's inland waters, including streams, rivers, ponds, lakes and reservoirs is subject to occasional, recurrent or even permanent drying. Moreover, the occurrence and intensity of drying events are increasing in many areas of the world because of climate change, water abstraction, and land use alteration. Yet, information on the gaseous carbon (C) fluxes from dry inland waters is scarce, thus precluding a comprehensive assessment of C emissions including all, also intermittently dry, inland waters. Here, we review current knowledge on gaseous C fluxes from lotic (streams and rivers) and lentic (ponds, lakes, and reservoirs) inland waters during dry phases and the response to rewetting, considering controls and sources as well as implications of including ‘dry’ fluxes for local and global scale estimates. Moreover, knowledge gaps and research needs are discussed. Our conservative estimates indicate that adding emissions from dry inland waters to current global estimates of CO2 emissions from inland waters could result in an increase of 0.22 Pg C year?1, or ~10% of total fluxes. We outline the necessary conceptual understanding to successfully include dry phases in a more complete picture of inland water C emissions and identify potential implications for global C cycle feedbacks.Marlot, L., Batteau, M., De Beer, D., Faure, K., 2018. In silico screening of comprehensive two-dimensional centrifugal partition chromatography × liquid chromatography for multiple compound isolation. Analytical Chemistry 90, 14279-14286 of unknown compounds for structural identification and the collection of target molecules to generate unavailable standards remain a challenge when dealing with complex samples. While tedious multistep purification is commonly used, it is not appropriate for a limited amount of sample or when a full recovery of expensive molecules is required. Two-dimensional preparative chromatography in a comprehensive mode provides an effective means to collect a large number of molecules in such a case. However, there is currently a lack of metrics to estimate preparative performances with a minimal number of experiments. An in silico comparative study of various pairs of chromatographic systems is proposed, focusing on the occupation rate and the homogeneity of peak spreading in the 2D separation space. Off-line combination of centrifugal partition chromatography (CPC) with liquid chromatography (LC) exhibits numerous advantages for 2D preparative separation. Our in silico approach was illustrated through the isolation of eight bioactive compounds with very similar structures from Cyclopia genistoides plant by CPC×LC. The column screening was performed considering predictive 2D plots in light of the preparative performance descriptors and compared to real 2D preparative separations.Martindale, R.C., Foster, W.J., Velledits, F., 2019. The survival, recovery, and diversification of metazoan reef ecosystems following the end-Permian mass extinction event. Palaeogeography, Palaeoclimatology, Palaeoecology 513, 100-115. Triassic Period records important ecological transitions in the aftermath of the end-Permian mass extinction and is a key interval in the evolution of modern coral reefs. There have been several critical developments in our understanding of Triassic reef evolution over the past decade: the timing of events and duration of stages have changed dramatically; the discovery of metazoan reefs in the Early Triassic; details about the environmental perturbations that drove the extinction; the relationship between tectonic activity and platform margin reef proliferation; and additional proxy evidence for the co-evolution of coral reef-builders and their photosymbionts. Here, we provide an up-to-date synthesis of reef collapse and recovery dynamics following the end-Permian extinction, specifically integrating recent discoveries. The evolution of reef ecosystems can be divided into five phases based on their composition. 1) Microbial-metazoan reefs represent survival communities that characterize the immediate extinction aftermath. 2) The re-establishment of reefs built by metazoans (small sponge biostromes and bivalve buildups) is observed in oxygenated settings in the Olenekian (Early Triassic). 3) Towards the end of the Olenekian and into the Anisian (Middle Triassic) low-diversity, “Tubiphytes”-dominated reefs formed, which represent the first Triassic platform-margin reefs; platform-margin reefs, however, are not widespread until the late Anisian. 4) Late Anisian reefs also record a composition change and increase in species richness with sponges and “Tubiphytes” as the main reef builders. 5) The first scleractinian corals (which are the main reef builder in modern marine reef ecosystems) evolved during the Anisian but are not reported as dominant reef builders until the Late Triassic. The radiation of coral reefs is posited to be coupled to the acquisition of photosymbionts (e.g., zooxanthellae). There is clearly a stepwise evolution of reef types during the Triassic; however, once each reef type appears it persists throughout the remainder of the Triassic. The survival, recovery, and diversification of reef ecosystems is, therefore, more complex than previously outlined, particularly with respect to the earliest post-extinction ecosystems. These recent advances highlight the need to thoroughly document the faunal compositions of understudied reef systems as well as to continue the exploration of Triassic ecosystems in underrepresented regions.Marynowski, L., Goryl, M., Bucha, M., Smolarek-Lach, J., Detman, A., Sikora, A., Chojnacka, A., Simoneit, B.R.T., 2019. Trehalose, mannitol and arabitol as indicators of fungal metabolism in Late Cretaceous and Miocene deposits. International Journal of Coal Geology 201, 51-61., mannitol and arabitol are the main saccharides of extant fungal metabolism, but their occurrence and distribution in geological materials have rarely been considered. Here, we identify these sugars in Miocene lignites and for the first time in Late Cretaceous mudstones and coals. The co-occurrence of trehalose, mannitol and arabitol in the sedimentary rocks investigated suggests their fungal origin, because these three saccharides are major compounds present in most modern fungi, including the very common mycorrhizal and wood-rotting groups. Therefore, we conclude that these sugars should be treated as new fungal biomarkers (biomolecules) present in geological rocks. Trehalose and mannitol are major compounds in total extracts of the samples and a sum of their concentration reaches 4.6?μg/g of sample. The arabitol concentrations do not exceed 0.5?μg/g, but in contrast to trehalose, the concentration correlates well with mannitol (R2?=?0.94), suggesting that they have the same, translocatory role in fungi. Based on the trehalose vs. mannitol and arabitol distributions in Cretaceous samples and their comparison with data for modern fungi, we preliminarily conclude that the coal seams from the Rakowice Ma?e (SW Poland) section were formed during warmer climatic periods than the overlying sediments. Furthermore, no DNA could be isolated from the samples of lignites and overlying sediments, whereas it was abundant in the control samples of maple, birch and oak wood degraded by fungi. This indicates an absence of recent fungi responsible for decay in lignites and implies that the saccharide origin is connected with ancient fungi. Other sugar alcohols and acids like D-pinitol, quinic acid and shikimic acid, were found for the first time in sedimentary rocks, and their source is inferred to be from higher plants, most likely conifers. The preservation of mono- and disaccharides of fungal origins in pre-Palaeogene strata implies that compounds previously thought as unstable can survive for tens to hundreds of millions of years without structural changes in immature rocks unaffected by secondary processes.Matus, F., Stock, S., Eschenbach, W., Dyckmans, J., Merino, C., Nájera, F., K?ster, M., Kuzyakov, Y., Dippold, M.A., 2019. Ferrous Wheel Hypothesis: Abiotic nitrate incorporation into dissolved organic matter. Geochimica et Cosmochimica Acta 245, 514-524. evaluated the abiotic formation of dissolved organic nitrogen (DON) by the fast reaction of iron (Fe) with nitrate (NO3?) in the dissolved organic matter (DOM) of volcanic soils in a temperate rainforest (>5000?mm precipitation per year). During five days, the educts and products of abiotic reactions under anoxic conditions were measured in a microcosm experiment depending on the Fe and NO3? concentrations. A control zero-Fe was not used because there was no chemical reaction with nitrate addition. Using a novel technique of automated sample preparation for inorganic N (SPIN) attached to a membrane inlet quadrupole mass spectrometry (MIMS), the 15N abundances and inorganic N concentrations were determined directly in aqueous solutions. The results were explained in the context of the Ferrous Wheel Hypothesis which states that Fe(II) is utilized to reduce NO3? to nitrite (NO2?) that is incorporated into DOM. Fe(II) is regenerated from Fe(III) in anaerobic soil microsites. Here we tested one part of this hypothesis, the processes occurring in DOM (instead of soil organic matter). Using the SPIN-MIMS technique, we could overcome Ferrous Wheel Hypothesis criticism regarding possible Fe interference during NO3? analysis. The total recovery of 15N added as NO3? fluctuated between 63 and 101%, and the remaining 15N was measured as gaseous N2O. The 15N-labelled NO3? added decreased immediately after 15?min of incubation. After five days of incubation, approximately 25% of the labelled NO3? (e? acceptors) added was transformed to DON in the presence of a high amount of Fe(II) (e? donors). Small amounts of N2O and CO2 provided further evidence of NO3? reduction and DOM oxidation, respectively. From these results, we propose a new theoretical model that includes the Ferrous Wheel Hypothesis, where only the transformation of NO3? to DON was proven. The present results explain the high retention of NO3? in DOM from volcanic soils in ecosystems with high precipitation.Mehana, M., Abraham, J., Fahes, M., 2019. The impact of asphaltene deposition on fluid flow in sandstone. Journal of Petroleum Science and Engineering 174, 676-681. deposition in oil reservoirs is a contentious issue affecting both well and reservoir productivity. Though the phenomenon has been previously studied in several laboratory experiments, the uniformity aspects of the asphaltene deposit are usually overlooked. We have previously developed an experimental workflow to create a uniform deposit of asphaltene inside the core sample. In this study, the impact of this uniform deposit on fluid flow is quantified through imbibition, corefloods and relative permeability experiments. In addition, the lab results are used in a field scale simulation to investigate the impact of deposition on field performance. The results exhibit a shift in the wettability state where a reduction in both water imbibition rate and capacity are observed after deposition. Besides, up to 25% reduction in absolute permeability is detected. Results of pressure drop experiments across the core conducted on the exposed rocks indicate a change in the wetting characteristics, with the exposed rocks becoming more mixed/intermediate wet and varying with the change in the initial brine saturation in the rock. Subsequently, the relative permeability set is affected where a shift in the oil residual saturation, a downgrade in the oil curve and an upgrade in the water curve are observed. Upscaling this new data to field scale indicated a loss of more than half of the well productivity and an earlier breakthrough if waterflooding is implemented.Ménez, B., Pisapia, C., Andreani, M., Jamme, F., Vanbellingen, Q.P., Brunelle, A., Richard, L., Dumas, P., Réfrégiers, M., 2018. Abiotic synthesis of amino acids in the recesses of the oceanic lithosphere. Nature 564, 59-63. hydrocarbons and carboxylic acids are known to be formed on Earth, notably during the hydrothermal alteration of mantle rocks. Although the abiotic formation of amino acids has been predicted both from experimental studies and thermodynamic calculations, its occurrence has not been demonstrated in terrestrial settings. Here, using a multimodal approach that combines high-resolution imaging techniques, we obtain evidence for the occurrence of aromatic amino acids formed abiotically and subsequently preserved at depth beneath the Atlantis Massif (Mid-Atlantic Ridge). These aromatic amino acids may have been formed through Friedel–Crafts reactions catalysed by an iron-rich saponite clay during a late alteration stage of the massif serpentinites. Demonstrating the potential of fluid-rock interactions in the oceanic lithosphere to generate amino acids abiotically gives credence to the hydrothermal theory for the origin of life, and may shed light on ancient metabolisms and the functioning of the present-day deep biosphere.Meng, Q.T., Bechtel, A., Sachsenhofer, R.F., Liu, Z.J., Gross, D., Sun, P.C., Hu, F., Li, L., Wang, K.B., Xu, C., Chen, L.L., Zeng, W.R., 2019. Hydrocarbon potential and palaeo-depositional environment of lacustrine source rocks: Middle Jurassic Shimengou Formation, northern Qaidam Basin, NW China. Journal of Petroleum Geology 42, 37-58. Middle Jurassic Shimengou Formation in the Qaidam Basin, NW China, includes coals and lacustrine source rocks which locally reach oil shale quality (i.e. yielding >3.5 % oil on low‐temperature distillation). In the present study, the palaeo‐depositional environment and hydrocarbon potential of the 84.5 m thick Shale Member of the Shimengou Formation are investigated based on bulk geochemical parameters, organic petrographic data, biomarker analysis, and stable isotope geochemistry of 88 core samples.The Shale Member was deposited in an anoxic freshwater lake which formed following the drowning of a precursor low‐lying mire. Variations in bulk geochemical parameters allow four informal units to be identified, referred to (from the base up) as Units 1 to 4. These contain intervals of oil shale of varying thicknesses. In Unit 1, mudstones in the interval referred to as oil shale Layer 1 (true thickness [TD]: 2.06 m) are OM‐rich as a result of algal blooms and photic zone anoxia, and correspond to an initial flooding event. Subsequently, productivity of aquatic organisms decreased, resulting in the deposition of organic‐lean mudstones in Unit 2. Oil shale Layers 2 (TD: 2.03 m) and 3 (TD: 8.03 m) near the base of Unit 3 were deposited during maximum water depths. As with Layer 1, high productivity by algal blooms resulted in photic zone anoxia in a stratified water column. The shales in the upper part of Unit 3 are characterized by high TOC contents and a gradual increased input of terrigenous OM, and were deposited in a stable semi‐deep lake. Finally, organic‐lean mudstones in Unit 4 were deposited in shallow lacustrine conditions. The reconstruction of depositional environments in thick, non‐marine shale‐rich successions by mineralogical, petrographic and inorganic geochemical methods may be challenging as a result of the homogenous composition of component mudstones. The results of this study indicate, however, that sub‐division and basin‐wide correlation of such intervals can be achieved by organic geochemical analyses.Oil shales and organic‐rich mudstones in Units 1 and 3 of the Shimengou Formation Shale Member are excellent oil‐prone source‐rocks with a Source Potential Index of 3.2 t HC/m2. Considering the large area covered by the Shimengou Formation in the northern Qaidam Basin (～34,000 km2), the results of this study highlight the regional significance for future petroleum exploration. They indicate that variations in organic productivity and dilution by minerals are key factors controlling the abundance and type of organic matter in the formation. An understanding of these factors will assist with the identification of exploration targets. Merdith, A.S., Williams, S.E., Brune, S., Collins, A.S., Müller, R.D., 2019. Rift and plate boundary evolution across two supercontinent cycles. Global and Planetary Change 173, 1-14. extent of continental rifts and subduction zones through deep geological time provides insights into the mechanisms behind supercontinent cycles and the long term evolution of the mantle. However, previous compilations have stopped short of mapping the locations of rifts and subduction zones continuously since the Neoproterozoic and within a self-consistent plate kinematic framework. Using recently published plate models with continuously closing boundaries for the Neoproterozoic and Phanerozoic, we estimate how rift and peri-continental subduction length vary from 1?Ga to present and test hypotheses pertaining to the supercontinent cycle and supercontinent breakup. We extract measures of continental perimeter-to-area ratio as a proxy for the existence of a supercontinent, where during times of supercontinent existence the perimeter-to-area ratio should be low, and during assembly and dispersal it should be high. The amalgamation of Gondwana is clearly represented by changes in the length of peri-continental subduction and the breakup of Rodinia and Pangea by changes in rift lengths. The assembly of Pangea is not clearly defined using plate boundary lengths, likely because its formation resulted from the collision of only two large continents. Instead the assembly of Gondwana (ca. 520?Ma) marks the most prominent change in arc length and perimeter-to-area ratio during the last billion years suggesting that Gondwana during the Early Palaeozoic could explicitly be considered part of a Phanerozoic supercontinent. Consequently, the traditional understanding of the supercontinent cycle, in terms of supercontinent existence for short periods of time before dispersal and re-accretion, may be inadequate to fully describe the cycle. Instead, either a two-stage supercontinent cycle could be a more appropriate concept, or alternatively the time period of 1 to 0?Ga has to be considered as being dominated by supercontinent existence, with brief periods of dispersal and amalgamation.Meringer, M., Giri, C., Cleaves II, H.J., 2018. Fitting cometary sampling and composition mass spectral results using non-negative least squares: Reducing detection ambiguity for in situ solar system organic compound measurements. ACS Earth and Space Chemistry 2, 1256-1261. chemistry occurring in the universe generates a huge variety of organic compounds abiotically. Significant progress has been made in understanding the types and distributions of these compounds in various planetary, asteroidal, cometary, nebular, and molecular cloud environments. One of the most exciting recent discoveries was the detection of low-molecular-weight organic species native to the surface of comet 67P/Churyumov–Gerasimenko by the cometary sampling and composition experiment that was aboard the Philae lander of the European Space Agency. The identities of these species were estimated using a simple hand-fitting method. Here, we use a more rigorous statistical method to fit the same data and find that there is some variance between results obtained using the two methods. This paper offers recommendations to improve the numerical methods for fitting of mass spectra, which would lead to more confident identification of ambiguous-mass compounds. Such methods may also help maximize the gains of future sampling-driven space missions, to Europa, Titan, Mars and its moons, comets, and asteroids, by filling in gaps in current scientific knowledge regarding electron impact mass spectra of ambiguous-mass compounds.Miao, L., Moczyd?owska, M., Zhu, S., Zhu, M., 2019. New record of organic-walled, morphologically distinct microfossils from the late Paleoproterozoic Changcheng Group in the Yanshan Range, North China. Precambrian Research 321, 172-198. life has likely existed since the late Paleoproterozoic, yet little is known about its early diversity and phylogenetic relationships. Organic-walled microfossils (OWMs) with conspicuous morphology provide a unique material to investigate the deep evolution of eukaryotic and prokaryotic microbial clades. Here we report a diverse assemblage of OWMs from the lower Changcheng Group (c. 1673–1638?Ma, Changzhougou and Chuanlinggou formations) in the Yanshan Range, North China, which consists of 15 species, including 2 that are newly described. The fossil assemblage is dominated by spheromorphs with less numerous process-bearing vesicles, as are colonial and filamentous forms. Among these, 6 morphologically complex taxa (Dictyosphaera, 2 species of Germinosphaera, Pterospermopsimorpha, Simia, and Valeria) are identified as unambiguous unicellular eukaryotes. Four species (Cucumiforma, Navifusa, Schizofusa and large Leiosphaeridia) with relatively simple morphology but having large size, thick wall, and some showing median-split excystment structures, are of probable eukaryotic affinity. However, various colonial microfossils could be either eukaryotes or prokaryotes. The new record of morphologically disparate OWMs represents one of the earliest occurrences of eukaryotes in both China and the world, and indicates that the eukaryotic life was already well established in the late Paleoproterozoic and was of moderate diversity, similar to that of the Mesoproterozoic.Minami, A., Ozaki, T., Liu, C., Oikawa, H., 2018. Cyclopentane-forming di/sesterterpene synthases: widely distributed enzymes in bacteria, fungi, and plants. Natural Product Reports 35, 1330-1346.: 2000 to 2018 In the late 1960s, structurally unique fusicoccane- and ophiobolane-type di/sesterterpenes were isolated and their homologs were found to be widely distributed in various organisms. Nearly a half century later, the first terpene synthase PaFS was identified, which triggered the discovery of a number of di/sesterterpene synthases, which were named as cyclopentane-forming terpene synthases (CPF-TSs). In the past 10 years, CPF-TSs have emerged as a new type of class I terpene synthases, which afford di/sesterterpenes with characteristic polycyclic molecular skeletons; they catalyze two different types of cyclizations, defined as type A and B, which are relevant to the initial cyclization mode of a polyprenyl diphosphate. This review summarizes the characteristic features of CPF-TSs from various sources and detailed cyclization mechanisms; we have also discussed the structural diversification strategy of these novel enzymes.Mironov, N.A., Abilova, G.R., Borisova, Y.Y., Tazeeva, E.G., Milordov, D.V., Yakubova, S.G., Yakubov, M.R., 2018. Comparative study of resins and asphaltenes of heavy oils as sources for obtaining pure vanadyl porphyrins by the sulfocationite-based chromatographic method. Energy & Fuels 32, 12435-12446. resins and asphaltenes of three heavy oils differing in origin (Permian and Carboniferous) and vanadium content (0.025–0.165 wt %) have been studied as sources for isolation of spectrally pure vanadyl porphyrins by sulfocationite-based chromatographic method developed by us recently. This method consists of removing the low polar nonporphyrin components from the resins or DMF extract of asphaltenes on SiO2-column followed by chromatographic isolation of vanadyl porphyrins on the sulfocationite. The asphaltenes were revealed to be a more promising source of vanadyl porphyrins because they possess ≥5 times higher content of vanadium, provide better accumulation of vanadyl porphyrins during deposition extraction by N,N-dimethylformamide, and are less contaminated by low polar nonporphyrin compounds capable of coeluting with vanadyl porphyrins through the sulfocationite column. According to matrix-assisted laser desorption/ionization time-of-flight mass spectroscopy, DPEP vanadyl porphyrins were found to be the most abundant type for all studied samples (34.1–54.5%). Rhodo vanadyl porphyrins belong to minor components (3.3–8.7% for each subtype) while Etio and Di-DPEP types take the intermediate position (9.8–28.7%). The resins and asphaltenes of the same oil showed significant difference in the group composition of purified vanadyl porphyrins. For the resins, a ～1.3-fold decreased content of DPEP vanadyl porphyrins was found, which was compensated by a ～1.5- and/or ～1.8-fold increase in the content of Etio and Rhodo vanadyl porphyrins, respectively. However, this change in the composition of vanadyl porphyrins is not accompanied by a notable change of their average molecular weight despite the fact that increased concentration of more substituted (i.e., more hydrophobic) vanadyl porphyrins could be expected for less polar resins. This fact was interpreted in favor of association of vanadyl porphyrins with nonporphyrin components of the oil.Mogul, R., Barding, G.A.J., Lalla, S., Lee, S., Madrid, S., Baki, R., Ahmed, M., Brasali, H., Cepeda, I., Gornick, T., Gunadi, S., Hearn, N., Jain, C., Kim, E.J., Nguyen, T., Nguyen, V.B., Oei, A., Perkins, N., Rodriguez, J., Rodriguez, V., Savla, G., Schmitz, M., Tedjakesuma, N., Walker, J., 2018. Metabolism and biodegradation of spacecraft cleaning reagents by strains of spacecraft-associated Acinetobacter. Astrobiology 18, 1517-1527. assembly facilities are oligotrophic and low-humidity environments, which are routinely cleaned using alcohol wipes for benchtops and spacecraft materials, and alkaline detergents for floors. Despite these cleaning protocols, spacecraft assembly facilities possess a persistent, diverse, dynamic, and low abundant core microbiome, where the Acinetobacter are among the dominant members of the community. In this report, we show that several spacecraft-associated Acinetobacter metabolize or biodegrade the spacecraft cleaning reagents of ethanol (ethyl alcohol), 2-propanol (isopropyl alcohol), and Kleenol 30 (floor detergent) under ultraminimal conditions. Using cultivation and stable isotope labeling studies, we show that ethanol is a sole carbon source when cultivating in 0.2?×?M9 minimal medium containing 26?μM Fe(NH4)2(SO4)2. Although cultures expectedly did not grow solely on 2-propanol, cultivations on mixtures of ethanol and 2-propanol exhibited enhanced plate counts at mole ratios of ≤0.50. In support, enzymology experiments on cellular extracts were consistent with oxidation of ethanol and 2-propanol by a membrane-bound alcohol dehydrogenase. In the presence of Kleenol 30, untargeted metabolite profiling on ultraminimal cultures of Acinetobacter radioresistens 50v1 indicated (1) biodegradation of Kleenol 30 into products including ethylene glycols, (2) the potential metabolism of decanoate (formed during incubation of Kleenol 30 in 0.2?×?M9), and (3) decreases in the abundances of several hydroxy- and ketoacids in the extracellular metabolome. In ultraminimal medium (when using ethanol as a sole carbon source), A. radioresistens 50v1 also exhibits a remarkable survival against hydrogen peroxide (～1.5-log loss, ～108 colony forming units (cfu)/mL, 10?mM H2O2), indicating a considerable tolerance toward oxidative stress under nutrient-restricted conditions. Together, these results suggest that the spacecraft cleaning reagents may (1) serve as nutrient sources under oligotrophic conditions and (2) sustain extremotolerances against the oxidative stresses associated with low-humidity environments. In perspective, this study provides a plausible biochemical rationale to the observed microbial ecology dynamics of spacecraft-associated environments.Mohammadzadeh Shirazi, M., Ayatollahi, S., Ghotbi, C., 2019. Damage evaluation of acid-oil emulsion and asphaltic sludge formation caused by acidizing of asphaltenic oil reservoir. Journal of Petroleum Science and Engineering 174, 880-890. is one of the most effective techniques to remove the formation damage and restore (or even increase) the permeability of the near wellbore region. Although this technique is widely used to resolve the skin problem, it could initiate new damages itself that hinder the fluid flow and decrease the well production, consequently. Acid-oil emulsion and sludge formation are known as two major induced formation damage and the main reasons for the oil well acid treatment failures. Despite its critical effects, no comprehensive study has been addressed this specific type of formation damages in details. In this study, the acid-oil emulsion and asphaltic sludge formation were evaluated quantitatively. Multiple compatibility tests were conducted using HCl and six Iranian acid sensitive crude oil samples. The acid concentration, ferric ion presence, and acid-mixture ratio were selected as the main factors affecting the emulsion stability and the amount of sludge. To mimic the real condition the interference of the effects of these factors was noticed besides the crude oil type which has not been addressed before. The results revealed that controlling the iron ion presence, choosing the best acid concentration, and regulating the acid-mixture ratio would drastically reduce the risk of emulsion and sludge formation without any preventative additives presence. The quantitative values derived from this experimental work showed that the weight of dried asphaltic sludge formed was diminished to 7%, 5.6%, 2.4%, 22%, 7.5% and 10% of the most critical sludging condition for the crude oil samples A, B, C, D, E, and F respectively. Besides, for the first time, the volumetric measurement of the massive asphaltic sludge was performed to approach more realistic damage evaluation. The results confirmed it is possible that the solid sludge occupies 60?vol % of the primitive acid-oil mixture volume at high concentration of HCl and ferric besides high acid-oil ratio condition.Mohammedyasin, M.S., Wudie, G., Anteneh, Z.L., Bawoke, G.T., 2019. Paleoredox conditions of the Middle-Upper Jurassic black shales in the Blue Nile Basin, Ethiopia. Journal of African Earth Sciences 151, 136-145. elements (Mo, V, U, Re, Cd, Co, As, Sb, Tl, Ni, Cr, Mn, Fe, Pb, Cu, Zn, Se) and proxies for detrital clastic sedimentation (Al, Ti, Sc, Th) along with total organic carbon (TOC) and total sulfur (TS) were analysed to constrain the paleoredox conditions of the Middle-Upper Jurassic black shales in the Blue Nile (Abay) Basin, Ethiopia. These samples were collected from the deep marine Antalo Limestone (Oxfordian-Kimmeridgian), Gohatsion Formation (Bathonian) and glauconitic shale-mudstone unit (Aalenian-Toarcian). Significant variations in redox-sensitive elements concentration within and between these shales were evident for variable redox conditions. In general, the concentration of proxies for detrital clastic sedimentation increases from the Antalo Limestone to Gohatsion Formation and further to glauconitic shale-mudstone unit shales, respectively. The Antalo Limestone shales show slightly higher enrichment in redox-sensitive elements than the Gohatsion Formation and glauconitic shale-mudstone unit shales. The Antalo Limestones shales have higher TOC content than the glauconitic shale-mudstone unit shales and become very low in the Gohatsion Formation shales. The TS content in contrast, is relatively lower in the Antalo Limestone shales, intermediate in the Gohatsion Formation shales and becomes higher in the glauconitic shale-mudstone unit shales. The Antalo Limestone shales were deposited under anoxic-suboxic conditions whereas the Gohatsion Formation and glauconitic shale-mudstone unit shales were deposited under suboxic-oxic conditions. The TOC content and redox conditions of the Antalo Limestone shales implies favourable organic matter preservation and future source rock explorations in the basin should be targeted there.Mokhtari, B., Bahramian, A., 2019. Production monitoring of multilateral wells by multivariate dynamic interfacial tension. Measurement 134, 794-803. information about the inflow distribution in a multilateral well is of great importance and an ongoing challenge in the oil industry. In this work, we present a standard method for online monitoring of inflow distribution based on multivariate analysis of the dynamic surface tension (DST) of the produced oil. The method is reliant upon the assumption that the DST of the produced oil is a functional that takes the DST functions of each producing branch or layer as input. We measured the DST of water and crude oils, sampled from the sub-layers of a multilateral well, in ambient conditions. We found that the DST of crude oil samples fit three equations at three intervals which led to easier optimization of the error function of partial least squares (PLS). We, moreover, analyzed the impact of droplet normalization on the accuracy of the predicted results. The developed method was reliably used for an accurate and fast determination of the inflow distribution in a three-lateral well.Monteil, C.L., Perrière, G., Menguy, N., Ginet, N., Alonso, B., Waisbord, N., Cruveiller, S., Pignol, D., Lefèvre, C.T., 2018. Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis. Environmental Microbiology 20, 4415-4430. and evolutionary processes involved in magnetotactic bacteria (MTB) adaptation to their environment have been a matter of debate for many years. Ongoing efforts for their characterization are progressively contributing to understand these processes, including the genetic and molecular mechanisms responsible for biomineralization. Despite numerous culture‐independent MTB characterizations, essentially within the Proteobacteria phylum, only few species have been isolated in culture because of their complex growth conditions. Here, we report a newly cultivated magnetotactic, microaerophilic and chemoorganoheterotrophic bacterium isolated from the Mediterranean Sea in Marseille, France: Candidatus Terasakiella magnetica strain PR‐1 that belongs to an Alphaproteobacteria genus with no magnetotactic relative. By comparing the morphology and the whole genome shotgun sequence of this MTB with those of closer relatives, we brought further evidence that the apparent vertical ancestry of magnetosome genes suggested by previous studies within Alphaproteobacteria hides a more complex evolutionary history involving horizontal gene transfers and/or duplication events before and after the emergence of Magnetospirillum, Magnetovibrio and Magnetospira genera. A genome‐scale comparative genomics analysis identified several additional candidate functions and genes that could be specifically associated to MTB lifestyle in this class of bacteria.Morantes, L.R., Percebom, A.M., Mejía-Ospino, E., 2019. On the molecular basis of aggregation and stability of Colombian asphaltenes and their subfractions. Fuel 241, 542-549. residue (VR) is the heaviest fraction obtained by fractional distillation of the crude oil. Crude oil and its fractions, such as VR, can be separated in its components saturates, aromatics, resins, and asphaltenes (SARA fractions). Asphaltenes are of particular importance for up- and down-stream processes due to their molecular complexity, high heteroatom content, and strong tendency to self-aggregate. To evaluate the molecular characteristics of asphaltenes responsible for aggregation, we used a fractionation method based on mixtures of toluene and acetone to separate asphaltenes, isolated from a heavy Colombian residue, into different solubility subfractions. In this contribution, we show correlations between elemental composition and average molecular properties of subfractions and their solubility behavior. In addition, we were able to differentiate asphaltenes into ‘unstable’ and ‘stable’ subfractions in toluene solution by an analytical centrifugation method. From the stability analysis, we demonstrated that less soluble subfractions (consisting of more aromatic, heavier, and more condensed asphaltenes) are more prone to flocculation, and hence, they are less stable than more soluble subfractions. The results of colloidal characterization prove that less soluble subfractions form large fractal structures of small nanoaggregates, whereas the most soluble subfraction form highly stabilized dispersions of non-flocculating nanoaggregates. Results obtained in this work are expected to provide insights regarding the importance of solubility-based fractionation method as a basis for understanding asphaltene aggregation in heavy crude oils.Morée, A.L., Schwinger, J., Heinze, C., 2018. Southern Ocean controls of the vertical marine δ13C gradient – a modelling study. Biogeosciences 15, 7205-7223.δ13C, the standardised 13C∕12C ratio expressed in per mille, is a widely used ocean tracer to study changes in ocean circulation, water mass ventilation, atmospheric pCO2, and the biological carbon pump on timescales ranging from decades to tens of millions of years. δ13C data derived from ocean sediment core analysis provide information on δ13C of dissolved inorganic carbon and the vertical δ13C gradient (i.e. Δδ13C) in past oceans. In order to correctly interpret δ13C and Δδ13C variations, a good understanding is needed of the influence from ocean circulation, air–sea gas exchange and biological productivity on these variations. The Southern Ocean is a key region for these processes, and we show here that Δδ13C in all ocean basins is sensitive to changes in the biogeochemical state of the Southern Ocean. We conduct a set of idealised sensitivity experiments with the ocean biogeochemistry general circulation model HAMOCC2s to explore the effect of biogeochemical state changes of the Southern and Global Ocean on atmospheric δ13C, pCO2, and marine δ13C and Δδ13C. The experiments cover changes in air–sea gas exchange rates, particulate organic carbon sinking rates, sea ice cover, and nutrient uptake efficiency in an unchanged ocean circulation field. Our experiments show that global mean Δδ13C varies by up to about ±0.35‰ around the pre-industrial model reference (1.2‰) in response to biogeochemical change. The amplitude of this sensitivity can be larger at smaller scales, as seen from a maximum sensitivity of about ?0.6‰ on ocean basin scale. The ocean's oldest water (North Pacific) responds most to biological changes, the young deep water (North Atlantic) responds strongly to air–sea gas exchange changes, and the vertically well-mixed water (SO) has a low or even reversed Δδ13C sensitivity compared to the other basins. This local Δδ13C sensitivity depends on the local thermodynamic disequilibrium and the Δδ13C sensitivity to local POC export production changes. The direction of both glacial (intensification of Δδ13C) and interglacial (weakening of Δδ13C) Δδ13C change matches the direction of the sensitivity of biogeochemical processes associated with these periods. This supports the idea that biogeochemistry likely explains part of the reconstructed variations in Δδ13C, in addition to changes in ocean circulation.Moreno-Mayar, J.V., Vinner, L., de Barros Damgaard, P., de la Fuente, C., Chan, J., Spence, J.P., Allentoft, M.E., Vimala, T., Racimo, F., Pinotti, T., Rasmussen, S., Margaryan, A., Iraeta Orbegozo, M., Mylopotamitaki, D., Wooller, M., Bataille, C., Becerra-Valdivia, L., Chivall, D., Comeskey, D., Devièse, T., Grayson, D.K., George, L., Harry, H., Alexandersen, V., Primeau, C., Erlandson, J., Rodrigues-Carvalho, C., Reis, S., Bastos, M.Q.R., Cybulski, J., Vullo, C., Morello, F., Vilar, M., Wells, S., Gregersen, K., Hansen, K.L., Lynnerup, N., Mirazón Lahr, M., Kj?r, K., Strauss, A., Alfonso-Durruty, M., Salas, A., Schroeder, H., Higham, T., Malhi, R.S., Rasic, J.T., Souza, L., Santos, F.R., Malaspinas, A.-S., Sikora, M., Nielsen, R., Song, Y.S., Meltzer, D.J., Willerslev, E., 2018. Early human dispersals within the Americas. Science 362, Article eaav2621.: Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are ≥10,000 years old (up to ~18× coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct “Paleoamericans.” We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America.Editor's Summary, Complex processes in the settling of the Americas: The expansion into the Americas by the ancestors of present day Native Americans has been difficult to tease apart from analyses of present day populations. To understand how humans diverged and spread across North and South America, Moreno-Mayar et al. sequenced 15 ancient human genomes from Alaska to Patagonia. Analysis of the oldest genomes suggests that there was an early split within Beringian populations, giving rise to the Northern and Southern lineages. Because population history cannot be explained by simple models or patterns of dispersal, it seems that people moved out of Beringia and across the continents in a complex manner.Structured AbstractIntroduction: Genetic studies of the Pleistocene peopling of the Americas have focused on the timing and number of migrations from Siberia into North America. They show that ancestral Native Americans (NAs) diverged from Siberians and East Asians ~23,000 years (~23 ka) ago and that a split within that ancestral lineage between later NAs and Ancient Beringians (ABs) occurred ~21 ka ago. Subsequently, NAs diverged into northern NA (NNA) and southern NA (SNA) branches ~15.5 ka ago, a split inferred to have taken place south of eastern Beringia (present-day Alaska and western Yukon Territory).Rationale: Claims of migrations into the Americas by people related to Australasians or by bearers of a distinctive cranial morphology (“Paleoamericans”) before the divergence of NAs from Siberians and East Asians have created controversy. Likewise, the speed by which the Americas were populated; the number of basal divergences; and the degrees of isolation, admixture, and continuity in different regions are poorly understood. To address these matters, we sequenced 15 ancient human genomes recovered from sites spanning from Alaska to Patagonia; six are ≥10 ka old (up to ~18× coverage).Results: All genomes are most closely related to NAs, including those of two morphologically distinct Paleoamericans and an AB individual. However, we also found that the previous model is just a rough outline of the peopling process: NA dispersal gave rise to more complex serial splitting and early population structure—including that of a population that diverged before the NNA-SNA split—as well as admixture with an earlier unsampled population, which is neither AB nor NNA or SNA. Once in the Americas, SNAs spread widely and rapidly, as evidenced by genetic similarity, despite differences in material cultural, between >10-ka-old genomes from North and South America. Soon after arrival in South America, groups diverged along multiple geographic paths, and before 10.4 ka ago, these groups admixed with a population that harbored Australasian ancestry, which may have been widespread among early South Americans. Later, Mesoamerican-related population(s) expanded north and south, possibly marking the movement of relatively small groups that did not necessarily swamp local populations genetically or culturally.Conclusion: NAs radiated rapidly and gave rise to multiple groups, some visible in the genetic record only as unsampled populations. At different times these groups expanded to different portions of the continent, though not as extensively as in the initial peopling. That the early population spread widely and rapidly suggests that their access to large portions of the hemisphere was essentially unrestricted, yet there are genomic and archaeological hints of an earlier human presence. How these early groups are related or structured, particularly those with Australasian ancestry, remains unknown. Rapid expansion, compounded by the attenuating effect of distance and, in places, by geographic and social barriers, gave rise to complex population histories. These include strong population structure in the Pacific Northwest; isolation in the North American Great Basin, followed by long-term genetic continuity and ultimately an episode of admixture predating ~0.7 ka ago; and multiple independent, geographically uneven migrations into South America. One such migration provides clues of Late Pleistocene Australasian ancestry in South America, whereas another represents a Mesoamerican-related expansion; both contributed to present-day South American ancestry.Morrow, D.W., 2018. Devonian of the Northern Canadian Mainland Sedimentary Basin: A Review. Bulletin of Canadian Petroleum Geology 66, 623-694. Devonian succession of the Northern Canadian Mainland Sedimentary Basin is considerably thicker, and exhibits greater lithofacies variability, than its counterpart across the Western Canada Sedimentary Basin south of 60°. In the Northern Canadian Mainland Sedimentary Basin, Devonian strata are comprised of three complete second order transgressive-regressive cycles of deposition including the depositional sequences of T-R Cycles A, B, and C, and the lower transgressive sequence tract portion of a fourth second order sequence, T-R Cycle D. The carbonate-dominated Lower Devonian succession, including T-R Cycle A and part of Cycle B, is widespread, and has a thickness of up to 3000 metres locally, in contrast to the much thinner and more discontinuous Lower Devonian of the Western Canadian Sedimentary Basin south of 60°. Middle and Upper Devonian strata in the Northern Canadian Sedimentary Basin, like those of the Western Canada Sedimentary Basin, are widespread, but are dominantly siliciclastic. These strata include the upper part of T-R Cycle B, T-R Cycle C, and the lower part of T-R Cycle D. The profound change in sedimentary character from dominantly carbonate, to siliciclastic deposition, from early to late Devonian time reflects an overall evolution in tectonic regime from passive margin rifting to one of active orogenesis.Mulla, A., Fernandes, G., Menezes, L., Meena, R.M., Naik, H., Gauns, M., Damare, S., 2018. Diversity of culturable nitrate-reducing bacteria from the Arabian Sea oxygen minimum zone. Deep Sea Research Part II: Topical Studies in Oceanography 156, 27-33. subsurface waters of the northern Arabian Sea display a pronounced oxygen minimum layer associated with high nitrite maxima which provide an ideal niche for organisms that can respire nitrate. Culture-based studies elaborate the physiological characteristics of the organisms and their metabolic activities in biogeochemical cycles. In this study, the bacterial diversity and nitrate utilizing activity of the culturable heterotrophic bacteria inhabiting the water column oxygen minimum zone of Arabian Sea were investigated. Nitrate-reducing bacteria were isolated from the water column in the central Arabian Sea. Genotypic characterization of the isolates using 16?S rDNA gene sequencing grouped them into three phylogenetic groups i.e. Proteobacteria, Firmicutes, and Actinobacteria. Out of the 56 isolated bacteria, 45 strains belonged to Proteobacteria, 6 to Firmicutes and 5 to Actinobacteria. The nitrate reducing ability of the isolates was tested using Griess test. Thirty-six species belonging to genera Alcanivorax, Alteromonas, Halomonas, Pseudoalteromonas, Marinobacter, Bacillus, and Vibrio were positive for NO2-/NO3- reduction. Our results imply that cultivable bacteria capable of utilizing NO3- available in the system are present in the Arabian Sea oxygen minimum zone and the conditions existing therein must be favorable for their growth and functionality.Müller, O., Bang-Andreasen, T., White III, R.A., Elberling, B., Ta?, N., Kneafsey, T., Jansson, J.K., ?vre?s, L., 2018. Disentangling the complexity of permafrost soil by using high resolution profiling of microbial community composition, key functions and respiration rates. Environmental Microbiology 20, 4328-4342. permafrost can stimulate microbial activity, leading to faster decomposition of formerly preserved organic matter and CO2 release. Detailed knowledge about the vertical distribution of the responsible microbial community that is changing with increasing soil depth is limited. In this study, we determined the microbial community composition from cores sampled in a high Arctic heath at Svalbard, Norway; spanning from the active layer (AL) into the permafrost layer (PL). A special aim has been on identifying a layer of recently thawed soil, the transition zone (TZ), which might provide new insights into the fate of thawing permafrost. A unique sampling strategy allowed us to observe a diverse and gradually shifting microbial community in the AL, a Bacteroidetes dominated community in the TZ and throughout the PL, a community strongly dominated by a single Actinobacteria family (Intrasporangiaceae). The contrasting abundances of these two taxa caused a community difference of about 60%, just within 3 cm from TZ to PL. We incubated subsamples at about 5°C and measured highest CO2 production rates under aerobic incubations, yet contrasting for five different layers and correlating to the microbial community composition. This high resolution strategy provides new insights on how microbial communities are structured in permafrost and a better understanding of how they respond to thaw.Nalinakshan, S., Sivasubramanian, V., Ravi, V., Vasudevan, A., Sankar, M.S.R., Arunachalam, K., 2019. Progressive crude oil distillation: An energy-efficient alternative to conventional distillation process. Fuel 239, 1331-1337., the major process in crude oil refineries as of now. In this work we focused the attention to energy saving with respect to an industrial crude oil distillation unit. An alternative to the conventional crude oil distillation model present in the Bharat Petroleum Corporation, Kochi Refinery is proposed and simulated. The theoretical predictions as well as the simulated results indicate that the Progressive crude oil distillation reduces the utility burden as well as increase the extraction of more valuable light components. The simulation was carried out using Aspen HYSYS V8.8.2. Different crudes are taken into account and their properties and amount of distillate are analyzed. The optimization is done in an easy manner rather than the conventional mathematical method, together with the advanced process control tools; make it profitable in the operation in real time.Namouchi, A., Guellil, M., Kersten, O., H?nsch, S., Ottoni, C., Schmid, B.V., Pacciani, E., Quaglia, L., Vermunt, M., Bauer, E.L., Derrick, M., Jensen, A.?., Kacki, S., Cohn, S.K., Stenseth, N.C., Bramanti, B., 2018. Integrative approach using Yersinia pestis genomes to revisit the historical landscape of plague during the Medieval Period. Proceedings of the National Academy of Sciences 115, E11790-E11797.: While our knowledge of modern plague reservoirs and their hosts is extensive, we have little to no knowledge about the origin of the Medieval plague pandemics or the routes of transmission involved in their spread. Prior genomic data provide a patchy low-resolution picture of the transmission dynamics involved during the Second Plague Pandemic, with only five distinct genomes. We have reevaluated all Medieval strains under the light of archaeological and historical evidence to carefully discuss the involvement of different transmission routes during the Second Plague Pandemic. Our interpretation showcases the importance of trade routes and human movements and further supports the identification of Yersinia pestis as the pathogenic agent of the so-called pestis secunda (1357–1366).Abstract: Over the last few years, genomic studies on Yersinia pestis, the causative agent of all known plague epidemics, have considerably increased in numbers, spanning a period of about 5,000 y. Nonetheless, questions concerning historical reservoirs and routes of transmission remain open. Here, we present and describe five genomes from the second half of the 14th century and reconstruct the evolutionary history of Y. pestis by reanalyzing previously published genomes and by building a comprehensive phylogeny focused on strains attributed to the Second Plague Pandemic (14th to 18th century). Corroborated by historical and ecological evidence, the presented phylogeny, which includes our Y. pestis genomes, could support the hypothesis of an entry of plague into Western European ports through distinct waves of introduction during the Medieval Period, possibly by means of fur trade routes, as well as the recirculation of plague within the human population via trade routes and human movement.Nasiman, T., Kanoh, H., 2018. Preparation of the Na2CO3–carbon nanocomposite and its CO2 capture. Energy & Fuels 32, 12689-12694. Na2CO3–carbon nanocomposite (NaC-NC) was prepared from terephthalic acid and NaOH, and its CO2 capture under moist conditions was examined by thermogravimetric analysis and X-ray diffraction. CO2 capture was repeated twice. The first CO2 capture reaction of bulk Na2CO3 was faster than its second, while the second capture reaction of NaC-NC was faster than its first. This may be because of the nanostructural properties of NaC-NC. The regeneration from NaHCO3 to Na2CO3 of NaC-NC proceeded at a lower temperature than with the bulk NaHCO3. Thus, compared with the bulk Na2CO3, we found that NaC-NC could efficiently capture CO2, increasing the reaction rate and decreasing the regeneration temperature.Ndip, E.A., Agyingi, C.M., Nton, M.E., Hower, J.C., Oladunjoye, M.A., 2019. Organic petrography and petroleum source rock evaluation of the Cretaceous Mamfe Formation, Mamfe basin, southwest Cameroon. International Journal of Coal Geology 202, 27-37. Mamfe basin is thought to be a rift splay segment of the southern Benue Trough and is genetically link to the Abakaliki and Anambra sub-basins in Nigeria. In the Mamfe basin very little studies have been done on maceral characterization and hydrocarbon generative potential of the Cretaceous black shale. Organic petrography and Rock–Eval pyrolysis studies were done on the black shale outcropping in the basin. The objectives were to determine the types of macerals present, and their relative abundance as well as their hydrocarbon generation potential; to assess the black shale's source rocks richness and quality; and to evaluate the source rock thermal maturity and the relationship between maturity and hydrocarbon generation. The results of this investigation indicated that the maceral content include relatively low percentages of vitrinite (4.9%), inertinite (3.4%) and scare liptinite (0.5%). The total organic carbon of the samples vary from 0.17 to 4.53?wt%, (mean?=?1.11?wt%) indicating poor to good source rocks generative potential while the S1 values ranges from 0.04–1.25?mg HC/g rock, (mean?=?0.23?mg HC/g rock), indicating poor–fair source rocks generation potential. Most of the samples are mature-peak mature for gaseous hydrocarbon generation. Based on the organic petrography and geochemical analyses performed on the black shale samples of the Mamfe Formation, they are described as mainly humic type III-reworked/oxidized type IV kerogen. The genetic potential of these source rocks is low and free hydrocarbon are absent. Given the prevalence of type III/IV kerogen, thermal maturity levels and hydrocarbon yield, it can be concluded that the source rocks of the Mamfe Formation have some moderate to fair potential for gaseous hydrocarbon which have not yet been generated at the present outcrop levels.Ni, Y., Zou, C., Cui, H., Li, J., Lauer, N.E., Harkness, J.S., Kondash, A.J., Coyte, R.M., Dwyer, G.S., Liu, D., Dong, D., Liao, F., Vengosh, A., 2018. Origin of flowback and produced waters from Sichuan Basin, China. Environmental Science & Technology 52, 14519-14527. gas extraction through hydraulic fracturing and horizontal drilling is increasing in China, particularly in Sichuan Basin. Production of unconventional shale gas with minimal environmental effects requires adequate management of wastewater from flowback and produced water (FP water) that is coextracted with natural gas. Here we present, for the first time, inorganic chemistry and multiple isotope (oxygen, hydrogen, boron, strontium, radium) data for FP water from 13 shale gas wells from the Lower Silurian Longmaxi Formation in the Weiyuan gas field, as well as produced waters from 35 conventional gas wells from underlying (Sinian, Cambrian) and overlying (Permian, Triassic) formations in Sichuan Basin. The chemical and isotope data indicate that the formation waters in Sichuan Basin originated from relics of different stages of evaporated seawater modified by water–rock interactions. The FP water from shale gas wells derives from blending of injected hydraulic fracturing water and entrapped saline (Cl ～ 50,000 mg/L) formation water. Variations in the chemistry, δ18O, δ11B, and 87Sr/86Sr of FP water over time indicate that the mixing between the two sources varies with time, with a contribution of 75% (first 6 months) to 20% (>year) of the injected hydraulic fracturing water in the blend that compose the FP water. Mass-balance calculation suggests that the returned hydraulic fracturing water consisted of 28–49% of the volume of the injected hydraulic fracturing water, about a year after the initial hydraulic fracturing. We show differential mobilization of Na, B, Sr, and Li from the shale rocks during early stages of operation, which resulted in higher Na/Cl, B/Cl, Li/Cl, and 87Sr/86Sr and lower δ11B of the FP water during early stages of FP water formation relative to the original saline formation water recorded in late stages FP water. This study provides a geochemical framework for characterization of formation waters from different geological strata, and thus the ability to distinguish between different sources of oil and gas wastewater in Sichuan Basin.Nicewonger, M.R., Aydin, M., Prather, M.J., Saltzman, E.S., 2018. Large changes in biomass burning over the last millennium inferred from paleoatmospheric ethane in polar ice cores. Proceedings of the National Academy of Sciences 115, 12413-12418.: Biomass burning influences the climate system through direct emissions of aerosols, greenhouse gases, and chemically reactive gases. There is uncertainty and controversy regarding variations in past biomass burning, making it difficult to establish the climate sensitivity of biomass burning in current climate models. This study presents new measurements of ethane in air trapped in polar ice cores. The results indicate that biomass burning emissions exceeded modern levels during the Medieval Period (1000–1500 CE) but then decreased substantially during the Little Ice Age (1600–1800 CE), indicating the sensitivity of biomass burning to climate during the preindustrial era. Such positive feedbacks between biomass burning and climate may make it difficult to achieve societal climate goals.Abstract: Biomass burning drives changes in greenhouse gases, climate-forcing aerosols, and global atmospheric chemistry. There is controversy about the magnitude and timing of changes in biomass burning emissions on millennial time scales from preindustrial to present and about the relative importance of climate change and human activities as the underlying cause. Biomass burning is one of two notable sources of ethane in the preindustrial atmosphere. Here, we present ice core ethane measurements from Antarctica and Greenland that contain information about changes in biomass burning emissions since 1000 CE (Common Era). The biomass burning emissions of ethane during the Medieval Period (1000–1500 CE) were higher than present day and declined sharply to a minimum during the cooler Little Ice Age (1600–1800 CE). Assuming that preindustrial atmospheric reactivity and transport were the same as in the modern atmosphere, we estimate that biomass burning emissions decreased by 30 to 45% from the Medieval Period to the Little Ice Age. The timing and magnitude of this decline in biomass burning emissions is consistent with that inferred from ice core methane stable carbon isotope ratios but inconsistent with histories based on sedimentary charcoal and ice core carbon monoxide measurements. This study demonstrates that biomass burning emissions have exceeded modern levels in the past and may be highly sensitive to changes in climate.Nichols, C.M., Dodds, J.N., Rose, B.S., Picache, J.A., Morris, C.B., Codreanu, S.G., May, J.C., Sherrod, S.D., McLean, J.A., 2018. Untargeted molecular discovery in primary metabolism: Collision cross section as a molecular descriptor in ion mobility-mass spectrometry. Analytical Chemistry 90, 14484-14492. this work, we established a collision cross section (CCS) library of primary metabolites based on analytical standards in the Mass Spectrometry Metabolite Library of Standards (MSMLS) using a commercially available ion mobility-mass spectrometer (IM-MS). From the 554 unique compounds in the MSMLS plate library, we obtained a total of 1246 CCS measurements over a wide range of biochemical classes and adduct types. Resulting data analysis demonstrated that the curated CCS library provides broad molecular coverage of metabolic pathways and highlights intrinsic mass–mobility relationships for specific metabolite superclasses. The separation and characterization of isomeric metabolites were assessed, and all molecular species contained within the plate library, including isomers, were critically evaluated to determine the analytical separation efficiency in both the mass (m/z) and mobility (CCS/ΔCCS) dimension required for untargeted metabolomic analyses. To further demonstrate the analytical utility of CCS as an additional molecular descriptor, a well-characterized biological sample of human plasma serum (NIST SRM 1950) was examined by LC-IM-MS and used to provide a detailed isomeric analysis of carbohydrate constituents by ion mobility.Nicolaisen, J.B., Elvebakk, G., Ahokas, J., Bojesen-Koefoed, J.A., Olaussen, S., Rinna, J., Skeie, J.E., Stemmerik, L., 2019. Characterization of Upper Palaeozoic organic-rich units in Svalbard: Implications for the petroleum systems of the Norwegian Barents Shelf. Journal of Petroleum Geology 42, 59-78. discoveries of hydrocarbons along the western margin of the Norwegian Barents Shelf have emphasised the need for a better understanding of the source rock potential of the Upper Palaeozoic succession. In this study, a comprehensive set of organic geochemical data have been collected from the Carboniferous – Permian interval outcropping on Svalbard in order to re‐assess the offshore potential. Four stratigraphic levels with organic‐rich facies have been identified: (i) Lower Carboniferous (Mississippian) fluvio‐lacustrine intervals with TOC between 1 and 75 wt.% and a cumulative organic‐rich section more than 100 m thick; (ii) Upper Carboniferous (Pennsylvanian) evaporite‐associated marine shales and organic‐rich carbonates with TOC up to 20 wt.%; (iii) a widespread lowermost Permian organic‐rich carbonate unit, 2–10 m thick, with 1–10 wt. % TOC; and (iv) Lower Permian organic‐rich marine shales with an average TOC content of 10 wt.%.Petroleum can potentially be tied to organic‐rich facies at formation level based on the gammacerane index, δ13C of the aromatic fraction and/or the Pr/Ph ratio. Relatively heavy δ13C values, a low gammacerane index and high Pr/Ph ratios characterize Lower Carboniferous non‐marine sediments, whereas evaporite‐associated facies have lighter δ13C, a higher gammacerane index and lower Pr/Ph ratios. Nie, H., Sun, C., Liu, G., Du, W., He, Z., 2019. Dissolution pore types of the Wufeng Formation and the Longmaxi Formation in the Sichuan Basin, south China: Implications for shale gas enrichment. Marine and Petroleum Geology 101, 243-251. shale gas reservoirs, scientific consensus indicates that the main pore types are organic matter pores, mineral pores and micro-fractures. The organic matter pores are crucial to porosity, and in many cases they form the main pore type favorable for shale gas enrichment. Dissolution pores can influence shale gas enrichment and preservation. Although the various types of dissolution pores have been reported, few studies have identified the characteristics of mineral dissolution pores, let alone the development of dissolution pores and their effect on shale gas enrichment. Based on observations from shale gas wells in the Sichuan Basin, this paper studied the types of dissolution pores in the Wufeng Formation and the Longmaxi Formation. The study shows that the types of dissolution pores are carbonate dissolution pores, feldspar dissolution pores, and quartz dissolution pores and that carbonate dissolution pores are the main type. The formation time of the dissolution pores can be identified through analyzing the time of the mineral generation and the time at which the solid bitumen and/or minerals filled in the dissolution pores. We found that the dissolution pores in the secondary enlargement of minerals formed later than those in the original minerals. The dissolution pores without solid bitumen may have formed later than the dissolution pores with solid bitumen filling. Given that the dissolution pores had formed before the peak stage of oil generation, the dissolution pores should be well connected through the dissolved trench, which would largely improve the reservoir volume for hydrocarbon storage and matrix permeability. If there is no solid bitumen filling in the dissolution pores and the formation of the dissolution pores began after the crude oil was charged but before the peak stage of gas generation, these conditions will have some destructive effects on shale gas enrichment. In the worst-case scenario, if the dissolution pores formed after the peak stage of gas generation, the development of the pores will likely destroy the shale gas enrichment and can convert reservoir pressure to a normal pressure. The new findings in this paper reveal that the formation time of the dissolution pores has a controlling effect on shale gas enrichment in the Wufeng Formation and the Longmaxi Formation in the Sichuan Basin; these findings also provide valuable guidance for future research on shale gas reservoirs around the world.Niehus, N.C., Brockmeyer, B., Witt, G., 2019. Bioavailability and distribution of PAHs and PCBs in the sediment pore water of the German Bight and Wadden Sea. Marine Pollution Bulletin 138, 421-427. freely dissolved concentration (Cfree) was measured for PAHs and PCBs in sediments of the German Bight and Wadden Sea. Ex-situ Solid Phase Microextraction (SPME) was applied using Polydimethlysiloxane (PDMS) coated glass fibers followed by automated thermal desorption and GC–MS analysis. This study provides the first dataset on the spatial distribution of Cfree for PAHs and PCBs in the German Bight and the Wadden Sea. We found elevated PCB concentrations in the Wadden Sea and especially in the Weser estuary. Sandy North Sea sediments were rather less contaminated, except for some former dumping sites. The sorption strength of PAHs was generally stronger, while PCBs in the Wadden Sea sediments were only weakly bound. This SPME method is a rapid and sensitive tool to study Cfree of hydrophobic organic chemicals to improve todays sediment risk assessment.Nordeng, S.H., 2019. The statistical compensation effect in nonisothermal kinetics: Theory, simulations and experimental evidence. Organic Geochemistry 127, 124-135. “compensation effect” refers to the general presence of a linear relationship between experimental activation energies (Ea) and the logarithm of the corresponding frequency factor (A). This study examined the compensation effect with regard to petroleum generation and source rocks found in the Bakken Formation in the Williston Basin. The specific purpose was to test whether or not these compensation effects are caused by experimental conditions or actual differences in source rock kinetics.An analytical solution for the compensation effect developed for isothermal kinetics experiments is adapted for use with the Kissinger method for obtaining activation energies (Ea) and frequency factors (A) from nonisothermal experiments (programed pyrolysis). This results in an expression that shows that the linear relationship between Ea and ln(A) or compensation effect, present in most if not all, kinetic analyses of source rocks, is an artifact of experimental design and error and is not caused by an underlying physiochemical property. The compensation effect described by this expression, caused by experimental errors, forms an extremely elongated error ellipse in the Ea-ln(A) plane that is closely approximated by a line that corresponds its principal or major axis. The gradient of the principal axis is equal to the product of the harmonic mean of the peak reaction temperatures and the gas constant.Simulated programmed pyrolysis experiments demonstrate that the reformulated analytical solution, when applied to the Kissinger Equation, predicts the slope of the linear dependence between different apparent values of Ea and ln(A) caused by experimental imprecision. This result is present in rearranged and multiple split experimental data. Even though the apparent kinetic parameters may vary between analyses within a single set of sample splits, all share the same statistical compensation effect and demonstrate equivalent kinetics, whereas sample splits with different kinetic parameters lie along different statistical compensation effects. The results show that it is not possible to differentiate source rocks on the basis of apparent values of Ea and A without also demonstrating that these kinetic parameters lie along statistically different compensation effects. Failure to recognize this behavior leads to serious errors when extrapolated to geologic time and temperature scales.Nutz, A., Schuster, M., 2018. Comments on: “A leaf wax biomarker record of early Pleistocene hydroclimate from West Turkana, Kenya” by Lupien et?al. [Quat. Sci. Rev. 186 (2018), 225–235]. Quaternary Science Reviews 201, 505-507. to: R.L. Lupien, J.M. Russell, C. Feibel, C. Beck, I. Casta?eda, A. Deino, A.S. Cohen. A leaf wax biomarker record of early Pleistocene hydroclimate from West Turkana, Kenya. Quaternary Science Reviews, Volume 186, 15 April 2018, Pages 225-235Referred to by: R.L. Lupien, J.M. Russell, C. Feibel, C. Beck, I. Cast?neda, A. Deino, A.S. Cohen. Reply to comments by Nutz and Schuster (2018) on “A leaf wax biomarker record of early Pleistocene hydroclimate from West Turkana, Kenya” Quaternary Science Reviews, Volume 201, 1 December 2018, Pages 508-510In a recent paper, Lupien et al. (2018) present an innovative study of an HSPDP drill core recovered from West Turkana (Kenya) (Cohen et al., 2016). The authors use shifts in the hydrogen-isotope composition of terrestrial leaf waxes as a proxy of changes in regional hydrology between 1.86 and 1.37 Ma, a critical period for human evolution . This remarkable study provides valuable and novel Quaternary paleoclimate proxy data for the Turkana Depression and, as such, represents an important contribution to geological and paleoenvironmental investigations in this area. Nonetheless, some interpretations of this recent paper are in contradiction with field interpretations published by Nutz et al. (2017), a paper not cited nor discussed by Lupien et al. (2018). Hence, we believe that some of the interpretations of Lupien et al. (2018) should be discussed and nuanced.Nutz et al. (2017) applied facies and sequence stratigraphy analyses to exposed sediments of the Nachukui Fm (Omo Group) along the western shore of Lake Turkana. Dated between 1.95 and 1.72 Ma, the period discussed in Nutz et al. (2017) covers ca. 29% of the period discussed by Lupien et al. (2018). Based on a sedimentary succession that ranged from offshore to coastal lake depositional environments, Nutz et al. (2017) traced the progradation-retrogradation patterns of the paleoshoreline. They reflect regression-transgression of paleolake Turkana, and serve as a proxy of regional hydroclimate evolution. Nutz et al. (2017) demonstrated that from 1.95 to 1.72 Ma (i) the expansion and contraction of paleolake Turkana occurred at an orbital scale with a first-order trend of 400 ka (eccentricity) having superimposed higher frequency cycles at 20 ka (precession), (ii) the 400-ka periodicity drove important changes in bathymetry (>40 m), and (iii) the 20-ka periodicity triggered more limited changes in bathymetry (<25 m) associated with a relatively restricted lateral shift of the shoreline (3–4 km); these changes are of a lower magnitude than those of the last African Humid Period (Holocene). Finally, Nutz et al. (2017) conclude that from 1.95 to 1.72 Ma the lake level of paleolake Turkana was relatively stable. Thus, this period does not reflect a period of marked climate variability.Hereafter, we focus on five points of Lupien et al. (2018) for which interpretations are, in our view, not accurate or that are contradicted by direct field observations. (i) “Our data indicate little change in the long-term mean hydroclimate during this interval, in contrast to inferred changes in the level of Lake Turkana.” (Lupien et al., 2018: 225). There is no continuous reconstruction of paleolake Turkana lake levels existing in the literature for this time interval, nor any actual estimates of the amplitude of lake-level change. The sole exception to this statement is the uncited Nutz et al. (2017); however, they refer only to the 1.95–1.72 Ma interval. References cited by Lupien et al. (2018: 226), i.e., Feibel (2011) and Feibel et al. (1989), do not present a curve of paleolake Turkana water level changes, nor do they provide an estimate of the amplitude of lake-level variation. Thus, they do not provide a sufficiently constrained or continuous reconstruction of lake-level fluctuations (from 1.86 to 1.37 Ma) to suggest, “dramatic lake level changes”. Thus, this affirmation is unfounded, and the new results of Lupien et al. (2018) support previous studies (Joordens et al. (2011); Nutz et al., 2017) that demonstrate a relatively low amplitude of paleolake Turkana fluctuations for the investigated period.Furthermore, we do not understand why Lupien et al. (2018) state that published changes in lake level do not agree with their new results. By arguing this, the authors are forced to hypothesize that “lake level may be responding dominantly to deltaic progradation or tectonically-driven changes in the basin configuration as opposed to hydroclimate.“ (Lupien et al., 2018: 225). This is highly improbable and, at the least, requires further explanation and geological data to support this contention. Lake-level fluctuation controlled by deltaic progradation-retrogradation is very speculative and, to our knowledge, has yet to be described. Deltaic progradation-retrogradation is, in most cases, considered to follow the evolution of base level rather than controlling base level evolution in of itself. This is a basic concept of sequence stratigraphy (e.g., Catuneanu, 2002; Swift et al., 2003; Helland-Hansen and Hampson, 2009).In regard to rift lake evolution, the main potential tectonic process responsible for changing lake level is subsidence, which would modify basin physiography. However, acceleration in subsidence has a longer-term periodicity of 105–106 years, rather than the 104 years of the precessional periodicity. As such, even if tectonic processes and the related time scale both control the long-term evolution of lake levels, tectonic processes cannot explain lake level variation tuned by precessional cycles. The authors could have also proposed volcanism as a potential driver of paleolake-level fluctuations. The successive and repeated emptying of magma chambers can modify basin physiography. However, this hypothesis has also been rejected (see discussion in Nutz et al., 2017). Interpreting lake-level fluctuations as not being derived from climate (sensuLupien et al. 2018) is very complicated, especially when considering the time scale of the climate shifts. (ii) “Time-series spectral analyses of the isotopic data reveal strong precession-band (21 kyr) periodicity, indicating that regional hydroclimate was strongly affected by changes in insolation .” (Lupien et al., 2018: 225). Here, we question the direct relationships proposed by Lupien et al. (2018) between the identification of a strong precession-band periodicity and the strong hydroclimatic response. The identification of a precessional periodicity agrees with Joordens et al. (2011) and Nutz et al. (2017), both of whom identified a similar periodicity, albeit over shorter periods. However, spectral analyses of the time series do not provide any estimate of the amplitude of hydroclimatic change. Therefore, it is not possible to infer the impacts on paleolake levels, paleolandscapes, and paleoenvironments. Thus, we believe that the term “strongly affected” is an over-interpretation. This raises the question of how to conciliate the identification of a particular climate process from a drill core and its real impact on paleoenvironments and paleolandscapes.(iii) “We observe an interval of particularly high-amplitude hydrologic variation at ～1.7 Ma, which occurs during a time of high orbital eccentricity hence large changes in precessionally-driven insolation amplitude.” (Lupien et al., 2018: 225). Moreover, Lupien et al. (2018: 232) conclude that “The time interval from ～1.8 to 1.7 Ma is marked by extremely high amplitude hydrologic change that greatly exceeds the variance observed during the last ～20 kyr, including the well-known African Humid Period.” Lupien et al. (2018) suggest that hydrologic changes between 1.8 and 1.7 Ma were greater than those recorded for the last 20 kyr. Nutz et al. (2017) conclude the opposite. Based on the tracking of paleoshoreline migration Nutz et al. (2017) demonstrated that fluctuations of paleolake bathymetr between 1.95 and 1.72 Ma were of much lower magnitude (<25 m) than fluctuations during the Late Quaternary (i.e., ～100 m below present-day lake level; Morrissey and Scholz, 2014) and the Holocene </topics/earth-and-planetary-sciences/holocene> (i.e., ～100 m above present-day lake level; Garcin et al. 2012; Nutz and Schuster, 2016). This shows that the amplitude of proxy fluctuations cannot be directly correlated to amplitudes of hydrologic change.(iv) Lupien et al. (2018: 231) state that “… lake depth records derived from outcrops </topics/earth-and-planetary-sciences/outcrop> exhibit a binary response to climate (i.e. lake vs. no lake), making it difficult to investigate the extent of aridity during insolation minima.” We disagree with this archaic and simplistic view of lacustrine depositional systems. For several decades now, conventional sedimentological tools, i.e., facies </topics/earth-and-planetary-sciences/facies> and sequence analyses, have demonstrated their ability to differentiate various lacustrine depositional sub-environments, such as direct proxies for relative changes in bathymetry and changes in paleohydrology </topics/earth-and-planetary-sciences/paleohydrology>. A number of publications provide examples in which paleolake systems present alternate depositional environments that are associated with various paleobathymetries represented by different facies associations (e.g., Létteron et al., 2018; Schuster and Nutz, 2018; Renaut and Gierlowski-Kordesch, 2010; Keighley, 2008; Adams, 2007; Orti et al., 2007; Dam and Surlik, 1992; Martel and Gibling, 1991; Renaut and Owen, 1991).(v) Additionally, we note two mistakes on Figure 1 (Lupien et al., 2018: 226): first, the given core location is some 30 km north of the actual drill site (e.g.,Sier et al., 2017), and second, the proposed outline of “paleolake Lorenyang” is not found within the cited references (Brown and Feibel, 1991).To conclude, core analysis such as the one provided by Lupien et al. (2018) is essential for identifying the climate processes that have impacted a particular region. However, the study of outcrops </topics/earth-and-planetary-sciences/outcrop>, such as presented in Nutz et al. (2017), remains the only approach permitting the deciphering of the real impacts of the different climate processes on paleoenvironments and paleolandscapes. Since both of these aspects are crucial, especially when discussing the context of human evolution, we believe that future methodological breakthroughs will involve a combined approach to prevent over-interpretations of both 1-D high-resolution proxy analysis and 2.5-D outcrop-based studies.Oliveira, I., Gomes, L., Franceschi, E., Borges, G., de Conto, J.F., Albuquerque, F.C., Dariva, C., 2018. Surface and interface characterization of asphaltenic fractions obtained with different alkanes: A study by atomic force microscopy and pendant drop tensiometry. Energy & Fuels 32, 12174-12186. is recognized that asphaltenes have a tendency toward aggregation and precipitation. Even at low concentrations, they can adsorb at interfaces/surfaces where each type of interaction plays an important role in different stages of oil production. In order to evaluate the behavior of asphaltenes, it is necessary to conduct studies that allow the understanding of their chemical and physical structure, as well as to assess how they behave interfacially and superficially. By using the Pendant Drop Tensiometry and Atomic Force Microscopy techniques, the present work aims to characterize the interfacial behavior and the surface structure of two asphaltenic fractions obtained through the precipitation using n-heptane and propane as flocculants. Asphaltenic fractions were characterized by Fourier transform infrared spectroscopy, elementary analysis, gel permeation chromatography, and differential scanning calorimetry, to obtain their physicochemical characteristics. Fractions were deposited in glass substrates at different concentrations, and the contact angle between water and the substrate was determined, identifying how the different asphaltenic fractions influence the wettability of the surface, even at low concentrations. When precipitation was conducted using propane, the asphaltenic fraction showed distinct structural characteristics that were obtained by precipitation with heptane. Atomic force microscopy suggested the formation of different surface arrangements between the fractions, caused by the higher presence of resins in the fractions precipitated by propane. The pendant drop tensiometry evidenced that the asphaltenic fraction insoluble in heptane showed greater affinity to migration to the interface, producing films more resistant to the deformation, than the asphaltene fraction insoluble in propane.Olivon, F., Elie, N., Grelier, G., Roussi, F., Litaudon, M., Touboul, D., 2018. MetGem software for the generation of molecular networks based on the t-SNE algorithm. Analytical Chemistry 90, 13900-13908. networking (MN) is becoming a standard bioinformatics tool in the metabolomic community. Its paradigm is based on the observation that compounds with a high degree of chemical similarity share comparable MS2 fragmentation pathways. To afford a clear separation between MS2 spectral clusters, only the most relevant similarity scores are selected using dedicated filtering steps requiring time-consuming parameter optimization. Depending on the filtering values selected, some scores are arbitrarily deleted and a part of the information is ignored. The problem of creating a reliable representation of MS2 spectra data sets can be solved using algorithms developed for dimensionality reduction and pattern recognition purposes, such as t-distributed stochastic neighbor embedding (t-SNE). This multivariate embedding method pays particular attention to local details by using nonlinear outputs to represent the entire data space. To overcome the limitations inherent to the GNPS workflow and the networking architecture, we developed MetGem. Our software allows the parallel investigation of two complementary representations of the raw data set, one based on a classic GNPS-style MN and another based on the t-SNE algorithm. The t-SNE graph preserves the interactions between related groups of spectra, while the MN output allows an unambiguous separation of clusters. Additionally, almost all parameters can be tuned in real time, and new networks can be generated within a few seconds for small data sets. With the development of this unified interface (<;), we fulfilled the need for a dedicated, user-friendly, local software for MS2 comparison and spectral network generation.Omran, B.A., Nassar, H.N., Younis, S.A., Fatthallah, N.A., Hamdy, A., El-Shatoury, E.H., El-Gendy, N.S., 2019. Physiochemical properties of Trichoderma longibrachiatum DSMZ 16517-synthesized silver nanoparticles for the mitigation of halotolerant sulphate-reducing bacteria. Journal of Applied Microbiology 126, 138-154.: In order to efficiently control the corrosive sulphate‐reducing bacteria (SRB), the main precursor of the microbial influenced corrosion (MIC) in oil industry, the ability of Trichoderma longibrachiatumDSMZ 16517 to synthesize silver nanoparticles (AgNPs) was investigated and their biocidal activity against halotolerant SRB was tested. Methods and Results: The mycelial cell‐free filtrate (MCFF) bioreduced the silver ions (Ag+) to their metallic nanoparticle state (Ag0), which was presumptively indicated by the appearance of a dark brown suspension and confirmed by the characteristic absorbance of AgNPs at ?422nm. One‐factor‐at‐a‐time technique was used to optimize the effect of temperature, time, pH, fungal biomass and silver nitrate concentrations, stirring rates and dark effect. The dynamic light scattering (DLS) analysis revealed average AgNPs size and zeta potential values of 17·75 nm and ?26·8 mV, respectively, indicating the stability of the prepared AgNPs. The X‐ray diffraction (XRD) pattern assured the crystallinity of the mycosynthesized AgNPs, with an average size of 61 nm. The field emission scanning electron microscope (FESEM) and high‐resolution transmission electron microscope (HRTEM) showed nonagglomerated spherical, triangular and cuboid AgNPs ranging from 5 to 11 ± 0·5 nm. The Fourier transform infrared spectroscopy (FT‐IR) analysis of the mycosynthesized AgNPs affirmed the role of MCFF as a reducing and capping agent. A preliminary suggested mechanism for mycosynthesis of AgNPs was elucidated. The mycosynthesized AgNPs expressed high biocidal activity against a halotolerant planktonic mixed culture of SRB. The HRTEM analysis showed a clear evidence of an alteration in cell morphology, a disruption of SRB cell membranes, a lysis in cell wall and a cytoplasmic extraction after treatment with AgNPs. This confirmed the bactericidal effect of the mycosynthesized AgNPs. Conclusion: The biocidal activity of the mycosynthesized AgNPs against halotolerant planktonic SRB makes it an attractive option to control MIC in the petroleum industry.Significance and Impact of the Study: This research provides a helpful insight into the development of a new mycosynthesized biocidal agent against the corrosive sulphate‐reducing bacteria.Orland, C., Emilson, E.J.S., Basiliko, N., Mykytczuk, N.C.S., Gunn, J.M., Tanentzap, A.J., 2019. Microbiome functioning depends on individual and interactive effects of the environment and community structure. ISME Journal 13, 1-11. ecosystem functioning changes with microbial communities remains an open question in natural ecosystems. Both present-day environmental conditions and historical events, such as past differences in dispersal, can have a greater influence over ecosystem function than the diversity or abundance of both taxa and genes. Here, we estimated how individual and interactive effects of microbial community structure defined by diversity and abundance, present-day environmental conditions, and an indicator of historical legacies influenced ecosystem functioning in lake sediments. We studied sediments because they have strong gradients in all three of these ecosystem properties and deliver important functions worldwide. By characterizing bacterial community composition and functional traits at eight sites fed by discrete and contrasting catchments, we found that taxonomic diversity and the normalized abundance of oxidase-encoding genes explained as much variation in CO2 production as present-day gradients of pH and organic matter quantity and quality. Functional gene diversity was not linked to CO2 production rates. Surprisingly, the effects of taxonomic diversity and normalized oxidase abundance in the model predicting CO2 production were attributable to site-level differences in bacterial communities unrelated to the present-day environment, suggesting that colonization history rather than habitat-based filtering indirectly influenced ecosystem functioning. Our findings add to limited evidence that biodiversity and gene abundance explain patterns of microbiome functioning in nature. Yet we highlight among the first time how these relationships depend directly on present-day environmental conditions and indirectly on historical legacies, and so need to be contextualized with these other ecosystem properties.Orr, F.M., Jr., 2018. Carbon capture, utilization, and storage: An update. SPE Journal 23, 2444-2455, SPE-194190-PA. progress in carbon capture, utilization, and storage (CCUS) is reviewed. Considerable research effort has gone into carbon dioxide (CO2) capture, with many promising separation processes in various stages of development, but only a few have been tested at commercial scale, and considerable additional development will be required to determine competitiveness of new technologies. Processes for direct capture of CO2 from the air are also under development and are starting to be tested at pilot scale. Transportation of CO2 to storage sites by pipeline is well-established, though substantially more pipeline capacity will be required if CCUS is to be undertaken at a large scale. Considerable experience has now been built up in enhanced-oil-recovery (EOR) operations, which have been under way since the 1970s. Storage in deep saline aquifers has also been achieved at scale. Recent large-scale projects that capture and store CO2 are described, as are current and potential future markets for CO2. Potential effects of changes in the US tax code Section 45Q on those markets are summarized. Future deployment of CCUS will depend more on cost reductions for CO2 separations, development of new markets for CO2, and the complexities of project finance than on technical issues associated with storage of CO2 in the subsurface.Ospadov, E., Tao, J., Staroverov, V.N., Perdew, J.P., 2018. Visualizing atomic sizes and molecular shapes with the classical turning surface of the Kohn–Sham potential. Proceedings of the National Academy of Sciences 115, E11578-E11585.: Can quantum mechanics predict a well-defined and chemically intuitive size and shape for an atom or a molecule? We show that the bounding surface of a chemical species can be naturally defined as the classical turning surface of the Kohn–Sham potential—an effective potential that, acting on noninteracting electrons, yields the ground-state density of the real system. The atomic and ionic radii defined in this manner display all expected periodic trends, while the ratio of a bond length to the sum of atomic or ionic radii identifies the type of the bond (covalent, ionic, hydrogen, or van der Waals). The proposed approach permits a visual representation of chemical species that is intuitive and quantum-mechanically rigorous at the same time.Abstract: The Kohn–Sham potential v eff (r) veff(r) is the effective multiplicative operator in a noninteracting Schr?dinger equation that reproduces the ground-state density of a real (interacting) system. The sizes and shapes of atoms, molecules, and solids can be defined in terms of Kohn–Sham potentials in a nonarbitrary way that accords with chemical intuition and can be implemented efficiently, permitting a natural pictorial representation for chemistry and condensed-matter physics. Let ? max ?max be the maximum occupied orbital energy of the noninteracting electrons. Then the equation v eff (r)=? max veff(r)=?max defines the surface at which classical electrons with energy ?≤? max ?≤?max would be turned back and thus determines the surface of any electronic object. Atomic and ionic radii defined in this manner agree well with empirical estimates, show regular chemical trends, and allow one to identify the type of chemical bonding between two given atoms by comparing the actual internuclear distance to the sum of atomic radii. The molecular surfaces can be fused (for a covalent bond), seamed (ionic bond), necked (hydrogen bond), or divided (van der Waals bond). This contribution extends the pioneering work of Z.-Z. Yang et al. [Yang ZZ, Davidson ER (1997) Int J Quantum Chem 62:47–53; Zhao DX, et al. (2018) Mol Phys 116:969–977] by our consideration of the Kohn–Sham potential, protomolecules, doubly negative atomic ions, a bond-type parameter, seamed and necked molecular surfaces, and a more extensive table of atomic and ionic radii that are fully consistent with expected periodic trends.Otwell, A.E., López García de Lomana, A., Gibbons, S.M., Orellana, M.V., Baliga, N.S., 2018. Systems biology approaches towards predictive microbial ecology. Environmental Microbiology 20, 4197-4209. complex interspecies interactions, microbial processes drive nutrient cycling and biogeochemistry. However, we still struggle to predict specifically which organisms, communities and biotic and abiotic processes are determining ecosystem function and how environmental changes will alter their roles and stability. While the tools to create such a predictive microbial ecology capability exist, cross‐disciplinary integration of high‐resolution field measurements, detailed laboratory studies and computation is essential. In this perspective, we emphasize the importance of pursuing a multiscale, systems approach to iteratively link ecological processes measured in the field to testable hypotheses that drive high‐throughput laboratory experimentation. Mechanistic understanding of microbial processes gained in controlled lab systems will lead to the development of theory that can be tested back in the field. Using N2O production as an example, we review the current status of field and laboratory research and layout a plausible path to the kind of integration that is needed to enable prediction of how N‐cycling microbial communities will respond to environmental changes. We advocate for the development of realistic and predictive gene regulatory network models for environmental responses that extend from single‐cell resolution to ecosystems, which is essential to understand how microbial communities involved in N2O production and consumption will respond to future environmental conditions.Pan, S., Wang, Q., Bai, J., Chi, M., Cui, D., Wang, Z., Liu, Q., Xu, F., 2018. Molecular structure and electronic properties of oil shale kerogen: An experimental and molecular modeling study. Energy & Fuels 32, 12394-12404. this study, structural parameters of Longkou oil shale kerogen were examined and identified by the combination of pyrolysis–gas chromatography–mass spectrometry, Fourier transform infrared spectroscopy, 13C nuclear magnetic resonance spectroscopy, and X-ray photoelectron spectroscopy. Based on the experimental data, a three-dimensional kerogen model was generated using quantum chemistry and molecular dynamics methods. The optimized molecular configuration was discussed, which showed good agreement with the experimental results in terms of structural characteristics. Electron density analysis was performed to examine the bonding characteristics of kerogen, and the bond length distribution of the Longkou kerogen model was analyzed, revealing that the S atom exhibits higher affinity for the H atom compared to the aliphatic carbon from the comparison of the electron density of the C–S and S–H bonding regions. Mulliken charge analysis was carried out to evaluate the partial atomic charges of heteroatoms. The charges on the cyclic structure tended to be equally distributed because of the presence of conjugated π bond, leading to the loss of charges on the N atoms. Besides, the HOMO–LUMO properties of Longkou kerogen were calculated, and a detailed picture of the frontier orbitals of kerogen for the inter- or intramolecular chemical reactions was obtained. This study validated that polycyclic aromatic structures in kerogen play a crucial role in the reactive sites for bond cleavage during the deformation of kerogen.Pang, Y., Tian, Y., Soliman, M.Y., Shen, Y., 2019. Experimental measurement and analytical estimation of methane absorption in shale kerogen. Fuel 240, 192-205. storage in shale (organic-rich mudstone) consists of three different states: free gas in pores and natural fractures; adsorbed gas on organic and inorganic pore walls; and absorbed gas into organic matter (kerogen). Since it is difficult to differentiate absorbed gas from adsorbed gas, most current studies combine the adsorbed gas with absorbed gas and call the combination as gas sorption. In this study, a conceptual model of gas sorption is proposed to account for the contributions from adsorption and absorption to gas storage in shale, respectively. Methane sorption capacity of Barnett and Eagle Ford shale core samples is measured by magnetic suspension sorption system. Regression analysis is performed on the measured data by Simplified Local-Density model coupled with modified Peng-Robinson Equation of State (SLD-PR). Absolute sorption capacity of these two shale core samples is estimated based on the density profile of SLD-PR model. Additionally, the absorbed gas, which is regarded as the gas molecules dissolving/diffusing into the bulk of solid kerogen, is distinguished from the adsorbed gas through interpreting the results of gas expansion measurements using Fick’s law of diffusion. Moreover, methane diffusion coefficients for the two shale core samples are determined, which range from 10?22?m2/s to 10?21?m2/s. The percentage of absorbed gas accounting for total sorbed gas increases with pore pressure. When the pore pressure increases, more gas molecules attempt to adsorb on the surface of kerogen and create a larger gas concentration gradient for gas diffusing into the kerogen. The gas molecules, which adsorb on the pore walls of kerogen and then diffuse into the solid lattice of kerogen, may lead to the swelling of kerogen and thus reduce the pore width for free gas transportation. Therefore, the accurate prediction of the gas absorption capacity of kerogen is significant to understand gas storage mechanism and characterize original gas in place (OGIP) in shale gas reservoirs.Pang, Z., Tao, S., Zhang, Q., Zhang, T., Yang, J., Fan, J., Yuan, M., 2018. Secondary migration mechanism and accumulation controlling factors of Jurassic tight oil in Sichuan Basin. Acta Petrolei Sinica 39, 1211-1222. physical analog experiment, cast and fluorescent thin sections, field emission scanning electron microscope (FESEM)and environment scanning electron microscope (ESEM)were utilized to study the secondary migration mechanism and accumulation controlling factors of Jurassic tight oil in central Sichuan Basin. It was revealed that under the huge migration driving force, tight oil in the study area migrated with low speed non-Darcy flow through a low efficient migration path, and underwent three migration and seepage phases, including viscous flow, nonlinear flow, and quasi-linear flow. The mode was characterized by microscopic pore-facture complex conduction and macroscopic large-scale short-distance migration. Based on the migration mechanisms, the favorable tight oil play was controlled by the distribution of profitable source rocks. The hydrocarbon generating intensity of 4.0×105t/km2 indicated the distribution boundary of favorable tight oil play in the study area. High permeability and porosity reservoir formed tight oil sweet spots, and high-capacity wells were closely related to the development of fracures in a majority.Panja, P., Pathak, M., Deo, M., 2019. Productions of volatile oil and gas-condensate from liquid rich shales. Advances in Geo-Energy Research 3, 29-42. growth in productions of liquid hydrocarbons from tight formations (shales) has been phenomenal in recent years. During the production of liquids (oil and condensate), large amounts of associated gas are also produced. The economic viability of a producing well depends on maintaining a reasonable proportion of liquid. The compositions and state of reservoir fluid play an important role in producing liquids from tight formations or shales in the USA such as Eagle Ford in Texas, Niobrara in Wyoming-Colorado, and Bakken in North Dakota. Small deviation in reservoir temperature around the critical point changes the state of the fluid (volatile oil or condensate) and as a result, the production of liquid is affected. Impacts of the state of the fluid (volatile oil or condensate), reservoir permeability and operating conditions on ultimate recoveries and produced gas liquid ratio are studied here. Five different reservoir fluids representing low to high liquid hydrocarbon contents are considered. Around 2% increment in condensate recovery after 10 years of production is observed from 100 nD permeability reservoir filled with the richest fluid (fluid 5) when the well is operated at 3000 psia compared to 1000 psia. At the same conditions, 9.3% more condensate is recovered for the leanest fluid (fluid 1). Therefore, operating the well at higher flowing bottom hole pressure (BHP) maximized the liquid recoveries of volatile oils and condensates in case of low permeability reservoirs (100 nD). However, in case of higher permeability (1000 nD) reservoir, lower operating pressure was preferable to increase the recovery. Conclusively, bottom hole pressure has less impact on the richer fluids and higher permeability reservoir. Operating well at higher BHP (3000 psia) also suppresses the production of gas and relatively enhances the production of liquid. Liquid to gas ratio (LGR) declines more rapidly for 100 nD permeability reservoirs compared to 1000 nD at BHP of 1000 psia. High fracture permeability (1000mD and above) appeared to negatively affect liquid recoveries at higher BHP resulting in reduction of recovery by around 2%. An optimum fracture permeability may be necessary based on reservoir permeability, operating pressure and type of fluid.Parasyri, A., Papazi, A., Stamatis, N., Zerveas, S., Avramidou, E.V., Doulis, A.G., Pirintsos, S., Kotzabasis, K., 2018. Lichen as micro-ecosystem: Extremophilic behavior with astrobiotechnological applications. Astrobiology 18, 1528-1542. work demonstrates the tolerance of lichen Pleurosticta acetabulum under extreme conditions similar to those encountered in extraterrestrial environments. Specifically, the impact of three extreme Mars-like conditions—complete dehydration, extremely low temperature (-196°C/77K), and oxygen depletion—on lichens was investigated. The symbiosis of mycobiont and photobiont partners creates a micro-ecosystem that ensures viability of both symbiotic partners under prolonged desiccation and extremely low temperatures without any cultivation care. Changes in the molecular structure and function of the photosynthetic apparatus, in the level of chlorophylls, polyamines, fatty acids, carbohydrates, ergosterol, efflux of K+, and DNA methylation ensure the ecological integrity of the system and offer resistance of lichens to above-mentioned extreme environmental conditions. For the first time, we also demonstrate that the unprecedented polyextremophilic characteristic of lichens could be linked to biotechnological applications, following exposure to these extreme conditions, such that their ability to produce a high yield of hydrogen was unchanged. All these support that lichens are (a) ideal model systems for a space mission to inhabit other planets, supporting also the aspect that the panspermia theory could be extended to incorporate in the traveling entities not only single organisms but micro-ecosystems like lichens, and (b) ideal model systems for astrobiotechnological applications (hydrogen production), such as in the development of bioregeneration systems for extraterrestrial environments.Park, G., Brunswick, P., Kwok, H., Haberl, M., Yan, J., MacInnis, C., Kim, M., Helbing, C., van Aggelen, G., Shang, D., 2018. A rapid gas chromatography tandem mass spectrometry method for the determination of 50 PAHs for application in a marine environment. Analytical Methods 10, 5559-5570. micro-extraction gas chromatography pseudo-MRM mass spectrometry method was developed for the rapid determination of 50 selected polycyclic aromatic hydrocarbons (PAHs) and alkylated-PAHs (APAHs) in seawater. The combined PAHs and APAHs, referred to as total polycyclic aromatic hydrocarbons (TPAHs), include dibenzothiophenes and naphthabenzothiophenes. The method was aimed at the assessment of TPAH compounds in the water accommodated fraction of oil in seawater, now promoted for use in toxicity evaluation following an oil spill incident. The presented method applies a unique multi-level quantitative calibration method for many alkylated PAHs for which the authentic standards are either extremely expensive or difficult to obtain. This new method was able to determine all 50 TPAH compounds while avoiding excessive cost. The reliability of this isotope dilution micro-extraction method was shown by extraction and analysis of Prudhoe Bay oil, with comparable compound results corresponding to published data. The developed method was successfully applied to water accommodated fraction (WAF) samples prepared with Low Sulfur Marine Diesel, High Sulfur Fuel Oil and Diluted Bitumen in seawater. With reduced cost and a single injection for all the 50 target compounds, this rapid quantitative method allows for routine environmental monitoring of a larger suite of TPAH analytes.Pascoe, S., 2018. Assessing relative potential economic impacts of an oil spill on commercial fisheries in the Great Australian Bight using a Bayesian Belief Network framework. Deep Sea Research Part II: Topical Studies in Oceanography 157-158, 203-210. based experiences of oil-spill induced impacts on fisheries were used to develop a Bayesian Belief Network (BBN) to evaluate the potential economic consequences of a (hypothetical) oil spill in the Great Australian Bight, an area currently being explored by several major international oil companies. The model differs from most previous BBN analyses in that it also considers the relatively short term economic impacts of such a spill, encompassing market and fisher behaviour, as well as impacts on the stocks affected directly by the spill. The results suggest that impacts vary depending on the characteristics of the fishery (i.e. main species, location etc.) and the timing and extent of the oil spill, but market, management and fisher behavioural responses (and their ability to respond) were found to have the greatest impact on the final economic outcomes.Peacock, M., Materi?, D., Kothawala, D.N., Holzinger, R., Futter, M.N., 2018. Understanding dissolved organic matter reactivity and composition in lakes and streams using proton-transfer-reaction mass spectrometry (PTR-MS). Environmental Science & Technology Letters 5, 739-744., we present a novel approach for investigating dissolved organic matter (DOM) composition using thermal desorption proton-transfer-reaction mass spectrometry (PTR-MS), a technique that provides insight into the molecular composition of DOM < m/z 500 (termed “PTR-DOC”). The applicability of PTR-MS for understanding the relationship between DOM composition and reactivity has yet to be explored. We present results from a synoptic sampling campaign of streams and lakes in a Swedish forest catchment where we measured DOM composition using PTR-MS and traditional optical methods and conducted DOM biodegradability assays. PTR-DOC comprised ≤12% of the total DOC pool. We found significant relationships between PTR-DOC and DOM degradability; reduced chemodiversity and low concentrations of PTR-DOC were both associated with the total DOM pool being more susceptible to microbial degradation. Furthermore, molecular differences were apparent among headwater lakes, headwater streams, and lakes further down the catchment. Direct linkages between PTR-DOC and optical methods were observed. Using the quantitative data that PTR-MS generates, it could become possible to identify the fluorescing components of DOM, and the method may be particularly informative in low-DOC waters such as marine environments where PTR-DOC may dominate the total DOM pool.Pearce, J.K., Dawson, G.K.W., Golab, A., Knuefing, L., Sommacal, S., Rudolph, V., Golding, S.D., 2019. A combined geochemical and μCT study on the CO2 reactivity of Surat Basin reservoir and cap-rock cores: Porosity changes, mineral dissolution and fines migration. International Journal of Greenhouse Gas Control 80, 10-24. storage of CO2 generally involves injection of a CO2 stream into a high porosity and permeability reservoir, contained by one or more overlying low permeability formations. Sandstone reservoirs and associated cap-rocks of targeted CO2 storage sites therefore have distinct properties such as porosity and mineral contents. Their geochemical response or reactivity to injected supercritical CO2 and associated changes in porosity, and permeability affecting scaling, mineral trapping, injectivity, or migration can therefore be very different. Six drill core samples including quartz-rich sandstones, calcite cemented sandstones, and feldspar or clay-rich cap-rocks from a proposed demonstration site in the Surat Basin, Australia, were characterized before and after reaction with pure supercritical CO2 and low salinity formation water. The quartz-rich sandstones have low reactivity, and maintain high porosities with visible pore connectivity after reaction, they are unlikely to be affected by scaling. Kaolin and fine grain movement observed via μCT and SEM could have the potential to open or plug pores, potentially increasing or decreasing permeability and CO2 injectivity. Calcite cemented sandstones had the greatest measured change in porosity after reaction via calcite dissolution. Narrow angular channels were formed in the calcite cement around framework grains, extending through to the center of the sub-plug in the courser grained rock, and surface roughness increased. Solution pH was however quickly passivated. The highest concentrations of Ca, Mn, Sr, and Mg were released to solution from calcite dissolution. Clay (and feldspar) rich cap-rock core had mainly microporosity and the smallest initial pore throat diameters associated with clays. Small changes to μCT calculated porosities after reaction were related to a decrease in chlorite X-ray density, and dissolution of patchy carbonate minerals. Pores were disconnected in μCT images, except for some created horizontal connection along a sandy lamination in a cap-rock. Dissolved concentrations of Ca, Fe, Si, Sr, Mn, Li and Mg increased via dissolution of both carbonate and silicate minerals. Dissolved Ca, Fe, Mn and Mg from silicate minerals in the cap-rock were available for longer term mineral trapping of CO2. Potential increases in porosity and migration will be highest in the calcite cemented zones, while clay-rich cap-rocks could be expected to maintain integrity. There is a low likelihood of mineral trapping or scaling in the quartz rich lower Precipice Sandstone. Overlying rocks can provide Fe, Mg, Ca for mineral trapping of CO2 as ferroan carbonates such as siderite, ankerite and dolomite over longer time scales when pH is buffered. Changes to porosity, mineral content, and water chemistry after pure CO2 reaction observed here and in other published studies were dependent on mineral content and fluid accessibility. These results could be generalized to other sandstone reservoirs where it is expected to inject CO2. The results can also be used to validate geochemical models to build longer term predictions.Pei, L., Gang, W., Zhu, C., Liu, Y., He, W., Dong, Y., Xiang, B., 2018. Carbon isotope and origin of the hydrocarbon gases in the Junggar Basin, China. Journal of Natural Gas Geoscience 3, 253-261. genetic type, source and distribution of hydrocarbon gases in the Junggar Basin were clarified through the carbon isotope analysis. Mature to post mature oil-type gas, mature to post mature coal-type gas, transition gas and biogas are identified in the Junggar Basin. Partly reversed order of carbon isotope of hydrocarbon gases in the Junggar Basin are attributed to one or several of the following reasons: mixing of oil-type and coal-type gases, mixing of coal-type gases of different source, mixing of coal-type gases of varied maturity, and microbial action. Three types of coal-type gases in the Junggar Basin are identified. The first type of coal-type gases characterized with high δ13C values of heavy hydrocarbon gases (δ13C2>?26.0‰) are the mature to high mature gases that are generated from Jurassic source rocks. The second type of coal-type gases characterized with low δ13C values of heavy hydrocarbon gases (δ13C2<?26.0‰) and wide maturity range, are generated from one or several source rocks in the Jurassic and the Wuerhe and Jiamuhe Formations of Permian. The third type of coal-type gases characterized with a wide δ13C value of heavy hydrocarbon gases and the high-post maturity are generated from the Carboniferous source rocks.Peng, W., Hu, G., Liu, Q., Jia, N., Fang, C., Gong, D., Yu, C., Lyu, Y., Wang, P., Feng, Z., 2018. Research status on thermal simulation experiment and several issues of concern. Journal of Natural Gas Geoscience 3, 283-293. study the research status of thermal simulation experiment and put forward three issues worthy of attention and five important development directions. Classification according to thermal simulation system is the most widely used classification scheme. Different thermal simulation experimental systems have their own characteristics, and according to different experimental purpose, a suitable thermal simulation experiment system can be selected according to different experimental purposes. The closed experimental system is more suitable for the thermal simulation experiment of humic source rocks. The online analysis of open system has unique advantages in the study of volatile components. The semi-open system is the most closest to the thermal simulation system of the thermal evolution of the source rocks in the actual geological condition. Three key issues are presented concerning the thermal simulation experiment are presented. The first is the influence of water on the thermal simulation experiment. The second is whether convincing isotope reversal can be presented expect Fischer–Tropsch synthesis. The third is that, in the study of the thermal simulation experiment, the model of hydrocarbon generation must be built in combination with the actual geological background. Five key development directions concerning the thermal simulation experiment are proposed. The first is thermal simulation experimental study on a relatively low temperature and a long time with water participation. The second is experimental research on thermal simulation of unconventional petroleum. The third is a study on the development of pore microcracks in source rocks and the correlation of the interaction of fluid discharge in thermal simulation experiments. The fourth is an experimental study on thermal simulation of carbonate source rock. The fifth is an experimental study of thermal simulation related to abnormal pressure.Peng, X., Chen, M., Chen, S., Dasgupta, S., Xu, H., Ta, K., Du, M., Li, J., Guo, Z., Bai, S., 2018. Microplastics contaminate the deepest part of the world’s ocean. Geochemical Perspectives Letters 9, 1-5. of metric tons of plastics are produced annually and transported from land to the oceans. Finding the fate of the plastic debris will help define the impacts of plastic pollution in the ocean. Here, we report the abundances of microplastic in the deepest part of the world’s ocean. We found that microplastic abundances in hadal bottom waters range from 2.06 to 13.51 pieces per litre, several times higher than those in open ocean subsurface water. Moreover, microplastic abundances in hadal sediments of the Mariana Trench vary from 200 to 2200 pieces per litre, distinctly higher than those in most deep sea sediments. These results suggest that manmade plastics have contaminated the most remote and deepest places on the planet. The hadal zone is likely one of the largest sinks for microplastic debris on Earth, with unknown but potentially damaging impacts on this fragile ecosystem.Peng, X., Wang, Y., Diao, Y., Zhang, L., Yazid, I.M., Ren, S., 2019. Experimental investigation on the operation parameters of carbon dioxide huff-n-puff process in ultra low permeability oil reservoirs. Journal of Petroleum Science and Engineering 174, 903-912. oil reservoirs featured with ultra low permeability, CO2 huff-n-puff can be a promising approach for enhanced oil recovery. To understand its production performance and the effects of different factors in field operation, a series of CO2 huff-n-puff experiments under various conditions were conducted using a 1D sandpack model, and the extraction effect of CO2 and its influence on oil production have been analyzed. The experimental results show that, as cyclic CO2 injection quantity increases, the cyclic oil recovery factor is improved, but the CO2 utilization factor is reduced, and there will be an optimum cyclic injection quantity from economic point of view. Both cyclic oil recovery factor and CO2 utilization factor are improved with the increasing reservoir temperature, while injection of low temperature CO2 may impose an adverse influence on oil recovery performance. In addition, the cyclic oil recovery factor and CO2 utilization factor firstly rise and then fall with the increasing soaking period. The results presented in this study are expected to provide some guidance to the field implementation of CO2 huff-n-puff technique in ultra low permeability oil reservoirs.Peng, X., Zhu, X.-K., Shi, F., Yan, B., Zhang, F., Zhao, N., Peng, P., Li, J., Wang, D., Shields, G.A., 2019. A deep marine organic carbon reservoir in the non-glacial Cryogenian ocean (Nanhua Basin, South China) revealed by organic carbon isotopes. Precambrian Research 321, 212-220. late-Cryogenian warm (non-glacial) interval (c.660???c.650?Ma) is potentially of great significance to the co-evolution between life and the surface environment during the emergence of animal life on Earth. In this study, three high-resolution organic carbon isotopic (δ13Corg) records for the Datangpo/Xiangmeng Formation on the Yangtze Craton are presented. The data derive from drill cores representing different depositional settings at Daotuo (slope setting), Minle (shallow-water basin), and Xiangtan (basin), respectively. The Daotuo and Minle samples exhibit an overall increase of 6–8‰ as well as significant isotopic fluctuations following the Tiesi’ao/Sturtian glaciation, while samples from the deeper Xiangtan section show relatively muted fluctuations (±1‰) and no overall trend over the same interval. These findings can be plausibly explained by a much longer residence time for marine organic matter, which may have acted as a redox buffer against oxygenation and climate change. The build-up and eventual oxidation of a sub-pycnocline organic carbon reservoir in the redox stratified non-glacial ocean could help to explain the extreme positive and negative carbon isotope perturbations, respectively, in time-equivalent shallow-marine carbonate Platform successions from Mongolia, Australia and Namibia.Penn, J.L., Deutsch, C., Payne, J.L., Sperling, E.A., 2018. Temperature-dependent hypoxia explains biogeography and severity of end-Permian marine mass extinction. Science 362, Article eaat1327.: Rapid climate change at the end of the Permian Period (~252 million years ago) is the hypothesized trigger for the largest mass extinction in Earth’s history. We present model simulations of the Permian/Triassic climate transition that reproduce the ocean warming and oxygen (O2) loss indicated by the geologic record. The effect of these changes on animal survival is evaluated using the Metabolic Index (Φ), a measure of scope for aerobic activity governed by organismal traits sampled in diverse modern species. Modeled loss of aerobic habitat predicts lower extinction intensity in the tropics, a pattern confirmed with a spatially explicit analysis of the marine fossil record. The combined physiological stresses of ocean warming and O2 loss can account for more than half the magnitude of the “Great Dying.”Editor's Summary, Drivers of the “Great Dying”: Though our current extinction crisis is substantial, it pales in comparison to the largest extinction in Earth's history, which occurred at the end of the Permian Period. Referred to as the “Great Dying,” this event saw the loss of up to 96% of all marine species and 70% of terrestrial species. Penn et al. explored the extinction dynamics of the time using Earth system models in conjunction with physiological data across animal taxa (see the Perspective by Kump). They conclude that increased marine temperatures and reduced oxygen availability were responsible for a majority of the recorded extinctions. Because similar environmental alterations are predicted outcomes of current climate change, we would be wise to take note.Structured AbstractIntroduction: Climate change triggered by volcanic greenhouse gases is hypothesized to have caused the largest mass extinction in Earth’s history at the end of the Permian Period (~252 million years ago). Geochemical evidence provides strong support for rapid global warming and accompanying ocean oxygen (O2) loss, but a quantitative link among climate, species’ traits, and extinction is lacking. To test whether warming and O2 loss can mechanistically account for the marine mass extinction, we combined climate model simulations with an established ecophysiological framework to predict the biogeographic patterns and severity of extinction. Those predictions were confirmed by a spatially explicit analysis of the marine fossil record.Rationale: The impact of climate change on marine biodiversity depends on both its magnitude and on species’ diverse biological sensitivities. Tolerances of marine animals to warming and O2 loss are physiologically related and can be represented in a single metric: the ratio of temperature-dependent O2 supply and demand rates. This ratio, termed the Metabolic Index (Φ), measures the environmental scope for aerobic activity and is governed by ocean conditions as well as thermal and hypoxia sensitivity traits that vary across species. If climate warming and O2 loss reduce Φ below the species-specific minimum requirement for sustained ecological activity (Φcrit), the ocean would no longer support active aerobic metabolism and, by extension, long-term population persistence.Results: We simulated the greenhouse gas–driven global warming at the end of the Permian using a model of Earth’s climate and coupled biogeochemical cycles that matches geochemical proxy data. The imposed increase in atmospheric greenhouse gas levels raises near-surface ocean temperatures by more than ~10°C and depletes global marine O2 levels by almost 80%.To predict the impact of these changes on animal habitat and survival, we measured the frequencies of Metabolic Index traits in diverse living species and used them to define a set of model ecophysiotypes. We populated the model Permian ocean with each ecophysiotype wherever conditions provide viable habitat (Φ ≥ Φcrit), yielding an ocean with diverse, locally adapted ecophysiotypes throughout all regions. Across the climate transition, however, ocean warming increases the metabolic O2 demand amid declining supply; this removes large fractions of global aerobic habitat for the vast majority of ecophysiotypes and implies a high likelihood of extinction. We simulated the resulting mass extinction of ecophysiotypes and found a robust geographic pattern: Extinction intensity should have been lower in the tropics than at high latitudes. The cause of lower tropical extinction is that organisms initially inhabiting these warm, low-O2 environments can better exploit those conditions when they arise globally, whereas the habitats of more polar species disappear completely.To test the geographic selectivity of the model extinction, we compared model predictions to spatially explicit reconstructions of genus extinction from the marine fossil record. We found that across diverse taxonomic groups, the observed extinction intensity indeed increases with latitude, consistent with the predicted signature of aerobic habitat loss. Comparison of the model to the fossil record implies that temperature-dependent hypoxia can account for more than half of the observed magnitude of regional extinction (i.e., extirpation).Conclusion: Ocean warming and O2 loss simulated in an Earth System Model of end-Permian climate change imply widespread loss of aerobic habitat among animal types with diverse thermal and hypoxia tolerances. The resulting extinctions are predicted to select most strongly against higher-latitude species, whose biogeographic niche disappears globally. The combined physiological stresses of ocean warming and O2 loss largely account for the spatial pattern and magnitude of extinction observed in the fossil record of the “Great Dying.” These results highlight the future extinction risk arising from a depletion of the ocean’s aerobic capacity that is already under way.Pennisi, E., 2018. Fossils push back origin of key plant groups millions of years. Science 362, 1340. exploring a site near the Dead Sea have unearthed a startling connection between today's conifer forests in the Southern Hemisphere and an unimaginably distant time torn apart by a global cataclysm. Exquisitely preserved plant fossils show the podocarps, a group of ancient evergreens that includes the massive yellowwood of South Africa and the red pine of New Zealand, thrived in the Permian period, more than 250 million years ago. That's tens of millions of years earlier than thought, and it shows that early podocarps survived the “great dying” at the end of the Permian, the worst mass extinction the planet has ever known.Reported on p. 1414, the fossils push back the origins not just of podocarps, but also of groups of seed ferns and cycadlike plants. Beyond altering notions of plant evolution, the discoveries lend support to a 45-year-old idea that the tropics serve as a “cradle” of evolution. “This is an exciting paper,” says Douglas Soltis, a plant evolutionary biologist at the University of Florida (UF) in Gainesville. By revealing the richness of the Permian tropics, he adds, “The findings may also help researchers decide where to look for crucial fossil discoveries.”During the Permian, from 299 million to 251 million years ago, Earth's landmasses had merged to form a supercontinent, bringing a cooler, drier climate. Synapsids, thought to be ancient predecessors of mammals, and sauropsids, ancestors to reptiles and birds, roamed the landscape. Simple seed-bearing plants had already appeared on the scene. Family trees reconstructed from the genomes of living plants suggest more sophisticated plant groups might also have evolved during the Permian, but finding well-preserved plant fossils from that time has been difficult.About 50 years ago, a German geologist described the Umm Irna formation, a series of sedimentary layers exposed along the Jordanian coast of the Dead Sea. Working at the site in the early 2000s, paleontologist Abdalla Abu Hamad, now with the University of Jordan in Amman, discovered some exquisitely preserved plants from Permian swamps and drier lowlands.After moving to the University of Münster in Germany for a Ph.D., he teamed up with paleobotanists there to analyze hundreds of newly collected plant fossils, including leaves, stems, and reproductive organs. Many of the fossils preserve the ancient plants' cuticle, a waxy surface layer that captures fine features, such as the leaf pores called stomata. That made it possible for the team to positively identify many of the plants.“At first, we couldn't really believe our eyes,” Benjamin Bomfleur, a study co-author at the University of Münster, recalls. Many were plants thought have gotten their start later in the Mesozoic, the period when dinosaurs ruled. Along with the podocarps, they identified corystosperms, seed ferns common in the dinosaur age but extinct now, and cycadlike Bennettitales, another extinct group that had flowerlike reproductive structures.Such finds could help resolve an ongoing debate about why the tropics have more species than colder latitudes do. Some have suggested that species originate at many latitudes but are more likely to diversify in the tropics, with its longer growing seasons, higher rainfall and temperatures, and other features. But another theory proposes that most plant—and animal—species actually got their start near the equator, making the low latitudes an evolutionary “cradle” from which some species migrate north and south. The new work “supports the idea of the evolution cradle,” Bomfleur says. Philip Mannion, a paleontologist at Imperial College London agrees, but says the case is not fully settled. “Our sampling of the fossil record is extremely patchy throughout geological time and space,” he cautions.It's not clear how the newfound Permian plants made it through the great dying, a 100,000-year period when, for reasons that are still unclear, 90% of marine life and 70% of life on land disappeared. But their presence in the Permian raises the possibility that other plant groups thought to have later origins actually emerged then in the tropics, says UF plant evolutionary biologist Pamela Soltis. If these select plants survived the mass extinction, she says, “Perhaps the communities they supported may have been more stable as well.”Peper, S., Fonseca, J.M.S., Dohrn, R., 2019. High-pressure fluid-phase equilibria: Trends, recent developments, and systems investigated (2009–2012). Fluid Phase Equilibria 484, 126-224. of the continuation of a review series covering the period 2009 to 2012 on high-pressure phase equilibria are given, including a compilation of systems investigated, recent developments, and trends. As in the previous review articles, the systems, the reference, the temperature and pressure range of the data, and the experimental method used for the measurements is given in 57 tables. Phase equilibria including vapor, liquid, and solid phases, hydrate equilibria, critical points, the solubility of high-boiling substances in supercritical fluids, the solubility of gases in liquids, and the solubility (sorption) of volatile components in polymers and ionic liquids are included.Peter, K.T., Herzog, S., Tian, Z., Wu, C., McCray, J.E., Lynch, K., Kolodziej, E.P., 2019. Evaluating emerging organic contaminant removal in an engineered hyporheic zone using high resolution mass spectrometry. Water Research 150, 140-152. hyporheic zone (HZ), located at the interface of surface and groundwater, is a natural bioreactor for attenuation of chemical contaminants. Engineered HZs can be incorporated into stream restoration projects to enhance hyporheic exchange, with flowpaths optimized to promote biological habitat, water quantity, and water quality improvements. Designing HZs for in-stream treatment of stormwater, a significant source of flow and contaminant loads to urban creeks, requires assessment of both the hydrology and biogeochemical capacity for water quality improvement. Here, we applied tracer tests and high resolution mass spectrometry (HRMS) to characterize an engineered hyporheic zone unit process, called a hyporheic design element (HDE), in the Thornton Creek Watershed in Seattle, WA. Dye, NaCl, and bromide were used to hydrologically link downwelling and upwelling zones and estimate the hydraulic retention time (HRT) of hyporheic flowpaths. We then compared water quality improvements across hydrologically-linked surface and hyporheic flowpaths (3–5?m length; ～30?min to >3?h) during baseflow and stormflow conditions. We evaluated fate outcomes for 83 identified contaminants during stormflow, including those correlated with an urban runoff mortality syndrome in coho salmon. Non-target HRMS analysis was used to assess holistic water quality improvements and evaluate attenuation mechanisms. The data indicated substantial water quality improvement in hyporheic flowpaths relative to surface flow and improved contaminant removal with longer hyporheic HRT (for ～1900 non-target compounds detected during stormflow, <17% were attenuated >50% via surface flow vs. 59% and 78% via short and long hyporheic residence times, respectively), and strong contributions of hydrophobic sorption towards observed contaminant attenuation.Peters, B., Horak, R., Devol, A., Fuchsman, C., Forbes, M., Mordy, C.W., Casciotti, K.L., 2018. Estimating fixed nitrogen loss and associated isotope effects using concentration and isotope measurements of NO3–, NO2–, and N2 from the Eastern Tropical South Pacific oxygen deficient zone. Deep Sea Research Part II: Topical Studies in Oceanography 156, 121-136. the pathways of fixed nitrogen (N) loss in marine oxygen deficient zones (ODZs) and the isotopic fractionation caused by these processes are important for understanding the marine fixed N budget and its potential for change. In this study, a variety of approaches were used to quantify fixed N loss in the eastern tropical South Pacific Ocean (ETSP). The required measurements included nutrient concentration (nitrate—NO3-, nitrite—NO2-, and phosphate—PO43-), gas ratio (N2/Ar) measurements, and stable N and O isotopes in NO3-, NO2-, and nitrogen gas (N2). The dissolved inorganic nitrogen deficit calculated from [PO43-] ([DIN]def,P) exceeded the concentration of N2 gas biologically produced in the ODZ (local [N2]bio) throughout the ODZ at most stations, likely due to release of PO43- from sediments driving up [DIN]def,P. Calculating DIN deficit using water mass analysis and local oxygen (O2) consumption ([DIN]def,OMP) yielded better agreement with local [N2]bio than [DIN]def,P, except at the maximum [N2]bio, where [DIN]def,OMP misses contributions of anaerobic ammonia oxidation (anammox) to N2 production. We used the mismatch between [DIN]def,OMP and [N2]bio to estimate a 29% contribution of anammox to [N2]bio. Stable isotopic measurements of NO2-, NO3-, and N2 were used alongside [N2]bio and new estimates of [DIN]def to calculate N and O isotope effects for NO3- reduction (15εNAR and 18εNAR, respectively), and N isotope effects for DIN removal (15εDIN-R). While the various methods for estimating [DIN]def had little effect on the isotope effects for DIN removal, differences between 15εNAR and 15εDIN-R, and variations with depth in the ODZ were observed. Using a simple time-dependent ODZ model, we interpreted these patterns to reflect the influences of NO2- oxidation and NO2- accumulation on expression of isotopic fractionation in the ODZ.Petsios, E., Thompson, J.R., Pietsch, C., Bottjer, D.J., 2019. Biotic impacts of temperature before, during, and after the end-Permian extinction: A multi-metric and multi-scale approach to modeling extinction and recovery dynamics. Palaeogeography, Palaeoclimatology, Palaeoecology 513, 86-99. and delayed recovery during the end-Permian extinction and Early Triassic has been linked to environmental instability brought on by volcanic outgassing and greenhouse conditions, but the relative importance of the myriad of environmental stressors at this time on recovery dynamics is not well understood. Previous workers have documented both overall delayed biotic recovery for the entirety of the Early Triassic, but also incipient recoveries that appear to occur relatively early after the initial extinction event. Here, we explore the patterns of extinction and recovery using several metrics of ecological complexity in marine benthic communities using a global dataset, and compare several multiple regression models to determine which set of abiotic factors best predicts extinction and recovery dynamics. We additionally test the importance of temporal scale of analysis in interpretations of recovery dynamics and modeling results, by including analyses at the epoch, stage, and substage scales bracketing the interval of extinction and recovery. We find differences in mode of recovery between the ecological metrics analyzed, with some metrics exhibiting an Early Triassic recovery lag, while others recover continuously or immediately following the initial extinction event. We also find evidence of a global ‘Dienerian minimum’, with overall levels of community complexity significantly lower than earlier Griesbachian communities, suggesting a synchronous disturbance to the progression of recovery at this time. The regression model with δ18Oapatite mean values as the response variable is most often found to be the best-fit model across all time scales analyzed, though proxies of rock record fidelity and paleontological sampling effort become more important in finer timescale analyses, likely due to dwindling sample numbers. Out of the models tested, these results suggest that global ocean temperatures best predict patterns of extinction and recovery across several ecological metrics, and that thermal episodes during the initial extinction event and subsequently in the Early Triassic recovery period significantly suppressed benthic marine community health.Pirok, B.W.J., Molenaar, S.R.A., Roca, L.S., Schoenmakers, P.J., 2018. Peak-tracking algorithm for use in automated interpretive method-development tools in liquid chromatography. Analytical Chemistry 90, 14011-14019. peak-tracking algorithm for chromatograms recorded using liquid chromatography and mass spectrometry was developed. Peaks are tracked across chromatograms using the spectrometric information, the statistical moments of the chromatographic peaks, and the relative retention. The algorithm can be applied to pair chromatographic peaks in two very different chromatograms, obtained for different samples using different methods. A fast version of the algorithm was specifically tailored to process chromatograms obtained during method development or optimization, where a few similar mobile-phase-composition gradients (same eluent components, but different ranges and programming rates) are applied to the same sample for the purpose of obtaining model parameters to describe the retention of sample components. Due to the relative similarity between chromatograms, time-saving preselection protocols can be used to locate a candidate peak in another chromatogram. The algorithm was applied to two different samples featuring isomers. The automatically tracked peaks and the resulting retention parameters generally yielded prediction errors of less than 1%.Prince, R.C., 2018. An opportunity lost? Research on alternative oil spill response technologies requires active engagement with the professionals. Environmental Science & Technology 52, 14029-14030. marine oil spills (Figure 1) rightly garner the public’s attention; oil slicks threaten the lives of charismatic birds and animals and the beauty of shorelines. They disrupt the fishing and hospitality industries, and unsettle the lives of many. Expectations that everything will return to normal by the next news broadcast, or at least in the next few days, are invariably disappointed, and initial responders always seem overwhelmed. Not surprisingly, many researchers want to help, and our community ought to be among the leaders in such efforts, providing expert advice and helping to develop new or improved response options. Alas, much of the effort and investment of public and private research funding results in publications that have little chance of being put into practice.One reason that our community’s research often fails to have an impact is that many researchers are not fully aware of the substantial resources already available for oil-spill response, the accumulated knowledge on successes and failures gained over the past 50 years, and the general complexity of oil spill cleanup.(1) Professional organizations stand ready to respond to oil spills on short notice, and they have to balance the efficacy of a technology with its feasibility of deployment, the capabilities of available equipment, and worker safety. In the United States these organizations are mandated by the Oil Pollution Act (1990), and about 800 Oil Spill Removal Organizations stand ready around the country.(2) Because our research community has little interaction with this enormous reservoir of accumulated expertise, it tends to pursue mirages rather than the critical issues that constrain the cleanup-process. Two examples serve to illustrate the problem: sorbents and dispersants.The scale of major oil spills means that sorbents(3) can only play a minor role in cleanup operations. Sorbents are used on land and confined surface waters, but not on the open sea.(4) Loose sorbents work well for spills on dry hard surfaces, but maritime use requires the sorbent both have a substantial preference for absorbing oil over water, and be deployed in booms or sheets that can be retrieved. Research that merely develops a new sorbent without testing it as it would be deployed in a real spill is very unlikely to help responders, even if it results in a paper that receives numerous citations. For example, the obvious benefits of sorbents exhibiting very large surface areas must be balanced against their structural integrity, because the release of oiled particles or fibers into the marine environment would be unacceptable. Sorbent booms are important for protecting especially sensitive sites, but given the existing stockpiles of effective equipment,(4) a new product would have to be markedly better to be considered. And at the end of the day, no matter how effective, sorbents will not be an important part of efforts to address large oil spills. When they are used, they increase the amount of waste material that must be handled and do nothing to stimulate biodegradation, the major process that actually removes oil from the environment.When it is recognized that oil cannot be collected in booms and skimmed or burnt, responders turn to dispersants to get oil off the water surface. They can rapidly treat large spills because they can be applied by air. This protects birds and shorelines and dramatically stimulates biodegradation, but in some circumstances might harm fisheries.(5) Current products have been refined since their introduction in the early 1970s,(6) and after extensive study their properties are well understood. They are applied far from land at a notional rate of 5 gal/acre (47 L/Ha; a teaspoon for every 10 square feet), with appropriate personal protective equipment (PPE) for workers who might come in contact with the product. Substantial exclusion zones are established around vessels and marine mammals during deployment. While of course dispersants are not entirely benign, their acute toxicity to marine life is similar to that of common dishwashing liquids,(7) their acute toxicity to mammals is comparable to that of ethanol,(8) and they are promptly biodegraded once applied.(9) Since it is well understood that the toxicity of dispersed oil comes from the oil, not from the dispersant,(10) research at finding “nontoxic” dispersants is doomed to irrelevance. Even if research were to lead to a significantly more-effective dispersant, the expense of getting it licensed on the National Contingency Plan,(11) and the investment in the enormous current stockpiles would be substantial hurdles for its adoption.So is there anything that environmental chemists, engineers and ecotoxicologists might offer to improve oil spill response? Absolutely. But if research is going to affect practice, it must be relevant. Researchers need to familiarize themselves with the basic knowledge already accumulated on oil behavior and the performance of various technologies, and then consult with manufacturers, regulators, and responders in the early days of their projects. New technology must fit within the complexities and limitations of oil spill response, and recognize both the scale of the operations, and the enormous dilutions that occur once oil is dispersed.(12) Excellent scientific research is certainly essential, but without guidance and support from the Oil Spill Removal Organizations it will not be enough. Connections might be made at the International Oil Spill Conference in the U.S.,(13) a long-running exposition with affiliated meetings in Europe and Asia which makes its papers freely available, or the smaller AMOP meeting in Canada.(14) These might be beyond the comfort zone of academic researchers, but they will provide a window on the real needs in oil spill response.References1. Fingas, M. The Basics of Oil Spill Cleanup; CRC press, 2015.2. United States Coast Guard Response Resource Inventory System. 2018, . USEPA Sorbents 2018, . CEDRE Use of Sorbents for Spill Response - Operational Guide – 2018, . Prince, R. C. Oil spill dispersants: boon or bane?. Environ. Sci. Technol. 2015, 49, 6376– 84, DOI: 10.1021/acs.est.5b009616. Canevari, G. Oil slick dispersant and method. 1974, US Patent US3,793,218.7. Word, J. Q.; Clark, J. R.; Word, L. S. Comparison of the acute toxicity of Corexit 9500 and household cleaning products. Hum. Ecol. Risk Assess. 2015, 21, 707– 25, DOI: 10.1080/10807039.2014.9202278. George, S. E.; Nelson, G. M.; Kohan, M. J.; Warren, S. H.; Eischen, B. T.; Brooks, L. R. Oral treatment of Fischer 344 rats with weathered crude oil and a dispersant influences intestinal metabolism and microbiota. J. Toxicol. Environ. Health, Part A 2001, 63, 297– 316, DOI: 10.1080/15287390151143686 9. Brakstad, O. G.; St?rseth, T. R.; Brunsvik, A.; Bonaunet, K.; Faksness, L.-G. Biodegradation of oil spill dispersant surfactants in cold seawater. Chemosphere 2018, 204, 290– 293, DOI: 10.1016/j.chemosphere.2018.04.05110. Barron, M. G.; Hemmer, M. J.; Jackson, C. R. Development of aquatic toxicity benchmarks for oil products using species sensitivity distributions. Integr. Environ. Assess. Manage. 2013, 9, 610– 615, DOI: 10.1002/ieam.1420 11. USEPA National Contingency Plan Subpart J, 2018, . Lee, K.; Nedwed, T.; Prince, R. C.; Palandro, D. Lab tests on the biodegradation of chemically dispersed oil should consider the rapid dilution that occurs at sea. Mar. Pollut. Bull. 2013, 73, 314– 318, DOI: 10.1016/j.marpolbul.2013.06.00513. International Oil Spill Conference. 2018, . AMOP 2018, , J.C., Gutiérrez Sama, S., Barrère-Mangote, C., Rodgers, R.P., Lobinski, R., Marshall, A.G., Bouyssière, B., Giusti, P., 2018. Analysis of petroleum products by gel permeation chromatography coupled online with inductively coupled plasma mass spectrometry and offline with Fourier transform ion cyclotron resonance mass spectrometry. Energy & Fuels 32, 12198-12204. have examined the aggregation behavior of a typical atmospheric residue feedstock by gel permeation chromatography (GPC). The size profiles for compounds containing sulfur, vanadium, and nickel were determined online from elemental detection by inductively coupled plasma (ICP) mass spectrometry. Four fractions that vary in aggregation state were analyzed by positive atmospheric pressure photoionization (APPI) 9.4 T Fourier transform ion cyclotron resonance mass spectrometry (APPI FT-ICR MS). Results showed an inverse relationship between fraction aggregate size and monomer ion yield and revealed that aggregation tendency did not correlate with higher polar or aromatic species abundance. Aggregation in the atmospheric residue more closely correlated with increased relative abundance of larger and more aliphatic compounds. The molecular composition of the GPC aggregate fractions suggests that nonpolar intermolecular forces between saturated, long-chain alkyl substituents contribute more to aggregation than pi–pi interactions.Qian, Z., Tianwei, H., Mackey, H.R., van Loosdrecht, M.C.M., Guanghao, C., 2019. Recent advances in dissimilatory sulfate reduction: From metabolic study to application. Water Research 150, 162-181. bacteria (SRB) are a group of diverse anaerobic microorganisms omnipresent in natural habitats and engineered environments that use sulfur compounds as the electron acceptor for energy metabolism. Dissimilatory sulfate reduction (DSR)-based techniques mediated by SRB have been utilized in many sulfate-containing wastewater treatment systems worldwide, particularly for acid mine drainage, groundwater, sewage and industrial wastewater remediation. However, DSR processes are often operated suboptimally and disturbances are common in practical application. To improve the efficiency and robustness of SRB-based processes, it is necessary to study SRB metabolism and operational conditions. In this review, the mechanisms of DSR processes are reviewed and discussed focusing on intracellular and extracellular electron transfer with different electron donors (hydrogen, organics, methane and electrodes). Based on the understanding of the metabolism of SRB, responses of SRB to environmental stress (pH-, temperature-, and salinity-related stress) are summarized at the species and community levels. Application in these stressed conditions is discussed and future research is proposed. The feasibility of recovering energy and resources such as biohydrogen, hydrocarbons, polyhydroxyalkanoates, magnetite and metal sulfides through the use of SRB were investigated but some long-standing questions remain unanswered. Linking the existing scientific understanding and observations to practical application is the challenge as always for promotion of SRB-based techniques.Quan, Y., Liu, J., Hao, F., Bao, X., Xu, S., Teng, C., Wang, Z., 2019. Geochemical characteristics and origins of natural gas in the Zhu III sub-basin, Pearl River Mouth Basin, China. Marine and Petroleum Geology 101, 117-131. Zhu III sub-basin is an important petroliferous region in the South China Sea where hydrocarbon distribution shows strong heterogeneity with oil primary produced from the Wenchang B depression, and gases from the Wenchang A depression. However, a mixture of oil and gases are produced from the surrounding Qionghai and Shenhu uplifts. The origin, generation history and migration pathway of oil have been intensively studied but no study have been done directly on the gas, which restricts future petroleum exploration. In this study, natural gas molecular compositions were measured on 46 samples, stable carbon isotopic composition were measured on 39 samples and light hydrocarbon composition were measured on 30 samples. Results indicate that natural gases in the Zhu III sub-basin are mainly composed of hydrocarbon gases with abundant CO2 and N2. The hydrocarbon gases are all thermogenic gases which are mainly derived from the Oligocene Enping Formation (E3e, 35-30?Ma). The contribution of the Eocene Wenchang Formation (E2w, 56-35?Ma) to natural gases increases from the Wenchang A depression to the South Boundary Fault (SBF) and surrounding uplifts. This is caused by the early generated natural gases with more contribution from the E2w and dissolved in oils that migrated to the surrounding Qionghai and Shenhu uplifts. Natural gases and oil in the surrounding uplifts and near the SBF, therefore, avoided secondary cracking due to the high gas migration rate through the SBF and lateral sandstone carrier beds, whereas natural gases in the Wenchang A depression mainly originated from the secondary cracking of oil. The equivalent vitrinite reflectance values of source rocks when the natural gases were generated varied from 0.6% to 1.5% based on carbon isotope differences between hydrocarbons, indicating mature to high mature stage. CO2 with abundance less than 10% mainly originated from organic matter decomposition. CO2 with abundance more than 15% was sourced from the deep mantle and crust and mainly concentrated in the deep layers near the SBF which cuts into the basement. N2 is probably the product of in-situ reservoir alteration, such as biodegradation in shallower layers. Our study on the geochemical characteristics and origins of the natural gas will enable a better understanding of petroleum system in the Zhu III sub-basin and provide theoretical basis for optimizing future petroleum exploration strategy. Detailed study on shallow layers in the Qionghai and Shenhu uplifts and deep layers near the SBF are needed because exploration risks are relatively high in these plays.Raghav Chaturvedi, K., Kumar, R., Trivedi, J., Sheng, J.J., Sharma, T., 2018. Stable silica nanofluids of an oilfield polymer for enhanced CO2 absorption for oilfield applications. Energy & Fuels 32, 12730-12741. injected with water often gives premature breakthrough and reduces its absorption during sequestration and oil recovery applications. Water-soluble polymers are used to increase CO2 absorption via an increase in water viscosity that restricts CO2 movement and thus its early release. The efficacy of polymer CO2 absorption methods can be further increased in the presence of nanoparticles (NPs) that interact with polymer chains and create a steric barrier to improve CO2 absorption. Thus, nanofluids prepared with compatible NPs might be a safe and reliable method to improve CO2 absorption of polymer methods. In this work, a nanofluid prepared with silica NPs (0.1–1.0 wt %) in base fluid of oilfield polymer [(polyacrylamide (PAM) with typical oilfield concentration (1000 ppm)] was tested for CO2 absorption and compared with the one of PAM fluid at different temperatures (303 and 353 K). The inclusion of SiO2 in PAM fluid provided stable nanofluids that exhibited good dispersion stability without NP settlement for days. Thus, the efficacy of PAM fluid CO2 absorption significantly increased with nanofluids as reported through microscopic, kinetics, and molality results. The increase in NP concentration and temperature (353 K) showed an inverse relationship with CO2 absorption in nanofluids, mainly due to enhanced NP aggregation; thus, the use of nanofluids for CO2 absorption is critical at high temperature and high NP concentration. The NP effect on CO2 stabilization and absorption is finally supported through UV–vis measurements. The study highlighted important aspects of CO2 absorption and is a forward step toward the use of nanofluid together with the considerable possibility of enhanced CO2 miscible oil recovery.Ramírez, G.A., J?rgensen, S.L., Zhao, R., D’Hondt, S., 2018. Minimal influence of extracellular DNA on molecular surveys of marine sedimentary communities. Frontiers in Microbiology 9, 2969. doi: 10.3389/fmicb.2018.02969. DNA has been reported to comprise a large fraction of total DNA in near-seafloor sediment. However, the potential effect of extracellular DNA, arising from dead or moribund cells, on sequencing surveys is a critical concern that has largely not been addressed for marine sedimentary habitats. To address this concern, we interrogated freshly collected Arctic and Pacific sediment for extracellular 16S rRNA genes using the photoactive DNA-binding dye Propidium Monoazide. Significant differences between relative abundances of total (intracellular + extracellular) Bacterial 16S rRNA genes and relative abundances of intracellular Bacterial 16S rRNA genes are only detected in three of twelve shallow [10 cm below seafloor (cmbsf)] samples. Relative abundances of total Bacterial 16S rRNA genes are statistically indistinguishable from relative abundances of intracellular Bacterial 16S rRNA genes in all interrogated samples from depths greater than 10 cmbsf. 16S rRNA gene sequencing shows that even where significantly higher abundances of extracellular genes are detected, they have little or no influence on prokaryote community composition. Taxon-level analyses suggest that extracellular DNA, arising from in situ death, may be sourced from different organisms in sediment of different ages. However, the overall effect of extracellular genes on sequencing surveys of marine sedimentary prokaryotes is minimal.Rehman, K., Imran, A., Amin, I., Afzal, M., 2019. Enhancement of oil field-produced wastewater remediation by bacterially-augmented floating treatment wetlands. Chemosphere 217, 576-583. and bacteria individually as well as in synergism with each other hold a great potential to degrade a wide range of environmental pollutants. Floating treatment wetlands (FTWs) is an efficient and low-cost technology that uses the synergistic interaction between plant roots and microbes for in situ remediation of wastewater. The present study aims to assess the feasibility of FTW-based remediation of oil field-produced wastewater using an interaction between two plant species, Typha domingensis and Leptochloa fusca, in partnership with a consortium of crude oil-degrading bacterial species, Bacillus subtilis LORI66, Klebsiella sp. LCRI87, Acinetobacter Junii TYRH47, and Acinetobacter sp. BRSI56. All the treatments reduced contaminant levels, but T.?domingensis, in combination with bacterial inoculation, exhibited the highest reduction in hydrocarbon (95%), COD (90%), and BOD content (93%) as compared to L.?fusca. This combination maximally promoted increases in fresh biomass (31%), dry biomass (52%), and length (25%) of plants as well. This effect was further signified by the persistence of bacteria (40%) and considerable abundance (27%) and expression (28.5%) of the alkB gene in the rhizoplane of T.?domingensis in comparison to that of L.?fusca. The study, therefore, suggests that T.?domingensis, in combination with bacterial consortium, has significant potential for treatment of oil field-produced water and can be exploited on large scale in FTWs.Rezaveisi, M., Sepehrnoori, K., Pope, G.A., Johns, R.T., 2018. Thermodynamic analysis of phase behavior at high capillary pressure. SPE Journal 23, 1977-1990, SPE-175135-PA. capillary pressure has a significant effect on the phase behavior of fluid mixtures. The capillary pressure is high in unconventional reservoirs because of the small pores in the rock, so understanding the effect of capillary pressure on phase behavior is necessary for reliable modeling of unconventional shale-gas and tight-oil reservoirs. As the main finding of this paper, first we show that the tangent-plane-distance method cannot be used to determine phase stability and present a rigorous thermodynamic analysis of the problem of phase stability with capillary pressure. Second, we demonstrate that there is a maximum capillary pressure (Pcmax) where calculation of capillary equilibrium using bulk-phase thermodynamics is possible and derive the necessary equations to obtain this maximum capillary pressure. We also briefly discuss the implementation of the capillary equilibrium in a general-purpose compositional reservoir simulator. Two simulation case studies for synthetic gas condensate reservoirs were performed to illustrate the influence of capillary pressure on production behavior for the fluids studied.Roland, F.A.E., Morana, C., Darchambeau, F., Crowe, S.A., Thamdrup, B., Descy, J.-P., Borges, A.V., 2018. Anaerobic methane oxidation and aerobic methane production in an east African great lake (Lake Kivu). Journal of Great Lakes Research 44, 1183-1193. investigated CH4 oxidation in the water column of Lake Kivu, a deep meromictic tropical lake with CH4-rich anoxic deep waters. Depth profiles of dissolved gases (CH4 and N2O) and a diversity of potential electron acceptors for anaerobic CH4 oxidation (NO3?, SO42?, Fe and Mn oxides) were determined during six field campaigns between June 2011 and August 2014. Denitrification measurements based on stable isotope labelling experiments were performed twice. In addition, we quantified aerobic and anaerobic CH4 oxidation, NO3? and SO42? consumption rates, with and without the presence of an inhibitor of SO42?-reducing bacteria activity. Aerobic CH4 production was also measured in parallel incubations with the addition of an inhibitor of aerobic CH4 oxidation. The maximum aerobic and anaerobic CH4 oxidation rates were estimated to be 27?±?2 and 16?±?8?μmol/L/d, respectively. We observed a difference in the relative importance of aerobic and anaerobic CH4 oxidation during the rainy and the dry season, with a greater role for aerobic oxidation during the dry season. Lower anaerobic CH4 oxidation rates were measured in presence of molybdate in half of the measurements, suggesting the occurrence of linkage between SO42? reduction and anaerobic CH4 oxidation. NO3? consumption and dissolved Mn production rates were never high enough to sustain the measured anaerobic CH4 oxidation, reinforcing the idea of a coupling between SO42? reduction and CH4 oxidation in the anoxic waters of Lake Kivu. Finally, significant rates (up to 0.37?μmol/L/d) of pelagic CH4 production were also measured in oxygenated waters.Romaniuk, K., Golec, P., Dziewit, L., 2018. Insight into the diversity and possible role of plasmids in the adaptation of psychrotolerant and metalotolerant Arthrobacter spp. to extreme Antarctic environments. Frontiers in Microbiology 9, 3144. doi: 10.3389/fmicb.2018.03144. spp. are coryneform Gram-positive aerobic bacteria, belonging to the class Actinobacteria. Representatives of this genus have mainly been isolated from soil, mud, sludge or sewage, and are usually mesophiles. In recent years, the presence of Arthrobacter spp. was also confirmed in various extreme, including permanently cold, environments. In this study, 36 psychrotolerant and metalotolerant Arthrobacter strains isolated from petroleum-contaminated soil from the King George Island (Antarctica), were screened for the presence of plasmids. The identified replicons were thoroughly characterized in order to assess their diversity and role in the adaptation of Arthrobacter spp. to harsh Antarctic conditions. The screening process identified 11 different plasmids, ranging in size from 8.4 to 90.6 kb. A thorough genomic analysis of these replicons detected the presence of numerous genes encoding proteins that potentially perform roles in adaptive processes such as (i) protection against ultraviolet (UV) radiation, (ii) resistance to heavy metals, (iii) transport and metabolism of organic compounds, (iv) sulfur metabolism, and (v) protection against exogenous DNA. Moreover, 10 of the plasmids carry genetic modules enabling conjugal transfer, which may facilitate their spread among bacteria in Antarctic soil. In addition, transposable elements were identified within the analyzed plasmids. Some of these elements carry passenger genes, which suggests that these replicons may be actively changing, and novel genetic modules of adaptive value could be acquired by transposition events. A comparative genomic analysis of plasmids identified in this study and other available Arthrobacter plasmids was performed. This showed only limited similarities between plasmids of Antarctic Arthrobacter strains and replicons of other, mostly mesophilic, isolates. This indicates that the plasmids identified in this study are novel and unique replicons. In addition, a thorough meta-analysis of 247 plasmids of psychrotolerant bacteria was performed, revealing the important role of these replicons in the adaptation of their hosts to extreme environments.Rose, C.V., Fischer, W.W., Finnegan, S., Fike, D.A., 2019. Records of carbon and sulfur cycling during the Silurian Ireviken Event in Gotland, Sweden. Geochimica et Cosmochimica Acta 246, 299-316. Silurian (～431?Ma) carbonate rocks record a ca. 4.5‰ positive excursion in the stable isotopic composition of carbonate carbon (δ13Ccarb). Associated with this isotopic shift is a macroevolutionary turnover pulse known as the ‘Ireviken Event’. The onset of this carbon isotope excursion is commonly associated with a shallowing-upward facies transition that may have been accompanied by climatic change, as indicated by a parallel positive shift (～0.6‰) in the stable isotopic composition of carbonate oxygen (δ18Ocarb). However, the relationships among carbon cycle perturbations, faunal turnover, and environmental changes remain enigmatic. Here we present a suite of new isotopic data across the Ireviken Event from multiple sections in Gotland, Sweden. These samples preserve no systematic change in δ18Ocarb but show positive excursions of equal magnitude in both carbonate (δ13Ccarb) and organic (δ13Corg) carbon. In addition, the data reveal a synchronous perturbation in sulfur isotope ratios, manifest as a ca. 7‰ positive excursion in carbonate-associated sulfate (δ34SCAS) and a ca. 30‰ positive excursion in pyrite (δ34Spyr). The increase in δ34Spyr values is accompanied by a substantial, concomitant increase in stratigraphic variability of δ34Spyr.The relatively constant offset between the δ13Ccarb and δ13Corg excursions throughout the Ireviken Event could be attributed to increased organic carbon burial, or possibly a change in the isotopic composition of CO2 sources from weathering. However, a positive correlation between carbonate abundance and δ13Ccarb suggests that local to regional changes in dissolved inorganic carbon (DIC) during the shallowing-upward sequence may have been at least partly responsible for the observed excursion. The positive excursion recorded in δ34SCAS suggests a perturbation of sufficient magnitude and duration to have impacted the marine sulfate reservoir. An inverse correlation between CAS abundance and δ34SCAS supports the notion of decreased sulfate concentrations, at least locally, consistent with a concomitant increase in pyrite burial. A decrease in the offset between δ34SCAS and δ34Spyr values during the Ireviken Event suggests a substantial reduction in the isotopic fractionations (εpyr) expressed during microbial sulfur cycling and pyrite precipitation through this interval. Decreased εpyr and the concomitant increase in stratigraphic variation in δ34Spyr are typical of isotope systematics observed in modern shallow-water environments, associated with increased closed-system behavior and/or oxidative sedimentary reworking during early sediment diagenesis. While the isotopic trends associated with the Ireviken Event have been observed in multiple locations around the globe, many sections display different magnitudes of isotopic change, and moreover, are typically associated with local facies changes. Due to the stratigraphic coherence of the carbon and sulfur isotopic and abundance records across the Ireviken Event, and their relationship to changes in local depositional environment, we surmise that these patterns more closely reflect biogeochemical processes related to deposition and lithification of sediment than global changes in carbon and sulfur burial fluxes.Rostami, S., Abessi, O., Amini-Rad, H., 2019. Assessment of the toxicity, origin, biodegradation and weathering extent of petroleum hydrocarbons in surface sediments of Pars Special Economic Energy Zone, Persian Gulf. Marine Pollution Bulletin 138, 302-311. the last years, the oil and gas explorations, extractions and refineries have led to severe ecological damages into the sensitive environment of the Persian Gulf. In this study, the level of oil contamination, the source of hydrocarbons and the degree of weathering or degradation extent were investigated in the Surface Sediments of Pars Special Zone, Persian Gulf. Fifteen sediment samples were collected. The Gas Chromatography-Mass Spectrometry used to analyze Aliphatic Hydrocarbons (AHC) and EPA's sixteen compounds of Polycyclic Aromatic Hydrocarbons (PAHs). The total concentration of Aliphatic Hydrocarbons found to be in the range of 693 to 3752?μg/g and the 16 EPA PAHs compounds varied between 46.6 and 84.7?ng/g dry weight in the region. The concentration of hydrocarbons found to be lower than the level of threshold effects. The source of compounds was also identified by developing the multiple indices.Ruff, S.E., Felden, J., Gruber-Vodicka, H.R., Marcon, Y., Knittel, K., Ramette, A., Boetius, A., 2019. In situ development of a methanotrophic microbiome in deep-sea sediments. ISME Journal 13, 197-213. of the greenhouse gas methane from the seabed is globally controlled by marine aerobic and anaerobic methanotrophs gaining energy via methane oxidation. However, the processes involved in the assembly and dynamics of methanotrophic populations in complex natural microbial communities remain unclear. Here we investigated the development of a methanotrophic microbiome following subsurface mud eruptions at H?kon Mosby mud volcano (1250?m water depth). Freshly erupted muds hosted deep-subsurface communities that were dominated by Bathyarchaeota, Atribacteria and Chloroflexi. Methanotrophy was initially limited to a thin surface layer of Methylococcales populations consuming methane aerobically. With increasing distance to the eruptive center, anaerobic methanotrophic archaea, sulfate-reducing Desulfobacterales and thiotrophic Beggiatoaceae developed, and their respective metabolic capabilities dominated the biogeochemical functions of the community. Microbial richness, evenness, and cell numbers of the entire microbial community increased up to tenfold within a few years downstream of the mud flow from the eruptive center. The increasing diversity was accompanied by an up to fourfold increase in sequence abundance of relevant metabolic genes of the anaerobic methanotrophic and thiotrophic guilds. The communities fundamentally changed in their structure and functions as reflected in the metagenome turnover with distance from the eruptive center, and this was reflected in the biogeochemical zonation across the mud volcano caldera. The observed functional succession provides a framework for the response time and recovery of complex methanotrophic communities after disturbances of the deep-sea bed.Runnels, C.M., Lanier, K.A., Williams, J.K., Bowman, J.C., Petrov, A.S., Hud, N.V., Williams, L.D., 2018. Folding, assembly, and persistence: The essential nature and origins of biopolymers. Journal of Molecular Evolution 86, 598-610. as we know it requires three basic types of polymers: polypeptide, polynucleotide, and polysaccharide. Here we evaluate both universal and idiosyncratic characteristics of these biopolymers. We incorporate this information into a model that explains much about their origins, selection, and early evolution. We observe that all three biopolymer types are pre-organized, conditionally self-complementary, chemically unstable in aqueous media yet persistent because of kinetic trapping, with chiral monomers and directional chains. All three biopolymers are synthesized by dehydration reactions that are catalyzed by molecular motors driven by hydrolysis of phosphorylated nucleosides. All three biopolymers can access specific states that protect against hydrolysis. These protected states are folded, using self-complementary interactions among recurrent folding elements within a given biopolymer, or assembled, in associations between the same or different biopolymer types. Self-association in a hydrolytic environment achieves self-preservation. Heterogeneous association achieves partner-preservation. These universal properties support a model in which life’s polymers emerged simultaneously and co-evolved in a common hydrolytic milieu where molecular persistence depended on folding and assembly. We believe that an understanding of the structure, function, and origins of any given type of biopolymer requires the context of other biopolymers.Safi, E., Thompson, S.P., Evans, A., Day, S.J., Murray, C.A., Baker, A.R., Oliveira, J.M., van Loon, J.T., 2019. X-ray powder diffraction study of the stability of clathrate hydrates in the presence of salts with relevance to the Martian cryosphere. Geochimica et Cosmochimica Acta 245, 304-315. on the present day Martian surface is thought to exist in two thermally distinct sub-surface reservoirs: as ice in the cryosphere and as groundwater located deeper in the crust. These sub-surface environments are thought to contain saline, rather than pure, water and laboratory studies on whether or not clathrate hydrates can form in such environments are lacking. We fill this gap by performing synchrotron radiation X-ray powder diffraction to investigate the formation and evolution of clathrate hydrates in weak chloride solutions at CO2 pressures, and over temperature ranges, that are similar to those found in the Martian regolith. We have found that clathrate hydrates can form under conditions relevant to the Martian cryosphere, despite the presence of chloride salts. We find that the dissociation temperatures for CO2 clathrate hydrates formed in saline solutions are depressed by 10–20?K relative to those formed in pure water, depending on the nature of the salt and the CO2 pressure. We suggest that the inhibiting effect that salts such as MgCl2, CaCl2 and NaCl have on clathrate hydrate formation could also be related to the salts’ effect on the formation of the low temperature phase of ice. However, despite the inhibiting effect of the salts, we conclude that the presence of clathrate hydrates should still be possible under conditions likely to exist within the Martian cryosphere.Sahoo, S.K., Madhusudhan, B.N., Marín-Moreno, H., North, L.J., Ahmed, S., Falcon-Suarez, I.H., Minshull, T.A., Best, A.I., 2018. Laboratory insights into the effect of sediment-hosted methane hydrate morphology on elastic wave velocity from time-lapse 4-D synchrotron X-ray computed tomography. Geochemistry, Geophysics, Geosystems 19, 4502-4521. better understanding of the effect of methane hydrate morphology and saturation on elastic wave velocity of hydrate‐bearing sediments is needed for improved seafloor hydrate resource and geohazard assessment. We conducted X‐ray synchrotron time‐lapse 4‐D imaging of methane hydrate evolution in Leighton Buzzard sand and compared the results to analogous hydrate formation and dissociation experiments in Berea sandstone, on which we measured ultrasonic P and S wave velocities and electrical resistivity. The imaging experiment showed that initially hydrate envelops gas bubbles and methane escapes from these bubbles via rupture of hydrate shells, leading to smaller bubbles. This process leads to a transition from pore‐floating to pore‐bridging hydrate morphology. Finally, pore‐bridging hydrate coalesces with that from adjacent pores creating an interpore hydrate framework that interlocks the sand grains. We also observed isolated pockets of gas within hydrate. We observed distinct changes in gradient of P and S wave velocities increase with hydrate saturation. Informed by a theoretical model of idealized hydrate morphology and its influence on elastic wave velocity, we were able to link velocity changes to hydrate morphology progression from initial pore‐floating, then pore‐bridging, to an interpore hydrate framework. The latter observation is the first evidence of this type of hydrate morphology and its measurable effect on velocity. We found anomalously low S wave velocity compared to the effective medium model, probably caused by the presence of a water film between hydrate and mineral grains.Sandau, C.D., Prokipchuk, M., Dominato, K.R., Mundle, S.O.C., 2019. Soil gas investigation of an alleged gas migration issue on a residential farm located above the Weyburn-Midale CO2 enhanced oil recovery project. International Journal of Greenhouse Gas Control 81, 11-20. (13C) and radiogenic (14C) carbon isotope tracers are recognized approaches to identify gas sources using soil gas monitoring techniques; however, definitive characterization from a subsurface injection/storage reservoir can be complicated by processes that produce and consume CO2. Few studies assess the combined use of compositional (fixed gases, hydrocarbons, and sulphurous compounds) and isotopic (13C, 18O and 14C) indicators from soil gases as tools to evaluate CO2 storage reservoir leaks. Compositional and isotopic indicators from soil gases were compared at an investigation site (IS) alleged to be impacted by CO2 leaking from an underlying injection reservoir with a baseline control site (BCS) outside of the injection area. Soil gas δ13CCO2 values collected from the IS (?23.4‰to ?22.6‰) were comparable with the range observed at the BCS (?22.8‰ and ?23.3‰), falling within the range anticipated for both biogenic and injected CO2. 14C values were also comparable between IS (98.0 pMC to 107.0 pMC) and BCS (102.8 pMC to 105.3 pMC) sites, representing a modern carbon source that was distinct from the CO2 injection gas (0.34 pMC). The results provide several lines of evidence that CO2 fluxes in soil gases at the IS were related to naturally occurring processes and were not caused by a gas migration issue from a geological CO2 storage reservoir.Santibanez-Borda, E., Govindan, R., Elahi, N., Korre, A., Durucan, S., 2019. Maximising the dynamic CO2 storage capacity through the optimisation of CO2 injection and brine production rates. International Journal of Greenhouse Gas Control 80, 76-95. O2 storage capacity in saline aquifers can dramatically be reduced by pressure build up due to the CO2 injection process. In this paper, a novel optimisation strategy that maximises the CO2 storage capacity utilisation and net profits before tax is presented in a scenario of simultaneous CO2 injection and brine production to help control pressure build up and increase the effective storage capacity. The strategy is tested at the region surrounding the Forties and Nelson fields, assuming both as pure saline aquifer traps. The optimisation was performed considering constraints such that the CO2 plume distribution does not migrate outside the license boundaries, the fracture pressure is not reached within the reservoir, and the CO2 injection and brine production rates occur within feasible limits. The problem was first formulated analytically with the aid of surrogate models, and then optimised using the SIMPLEX and Generalized Reduced Gradient methods. Results for the Forties and Nelson fields show that by allowing five brine production wells producing up to 2.2 MMtonnes/year, the CO2 storage capacity increased between 112-145% compared to the case where no brine production is practiced.Santoro, V., Baiocchi, C., Dal Bello, F., Gastaldi, D., Aigotti, R., Zorzi, M., Pellegrino, A., Forte, E., Romaniello, F., Magni, M., Fontana, M., Somenzi, M., Medana, C., 2018. Formation of by-products during chemical interesterification of lipids. Detection and characterization of dialkyl ketones by non-aqueous reversed-phase liquid chromatography-high resolution mass spectrometry and gas chromatography-mass spectrometry. Journal of Chromatography A 1581-1582, 63-70. new class of foreign substances present in the unsaponifiable fraction of vegetable oils undergone to chemical interesterification was systematically investigated. Their chemical structure, corresponding to dialkyl ketones (DAK) molecules, was elucidated both by gas chromatography-mass spectrometry (GC–MS), and liquid chromatography-high resolution mass spectrometry (LC-HRMS). An analytical protocol aimed to qualitative and quantitative detection of DAK molecules in vegetable oils of confectionery industry interest was developed. Being the range of concentration levels to be evaluated dependent on the technological task of interesterification process, the quantitation step was thoroughly examined. All the validation parameters were satisfactory and particularly the concentration determinations were made more reliable by the contemporary use of several quantitation standards. GC–MS and LC-HRMS analytical techniques exhibited comparable performances even if the second one shown better detection sensitivity.Savareear, B., Escobar-Arnanz, J., Brokl, M., Saxton, M.J., Wright, C., Liu, C., Focant, J.-F., 2018. Comprehensive comparative compositional study of the vapour phase of cigarette mainstream tobacco smoke and tobacco heating product aerosol. Journal of Chromatography A 1581–1582, 105-115. simple direct sample collection/dilution and introduction method was developed using quartz wool and Tenax/sulficarb sorbents for thermal desorption and comprehensive two-dimensional gas chromatography (TD-GC?×?GC) analyses of volatile organic compounds from vapour phase (VP) fractions of aerosol produced by tobacco heating products (THP1.0) and 3R4F mainstream tobacco smoke (MTS). Analyses were carried out using flame ionisation detection (FID) for semi-quantification and both low and high resolution time-of-flight mass spectrometry (LR/HR-TOFMS) for qualitative comparison and peak assignment. Qualitative analysis was carried out by combining identification data based on linear retention indices (LRIs) with a match window of ±10 index units, mass spectral forward and reverse library searches (from LR and HRTOFMS spectra) with a match factor threshold of >700 (both forward and reverse), and accurate mass values of?±?3?ppm for increased confidence in peak identification. Using this comprehensive approach of data mining, a total of 79 out of 85 compounds and a total of 198 out of 202 compounds were identified in THP1.0 aerosol and in 3R4F MTS, respectively. Among the identified analytes, a set of 35 compounds was found in both VP sample types. Semi-quantitative analyses were carried out using a chemical class-based external calibration method. Acyclic, alicyclic, aromatic hydrocarbons and ketones appeared to be prominent in 3R4F MTS VP, whereas larger amounts of aldehydes, ketones, heterocyclic hydrocarbons and esters were present in THP1.0 aerosol VP. The results demontsrate the capability and versatility of the method for the characterization and comparison of complex aerosol samples and highlighted the relative chemical simplicity of THP1.0 aerosol in comparison to MTS.Sazali, Y.A., Sazali, W.M.L., Ibrahim, J.M., Dindi, M., Graham, G., G?deke, S., 2019. Investigation of high temperature, high pressure, scaling and dissolution effects for Carbon Capture and Storage at a high CO2 content carbonate gas field offshore Malaysia. Journal of Petroleum Science and Engineering 174, 599-606. is considering Carbon Capture and Storage (CCS) as a possible way to reduce its greenhouse gas emission footprint. An offshore carbonate reservoir has been identified in which all aspects of CCS are investigated in detail. There, the CO2 is planned to be re-injected into a saline aquifer. However, formation damage in underground formations linked with permeability reduction can significantly impact oil and gas production and could render CCS infeasible. Thus, in order to manage the injection of CO2 from the subsurface side a study was conducted investigating geomechanical aspects, rock fluid interactions as well as production aspects from the gas field. Only very few studies exist that investigate scaling and dissolution effects at elevated pressures and temperatures. Here, results from 3 high pressure high temperature scaling and dissolution core floods for the scheduled to be developed carbonate field are presented in detail. Core floods were performed under temperatures ranging between 121?°C to 136?°C and CaCO3 scaling tendencies between 0.24 and 1.47. The scaling tendency of each brine was adjusted to represent, baseline, assumed worst case scaling as well as worst case dissolution scenarios identified based on fluid and gas samples and prior geochemical modelling. Bicarbonate, Calcium and pH were analysed from samples taken during the core flood. SEM-EDX analysis was done on core flood effluent particles. A calcite dissolution rate of 0.008?mol/m2/sec was calculated for the core flood with the scaling tendency of 0.24. The specific surface area of the calcite was estimated at 0.17?cm2/mol. Overall the results indicate that only minor dissolution can be anticipated during production from the CO2 rich gas field.Scarlett, A.G., Spaak, G., Mohamed, S., Plet, C., Grice, K., 2019. Comparison of tri-, tetra- and pentacyclic caged hydrocarbons in Australian crude oils and condensates. Organic Geochemistry 127, 115-123. stable and biodegradation resistant, the tricyclic and pentacyclic diamondoid caged hydrocarbons are commonly used as source and maturity indicators of oils and potential source-rocks, but similar tetracyclic structures appear to have received much less attention. Using two-dimensional (2D) gas chromatography – time of flight mass spectrometry (GC?×?GC-TOFMS), 29 Australian crude oils and condensates were analysed for the presence of caged C12H18 tetracyclics such as ethanoadamantane and iceane. The thermodynamically more stable 2,4-ethanoadamantane was identified by comparison with a synthesised authentic standard. Three of its bridgehead methyl-substituted isomers, 6-methylethanoadamantane (6-ME), 1-ME and 2-ME, were tentatively assigned based on mass spectral comparison and relative elution order. Further series of non-bridgehead methyl isomers, plus dimethyl isomers, were also inferred based on mass spectra and 2D elution positions. The tri-, tetra and pentacyclic caged hydrocarbons and their methyl-substituted homologues were semi-quantified in the Australian oils. The potential of a novel index, the methylethanoadamantane index (MEI), based on the ratio of the more stable bridgehead isomers divided by the sum of all the methyl substituted isomers (MEI?=?Σ(6-ME?+?1-ME?+?2-ME)/ΣTotal methylethanoadamantanes), was explored. A significant positive association was found between the MEI and MAI (r2?=?0.203, p?<?0.05) and a significant negative association was found between MEI and MDI (r2?=?0.246, p?<?0.05). Stronger relationships were found for other commonly applied diamondoid ratio indices, including Σ Methyl Adamantanes/Σ Methyl Diamantanes (ΣMA/ΣMD) versus ΣMA/ΣME (r2?=?0.781, p?<?0.0001, n?=?26). The relatively low volatility of the ethanoadamantanes compared to the adamantanes and their likely greater resistance to microbial attack than the ethyladamantanes, may make analysis of these compounds a useful addition to the commonly measured diamondoids.Schinkel, L., Bogdal, C., Canonica, E., Cariou, R., Bleiner, D., McNeill, K., Heeb, N.V., 2018. Analysis of medium-chain and long-chain chlorinated paraffins: The urgent need for more specific analytical standards. Environmental Science & Technology Letters 5, 708-717. paraffins (CPs) are high-production volume chemicals and ubiquitous environmental pollutants. In particular, data about the environmental fate of medium-chain (MCCPs, C14–C17) and long-chain (LCCPs, C≥18) CPs are urgently needed. Their analysis requires elaborate analytical methods and representative analytical standards. Complex mixtures that contain CPs of different carbon chain lengths and degrees of chlorination are currently used for quantification but are impractical when chain length distributions substantially differ between samples and standards. Single-chain CP mixtures of only one carbon chain length but varying degrees of chlorination are more suitable for accurate quantification but are not available for MCCPs and LCCPs. Such standards are useful for homologue pattern deconvolution and response factor calculations. Toxicity and transformation studies on MCCPs and LCCPs are scarce. Studies would also benefit from less complex CP standards, e.g., single-chain mixtures or even constitutionally defined CPs. Currently available analytical standards are inadequate for the demanding task of quantifying MCCPs and LCCPs. Improved standards are required. This review provides an overview of the available analytical CP materials, discusses advantages and disadvantages of accurate CP analysis, and gives a recommendation for improvements. Recommendations for improved analytical standards include (A) complex CP mixtures that better resemble technical CP mixtures, (B) single-chain CP mixtures of different carbon chain lengths (C10–C30) and varying degrees of chlorination (40–70 wt % Cl), (C) constitutionally defined CPs with representative chlorination patterns, and (D) isotopically labeled CP isomers that represent a broad range of CPs.Schmidt, D.R., Woolf, N.J., Zega, T.J., Ziurys, L.M., 2018. Extreme 13C, 15N and 17O isotopic enrichment in the young planetary nebula K4-47. Nature 564, 378–381., nitrogen and oxygen are the three most abundant elements in the Galaxy after hydrogen and helium. Whereas hydrogen and helium were created in the Big Bang, carbon, nitrogen and oxygen arise from nucleosynthesis in stars. Of particular interest\ are the isotopic ratios 12C/13C, 14N/15N and 16O/17O because they are effective tracers of nucleosynthesis and help to benchmark the chemical processes that occurred in primitive interstellar material as it evolved into our Solar System\. However, the origins of the rare isotopes 15N and 17O remain uncertain, although novae and very massive stars that explode as supernovae are postulated\ to be the main sources of 15N. Here we report millimetre-wavelength observations of the young bipolar planetary nebula K4-47 that indicate another possible source for these isotopes. We identify various carbon-bearing molecules in K4-47 that show that this object is carbon-rich, and find unusually high enrichment in rare carbon (13C), oxygen (17O) and nitrogen (15N) isotopes: 12C/13C = 2.2 ± 0.8, 16O/17O = 21.4 ± 10.3 and 14N/15N = 13.6 ± 6.5 (uncertainties are three standard deviations); for comparison, the corresponding solar ratios\ are 89.4 ± 0.2, 2,632 ± 7 and 435 ± 57. One possible interpretation of these results is that K4-47 arose from a J-type asymptotic giant branch star that underwent a helium-shell flash (an explosive nucleosynthetic event that converts large quantities of helium to carbon and other elements), enriching the resulting planetary nebula in 15N and 17O and creating its bipolar geometry. Other possible explanations are that K4-47 is a binary system or that it resulted from a white dwarf merger, as has been suggested for object CK Vu. These results suggest that nucleosynthesis of carbon, nitrogen and oxygen is not well understood and that the classification of certain stardust grains must be reconsidered.Schmidt, J.S., Menezes, T.R., Souza, I.V.A.F., Spigolon, A.L.D., Pestilho, A.L.S., Coutinho, L.F.C., 2019. Comments on empirical conversion of solid bitumen reflectance for thermal maturity evaluation. International Journal of Coal Geology 201, 44-50. studies raised doubts about the reliability of the correlation function between solid bitumen and vitrinite reflectance in diagenesis to catagenesis stages. Addressing this issue, data was surveyed from recent and classical studies following strict criteria. This compilation comprised an expressive sampling in the vitrinite reflectance range of 0.19 to 5.79% and was used to generate a new correlation function. This function was compared to previous ones and against data from recent studies. The results confirm that the reflectance of solid bitumen with homogeneous texture can be used as a thermal maturity index. Furthermore, the results also bring new insights on the identification of vitrinite-like solid bitumen when the petrographic criteria are ineffective.Schmitz, O.J., Wilmers, C.C., Leroux, S.J., Doughty, C.E., Atwood, T.B., Galetti, M., Davies, A.B., Goetz, S.J., 2018. Animals and the zoogeochemistry of the carbon cycle. Science 362, Article eaar3213.: Predicting and managing the global carbon cycle requires scientific understanding of ecosystem processes that control carbon uptake and storage. It is generally assumed that carbon cycling is sufficiently characterized in terms of uptake and exchange between ecosystem plant and soil pools and the atmosphere. We show that animals also play an important role by mediating carbon exchange between ecosystems and the atmosphere, at times turning ecosystem carbon sources into sinks, or vice versa. Animals also move across landscapes, creating a dynamism that shapes landscape-scale variation in carbon exchange and storage. Predicting and measuring carbon cycling under such dynamism is an important scientific challenge. We explain how to link analyses of spatial ecosystem functioning, animal movement, and remote sensing of animal habitats with carbon dynamics across landscapes.Editor's Summary, Animals count: Flux across the carbon cycle is generally characterized by contributions from plants, microbes, and abiotic systems. Animals, however, move vast amounts of carbon, both through ecosystem webs and across the landscape. Schmitz et al. review the different contributions that animal populations make to carbon cycling and discuss approaches that allow for better monitoring of these contributions.Structured AbstractBackground: Modern advances in remote-sensing technology are providing unprecedented opportunities to accurately measure the global distribution of carbon held in biomass within ecosystems. Such highly spatially resolved measures of biomass carbon are intended to provide an accurate inventory of global carbon storage within ecosystems. They are also needed to test the accuracy of carbon cycle models that predict how global changes that alter biogeochemical functions—such as carbon assimilation via photosynthesis, carbon losses via plant and microbial respiration, and organic matter deposition in soils and sediments—will affect net ecosystem carbon uptake and storage. Emerging ecological theory predicts that wild animals stand to play an important role in mediating these biogeochemical processes. Furthermore, many animal species roam widely across landscapes, creating a spatial dynamism that could regulate spatial patterning of vegetation biomass and carbon uptake and soil carbon retention. But such zoogeochemical effects are not measured by current remote-sensing approaches nor are they factored into carbon cycle models. Studies are now providing new quantitative insights into how the abundance, diversity, and movement of animal species across landscapes influence the nature and magnitude of zoogeochemical affects. These insights inform how to account for animals in remote-sensing applications and in carbon cycle models to more accurately predict carbon exchange between ecosystems and the atmosphere in the face of global environmental change.Advances: Zoogeochemical effects have been measured using manipulative experiments that exclude or add focal wild animal species or along landscape gradients where animal abundances or diversity vary naturally. Our review of these studies, which cover a wide diversity of taxa (vertebrates and invertebrates and large- and small-bodied organisms) and ecosystems, reveals that animals can increase or decrease rates of biogeochemical processes, with a median change of 40% but ranging from 15 to 250% or more. Moreover, models that embody zoogeochemical effects reveal the potential for considerable under- or overestimates in ecosystem carbon budgets if animal effects are not considered. The key challenge, in light of these findings, is comprehensively accounting for spatially dynamic animal effects across landscapes. We review new developments in spatial ecosystem ecology that offer the kind of analytical guidance needed to link animal movement ecology to geospatial patterning in ecosystem carbon uptake and storage. Considerations of animal movement will require highly resolved spatially explicit understanding of landscape features, including topography, climate, and the spatial arrangement of habitat patches and habitat connectivity within and among ecosystems across landscapes. We elaborate on advances in remote-sensing capabilities that can deliver these critical data. We further review new geospatial statistical methods that, when combined with remote-sensing data and spatial ecosystem modeling, offer the means to comprehensively understand and predict how zoogeochemical-driven landscape processes regulate spatial patterns in carbon distribution.Outlook: There is growing interest to slow climate change by enlisting ecological processes to recapture atmospheric carbon and store it within ecosystems. Wild animal species are rarely considered as part of the solution. Instead, it is often held that managing habitat space to conserve wild animals will conflict with carbon storage. Our integrative review offers a pathway forward for deciding when and how conserving or managing a diversity of animal species could in fact enhance ecosystem carbon uptake and storage. Such understanding informs international climate and biodiversity initiatives such as those described by the United Nations Convention on Biological Diversity and national biodiversity strategies and climate action plans. All of these initiatives require better resolution of how biodiversity effects on ecosystem structure and biogeochemical functioning will become altered by global change.Schwaiger, M., Schoeny, H., El Abiead, Y., Hermann, G., Rampler, E., Koellensperger, G., 2019. Merging metabolomics and lipidomics into one analytical run. Analyst 144, 220-229. novel integrated metabolomics/lipidomics workflow is introduced enabling high coverage of polar metabolites and non-polar lipids within one analytical run. Dual HILIC and RP chromatography were combined to high-resolution mass spectrometry. As a major advantage, only one data file per sample was obtained by fully automated simultaneous analysis of two extracts per sample. Hence, the unprecedented high coverage without compromise on analytical throughput was not only obtained by the orthogonality of the chromatographic separations, but also by the implementation of dedicated sample preparation procedures resulting in optimum extraction efficiency for both sub-omes. Thus, the method addressed completely hydrophilic sugars and organic acids next to water-insoluble triglycerides. As for the timing of the dual chromatography setup, HILIC and RP separation were performed consecutively. However, re-equilibration of the HILIC column during elution of RP compounds and vice versa reduced the overall analysis time by one third to 32 min. Application to the Standard Reference Material SRM 1950 – Metabolites in Frozen Human Plasma resulted in >100 metabolite and >380 lipid identifications based on accurate mass implementing fast polarity switching and acquiring data dependent MS2 spectra with the use of automated exclusion lists. Targeted quantification based on external calibrations and 13C labeled yeast internal standards was successfully accomplished for 59 metabolites. Moreover, the potential for lipid quantification was shown integrating non-endogenous lipids as internal standards. In human plasma, concentrations ranging over 4 orders of magnitude (low nM to high μM) were assessed.Schweitzer, H., Ritter, D., McIntosh, J., Barnhart, E., Cunningham, A.B., Vinson, D., Orem, W., Fields, M.W., 2019. Changes in microbial communities and associated water and gas geochemistry across a sulfate gradient in coal beds: Powder River Basin, USA. Geochimica et Cosmochimica Acta 245, 495-513. between microbial sulfate reduction and methanogenesis drives cycling of fossil carbon and generation of CH4 in sedimentary basins. However, little is understood about the fundamental relationship between subsurface aqueous geochemistry and microbiology that drives these processes. Here we relate elemental and isotopic geochemistry of coal-associated water and gas to the microbial community composition from wells in two different coal beds across CH4 and SO42? gradients (Powder River Basin, Montana, USA). Areas with high CH4 concentrations generally have higher alkalinity and δ13C-DIC values, little to no SO42?, and greater conversion of coal-biodegradable organics to CH4 (based on δ13C-CH4 and δ13C-CO2 values). Wells with SO42? concentrations from 2 to 10?mM had bacterial populations dominated by several different sulfate-reducing bacteria and archaea that were mostly novel and unclassified. In contrast, in wells with SO42? concentrations <1?mM, the sequences were dominated by presumptive syntrophic bacteria as well as archaeal Methanosarcinales and Methanomicrobiales. The presence of sequences indicative of these bacteria in low SO42? methanogenic wells may suggest a syntrophic role in coal biodegradation and/or the generation of methanogenic substrates from intermediate organic compounds. Archaeal sequences were observed in all sampled zones, with an enrichment of sequences indicative of methanogens in low SO42? zones and unclassified sequences in high SO42? zones. However, sequences indicative of Methanomassiliicoccales were enriched in intermediate SO42? zones and suggest tolerance to SO42? and/or alternative metabolisms in the presence of SO42?. Moreover, sequences indicative of methylotrophic methanogens were more prevalent in an intermediate SO42? and CH4 well and results suggest an important role for methylotrophic methanogens in critical zone transitions. The presented results demonstrate in situ changes in bacterial and archaeal population distributions along a SO42? gradient associated with recalcitrant, organic carbon that is biodegraded and converted to CO2 and/or CH4.Sclafani, J.A., Congreve, C.R., Krug, A.Z., Patzkowsky, M.E., 2018. Effects of mass extinction and recovery dynamics on long-term evolutionary trends: a morphological study of Strophomenida (Brachiopoda) across the Late Ordovician mass extinction. Paleobiology 44, 603-619. extinctions affect the history of life by decimating existing diversity and ecological structure and creating new evolutionary and ecological pathways. Both the loss of diversity during these events and the rebound in diversity following extinction had a profound effect on Phanerozoic evolutionary trends. Phylogenetic trees can be used to robustly assess the evolutionary implications of extinction and origination.We examine both extinction and origination during the Late Ordovician mass extinction. This mass extinction was the second largest in terms of taxonomic loss but did not appear to radically alter Paleozoic marine assemblages. We focus on the brachiopod order Strophomenida, whose evolutionary relationships have been recently revised, to explore the disconnect between the processes that drive taxonomic loss and those that restructure ecological communities.A possible explanation for this disconnect is if extinction and origination were random with respect to morphology. We define morphospace using principal coordinates analysis (PCO) of character data from 61 Ordovician–Devonian taxa and their 45 ancestral nodes, defined by a most parsimonious reconstruction in Mesquite. A bootstrap of the centroid of PCO values indicates that genera were randomly removed from morphospace by the Late Ordovician mass extinction, and new Silurian genera were clustered within a smaller previously unoccupied region of morphospace. Diversification remained morphologically constrained throughout the Silurian and into the Devonian. This suggests that the recovery from the Late Ordovician mass extinction resulted in a long-term shift in strophomenide evolution. More broadly, recovery intervals may hold clues to understanding the evolutionary impact of mass extinctions.Scully, M.E., 2018. A diel method of estimating gross primary production: 1. Validation with a realistic numerical model of Chesapeake Bay. Journal of Geophysical Research: Oceans 123, 8411-8429.: A method for estimating gross primary production (GPP) is presented and validated against a numerical model of Chesapeake Bay that includes realistic physical and biological forcing. The method statistically fits a photosynthesis‐irradiance response curve using the observed near‐surface time rate of change of dissolved oxygen and the incoming solar radiation, yielding estimates of the light‐saturated photosynthetic rate and the initial slope of the photosynthesis‐irradiance response curve. This allows estimation of GPP with 15‐day temporal resolution. The method is applied to the output from a numerical model that has high skill at reproducing both surface and near‐bottom dissolved oxygen variations observed in Chesapeake Bay in 2013. The rate of GPP predicted by the numerical model is known, as are the contributions from physical processes, allowing the proposed diel method to be rigorously assessed. At locations throughout the main stem of the Bay, the method accurately extracts the underlying rate of GPP, including pronounced seasonal variability and spatial variability. Errors associated with the method are primarily the result of contributions by the divergence in turbulent oxygen flux, which changes sign over the surface mixed layer. As a result, there is an optimal vertical location with minimal bias where application of the method is most accurate.Plain Language Summary: This paper presents and evaluates a method for estimating gross primary production from time variations of dissolved oxygen. The evaluation is performed on the output from a three‐dimensional circulation model of Chesapeake Bay that can simulate dissolved oxygen with high skill.Scully, M.E., 2018. A diel method of estimating gross primary production: 2. Application to 7?years of near-surface dissolved oxygen data in Chesapeake Bay. Journal of Geophysical Research: Oceans 123, 8430-8443.: A diel method for estimating gross primary production (GPP) is applied to nearly continuous measurements of near‐surface dissolved oxygen collected at seven locations throughout the main stem of Chesapeake Bay. The data were collected through the Chesapeake Bay Interpretive Buoy System and span the period 2010–2016. At all locations, GPP exhibits pronounced seasonal variability consistent temperature‐dependent phytoplankton growth. At the Susquehanna Buoy, which is located within the estuarine turbidity maximum, rates of GPP are negatively correlated with uncalibrated turbidity data consistent with light limitation at this location. The highest rates of GPP are located immediately down Bay from the estuarine turbidity maximum and decrease moving seaward consistent with nutrient limitation. Rates of GPP at the mouth (First Landing Buoy) are roughly a factor of 3 lower than the rates in the upper Bay (Patapsco). At interannual time scales, the summer (June–July) rate of GPP averaged over all stations is positively correlated (r2 = 0.62) with the March Susquehanna River discharge and a multiple regression model that includes spring river discharge, and summer water temperature can explain most (r2 = 0.88) of the interannual variance in the observed rate of GPP. The correlation with river discharge is consistent with an increase in productivity fueled by increased nutrient loading. More generally, the spatial and temporal patterns inferred using this method are consistent with our current understanding of primary production in the Bay, demonstrating the potential this method has for making highly resolved measurements in less well studied estuarine systems.Plain Language Summary: A new method for estimating gross primary production from in situ dissolved oxygen data is applied to 7 years of data from Chesapeake Bay. Application of the method highlights pronounced spatial and temporal variability consistent with previous studies employing more labor intensive methods. The method shows significant promise for making high‐quality measurements of productivity with high temporal resolution in estuarine systems.Seviour, T., Derlon, N., Dueholm, M.S., Flemming, H.-C., Girbal-Neuhauser, E., Horn, H., Kjelleberg, S., van Loosdrecht, M.C.M., Lotti, T., Malpei, M.F., Nerenberg, R., Neu, T.R., Paul, E., Yu, H., Lin, Y., 2019. Extracellular polymeric substances of biofilms: Suffering from an identity crisis. Water Research 151, 1-7. biofilms can be both cause and cure to a range of emerging societal problems including antimicrobial tolerance, water sanitation, water scarcity and pollution. The identities of extracellular polymeric substances (EPS) responsible for the establishment and function of biofilms are poorly understood. The lack of information on the chemical and physical identities of EPS limits the potential to rationally engineer biofilm processes, and impedes progress within the water and wastewater sector towards a circular economy and resource recovery. Here, a multidisciplinary roadmap for addressing this EPS identity crisis is proposed. This involves improved EPS extraction and characterization methodologies, cross-referencing between model biofilms and full-scale biofilm systems, and functional description of isolated EPS with in situ techniques (e.g. microscopy) coupled with genomics, proteomics and glycomics. The current extraction and spectrophotometric characterization methods, often based on the principle not to compromise the integrity of the microbial cells, should be critically assessed, and more comprehensive methods for recovery and characterization of EPS need to be developed.Shen, W., Chen, J., Wang, Y., Zhang, K., Chen, Z., Luo, G., Fu, X., 2019. The origin, migration and accumulation of the Ordovician gas in the Tazhong III region, Tarim Basin, NW China. Marine and Petroleum Geology 101, 55-77. Ordovician large-scale gas reservoir in the Tazhong III region (burial depth?>?6000?m) is a typical deep strata gas reservoir in the Tarim Basin of NW China. The origin, migration and accumulation of the Ordovician natural gas in the Tazhong III region were investigated by integrating geological, geophysical, and geochemical parameters. The parameters that were successfully analyzed included the gas compositions and carbon isotope ratios, production data, burial and geothermal histories, oil compositions and properties, together with the diamantane index. The results indicated that the Ordovician natural gas in the Tazhong III region originated from Cambrian-Ordovician paleo-oil cracking, accompanied by a large amount of H2S generated from thermochemical sulfate reduction (TSR). When the oil cracking gas migrated vertically into the Ordovician reservoir through the Tazhong I fault and strike-slip faults, it was preferentially charged in the pinnate fault zones of strike-slip faults with high porosity and permeability, leading to the enrichment of natural gas and an abnormal distribution of the compositions and properties of hydrocarbon. Then, oil cracking gas intruded into and altered the previous oil reservoir from northeast to southwest through the strike-slip faults, unconformities and pore-fracture reservoir belt, leading to the differential accumulation of hydrocarbon in districts of the Tazhong III region. The Ordovician natural gas migration-accumulation model in the Tazhong III region indicates a great exploration potential in the deep or super-deep strata of the Tarim Basin. Further exploration activities in the Ordovician reservoir of the Tarim Basin should be conducted in the regions where Cambrian-Ordovician source rocks are well developed, and the stress fracture zones-related deep fault should be emphasized.Shevchenko, A., Schuhmann, A., Thomas, H., Wetzel, G., 2018. Fine endmesolithic fish caviar meal discovered by proteomics in foodcrusts from archaeological site Friesack 4 (Brandenburg, Germany). PLOS ONE 13, Article e0206483. role of aquatic resources in ancient economies and paleodiet is important for understanding the evolution of prehistorical societies. Charred food remains from ancient pottery are valuable molecular evidence of dietary habits in antiquity. However, conventional archaeometric approaches applied in their analysis lack organismal specificity, are affected by abundant environmental contaminants, do not elucidate food processing recipes and are limited in the inland regions where diverse dietary resources are available. We performed proteomics analysis of charred organic deposits adhered on early ceramics from Mesolithic-Neolithic inland site Friesack 4 (Brandenburg, Germany). One of pots—a small coarse bowl radiocarbon dated to the end of the 5th millennium BC—was attributed to Endmesolithic pottery. Proteomics of foodcrust from this vessel identified fine carp roe meal and revealed details of a prehistorical culinary recipe. Ancient proteins were unequivocally distinguished from contemporary contaminants by computing deamidation ratios of glutamine residues. These data paint a broader picture of the site-specific exploitation of aquatic resources and contribute to better understanding of the dietary context of Neolithic transition in European inland.Shi, Y., Yassin, M.R., Yuan, L., Dehghanpour, H., 2019. Modelling imbibition data for determining size distribution of organic and inorganic pores in unconventional rocks. International Journal of Coal Geology 201, 26-43. studies show that the pore network of unconventional rocks generally consists of inorganic and organic parts, forming a dual-wet medium. The organic part has high wetting affinity to oleic phase but low wetting affinity to aqueous phase. In contrast, the inorganic part has high wetting affinity to both oleic and aqueous phases. The objective of this study is to estimate the organic and inorganic pore size distributions (PSDs) of the unconventional rocks by analyzing the comparative oil and brine imbibition data. A previously-proposed fractal model which considers the non-piston-like imbibition front is used to achieve this objective. We use a history matching technique to fit the measured imbibition data with the proposed fractal model, and determine unknown parameters such as fractal dimension (FD), minimum pore diameter (Dmin), and tortuosity (τ) that control the imbibition profile. The determined parameters are then used to estimate PSD. The PSD of inorganic and organic pores (PSDinorg+org) is calculated by oil imbibition data and the PSD of inorganic pores (PSDinorg) is calculated by brine imbibition data. The PSD of organic pores (PSDorg) is calculated by decoupling of PSDinorg+org and PSDinorg. Comparing the estimated PSDorg and PSDinorg shows that organic pores are generally smaller than inorganic pores, consistent with the results of scanning electron microscopy (SEM) and energy-dispersive X-ray spectroscopy (EDS) analyses, indicating the abundance of nanopores within the organic matter. Moreover, compared with the PSD from mercury injection capillary pressure (MICP) test, PSD estimated by oil imbibition shows very small pores (< 3?nm in diameter) which are not accessible by mercury, especially for the low-permeability rock samples. The method proposed in this study can complement the conventional MICP technique for a more comprehensive characterization of the pore network of unconventional rocks with dual-wet pore network.Shiraishi, F., Ohnishi, S., Hayasaka, Y., Hanzawa, Y., Takashima, C., Okumura, T., Kano, A., 2019. Potential photosynthetic impact on phosphate stromatolite formation after the Marinoan glaciation: Paleoceanographic implications. Sedimentary Geology 380, 65-82. study investigated the origin and the depositional age of phosphate stromatolites contained in the Neoproterozoic Salitre Formation, Brazil. The stromatolites exhibited columnar shapes and were intercalated with laminated dolostones. Their depositional environment was interpreted to have been an evaporitic ramp where erosion and reworking by waves prevailed. Laser ablation-inductively coupled plasma-mass spectrometry measurements of the stromatolites yielded a U–Pb age of 616?±?32?Ma, suggesting that they were deposited after the Marinoan glaciation. Several types of filamentous structures were recognized in the stromatolites; many of them were “pseudofossil” ambient inclusion trails, but some were possibly microfossils. To consider the general presence of photosynthetic microorganisms on the surface of shallow-water stromatolites, the involvement of microbial photosynthesis in phosphate stromatolite formation was expected. Numerical calculations determined that photosynthesis could have induced phosphate mineral precipitation at the time of deposition if the phosphorus concentration was above ca. 5?μM. To achieve such high concentration at the shallow ocean, globally elevated phosphorus concentration was considered to be the ultimate factor in addition to the local process(es) including upwelling and/or evaporation. Therefore, the phosphate stromatolites in the Salitre Formation are evidence of the development of a phosphorus-rich ocean after the Marinoan glaciation.Simon, M.N., Buxner, S., Impey, C., 2018. A survey and analysis of college students' understanding of planet formation before instruction. Astrobiology 18, 1594-1610. topic of solar system formation has become essential to the teaching of astrobiology due to the discovery of more than 3700 exoplanets, some orbiting within their host star's habitable zone. The architecture of planetary systems is more easily understood when students are able to comprehend how solar systems form. There has yet to be a study that addresses the topic of planet formation at the college level using a large sample of introductory astronomy students. We collected responses from students in 13 introductory astronomy and planetary science courses (n?=?1050) at the University of Arizona, who each completed 1 of 6 short-answer questions on the topic of planet formation. The questions were administered on the first day of the Fall 2016 and Spring 2017 semesters before any relevant material was taught. After analyzing their responses, we found that the most common misconception students held was that our Solar System formed as a direct result of the Big Bang, but a substantial percentage of students lacked a more general understanding of fundamental astronomical topics (gravity, definitions of a planet and solar system, density, and the physical processes associated with solar system formation). This lack of foundational knowledge prevented students from explaining and understanding the process of planet formation at a scientific level.Singh, P., Patil, Y., Rale, V., 2019. Biosurfactant production: emerging trends and promising strategies. Journal of Applied Microbiology 126, 2-13. are economically most sought after biotechnological compounds of the 21st century. However, inefficient bioprocessing has mitigated the economical commercial production of these compounds. Although much work is being done on the use of low-cost substrates for their production, a paucity of literature exists on the upcoming bioprocess optimization strategies and their successes and potential for economical biosurfactant production. This review discusses some of the latest developments and most promising strategies to enhance and economize the biosurfactant production process. Recent market analysis, developments in the field of optimally formulated cost credit substrates for enhanced product formation and subsequent process economization are few of the critical aspects highlighted here. Use of nanoparticles and coproduction of biosurfactant along with other commercially important compounds like enzymes, are other upcoming bioprocess intensification strategies. The recent developments discussed here would not only give an overview of pertinent parameters for economic biosurfactant production but would also bring to fore multiple strategies that would open up new avenues of research on biosurfactant production. This would go a long way in making biosurfactants a commercially successful compound of the current century.Slomberg, D.L., Ollivier, P., Miche, H., Angeletti, B., Bruchet, A., Philibert, M., Brant, J., Labille, J., 2019. Nanoparticle stability in lake water shaped by natural organic matter properties and presence of particulate matter. Science of The Total Environment 656, 338-346. nanoparticle (NP) fate in the environment continues to remain a challenge, especially for natural surface water systems, where NPs can hetero-aggregate with natural organic and mineral suspended matter. Here we present the interactions and aggregation behavior of TiO2 NPs with natural organic matter (NOM) in a natural lake water. NP fate in a synthetic water of the same pH and ionic composition was also tested in the presence and absence of NOM analogs to gain insight into the different stabilizing effects of each NOM type. Several complementary analytical techniques were utilized to assess lake NOM composition, including pyrolysis?gas chromatography–mass spectrometry, gel permeation chromatography, the polarity rapid-assessment method, and Nanoparticle Tracking Analysis. In the natural lake water, the TiO2 NPs preferentially interacted with mostly anionic NOM of high and medium molecular weight (~1200–1450 and 400–520?Da). Specifically, strong interactions with proteins and polyhydroxy aromatics were observed. NP fate and stability were determined in both raw lake water containing mineral particulate matter and total NOM (NOMtot) and filtered lake water containing only NOM <0.8?μm (NOM<0.8), with different aggregation profiles observed over time. Additionally, three times the number of TiO2 NPs remained in suspension when only NOM<0.8 was present compared to the unfiltered water containing mineral particulate matter and NOMtot. These results demonstrate the contrasting NP fates in the aquatic environment according to the presence of NOMtot vs. NOM<0.8 and further suggest that the use of pure NOM analogs may not accurately represent NP interactions and fate in the natural system.Slotznick, S.P., Swanson-Hysell, N.L., Sperling, E.A., 2018. Oxygenated Mesoproterozoic lake revealed through magnetic mineralogy. Proceedings of the National Academy of Sciences 115, 12938-12943.: Constraining oxygen levels and redox chemistry of Proterozoic oceans and lakes is vital for placing environmental constraints on early aerobic eukaryotic evolution. Recent work has used iron-based geochemical proxies—however, interpretation of such measurements can be difficult due to uncertainties related to baselines for lake sediments and equivocal zones associated with empirically calibrated proxies. We integrate magnetic, geochemical, and microscale imaging techniques to analyze the iron mineralogy of the 1.1-billion-year-old Paleolake Nonesuch, one of the few lacustrine records of this era. With these methods, we resolve ambiguous geochemical signals and document an oxycline with oxygenated shallow waters and decreasing oxygen with depth. These results indicate a stable oxygenated environment in the terrestrial realm 1.1 billion years ago.Abstract: Terrestrial environments have been suggested as an oxic haven for eukaryotic life and diversification during portions of the Proterozoic Eon when the ocean was dominantly anoxic. However, iron speciation and Fe/Al data from the ca. 1.1-billion-year-old Nonesuch Formation, deposited in a large lake and bearing a diverse assemblage of early eukaryotes, are interpreted to indicate persistently anoxic conditions. To shed light on these distinct hypotheses, we analyzed two drill cores spanning the transgression into the lake and its subsequent shallowing. While the proportion of highly reactive to total iron (FeHR/FeT) is consistent through the sediments and typically in the range taken to be equivocal between anoxic and oxic conditions, magnetic experiments and petrographic data reveal that iron exists in three distinct mineral assemblages resulting from an oxycline. In the deepest waters, reductive dissolution of iron oxides records an anoxic environment. However, the remainder of the sedimentary succession has iron oxide assemblages indicative of an oxygenated environment. At intermediate water depths, a mixed-phase facies with hematite and magnetite indicates low oxygen conditions. In the shallowest waters of the lake, nearly every iron oxide has been oxidized to its most oxidized form, hematite. Combining magnetics and textural analyses results in a more nuanced understanding of ambiguous geochemical signals and indicates that for much of its temporal duration, and throughout much of its water column, there was oxygen in the waters of Paleolake Nonesuch.Sokol, A.G., Kupriyanov, I.N., Tomilenko, A.A., Bul’bak, T.A., Palyanov, Y.N., Sobolev, N.V., 2018. Formation of water-bearing defects in olivine in the presence of water–hydrocarbon fluid at 6.3 GPa and 1200°C. Doklady Earth Sciences 483, 1451-1453. main trends of water dissolution in Fe-bearing olivine have been investigated in the olivine–H2O–hydrocarbon fluid system in experiments at a pressure of 6.3 GPa, a temperature of 1200°C, and hydrogen fugacity ( fH2) buffered by the Mo–MoO2 equilibrium. The content and contribution of ОH defects of different types in Fe-bearing olivines depend on the composition of reduced fluids in the system. As the fraction of hydrocarbons in the fluid increases, the H2O content in olivine crystals decreases from 900 to 160–180 ppm, while the ОН absorption peaks become lower at high frequencies and occupy a larger part of the infrared spectrum in the low-frequency region. According to the experimental results, even the deepest seated mantle olivines with OH defects were not equilibrated with a fluid rich in light alkanes or oxygenated hydrocarbons.Song, D., Tuo, J., Zhang, M., Wu, C., Su, L., Li, J., Zhang, Y., Zhang, D., 2019. Hydrocarbon generation potential and evolution of pore characteristics of Mesoproterozoic shales in north China: Results from semi-closed pyrolysis experiments. Journal of Natural Gas Science and Engineering 62, 171-183. shale and Hongshuizhuang shale were used to study the potential for shale gas formation in the Mesoproterozoic shales from North China by semi-closed pyrolysis experiments. Nitrogen adsorption experiments were performed on the original samples and solid residues after pyrolysis at different simulated temperatures to characterize changes of pore characteristics in the studied shales. The results of semi-closed pyrolysis experiments showed that good potential of hydrocarbon gas generation in the studied shales. At temperature of 550?°C, yield of hydrocarbon gas generated from the Xiamaling shale was 222.31?mL/g TOC with initial TOC of 3.76% and Tmax?=?450?°C, while yield of hydrocarbon gas generated from the Hongshuizhuang shale was 364.79?mL/g TOC with initial TOC of 5.18% and Tmax?=?440?°C. The results of the lower pressure nitrogen adsorption experiments demonstrated that relatively larger-size pores would be dominated with the increasing temperature. Pattern of pore size distribution changed during the pyrolysis experiments. Pore size distribution of original samples was unimodal with pore size of 2?nm, bimodal shape with peak apertures of 2?nm and 30?nm was beginning to dominated with the increase of pyrolysis temperature, and finally, shape of unimodal with aperture of 30?nm tended to more predominant at higher temperatures. In addition, evolutionary scenarios of nanopores for the two studied shales were composed by three stages with increasing of pyrolysis temperature, including pore decreasing, increasing and transforming stages. This study revealed the shales in the Mesoproterozoic of North China have good potential for the formation of shale gas.Song, K., Shang, Y., Wen, Z., Jacinthe, P.-A., Liu, G., Lyu, L., Fang, C., 2019. Characterization of CDOM in saline and freshwater lakes across China using spectroscopic analysis. Water Research 150, 403-417. dissolved organic matter (CDOM) is a major component of DOM in waters, and plays a vital role in carbon cycling in inland waters. In this study, the light absorption and three-dimensional excitation-emission matrix spectra (EEMs) of CDOM of 936 water samples collected in 2014–2017 from 234 lakes in five regions across China were examined to determine relationships between lake water sources (fresh versus saline) and their fluorescence/absorption characteristics. Results indicated significant differences regarding DOC concentration and aCDOM(254) between freshwater (6.68?mg?C L?1, 19.55?m-1) and saline lakes (27.4?mg?C L?1, 41.17?m-1). While humic-like (F5) and fulvic-like (F3) compounds contributed to CDOM fluorescence in all lake waters significantly, their contribution to total fluorescence intensity (FT) differed between saline and freshwater lakes. Significant negative relationships were also observed between lake altitude with either F5 (R2?=?0.63, N?=?306) or FT (R2??=?0.64, N?=?306), suggesting that the abundance of humic-like materials in CDOM tends to decrease with increased in lakes altitude. In high-altitude lakes, strong solar irradiance and UV exposure may have induced photo-oxidation reactions resulting in decreased abundance of humic-like substances and the formation of low molecular weight compounds. These findings have important implications regarding our understanding of C dynamics in lacustrine systems and the contribution of these ecosystems to the global C cycle.Song, S., Zhang, H., Sun, L., Shi, J., Cao, X., Yuan, S., 2018. Molecular dynamics study on aggregating behavior of asphaltene and resin in emulsified heavy oil droplets with sodium dodecyl sulfate. Energy & Fuels 32, 12383-12393. aggregates of asphaltene and resin molecules play an important role in stabilizing heavy crude oil. Although many experiments are applied to investigate the complex aggregating structure of asphaltene and resin molecules in heavy crude oil, those microstructure and properties are still not clear at the molecular level. As another auxiliary tool, molecular dynamics (MD) simulation can be used to simulate the behavior of asphaltene and resin in the heavy oil droplet or emulsified oil droplet. The simulation results showed the following: (i) Asphaltene and resin molecules can form a netlike structure in heavy oil through face-to-face or edge-to-face stacking interaction, and the aggregating structure is considered to be the main reason that heavy crude oil has high viscosity. (ii) When surfactant molecules were added to the heavy oil phase, the asphaltene molecules moved to the center of emulsified oil droplet from the oil/water interface. The adsorption of surfactant molecules at the interface resulted in an increase in the hydrophilic surface area of the oil droplet. We think that the changed hydrophilicity of emulsified oil droplet is the key to the viscosity reduction of heavy oil. (iii) The steered MD simulation can prove that the interaction among asphaltene and resin molecules becomes fragile in emulsified heavy oil droplet, and it indicates that the added surfactant molecules are beneficial to the viscosity reduction in crude oil.Song, W., Wang, D., Yao, J., Li, Y., Sun, H., Yang, Y., Zhang, L., 2019. Multiscale image-based fractal characteristic of shale pore structure with implication to accurate prediction of gas permeability. Fuel 241, 522-532. heterogeneities of shale are manifested in the complex pore spatial configurations and the wide distribution of pore sizes. The recent advances of high-resolution imaging techniques such as Scanning Electron Microscope (SEM) and Focussed Ion Beam Scanning Electron Microscopes (FIB-SEM) enable accurate characterization of shale pore structure in the limited imaging area. Due to the nature of multiscale pore size, image-based petrophysical properties are highly dependent on the selection of image resolution. Fractal theory proves to be an effective approach to characterize pore structure as well as calculate fluid transport properties. In this study, the image-based fractal characteristic of shale pore structure at multiscale resolutions is investigated and its impact on the accurate prediction of gas permeability is analyzed. The fractal dimensions of pore phase in 100 SEM images at resolutions ranging from 15.5?nm to 420?nm are calculated by the box counting method and Sierpinski carpets analytical solution. The real gas permeability model in consideration of second order slip is derived based on the fractal theory. Two groups of gas permeabilities at different resolutions are estimated respectively based on the fractal dimensions obtained from the box counting method and Sierpinski carpets analytical solution. The results found that fractal dimensions obtained from the box counting method at different resolutions are more close to the exact fractal dimension compared with that obtained from the Sierpinski carpets analytical solution at low resolutions and gas permeabilities calculated at different resolutions based on the box counting estimated fractal dimensions are more close to the exact gas permeability. The image resolution for accurate calculation of shale pore structure properties and gas permeability should be less than 50?nm based on our analysis results.Song, Y., Li, S., Hu, S., 2019. Warm-humid paleoclimate control of salinized lacustrine organic-rich shale deposition in the Oligocene Hetaoyuan Formation of the Biyang Depression, East China. International Journal of Coal Geology 202, 69-84. organic-rich shales are widely developed within the Oligocene Biyang Depression in the Nanxiang Basin in east China and across Southeast Asia. These shales have been proven as hydrocarbon source rocks of crude oil, as well as sources and reservoirs of shale oil. Understanding the deposition of these shales is essential to reconstruct the paleoenvironment and paleoclimate during the Oligocene in east China, as well as target the potential shale oil resources. Based on X-ray diffraction, organic and inorganic petrologic, organic and inorganic geochemical, and stable isotopic analyses, paleoenvironment, paleoclimate and hydrocarbon potential of the lacustrine organic-rich shales in the Oligocene Hetaoyuan Formation were investigated. The mineral composition of Hetaoyuan Formation organic-rich shales is dominated by clay minerals, followed by quartz, plagioclase, calcite, dolomite, pyrite and gypsum. Six lithotypes are identified, including siltstone, silty shale, clay shale, calcareous shale, dolomite shale and massive mudstone. The organic matter (OM) of the organic-rich shales is dominated by type I kerogen (lamalginite). Maturity parameters (Tmax, biomarker ratios and calculated vitrinite reflectance) suggest that the OM enters the oil window maturity. High TOC and generative potential, together with high contents of brittle minerals (including quartz, plagioclase and carbonates) reveal the Oligocene Hetaoyuan Formation hold good to very good potential of shale oil exploitation. Six organic-rich shale layers have been identified in the Hetaoyuan Formation (shale layer 1 to 6, from top to bottom). Among them shale layers 5 and 3 hold the best shale oil potential and therefore be investigated in the present paper. Shale layer 5 was deposited in a semi-deep lacustrine environment under the moderately warm-humid paleoclimate, further dividing into lower, middle and upper units. Relatively low TOC contents (av. 2.6?wt%) in the lower unit are probably caused by high sedimentation rate. High bioproductivity under favorable preservation conditions led to relatively high TOC contents (av. 3.6?wt%) in the middle unit. Less reducing conditions together with moderate-low bioproductivity resulted in relatively low TOC contents (av. 2.6?wt%) in the upper unit. Warm-humid paleoclimate prevailed during deposition of shale layer 3, deepened water depth and formed a deep lacustrine environment. The stratified water column led to stable anoxic condition and photic zone euxinia in the saline, deep lacustrine environment, which enabled the accumulation of high amounts of OM (av. 4.9?wt% TOC) under excellent preservation (av. HI: 710?mg HC/g TOC). The results of core scanning analysis indicate that formation of the laminated shales probably controlled by seasonal fluctuations of paleoclimate.Song, Y., Tian, Y., Li, X., Wei, J., Zhang, H., Bond, P.L., Yuan, Z., Jiang, G., 2019. Distinct microbially induced concrete corrosion at the tidal region of reinforced concrete sewers. Water Research 150, 392-402. induced concrete corrosion (MICC) is a major deterioration affecting sewers worldwide. MICC is not uniform on sewer inner walls and often occurs at hot spots such as crown and tidal regions, which are critical to determine sewer service life. Especially, concrete corrosion in tidal regions is complicated due to the fluctuation of wastewater levels and the hydraulic scouring effects. The traditional methodology of corrosion monitoring also limits the study of the tidal corrosion. In this study, by using a combination of various advanced mineral analytical techniques and culture-independent 16S rRNA gene amplicon sequencing, the development of corrosion, the formation of corrosion products and the variation of microbial communities in tidal regions were investigated systematically. The physical-chemical characteristics in tidal regions varied with the distance from the wastewater surface. Above the wastewater, more severe corrosion was detected with a closer distance to wastewater, producing gypsum as the major corrosion products. The microbial succession in tidal regions occurred, with the coexistence of conventional autotrophic SOB and acidophilic heterotrophic bacteria initially, and shifting to the predominant colonization of Mycobacterium when pH reached around 1. The heterotrophic bacteria, i.e. Mycobacterium and Bacillus, were likely responsible for the observed corrosion due to the potential capability in generating sulfuric acid. The applications of advanced mineral and microbial analytical techniques were demonstrated effective in improving the understanding of concrete sewer corrosion.Stamenkovi?, V., Ward, L.M., Mischna, M., Fischer, W.W., 2018. O2 solubility in Martian near-surface environments and implications for aerobic life. Nature Geoscience 11, 905-909. to the scarcity of O2 in the modern Martian atmosphere, Mars has been assumed to be incapable of producing environments with sufficiently large concentrations of O2 to support aerobic respiration. Here, we present a thermodynamic framework for the solubility of O2 in brines under Martian near-surface conditions. We find that modern Mars can support liquid environments with dissolved O2 values ranging from ~2.5?×?10?6?mol?m?3 to 2?mol?m?3 across the planet, with particularly high concentrations in polar regions because of lower temperatures at higher latitudes promoting O2 entry into brines. General circulation model simulations show that O2 concentrations in near-surface environments vary both spatially and with time—the latter associated with secular changes in obliquity, or axial tilt. Even at the limits of the uncertainties, our findings suggest that there can be near-surface environments on Mars with sufficient O2 available for aerobic microbes to breathe. Our findings may help to explain the formation of highly oxidized phases in Martian rocks observed with Mars rovers, and imply that opportunities for aerobic life may exist on modern Mars and on other planetary bodies with sources of O2 independent of photosynthesis.Stebbins, A., Williams, J., Brookfield, M., Nye, S.W., Hannigan, R., 2019. Frequent euxinia in southern Neo-Tethys Ocean prior to the end-Permian biocrisis: Evidence from the Spiti region, India. Palaeogeography, Palaeoclimatology, Palaeoecology 516, 1-10. this study, we reconstruct water-column oxygen availability during the deposition of Late Permian shales (Wuchiapingian to approximately early Changhsingian) using the geochemistry and morphology of sedimentary pyrite (FeS2). Deposition of the shales occurred prior to the end-Permian mass extinction within the southern Neo-Tethys Ocean (Spiti region, Himachal Pradesh, India). We found that the variability of pyritic sulfur to organic carbon (Spyr/Corg) and the pyritic sulfur isotopic composition (δ34Spyr) did not record changes in oxygen availability at Spiti sections. This was due to the removal of original pyritic sulfur by modern oxidative weathering and diagenetic pyrite formation which overwhelmed the original δ34Spyr values. However, pyrite framboid size distributions was a reliable recorder of paleoredox conditions. The degree of oxygen limitation varied with multiple transient euxinic events interrupting a predominantly oxic-dysoxic trend near the top of the Gungri Formation upper member (approximately late Wuchiapingian to early Changhsingian). These transient euxinic intervals provide important insight and regional evidence of environmental stress and instability in the southern Neo-Tethys well prior to the end-Permian mass extinction.Sun, B., Jinshan, L., Cheng, L., Yang, Q., Tian, W., Li, X., Chen, H., Qi, L., 2018. The feasibility of biological gas recovery in low-rank coal: a case study of Jiergalangtu depression in Erlian Basin. Acta Petrolei Sinica 39, 1272-1278. biological gas recovery technology has been applied successfully in the Powder River Basin of U.S., so that the depleted low-rank-coal gas field can re-achieve high yield, thus proving that biological gas recovery is one of effective approaches for the high efficiency development of coalbed methane (CBM). In order to effectively develop the low-rank CBM in China, a simulation experiment was conducted to test the flora types and make clear the gas production means and biological gas recovery potential in the coal seams of Jiergalangtu depression, Erlian Basin. The results indicate that a massive amount of methanogen exists in the coal samples and coalbed water of Jiergalangtu Depression, and acetic acid dissociation and CO2 reduction both lead to the production of CBM. All coal samples have methane production potential capacity under the in-situ condition, and the Ⅳ coal seam group produced 11±1.4 μmol/g of methane (equivalent to 0.25-0 28 m3/t) of coal sample in five months. In the experiment with exogenous bacteria, the Ⅲ coal seam group produced 18.40 μmol/g of methane (equivalent to 0.41 m3/t) of coal sample. The studies reveal that the Jiergalangtu depression of Erlian Basin can provide the conditions for biological gas recovery, especially for the Ⅲ coal seam group with low gas content. For the Ⅳ coal seam, after gas is depleted using conventional methods, biological gas recovery technology is used as an effective means to improve the single-well production and recovery. At present, six favorable depressions with the geological conditions of coalbed methane similar to Erlian Basin are selected in this study, and the total amount of resources is 4 180×1012m3.Sun, L., Bai, B., Wei, B., Pu, W., Wei, P., Li, D., Zhang, C., 2019. Recent advances of surfactant-stabilized N2/CO2 foams in enhanced oil recovery. Fuel 241, 83-93. foams are two of the most widely used foams in foam EOR processes, and numerous oil reservoirs could potentially benefit from them. This paper comprehensively reviews the development of these foams over the past decade. We focused on the promising surfactant formulas and their corresponding mechanisms under different reservoir conditions, especially harsh conditions. The most recent studies have shown that low interfacial tension foaming surfactants are efficient in fractured/tight reservoirs, while CO2-switchable surfactants are well suited to CO2 foam in carbonate reservoirs with high temperatures. Pure surfactants and mixed surfactants that combine anions and cations contain superior foam properties. The surfactant aggregates, such as vesicles and wormlike micelles, could distinctly enhance the foam stability. However, the adsorption of the mixed surfactants on reservoir rocks and the temperature of the complex structures should be given particular consideration. The phase behaviors </topics/chemistry/phase-behavior> involved in foam EOR processes are vital and much more complicated than those in other EOR processes. Thus, a better knowledge of the phase behaviors could further improve foam EOR performance. The results of this paper provide clues to N2/CO2 foam EOR design and also promote the development of harsh reservoirs.Sun, M.-T., Yang, Z.-M., Fan, X.-L., Wang, F., Guo, R.-B., Xu, D.-Y., 2019. Improved methane elimination by methane-oxidizing bacteria immobilized on modified oil shale semicoke. Science of The Total Environment 655, 915-923. is a greenhouse gas with significant global warming potential. The methane-oxidizing bacteria (MOB) immobilized on biocarrier could perform effectively and environmentally in methane elimination. To further improve the efficiencies of MOB immobilization and methane elimination, the surface biocompatibility of biocarrier needs to be improved. In this work, the oil shale semicoke (SC) was chemically modified by sodium p-styrenesulfonate hydrate (SS) and 2-(methacryloyloxy)ethyltrimethylammonium chloride (DMC) to promote surface hydrophilicity and positive charge, respectively. Results revealed that, under methane concentrations of ~10% (v/v) and ~0.5% (v/v), the MOB immobilized on semicoke modified with 1.0?mol?L?1 of SS permitted improved methane elimination capacities (ECs), which were 15.02% and 11.11% higher than that on SC, respectively. Additionally, under methane concentrations of ~10% (v/v) and ~0.5% (v/v), the MOB immobilized on semicoke modified with 0.4?mol?L?1 of DMC held superior ECs, which were 17.88% and 11.29% higher than that on SC, respectively. The qPCR analysis indicated that the MOB abundance on modified semicoke were higher than that on SC. In consequence, the surface biocompatibility of semicoke could be promoted by SS and DMC modifications, which potentially provided methods for other biocarriers to improve surface biocompatibility.Tamamura, S., Murakami, T., Aramaki, N., Ueno, A., Tamazawa, S., Badrul, A.A.K.M., Haq, S.R., Igarashi, T., Aoyama, H., Yamaguchi, S., Kaneko, K., 2019. The role of meteoric water recharge in stimulating biogenic methane generation: A case study from the Tempoku Coal Field, Japan. International Journal of Coal Geology 202, 14-26. meteoric water recharge is known to stimulate biogenic methane formation in shale and coal seams, the underlying mechanisms are currently unresolved. To this end, we conducted fieldwork in the Tempoku Coal Field, Japan. Pore water in core samples and well water in boreholes were analyzed for dissolved components and isotopic compositions. The hydraulic gradient was determined using values of borehole hydraulic head. Cl? concentrations (38?mg?L?1 to 16,600?mg?L?1), δ18O(H2O) values (?10.5‰ to ?2.4‰), and δD(H2O) values (?71.6‰ to ?17.8‰) increased with depth (<200?m), indicating meteoric water recharge. The positive correlation between δ13C(CH4) values (?74.9‰ to ?42.7‰) and δ13C(CO2) values (?27.5‰ to +13.3‰), as well as between δD(H2O) and δD(CH4) values (?264‰ to ?200‰), in the core samples and groundwater, indicted in situ methanogenesis in the zone of mixing and migration of meteoric water and saline groundwater. Some of the pore water samples contained biogenic acetate, propionate, and succinate at remarkably high concentrations (~200?mg?L?1), implying: (i) the thermodynamic inhibition of fermentation at fermentation sites, and (ii) spatial separation between the fermentation sites and methanogenesis sites. Planar fracture modeling indicates that at distances greater than a millimeter between fermentation and methanogenesis sites, the advective transport of fermentation products dominates rather than diffusive transport of those. Hence, meteoric water recharge would stimulate biogenic methane formation by inducing advective transport of the fermentation products, thus (i) relaxing the thermodynamic inhibition of fermentation at the site of the fermentation, and (ii) enhancing the rate of transport of the fermentation products to the site of methanogenesis.Tan, Z., Wang, W., Li, W., Lu, S., He, T., Cheng, Z., 2018. The sedimentary environment and deposition mode of organic-rich mudstone from the third member of Hetaoyuan Formation in the Biyang Depression. Acta Sedimentologica Sinica 36, 1256-1266 to various test methods, including Rock-Eval, GC-MS, ICP-MS, XRF and others, the abundance and type of organic matter, the major/trace elements, and the biomarker characteristics of the mudstone from the second and third beds of the third member of the Hetaoyuan Formation from the Biyang depression of the Nanxiang Basin were investigated. Based on this analysis, the geochemical characteristics and sedimentary environment of the lacustrine organic-rich mudstone have been discussed, and the deposition mode of the organic-rich mudstone has been definitively established. The results show that, during the depositional period of the second bed, the TOC values of the mudstone were relatively lower, and the organic matter of the lacustrine basin consisted of aquatic organisms and terrigenous organic matter. The kerogen types of the second-bed source rocks ranged from I to Ⅲ. The water column caused by high-salinity water and a reducing environment provided excellent preservation conditions for organic matter enrichment. However, high-salinity water conditions tend to lead to reduced primary productivity in lakes. In addition, the relatively higher terrigenous detrital matter input decreased lake productivity and was not conducive to organic matter accumulation. In contrast, during the sedimentary period of the third bed, the TOC values of the mudstone were relatively higher. The kerogen types of third-bed source rocks were mainly I and Ⅱ1. The lacustrine salinity decreased dramatically, and the water column was not obvious, meaning that the anoxic bottom water environment was responsible for organic matter preservation. Under such circumstances, high productivity is the controlling factor for organic matter accumulation in third-bed mudstone.Tang, Y., Yang, R., Kang, X., 2018. Modeling the effect of water vaporization and salt precipitation on reservoir properties due to carbon dioxide sequestration in a depleted gas reservoir. Petroleum 4, 385-397. of water during both gas reservoir development and CO2 geological sequestration in saline formations can cause salt precipitation with rapid loss of formation porosity and permeability. Water vaporization and precipitation of halite around a single well from stage production to CO2 injection are studied to investigate the effect on reservoir properties in a gas reservoir. This paper identifies and quantifies post-flood dry zones and permeability changes in depleted gas reservoir after CO2 exposure with the comparison in gas production period by performing the numerical simulation with the compositional simulator. Simulation results indicate that water vaporization and salt precipitation occur during gas production, and can be intensified by CO2 injection. Dry supercritical CO2 injection vaporizes the brine promoting brine concentration and halite precipitation. The simulation indicates a drying area with a radius of 78 m around wellbore after CO2 injection. Porosity reduces with the most scope of 58%, and permeability can be decreased by up to 93.9% due to salt precipitation. And the injectivity is damaged by 99.77% at the end of injection period based on maximum permeability reduction. Moreover, six factors are investigated to conduct the influence analysis, showing that higher salinity brine, higher injection rate, higher irreducible water saturation, lower initial permeability, higher temperature and with capillary flow are conditions enhancing the salt precipitation due to dry CO2 injectionTang, Y., Yang, R., Yin, S., Fan, T., Dong, L., Hou, Y., 2019. Analysis of continental shale gas accumulation conditions in a rifted basin: A case study of Lower Cretaceous shale in the southern Songliao Basin, northeastern China. Marine and Petroleum Geology 101, 389-409. analysis of shale gas accumulation conditions is the basis of shale gas exploration. Previous research has mainly focused on the Upper Cretaceous shale in the Songliao Basin of northeastern China, and few studies have analyzed the Lower Cretaceous shale in this area. Based on an integrated analysis of the sedimentary facies, shale samples and seismic interpretation from the Lower Cretaceous Shahezi, Yingcheng and Denglouku Formations of the Fulongquan Depression in the Songliao Basin, the distribution of the shale and the generation, accumulation and preservation conditions of the shale gas are evaluated and discussed. Core observations and sedimentary facies analysis show that the sedimentary facies types in the Shahezi, Yingcheng and Denglouku Formations are mainly fan delta, braided river delta, sublacustrine fan and lacustrine facies. The semideep lake, shallow lake and delta front sedimentary subfacies are favorable for the deposition of shale. The study of the shale distribution indicates that the shale was mainly deposited near the maximum flooding surface of the third-order sequences, and the shales in the Shahezi and Yingcheng Formations are darker and thicker than those in the Denglouku Formation. In addition, the shale in this study area is laterally distributed in the depression belt and the steep slope belt near the boundary faults of the basin. According to the geochemistry tests, rock properties and mineral constituents, the shales in the Shahezi and Yingcheng Formations have favorable gas generation potential. Compared with the properties of the major gas-producing shales in China and the United States, the shales in the Shahezi and the Yingcheng Formations are thick and have a favorable organic matter type, high average organic matter abundance, high organic matter thermal maturity that reached a high maturation stage, high porosity and high gas contents; these properties meet the standards of industrial exploitation, and these shales can therefore be considered favorable targets for unconventional energy exploration.Taylor, G.T., Suter, E.A., Pachiadaki, M.G., Astor, Y., Edgcomb, V.P., Scranton, M.I., 2018. Temporal shifts in dominant sulfur-oxidizing chemoautotrophic populations across the Cariaco Basin's redoxcline. Deep Sea Research Part II: Topical Studies in Oceanography 156, 80-96. pronounced and relatively stable peak in dark carbon assimilation (DCA) has been observed within the Cariaco Basin's redoxcline over a 19-year observation period, presumably driven largely by sulfur-oxidizing chemoautotrophic bacteria (thioautotrophs). As documented in previous reports, this midwater productivity hotspot is associated with prominent biomass peaks, consisting of prokaryoplankton, protists and viruses. Early in the time-series, phylogenetic studies (small subunit ribosomal RNA gene libraries) and fluorescent in situ hybridization (FISH) surveys documented that the chemoautotrophic layer was overwhelmingly populated by ε-proteobacteria related to sulfur-oxidizing symbionts from hydrothermal vent systems and β-proteobacteria. However, after May 2009, β- and ε-proteobacteria were no longer detected in significant numbers by FISH or by more exhaustive sequencing efforts (454 pyrosequencing and MiSeq iTag libraries). Sulfur oxidation gene quantification (qPCR) also confirmed that ε-proteobacteria were rare in samples collected after mid-2009 and that the chemoautotrophic layer became dominated by γ-proteobacterial sulfur-oxidizers (GSOs). Monthly hydrographic and chemical data from the CARIACO Ocean Time-Series were examined for temporal changes that might have driven this shift in the dominant thioautotrophs. Within the redoxcline (250–450 m), significant shifts occurred in water density structure and distributions of H2S, NH4+, O2, and NO2- between the β-/ε-proteobacteria-dominated and the γ-proteobacteria-dominated periods. How these changing hydrographic and geochemical conditions might have selected for one sulfur-oxidizing lineage over another cannot be directly determined. However, spatiotemporal variations in water density and concentration gradients altered vertical fluxes of the major reductant (H2S) and oxidants (O2, NO3-, NO2-), which we postulate provided a more geochemically stable environment favoring GSOs.Teramoto, E.H., Chang, H.K., 2019. Geochemical conceptual model of BTEX biodegradation in an iron-rich aquifer. Applied Geochemistry 100, 293-304. geochemical conceptual model was developed to interpret long-term field monitoring data of the chemical speciation related to BTEX biodegradation in a tropical iron-rich aquifer that was contaminated by a large volume of jet fuel. Biodegradation under dissimilatory iron reduction is widely favored due to the abundance of iron oxides in the sediment. Concomitantly with iron-reduction, the methanogenesis pathway plays an important role in the microbial degradation of BTEX. The conceptual model was proposed to link the geochemical zonation with BTEX mineralization and secondary reactions. The representativeness of the chemical speciation of the studied hydrocarbon-contaminated aquifer is best supported when PCO2 is fixed and dissolved oxygen, potentially present due to mass transfer from entrapped air, is considered in the model. These findings emphasize the need of both constraints to properly interpret BTEX biodegradation in a tropical iron-rich aquifer.Them, T.R., Jagoe, C.H., Caruthers, A.H., Gill, B.C., Grasby, S.E., Gr?cke, D.R., Yin, R., Owens, J.D., 2019. Terrestrial sources as the primary delivery mechanism of mercury to the oceans across the Toarcian Oceanic Anoxic Event (Early Jurassic). Earth and Planetary Science Letters 507, 62-72. study evaluates the utility of sedimentary mercury (Hg) contents as a proxy for fingerprinting ancient massive volcanism, which is often associated with biogeochemical perturbations. Herein we present new Hg geochemical data from anoxic marine basins across the Toarcian Oceanic Anoxic Event (T-OAE; ～183 Ma) as a test of the complex Hg cycle. The T-OAE was likely initiated by the main eruptive phase of the Karoo–Ferrar large igneous province, which caused a subsequent cascade of environmental perturbations and resulting mass extinction. At present the leading interpretation of sedimentary Hg anomalies has been volcanogenic outgassing as the primary source. Our study and compilation results suggest, however, that Hg/TOC anomalies were restricted to shallow-water, and/or proximal environments, while deep-water, more distal depositional settings document no significant Hg-related anomalies. Furthermore, asynchronous stratigraphic deviations in Hg enrichments favor terrestrially sourced materials and local redox variability, rather than direct volcanogenic emissions, as a primary control mechanism. Additionally, Hg isotope signatures from our only study site documenting an Hg anomaly are also consistent with a terrestrial Hg origin during the T-OAE. Therefore, our results suggest that Hg anomalies in the geological record need to be re-evaluated as a “smoking gun” proxy that only infers volcanogenic inputs.Thi?ner, J.B., Richter-Brockmann, S., Achten, C., 2018. Analysis of 6- and 7-ring PAH and other non-EPA PAH by atmospheric pressure laser ionization – mass spectrometry (APLI-MS) in environmental certified reference materials NIST 1941b, NIST 1649b, BAM CC013a and IRMM BCR 535. Journal of Chromatography A 1581-1582, 91-99. in environmental analytical chemistry of polycyclic aromatic hydrocarbons (PAH) in the past decades cover improvements in laboratory methods as well as new insights in the toxicology of single PAH compounds. A re-evaluation of the established list of 16 priority PAH published by the U. S. Environmental Protection Agency seems overdue. In this study we have applied PAH analysis by atmospheric pressure laser ionization – mass spectrometry (APLI-MS) to NIST 1941b, NIST 1649b, BAM CC013a and IRMM BCR 535 giving further references in addition to the certificates of analysis. Gas chromatography enables to distinguish between different alkylated PAH derivatives whereas liquid chromatography additionally allows detection of PAH tentatively with six or more aromatic rings on the level of chemical formula. For an optimal isomer-specific differentiation, LC-APLI-MS should be used in combination with fluorescence detection. Distribution patterns of 6 and 7-ring PAH are presented for urban dust, marine and harbor sediments and the soil sample. Additionally, a set of 14 nitrogen, sulfur and oxygen-containing polycyclic aromatic compounds were analyzed by APLI and quantified in all reference materials for the first time.Thibon, F., Blichert-Toft, J., Tsikos, H., Foden, J., Albalat, E., Albarede, F., 2019. Dynamics of oceanic iron prior to the Great Oxygenation Event. Earth and Planetary Science Letters 506, 360-370. report Fe isotope compositions in banded iron formations (BIF) from three cores from the pre-GOE Transvaal Supergroup, South Africa, and one core from the pre-GOE Joffre Member of the Hamersley Group, Australia. The low abundances of detrital elements such as Al, Ti, Sc, and V suggest that these BIF were deposited in distal positions with respect to Precambrian continents, while the very low P abundances are incompatible with strong biological productivity at these localities. A combination of U–Pb chronology and cobalt accumulation rates is used to establish a high-resolution time scale and deduce chemical fluxes. The e-folding time of δ56Fe variations up stratigraphy is used to determine Fe oceanic residence times and Fe concentrations as well as the dissolved carbonate content of Early Proterozoic seas. Iron oceanic residence times increased from 0.2 to 2.3 Ma during the time interval between 2521 and 2394 Ma covered by the present cores, translating into ocean Fe concentrations increasing from 6.4 to 37 mmolkg?1. Massive BIF precipitation was triggered by release of CO2 into the atmosphere and subsequent surges of alkalinity into the ocean due to the weathering of large subaerial volcanic systems. We argue that a suitable electron acceptor for Fe2+ oxidation to magnetite is the inorganic conversion of CO2 (or dissolved inorganic carbon) to CH4. In the process, H+ is produced, which is reinjected into oceanic hydrothermal systems liberating Fe2+. The couple Fe2+-magnetite may, in the Archean, have played the same buffering role as the couple Ca2+-calcite plays today. Massive injection of methane into the atmosphere would accompany BIF deposition and make the early Earth similar to modern Titan. Therefore, although biological processes may have assisted iron oxidation and precipitation, they are not a prerequisite for BIF deposition.Thompson, R.L., Nisbet, E.G., Pisso, I., Stohl, A., Blake, D., Dlugokencky, E.J., Helmig, D., White, J.W.C., 2018. Variability in atmospheric methane from fossil fuel and microbial sources over the last three decades. Geophysical Research Letters 45, 11,499-11,508.: Atmospheric measurements show an increase in CH4 from the 1980s to 1998 followed by a period of near‐zero growth until 2007. However, from 2007, CH4 has increased again. Understanding the variability in CH4 is critical for climate prediction and climate change mitigation. We examine the role of CH4 sources and the dominant CH4 sink, oxidation by the hydroxyl radical (OH), in atmospheric CH4 variability over the past three decades using observations of CH4, C2H6, and δ13CCH4 in an inversion. From 2006 to 2014, microbial and fossil fuel emissions increased by 36 ± 12 and 15 ± 8 Tg y?1, respectively. Emission increases were partially offset by a decrease in biomass burning of 3 ± 2 Tg y?1 and increase in soil oxidation of 5 ± 6 Tg y?1. A change in the atmospheric sink did not appear to be a significant factor in the recent growth of CH4. Plain Language Summary: Methane is the second most important greenhouse gas and is responsible for approximately 17% of the direct radiative forcing from all long‐lived greenhouse gases. Observations of methane in the atmosphere have shown a dramatic increase from 2007 after a period of relative stability between the late 1990s and early 2000s, but the cause of this increase is still under scientific debate. This study uses atmospheric observations of methane and two related tracers, the isotopic ratio of carbon in methane and ethane, to constrain the sources and sinks of methane over the past three decades. The increase in methane between 2007 and 2014 is likely due to an increase in microbial sources, of 24–48 Tg/y (predominantly natural wetlands and agricultural), as well as fossil fuel sources, of 7–23 Tg/y. In contrast to other recent studies, a reduction in the atmospheric sink of methane was found not to be a significant factor in explaining the recent atmospheric increase.Tian, D., Jiang, T., Liu, B., Liu, J., Zhang, Z., Xu, H., Cheng, C., 2019. Early Miocene sedimentary processes and their hydrocarbon implications in the Baiyun Sag of Pearl River Mouth Basin, northern south China sea. Marine and Petroleum Geology 101, 132-147. shelf-slope zone has received considerable attention for hydrocarbon exploration due to its unique location, where the sediments are delivered to deep-water environment and deposited as hydrocarbon reservoirs that have been discovered around the world. However, it is realized that the sedimentary processes are very complex, and various depositional bodies develop in the shelf-slope zone. Constrained by 3D seismic, core and well log data, numerical simulations can be applied to better understand the sedimentary processes, and predict the distribution and characteristics of deposits as hydrocarbon reservoirs. Based on core-log-seismic integration, the Early Miocene shelf-margin delta and channelized submarine fan systems along the northern slope of Baiyun Sag in the Pearl River Mouth Basin are distinguished and they are mainly composed of debris, turbidites and slumps. The numerical model is built based on Early Miocene topography acquired by back-stripped well-tied seismic profiles, and the initial boundary conditions, including sediment concentration, velocity and, grain size, and so on, behaviors and structures of slope system are set according to the results of marine surveys around the world. The Computational Fluid Dynamic software ANSYS-FLUENT was applied for the modelling. As a results, the distributions and geometries of the simulated deposits are compared with the depositional bodies interpreted from seismic data. The hydrodynamic simulations of the two sedimentary systems indicate that depositional bodies converge to the downstream of the slope and the basin floor, and turn tractive current into turbidity current during the sedimentary processes, which result in obviously various sedimentary characteristics in different locations. The identification of sedimentary processes in the shelf-margin delta and channelized submarine fan systems has been beneficial for predicting reservoirs and exploring hydrocarbons in the Baiyun Sag, Pearl River Mouth Basin, which is also contributing to the understanding of sedimentary process and reservoir prediction in deep-water areas around the world.Timmers, P.H.A., Vavourakis, C.D., Kleerebezem, R., Sinninghe Damsté, J.S., Muyzer, G., Stams, A.J.M., Sorokin, D.Y., Plugge, C.M., 2018. Metabolism and occurrence of methanogenic and sulfate-reducing syntrophic acetate oxidizing communities in haloalkaline environments. Frontiers in Microbiology 9, 3039. doi: 10.3389/fmicb.2018.03039. syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the metabolism and occurrence of SAOB at extremely haloalkaline conditions were investigated, using highly enriched methanogenic (M-SAO) and sulfate-reducing (S-SAO) cultures from south-western Siberian hypersaline soda lakes. Activity tests with the M-SAO and S-SAO cultures and thermodynamic calculations indicated that H2 and formate are important IECs in both SAO cultures. Metagenomic analysis of the M-SAO cultures showed that the dominant SAOB was ‘Candidatus Syntrophonatronum acetioxidans,’ and a near-complete draft genome of this SAOB was reconstructed. ‘Ca. S. acetioxidans’ has all genes necessary for operating the Wood–Ljungdahl pathway, which is likely employed for acetate oxidation. It also encodes several genes essential to thrive at haloalkaline conditions; including a Na+-dependent ATP synthase and marker genes for ‘salt-out‘ strategies for osmotic homeostasis at high soda conditions. Membrane lipid analysis of the M-SAO culture showed the presence of unusual bacterial diether membrane lipids which are presumably beneficial at extreme haloalkaline conditions. To determine the importance of SAO in haloalkaline environments, previously obtained 16S rRNA gene sequencing data and metagenomic data of five different hypersaline soda lake sediment samples were investigated, including the soda lakes where the enrichment cultures originated from. The draft genome of ‘Ca. S. acetioxidans’ showed highest identity with two metagenome-assembled genomes (MAGs) of putative SAOBs that belonged to the highly abundant and diverse Syntrophomonadaceae family present in the soda lake sediments. The 16S rRNA gene amplicon datasets of the soda lake sediments showed a high similarity of reads to ‘Ca. S. acetioxidans’ with abundance as high as 1.3% of all reads, whereas aceticlastic methanogens and acetate oxidizing sulfate-reducers were not abundant (≤0.1%) or could not be detected. These combined results indicate that SAO is the primary anaerobic acetate oxidizing pathway at extreme haloalkaline conditions performed by haloalkaliphilic syntrophic consortia.Torti, A., J?rgensen, B.B., Lever, M.A., 2018. Preservation of microbial DNA in marine sediments: insights from extracellular DNA pools. Environmental Microbiology 20, 4526-4542. sediments harbour extracellular DNA (exDNA) not associated with currently living organisms. Including this exDNA in genetic surveys may distort abundance and diversity estimates of living prokaryotic communities. We separately extract exDNA and intracellular DNA (inDNA) from 11 horizons in a 10-m deep sediment core from Aarhus Bay (Denmark) that spans > 9000 years of Holocene sedimentation. We compare depth profiles of bacterial and archaeal 16S rRNA gene compositions to those of macrofaunal activity (bioturbation), sulfate and methane concentrations, sediment age and lithology. Among these variables, bioturbation shows the strongest relationship with the two DNA pools. In bioturbated surface sediments, the majority of Operational Taxonomic Units (OTUs) present in exDNA is absent from inDNA, thus belonging to microorganisms that were not alive at the time of sampling. Below the bioturbation zone, the two DNA pools display a much higher phylogenetic similarity. At all depths, the majority of exDNA and inDNA sequences show highest sequence similarities to sediment microorganisms, a finding that is additionally supported by separate analyses on low- and high-molecular weight exDNA. Our results indicate that in Aarhus Bay the vast majority of prokaryotic exDNA is turned over, thus not contributing to a genetic archive of past environmental change.Turgeman-Grott, I., Joseph, S., Marton, S., Eizenshtein, K., Naor, A., Soucy, S.M., Stachler, A.-E., Shalev, Y., Zarkor, M., Reshef, L., Altman-Price, N., Marchfelder, A., Gophna, U., 2019. Pervasive acquisition of CRISPR memory driven by inter-species mating of archaea can limit gene transfer and influence speciation. Nature Microbiology 4, 177-186.–Cas systems provide prokaryotes with sequence-specific immunity against viruses and plasmids based on DNA acquired from these invaders, known as spacers. Surprisingly, many archaea possess spacers that match chromosomal genes of related species, including those encoding core housekeeping genes. By sequencing genomes of environmental archaea isolated from a single site, we demonstrate that inter-species spacers are common. We show experimentally, by mating Haloferax volcanii and Haloferax mediterranei, that spacers are indeed acquired chromosome-wide, although a preference for integrated mobile elements and nearby regions of the chromosome exists. Inter-species mating induces increased spacer acquisition and may result in interactions between the acquisition machinery of the two species. Surprisingly, many of the spacers acquired following inter-species mating target self-replicons along with those originating from the mating partner, indicating that the acquisition machinery cannot distinguish self from non-self under these conditions. Engineering the chromosome of one species to be targeted by the other’s CRISPR–Cas reduces gene exchange between them substantially. Thus, spacers acquired during inter-species mating could limit future gene transfer, resulting in a role for CRISPR–Cas systems in microbial speciation.Umeozor, E.C., Gates, I.D., 2018. Predictive modeling of energy and emissions from shale gas development. Environmental Science & Technology 52, 14547-14555. of individual preproduction activities to overall energy use and greenhouse gas (GHG) emissions during shale gas development are not well understood nor quantified. This paper uses predictive modeling combining the physics of reservoir development operations with depositional attributes of shale gas basins to account for energy requirements and GHG emissions during shale gas well development. We focus on shale gas development from the Montney basin in Canada and account for the energy use during drilling and fluid pumping for reservoir stimulation, in addition to preproduction emissions arising from energy use and potential gas releases during operations. Detailed modeling of activities and events that take place during each stage of development is described. Relative to the hydraulic fracturing activity, we observe significantly higher energy intensity for the well drilling and mud circulation activities. Well completion flowback gas is found to be the predominant potential source of GHG emission. When these results are expressed on an annual basis, consistent with the convention of most climate policy goals and directives, environmental impacts of our growing natural gas economy are better appreciated. Estimated likely GHG emission from new development wells in 2017 in the Montney Formation alone is 2.68 Mt CO2e. However, on a preproduction requirements basis and dependent on mean estimated ultimate recovery (EUR), energy return on invested energy for shale gas from the Montney Formation in Canada is estimated to be about 3400. The approach described here can be reliably extended to areas, globally, where natural gas development is becoming prominent.Urai, A., Takahashi, K., Chikaraishi, Y., Fukushima, K., 2018. Algal-derived 24-ethylcholesta-5,22-dien-3β-ol (stigmasterol) is frequently found in high-molecular-weight dissolved organic matter (HMW-DOM) during summer in freshwater and brackish lakes. Geochemical Journal 52, e15-e20. this study, we evaluated the saponification effect on alkenone quantification and the U37K′ paleothermometer using two internal standards (2-nonadecanone and squalane) by analyzing in-house reference sediment and eleven surface sediments taken from the Yellow Sea. The C37:3 and C37:2 alkenone concentrations of the in-house reference sediment showed significant differences between before and after the saponification (ΔC37:3 and ΔC37:2) depending on the internal standards used. However, the differences in the U37K′ and the estimated sea surface temperatures were insignificant. The ΔC37:3 and ΔC37:2 concentrations were larger when calculating based on 2-nonadecanone (46 ± 26 and 136 ± 67 ng/g, respectively) than those based on squalane (?7 ± 4 and ?12 ± 10 ng/g, respectively) in the surface sediments. Interestingly, the ΔC37:3 and ΔC37:2 concentrations based on 2-nonadecanone showed a strong correlation with the loss of 2-nonadecanone that occurred during saponification. Accordingly, our study indicated that preferential loss of internal standards (e.g., 2-nonadecanone) can occur during saponification, which affects alkenone quantification and, thus, attention should be paid when choosing an internal standard. Valentine, B.J., Hackley, P.C., Hatcherian, J., Yu, J.-J., 2019. Reflectance increase from broad beam ion milling of coals and organic-rich shales due to increased surface flatness. International Journal of Coal Geology 201, 86-101. ion beam (BIB) milling is useful in organic petrology because it can yield flat sample surfaces and avert the ‘smearing’ of organic matter (OM) that results from traditional mechanical polishing. This potentially makes BIB especially useful in the study of nano-porosity, where even minor mechanical disruption of the sample surface distorts the sample characteristic of interest—the pore structure. However, several studies have observed an OM reflectance increase after BIB milling, concluding that ion milling may cause thermal alteration to OM surfaces. To better understand ion milling effects on organic matter, coal (subbituminous, high volatile bituminous, medium volatile bituminous, anthracite) and shale [Bakken Formation, Ohio Shale-Huron Member (5), Kimmeridge Clay Formation, Alum Shale, New Albany Shale] samples were prepared using traditional mechanical polishing methods. Reflectance measurements (% Ro) were gathered on all maceral types present before BIB milling, followed by re-measurement of OM reflectance at the same locations after milling. Most OM increased in reflectance after BIB milling, with some exceptions in high maturity samples. Liptinite macerals in both coal and shale samples showed the greatest percent reflectance increase on average (+133%; n?=?338), followed by solid bitumen (+49%; n?=?313), vitrinite (+26%; n?=?413), and inertinite (+9%; n?=?220). Despite the increases to OM reflectance caused by BIB milling, no evidence was found for kerogen conversion (e.g., change in maceral abundances), or for migration of newly generated petroleum (e.g., pseudomorphic replacement of kerogen by solid bitumen). Such changes occur when samples are thermally altered from immature conditions into the oil window (e.g., by hydrous pyrolysis), and, if the increases in OM reflectance were thermally driven (by BIB milling), they should have been observed in the above experiments. Herein, we also used atomic force microscopy to document a decrease in surface roughness of correlative locations of OM on pre- and post-ion milled samples. This improved surface polish caused by BIB milling appears to be the root cause of increased OM reflectance, as no other supporting evidence of thermal alteration could be found. That is, the fraction of light formerly lost to oblique scatter in diffuse reflectance from a mechanically polished surface is converted to specular reflectance after BIB ion milling. Thus the light leaves the surface at a near normal angle and returns to the detector, resulting in increased OM reflectance.Vander Roost, J., Daae, F.L., Steen, I.H., Thorseth, I.H., Dahle, H., 2018. Distribution patterns of iron-oxidizing Zeta- and Beta-proteobacteria from different environmental settings at the Jan Mayen vent fields. Frontiers in Microbiology 9, 3008. doi: 10.3389/fmicb.2018.03008. oxidizers are widespread in marine environments and play an important role in marine iron cycling. However, little is known about the overall distribution of iron oxidizers within hydrothermal systems, including settings with little hydrothermal activity. Moreover, the extent to which different phylogenetic groups of iron oxidizers exhibit niche specialization toward different environmental settings, remains largely unknown. Obtaining such knowledge is critical to unraveling the impact of the activity of iron oxidizers and how they are adapted. Here, we used 16S rRNA sequencing to characterize the distribution of iron oxidizers in different environmental settings within the Jan Mayen hydrothermal vent fields (JMVFs). Putative iron oxidizers affiliated to Zetaproteobacteria and Betaproteobacteria were detected within iron mounds, bottom seawater, basalt surfaces, and surface layers of sediments. The detected iron oxidizers were compared to sequence types previously observed in patchily distributed iron mats associated with diffuse venting at the JMVFs. Most OTUs of iron oxidizers reoccurred under different environmental settings, suggesting a limited degree of niche specialization. Consequently, most of the detected iron oxidizers seem to be generalists with a large habitat range. Our study highlights the importance of gathering information about the overall distribution of iron oxidizers in hydrothermal systems to fully understand the role of this metabolic group regarding cycling of iron. Furthermore, our results provide further evidence of the presence of iron-oxidizing members of Betaproteobacteria in marine environments.Villanea, F.A., Schraiber, J.G., 2019. Multiple episodes of interbreeding between Neanderthal and modern humans. Nature Ecology & Evolution 3, 39-44. and anatomically modern humans overlapped geographically for a period of over 30,000?years following human migration out of Africa. During this period, Neanderthals and humans interbred, as evidenced by Neanderthal portions of the genome carried by non-African individuals today. A key observation is that the proportion of Neanderthal ancestry is ~12–20% higher in East Asian individuals relative to European individuals. Here, we explore various demographic models that could explain this observation. These include distinguishing between a single admixture event and multiple Neanderthal contributions to either population, and the hypothesis that reduced Neanderthal ancestry in modern Europeans resulted from more recent admixture with a ghost population that lacked a Neanderthal ancestry component (the ‘dilution’ hypothesis). To summarize the asymmetric pattern of Neanderthal allele frequencies, we compiled the joint fragment frequency spectrum of European and East Asian Neanderthal fragments and compared it with both analytical theory and data simulated under various models of admixture. Using maximum-likelihood and machine learning, we found that a simple model of a single admixture did not fit the empirical data, and instead favour a model of multiple episodes of gene flow into both European and East Asian populations. These findings indicate a longer-term, more complex interaction between humans and Neanderthals than was previously appreciated.Vuillemin, A., Horn, F., Friese, A., Winkel, M., Alawi, M., Wagner, D., Henny, C., Orsi, W.D., Crowe, S.A., Kallmeyer, J., 2018. Metabolic potential of microbial communities from ferruginous sediments. Environmental Microbiology 20, 4297-4313. (Fe‐rich, SO4‐poor) conditions are generally restricted to freshwater sediments on Earth today, but were likely widespread during the Archean and Proterozoic Eons. Lake Towuti, Indonesia, is a large ferruginous lake that likely hosts geochemical processes analogous to those that operated in the ferruginous Archean ocean. The metabolic potential of microbial communities and related biogeochemical cycling under such conditions remain largely unknown. We combined geochemical measurements (pore water chemistry, sulfate reduction rates) with metagenomics to link metabolic potential with geochemical processes in the upper 50 cm of sediment. Microbial diversity and quantities of genes for dissimilatory sulfate reduction (dsrAB) and methanogenesis (mcrA) decrease with increasing depth, as do rates of potential sulfate reduction. The presence of taxa affiliated with known iron‐ and sulfate‐reducers implies potential use of ferric iron and sulfate as electron acceptors. Pore‐water concentrations of acetate imply active production through fermentation. Fermentation likely provides substrates for respiration with iron and sulfate as electron donors and for methanogens that were detected throughout the core. The presence of ANME‐1 16S and mcrA genes suggests potential for anaerobic methane oxidation. Overall our data suggest that microbial community metabolism in anoxic ferruginous sediments support coupled Fe, S and C biogeochemical cycling.Vuppaladadiyam, A.K., Prinsen, P., Raheem, A., Luque, R., Zhao, M., 2018. Sustainability analysis of microalgae production systems: A review on resource with unexploited high-value reserves. Environmental Science & Technology 52, 14031-14049., at present, is a prominent component in the development of production systems that aim to provide the future energy and material resources. Microalgae are a promising feedstock; however, the sustainability of algae-based production systems is still under debate. Commercial market volumes of algae-derived products are still narrow. The extraction and conversion of primary metabolites to biofuels requires cultivation at large scales; cost-effective methods are therefore highly desirable. This work presents a complete and up to date review on sustainability analysis of various microalgae production scenarios, including techno-economic, environmental, and social impacts, both in large-scale plants for bioenergy production and in medium-scale cultivars intended for the production of high added-value chemicals. The results show that further efforts in algal-based research should be directed to improving the productivity, the development of multi product scenarios, a better valorization of coproducts, the integration with current industrial facilities to provide sustainable nutrient resources from waste streams, and the integration of renewable technologies such as wind energy in algae cultivars.Wade, D.C., Abraham, N.L., Farnsworth, A., Valdes, P.J., Bragg, F., Archibald, A.T., 2018. Simulating the climate response to atmospheric oxygen variability in the Phanerozoic. Climate of the Past Discussions 2018, 1-35. amount of dioxygen (O2) in the atmosphere may have varied from as little as 10% to as high as 35% during the Phanerozoic eon (541 Ma–Present). These changes in the amount of O2 are large enough to have lead to changes in atmospheric mass, which may alter the radiative budget of the atmosphere, leading to this mechanism being invoked to explain discrepancies between climate model simulations and proxy reconstructions of past climates. Here we present the first fully 3D numerical model simulations to investigate the climate impacts of changes in O2 during different climate states using the HadGEM3-AO and HadCM3-BL models. We show that simulations with an increase in O2 content result in increased global mean surface air temperature under conditions of a pre-industrial Holocene climate state, in agreement with idealised 1D and 2D modelling studies. We demonstrate the mechanism behind the warming is complex and involves trade-off between a number of factors. Increasing atmospheric O2 leads to a reduction in incident shortwave radiation at Earth's surface due to Rayleigh scattering, a cooling effect. However, there is a competing warming effect due to an increase in the pressure broadening of greenhouse gas absorption lines and dynamical feedbacks, which alter the meridional heat transport of the ocean, warming polar regions and cooling tropical regions.Case studies from past climates are investigated using HadCM3-BL which show that in the warmest climate states, increasing oxygen may lead to a temperature decrease, as the equilibrium climate sensitivity is lower. For the Maastrichtian (72.1–66.0Ma), increasing oxygen content leads to a better agreement with proxy reconstructions of surface temperature at that time irrespective of the carbon dioxide content. For the Asselian (298.9–295.0Ma), increasing oxygen content leads to a warmer global mean surface temperature and reduced carbon storage on land, suggesting that high oxygen content may have been a contributing factor in preventing a Snowball Earth during this period of the early Permian. These climate model simulations reconcile the surface temperature response to oxygen content changes across the hierarchy of model complexity and highlight the broad range of Earth system feedbacks that need to be accounted for when considering the climate response to changes in atmospheric oxygen content.Walker, S.W.C., Anwar, A., Psutka, J.M., Crouse, J., Liu, C., Le Blanc, J.C.Y., Montgomery, J., Goetz, G.H., Janiszewski, J.S., Campbell, J.L., Hopkins, W.S., 2018. Determining molecular properties with differential mobility spectrometry and machine learning. Nature Communications 9, Article 5096. fast and accurate determination of molecular properties is highly desirable for many facets of chemical research, particularly in drug discovery where pre-clinical assays play an important role in paring down large sets of drug candidates. Here, we present the use of supervised machine learning to treat differential mobility spectrometry – mass spectrometry data for ten topological classes of drug candidates. We demonstrate that the gas-phase clustering behavior probed in our experiments can be used to predict the candidates’ condensed phase molecular properties, such as cell permeability, solubility, polar surface area, and water/octanol distribution coefficient. All of these measurements are performed in minutes and require mere nanograms of each drug examined. Moreover, by tuning gas temperature within the differential mobility spectrometer, one can fine tune the extent of ion-solvent clustering to separate subtly different molecular geometries and to discriminate molecules of very similar physicochemical properties.Wang, B., Yu, Z., Zhang, Y., Zhang, H., 2019. Microbial communities from the Huaibei Coalfield alter the physicochemical properties of coal in methanogenic bioconversion. International Journal of Coal Geology 202, 85-94. relationships among the production of methane, the physicochemical properties of coal, and the composition of microbial communities are poorly understood in methanogenic bioconversion. In this study, we investigated the changes in microbial communities during the methanogenic process of coal based on culture-dependent methods as well as the physicochemical properties of the coal samples. The process of methane production could be clearly divided into four phases (lag, log, peak, and stationary phases). The initial bacterial communities in the cultivation were predominantly Bacteroidales, Actionmycetales, and Bacillales; the archaeal community was present at values below the detection limit. However, distinct changes in bacterial communities were noted at the log phase of methane production. Bacteroides species accounted for >80% of the total bacterial community, and acetotrophic Methanosarcina was the only archaeal community. Interestingly, Clostridiales increased considerably during the first 2?weeks, but decreased thereafter, indicating that Clostridiales may play a unique role during the initial stage of methanogenic coal bioconversion. Furthermore, the final coal sample showed decreased C and O contents and increased N and H contents. Volatile and ash contents as well as microporosity were also higher than those in the initial state. These results suggested that methanogenic coal bioconversion was a complex biochemical process and that the physicochemical properties of coal were altered in methanogenic bioconversion. Moreover, these findings may facilitate the development of strategies to improve the production of biomethane utilizing coal.Wang, C., Shi, G., 2019. Redox condition and organic carbon accumulation mechanism in the Cryogenian Nanhua Basin, South China: Insights from iron chemistry and sulfur, carbon, oxygen isotopes of the Datangpo Formation. Advances in Geo-Energy Research 3, 67-75. glaciation, oxidation event and eukaryotic expansion and diversification in the Neoproterozoic period are marked events that characterize the early evolution of the Earth, but how the interactions occurred among these events is not well understood. The organic matters preserved in the black shales of the Datangpo Formation (Cryogenian period) are sensitive to redox conditions, and thus its accumulation and preservation offer beneficial clues to unravel the early evolutional history of the Earth. This study presents new chemostratigraphic data of iron component, TOC content, sulfur isotope of pyrite, carbon and oxygen isotopes of carbonaceous shale of the Datangpo Formation (Cryogenian period) in the Datangpo section, South China. The analyzed results imply abundant nutrients existing in the ocean in the Early Cryogenian. The nutrients, such as phosphorus, resulting from neighbor volcanic eruptions, provided nutrients that enabled microbes to flourish during the Cryogenian interglacial gap. Iron components and sulfur isotopes indicated anoxic, euxinic deep water environments for the black shales in the lower portion of the Datangpo Formation. The anoxic setting was good for the preservation of organic matter, but terrigenous materials inputs, as revealed by the high Al2O3 contents, diluted the organic carbon content (TOC).Wang, C., Zhang, B., Lu, Y., Shu, Z., Lu, Y., Bao, H., Meng, Z., Chen, L., 2018. Lithofacies distribution characteristics and its controlling factors of shale in Wufeng Formation-Member 1 of Longmaxi Formation in the Jiaoshiba area. Petroleum Research 3, 306-319. is essential to investigate shale lithofacies distribution and controlling factor of the shale for geological evaluation of shale gas exploration and development. Through comprehensive analysis of cores, thin sections, cathode luminescence, whole-rock X-ray diffraction, element capture spectroscopy, major/trace element and other data, three major types and eight sub-type shale lithofacies in the shale of Wufeng Formation-Member 1 of Longmaxi Formation in Jiaoshiba area are identified by the three-end-member method and shale lithological classification nomenclature, and the spatiotemporal distribution law and main development controlling factors of shale lithofacies are well studied. In the Jiaoshiba area, vertically, the marine shale develops siliceous shale, mixed shale and argillaceous shale from bottom to top. Besides, lateral distribution of the shale is different from north to south; the shale lithofacies in the north area changes rapidly, the mixed shale in the north area is much thicker than that in the south area, while the siliceous shale in the south area is relatively thicker. Difference in the shale lithofacies is controlled by special sedimentary geologic events; development of the siliceous shale is controlled by the Ordovician-Silurian global volcanic event to some extent, while the mixed shale is significantly influenced by effect of bottom current, and the argillaceous shale is mainly affected by supply of terrestrial clastic material.Wang, J., Song, X., Li, Q., Bai, H., Zhu, C., Weng, B., Yan, D., Bai, J., 2019. Bioenergy generation and degradation pathway of phenanthrene and anthracene in a constructed wetland-microbial fuel cell with an anode amended with nZVI. Water Research 150, 340-348. frequent occurrence of polycyclic aromatic hydrocarbons (PAHs) in aquatic environments is of great concern because of their teratogenicity, toxicity, carcinogenicity, and mutagenicity to plants, animals and human beings. In this study the bioelectricity generation, biodegradation, phytoextraction and substrate adsorption of phenanthrene and anthracene in a constructed wetland-microbial fuel cell (CW-MFC) were investigated with an anode electrode amended with or without biochar-nZVI. During a 182-day operation period, the average removal efficiency for phenanthrene and anthracene ranged from 88.5% to 96.4%. The concentration of phenanthrene in roots, stems and laminas of T.?orientalis was 14.9, 3.9 and 2.3?ng?g?1 respectively, while that of anthracene was 22.2, 3.1 and 1.3?ng?g?1, respectively. In addition, the application of nZVI was conducive to bioelectricity generation and organic compound degradation in the CW-MFC reactor. The distribution of the bacterial community indicated that the relative abundance of Bacillus, Paludibacter, Desulfovibrio and Lactococcus with a degradation capability for refractory organics was significantly increased. Especially the genus Bacillus for excreting catalase became more abundant. The results of our study indicate how to promote bioelectricity generation and biodegradation of refractory organic compounds in a CW-MFC by improving the culture conditions for bacteria.Wang, K., Pang, Y., He, C., Li, P., Xiao, S., Sun, Y., Pan, Q., Zhang, Y., Shi, Q., He, D., 2018. Optical and molecular signatures of dissolved organic matter in Xiangxi Bay and mainstream of Three Gorges Reservoir, China: Spatial variations and environmental implications. Science of The Total Environment 657, 1274-1284. the on-going boom in the construction of dam reservoirs all over the world, the sources and composition of dissolved organic matter (DOM) in fluvial networks are expected to be altered. Considering the importance of DOM as a key biogeochemical component in inland waters, this might bring important ecological and environmental influences. However, limited information is available on the molecular composition of DOM in dam reservoirs. In this study, the spatial characteristics of DOM composition were investigated in Xiangxi tributary and mainstream of the Three Gorges Reservoir (TGR), the largest freshwater reservoir in the world. The concentration alteration of conservative cations revealed the water intrusion from mainstream into Xiangxi tributary, which mainly controlled the hydrological gradient. One tyrosine-like (C4), one tryptophan-like (C2), and two humic-like (C1 and C3) fluorescent components were identified in fluorescent DOM (FDOM) by parallel factor analysis (PAFACAC), potentially indicating algal, anthropogenic, and terrestrial inputs, respectively. Decreasing trends of C1, C3 and C4 components and an increasing trend of C2 component were observed from Xiangxi tributary to mainstream, indicating higher terrestrial and algal inputs but lower anthropogenic inputs in Xiangxi tributary compared to mainstream. The Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) characterization further revealed substantial heterogeneity of DOM at the molecular level. Interestingly, S-containing compounds related to synthetic surfactants were consistently detected, and their relative abundances showed an increasing trend from Xiangxi tributary to mainstream, in agreement with the distribution of the anthropogenic derived C2 component. Meanwhile, numerous lignin-like S-containing compounds were identified, likely the result of the incorporation of sulfide ions to lignin-like CHO compounds. This study represents the first molecular level characterization of DOM in the TGR system, which should aid the design and implementation of more detailed future studies.Wang, Q., Wang, T., Liu, W., Zhang, J., Feng, Q., Lu, H., Peng, P.a., 2019. Relationships among composition, porosity and permeability of Longmaxi Shale reservoir in the Weiyuan Block, Sichuan Basin, China. Marine and Petroleum Geology 102, 33-47. composition might influence the petrophysical properties of shale reservoirs. The relationships among composition, porosity and permeability of Longmaxi Shale in Weiyuan area, Sichuan Basin, China, were systematically investigated by the integration of geochemical, mineralogical and petrophysical data. The cumulative pore volume of the organic-rich Longmaxi Shale is mainly contributed of pores with diameter of 2?nm–100?nm. The total organic carbon (TOC) content is the main control on porosity, as the percentage of organic porosity is >60% for the organic-rich shales. The clay content is positively correlated with porosity, partly due to the clay associated interparticle pores and pores developed in organo-clay complex. Carbonate and quartz content dilute the TOC and clay content, which accounts for their negative relationships with porosity. In terms of shale composition, the clay content exerts the strongest influence on permeability. At low clay contents (<30%), the clay content shows a positive correlation with permeability due to the good pore connectivity caused by pores developed in organo-clay complexes, whereas at high clay content (>30%), the clay content exhibits a negative impact on permeability because abundant clay minerals block pore throats, reduce the resistance to mechanical compaction and result in low permeability. The influence of the pore network on permeability is evident from a positive correlation between the pore volume percentage of meso-pores (VOLmes) and permeability, which is due to (a) fine and coarse meso-pores including a large fraction of organic pores, which have better connectedness than other interparticle (mostly >50?nm) and intraparticle (mainly isolated) pores; and (b) large quantities of fine and coarse meso-pores increasing the capacity to access other pores, which form the dominated pathways for gas flows. According to the above illustrated relationships, appropriate porosity and permeability indicating fine storage capacity and favorable flow capacity occur in the Longmaxi Shale in Weiyuan Block, which implies good reservoir quality and excellent exploration prospects in this region.Wang, Q., Wang, X., Wei, H., Khormali, F., Xie, H., Zhang, J., Chen, F., 2019. Climatic significance of the stable carbon isotopic composition of surface soils in northern Iran and its application to an Early Pleistocene loess section. Organic Geochemistry 127, 104-114. stable carbon isotopic composition of bulk organic matter (δ13Corg) in paleosols has been widely used as a proxy indicator for reconstructing past vegetation and climate. Previous studies generally show a negative correlation between the δ13Corg values of modern C3 plants and surface soils under C3 plant-dominated ecosystems and mean annual precipitation (MAP). However, the relationship between δ13Corg and MAP varies among different climatic regimes, resulting in uncertainties in paleo-precipitation reconstructions. In this study, we analyzed the δ13Corg values of surface soil samples collected along a north-south climatic gradient in northern Iran, in the western part of arid central Asia (ACA). Our aims were to explore the relationship between surface soil δ13Corg values and climatic factors; to use it to develop a transfer function for ACA; and then to apply the transfer function to a well-dated loess-paleosol sequence (AB1) to reconstruct early Pleistocene (2.4–1.8?Ma) MAP in northern Iran. The results show that: (1) the δ13Corg values of 44 surface soil samples range from ?27.56‰ to ?23.61‰, with an average of ?25.77‰, indicating that the modern natural ecosystem in northern Iran is dominated by C3 vegetation; (2) The δ13Corg values of the surface soil samples are strongly negatively correlated with MAP (y?=??0.0079x???22.8418, R2?=?0.4419, p?<?0.001), with a coefficient of ?0.79‰/100?mm. We infer that the effects of mean annual temperature (MAT) and elevation on the relationship are minimal; (3) Reconstructed early Pleistocene MAP in northern Iran was ～649?mm, much wetter than the present day (～331?mm); (4) The loess δ13Corg values from ACA exhibit similar trends to records from monsoonal Asia, suggesting a similar history of Quaternary climate change between ACA and monsoonal Asia, which is likely related to the growth and decay of Northern Hemisphere ice sheets.Wang, S., Liu, G., Zhang, J., Zhou, L., Lam, P.K.S., 2019. An effective method for reconstructing the historical change in anthropogenic contribution to sedimentary organic matters in rivers. Science of The Total Environment 655, 968-976. water quality has been greatly affected by anthropogenic activities around the world in the past decades. Scientists and policymakers should pay close attention to quantify historical change in human impacts on aquatic environment. An effective method for reconstructing the historical input of anthropogenic organic matters in aquatic environment is urgently required. Here, five sediment cores from the Huaihe River were analyzed for n-alkanes (C8–C40) and isoprenoid alkanes (pristane and phytane) using gas chromatography–mass spectrometry (GC–MS). Sixty years (1955–2014) sedimentary history of n-alkanes was reconstructed using 210Pb method. The evaluation of wax n-alkanes percentage (WNA) indicated that the terrestrial higher plant input was predominant in most samples. The main anthropogenic sources were the petroleum hydrocarbon, fossil fuel combustion and the discharge of industrial wastewater and domestic sewage. The results of principal component analysis-multiple linear regression (PCA-MLR) indicated that the respective contributions of anthropogenic and biogenic sources to sedimentary organic matters were 47.8% and 48.1% in the Huaihe River. Furthermore, the anthropogenic contribution displayed a decrease trend from 1991 to 2014, which probably attributed to the effective pollution control measures taken by the local government. However, the anthropogenic contribution was still considerable during this period. Thus, the government should pay attention to organic pollution control in the Huaihe River sediments continuously. In summary, this study provides an effective method for reconstructing the historical change in anthropogenic contribution to sedimentary organic matters in rivers, which can probably be applied to other aquatic environment around the world.Wang, S., Zhuang, Q., L?hteenoja, O., Draper, F.C., Cadillo-Quiroz, H., 2018. Potential shift from a carbon sink to a source in Amazonian peatlands under a changing climate. Proceedings of the National Academy of Sciences 115, 12407-12412.: We use a process-based biogeochemistry model to quantify the carbon accumulation for peatland ecosystems in the Pastaza-Mara?on foreland basin in the Peruvian Amazon from 12,000 y before present to AD 2100. We find that warming accelerates peat carbon loss, while increasing precipitation slightly enhances peat carbon accumulation at millennial time scales. With these impacts, our simulations suggest that the basin might lose up to 0.4 Pg?C by AD 2100, with the largest loss from palm swamp. If this loss rate is true for all Amazonia peatlands, we project that these carbon-dense peatlands may switch from a current carbon sink into a future source in this century.Abstract: Amazonian peatlands store a large amount of soil organic carbon (SOC), and its fate under a future changing climate is unknown. Here, we use a process-based peatland biogeochemistry model to quantify the carbon accumulation for peatland and nonpeatland ecosystems in the Pastaza-Mara?on foreland basin (PMFB) in the Peruvian Amazon from 12,000 y before present to AD 2100. Model simulations indicate that warming accelerates peat SOC loss, while increasing precipitation accelerates peat SOC accumulation at millennial time scales. The uncertain parameters and spatial variation of climate are significant sources of uncertainty to modeled peat carbon accumulation. Under warmer and presumably wetter conditions over the 21st century, SOC accumulation rate in the PMFB slows down to 7.9 (4.3–12.2) g?C?m?2?y?1 from the current rate of 16.1 (9.1–23.7) g?C?m?2?y?1, and the region may turn into a carbon source to the atmosphere at ?53.3 (?66.8 to ?41.2) g?C?m?2?y?1 (negative indicates source), depending on the level of warming. Peatland ecosystems show a higher vulnerability than nonpeatland ecosystems, as indicated by the ratio of their soil carbon density changes (ranging from 3.9 to 5.8). This is primarily due to larger peatlands carbon stocks and more dramatic responses of their aerobic and anaerobic decompositions in comparison with nonpeatland ecosystems under future climate conditions. Peatland and nonpeatland soils in the PMFB may lose up to 0.4 (0.32–0.52) Pg?C by AD 2100 with the largest loss from palm swamp. The carbon-dense Amazonian peatland may switch from a current carbon sink into a source in the 21st century.Wang, W., Jiang, Y., Swennen, R., Yuan, J., Liu, J., Zhang, S., 2019. Utility of inclusions for interpreting reservoir thresholds for tight sandstone gas accumulation in the Longfengshan and Dongling sags, Southeast China. Journal of Natural Gas Science and Engineering 61, 270-283. better understand the thresholds for hydrocarbon migration in tight sandstone, we studied the gas migration and accumulation processes in the Longfengshan and Dongling sags in the Songliao Basin by determining the ancient pore pressure evolution and gas fractionation. The trapping pressure of coeval aqueous inclusions can be used to identify systematic overpressure trends, which increase during gas charging. Early formation of overpressure and a maximum surplus pressure greater than 6?MPa in reservoirs adjacent to high-quality source rocks (total organic carbon?>?1.2%) indicate that the formation of surplus pressure is related to the gas generation capacity. The gas-bearing inclusion distribution and systematic geochemical trends suggest that dynamic gas migration was accompanied by gas fractionation. The results indicate that dissolved gas mainly accumulated in reservoirs with a maximum surplus pressure greater than 6?MPa and that the free gas diffused toward reservoirs with maximum surplus pressures less than 6?MPa. The gas saturations were generally stable and greater than 50% in the high surplus pressure zone. However, in the low surplus pressure zone, the gas saturation was less than 25%, although this value was relatively higher in reservoirs where the maximum surplus pressure was less than 3?MPa. Our results demonstrate that the resistance thresholds for the migration of dissolved gas and free gas differ in tight sandstone reservoirs. The surplus pressures greater than 6?MPa are advantageous for dissolved gas accumulation. An obvious resistance threshold is not observed for free gas migration, although the migration of this gas was relatively inefficient and occurred mainly via diffusion in the direction of decreasing surplus pressure. The results of this study confirm the importance of considering the driving force for natural gas in different phases as a key factor when determining optimal exploration targets.Wang, X., Li, X., Yu, L., Li, Y., Huang, L., Lin, W., Li, D., 2019. Distinctive microbial communities imply the main mechanism in a MEOR trial in high pour-point reservoir. Journal of Petroleum Science and Engineering 175, 97-107. on preliminary research in laboratory, a microbial enhanced oil recovery (MEOR) field trial was carried out in three production wells in Liaohe high pour-point oil reservoir. The three wells are located closely in the same block, share similar geological characteristics. Since all of them held a lower bottom temperature which accounted for serious wax precipitation underground, the microbial agents were injected to remove the waxy blockage for enhancing oil recovery. The results of the pilot showed two of the wells were effective while another well had little effect. In order to identify the functional bacteria and reveal the main mechanism of MEOR in high pour-point oil reservoirs, combined the MEOR field trial, laboratory comparative study on the positive wells and the negative well was carried out. First of all, the microbial communities in the three pilot wells were analyzed by 16S rRNA gene clone library. The results showed the original microorganisms in the two effective wells were highly similar and significantly different from those in the non-effective well. After MEOR treatment, the exogenous surfactant-producing bacteria (ESPB) and the nitrate reducing bacteria (NRB) including Lysinibacillus, Acinetobacter junnii, Sulfurihydrogenibium were abundantly stimulated and shared in the effective wells, which are thought to be the functional microorganisms in this study. Secondly, the oil components were characterized by chromatography and mass spectroscopy, the results indicated resins in the effective well samples were degraded by 5.53%–5.81% after the MEOR treatment, however, the saturated hydrocarbons exhibited little change as well as the oil pour-point. Finally, further comparative analysis for the effluents’ physical characteristics demonstrated the bio-emulsification rather than biodegradation played an important role in improving oil mobility and was the main mechanism in this trial.Wang, Y., Chen, X., Guo, W., Zhou, H., 2018. Distinct bacterial and archaeal diversities and spatial distributions in surface sediments of the Arctic Ocean. FEMS Microbiology Letters 365, fny273-fny273. changes in the polar oceans are more pronounced than in other regions. The lack of knowledge regarding the microbial diversity, distribution and succession in the polar oceans has hampered our understanding about the effects of environmental changes on microbial ecosystems. This study investigated bacterial and archaeal diversities and spatial distributions in surface sediments of the Bering Sea and the Chukchi Sea. The results showed that bacterial α-diversity was higher than archaea, and these differences were due to compositional changes. β-diversities were not significantly different for bacterial and archaeal communities. Proteobacteria and Bacteroidetes were the dominant bacterial phyla, and the subdivisions of Proteobacteria changed obviously when compared with previous results. However, different assemblages dominated archaeal communities in different regions. Bacterial and archaeal communities were mainly determined by metallic ions, and geochemical properties were the major contributors to community dissimilarities. Interactions between geographical and geochemical properties had more pronounced impacts on archaeal communities.Wang, Y., Hou, Z.Q., Hu, Y.Z., 2018. In situ X-ray micro-CT for investigation of damage evolution in black shale under uniaxial compression. Environmental Earth Sciences 77, 717. damage evolution of shale is crucial to the hydraulic fracturing treatment and engineering stability. Although many effects have been done on the macroscopic characteristics of shale, yet the microscopic failure mechanism is not well understood. A uniaxial compressive test on black shale was conducted under topographic monitoring using in situ X-ray micro-tomography (?CT). A series of high-resolution reconstruction images were obtained by carrying out CT scans at six key points throughout the test to obtain the internal structure of shale sample. In addition, the CT values for the purpose of crack damage evolution in shale were identified. Clear 2D/3D CT images, CT value analysis and image segmentation analysis reveal that the sample experiences compression, damage, cracking, crack propagation, and collapse stages. Crack geometry and distribution in the shale sample is visualized by rendered CT images, and a combined tension and shear failure mode is observed from the fracture rose diagram. This work suggests that formation and propagation of fractures are influenced by the stratified structure and weak cementation medium between layers.Wang, Y., Ma, L., Zhang, M., Chen, M., Li, P., He, C., Yan, C., Wan, J.-B., 2019. A simple method for peak alignment using relative retention time related to an inherent peak in liquid chromatography-mass spectrometry-based metabolomics. Journal of Chromatographic Science 57, 9-16. time (RT) shifts are inevitable in liquid chromatography-mass spectrometry (LC–MS)-based metabolomics studies. RT alignment, aligning peaks originating from the same feature to an identical RT, is a necessary step prior to multivariate data analysis. Many RT alignment software packages and various algorithms have been developed. In the present study, a simple method for peak alignment was proposed using relative RT related to an inherent peak in the chromatogram, and its performance on RT alignment in untargeted metabolomics was evaluated using an LC–MS dataset acquired from plasma samples from osteoporotic rats, and compared with the common MarkerLynx XS method using different RT window. RT alignment accuracy and relative standard deviation (RSD) value of the intensity of 79 selected ions in a chromatogram were employed to assess the alignment effectiveness of Method I (0.2 RT window), Method II (0.5 RT window) and Method III (relative RT). The overall RT alignment accuracy of these three methods was 67.7%, 77.2% and 90.9%, and 44.3%, 72.2% and 82.3% of the ions had intensity RSD values &lt;30%, respectively. The results demonstrated that Method III using relative RT significantly reduced the influence caused by RT shifts in LC–MS-based metabolomics. Furthermore, Method I and Method III were applied to discover plasma biomarkers for osteoporosis in rats. Thirteen and nineteen ions were selected as potential biomarkers, respectively. Among them, only eight common ions were found, which demonstrated that different sets of biomarkers were obtained using those two RT alignment methods. The relative RT method exhibited fewer missing values, a lower RSD of peak intensity and better performance in pattern recognition, thereby showing the great potential in future metabolomics studies.Wang, Y., Qin, Y., Zhang, R., He, L., Anovitz, L.M., Bleuel, M., Mildner, D.F.R., Liu, S., Zhu, Y., 2018. Evaluation of nanoscale accessible pore structures for improved prediction of gas production potential in Chinese marine shales. Energy & Fuels 32, 12447-12461. Lower Cambrian Niutitang and Lower Silurian Longmaxi shales in the Upper Yangtze Platform (UYP) are the most promising strata for shale gas exploration in China. Knowledge of the nanoscale pore structure may improve the prediction of the gas production potential in Chinese marine shales. A systematic investigation of the pore accessibility and its impact on methane adsorption capacity has been conducted on shale samples using various techniques including geochemical and mineralogical analyses, field-emission scanning electron microscopy (FE-SEM), small-angle neutron scattering (SANS), helium porosimetry, and methane adsorption. The results show that organic matter (OM) pores with various shapes dominate the pore systems of these shales. OM tended to mix with clay minerals and converted to organoclay complexes, developing plentiful micro- and mesopores. A unified fit model with two pore structures, fractal pores and finite pores, was used to model the SANS data to characterize the pore structure of the shales. Both mass and surface fractals are identified for each pore structure. The total porosity estimated by the Porod invariant method ranges between 2.35 and 16.40%, of which the porosity for finite pores ranges between 0.35 and 6.36%, and the porosity for the fractal pores ranges between 2.07 and 8.51%. The fraction of open pores was evaluated by comparing the porosities estimated by He porosimetry and SANS. We find that the fraction of open pores is higher than 64% for most of these shales. Correlation analyses suggest that clay and total organic carbon (TOC) have opposite effects on pore structure and methane adsorption capacity. Samples with higher clay contents have higher pore accessibility and lower total porosity, surface area, and maximum methane adsorption, whereas samples with higher TOC content show the inverse relationships. The high percentage of open pores may reduce methane adsorption capacity in these shales, whereas low pore accessibility may reduce methane production at specific pressure differences. Thus, both TOC and pore accessibility may be essential controlling factors in methane production from shale gas reservoirs.Wang, Y., Sun, J., Qiao, J., Ouyang, J., Na, N., 2018. A “soft” and “hard” ionization method for comprehensive studies of molecules. Analytical Chemistry 90, 14095-14099. mass spectrometry can be rapidly and directly effective for molecular studies, while there still seems to be a gap between two major groups of electrospray ionization (ESI)- and atmospheric pressure chemical ionization (APCI)-related techniques, for detection of moderately polar to polar and low polar to nonpolar molecules in a relatively low mass range, respectively. Here, an extensively applicable “soft” and “hard” ionization method, spray-dependent plasma mass spectrometry (SDP MS), was established for detecting various molecules with diverse polarities or molecular weights. By SDP MS, both fragment ions and intact molecular ions can be obtained. Significantly, cluster ions of aggregates in high mass range formed by weak molecular interactions can also be well recorded, much softer than traditional ESI MS. By filling the gap between ESI-based and APCI-based ionization techniques, SDP MS would enhance MS performance for comprehensive molecular studies and be extensively applicable in fields of organic synthesis, biological chemistry, medical chemistry, and clinical diagnosis.Ward, B., Ramaiah, N., Edgcomb, V., Crowe, S., 2018. Preface: Microbial community response to ocean deoxygenation. Deep Sea Research Part II: Topical Studies in Oceanography 156, 1-3. oceans are losing oxygen as the combined result of warming climate and increasing nutrient fluxes from land to the sea. This ocean deoxygenation is most obvious in reports that the volume, area, and severity of oxygen minimum zones and hypoxic coastal sites are expanding. The distribution of oxygen in the ocean is controlled by physical, chemical and biological processes, on scales from global ocean currents and atmospheric circulation, to microbial metabolisms. Climate change has increased water column stratification decreasing the mixing of oxygen from the atmosphere and surface-ocean into deep waters and driving deoxygenation throughout the much of the ocean. At the same time, anthropogenic discharges are loading coastal waters with nutrients, in particular nitrogen, causing eutrophication that enhances biological oxygen demand and promotes hypoxia (Diaz and Rosenberg, 2008, Whitney et al., 2007, Stramma et al., 2008, Emerson et al., 2004, Conley et al., 2011). Ocean deoxygenation directly impacts marine ecosystem functions and services through changes in food web structure and biodiversity, which have direct impacts on fisheries and thus pose serious risks to food security (Vaquer-Sunyer and Duarte, 2008, Breitburg et al., 2018). As oxygen levels decline, energy is increasingly diverted away from higher trophic levels into microbial community metabolism, which not only compresses the habitable portion of the water column for fish, but changes predator-prey dynamics and trophic structure throughout the food web, enhances fixed nitrogen loss, leads to accumulation of hydrogen sulfide, and induces the production of climate active trace gases. Sound management of marine ecosystems, and mitigation of the many risks associated with ocean deoxygenation, requires reliable predictions of deoxygenation rates and impacts under a range of future scenarios with well-constrained uncertainties. State-of-the-art numerical models predict oxygen loss of several percent by the end of the century, with substantial ecological and biogeochemical effects. Understanding microbial and biogeochemical responses to declining ocean oxygen is central to forecasting deoxygenation and its impacts, ranging from climate feedbacks to fisheries productivity and food security.SCOR Working Group 144 was convened to address knowledge gaps in the microbiology and biogeochemistry of low oxygen marine environments. Our work culminated in the International Symposium on Microbial Responses to Ocean Deoxygenation, held at the CSIR-National Institute of Oceanography (CSIR-NIO) in Goa, India in December 2016. Dr. SWA Naqvi, former director of NIO and leading researcher in the biogeochemistry of oxygen minimum zones, was honored during this Symposium and delivered a key note talk. Symposium sessions included Biogeochemical Processes, Microbial Ecology and Communities, Omics of Deoxygenated Waters, Instrumentation and Methods for OMZ Studies, and Societal Impacts of Marine Deoxygenation. Much of the research presented at the symposium is collected into this Special Issue on Ocean Deoxygenation, which we hope will serve as a resource to the broader oceanographic community and raise knowledge and awareness of ocean deoxygenation in the ocean sciences. All of the authors gratefully acknowledge the support of SCOR and the Ocean Carbon and Biogeochemistry (OCB) group at NSF, the Council of Scientific and Industrial Research (CSIR), and the Ministry of Earth Sciences, Government of India for their support of the meeting.The 15 papers collected in this special issue of Deep Sea Research II focus on the microbial ecology and biogeochemistry of marine oxygen minimum zones. Eleven papers in the collection are concerned with the diversity and distribution of marine microorganisms in space and time in relation to oxygen in the environment. Several authors reported on the diversity of microorganisms involved in nitrogen and sulfur cycling at the Arabian Sea Time Series (ASTS) and nearby stations. The Arabian Sea is one of the three main oceanic OMZs, but it has been less studied than the two analogous systems in the Eastern Tropical Pacific Ocean. Thus, this new work on the diversity and distribution of microbes reported here not only adds greatly to the knowledge of this system but enables new syntheses between all three OMZs. Bandekar et al. (2018a) characterized the microbial assemblage, both bacteria and archaea, at the ASTS using 16S rRNA clone libraries. They found that communities clustered more by depth than by season. This is consistent with the idea that vertical redox structuring in OMZs shapes the nature of marine communities. Bacteria and archaea implicated in N cycling were minor components of clone libraries, which suggests very diverse assemblages at all depths. Oxygen and major inorganic nutrients were all significant determinants of community composition. Bandekar et al. (2018b) also used clone libraries from the ASTS to investigate bacteria specifically associated with N cycling, based on their key functional genes, nirS (nitrite reductase) and hzo (hydrazine oxidase). The marine anammox genus Scalindua was the only anammox bacterium detected, while many diverse Proteobacteria (mainly gamma-Proteobacteria), were detected with nirS. Hzo was more abundant and both genes exhibited appreciable differences in abundance between seasons and depths. Mulla et al. (2018) isolated nitrate reducing bacteria from several stations in the Arabian Sea, including the ASTS. Cultures were characterized by 16S rRNA sequencing and most were related to known bacterial denitrifying strains in the Proteobacteria, Actinobacteria, and Firmicutes. This study described and characterized many new cultures, which will undoubtedly represent a key resource for future research on this important step in the N cycle of low oxygen waters. Gomes et al. (2018) focused on the microbes involved in N loss processes in the water column of the Arabian Sea. They characterized denitrifying bacterial diversity and the distribution of three functional genes involved in nitrate- (narG), nitrite- (nirS) and nitrous oxide (nosZ) reduction at three coastal sites and found that bacterial community structure varied seasonally with the monsoons and with depth across the oxygen gradients. Collectively, these contributions paint an emerging picture of OMZs characterized by vertically structured microbial communities with the metabolic potential for N metabolisms distributed across taxonomically diverse functional genes and host microorganisms.In addition to loss of fixed nitrogen as N2 gas, denitrification also results in the production and consumption of nitrous oxide. Jayakumar et al. (2018) investigated the diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, in marine (including the three largest oceanic OMZs) and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones. Atypical nosZ genes, usually associated with incomplete denitrification pathways, were detected in all the environments, including surface ocean waters.It has been hypothesized (Deutsch et al. 2007) that N fixation might be favored in environments where N loss was also occurring, e.g., in the oxygen minimum zone of the Arabian Sea. Thajudeen et al. (2018) addressed this question by investigating nitrogen fixation in Arabian Sea coastal sediments using clone libraries of nifH genes from sediment communities and 16S rRNA gene sequencing of bacterial diazotrophs cultivated from those sediments. Diverse assemblages of Proteobacteria, Firmicutes and unknown nifH genes were identified. N fixation was detected in the sediments at relatively low rates compared to eutrophic estuaries, and most of the diazotrophs were identified as Proteobacteria.While anammox and denitrification are recognized as important processes in oxygen minimum zones, we tend not to look for those processes or the microbes that perform them in well oxygenated regions of the ocean. Hamasaki et al. (2018) did just that, by investigating the distribution and phylogeny of anammox bacteria in the central Pacific Ocean. Three clades of the marine anammox genus Scalindua were detected in waters with oxygen concentrations up to ~50 μM, although the anammox process itself was undetectable.The Eastern Tropical South Pacific is probably the best studied major oceanic OMZ, but it continues to yield new insights. Aldunate et al. (2018) used three different methods based on 16S rRNA sequence data to characterize microbial assemblages at the coastal time series station in the seasonal OMZ off Chile. Reproducible patterns of community assembly were observed over three years. Oxygen conditions were a major determinant of community composition, with a threshold around 70 μM, strikingly similar to canonical thresholds for marine hypoxia (62.5 μM). Microbes involved in S cycling were more abundant at lower O2 conditions, suggesting the potential for metabolic redox sulfur cycling in this coastal location even when dissolved sulfide was not detectable.The long running (20 years) Cariaco Basin time series station was the focus of the study by Taylor et al. (2018), which documented a regime shift in the dominant sulfur oxidizing clades over time. By synthesizing data produced through different methods over time, they showed that divergent community assemblages are associated with different magnitudes and variability in sulfide fluxes. The two different sulfur oxidizing assemblages were associated with changes in density and chemical distributions, although a specific mechanism or physiological basis for the regime shift is unknown.Saanich Inlet, B.C., Canada is a seasonally anoxic fjord, rather than an oxygen minimum zone, and thus it offers the opportunity to investigate the real-time responses of microbial communities to seasonal transitions between oxic and anoxic conditions. Torres-Beltran et al. (2018) used pyrotag sequencing of 16S rRNA genes and gene transcripts to investigate the patterns and interactions among microbial eukaryotes at the time series station in Saanich Inlet. They discovered evidence of interactions between the parasitic dinoflagellates Syndiniales and many other eukaryotic groups. The progression of co-occurrences between different groups of eukaryotic microbes as the water column stratified and bottom waters became anoxic suggests a role for parasitic interactions in shaping phytoplankton bloom dynamics, controlling the abundance of grazers, and shaping pools of dissolved and particulate organic carbon.In the only other study in this collection to focus on eukaryotes, Dsouza and Gauns (2018) sampled zooplankton on an offshore transect from Goa in the coastal Arabian Sea. Zooplankton communities clustered by location, with distinct assemblies in the coastal, shelf break and offshore regions, likely related to phytoplankton and oxygen distributions. This paper presents a unique and extensive data set of abundances of copepod species in spring.All these microbial diversity studies add hugely to the database of environmental sequences, and to the culture collection of environmentally relevant microorganisms. They provide evidence that microbial communities assemble in response to environmental conditions, and find in many cases that oxygen is a critical variable in determining community composition and interactions. In addition to the focus on oxygen gradients and low oxygen systems, this collection also illustrates the importance and utility of time series studies for detecting the manner and time-scale of community responses to changing conditions.Four papers in the issue focus directly on the chemistry that shapes and results from the microbial metabolisms. New methods and isotope technologies make it possible to model microbial processes independent of biological measurements or manipulative experiments. Peters et al. (2018) carried out a comprehensive examination of N cycling processes in the ETSP based on stable isotopic compositions and nutrient concentration distributions. Using a novel water mass mixing approach, they examined the underlying physical mechanisms responsible for changes in concentrations of dissolved inorganic nitrogen (DIN), phosphate and dissolved O2. The mismatch between DIN deficit and N2 excess implies a source of phosphate from sediments, which the model allows them to quantify. The authors were also able to quantify the magnitude of N2 excess in the water column and developed a framework for evaluating its production via denitrification and anammox. They found that anammox was responsible for 28% of the total N2 production, the rest presumably deriving from denitrification.Fuchsman et al. (2018) measured isotopic signatures of nitrate, nitrite and N2 in an offshore transect in the ETNP to obtain an isotope mass balance and thus estimate the relative magnitudes of water column and sedimentary denitrification. They estimated the Rayleigh fractionation effect at 26-27 per mil. (from both nitrate and N2 perspectives), higher than the previous consensus for the fractionation effect of pelagic denitrification. A very similar value (24 – 26 per ml) was found for the Arabian Sea. These high fractionation effects imply a correspondingly large contribution to denitrification in sediments in order to account for the isotope content of oceanic nitrate. The combination of high denitrification rates in both water column and sediments implies the need for high N fixation rates in order to balance the oceanic N budget.Nitric oxide (NO), the most transient of denitrification intermediates, was measured in the ETSP by Lutterbeck et al. (2018) using a new very sensitive chemiluminescence method. NO concentration correlated with distributions of both nitrite and ammonia oxidizing archaea (AOA), suggesting that AOA are the source of NO in the low oxygen waters. NO is an intermediate in archaeal nitrification, so the authors hypothesize that some form of archaeal nitrifier-denitrification is responsible for the distribution of this very labile species.Nitrification and denitrification are both implicated in the production of nitrous oxide and their relative importance varies depending on the oxygen conditions of the environment. Casciotti et al. (2018) measured the concentration and isotope/isotopomer signature of N2O, to investigate the sources and sinks of N2O across dissolved oxygen gradients and throughout the water column in the eastern tropical South Pacific. Nitrification was the dominant source of N2O in the deep waters below the ODZ, while nitrate, via denitrification, was the dominant source of N2O within the offshore oxygen deficient layers.The potential long term expansion of oxygen minimum zones and ocean deoxygenation, especially in coastal regions, provides motivation for the study of the microbial biogeochemistry of low oxygen marine environments. The research presented in this volume illustrates the power of new methods, particularly in molecular biology and isotope analyses, directed towards specific microbial systems and biogeochemical regimes. Time series programs provide unprecedented temporal resolution for investigating and monitoring the response of the ocean and its inhabitants to deoxygenation. We hope that future research will build on the research contained in this volume to improve our knowledge of microbial and biogeochemical responses to ocean deoxygenation on scales ranging from microbial genomes to ecosystem structure to the functioning of the global ocean and atmosphere. We also hope these reports inspire more communication between research groups to coordinate future studies that employ consistent experimental approaches that will allow direct comparisons of data from different oxygen depleted habitats. Such concerted and global efforts are needed to develop the deep mechanistic insight into microbial and biogeochemical responses to ocean deoxygenation that will enable more robust predictions of ocean oxygen loss and its impacts on climate, marine ecosystems, fisheries, and food security.ReferencesM. Aldunate, R. De la Igelsia, A.D. Bertagnolli, O. Ulloa, Oxygen modulates bacterial community composition in the coastal upwelling waters off central Chile, Deep-Sea Res. II., 156 (2018), pp. 68-79M. Bandekar, N. Ramaiah, A. Jain, R.M. Meena, Seasonal and depth-wise variations in bacterial and archaeal groups in the Arabian Sea oxygen minimum zone. Deep-Sea Res. II., 156 (2018), pp. 4-18M. Bandekar, N. Ramaiah, R.M. Meena, Diversity and abundance of denitrifying and anammox bacteria from the Arabian Sea oxygen minimum zone. Deep-Sea Res. II., 156 (2018), pp. 19-26D. Breitburg, L.A. Levin, A. Oschlies, M. Gregoire, F.P. Chavez, D.J. Conley, V. Garcon, D. Gilbert, D. Gutierrez, K. Isensee, G.S. Jacinto, K.E. Limburg, I. Montes, S.W.A. Naqvi, G.C. Pitcher, N.N. Rabalais, M.R. Roman, K.A. Rose, B.A. Seibel, M. Telszewski, M. Yasuhara, J. Zhang, Declining oxygen in the global ocean and coastal waters. Science, 359 (2018), 10.1126/science.aam7240K.L. Casciotti, M. Forbes, J. Vedamati, B. Peters, T. Martin, C. Mordy, Nitrous oxide cycling in the Eastern Tropical South Pacific as inferred from isotopic and isotopomeric data, Deep-Sea Res. II., 156 (2018), pp. 155-167D.J. Conley, J. Carstensen, J. Aigars, P. Axe, E. Bonsdorff, T. Eremina, B.M. Haahti, C. Humborg, P. Jonsson, J. Kotta, C. Lannegren, U. Larsson, A. Maximov, M.R. Medina, E. Lysiak-Pastuszak, N. Remeikaite-Nikiene, J. Walve, S. Wilhelms, L. Zillen, Hypoxia is increasing in the Coastal Zone of the Baltic Sea, Environ. Sci. Technol., 45 (2011), pp. 6777-6783C. Deutsch, J.L. Sarmiento, D.M. Sigman, N. Gruber, J.P. Dunne, Spatial coupling of nitrogen inputs and losses in the ocean, Nature, 445 (2007), pp. 163-167R.J. Diaz, R. Rosenberg, Spreading dead zones and consequences for marine ecosystems, Science, 321 (2008), pp. 926-929S. Emerson, Y.W. Watanabe, T. Ono, S. Mecking, Temporal trends in apparent oxygen utilization in the upper pycnocline of the North Pacific: 1980-2000, J. Oceanogr., 60 (2004), pp. 139-147C.A. Fuchsman, A.H. Devol, K.L. Casciotti, C. Buchwald, B.X. Chang, R.E.A. Horak, An N isotopic mass balance of the Eastern Tropical North Pacific oxygen deficient zone, Deep-Sea Res. II., 156 (2018), pp. 137-147J. Gomes, R. Khandeparker, M. Bandekar, R.M. Meena, N. Ramaiah, Quantitative analyses of denitrifying bacterial diversity from a seasonally hypoxic monsoon governed tropical coastal region, Deep-Sea Res. II., 156 (2018), pp. 34-43K. Hamasaki, R. Shishikura, S. Suzuki, T. Shiozaki, H. Ogawa, T. Nakamura, Y. Suwa, Distribution and phylogeny of anaerobic anammonium-oxidizing (anammox) bacteria in water column of the central Pacific Ocean, Deep-Sea Res. II., 156 (2018), pp. 60-67A. Jayakumar, D. Balachandran, A.P. Rees, P.J. Kearns, J.L. Bowen, B.B. Ward, Community composition of nitrous oxide reducing bacteria investigated using a functional gene microarray, Deep-Sea Res. II., 156 (2018), pp. 44-50H. Lutterbeck, D.L. Arévalo-Martínez, C. L?scher, H.W. Bange, Nitric oxide (NO) in the oxygen minimum zone off Peru, Deep-Sea Res. II., 156 (2018), pp. 148-154A.B. Mulla, G. Fernandes, L. Menezes, R.M. Meena, H.S. Naik, M. Gauns, S. Damare, Diversity of culturable nitrate-reducing bacteria from the Arabian Sea oxygen minimum zone, Deep-Sea Res. II., 156 (2018), pp. 27-33B. Peters, R.E.A. Horak, A.H. Devol, C.A. Fuchsman, M. Forbes, C. Mordy, K.L. Casciotti, Estimating fixed nitrogen loss and associated isotope effects using concentration and isotope measurements of NO3?, NO2?, and N2 from the Eastern Tropical South Pacific oxygen deficient zone, Deep-Sea Res. II., 156 (2018), pp. 121-136L. Stramma, G.C. Johnson, J. Sprintall, V. Mohrholz, Expanding oxygen minimum zones in the tropical oceans, Science, 320 (2008), pp. 655-658G. Taylor, E. Suter, M. Pachiadaki, Y. Astor, V. Edgcomb, M.I. Scranton, Temporal Shifts in Dominant Sulfur-Oxidizing Chemoautotrophic Populations across the Cariaco Basin’s Redoxcline, Deep-Sea Res. II., 156 (2018), pp. 80-96J. Thajudeen, J. Yousuf, P. Veetil, M. Vipindas, A.A. Hatha, Diversity of nitrogen fixing bacterial communities in the coastal sediments of southeastern Arabian Sea (SEAS), Deep-Sea Res. II., 156 (2018), pp. 51-59M. Torres-Beltran, T. Sehein, M. Pachiadaki, S. Hallam, V. Edgcomb, Parasitic protist interactions and dynamics along oxygen gradients in a seasonally anoxic fjord: Saanich Inlet, British Columbia, Deep-Sea Res. II. (2018)R. Vaquer-Sunyer, C.M. Duarte, Thresholds of hypoxia for marine biodiversity, Proc. Natl. Acad. Sci. USA, 105 (2008), pp. 15452-15457F.A. Whitney, H.J. Freeland, M. Robert, Persistently declining oxygen levels in the interior waters of the eastern subarctic Pacific, Prog. Oceanogr., 75 (2007), pp. 179-199Washburn, T.W., Yoskowitz, D.W., Montagna, P.A., 2018. Valuing nature waste removal in the offshore environment following the Deepwater Horizon oil spill. Frontiers in Marine Science 5, 477. doi: 10.3389/fmars.2018.00477. offshore and deep-sea marine environment provides many ecosystem services (i.e., benefits to humans), for example: climate regulation, exploitable resources, processes that enable life on Earth, and waste removal. Unfortunately, the remote nature of this environment makes it difficult to estimate the values of these services. One service in particular, waste removal, was examined in the context of the Deepwater Horizon oil spill. Nearly 5 million barrels of oil were released into the offshore Gulf of Mexico, and 14 billion dollars were spent removing about 25% of the oil spilled. Using values for oil spillcleanup efforts, which included capping the wellhead and collecting oil, surface combustion, and surface skimming, it was calculated that waste removal, i.e., natural removal of spilled oil, saved BP over $35 billion. This large amount demonstrates the costs of offshore disasters, the importance of the offshore environment to humans, as well as the large monetary values associated with ecosystem services provided.Welch, S.A., Sheets, J.M., Place, M.C., Saltzman, M.R., Edwards, C.T., Gupta, N., Cole, D.R., 2019. Assessing geochemical reactions during CO2 injection into an oil-bearing reef in the Northern Michigan basin. Applied Geochemistry 100, 380-392. Dover 33 Reef, part of the Niagaran Reef Complex in Northern Michigan (USA), has been the focus of an enhanced oil recovery/carbon capture utilization and storage (EOR/CCUS) project as part of the Phase III-Midwest Regional Carbon Sequestration Partnership (Gupta et al., 2013a,b). The Dover 33 structure has experienced significant CO2 flooding in the past two decades, and over the course of the current injection study (between February 2013 and July 2016) has received approximately 100 to 1000 tonnes/day into the central injection well (L-M) 1–33). As part of the geochemical monitoring effort of the study, gas and fluid samples were collected from Dover 33 reef, and several other nearby reef structures, to assess the impact of CO2 injection on the geochemical processes occurring within in the reef.The injected gas is composed of approximately 95% CO2, with a δ13CCO2 of ～20.5‰, which is consistent with previously published compositions of Antrim shale gas, the source of the CO2. The concentrations and isotopic compositions of higher pressure gas collected from the L-M 5–33 monitoring well were similar to those measured in the injection well, but did exhibit a small but systematic shift in isotopic composition towards lower values over the course of the study, suggesting mixing and dilution between the gas in the reservoir and the injected gas. In contrast the δ13CCO2 of gas samples from the monitoring well with the lower surface pressure, L-M 2–33, are consistently lower throughout the study, ～18.5‰, indicating that reactions with the injected CO2 are occurring within the reef or with the well casing.Fluid samples were collected to assess the extent of interaction among the injected gas, the reservoir rock, and the brine. The brine samples are acidic (pH?～?4.1 to 4.9) with a total salt content of nearly 400?g/L. Analysis of the isotopic composition of dissolved inorganic carbon (DIC) in the Dover 33 brine shows that δ13C is higher than the injected gas (27–33‰) suggesting that the gas is not in equilibrium with DIC in the brine, and that there has been little isotopic exchange with carbonate minerals in the reef. The water isotope composition of the brine, δ18O and δD, plot below the meteoric water line, indicating that the water is not of recent meteoric origin and has undergone isotopic exchange with both gas and minerals within the reef structure. The 87Sr/86Sr ratios of the brine samples range from 0.70865 to 0.70869, consistent with Silurian seawater composition.Geochemical modelling of the brine composition shows that the predicted CO2 solubility as DIC is much greater than the measured DIC, and that the brines are supersaturated with respect to carbonate minerals, suggesting the potential for significant trapping of CO2 in both dissolved and mineral form.Wilberforce, T., Baroutaji, A., Soudan, B., Al-Alami, A.H., Olabi, A.G., 2019. Outlook of carbon capture technology and challenges. Science of The Total Environment 657, 56-72. greenhouse gases emissions produced by industry and power plants are the cause of climate change. An effective approach for limiting the impact of such emissions is adopting modern Carbon Capture and Storage (CCS) technology that can capture more than 90% of carbon dioxide (CO2) generated from power plants. This paper presents an evaluation of state-of-the-art technologies used in the capturing CO2. The main capturing strategies including post-combustion, pre-combustion, and oxy – combustion are reviewed and compared. Various challenges associated with storing and transporting the CO2 from one location to the other are also presented. Furthermore, recent advancements of CCS technology are discussed to highlight the latest progress made by the research community in developing affordable carbon capture and storage systems. Finally, the future prospects and sustainability aspects of CCS technology as well as policies developed by different countries concerning such technology are presented.Woda, J., Wen, T., Oakley, D., Yoxtheimer, D., Engelder, T., Castro, M.C., Brantley, S.L., 2018. Detecting and explaining why aquifers occasionally become degraded near hydraulically fractured shale gas wells. Proceedings of the National Academy of Sciences 115, 12349-12358.: Development of shale gas has changed the economics of global energy. However, methane sometimes escapes from shale gas wells into aquifers and the atmosphere. Although many researchers investigate leakage of this greenhouse gas, detection can be difficult where natural sources of methane are present. Here, methane was studied in water near gas wells previously cited for well integrity issues. We identify chemical clues that can distinguish methane migration related to shale gas development from methane that was preexisting. We also document a geological setting—the upper part of a large geological fold at shallow depth—that may be prone to methane migration. Knowledge gained from this study may lessen the chances for fugitive methane emissions into aquifers in the future.Abstract: Extensive development of shale gas has generated some concerns about environmental impacts such as the migration of natural gas into water resources. We studied high gas concentrations in waters at a site near Marcellus Shale gas wells to determine the geological explanations and geochemical implications. The local geology may explain why methane has discharged for 7 years into groundwater, a stream, and the atmosphere. Gas may migrate easily near the gas wells in this location where the Marcellus Shale dips significantly, is shallow (～1 km), and is more fractured. Methane and ethane concentrations in local water wells increased after gas development compared with predrilling concentrations reported in the region. Noble gas and isotopic evidence are consistent with the upward migration of gas from the Marcellus Formation in a free-gas phase. This upflow results in microbially mediated oxidation near the surface. Iron concentrations also increased following the increase of natural gas concentrations in domestic water wells. After several months, both iron and SO42? concentrations dropped. These observations are attributed to iron and SO42? reduction associated with newly elevated concentrations of methane. These temporal trends, as well as data from other areas with reported leaks, document a way to distinguish newly migrated methane from preexisting sources of gas. This study thus documents both geologically risky areas and geochemical signatures of iron and SO42? that could distinguish newly leaked methane from older methane sources in aquifers.Wolf, E.T., Haqq-Misra, J., Toon, O.B., 2018. Evaluating climate sensitivity to CO2 across Earth's history. Journal of Geophysical Research: Atmospheres 123, 11,861-11,874.: CO2‐driven changes to climate have occurred during many epochs of Earth's history when the solar insolation, atmospheric CO2 concentration, and surface temperature of the planet were all significantly different than today. Each of these aspects affects the implied radiative forcings, climate feedbacks, and resultant changes in global mean surface temperature. Here we use a three‐dimensional climate system model to study the effects of increasing CO2 on Earth's climate, across many orders of magnitude of variation, and under solar inputs relevant for paleo, present, and future Earth scenarios. We find that the change in global mean surface temperature from doubling CO2 (i.e., the equilibrium climate sensitivity) may vary between 2.6 and 21.6 K over the course of Earth's history. In agreement with previous studies, we find that the adjusted radiative forcing from doubling CO2 increases at high concentrations up to about 1.5 bars partial pressure, generally resulting in larger changes in the surface temperature. We also find that the cloud albedo feedback causes an abrupt transition in climate for warming atmospheres that depends both on the mean surface temperature and the total solar insolation. Climate sensitivity to atmospheric CO2 has probably varied considerably across Earth's history. Plain Language Summary: It is evident that climate sensitivity to changing CO2 varies if the amount of solar energy received by Earth is different, if the starting CO2 amount is different, or if the mean temperature of the planet is significantly different. Wolfender, J.-L., Nuzillard, J.-M., van der Hooft, J.J.J., Renault, J.-H., Bertrand, S., 2018. Accelerating metabolite identification in natural product research: Toward an ideal combination of liquid chromatography–high-resolution tandem mass spectrometry and NMR profiling, in silico databases, and chemometrics. Analytical Chemistry 90, 14095-14099. product research aims to characterize specialized metabolites from various living organisms and assess their biological properties from either a chemical ecology or drug discovery viewpoint. These “specialized” metabolites, which are oftentimes referred to as “secondary metabolites”, are nonessential to sustain the life of a given organism but necessary for its survival in a given environment, in contrast to “primary metabolites”, including amino acids, lipids, and carbohydrates, which are necessary for physiology purposes.(1) Specialized metabolites are small-molecular-weight molecules (typically <1500 Da) mainly involved in processes like defense against other biotic as well as abiotic agents or used as attractants for reproduction purposes due to the sessile lifestyles of many organisms, such as plants and microorganisms.(2) Throughout this review, we will refer to such metabolites as natural products (NPs).NPs from all living organisms have evolved and diversified for increased fitness within a specific environment. This has resulted in plants and microorganisms achieving the synthesis of distinct sets of NPs. Such pressure of evolution has generated the huge chemodiversity of NPs in nature. In plants, for example, and as stated by Pichersky and Lewinsohn, the total number of NPs found in the kingdom by far exceeds the capacity of any one plant genome to encode the necessary enzymes, and just as a plant lineage acquires the ability to elaborate new specialized compounds during evolution, it also loses the ability to produce others.(2)NPs thus include a large and diverse group of compounds from a variety of sources, mainly plants, bacteria, and fungi, from terrestrial and aquatic biotopes. They play significant biological roles in all organisms and have evolved to interact with enzymes, receptors, and ion channels. Some are active in living cells and are able to cross cell membranes and interfere with enzymes or even act against parasites.(3) Due to their coevolution in natural systems, NPs are therefore encoded to be bioactive and of high interest in the drug discovery field. They have long been used as medicines, and today, they continue to be a reservoir of potential drugs.(3,4) Thus, NPs and their related structures serve as essential sources of new chemical entities for the pharmaceutical industry due to their immense variety of functionally relevant compounds.(5)The chemical space encompassed by NPs is very large,(6) and more than 250?000 NPs have been reported to date in the dictionary of natural products (DNP).(7) The DNP surveys literature data of all NPs characterized worldwide as the result of the isolation work and full de novo identification of varied organisms with their taxonomic origin.(7) It is important to note that the DNP mainly focuses on plant resources, implying that when the microbial chemical space is added, the number above can easily quadruple. The chemical space is characterized by a “multidimensional descriptor space” in which NPs can be associated with a wide range of “descriptors” and “properties”, such as their molecular mass, lipophily (their affinity for a lipidic environment), compound class, and the topological features of their molecular structure.(8) A measurement of the chemodiversity of NPs can be obtained by evaluating the size of the chemical space visualized by the principal component analysis (PCA) of sets of molecular descriptors. This space has been shown to be much larger for NPs than those occupied by new chemical entities coming from combinatorial chemistry.(9) Both drugs and NPs cover similar parts of chemical space, demonstrating the potential of many NPs to become leads for drug discovery.(10) The methods used to navigate this chemodiversity space have constantly evolved. For example, ChemGPS-NP assists in compound selection and prioritization, property description and interpretation, cluster analysis and neighborhood mapping, as well as the comparison and characterization of large compound data sets.(11)Notwithstanding the potential of NPs to become effective drugs, the drug discovery workflow that leads from crude natural extracts to well-characterized bioactive NPs as hits and then as lead compounds is considered complex, slow, costly, and often not compatible with the pace of high-throughput screening campaigns. This explains in part why many pharmaceutical industries slowed down and then terminated most of their NP-oriented research programs in the early 2000s.(3,12)This difficulty of working with NPs is in part related to the very high complexity of the biological matrixes (natural crude extracts) in which they are embedded, which in turn causes their chemical richness. NPs as pure active ingredients are typically extracted from plants and microorganisms with solvents of different polarities (usually hydroalcoholic mixtures, methanol, ethyl acetate, or methylene chloride). Each of these extracts typically contains tens of main NPs and hundreds or thousands of less abundant ones. In addition, polar extracts are dominated by primary metabolites, mainly saccharides, and lipophilic extracts are dominated by various types of lipids and pigments. These compounds are part of the metabolome but are often not of interest for bioactivity. There are, however, exceptions; for example, polysaccharides are known to exhibit immunostimulating effects(13) and the high number that are bioactive, suggesting their functional roles.(14) Potentially all NPs, even minor constituents, may have interesting biological properties (e.g., potent defense toxins, hormones). Their identification requires using metabolite profiling methods that are able to work over a large dynamic range and generate information-rich spectral data for their full or partial identification.(15)The identification of bioactive NPs from such complex matrixes is classically performed in pharmacognosy (search for bioactive compounds from natural sources) by bioactivity-guided isolation approaches. Here, crude extracts exhibiting given biological activity are fractionated by a combination of preparative chromatographic methods. All fractions are submitted to bioassays, and those fractions continuing to exhibit activity are carried through further isolation and purification steps until pure active ingredients are obtained. These ingredients are then fully characterized by a combination of nuclear magnetic resonance spectroscopy (NMR), high-resolution mass spectrometry (HRMS), and chiroptical spectroscopic methods (i.e., sensitive to molecular chirality, such as electronic circular dichroism (ECD) and vibrational circular dichroism (VCD)) until their structure and absolute configuration are obtained.(16) This process is slow but effective and has led to major breakthroughs in NP research, such as the discovery of artemisinin (a sesquiterpene lactone containing an unusual peroxide) isolated from Artemisia annua. Artemisinin has become a reference drug for the treatment of malaria, and its discovery by Professor Tu Youyou led her to be awarded the Nobel Prize of Medicine in 2015.(17)To rationalize the process that yields interesting active ingredients, the metabolite profiling of crude extracts and dereplication prior to isolation has been underway for years in classical NP research.(18) Dereplication is the process of differentiating novel compounds from those that have already been studied.(12,19) Since its appearance in 1990, dereplication has significantly evolved over the last decades. It has been used in different workflows ranging from major compound identification and the acceleration of activity-guided fractionation up to the chemical profiling of collections of extracts.(18)In parallel to these advances in metabolite profiling, the field of metabolomics appeared at the beginning of the millennium for life science applications(20) and experienced exponential growth until today, as is the case for other omics approaches. Metabolomics is defined as a nonselective, universally applicable, comprehensive analytical approach for the identification and quantitation of metabolites in a biological system. This area of research strives to obtain complete metabolite fingerprints, detect differences between metabolites, and generate hypotheses to explain these differences.(19) Metabolomics is practically considered the large-scale analysis of metabolites of a given organism during various physiological states,(21) but it also extends to the comparative comprehensive metabolite profiling for deep/full metabolome analyses for chemotaxonomic investigations and NP prioritization studies in drug discovery. Tools in metabolomics have tremendously evolved over the past decade because such an unbiased data-driven approach has served many fields of life sciences and has also strongly influenced various aspects of NP research, notably in giving additional dimensions to dereplication. These developments were partly driven by the progress made in the acquisition techniques for metabolite profiling in complex biological matrixes in both the MS and NMR fields in terms of sensitivity, resolution, and throughput but also more recently by the introduction of in silico and chemometric associated methods.(22) It was recognized that traditional analysis methods only slightly dipped into the complete pool of molecules present in complex mixtures, thereby leaving a large amount of “dark matter.”(23) These unknowns potentially represent much-needed novel bioactive molecules that could, for example, be used to combat antibiotic resistance.In metabolomics, putative or partial metabolite identification from metabolite profiles or fingerprints of complex extracts is referred to as “annotation”. Today, this process still represents a major bottleneck in metabolomics because annotation is often not unambiguous, and only putative or partial assignments can be made. When compared to biological fluid metabolomics, this aspect is even more striking in NP research because NP chemodiversity is very extensive, and sample compositions vary substantially based on the organisms that are screened. In contrast, in biological fluid analysis, redundant metabolites are often profiled, and in this case, quantitation aspects are key to observing sometimes minute but significant changes in profiles (e.g., those related to disease or diet changes).To assess the level of confidence of metabolite annotation, different reporting standards for identification have been defined by metabolomics researchers. This resulted in a four-level system ranging from Level 1 (identified compound) via Levels 2 and 3 (putatively annotated compounds and compound classes) to Level 4 (unidentified or unclassified metabolites that can be differentiated based on analytical data, see Quality of Reporting of Metabolite IDs).(24)In typical NP research, unknown metabolites must be fully characterized de novo after isolation.(25) This also occurs redundantly for known NPs when the dereplication process is not sufficiently efficient. The additional full assessment of their absolute configuration by chiroptical methods and sometimes X-ray crystallography is also often required because 3D structural characterization is key to understanding ligand–target interactions in pharmacological investigations of NPs.(26)Full characterization clearly provides the high-quality unambiguous identification of metabolites but is time-consuming and often not worth the effort, especially when known compounds are redundantly characterized and their spectroscopy data have been published several times. Moreover, the isolation and full identification of minor compounds requires large amounts of biological material. Additionally, the pace of this work is not compatible with the pace at which high-throughput screening (HTS) campaigns are performed on extracts for drug discovery purposes.(3)The rapid high-quality identification of NPs is not only necessary for rationally characterizing active ingredients but also increasingly needed for obtaining detailed exhaustive composition information for herbal products used in traditional medicine, nutraceutical products, or botanicals with claimed clinical efficacy.(27) This can facilitate linking composition with possible efficacy, screening for possible toxic NPs, and establishing composition trends for given therapeutic usage in evidence-based approaches.(28) It is also needed to support quality control studies that increasingly rely on fingerprints rather than on single marker determination for herbal products.(29) This need for accurate composition determination is even more complex when studying drugs used by traditional Chinese medicine (TCM), where multiherb preparations are often used.(30)Altogether, only a few “complete” workflows exist that can take the researcher from raw data to performing the robust annotations and identifications of metabolites in complex mixtures; in particular, when investigating completely novel bioresources, existing tools often fail to identify reliable candidate molecules. Moreover, their usage is not always straightforward for NP researchers, which hampers their interpretation of downstream results. Thus, there is a strong need for metabolite profiling methods and data mining workflows that provide a much higher confidence of NP identification with reliable annotation scores that can be achieved with a high degree of automation.In this review, we will describe state-of-the-art metabolite profiling and data analysis methods based on both liquid chromatography (LC)–MS and NMR profiling that are currently used in NP research and metabolomics or related fields or can be implemented. In particular, their coverage in terms of full metabolome analysis will be discussed; however, this review will focus on the structure elucidation of NPs from complex mixtures. The present spectral NMR and MS/MS databases (DBs) suitable for NP annotation will be surveyed together with the different tools that can be used to generate searchable spectra generated in silico from structural NP DBs. Various recent workflows that can lead to annotation will be described and assessed, especially in terms of their usage/implementation in NP research and their ease of operation and level of automation for natural product chemists. Because both MS and NMR data are important for the characterization of NPs, their corresponding dereplication workflows will be treated equally. Current approaches integrating both MS and NMR analytical dimensions will be highlighted, and ideas for progress that can be made for better practical integration will be provided. Future prospects that may also come from the addition of orthogonal methods to LC–MS, such as collisional cross section (CCS) obtained with ion mobility measurements or retention time (RT) predictions, will be put in perspective. Finally, we will share our views on the development that is needed in terms of the contextualization (e.g., taxonomical data) of the metabolomics data generated from NP extracts. The creation of a novel method to combine scores from different and, if possible, orthogonal spectral/physicochemical information for more reliable annotation and the expansion of in silico candidate DBs through predictions of structural variation by exploiting knowledge of natural biosynthesis pathways will also be discussed. We will end by presenting our views and recommendations on the most important and exciting avenues toward more efficient and automated large-scale metabolite annotation and identification workflows.Wolfshorndl, M., Danford, R., Sachs, J.P., 2019. 2H/1H fractionation in microalgal lipids from the North Pacific Ocean: Growth rate and irradiance effects. Geochimica et Cosmochimica Acta 246, 317-338. hydrogen isotope ratio (2H/1H) of microalgal lipids has become a useful tool for reconstructing hydrologic conditions in the geologic past from marine and lacustrine sediments. Culture studies have shown that, in addition to the 2H/1H ratio of growth water, parameters such as salinity, growth rate, and irradiance, can have a large effect on lipid 2H/1H ratios. But aside from salinity, these effects have not been well studied in the field. In this work, hydrogen isotope fractionation relative to growth water was measured in four algal lipids - C37:3 and C37:2 methyl alkenones </topics/earth-and-planetary-sciences/alkenone>, (3β,4α,5α,22E)-4,23-Dimethylergost-22-en-3-ol (dinosterol), and 24-methylcholesta-5,22E-dien-3β-ol (brassicasterol) – in the upper water column of two North Pacific Ocean locations. By comparing lipid 2H/1H variations as a function of depth at tropical Station ALOHA (22°45′N, 158°00′W) and mid-latitude Gyre (41°30′N, 132°00′W in the Transition Zone) it was possible to evaluate the H isotope effects of nutrient limitation and irradiance on natural phytoplankton populations by comparing measured fractionation factors (αlipid) with those derived from laboratory-based empirical relationships. Significant distinctions were observed between the inferred causes of H isotope fractionation in different algal lipids at the two locations. At Station Aloha, 2H/1H fractionation in coccolithophorid-derived alkenones was primarily caused by nutrient-limited growth, while at Gyre it was caused by light limitation. Distinctions were less clear for the two sterols. 2H/1H fractionation in dinosterol was possibly influenced by nutrient-limited growth or light limitation at greater depths at both stations, while 2H/1H fractionation in brassicasterol matched values expected for nutrient-limited growth at both locations. Although systematic trends with depth in αlipid on the order of 10–30‰ were observed for each lipid, inter-day variability was some 3–7‰ depending on the lipid and site, and the magnitude of αlipid changes observed in the field were much less than those expected based on culture studies. This implies that the effects of nutrient and light limitation on natural phytoplankton populations in the ocean may not have a large influence on hydroclimate reconstructions based on 2H/1H ratios of microalgal lipids in marine sediments.Wood, D.A., 2019. Establishing credible reaction-kinetics distributions to fit and explain multi-heating rate S2 pyrolysis peaks of kerogens and shales. Advances in Geo-Energy Research 3, 1-28. reaction-kinetic distributions, in terms of activation energies (E) and pre-exponential factors (A), from the S2 peak data generated by pyrolysis tests conducted at three or more distinct heating ramps, is a well-established technique. These reaction-kinetics distributions are of paramount importance in establishing the timing and degree of petroleum generation from shales undergoing a range of burial and thermal histories. A commonly adopted approach is to determine and define reaction kinetics using a derivative of the Arrhenius equation configured in terms of a fixed/constant A value. Although the fixed-A approach can obtain good fits to multi-rate pyrolysis data, here it is shown that a formulation of the Arrhenius equation that involves reactions with a range of E and A values provides equally good fits to the multi-rate pyrolysis data. Moreover, the kinetic distributions with variable E-A provide more credible reaction kinetics consistent with those established for a range of kerogen types known for decades. To establish accurate fits to multi-rate pyrolysis S2 peak data at 1 ?C intervals from 250 ?C to 700 ?C an optimizer is applied to the preferred Arrhenius equation formulation to derive reaction increments and transformation fractions to a range of reaction kinetics (E-A pairs). The methodology applied involves two steps: Step 1 finds the single E-A pair that best matches the S2 peak temperatures (three or more for multi-rate pyrolysis data); step 2 uses the E-A pair from step 1 as its modal focus and fits the full S2 peak shape using a distribution of 11 distinct reaction. This approach can replicate the fixed-A approach but is best applied using reactions with variable E-A values. The results of applying this method to multi-rate pyrolysis data for ten published kerogens and shales show credible kinetic distributions spread along the established E-A trend for kerogen/shales.Wu, D., Liu, X., Liang, B., Sun, K., Xiao, X., 2018. Experiments on displacing methane in coal by injecting supercritical carbon dioxide. Energy & Fuels 32, 12766-12771. of carbon dioxide in coal seams can reduce the effect of carbon dioxide on human lives and enhance the production of methane. The phase of carbon dioxide changes into the supercritical state in deep coal seams. This study reports two experiments at different conditions. In the first experiment, the permeability of supercritical carbon dioxide in briquettes is recorded, and in the second experiment, experiments of displacing methane by supercritical carbon dioxide are performed to better understand the displacement of methane by carbon dioxide. The experimental results show the exponential relation between the permeability and volume stresses. The amount of methane displaced by supercritical carbon dioxide is recorded with respect to volume stresses and temperatures. Sweep efficiency and displaced volume are used to estimate the production of methane.Wu, G., Ji, H., Tian, L., Chen, D., 2018. Effects of salt ions on the methane hydrate formation and dissociation in the clay pore water and bulk water. Energy & Fuels 32, 12486-12494. hydrates in marine sediments are promising energy resources, while an effective recovery of methane from clay pores relies on a comprehensive appreciation of the hydrate evolution inside and outside the pore especially at a saline environment. Molecular dynamics simulations were conducted to investigate the methane hydrate formation and dissociation in the sodium montmorillonite (Na-MMT) interlayer with fresh water and saline water, respectively, by characterizing the distribution and transportation of methane and ions (K+, Na+, and Ca2+), the overall and local four-body structural order parameter, and the radial distribution functions. Results indicated that it was much easier to form methane hydrates in the bulk water than in the pore water, while the hydrates in the pore region were more readily dissociated than in the bulk region. The effects of salt ions on the hydrate formation were opposite in these two regions, which highlighted the role of the salting-out effect and the ion exchange between bulk water and pore water on the hydrate formation dynamics. It also demonstrated the priority for the hydrate dissociation from the contact area between MMT edge and bulk water because this region is more favorable for the distribution of salt ions and is more susceptible to be perturbed by the diffusion of salt ions from the pore water. Overall results provided theoretical supports for better understanding the microscopic mechanisms for the methane hydrate evolution at the heterogeneous environment with salt ions.Wu, L., Lu, Y., Jiang, S., Liu, X., Liu, Z., Lu, Y., 2019. Relationship between the origin of organic-rich shale and geological events of the Upper Ordovician-Lower Silurian in the Upper Yangtze area. Marine and Petroleum Geology 102, 74-85. on detailed sedimentological observations and geochemical analyses, four geological events have been identified, and a genetic depositional model has been established within a sequence stratigraphic framework. The organic-rich siliceous shale interbedded with dense bentonite layers in the transgressive systems tract 1 (TST 1) is attributed to the first stage of high-frequency volcanism (which started at ～447.62?Ma) associated with the collision of the Cathaysia and Yangtze Blocks. The presence of the organic-fair lime mudstone/shelly limestone indicates that Hirnantian Glaciation in the highstand systems tract (HST). The occurrence of organic-rich siliceous shale interbedded with scarce bentonite layers in the transgressive systems tract 2 (TST 2) is attributable to the second stage of low-frequency volcanism (which started at ～443.83?Ma) and to postglacial effects. The formation of organic-fair mixed shale with silty laminae is attributed to bottom-current activity in the early highstand systems tract (EHST). The occurrence of organic-poor clay-rich shale is due to terrigenous input in the late highstand systems tract (LHST). Our research also shows that the high marine productivity caused by volcanic ash and a high burial rate in an anoxic depositional setting led to organic matter and siliceous mineral enrichment in the TST 1 and TST 2. The favorable organic matter preservation conditions and the postglacial biotic recovery played significant roles in the formation of the organic-rich shale in the TST 2.Wu, S., Zhao, Y., Chen, Y., Dong, X., Wang, M., Wang, G., 2019. Sulfur cycling in freshwater sediments: A cryptic driving force of iron deposition and phosphorus mobilization. Science of The Total Environment 657, 1294-1303. cycling in freshwater ecosystems has been previously considered minor, and the direct evidence of its impacts on iron and phosphorus cycles in freshwater sediments remains unclear. In this study, mesocosms with amended acetate and various sulfate concentrations (1.5–3.0?mmol?L?1) were set up to investigate sulfur cycling and its influences on iron-rich freshwater sediments. Acetate addition induced hypoxia and provided substrates, which stimulated the sulfur cycling with evidence of SO42? decline, ΣS2?, S0 increase and corresponding variations of sulfate-reducing bacteria (SRB) and sulfur-oxidizing bacteria. Meanwhile, the growth of iron-reducing bacteria (IRB) was suppressed, and lower Fe(II) release was correspondingly related to larger SRB abundance at higher sulfate level, indicating that microbial iron reduction might be blocked by SRB activities. However, continuous dissolution of Fe(III) oxides and generation of iron sulfides were observed, suggesting that sulfide-mediated chemical iron reduction (SCIR) became the dominant iron-reducing pathway, and Fe(II) was buried as iron sulfides instead of released to water column, which resulted in a transition of iron cycling into unidirectional SCIR. Consequently, continuous dissolution of Fe(III) oxides led to significant increase of PO43? concentration in the water column and sediment pore-water, revealing the phosphorus mobility in sediments derived from the SCIR process. To note, sustained accumulation of iron sulfides was observed even without ΣS2? presence, suggesting that ΣS2? precipitation occurred prior to diffusion. Thus, ΣS2?-missing sulfur cycling seemed “cryptic” in this study. To highlight, the transition of the iron-reducing pathway and resulting PO43? release can be induced even under current sulfate level of Lake Taihu, and elevated sulfate levels could significantly intensify SCIR and phosphorus mineralization. Thus, the stimulated iron deposition and the resulting phosphorus release derived from the sulfur cycling should be paid more attention to in the treatment of eutrophic freshwater ecosystems.Wu, W., Zhang, D., Chen, K., Zhou, P., Zhao, M., Qiao, L., Su, B., 2018. Highly efficient desalting by silica isoporous membrane-based microfluidic chip for electrospray ionization mass spectrometry. Analytical Chemistry 90, 14395-14401. buffers and inorganic salts used for isolation and stabilization of biological samples are essential to be cleaned up prior to mass spectrometry (MS) analysis because of their deleterious effects such as ion suppression and instrumental pollution. In this work, a centimeter-scale continuous silica isoporous membrane (SIM) was prepared and integrated into a facile microfluidic chip for the desalting of protein samples based on dialysis principle. Thanks to the uniform pore size (～2.3 nm in diameter), ultrasmall thickness (90 nm) and high pore density (4.0 × 1012 pores cm–2, corresponding to a porosity of 16.7%) of SIM, the device achieved ～99% desalting efficiency for the sample with 154 mM NaCl (isotonic saline) at a flow rate of 1 μL min–1, while protein loss was only 5%. High-quality electrospray ionization (ESI)-MS spectra of cytochrome c dissolved in isotonic saline was obtained after the desalting treatment. In addition, the SIM-based microfluidic device was successfully online-coupled with microchip ESI-MS for real-time desalting and characterization of proteins.Wünsch, U.J., Acar, E., Koch, B.P., Murphy, K.R., Schmitt-Kopplin, P., Stedmon, C.A., 2018. The molecular fingerprint of fluorescent natural organic matter offers insight into biogeochemical sources and diagenetic state. Analytical Chemistry 90, 14188-14197. the biogeochemistry of dissolved organic matter (DOM) requires the synthesis of data from several complementary analytical techniques. The traditional approach to data synthesis is to search for correlations between measurements made on the same sample using different instruments. In contrast, data fusion simultaneously decomposes data from multiple instruments into the underlying shared and unshared components. Here, Advanced Coupled Matrix and Tensor Factorization (ACMTF) was used to identify the molecular fingerprint of DOM fluorescence fractions in Arctic fjords. ACMTF explained 99.84% of the variability with six fully shared components. Individual molecular formulas were linked to multiple fluorescence components and vice versa. Molecular fingerprints differed in diversity and oceanographic patterns, suggesting a link to the biogeochemical sources and diagenetic state of DOM. The fingerprints obtained through ACMTF were more specific compared to traditional correlation analysis and yielded greater compositional insight. Multivariate data fusion aligns extremely complex, heterogeneous DOM data sets and thus facilitates a more holistic understanding of DOM biogeochemistry.Xia, L., Cao, J., Hu, S., Li, S., Shi, C., 2019. Organic geochemistry, petrology, and conventional and unconventional hydrocarbon resource potential of Paleogene saline source rocks in eastern China: The Biyang Sag of the Nanxiang Basin. Marine and Petroleum Geology 101, 343-354. containing Paleogene organic-rich shales formed in a saline lacustrine environment are widespread in eastern China, and they provide sources of hydrocarbons in numerous petroleum fields. However, research on these basins has been patchy, which limits our understanding of the hydrocarbon source rocks. To address this problem, we selected the relatively understudied Nanxiang Basin as the study area and, more specifically, the third member of the Paleogene Hetaoyuan Formation (Eh3), which is the main hydrocarbon-generating layer in the Biyang Sag of this basin. In this paper, we report on the organic petrology and geochemistry of Eh3, and further analyze both its conventional and unconventional hydrocarbon potential. Our results show that the organic matter (OM) within the shales of Eh3 had bioprecursors that were mainly phytoplankton, bacteria, and benthic algae, with relatively small contributions from animal and higher plant materials. The shales have an average OM abundance (total organic carbon, or TOC) of 2.96?wt%, thus meeting the criterion of a good-quality source rock. Their organic-matter is mainly type I to type II, and in terms of thermal maturity they range from low maturity to mature, thus displaying the characteristics required to generate oil. The results of our molecular geochemical analyses show that the sediments of Eh3 in the Biyang Sag belong predominantly to deep or semi-deep lake facies, and they were deposited in a reducing environment and may have been affected by a marine incursion. The evidence for this includes Pr/Ph values of <1.0, samples falling in the marine and salt lacustrine regions on the Pr/nC17–Ph/nC18 diagram and values of C26/C25 for the tricyclic terpanes that are <1.3, thereby indicating the influence of sea water. Eh3 in the Biyang Sag has good potential to be a conventional and unconventional petroleum resource, particularly at the depocenter of the sag. Vertically, the third submember of Eh3 (Eh33) is proven to be the most favorable conventional petroleum resource, whereas the second submember (Eh32) is the most favorable unconventional petroleum resource. Therefore, the saline lacustrine sequences are good for both conventional and unconventional petroleum resources.Xia, L., Liu, L., Dou, Y., Guo, L., Li, G., Sun, Z., You, J., 2018. A stable mesoporous metal-organic framework as highly efficient sorbent of dispersive micro solid-phase extraction for the determination of polycyclic aromatic hydrocarbons by HPLC. Journal of Separation Science 41, 4331-4339. to the large molecular sizes of polycyclic aromatic hydrocarbons, their adsorption using microporous sorbents leads to a low adsorption capacity. Here, to increase the extraction capacity and detection sensitivity of polycyclic aromatic hydrocarbons, a highly efficient dispersive micro solid‐phase extraction method was developed based on a stable mesoporous metal‐organic framework named Jilin University China 48. Jilin University China 48 is a super hybrid with large one‐dimensional hexagonal nanotube‐like channels of 24.5 × 27.9 ?, which exhibits high potential to be an efficient sorbent of dispersive micro solid‐phase extraction to adsorb polycyclic aromatic hydrocarbons. By combining with high‐performance liquid chromatography, a sensitive method was developed for the determination of seven polycyclic aromatic hydrocarbons. The synthesized Jilin University China 48 exhibited excellent characteristics of stability, good morphology, large surface area, and open adsorption sites. Under the optimized extraction conditions, better extraction results were obtained than that of other methods reported previously. The proposed method exhibited high sensitivity with the limit of detections in the range of 0.021–0.13 ng/mL, good linearity in the range of 0.068–50 ng/mL with related coefficients of >0.9988, satisfactory precision with relative standard deviation of <4.3%, and adequate recoveries between 85.8 to 109.55% for all the target compounds.Xiang, Z., Chen, X., Zhao, Z., Xiao, X., Guo, P., Song, H., Yang, X., Huang, M., 2018. Analysis of volatile components in Dalbergia cochinchinensis Pierre by a comprehensive two-dimensional gas chromatography with mass spectrometry method using a solid-state modulator. Journal of Separation Science 41, 4315-4322. components in Dalbergia cochinchinensis Pierre were analysed using a comprehensive two‐dimensional gas chromatography with mass spectrometry method featuring a new solid‐state modulator. Compared to one‐dimensional gas chromatography, the number of detected peaks were significantly increased. A total of 45 major compounds were identified in this study and the forward and reverse match factors of these compounds were both above 800. The results showed that the volatile components in Dalbergia cochinchinensis Pierre were primarily aldehyde and ketone compounds such as benzaldehyde, cinnamaldehyde, 4‐chromanone, 1‐(2‐hydroxyphenyl)ethanone and acetophenone. In addition, a semi‐quantitative analysis was conducted to determine the contents of the detected compounds based on peak area percentage. Moreover, the repeatability of the comprehensive two‐dimensional gas chromatography‐mass spectrometry analysis in this study was quite satisfactory with relative standard deviations less than 12.7% for intraday and 17.3% for interday measurements.Xie, Y., Zhang, G., Shen, P., Liu, L., Huang, S., Chen, S., Yang, S., 2018. Formation conditions and exploration direction of large gas field in Bozhong sag of Bohai Bay Basin. Acta Petrolei Sinica 39, 1199-1210. sag is not only the most oil-abundant but also the most gas-abundant sag in Bohai Bay Basin, which lies in the middle of Bohai region with an area of nearly 9 000 km2 and a thickness of Cenozoic strata more than 10 km. It is the largest and thickest sag in Bohai Bay Basin. Bozhong sag experienced two stages, i.e., Paleogene fault depression and Neogene regional depression. During the stage of Paleogene fault depression, a bi-extension occurred to form a pattern of "four subsag with one uplift". The fault depression experienced an evolutionary process from several separated subsags into a whole. Continuous sedimentation led to the formation of Paleogene and Neogene-Quaternary "double-thickness" structure during the depression stage. There are three sets of source rock layers in Bozhong sag, i.e., Members 1 and 3 of Shahejie Formation and Member 3 of Dongying Formation (Sha 1, Sha 3 and Dong 3). High-quality source rocks are mainly developed in the middle and upper part of Sha 3, and the lower part of Sha 1 and Dong 3. Since the overlying layers are ultra-thick, there occurred the high evolution of source rocks. Based on statistical research, this study has established the hydrocarbon generation and expulsion models for different layers of source rock in Bozhong sag. As viewed from the predicted results, the source rock in Bozhong sag has large oil and gas discharge of 512.5×108m3 and 311.64×1011m3, respectively. Reservoirs of Kongdian Formation and buried hill in Bozhong sag present good hydrocarbon source conditions and locate in the near-source zone. The regional caprock of deep reservoir is the thick mudstone in Dongying Formation with a high degree of diagenesis and a strong blocking ability. The buried hill formations are characterized by old age, hard lithology, multiple tectonic movements, fissure development, strong corrosion, favorable property and high yield. The glutenite in Kongdian Formation has a strong anti-compaction property. Large groups of deep traps are developed, showing great prospects for exploration. Thus, deep reservoirs in Bozhong sag have the conditions to form large gas field, which are favorable areas for the discovery of large gas fields.Xu, H., George, S.C., Hou, D., 2019. The occurrence of isorenieratane and 24-n-propylcholestanes in Paleogene lacustrine source rocks from the Dongying Depression, Bohai Bay Basin: Implications for bacterial sulfate reduction, photic zone euxinia and seawater incursions. Organic Geochemistry 127, 59-80. organic-rich source rocks (shales and mudstones) were examined to assess the depositional environment and organic input sources of the third and fourth members of the Eocene Shahejie Formation, Bohai Bay Basin, China. Major organic contributions to the Shahejie Formation from dinoflagellates, diatoms, Botryococcus and marine pelagophyte/chrysophyte algae were determined using n-alkane distributions, gammacerane index and diagnostic steranes. Traces of higher plant biomarkers suggest that terrigenous organic inputs were limited. The pervasive presence of β-carotane, aryl isoprenoids, paleorenieratane, renieratane, isorenieratane, 2α-methylhopanes and crocetane indicate significant organic contributions from bacterial communities including cyanobacteria, purple sulfur bacteria (Chromatiaceae), green sulfur bacteria (Chlorobiaceae), and sulfate-reducing bacteria. The extent of H2S content, bacterial sulfate reduction, and photic zone euxinia (PZE) were evaluated by determining the aryl isoprenoids ratio (AIR: 0.7–9.0), the presence of isorenieratene derivatives, and the fate of sulfur in the water column. There was a decrease of PZE extent and duration from the northeast to the southwest of the palaeo-lake, and there was a decrease of water body salinity and bottom water anoxia from the fourth to the third member of the Shahejie Formation. Abrupt environmental perturbations in the third member of the Shahejie Formation are indicated not only by significant changes in parameters such as the pristane/phytane and β-carotane/n-C20 alkane ratios, the gammacerane index, the isorenieratane/C18 aryl isoprenoid, and the AIR, but also by the time lag in the expansion of cyanobacterial lineages after the expansion of purple/green sulfur bacteria, as well as seawater incursions. The unexpected occurrence of intact C30 4-desmethylsteranes (24-n-propylcholestanes) in the Shahejie Formation is first reported here, after very careful checking, and provides unambiguous biological evidence for at least two marine transgression events reaching the Eocene Dongying palaeo-lake. The organic enrichment of the petroleum source rocks in the Shahejie Formation is a consequence of combined indigenous lacustrine algal production, the constrained and favourable preservation conditions, and significant bacterial contributions and marine organic matter inputs to the lake.Xu, H., Zhou, W., Zhang, R., Liu, S., Zhou, Q., 2019. Characterizations of pore, mineral and petrographic properties of marine shale using multiple techniques and their implications on gas storage capability for Sichuan Longmaxi gas shale field in China. Fuel 241, 360-371., mineral and petrographic properties of shale conjunctionally determine the gas storage and transport properties of gas shale reservoirs. To investigate how these characteristics and pore structure influence the methane adsorption capability of shale formation, a total of forty-nine over-matured shale outcrop samples, thirty samples from Upper Longmaxi Formation and nineteen samples from Lower Longmaxi Formation from southern Sichuan Basin in China, were collected. Multiple techniques, including geochemical and mineralogical measurements, field emission-scanning electron microscopy (FE-SEM), mercury intrusion porosimetry (MIP), low-pressure CO2 and N2 adsorption and high-pressure methane adsorption, were employed to characterize the geo-properties, pore structure and their impacts on methane adsorption capacity under different temperatures. Geochemical and mineralogical results show that both Upper and Lower Longmaxi shales are over-matured which have oil-prone type I kerogen. Based on the FE-SEM observation, most of the organic matter (OM) pores in the tested Longmaxi shales are spongy OM pores due to the over-maturity stage with Ro between 2.36% and 3.15%. In general, Lower Longmaxi shales are rich in micropores with larger pore volume and specific surface area (SSA) compared to those of the Upper ones. A combination of CO2/N2 adsorption and MIP analyses on the pore structure show a whole-aperture pore size distribution (PSD) ranging from 0.4?nm to 10?μm. The methane adsorption capacity increases with increasing TOC for Lower and Upper Longmaxi shales, respectively, while increases with increasing SSA for combined Lower and Upper ones. It is noted that, the numerous OM pores in Lower Longmaxi shale are the primary contribution to a better pore network and greater methane adsorption capacities compared to that of the Upper Longmaxi shale, but it all depends on the surface area. Shale samples with higher surface area have higher methane adsorption capacity no matter which Longmaxi shale Formations. In addition, temperature has an apparently negative effect on methane adsorption capacity for both Upper and Lower Longmaxi shales, where temperature is more sensitive to the shale sample with higher TOC content.Xu, J., Li, X., Shi, Z., Li, R., Li, Q., 2018. Bacterial carbon cycling in the river plume in the northern South China Sea during summer. Journal of Geophysical Research: Oceans 123, 8106-8121.: Heterotrophic bacterioplankton play a significant role in carbon cycle in oceans. It is crucial to identify regulators of bacterial carbon processing across marine environments. In summer 2016, a cruise was conducted to examine the links between bacterial metabolic rates and community composition, and potential mechanisms regulating bacterial growth efficiency in the plume‐impacted coastal area. Our results showed that the two aspects of bacterial metabolism responded differently. Bacterial production (3.69 to 57.1 μg C·L?1·day?1) at the surface increased by 40% to 21‐fold in response to the freshwater input. The enhanced bacterial production was attributed to an increase in bacterial abundance and cell‐specific bacterial production, which was linked to shifts in bacterial community composition and changing partition between anabolic and catabolic pathways. Bacterial groups that grew fast and preferred high molecular weight dissolved organic carbon were responsible for the increase in bacterial production. However, bacterial respiration increased (less than fourfold) to lesser extent than bacterial production. Consequently, bacterial growth efficiency increased dramatically (up to sevenfold) in response to the plume input. Bacterial respiration was primarily dependent on environmental conditions rather than bacterial community composition. The increased phytoplankton biomass modulated bacterial respiration in two contrasting ways likely by providing phytoplankton‐derived dissolved organic carbon, which not only improved bacterial abundance but also lowered cell‐specific bacterial respiration because of mitigating energy limitation. Our findings elucidated bacterial carbon processing in the plume‐impacted coastal waters and highlighted the potential role of bacterial community composition in regulating carbon cycling in oceans.Plain Language Summary: Heterotrophic bacterioplankton play a significant role in carbon cycle in oceans. The two aspects of bacterial metabolism responded differently to the river plume. Bacterial production increased by 40% to 21‐fold, in response to the river plume. The enhanced bacterial production was attributed to an increase in bacterial abundance and cell‐specific bacterial production, which was linked to shifts in bacterial community composition and changing partition between anabolic and catabolic pathways. Bacterial group that grew fast and preferred high molecular weight dissolved organic carbon (DOC) was responsible for the increase in bacterial production. However, bacterial respiration increased (less than fourfold) to lesser extent than bacterial production. Consequently, bacterial growth efficiency increased dramatically (up to sevenfold) in response to the plume input. Bacterial respiration was primarily dependent on environmental conditions rather than shifts in bacterial community composition. The increased phytoplankton biomass modulated bacterial respiration in two contrasting ways likely by providing phytoplankton‐derived DOC, which not only improved bacterial abundance but also lowered cell‐specific bacterial respiration because of mitigating energy limitation. Our findings elucidated bacterial carbon processing in the plume‐impacted coastal waters and highlighted the potential role of bacterial community composition in regulating carbon cycling in oceans.Xu, X., Liu, W., Tian, S., Wang, W., Qi, Q., Jiang, P., Gao, X., Li, F., Li, H., Yu, H., 2018. Petroleum hydrocarbon-degrading bacteria for the remediation of oil pollution under aerobic conditions: A perspective analysis. Frontiers in Microbiology 9, 2885. doi: 10.3389/fmicb.2018.02885. the sharp increase in population and modernization of society, environmental pollution resulting from petroleum hydrocarbons has increased, resulting in an urgent need for remediation. Petroleum hydrocarbon-degrading bacteria are ubiquitous in nature and can utilize these compounds as sources of carbon and energy. Bacteria displaying such capabilities are often exploited for the bioremediation of petroleum oil-contaminated environments. Recently, microbial remediation technology has developed rapidly and achieved major gains. However, this technology is not omnipotent. It is affected by many environmental factors that hinder its practical application, limiting the large-scale application of the technology. This paper provides an overview of the recent literature referring to the usage of bacteria as biodegraders, discusses barriers regarding the implementation of this microbial technology, and provides suggestions for further developments.Xu, Y., Liu, T., Zhu, X., Ji, G., 2019. Quantitative analysis of genetic associations in the biodegradative pathway of PAHs in wetland sediments of the Bohai coast region. Chemosphere 218, 282-291. present study characterized the distribution and sources of polycyclic aromatic hydrocarbons (PAHs) in 57 sediment cores collected from estuary and tidal flat wetlands in the Bohai coast region and investigated the molecular degradation mechanism of PAHs. The results showed that the PAH concentrations in estuary sediments were significantly higher than in tidal flat sediments. PAH patterns and pollutant sources were more complicated in estuary sediments. Quantitative response relationships showed that in estuary sediments, the key factors affecting PAH degradation changed from initial dioxygenase genes and C23O to salicylate hydroxylase genes and C23O with an increase in the PAH ring number. In contrast, for tidal flat sediments, the initial dioxygenase genes remained the key factors (nidA and nahAc/nagAc, except only nidA for 5-ring PAHs) related to PAHs with different ring numbers. Non-metric multidimensional scaling (NMDS) analysis revealed that the lower catechol dioxygenase pathway coupled with the upper pyrene dioxygenase pathway. The total polycyclic aromatic hydrocarbon (TPAH) level across the Bohai coast region was most affected by catechol dioxygenation (catA?+?C23O). Catechol dioxygenation was directly affected by naphthalene dioxygenation/nahG ((nahAc?+?nagAc)/nahG), indicating that the interaction within the upper pathway coupled with the lower pathway. In addition, TOC had direct positive effects on catechol dioxygenation and nidA. This study improves our understanding of the biodegradative pathway of PAHs with different ring numbers and the response of PAHs to biotic and abiotic factors.Xue, W., Zhu, W., Li, H., Song, Z., 2018. Pore-scale mechanisms of the synergistic effects between microbial cultures and chemical surfactants on oil recovery. Energy & Fuels 32, 12319-12327. significant synergistic effect has been reported between microbial cultures and chemical surfactants in crude oil recovery processes. A number of attempts have been made to understand the synergistic mechanism. However, the existing studies only addressed the aspects of wettability alteration and interfacial tension (IFT) reduction, although there are many more contributors to the mechanism, such as emulsification, functional microbial activities, and diverse byproducts. In addition, the previous knowledge on synergistic oil recovery was based on indirect evidence from core-scale flooding and test tube experiments. To fully exploit the synergistic effects in the future, a new experimental system must be introduced (i) to verify the existing mechanisms in situ in porous media during the flooding process and (ii) to address the other potential contributors for a more comprehensive insight into the actual major contributors. Therefore, a visual pore-scale flooding experimental system was introduced in the present study to mimic the pore networks and conditions of a reservoir (55 °C, 10 MPa). This system enabled direct observations of fluid dynamics in pores during flooding. The final oil recovery using indigenous microorganisms (8.3%) and an anionic surfactant [sodium alcohol ether sulphate (AES)] (15.5%) was considerably enhanced (22.4%) when the two solutions were equally mixed, which indicated significant synergistic effects between them, whereas no such effects were observed with a nonionic surfactant [polyoxyethylene nonylphenol ether (OP10)]. The pore-scale and macroscale analyses were combined to reveal the synergistic mechanisms between the microbial culture and AES. The results show that the IFT reduction and wettability alteration, traditionally considered to be synergistic mechanisms, contributed to the oil recovery but were not the major contributors to the synergistic effects. In this case, the synergistic mechanisms include the following aspects: the anionic surfactant promotes microbial metabolism, such as biogas production (significantly enhanced from 0.0018 mL/mL medium to 0.0196 mL/mL medium), and the microbial culture, in turn, reduces the critical micelle concentration of the surfactant and enhances the emulsion effectiveness, including reducing the oil droplet sizes (from D90 = 217 to 116 μm) and increasing the stability of the emulsion system from several minutes to a few days. The two synergistic mechanisms reflect the mutually positive effects between the chemical surfactant and the microbial system; these mutual effects are especially essential for long-term and long-distance oil migration and final recovery in a real reservoir-scale flooding process.Yan, B., Zhu, X., He, X., Tang, S., 2019. Zn isotopic evolution in early Ediacaran ocean: A global signature. Precambrian Research 320, 472-483. Zn isotope composition of sedimentary archives reveals key biosphere–lithosphere interactions throughout geologic history. A recent Zn isotope study of Ediacaran cap carbonates from South Australia revealed that the local isotopic profile reflects global changes in oceanic chemistry. To examine this critical assumption, this study investigates a high-resolution zinc isotope profile of Marinoan post-glacial cap carbonates from the Yangtze Platform, South China. Stratigraphic variations in Zn isotope data from this study are similar to previously reported sections in South Australia and South China. The remarkable isotopic similarity between the two sections that were deposited on distant, geographically separated continental blocks demonstrates that the Zn isotopic variations reflect changing global signatures of the early Ediacaran ocean. This study highlights the value of Zn isotopes in sediments as a global proxy for paleoceanographic studies.We interpret the systematic stratigraphic changes in the Zn isotope composition of the studied post-glacial Marinoan carbonates as a global oceanic trend controlled mainly by varying inputs and outputs of Zn to the ocean. Decreasing δ66Zn values in the lowermost part of the section are attributed to the global precipitation of carbonate enriched in the heavier Zn isotope. A positive shift in the middle part of the section is explained by the non-quantitative removal of isotopically lighter Zn by sulfide minerals. Lower δ66Zn values in the uppermost part likely reflect the changing contributions of continental weathering and sulfide precipitation. Our data suggest that non-quantitative removal of Zn by sulfides is a previously unrecognized sink for zinc in the oceans.Yan, J., Jiao, H., Li, Z., Lei, Z., Wang, Z., Ren, S., Shui, H., Kang, S., Yan, H., Pan, C., 2019. Kinetic analysis and modeling of coal pyrolysis with model-free methods. Fuel 241, 382-391. about the rate of coal pyrolysis is of great importance because it exerts remarkable effect on its thermal conversions such as combustion, gasification and liquefaction. Different approaches can be used to obtain the kinetics of coal pyrolysis, the simplest are empirical and global kinetics, where Arrhenius expression is used to correlate the mass loss with temperature. This work conducted pyrolysis of a lignite and a bituminite at various heating rates with a thermo-gravimetric analyzer (TGA). Thermogravimetry coupled with mass spectroscopy (TG-MS), solid state 13C Cross Polarization/ Magic Angle Spinning nuclear magnetic resonance (13C CP/MAS NMR) and Raman analyses were also conducted to correlate the structural characteristics and pyrolysis behavior of the coals. Kinetic analysis was performed by using three model-free methods including Distributed Activation Energy model (DAEM), Ozawa-Flynn-Wall (OFW) and Friedman method. Kinetic modeling was also performed based on the DAEM model with multiple Gaussian sub-distributions of activation energy. The results show that DAEM, OFW and Friedman methods are almost equally effective for analyzing activation energy, which gradually increases with the extent of pyrolysis. Pyrolysis of both the coals can be divided into three stages corresponding to the reactions of various covalent bonds. Three-Gaussian distributed activation energy model (DAEM-G3) is applicable to describing pyrolysis of both coals. The well-matched modeling results with the experimental data over the entire temperature range indicate the validity of DAEM-G3 model in studying and understanding the reaction mechanism of coal pyrolysis.Yan, J., Manelski, R., Vasilas, B., Jin, Y., 2018. Mobile colloidal organic carbon: An underestimated carbon pool in global carbon cycles? Frontiers in Environmental Science 6, 148. doi: 10.3389/fenvs.2018.00148. colloids, 1–1,000 nm particles, are ubiquitous in every ecosystem. They have small size, large specific surface area, and high mobility in the subsurface, and thus can regulate the fate and transport of sorbing constituents such as nutrients, contaminants, and organic carbon (OC). The movement of colloids and colloidal OC (COC) through soils is an important process in mass and energy transport (including carbon) both within and between ecosystems, e.g., from terrestrial to aquatic ecosystems, and likely contribute to the ecosystem- or global-scale carbon balance given their ubiquitous distribution and unique environmental functions. However, despite their importance for terrestrial and aquatic carbon transport and balance, colloids, and COC have not been adequately accounted for because of the current operational definition uses 0.45 μm as the cutoff size for colloids. In this study, we quantified and characterized loadings of colloids and COC in aqueous samples collected from agricultural, forestry, freshwater wetland, and estuary ecosystems. Results reveal that, in all samples regardless of sampling sources, the total colloidal loads were underestimated by ≥50% and considered as “dissolved” solutes when the (cutoff size of 0.45 μm) was used. Together with a large number of data from the literature, our results further demonstrate that colloids are quantitatively substantial, carbon-dense and that as much as 8–19% of operationally defined DOC is in fact COC. Conservatively, this suggests that COC potentially accounts for 13.6 TgC year?1 as a riverine flux and 530 ± 25 TgC of global DOC pool in the ocean in global carbon cycles. In addition, freshwater wetland was found to be a hotspot, which released more colloids and COC compared to the other sampled ecosystems. These findings clearly demonstrate the limitations of using the operational definition for colloids and DOC and highlight the need for improving quantification and characterization of size-dependent colloidal and OC loads. Such effort will allow direct fundamental research into questions toward microbial access to “protected” carbon by minerals and more accurate assessment of global carbon cycles.Yang, J., Jeppe, K., Pettigrove, V., Zhang, X., 2018. Environmental DNA metabarcoding supporting community assessment of environmental stressors in a field-based sediment microcosm study. Environmental Science & Technology 52, 14469-14479. ecological risk assessment on toxic stressors in sediment is limited to a small and selected fraction of benthic communities. Ecogenomic approaches provide unprecedented capacity to monitor the changes of biodiversity and community composition in the field, but how to utilize it to assess ecological impact by contaminates remains largely unexplored. Here, an environmental DNA (eDNA) metabarcoding approach was used to assess the effect of copper on changes in biodiversity and community composition across the tree of life (including bacteria, protists, algae, fungi, and metazoa) in a field-based microcosm. Many microorganisms across a broad range of taxa groups changed their relative abundance in response to increased copper concentrations in sediments. Changes in community structure of microbiota appeared to be more sensitive to copper than survival of laboratory-bred organisms and indigenous macroinvertebrates. Copper caused a significant shift in prokaryotic community composition via substitution of dominant species. Network heterogeneity and Shannon diversity of the bacterial community decreased in the high copper treatments. eDNA metabarcoding assessed the effects of copper-contaminated sediment with less effort than manually processing samples. Our study highlighted the value of community profiling by an eDNA-based approach in prospective and retrospective risk assessment of environmental stressors.Yang, R., He, S., Hu, Q., Zhai, G., Yi, J., Zhang, L., 2018. Comparative investigations on wettability of typical marine, continental, and transitional shales in the Middle Yangtze Platform (China). Energy & Fuels 32, 12187-12197. is a physico-chemical rock property that plays a crucial role in the efficient development of shale gas and oil. However, a precise characterization of wettability for shale reservoirs is still a challenging task because of their complex pore structure (with a large proportion of pores in nm scale) and shale composition (variable at μm scale). In this work, we conducted the fluid drop wettability test, air–liquid contact angle measurement, and spontaneous imbibition (SI) with two fluids [deionized (DI) water and n-decane (an oil phase)] to evaluate the wettability of typical organic-rich shales (marine Longmaxi, continental Dongyuemiao, and transitional Dalong and Longtan shales), as influenced by total organic carbon (TOC), thermal maturity, mineral composition, effective porosity, and pore size distribution. Marine Longmaxi shales have strong or moderately strong water-wet properties with measured DI water contact angles of 3.4°–16.5°. In contrast, continental Dongyuemiao and transitional Dalong–Longtan shales show a much stronger water-repellant property with contact angles in the ranges of 21.2°–46.4° and 57.8°–61.7°, respectively. N-decane spreads quickly on the flat sample surfaces to generate zero contact angles, indicating that all these shales are strongly oil-wet. This is consistent with the much larger imbibition slopes of n-decane in the plot of log dimensionless weight (WD) versus log dimensionless time (tD) than DI water. Shale samples with the higher TOC content, higher quartz content, and lower clay content have a stronger water-repellant property in marine Longmaxi and continental Dongyuemiao shales. In contrast, relationships between DI water contact angles and quartz content and clay content are not obvious in transitional shales. With thermal maturities increasing from mature to high-mature and overmature, wetting affinity to DI water tends to alter, which needs more comprehensive investigations in the future. Effective porosity has a positive effect on DI water contact angles for argillaceous limestones in continental Dongyuemaio, siliceous shales in marine Longmaxi, and transitional shales, whereas it has a negative effect in the silty shales from continental Dongyuemiao and argillaceous siliceous shales from marine Longmaxi.Yang, W., Casey, J.F., Gao, Y., Li, J., 2019. A new method of geochemical allocation and monitoring of commingled crude oil production using trace and ultra-trace multi-element analyses. Fuel 241, 347-359. allocation refers to the practice of quantifying proportions of extracted commingled hydrocarbons across various contributing sources. In this paper we tested a new geochemical technique of trace element production allocation by analyzing the mass fractions of specific target elements in five end-member natural crude oils and the manually mixed crude oil in precisely controlled proportions. We analyzed target elements by ICP-OES and Triple Quadrupole (QQQ)-ICP-MS techniques in tandem on each sample. In our test, the contributing fractions of the five end-member oils were measured by weight and mixed in proportions of ～30%, 25%, 20%, 15%, and 10% in the commingled oil. The obtained mass fractions for specific target elements in both the five end-member oils and the commingled oil are input into a program developed called “ALLO-TRACE”. ALLO-TRACE calculates the contributing fractions of all the end-member oils to the commingled oil using multiple analyte-based linear equations. Our repeated tests have shown that the calculated contribution fractions based on the mass fractions of multiple trace elements agree well with their known contribution fractions in the commingled oil. Accuracies of most calculations for all the five end-member oil target proportions are within 4%, and the best can be less than 0.6% for all end members (average 0.17% and median 0.1%). Most calculation uncertainties in terms of relative standard deviations of the five end-member oils are within 3%, and the best can be less than 2.3% for all end members (average 1.2% and median 0.9%).Yang, Z., Jiang, B., McNamara, M.E., Kearns, S.L., Pittman, M., Kaye, T.G., Orr, P.J., Xu, X., Benton, M.J., 2019. Pterosaur integumentary structures with complex feather-like branching. Nature Ecology & Evolution 3, 24-30. were the first vertebrates to achieve true flapping flight, but in the absence of living representatives, many questions concerning their biology and lifestyle remain unresolved. Pycnofibres—the integumentary coverings of pterosaurs—are particularly enigmatic: although many reconstructions depict fur-like coverings composed of pycnofibres, their affinities and function are not fully understood. Here, we report the preservation in two anurognathid pterosaur specimens of morphologically diverse pycnofibres that show diagnostic features of feathers, including non-vaned grouped filaments and bilaterally branched filaments, hitherto considered unique to maniraptoran dinosaurs, and preserved melanosomes with diverse geometries. These findings could imply that feathers had deep evolutionary origins in ancestral archosaurs, or that these structures arose independently in pterosaurs. The presence of feather-like structures suggests that anurognathids, and potentially other pterosaurs, possessed a dense filamentous covering that probably functioned in thermoregulation, tactile sensing, signalling and aerodynamics.Yang, Z., Zou, C., Wu, S., Lin, S., Pan, S., Niu, X., Men, G., Tang, Z., Li, G., Zhao, J., Jia, X., 2019. Formation, distribution and resource potential of the "sweet areas (sections)" of continental shale oil in China. Marine and Petroleum Geology 102, 48-60. oil refers to oil stored in organic-rich shale. It is an important part of unconventional oil and provides a large amount of resources. Based on the systematic study of the geological characteristics of shale oil in China's major continental basins, the geological connotation of the “sweet area (section)” in shale oil is proposed in this paper, and it refers to areas (sections) that can be preferentially explored and developed in oil-bearing shale formations under current economic and technical conditions. The formation conditions and distribution characteristics of continental shale oil in China are analyzed with a focus on the geological properties of the Triassic Yanchang Formation in the Ordos Basin, the Cretaceous Qingshankou Formation in the Songliao Basin and the Permian Lucaogou Formation of the Jimusar Sag in the Junggar Basin. It is found that the “sweet areas” of shale oil with medium-high maturation are mainly located in thick shales with a Ro greater than 0.9%, and the “sweet sections” are mainly located in the middle and lower parts of the shale formation. The geological resources of continental shale oil in the major continental basins in China are estimated to be approximately 3700?×?108 tons. The in situ conversion process (ICP) may be a key technology for the effective development of medium-to low-mature shale oil. The scale, maximum burial depth and present depth of the organic-rich shale are proposed as the three key parameters for the optimization of pilot sites by taking the Triassic Yanchang Formation in the Ordos Basin as an example. Using ICP, it is expected that the recoverable resources of China's continental shale oil will be approximately (400–500)?×?108 tons. The terminology of "man-made reservoir" is proposed in this paper. In an "man-made reservoir", the overall industrial output of the "sweet areas (sections)" is formed by artificial intervention and the construction of an underground fracture network system with "man-made permeability". Continental shale oil may be another revolutionary source of unconventional oil and is expected to be first successfully produced in China.Yao, Y., Liu, J., Liu, D., Chen, J., Pan, Z., 2019. A new application of NMR in characterization of multiphase methane and adsorption capacity of shale. International Journal of Coal Geology 201, 76-85. and free methane are the primary contributor for gas production from shale. To accurately quantify the multiphase methane in shale is of great significance for shale gas exploration and exploitation. The conventional calculation methods to quantify the multiphase methane in shale are typically mathematical extrapolation from reservoir information, which tend to generate large error and is hard to be applied for shale reservoir because of its heterogeneity characteristics. Meanwhile, the most commonly used volumetric or manometric experimental methods are tedious, time-consuming and indirect measurement that requires assuming adsorbed phase density. Any volumetric effect or impurities can distort the shape of the isotherm measured with volumetric or manometric method. Therefore, it is necessary to explore a new quantitative method that can directly detect the multiphase methane in shale. In this study, several special experimental setups and methods were designed to evaluate the multiphase methane in shale. By introducing the low-field nuclear magnetic resonance (NMR) into the isothermal methane adsorption experiments of shale samples, this study developed a methodology for quantitative identification of multiphase methane gases in shale. Results show that the transverse relaxation time (T2) spectra of methane in shale contain four distinctive peaks, among which the peak (P1) with shortest T2 (<~1?ms) represents adsorbed methane and the one (P2) with longer T2 (~ 1–50?ms) symbolizes free methane in shale. The P2 increased linearly with methane pressure, whereas the P1 increased with increasing pressure to a very limited extent and reached a limiting value, similar to Langmuir equation. The provided method can directly measure the absolute and relative amounts of free and adsorbed methane gases in shale at a certain pressure, which is applicable to measure the in-situ gas content of the pressure coring shale samples, or alternatively, to theoretically estimate maximum adsorbed and free gas content when only the conventional core sample is available for analysis. This study also reports a newly developed technique that directly measures methane adsorption capacity and adsorption isotherm of shale, without the application of the equation of state for methane or volumetric corrections of any kind. The results show that the proposed method that is based on analysis of NMR relaxation time of methane in shale with respect to increasing pressure, is in excellent agreement with the conventional gravimetric method performed paralleled with the NMR method using the same experimental conditions. The developed theory and analytical technique to determine the multiphase methane and methane adsorption isotherm of shale provide an alternative method for in-situ gas content test and monitoring gas transport processes in shale such as desorption, diffusion and seepage.Yao, Y., Mao, F., Xiao, Y., Luo, J., 2019. Modeling capillary fringe effect on petroleum vapor intrusion from groundwater contamination. Water Research 150, 111-119. contaminated sites, indoor inhalation of volatile organic compounds from groundwater contamination, known as vapor intrusion (VI), is an important exposure pathway to determine groundwater cleanup level. Based on empirical analysis, US EPA concluded that there is a low probability for vapors from fuel hydrocarbons dissolved in groundwater to induce indoor concentrations that exceed risk-based standards, and recommended 6 feet vertical building-source separation distance as the risk screening tool for such cases. In this study, we examine this recommendation by performing numerical modeling to investigate the detailed effects of the capillary fringe on petroleum vapor biodegradation and attenuation. First, the numerical model is validated by comparison with laboratory data and field measurements in US EPA's database. Then the verified model is used to simulate two scenarios involving the capillary fringe effect, one with a groundwater source at various depth and the other with a soil gas source located above the groundwater level. For a groundwater contaminant source, the capillary fringe plays a significant role in VI by controlling the soil moisture content and oxygen availability, thus affecting the soil gas concentration biodegradation and attenuation. Specifically, the capillary fringe effect can significantly decrease the indoor air concentration by decreasing upward diffusion rates of hydrocarbon, increasing the thickness of the aerobic zone, and enhancing aerobic biodegradation. As a result, it is highly unlikely for sources located at groundwater level to induce unacceptable vapor intrusion risks, supporting US EPA's recommendation. Moreover, the simulations suggest that the vertical smear zone of residual light non-aqueous liquid contamination, induced by temporal fluctuations of groundwater level, may lead to a potential threat to indoor air quality for a short vertical source-building separation distance, and thus requires more attention. The sensitivity test of the numerical model also indicates that it is the vertical separation distance between building foundation and the top of the smear zone instead of the smear zone thickness that should be given more attention during the investigation.Yoshida, H., Hasegawa, H., Katsuta, N., Maruyama, I., Sirono, S., Minami, M., Asahara, Y., Nishimoto, S., Yamaguchi, Y., Ichinnorov, N., Metcalfe, R., 2018. Fe-oxide concretions formed by interacting carbonate and acidic waters on Earth and Mars. Science Advances 4, Article eaau0872. Fe-oxide concretions on Earth, especially in Utah, USA, have been investigated as an analog of hematite spherules found in Meridiani Planum on Mars to support interpretations of water-rock interactions in early Mars. Although several formation mechanisms have been proposed for the Fe-oxide concretions on Earth, it is still unclear whether these mechanisms are viable because a precise formation process and precursor of the concretions are missing. This paper presents evidence that Fe-oxide concretions in Utah and newly found Fe-oxide concretions in Mongolia had spherical calcite concretions as precursors. Different formation stages of calcite and Fe-oxide concretions observed, both in Utah and Mongolia, indicate that calcite concretions initially formed within eolian sandstone strata and were dissolved by infiltrating Fe-rich acidic waters to form spherical FeO(OH) crusts due to pH buffering. The similarity between these Fe-oxide concretions on Earth and the hematite spherule occurrences in Meridiani Planum, combined with evidence of acid sulfate water influences on Mars, suggest that the hematite spherules also formed from dissolution of preexisting carbonate spherules possibly formed under a dense carbon dioxide early martian atmosphere.Yoshino, K., Yamada, K., Kimura, K., 2018. Does suspended matter drained from the Isahaya freshwater reservoir cause organic enrichment in the northern Ariake Bay? Journal of Oceanography 74, 619-628. inner part of Isahaya Bay was converted to a freshwater reservoir following the closure of the land claim dike in 1997. Turbid water drains into Isahaya Bay when water levels increase. We investigated whether particulate organic matter (POM) from the reservoir in Isahaya Bay has caused bottom organic enrichment in the northern part of Ariake Bay. Using potential end-members from before to after the rainy seasons, during which a frequent discharge from the reservoir was expected, stable isotope analyses were performed on sediments collected from Isahaya Bay and northern Ariake Bay. Each end-member was isotopically differentiated by δ13C and δ15N (riverine POM: ?28.5 to ?27.2‰ and 3.3–4.6‰; reservoir POM: ?25.7 to ?25.3‰ and 7.4–8.4‰; marine POM: ?21.8 to ?19.7‰ and 6.7–7.6‰; microphytobenthos estimated from consumers: ?16.1 to ?15.9‰ and 5.2–6.1‰, respectively). Sediment isotopic signatures fell within the mixing space defined by the signatures of the end-members. Marine POM contributed greatly to bottom sediments in both seasons in Isahaya Bay and Ariake Bay, ranging from ca. 60–70 and 40–60%, respectively. Reservoir POM contributed around 10% to bottom sediments. This percentage slightly increased in the sediment of Isahaya Bay after the rainy season, but decreased in the sediment of Ariake Bay. Thus, most of the POM discharged from the reservoir would not reach the northern part of Ariake Bay and would not be a major contributor to organic enrichment. This study is the first to quantitatively describe the contribution of drained reservoir POM outside Isahaya Bay.Yu, H., Susanti, D., McGlynn, S.E., Skennerton, C.T., Chourey, K., Iyer, R., Scheller, S., Tavormina, P.L., Hettich, R.L., Mukhopadhyay, B., Orphan, V.J., 2018. Comparative genomics and proteomic analysis of assimilatory sulfate reduction pathways in anaerobic methanotrophic archaea. Frontiers in Microbiology 9, 2917. doi: 10.3389/fmicb.2018.02917. is the predominant electron acceptor for anaerobic oxidation of methane (AOM) in marine sediments. This process is carried out by a syntrophic consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria (SRB) through an energy conservation mechanism that is still poorly understood. It was previously hypothesized that ANME alone could couple methane oxidation to dissimilatory sulfate reduction, but a genetic and biochemical basis for this proposal has not been identified. Using comparative genomic and phylogenetic analyses, we found the genetic capacity in ANME and related methanogenic archaea for sulfate reduction, including sulfate adenylyltransferase, APS kinase, APS/PAPS reductase and two different sulfite reductases. Based on characterized homologs and the lack of associated energy conserving complexes, the sulfate reduction pathways in ANME are likely used for assimilation but not dissimilation of sulfate. Environmental metaproteomic analysis confirmed the expression of 6 proteins in the sulfate assimilation pathway of ANME. The highest expressed proteins related to sulfate assimilation were two sulfite reductases, namely assimilatory-type low-molecular-weight sulfite reductase (alSir) and a divergent group of coenzyme F420-dependent sulfite reductase (Group II Fsr). In methane seep sediment microcosm experiments, however, sulfite and zero-valent sulfur amendments were inhibitory to ANME-2a/2c while growth in their syntrophic SRB partner was not observed. Combined with our genomic and metaproteomic results, the passage of sulfur species by ANME as metabolic intermediates for their SRB partners is unlikely. Instead, our findings point to a possible niche for ANME to assimilate inorganic sulfur compounds more oxidized than sulfide in anoxic marine environments.Yu, R., Andrachek, R.G., Lehmicke, L.G., Pierce, A.A., Parker, B.L., Cherry, J.A., Freedman, D.L., 2018. Diffusion-coupled degradation of chlorinated ethenes in sandstone: An intact core microcosm study. Environmental Science & Technology 52, 14321-14330. diffusion must be considered when assessing natural attenuation and remediation of chlorinated ethenes in fractured porous bedrock aquifers. In this study, intact sandstone rock and groundwater from a trichloroethene (TCE)-contaminated site were used in microcosms (maintained for approximately 600 days) to simulate a single fracture-matrix system with a chamber at the top of the core allowing advection to represent fracture flow. Diffusion-coupled degradation with and without biostimulation were evaluated and compared to crushed-rock, batch microcosms. In the diffusion-transport microcosms, lactate stimulated reductive dechlorination of TCE to cis-1,2-dichloroethene (cDCE) and sulfate reduction. Reduction of TCE to cDCE led to a higher rate of chlorinated ethene removal from the cores, likely due to higher concentration gradients, along with lower sorption and a higher diffusion coefficient for cDCE relative to TCE. Reduction of cDCE to vinyl chloride or ethene did not occur as in crushed rock microcosms, inferring an absence of Dehalococcoides in the intact cores. Abiotic transformation was evident in the core microcosms based on the appearance of acetylene and enrichment in δ13C-TCE and δ13C-cDCE. Core microcosms permit a more realistic representation of the behavior of chlorinated ethenes in water-saturated fractured porous rock by incorporating the combined influence of fracture flow and matrix diffusion on transport and transformation.Yu, T., Guan, G., Abudula, A., Yoshida, A., Wang, D., Song, Y., 2019. Application of horizontal wells to the oceanic methane hydrate production in the Nankai Trough, Japan. Journal of Natural Gas Science and Engineering 62, 113-131. to the complicated reservoir conditions in the oceanic methane hydrate (MH) reservoir in the Nankai Trough, Japan, the gas production rate for the economical extraction had not been achieved during the current field production tests in 2013 and 2017 using vertical wells. Therefore, this study aimed at the application of the horizontal wells to the oceanic MH production in the Nankai Trough. Since there existed three sub-hydrate-bearing layers with different physical properties (i.e., initial hydrate saturation, porosity, and intrinsic permeability) in the reservoir, some possible well configurations including single horizontal well patterns and dual horizontal well patterns were designed based on a multilayered geological model simulating the real oceanic MH reservoir in the Nankai Trough. Then, the effectiveness of these two kinds of well designs was verified via long-term simulations of the oceanic MH production by simple depressurization, and the optimal well configuration for each design was recommended. Furthermore, a combined method of depressurization and hot water injection was also tested based on the dual horizontal well pattern, and the sensitivity analyses indicated that a favorable gas production rate of 8.64?×?105?m3/day could be obtained within the first year, even under a relatively low injection temperature of 40?°C and a relatively small injection rate of 2?kg/s/m of well.Yu, T., Guan, G., Abudula, A., Yoshida, A., Wang, D., Song, Y., 2019. Heat-assisted production strategy for oceanic methane hydrate development in the Nankai Trough, Japan. Journal of Petroleum Science and Engineering 174, 649-662. heat-assisted production strategy was considered to be an effective approach for the oceanic methane hydrate (MH) development. In this study, the combined method of depressurization and hot water injection was applied to the multilayered MH reservoir in the Nankai Trough, Japan, by using dual horizontal wells. Some possible well placements by placing the two wells in the same sublayer and different sublayers were designed in this study, and their effectiveness on the gas recovery enhancement was verified via long-term simulations of the oceanic MH production. It was found that when the two wells were placed in different sublayers, with some horizontal distance and the injection well locating above the production well, a favorable average gas production rate of 2.0?×?106?m3/day could be obtained, and was up to 100 times of that confirmed during the 2013 offshore MH production test in the Nankai Trough (2.0?×?104?m3/day), which indicated the high efficiency of the method proposed in this study. Furthermore, sensitivity analyses on the well locations suggested that the production well should be placed near the bottom of the hydrate reservoir, and a mild well spacing should be carefully determined, both to promote the heat transfer in the reservoir by making the maximum use of the injected hot water, and obtain a higher gas production rate.Yuan, J., Zhang, B., Wang, C., Brüschweiler, R., 2018. Carbohydrate background removal in metabolomics samples. Analytical Chemistry 90, 14100-14104. is a powerful tool to comprehensively monitor chemical processes in biological systems. Key to its success is the accurate and complete metabolite identification and quantification. Due to the inherent complexity of most metabolic mixtures, NMR peak overlap can make data analysis of 1D or even 2D NMR spectra challenging, especially for the 1H spectral region from 3.2–4.5 ppm that is dominated by carbohydrates and their derivatives. To address this problem, we present an effective method for carbohydrate signal removal in complex metabolomics samples by oxidation via the addition of sodium periodate (NaIO4). In an optional step, reaction products can be removed with hydrazide beads. The treated samples show substantially simplified 1D and 2D NMR spectra with their carbohydrate peaks removed, whereas noncarbohydrate peaks remain mostly unaffected. This allows the unrestricted detection of those metabolites that are otherwise obscured by carbohydrate signals. The method was first tested for metabolite model mixtures and then applied to urine and serum samples. It revealed a significant number of noncarbohydrates that were made unambiguously observable and identifiable by this method. The proposed protocol is simple and it is suitable for high-throughput sample treatment for the comprehensive metabolite identification in a broad range of samples.Zeng, Z., Liu, X.-L., Wei, J.H., Summons, R.E., Welander, P.V., 2018. Calditol-linked membrane lipids are required for acid tolerance in Sulfolobus acidocaldarius. Proceedings of the National Academy of Sciences 115, 12932-12937.: It is thought that the distinct ether lipid membranes of archaea allow them to thrive in environmental extremes. However, it has been difficult to demonstrate this physiological role directly. Here, we identify a protein required for the biosynthesis of a unique archaeal lipid head group, calditol, whose production was considered to be restricted to a subset of archaeal thermoacidophiles. We show that deletion of this protein in Sulfolobus acidocaldarius prevents production of calditol-linked membrane lipids and, in turn, inhibits cell growth at extremely low pH. Our findings also suggest that archaea more broadly, like bacteria, employ radical S-adenosylmethionine proteins to modify membrane lipids in ways that confer protective effects when environmental conditions, such as pH, fluctuate significantly.Abstract: Archaea have many unique physiological features of which the lipid composition of their cellular membranes is the most striking. Archaeal ether-linked isoprenoidal membranes can occur as bilayers or monolayers, possess diverse polar head groups, and a multiplicity of ring structures in the isoprenoidal cores. These lipid structures are proposed to provide protection from the extreme temperature, pH, salinity, and nutrient-starved conditions that many archaea inhabit. However, many questions remain regarding the synthesis and physiological role of some of the more complex archaeal lipids. In this study, we identify a radical S-adenosylmethionine (SAM) protein in Sulfolobus acidocaldarius required for the synthesis of a unique cyclopentyl head group, known as calditol. Calditol-linked glycerol dibiphytanyl glycerol tetraethers (GDGTs) are membrane spanning lipids in which calditol is ether bonded to the glycerol backbone and whose production is restricted to a subset of thermoacidophilic archaea of the Sulfolobales order within the Crenarchaeota phylum. Several studies have focused on the enzymatic mechanism for the synthesis of the calditol moiety, but to date no protein that catalyzes this reaction has been discovered. Phylogenetic analyses of this putative calditol synthase (Cds) reveal the genetic potential for calditol–GDGT synthesis in phyla other than the Crenarchaeota, including the Korarchaeota and Marsarchaeota. In addition, we identify Cds homologs in metagenomes predominantly from acidic ecosystems. Finally, we demonstrate that deletion of calditol synthesis renders S. acidocaldarius sensitive to extremely low pH, indicating that calditol plays a critical role in protecting archaeal cells from acidic stress.Zhang, B., He, Y., Chen, Y., Meng, Q., Huang, J., Yuan, L., 2018. Petrologic and geochemical characteristics of high-quality saline lacustrine source rocks in western Qaidam Basin. Petroleum Research 3, 359-369. main oil source in western Qaidam Basin is the Paleogene saline lacustrine source rocks. Traditionally, it was considered that these source rocks were characterized by low abundance and poor type of organic matter as well as limited oil generation potential, but this poor source rock condition was very inconsistent with good hydrocarbon exploration results. A previous study has just confirmed that this area develops high-quality source rocks, which is of great significance for recognizing potential of hydrocarbon resource and consolidating confidence to search large and medium-sized oil and gas fields in western Qaidam Basin. Based on fine geochemical analysis of source rocks, petrology, element geochemistry and organic geochemistry are applied to discuss development conditions of high-quality source rocks in this area. The results showed that the saline lacustrine sediments in western Qaidam Basin were deposited in relatively shallow and quiet water with relatively high salinity and low nutrient content; influenced by the drought and cold climate, the terrigenous supply of fresh water was limited, and few aquatic organisms were developed. Good preservation condition is favorable for rapid preservation of oil generating biomass (such as aquatic organisms), to form source rocks rich in hydrogen element with high soluble organic matter content; but relatively lower paleo-productivity makes organic matter abundance lower than that in the eastern saline lacustrine basins. The semi-deep lake, with relatively low salinity and abundant nutrients, is the most favorable are for development of high-quality source rocks; the source rocks have large thickness in the sedimentary depression areas, but due to high water salinity and far away from the provenance area, the water stratification was obvious, so it have moderate to high organic matter abundance.Zhang, C., Huang, L., Tang, Q., Xu, Y., Lan, X., Li, J., Liu, W., Zhao, H., 2018. Electric field assisted technology for improving the screening and application of a thiophene-biodegrading strain. Energy & Fuels 32, 12495-12500. the screening of functional strain and biodegradation, two devices of electric field assisted screening (EFAS) and electric field assisted biodegradation (EFAB) were developed in the current work. Candida tropicalis CZ12 capable of thiophene degradation was enriched and isolated from oily soil by the EFAS device at a voltage range of 10–14 v. In EFAB, the thiophene degradation velocity of this strain was accelerated by an assisted electric field, and it could reach 74% at 2 h in aqueous thiophene solution. Furthermore, the removal efficiency of the continuous EFAB device for treating thiophene-containing model fuel was 79.76% under the following conditions: aqueous–hydrocarbon ratio of 5:1, electric field assisted voltage of 15 V, and residence time of 120 min. It was clear that the above advantages of EFAS and EFAB were conducive to facilitating applications in biorefractory organics.Zhang, C., Shan, W., Wang, X., 2019. Quantitative evaluation of organic porosity and inorganic porosity in shale gas reservoirs using logging data. Energy Sources, Part A: Recovery, Utilization, and Environmental Effects 41, 811-828. pores space characterization is the core content of shale gas reservoir evaluation. The reservoir pore space of shale gas reservoir is complex, which can be divided into organic pore, clay pore, crack pore, and debris pore. A method for evaluating the four porosity of shale gas reservoir by using logging data is presented in this paper. First, according to the volume model, shale rock is equivalent to three parts: matrix, organic matter, and pore. On this basis, response equations of density logging and neutron logging are constructed. The total porosity of shale reservoirs can be solved by combining the two equations. Second, organic pore is nanopore that remains in organic matter during the conversion of kerogen to oil and gas, which is related to the content and maturity of organic matter. An equation for calculating organic porosity using total organic carbon content and density logging is presented. The scale factor in the equation is obtained from argon ion polishing scanning electron microscope experimental data. Third, based on the GRI porosity experimental data of 8 samples in the study area, the relationship among clay porosity, clay bound water saturation, and clay content was analyzed. It is considered that the clay bound water saturation has a certain correlation with the clay content, but the correlation coefficient is not high, has a positive correlation with the clay content. Based on this, a statistical model of clay porosity, clay content, and total porosity was established. Fourth, based on the dual laterolog response characteristics of microcracks, the fracture porosity of shale reservoirs is calculated by positive and negative simulation proposed by Li et al. In addition, the detrital porosity is equal to the difference between total porosity and organic porosity, clay porosity, crack porosity. The above techniques are applied to the calculation of four porosities of two wells in the Longmaxi Formation of Sichuan basin, China, and good effect has been achieved.Zhang, D., Hou, L., Gao, M., Zhang, X., 2018. Experiment and modeling on thermal cracking of n-dodecane at supercritical pressure. Energy & Fuels 32, 12426-12434. comprehensive understanding of the thermal cracking behavior of hydrocarbon fuels is important for thermal protection applications and investigations into the combustion of thermally cracked fuels. In the present study, n-dodecane is selected as a surrogate for aviation kerosene and it is subjected to a series of thermal cracking experiments at supercritical pressure. According to variations in chemical heat sink, fuel-conversion rate, and gas-production rate, the thermal cracking of n-dodecane is divided into three regions: primary, secondary, and severe. In the primary cracking region, the fuel-conversion rate is lower than 13%, and the liquid products contain only chain alkanes and alkenes. Owing to the mass fraction of main products being proportional to the fuel-conversion rate, a one-step global reaction kinetics is constructed. The secondary cracking region is characterized by rapidly increasing chemical heat sink, fuel-conversion rates, and gas-production rates with increasing fuel temperature, and the appearance of monocyclic aromatic hydrocarbons (MAHs) and cycloalkenes. A kinetic model containing three reactions is proposed for this region. This also considers the thermal decomposition of chain alkanes and alkenes, which result in the formation of MAHs and cycloalkenes. Severe cracking is observed for fuel-conversion rates above 71% where a rapid increase in the concentration of monocyclic and polycyclic aromatic hydrocarbons (PAHs) occurs. The increasing rate of chemical heat sink slows in this region which is characterized by the formation of MAHs, PAHs, and coke. A three-dimensional numerical model is built for the primary and secondary cracking regions, taking the effects of the flow, heat transfer, and thermal cracking of n-dodecane into consideration. Predicted values for the outlet temperature, fuel-conversion rate, and distribution of the main species in all tested cases agree well with the experimental results, validating the numerical model and kinetics for the primary and secondary thermal cracking of n-dodecane.Zhang, F., Jiao, Y., Wu, L., Rong, H., Li, J., Wan, D., 2019. Enhancement of organic matter maturation because of radiogenic heat from uranium: A case study from the Ordos Basin in China. American Association of Petroleum Geologists Bulletin 103, 157-176. debris (CD) within uranium-bearing strata has been studied in the Daying uranium deposit of the northern Ordos Basin, northern China. The influence of radiogenic heat from uranium on organic matter maturation was investigated through a series of tests including measurements of vitrinite reflectance (Ro), fission-track (FT) analysis in quartz grains, and the calculation of the radiogenic heat production rate of the samples. The results show that Ro in uranium-bearing strata generally increases as the burial depth increases, indicating that CD experienced normal burial coalification. However, Ro values of the samples rich in uranium are 0.062% Ro higher than those without uranium mineralization. Vitrinite reflectance bears a positive relationship with uranium content, and an inverse relationship with distance to the closest sandstone rich in uranium, indicating that uranium enrichment enhances organic matter maturation. The production of uranium decay makes FT observable in quartz grains, and the intensity of decay increases with proximity to the uranium ore body. The calculated radioactive heat production rate from the uranium ore body is 6.857 × 10?5 W/m3. During the long-term stable decay, as the uranium ore body theoretically results in an abnormal increase in temperature of 52°C without consideration of the loss of heat conduction, heat convection, and thermal radiation, this would yield a theoretical Ro increase of 0.209% Ro, reasonably greater than the observed. Therefore, the long-term stable radiogenic heat produced by uranium ore body can slightly enhance organic matter maturation, which is instructive in uranium prospecting.Zhang, L., Qi, S., Takeda, N., Kudo, S., Hayashi, J., Norinaga, K., 2018. Characteristics of gas evolution profiles during coal pyrolysis and its relation with the variation of functional groups. International Journal of Coal Science & Technology 5, 452-463. relation between the substituents or functional groups attached to the coal macromolecules and the generation of the volatile products, e.g., CH4, H2O, CO, CO2, etc., during the coal pyrolysis is an important but confusing subject. In this paper, quadrupole mass spectrometry, gas chromatography, and 13C nuclear magnetic resonance are applied to real-time monitoring the formations of volatile products, off-line quantitative determination of the total products from the pyrolysis of a sub-bituminous coal (SC), and the changes of diverse substitents in the SC along with coke foamation, respectively. These measurements are also performed for the pyrolysis of a caking coal to contrast SC. The qualitative and quantitative data reveal that, during coal pyrolysis, the functional groups related with the formation of CO, i.e., ether, carbonyl, and anhydride, can directly generate CO via bond breaking, or take a detour of the formation of other intermediates via condensation and recombination firstly. Moreover, the formations of CO2 and CH4 are related to the direct removal of -COO- and -CH3, respectively.Zhang, N., Yin, M., Wei, M., Bai, B., 2019. Identification of CO2 sequestration opportunities: CO2 miscible flooding guidelines. Fuel 241, 459-467. dioxide (CO2) flooding has been demonstrated as an economically feasible technique for carbon capture and storage (CCS) via enhanced oil recovery (EOR). In the oil industry, most of the CO2-EOR projects were implemented in miscible phase (CO2 miscible flooding), and it has become the most productive EOR method in the United States since 2012. Successful implementation of CO2 miscible flooding requires comprehensive guidelines about where CO2 can be applied. With the development of new technology, the suitable conditions for CO2-EOR have changed. Therefore, updating the guidelines for CO2-EOR is necessary. In this study, we updated the guidelines for field CO2 miscible applications in the United States by collecting valuable information from about 100 publications. Significant parameters for CO2 miscible flooding such as minimum miscibility pressure (MMP) and pay zone net thickness were considered for the first time in comparison with existing research studies. After data processing/cleaning, 207 projects have remained in the dataset. Combination plots were created to explore the ranges, distributions, and cumulative frequencies of each property. Meanwhile, descriptive values were calculated based on statistical methods. The guidelines for CO2 miscible flooding were presented with important parameters, including porosity, permeability, depth, reservoir temperature, net thickness, oil saturation, oil gravity, oil viscosity, and MMP. The analyzed results show that the reservoir pressure should be greater than 1020?psi to achieve miscibility, and CO2 miscible flooding project could be successfully applied in a reservoir with an oil gravity greater than 25?°API, oil viscosity less than 4?cp, and a reservoir temperature less than 120?°F.Zhang, P., Hu, J., Liu, B., Yang, J., Hou, H., 2019. Recent advances in metalloporphyrins for environmental and energy applications. Chemosphere 219, 617-635. chemistry has reached an unprecedented period of rapid development after decades of study. Due to attractive multifunctional properties, porphyrins and their analogues have emerged as multifunctional organometals for environmental and energy purposes. In particular, pioneer works have been conducted to explore their application in pollution abatement, energy conversion and storage and molecule recognition. This review summarizes recent advances of porphyrins chemistry, focusing on elucidating the nature of catalytic process. The Fenton-like redox chemistry and photo-excitability of porphyrins and their analogues are discussed, highlighting the generation of high-valent iron oxo porphyrin species. Finally, challenges in current research are identified and perspectives for future development in this area are presented.Zhang, S., Wang, J., Liu, X., Qu, F., Wang, X., Wang, X., Li, Y., Sun, Y., 2019. Microplastics in the environment: A review of analytical methods, distribution, and biological effects. TrAC Trends in Analytical Chemistry 111, 62-72. (MP) (<5?mm) are crucial pollution which are widely distributes in the environment. Recently, the studies of MP have increased rapidly due to increasing awareness of the potential and growing risks of biological effects during storage and disposal. However, due to limitations in analytical methods and the methods of environmental risk assessment, the distribution and biological effects of MP are still debatable issues. To clarify the potentially environmental and biological impacts of MP in the consecutive environment, (1) analytical methods to assess MP, (2) environmental transportation and distribution of MP and (3) the effects of MP on biota, including the additives and sorption-desorption of MP in both terrestrial ecosystem and aquatic ecosystems were summarized. Based on the reviewed publications, we propose considerations for addressing the insufficiencies of analytical methods, distribution and biological effects of MP in ecosystems so we can adequately safeguard global ecosystems.Zhang, X., Pandiakumar, A.K., Hamers, R.J., Murphy, C.J., 2018. Quantification of lipid corona formation on colloidal nanoparticles from lipid vesicles. Analytical Chemistry 90, 14387-14394. of a protein corona around nanoparticles when immersed into biological fluids is well-known; less studied is the formation of lipid coronas around nanoparticles. In many cases, the identity of a nanoparticle-acquired corona determines nanoparticle fate within a biological system and its interactions with cells and organisms. This work systematically explores the impact of nanoparticle surface chemistry and lipid character on the formation of lipid coronas for three different nanoparticle surface chemistries (two cationic, one anionic) on 14 nm gold nanoparticles exposed to a series of lipid vesicles of four different compositions. Qualitative (plasmon band shifting, ζ potential analysis, dynamic light scattering on the part of the nanoparticles) and quantitative (lipid liquid chromatography/mass spectrometry) methods are developed with a “pull-down” scheme to assess the degree of lipid corona formation in these systems. In general, cationic nanoparticles extract 60-95% of the lipids available in vesicles under the described experimental conditions, while anionic nanoparticles extract almost none. While electrostatics apparently dominate the lipid-nanoparticle interactions, primary amine polymer surfaces extract more lipids than quaternary ammonium surfaces. Free cationic species can act as lipid-binding competitors in solution.Zhang, X., Zhao, Y., Cui, X., Wang, X., Shen, H., Chen, Z., Huang, C., Meruva, N., Zhou, L., Wang, F., Wu, L., Luo, F., 2018. Application and enantiomeric residue determination of diniconazole in tea and grape and apple by supercritical fluid chromatography coupled with quadrupole-time-of-flight mass spectrometry. Journal of Chromatography A 1581-1582, 144-155. chiral separation and residue determination method for diniconazole enantiomers in tea, apple, and grape was developed and validated by supercritical fluid chromatography coupled with quadrupole-time-of-flight mass spectrometry (SFC-Q-TOF/MS). The two diniconazole enantiomers were separated on a Chiral CCA column, and the chromatographic conditions (mobile phase proportion and modifier, column temperature, backpressure, and auxiliary solvent) were optimized. The optimal SFC-Q-TOF/MS conditions were selected as a mobile phase of CO2/isopropanol (IPA) (v/v, 96/4), flow rate at 2.0?mL/min, automated back pressure regulator (ABPR) at 2000?psi, column temperature at 25 ℃ and under electrospray ionization positive mode with the best auxiliary solvent of 2?mmol/L ammonium acetate in methanol/water (v/v, 1/1) at 0.20?mL/min flow rate. Residues in tea and fruit samples were extracted by acetonitrile/water (v/v, 4/1 for fruit and 2/1 for tea), purified by Cleanert TPT or Pesti-Carb solid phase extraction column, then analyzed by SFC-Q-TOF/MS with matrix-matched external standard quantification method. The elution order of diniconazole enantiomers on CCA column was R-(-)-diniconazole at first, and S-(+)-diniconazole at second. The standard curve concentration levels of R-(-)-diniconazole and S-(+)-diniconazole in samples ranged from 0.01?mg/L to 1.00?mg/L with the correlation coefficients greater than 0.99. The spiked recoveries of R-(-)-diniconazole and S-(+)-diniconazole in apple and grape at three levels of 0.005, 0.05 and 0.25?mg/kg were in the range of 69.8% to 102.1%, with relative standard deviations (RSDs) (n?=?6) between 3.5% and 10.4%, and the limits of quantitation (LOQs) below 0.005?mg/kg. The spiked recoveries in black tea at three levels of 0.01, 0.10, and 0.50?mg/kg were in the range of 85.6% to 90.6%, with the RSDs (n?=?6) ranging from 3.9% to 9.5%, and LOQ of 0.01?mg/kg. This residue analysis and determination method for diniconazole enantiomers in apple, grape and tea samples is convenient, reliable, and meets the residue analysis requirement. Also it is applicatied for the residue fates of R-(-)-diniconazole and S-(+)-diniconazole during the fresh tea leaves growing, green tea processing and black tea processing. The degradation half-times (DT50) between R-(-)-diniconazole and S-(+)-diniconazole in the fresh tea leaves growing were 2.9 d and 3.1 d, respectively. The concentrations of R-(-)-diniconazole and S-(+)-diniconazole decreased gradually with time and on the 14th day after application were lower than 10% of the initial concentration. The average enantiomer fractions (EFs) of R-(-)-diniconazole and S-(+)-diniconazole at 2?h, 2, 5, 7, 10 and 14 d after application in fresh tea leaves were 0.505, 0.526, 0.523, 0.558, 0.453 and 0.489, respectively. This result is similar to the result of our last research for the enantiomers of cis-epoxiconazole-another triazole fungicide residues in fresh tea leaves. And in the whole black tea processing, 37.1%–49.3% and 35.9%–57.9% of R-(-)-diniconazole and S-(+)-diniconazole decreased, respectively. The total processing factors (PFs) of R-(-)-diniconazole and S-(+)-diniconazole for the black tea procedure were 0.507-0.629 and 0.421-0.641, respectively. The EFs of R-(-)-diniconazole and S-(+)-diniconazole in black tea processing ranged from 0.432 to 0.532. However, in the whole green tea processing, 22.3%–32.6% and 21.7%–40.3% of R-(-)-diniconazole and S-(+)-diniconazole decreased, respectively. The difference between black tea and green tea is nearly 15%, and in green tea is less decreased than in black tea. The total PFs of R-(-)-diniconazole and S-(+)-diniconazole for the green tea procedure were 0.674-0.777 and 0.597-0.783, respectively. The EFs of R-(-)-diniconazole and S-(+)-diniconazole in green tea processing ranged from 0.473 to 0.504. The PFs illustrated that for R-(-)-diniconazole and S-(+)-diniconazole decrease, the rolling and fermentation were the critical steps in black tea processing, and the rolling was the critical step in green tea processing, respectively.Zhang, Y., Gao, M., You, Q., Fan, H., Li, W., Liu, Y., Fang, J., Zhao, G., Jin, Z., Dai, C., 2019. Smart mobility control agent for enhanced oil recovery during CO2 flooding in ultra-low permeability reservoirs. Fuel 241, 442-450. development of natural/artificial fractures leads to significant differences of the physical properties between the matrix and the fractures, which usually causes serious channeling and low sweep efficiency during CO2 flooding in ultra-low permeability reservoirs, the use of a CO2-responsive smart mobility control system to generate bulk gel by wormlike micelles (WLMs) to mitigate gas channeling has great potentials for enhanced oil recovery (EOR) in ultra-low permeability reservoirs. In this study, five kinds of chemicals with CO2-sensitive groups are screened to measure the apparent viscosity using a rheometer. The experimental results show that the optimum system consists of 4.4?wt%?N, N-dimethyl octylamide-propyl tertiary amine (DOAPA) and 2.0?wt% sodium p-toluenesulfonate (SPTS). Subsequently, the plugging capacity and EOR performance of the system are systematically evaluated using core flooding experiments. The optimized system (DOAPA/SPTS) exhibits outstanding plugging capacity for gas channeling with a plugging efficiency of 99.2%. The oil recovery of the CO2 flooding increases by 20.0%. In addition, the thickening mechanism of the CO2-responsive system is studied using rheological experiments and a cryogenic transmission electron microscopy (Cryo-TEM). The shear-thinning behavior demonstrates that the thickening effect of the high-viscosity WLMs is strong in the DOAPA/SPTS-CO2 solution, and the Cryo-TEM results indicate a transition from spherical micelles to the WLMs. The protonation contributes to the formation of the WLMs in the solution during phase transformation process. The results of this study are expected to provide benchmark to select the mobility control agent for CO2 flooding in ultra-low permeability reservoirs.Zhang, Y., Li, Z., 2019. Raman spectroscopic study of chemical structure and thermal maturity of vitrinite from a suite of Australia coals. Fuel 241, 188-198. deconvolution and resolution of overlapping bands in the Raman spectra of a suite of coals studied by curve-fitting methods has improved our understanding of the main structural changes in naturally matured coals. Even though much work on deconvolution of Raman spectra has been done, the systematic evolution of chemical structures is not well established. In this study we used a suite of 28 coal samples from Australia with vitrinite reflectance ranging from 0.38 to 3.52%. The micro-Raman spectra of vitrinite macerals from selected coals were acquired using a custom-made Raman spectrometer and supplemented by other Raman spectra previously acquired under the same experimental conditions. In the spectral deconvolution procedure, the second derivative curve-fitting method was used to determine the number of peaks and peak positions of the Raman spectra. Each band was tentatively assigned to a corresponding chemical structure by references to the interpreted major structural changes likely to have taken place during coalification. These parameters included PD (the position of D band), RBS (the distance between G band and D band), FWHMG (full width at half maximum of G band), IG/IGL (the intensity ratio of G band and GL band), and AR/b (the ratio of Raman integrated area and the slope of the spectral background). All of these Raman parameters are found to have a very good correlation with Ro% with R2 higher than 0.90. While five simple equations have been proposed and may be used to estimate thermal maturity of coals, two equations (Eq. (4) for Ro% from 0.38 to 1.5 and Eq. (5) for Ro% from 1.5 to 3.52) are best suitable to predict thermal maturity of coals with the most accuracyZhang, Y., Sun, J., Zheng, P., Chen, T., Liu, Y., Han, G., Simpson, I.J., Wang, X., Blake, D.R., Li, Z., Yang, X., Qi, Y., Wang, Q., Wang, W., Xue, L., 2019. Observations of C1–C5 alkyl nitrates in the Yellow River Delta, northern China: Effects of biomass burning and oil field emissions. Science of The Total Environment 656, 129-139. nitrates (RONO2) are important reservoirs of nitrogen oxides and play key roles in the tropospheric chemistry. Two phases of intensive campaigns were conducted during February–April and June–July of 2017 at a rural coastal site and in open oil fields of the Yellow River Delta region, northern China. C1-C5 alkyl nitrates showed higher concentration levels in summer than in winter-spring (p?<?0.01), whilst their parent hydrocarbons showed an opposite seasonal variation pattern. The C3–C5 RONO2 levels in the oil fields were significantly higher than those in the ambient rural air. Alkyl nitrates showed well-defined diurnal variations, elucidating the effects of in-situ photochemical production and regional transport of aged polluted plumes. Backward trajectory analysis and fire maps revealed the significant contribution of biomass burning to the observed alkyl nitrates and hydrocarbons. A simplified sequential reaction model and an observation-based chemical box model were deployed to diagnose the formation mechanisms of C1-C5 RONO2. The C3–C5 RONO2 were mainly produced from the photochemical oxidation of their parent hydrocarbons (i.e., C3–C5 alkanes), whilst C1-C5 RONO2 compounds have additional sources. In addition to parent hydrocarbons, longer alkanes with >4 carbon atoms were also important precursors of alkyl nitrates in the oil fields. This study demonstrates the significant effects of oil field emissions and biomass burning on the volatile organic compounds and alkyl nitrate formation, and provides scientific support for the formulation of control strategies against photochemical air pollution in the Yellow River Delta region.Zhang, Y., Xin, C.-X., Zhang, L.-T., Deng, Y.-L., Wang, X., Chen, X.-Y., Wang, Z.-Q., 2018. Detection of fungi from low-biomass spacecraft assembly clean room aerosols. Astrobiology 18, 1585-1593. sensitive and rapid detection of airborne fungi in space stations is essential to ensure disease prevention and equipment safety. In this study, quantitative loop-mediated isothermal amplification (qLAMP) was used to detect fungi in the aerosol of the low-biomass environment of China's space station assembly clean room (CSSAC). A qLAMP primer set for detecting a wide range of aerosol fungi was developed by aligning 34 sequences of isolated fungal species and 17 space station aerosol-related fungal species. Optimization of sample pretreatment conditions of the LAMP reaction increased the quantitative results by 1.29–1.96 times. The results showed that our qLAMP system had high amplification specificity for fungi, with a quantifiable detection limit as low as 102. The detected fungal biomass in the aerosol of CSSAC was 9.59?×?102–2.20?×?105 28S rRNA gene copy numbers/m3. This qLAMP assay may therefore replace traditional colony-forming unit and quantitative PCR methods as an effective strategy for detecting fungi in space stations.Zhang, Y., Yao, S., Zhang, M., Zhou, X., Mei, H., Zeng, F., 2018. Prediction of adsorption isotherms of multicomponent gas mixtures in tight porous media by the oil–gas-adsorption three-phase vacancy solution model. Energy & Fuels 32, 12166-12173. unconventional reservoirs, the effect of adsorption on phase equilibrium cannot be neglected because the process occurs in extremely tight porous media. This work focuses on the adsorption prediction of multicomponent mixture systems in tight porous media with the oil–gas-adsorption three-phase equilibrium model to a gas sample in the literature. The revisited vacancy solution model of adsorption by Bhatia and Ding is introduced to study the adsorption behaviors of the mixture. The gas and adsorbed phases are assumed to be the solutions of adsorbates with a hypothetical solvent called “vacancy”, and the vacancy is treated as an additional component engaged in the phase equilibrium in this theory. Instead of using parameters extracted from the multicomponent adsorption data, this method takes advantage because it accurately predicts the gas mixture adsorption equilibrium with consideration of non-ideal behavior in the adsorbed phase from pure gas adsorption isotherms over wide ranges of conditions, which could be efficient in terms of cost and time. It can explain the competitive adsorption phenomenon, which is proven during the adsorption process of the gas mixture. The experimental data in the literature of CH4–C2H6 binary gas mixtures of different compositions with a pressure ranging from 0 to 125 bar under the temperatures of 40, 50, and 60 °C are restudied in this work. The prediction results are compared to two other methods, including the extended Langmuir model and the multicomponent potential theory. This method shows an improved precision with less than 5% mean absolute percentage error in all cases. In addition to predications of desorption for the depletion process, the vacancy solution model has the potential in future work to give simulations for other production operations, such as CO2 or N2 injection for the displacement of hydrocarbons in shales.Zhao, C., Jiang, Z., Wu, Y., Liu, S., Cui, L., Zhang, J., Huang, X., 2019. Origins of sediment organic matter and their contributions at three contrasting wetlands in a coastal semi-enclosed ecosystem. Marine Pollution Bulletin 139, 32-39. origins of sediment organic matter (SOM) and their contributions were studied in three contrasting wetlands (mudflat, estuarine and mangrove) of Daya Bay, South China Sea. Lower sediment δ13C but higher δ15N values were observed in coastal wetland than in offshore water of the bay. Greater terrigenous organic matter (TOM) contribution to SOM was observed in lower tidal area in mudflat and estuarine wetland. Higher concentrations of total organic carbon and total nitrogen in the three wetlands, as well as lower sediment δ13C, were found in the wet season. Extremely lower sediment δ15N with higher seawater ammonia were observed in estuarine wetland than in mudflat and mangrove, which was caused by the input of 15N-depleted ammonia from petrochemical industrial wastewater. Mangrove contributed substantially to SOM, with a larger contribution in mangrove area than in non-mangrove area. The mean contribution of TOM to SOM was lower in mangrove than in mudflat.Zhao, H., Fang, Z., Jing, H., Liu, J., 2019. Modeling vapor-liquid phase equilibria of hydrogen sulfide and water system using a cubic EOS-GEX model. Fluid Phase Equilibria 484, 60-73. phase equilibria of the H2S–H2O mixture were correlated by use of a cubic EOS-GEX over temperature and pressure range of 0.1–30?MPa and 278–627K. Average absolute deviations (AAD%) between the modeling results and the experimental data taken from literature for both the H2S-rich and the aqueous phases were found less than 5%. The new sets of EOS-GEX model parameters for H2S–H2O mixture were evaluated from the experimental data over the above-mentioned temperature and pressure range. The proposed model was compared with the three previous published models and we discussed the advantages and the disadvantages for each of them. This study demonstrated that the advantages of the cubic EOS-GEX model in calculating phase equilibria of H2SH2O mixture over currently available models, especially at high pressures. The hydrate equilibrium, the salt effect, and the chemical reactions in the aqueous phase were not considered during phase equilibrium calculation in this study.Zhao, H., Liu, W., Borjigin, T., Zhang, J., Luo, H., Wang, X., 2019. Study of thermochemical sulfate reduction of different organic matter: Insight from systematic TSR simulation experiments. Marine and Petroleum Geology 100, 434-446. series of thermochemical sulfate reduction (TSR) simulation experiments were carried out involving different organic matter (crude oil, solid bitumen, type II kerogen, type III kerogen) and different sulfate species (anhydrite and MgSO4) to address the chemical and carbon isotopic variations of the hydrocarbon, H2S and CO2. The increase of main peak carbons of residual saturated hydrocarbon and the decrease of gaseous hydrocarbons from control treatment to corresponding sulfate treatments suggest that TSR promote the consumption of both liquid and gaseous hydrocarbons. The δ13C1-3 values generally shift positively from control treatment to sulfate treatments and the (δ13Cethane-δ13Cmethane) values in sulfate treatments are higher than that in control treatments. The variation of δ13C1-3 in TSR is controlled by the isotope fractionation during the generation and consumption of C1-3 in TSR. MgSO4 is more reactive than anhydrite in TSR. A certain amount of H2S is incorporated into solid bitumen as the result of secondary alteration. We believe that the reactivity order of different organic matter in TSR is crude oil > solid bitumen > type II kerogen > type III kerogen. The reactivity of organic matter in TSR depends on the hydrocarbon generation kinetics of each organic matter. The dissolution/decomposition and precipitation of carbonate control the yield of CO2 in sour reservoirs. The negative shift of δ13CO2 with increasing TSR extent is mainly due to the inheritance effect of carbon isotope from hydrocarbons. Inorganic CO2 sourced from the thermal decomposition or acid dissolution of carbonate mineral impose significant influence on δ13CO2. The H2S yields decrease with CH4 yields and increase with δ13CH4 value, the δ13CH4 values increase with residual amount of gaseous alkane (1- H2S/(residual alkane + H2S)), suggesting that methane acted as reactant in TSR. The (δ13CO2-δ13CH4) values decrease significantly with increasing temperature, and the δ13CO2 is even more negative than δ13CH4 in 450 °C MgSO4 treatments involving type II and type Ⅲ kerogen. Accordingly, methane acted as a predominant reactant in 450 °C sulfate treatments in our experiment. It is possible for natural gas with high gas dryness to experience methane-dominated TSR in geological reservoirs.Zhao, L., Kaiser, R.I., Xu, B., Ablikim, U., Ahmed, M., Evseev, M.M., Bashkirov, E.K., Azyazov, V.N., Mebel, A.M., 2018. Low-temperature formation of polycyclic aromatic hydrocarbons in Titan’s atmosphere. Nature Astronomy 2, 973–979. detection of benzene in Titan’s atmosphere led to the emergence of polycyclic aromatic hydrocarbons (PAHs) as potential nucleation agents triggering the growth of Titan’s orange-brownish haze layers. However, the fundamental mechanisms leading to the formation of PAHs in Titan’s low-temperature atmosphere have remained elusive. We provide persuasive evidence through laboratory experiments and computations that prototype PAHs like anthracene and phenanthrene (C14H10) are synthesized via barrierless reactions involving naphthyl radicals (C10H7?) with vinylacetylene (CH2=CH–C≡CH) in low-temperature environments. These elementary reactions are rapid, have no entrance barriers, and synthesize anthracene and phenanthrene via van der Waals complexes and submerged barriers. This facile route to anthracene and phenanthrene—potential building blocks to complex PAHs and aerosols in Titan—signifies a critical shift in the perception that PAHs can only be formed under high-temperature conditions, providing a detailed understanding of the chemistry of Titan’s atmosphere by untangling elementary reactions on the most fundamental level.Zhao, W., Shen, A., Qiao, Z., Pan, L., Hu, A., Zhang, J., 2018. Genetic types and distinguished characteristics of dolomite and the origin of dolomite reservoirs. Petroleum Exploration and Development 45, 983-997. find out the origin of dolomite, the precipitation of primary dolomite, and the formation of pores in dolomite, petrologic and geochemical characteristics of typical samples from Sichuan and Tarim Basin were analyzed based on the previous understandings, and three aspects of results were achieved. (1) A classification of dolomite origins based on petrologic features, forming environment, and time sequence was proposed, which shows clear boundaries of diagenetic and characteristic realms and evolved clues between different types of dolomite. (2) Petrographic and geochemical identification marks for different types of dolomite were presented, revealing that the orderly geochemical variation of different types of dolomite is the response to the change of forming environment of dolomite during continuous time sequence. (3) The contribution of dolomitization to the formation of porosity was re-evaluated, revealing that the porosity in dolomite was mostly attributed to the primary pores and supergene dissolution and burial dissolution, and early dolomitization was conducive to the preservation of primary pores. These understandings are of great theoretical significance for identifying the origins and types of dolomite, and can guide the prediction of dolomite reservoirs.Zhao, X., Zhou, L., Pu, X., Jiang, W., Jin, F., Xiao, D., Han, W., Zhang, W., Shi, Z., Li, Y., 2018. Hydrocarbon-generating potential of the Upper Paleozoic section of the Huanghua Depression, Bohai Bay Basin, China. Energy & Fuels 32, 12351–12364. origin of the Upper Paleozoic hydrocarbon accumulations in the Huanghua Depression of Bohai Bay Basin was studied by petrography and Rock-Eval pyrolysis on more than 90 coal, dark mudstone, and carbonaceous mudstone samples, with 4 samples of hydrous pyrolysis. Additionally, biomarker analysis of oils produced from the Upper Paleozoic reservoirs were conducted. The source rocks were evaluated for their amounts of type III kerogen and content of hydrogen-rich macerals. The samples can be graded between fair and excellent quality, showing that the source rocks possess good potential for gas and oil generation. The main stage of oil generation occurs around 2600–4000 m [with random vitrinite reflectance (Ro) values of 0.7–1.3%], and gas generation happens in a wide depth range (Ro up to 2.0%). Hydrous pyrolysis under a closed system exhibits large potential for gas generation, and the dark mudstone can generate 500–1000 mL/g of total organic carbon (TOC) at a temperature between 350 and 550 °C. Coal and carbonaceous mudstone exhibit a clear capacity for oil generation (5–25 mg/g of TOC), with dark mudstone showing the highest values (up to 84 mg/g of TOC at 400 °C). Two categories of crude oils produced from the Upper Paleozoic reservoirs can be recognized, indicating that the oils are mainly migrated from strata. The studied source rocks and its produced oil are of high concentrations of diasterane and gammacerane, Ts < Tm, and Pr/Ph ratios of 1.01–3.44, indicating the input of coaly organic matter under a marine to continental transitional environment. The results illustrate good gas generation and limited oil generation capacity for the Upper Paleozoic source rocks, and more attention should be focused on the natural gas exploration in the study area and also other coal-bearing basins.Zhao, Z., Zhou, X.-P., 2019. An integrated method for 3D reconstruction model of porous geomaterials through 2D CT images. Computers & Geosciences 123, 83-94. reconstruction technique plays a key role in understanding the characteristics of geomaterial pore structures through computed tomography images. In this paper, multiple-point statistics and a marching cube algorithm are integrated to reconstruct three-dimensional model to extract the pore structure, analyze connectivity and predict the permeability of the pore structure. This method is applicable not only to two-dimensional images to determine simple characteristics of geomaterials, but also to better understand inner pore structure via the reconstructed three-dimensional models. The results obtained by the proposed reconstruction method agree well with those obtained from the previous methods.Zhong, Y., Shi, L., 2018. Genomic analyses of the quinol oxidases and/or quinone reductases involved in bacterial extracellular electron transfer. Frontiers in Microbiology 9, 3029. doi: 10.3389/fmicb.2018.03029. exchange electrons with extracellular substrates, some microorganisms employ extracellular electron transfer (EET) pathways that physically connect extracellular redox reactions to intracellular metabolic activity. These pathways are made of redox and structural proteins that work cooperatively to transfer electrons between extracellular substrates and the cytoplasmic membrane. Crucial to the bacterial and archaeal EET pathways are the quinol oxidases and/or quinone reductases in the cytoplasmic membrane where they recycle the quinone/quinol pool in the cytoplasmic membrane during EET reaction. Up to date, three different families of quinol oxidases and/or quinone reductases involved in bacterial EET have been discovered. They are the CymA, CbcL/MtrH/MtoC, and ImcH families of quinol oxidases and/or quinone reductases that are all multiheme c-type cytochromes (c-Cyts). To investigate to what extent they are distributed among microorganisms, we search the bacterial as well as archaeal genomes for the homologs of these c-Cyts. Search results reveal that the homologs of these c-Cyts are only found in the Domain Bacteria. Moreover, the CymA homologs are only found in the phylum of Proteobacteria and most of them are in the Shewanella genus. In addition to Shewanella sp., CymA homologs are also found in other Fe(III)-reducing bacteria, such as of Vibrio parahaemolyticus. In contrast to CymA, CbcL/MtrH/MtoC, and ImcH homologs are much more widespread. CbcL/MtrH/MtoC homologs are found in 15 phyla, while ImcH homologs are found in 12 phyla. Furthermore, the heme-binding motifs of CbcL/MtrH/MtoC and ImcH homologs vary greatly, ranging from 3 to 23 and 6 to 10 heme-binding motifs for CbcL/MtrH/MtoC and ImcH homologs, respectively. Moreover, CymA and CbcL/MtrH/MtoC homologs are found in both Fe(III)-reducing and Fe(II)-oxidizing bacteria, suggesting that these families of c-Cyts catalyze both quinol-oxidizing and quinone-reducing reactions. ImcH homologs are only found in the Fe(III)-reducing bacteria, implying that they are only the quinol oxidases. Finally, some bacteria have the homologs of two different families of c-Cyts, which may improve the bacterial capability to exchange electrons with extracellular substrates.Zhong, Z., Carr, T.R., 2019. Geostatistical 3D geological model construction to estimate the capacity of commercial scale injection and storage of CO2 in Jacksonburg-Stringtown oil field, West Virginia, USA. International Journal of Greenhouse Gas Control 80, 61-75. concerns around global warming increase, carbon capture, utilization and geological storage (CCUS) is a promising way to reduce the emissions of anthropogenic CO2 into the atmosphere. Sequestering the CO2 into depleted hydrocarbon reservoirs with associated enhanced oil recovery (EOR) is the most achievable approach under current economic constraints since it increases recovery of existing oil reserves, and bridges the gap between regional-scale CO2 capture and geologic sequestration. However, one of the challenges is the paucity of modern subsurface data required for adequate reservoir characterization and storage estimates. The Upper Devonian fluvial sandstone reservoirs in the Jacksonburg-Stringtown oil field in West Virginia, which have produced over 22 million barrels of oil since 1895, are ideal candidates for CO2 sequestration coupled with EOR. Reservoir storage capacity and oil recovery factors are keys for the evaluation of coupled CO2 storage and CO2-EOR process. Regression relationships between wireline logs and core measured data for porosity, permeability are constructed by artificial neural network and support vector machine in core-scale; then extended from core-scale to well-scale, where wells do not have porosity and permeability wireline logs; finally a 3D static geological model is generated based on the Random Gaussian Function simulation method and well-established variogram models generated by detailed data analysis. A static 3D reservoir model, which integrates detailed geological knowledge and existing legacy geological data from Jacksonburg-Stringtown oil field, is constructed to estimate theoretical CO2 storage capacity. Depending on the proposed 3D geological model, the best regions for coupled CCUS-EOR are located in southern portions of the field, and the estimated CO2 theoretical storage capacity for Jacksonburg-Stringtown oil field varies from 24 to 383 million metric tons. The estimated results of CO2 sequestration indicate that the Jacksonburg-Stringtown oilfield has significant potential for CO2 storage and value-added EOR.Zhou, C., Liu, Y., Liu, C., Liu, Y., Tfaily, M.M., 2019. Compositional changes of dissolved organic carbon during its dynamic desorption from hyporheic zone sediments. Science of The Total Environment 658, 16-23. organic matter (DOM) is an important driver for biogeochemical reactions that affect microbial community function, and regulate changes in porewater chemical composition and redox properties in the environment. This study investigated the variation in DOM molecular composition during the detachment of organic matter (OM) from hyporheic zone (HZ) sediments using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS). Diffusive mass transfer and microbial degradation were the two primary processes controlling the rate of OM release and molecular composition changes during the detachment from sediments. The diffusive mass transfer process limited the rate of OM release from the sediments, but had negligible effect on the molecular signature of the released OM. Microbial degradation on the other hand preferentially consumed the protein- and lipid-like fractions of the DOM, characterized by lower nominal oxidation states of carbon (NOSC), lower molecular weight, and a higher saturation of chemical bonds. The results have strong implication to the organic carbon dynamics and related microbial activities and contaminant transformation in hyporheic zones, an important critical area in river systems.Zhou, H., Chen, B., Wang, S., Yang, M., 2019. CO2/N2 mixture sequestration in depleted natural gas hydrate reservoirs. Journal of Petroleum Science and Engineering 175, 72-82. dioxide (CO2) emission is one of the primary causes of global warming, while CO2 storage is an effective way to solve this problem. Moreover, CO2 storage as CO2 hydrate is regarded as a viable and promising way. The development of natural gas hydrate mining technologies has provided a safe and appropriate method to store CO2 in depleted gas hydrate reservoirs. In addition, different concentrations of N2 are contained in the captured CO2 from flue gas. Therefore, CO2 storage with different N2 concentrations in depleted natural gas hydrate reservoirs with excess water was investigated in this study. Three types of gas (pure CO2, 90?mol%CO2?+?10?mol%N2 and 80?mol%CCO2?+?20?mol%N2) and three pressures (3.0?MPa, 3.2?MPa and 3.5?MPa) in the constant pressure process were investigated. Magnetic Resonance Imaging (MRI) was employed to monitor the entire experimental process. The experimental results showed that the hydrate was nucleated and generated in different areas independently during the storage process. N2 was beneficial for quick hydrate formation; however, pure CO2 was most CO2 for hydrate formation from a long-term perspective. In addition, CO2 was primarily stored as hydrate; a portion of CO2 was stored in the form of gas; and a small amount of CO2 was dissolved in the pore water. Moreover, the CO2 storage density (226.56?kg/m3) was the highest at the conditions of 275.15?K and 3.5?MPa using 90?mol%CO2 +?10?mol%N2 in the experiments. The highest CO2 storage density (229.99?kg/m3) calculated through water conversion occurred at the conditions of 275.15?K and 3.5?MPa using pure CO2.Zhou, X., Lü, X., Song, X., Quan, H., Chen, K., Qian, W., Wang, Z., Bai, Z., Zhang, J., 2019. Petroleum source of oil seepages in the Kalpin area, NW Tarim Basin, China. Journal of Petroleum Science and Engineering 175, 83-96. rocks in Lower Cambrian (?1) and Middle-Upper Ordovician (O2+3) have low S2 values, ranging from 0.01 to 0.34 and 0.01–5.95?mg HC/g Rock, respectively. The averages of TOC are 1.07% and 0.84% for ?1 and O2+3 source rocks, respectively. The equivalent vitrinite reflectance values (VREs) indicate that ?1 rocks are in a high-over mature stage for oil generation, and O2+3 rocks are sufficiently mature.Four oil seepages from the Yingshan Formation in the Qingsong quarry of the Aksu area and 34 core samples from ?1 and O2+3 rocks in the Kalpin area were analyzed for stable carbon isotopes. Moreover, 4 oil seepages and 16 core samples were analyzed by gas chromatography-mass spectrometry (GC-MS). Compared with O2+3 rocks, ?1 rocks are characterized by lower values of Gammacerane/C30 hopane (G/H), C28/(C27 + C28 + C29) 20R ααα sterane (C28%), C29/(C27 + C28 + C29) 20R ααα sterane (C29%), C26 20S/C28 20S triaromatic steroids (C26/C28), (C26 + C27)/C28 triaromatic steroids and (C26 20R + C27 20S)/C28 20R triaromatic steroids, and higher values of C21/C23 tricyclic terpane (C21/C23), C27/(C27 + C28 + C29) 20R ααα sterane (C27%), and C35 αβ (22R + 22S) homohopane/αβ C30-hopane (C35?H/H). The two sets of source rocks have a ‘‘V (C27>C28<C29)”-shaped regular sterane distribution pattern, and O2+3 rocks contain triaromatic steranes in abundances as high as those of ?1 rocks. C28C34 25-norhopanes (NHs) indicates that the degree of degradation of oil seepages falls at approximately PM 6, rendering many biomarker parameters ineffective for oil-source correlations, except for triaromatic steriods and carbon isotopic compositions. The values of C26/C28, (C26 + C27)/C28 triaromatic steroids and (C26 20R + C27 20S)/C28 20R triaromatic steroids using 0.50, 1.45 and 1.80 as threshold values, respectively, can differentiate ?1 and O2+3 rocks, and oil seepages show a natural affinity to the ?1 source rocks. The ?1 rocks have lighter δ13C of kerogen and heavier δ13C of group compositions than those of O2+3 rocks. The group compositions of oil seepages are depleted in 13C by approximately 0–1.5‰ compared with kerogens of ?1 extracts, further suggesting that the oil seepages are comparable to ?1 source rocks consistent with the results of biomarker analysis.Zhou, Y., Li, L., Jin, L., Zhou, J., Shi, Z., Li, Y., Hu, H., 2019. Pyrolytic behavior of coal-related model compounds connected with C–C bridged linkages by in-situ pyrolysis vacuum ultraviolet photoionization mass spectrometry. Fuel 241, 533-541. pyrolysis is generally considered to initiate by cleavage of weak covalent bonds bridged between aromatic rings. The C–C covalent bonds are predominant bridged linkages among the framework of coal, which have a critical influence on coal pyrolysis reaction but lack of direct online observation. Five representative coal-related model compounds containing C–C bridged bonds, polypropylene (PP), polyvinylpyrrolidone (PVP), poly-4-vinylpyridine (P4VP), polystyrene (PS) and poly-4-vinylphenol, were selected to pyrolyze in an in-situ pyrolysis vacuum ultraviolet photoionization mass spectrometry (Py-VUV-PIMS). The soft ionized mass spectral detection can provide product distribution and evolved information of original products and intermediates, which are the key evidence to understand the initiation, recombination and reaction routes during pyrolysis process. Online analysis of pyrolysis reaction was found to be priority with cracking of C–C bond in the five polymer samples, and homologous free radicals and original products, which mainly include monomers, dimers and their alkyl and alkenyl radicals, were detected. The results reveal the cleavage temperature of C–C covalent bond is deeply related to its chemical environment, and obvious conjugation effect and steric effect for the bridged linkage were observed. In addition, the effect of hydrogen bond was also observed during the pyrolysis of model compounds containing hydroxyl groups, and intramolecular or intermolecular hydrogen bonding reduced the temperature at which C–C bridged bonds break. The analogous fracture mode and pyrolysis behavior of coal-related model compounds, which are beneficial to understand the reaction route and mechanism of coal pyrolysis, were discussed based on the experimental observations and theoretical calculation.Zhou, Y., Martin, P., Müller, M., 2018. Composition and cycling of dissolved organic matter from tropical peatlands of coastal Sarawak, Borneo, revealed by fluorescence spectroscopy and PARAFAC analysis. Biogeosciences Discussions 2018, 1-25. Asian peatlands supply ~10% of the global flux of dissolved organic carbon (DOC) from land to the ocean, but the biogeochemical cycling of this peat-derived DOC in coastal environments is still poorly understood. Here, we use fluorescence spectroscopy and parallel factor (PARAFAC) analysis to distinguish different fractions of dissolved organic matter (DOM) in peat-draining rivers, estuaries, and coastal waters of Sarawak, Borneo. The terrigenous fractions showed high concentrations at freshwater stations within the rivers, and conservative mixing with seawater across the estuaries. The autochthonous DOM fraction, in contrast, showed low concentrations throughout our study area at all salinities. The DOM pool was also characterized by a high degree of humification in all rivers and estuaries up to salinity 25. These results indicate a predominantly terrestrial origin of the riverine DOM pool. Only at salinities >25 did we observe an increase in the proportion of autochthonous relative to terrestrial DOM. Natural sunlight exposure experiments with river water and seawater showed high photolability of the terrigenous DOM fractions, suggesting that photodegradation may account for the observed changes in DOM composition in coastal waters. Nevertheless, we estimate based on our fluorescence data that at least 20%–25% of the DOC at even our most marine stations (salinity>31) was terrestrial in origin, indicating that peatlands likely play an important role in the carbon biogeochemistry of Southeast Asian shelf seas.Zhu, H., She, J., Zhou, M., Fan, X., 2019. Rapid and sensitive detection of formaldehyde using portable 2-dimensional gas chromatography equipped with photoionization detectors. Sensors and Actuators B: Chemical 283, 182-187. developed an automated and highly portable device for rapid and sensitive formaldehyde detection based on heart-cutting 2-dimensional gas chromatography. In this design, the air sample was first absorbed by a preconcentrator before it is injected into the 1st-dimensional column (Rtx?-VMS). The partial elution from the 1st-dimensional column containing formaldehyde was re-injected into the 2nd-dimensional column (Rt? Q-BOND column) for further separation. The detection of formaldehyde was achieved by using a micro-helium dielectric barrier discharge photoionization detector that is able to ionize formaldehyde (ionization potential?=?10.88?eV). Due to the use of many miniaturized components, the entire system has a weight of only 1.3?kg (excluding the helium cartridge) and dimensions of only 27?cm?x?24?cm x 12?cm. It is capable of detecting formaldehyde down to 0.5?ppb (V/V) with a signal-to-noise ratio of 6 in only 11?minutes. Meanwhile, simultaneous separation and detection of other air pollution related toxic compounds, such as benzene, toluene, ethylbenzene, and xylene, was also demonstrated by the 1-dimensional column and a flow-through micro-photoionization detector. The device developed here should have a broad range of applications in environmental protection, industries, space exploration, and battlefield.Ziegs, V., Poetz, S., Horsfield, B., Rinna, J., Hartwig, A., Skeie, J.E., 2018. Deeper insights into oxygen-containing compounds of the Mandal Formation, Central Graben, Norway. Energy & Fuels 32, 12030-12048. the kerogen composition, the amounts of generated bitumen play a major role when assessing the petroleum retention and expulsion behavior of a source rock. High-molecular weight (HMW) products dominate the source rock extracts during early stages of generation in the total organic carbon-rich, inefficiently expelling Mandal Formation. Such gas chromatography-unresolvable, bituminous compounds have not yet been structurally described. Based on 20 immature to peak-oil mature whole rock samples from different locations of the Central Graben, a compositional comparison of seven samples of different maturity stages is drawn to the excellently expelling Posidonia Shale, Germany, of similar maturity. Electrospray ionization negative Fourier transform ion cyclotron resonance mass spectrometry allows the investigation of the acidic heteroelemental interior of the in-source retained petroleum. Rather than the quantities of bitumen, its composition seems to be important for petroleum migration efficiency and fractionation. While Posidonia Shale extracts contain slightly higher proportions of NSO constituents than extracts of the Mandal Formation, they are dominated by lower polar nitrogen compounds. Instead, Mandal Formation extracts are strongly enriched in highly polar oxygen-containing (Ox) compounds (O2–O6) which are more aromatic but contain longer aliphatic chains than extracts of the Posidonia Shale samples, thus increasing their molecular size and the number of polar sites. In particular, it is the C16 and C18 aliphatic and C20 aromatic homologues occurring in O2+ classes which most likely represent fatty and aromatic acids linked with additional oxygen-functional groups. We suggest that these features might be specific to the Mandal Formation of the Central Graben and are related to complex interactions of geological/palaeogeographic evolution, climate fluctuations, and biological input during Upper Jurassic times. Consequently, the compositional features of petroleum generated from the Mandal Formation—highly polar, large aromatic core structures with long aliphatic chains attached—control its physical properties and cause interaction with polar phases, such as the residual kerogen or clay minerals, and nonpolar phases in the source rock.Zonneveld, K.A.F., Gray, D.D., Kuhn, G., Versteegh, G.J.M., 2019. Postdepositional aerobic and anaerobic particulate organic matter degradation succession reflected by dinoflagellate cysts: The Madeira Abyssal Plain revisited. Marine Geology 408, 87-109. report on the succession of selective degradation of dinoflagellate cyst species that can be considered representative for discrete particulate organic matter (POM) classes of different degradability. The effects of anaerobic and aerobic degradation as well as bioturbation in a natural setting are documented in high resolution by means of palynological and geochemical analyses on Madeira Abyssal Plain A- and F-turbidites. These turbidites are unique as their initial ungraded sediments are affected by a downward penetrating oxydation front.Geochemical analyses document the presence of an active downward penetrating oxidation front in the A turbidite, and a palaeo-oxidation front in the F-turbidite. In this latter turbidite, several zones can be distinguished from top to bottom: an oxidised bioturbated zone, an oxidised but not-bioturbated zone, a visible paleo-oxidation front, and a narrow nitrogenous zone overlying unoxidised sediments.We are the first to report that anaerobic degradation within the nitrogenous zones in both turbidites affects cysts of some heterotrophic dinoflagellates. The cyst species affected (Echinidinium aculeatum, Echinidinium spp., cysts of Protoperidinium monospinum and Brigantedinium spp.) exponentially decrease in this zone that is further characterised by a strong decrease in sulphur content due to sulphide oxidation. Degradation rates are different for each species. These cysts of heterotrophic dinoflagellates consist of a nitrogen-rich glycan in contrast to the cellulosic cysts walls of phototrophic dinoflagellates. Therefore, our observation supports the hypothesis that the quality of organic matter plays an important role in OM degradation in oxygen deficient environments with N-rich OM being more labile than other components in these environments.All heterotrophic species are strongly affected by aerobic degradation with their cyst concentrations exponentially decreasing with increasing oxygen exposure. Degradation rates vary between species and range von highly degradable to slightly degradable. Most strongly affected are cysts of Protoperidinium monospinum, Brigantedinium spp., and Echinidinium spp. Increasingly less affected are: Selenopemphix nephroides, Selenopemphix quanta, other Peridinioids and Echinidinium aculeatum. An effect of aerobic degradation on photosynthetic species could only be observed for Pentapharsodinium dalei. All Impagidinium species appeared to be resistant to aerobic degradation.Despite having analysed only a limited number of samples in the bioturbated zone of the F-turbidite, we have strong indications that the bioturbation can lead to the degradation of POM that is not affected by aerobic degradation alone. The cyst species Spiniferites ramosus, Impagidinium paradoxum, Lingulodinium machaerophorum, Nematosphaeropsis labyrinthus, Spiniferites spp., Impagidinium sphaericum, Spiniferites elongates and Spiniferites mirabilis do not show concentration changes in the non-bioturbated aerobic sediments but their concentrations are considerably decreased in the bioturbated part of the F-turbidite. This supports the hypothesis that bioturbation can increase the degradation of POM by e.g. increasing oxygen exposure time and/or by an alteration of aerobic and anaerobic conditions.We furthermore show that the degradation rates of POM components represented by individual cyst species differ between zones with different redox and biological conditions. This implies that POM degradation reaction rate coefficients are environment dependent. Our observation that dinoflagellate cyst species have different degradation rates ranging from extremely labile to extremely recalcitrant within the individual redox/bioturbation zones supports the hypothesis that cyst walls have a species specific molecular structure. Our results support continuum models of organic matter degradation that assume a continuous distribution of organic matter reactivity.Zou, Y., Niu, S., Dong, L., Hamada, N., Hashi, Y., Yang, W., Xu, P., Arakawa, K., Nagata, J., 2018. Determination of short-chain chlorinated paraffins using comprehensive two-dimensional gas chromatography coupled with low resolution mass spectrometry. Journal of Chromatography A 1581-1582, 135-143. chlorinated paraffins (SCCPs), recently listed as Persistent Organic Pollutants (POPs) under the Stockholm Convention, are contained in commercial chlorinated paraffin (CP) products, which are used in industries such as metalworking fluids, sealants, and textiles. A novel method to determine SCCPs by comprehensive two-dimensional gas chromatography coupled with low resolution mass spectrometry was developed. Calibration curves of response factor versus chlorine content in two chlorine content ranges (R2 were 0.9544 and 0.9736, respectively) were used for quantification of SCCP total concentration. Moreover, relative concentrations of 24 congener groups were also theoretically calculated. Results showed that this method was able to detect SCCP concentration in commercial CP products and urban air samples. SCCP contribution varied largely among different CP products, which is highly determined by carbon chain distribution in paraffins. SCCP concentration in urban air ranged between 12.8–49.1?ng m?3 during nine-month sampling period. The highest SCCP concentration appeared in summer, and the lowest concentration occurred in winter. Gas phase was dominantly occupied by lighter congeners such as C10 group and Cl6 group, while heavier congeners such as C13 group and Cl7 and Cl8 groups contributed more in particle phase. ................
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