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GEOCHEMISTRY ARTICLES – June 2019?Analytical ChemistryArgiriadis, E., Denniston, R.F., Barbante, C., 2019. Improved polycyclic aromatic hydrocarbon and n-alkane determination in speleothems through cleanroom sample processing. Analytical Chemistry 91, 7007-7011.Basheer, C., Kamran, M., Ashraf, M., Lee, H.K., 2019. Enhancing liquid-phase microextraction efficiency through chemical reactions. TrAC Trends in Analytical Chemistry 118, 426-433.Bystrzanowska, M., Tobiszewski, M., 2019. Multi-objective optimization of microextraction procedures. TrAC Trends in Analytical Chemistry 116, 266-273.Huang, J., Guo, X., Xu, T., Fan, L., Zhou, X., Wu, S., 2019. Ionic deep eutectic solvents for the extraction and separation of natural products. Journal of Chromatography A 1598, 1-19.Huang, X., Liu, M., Liu, X., Liu, Q., Chen, X., 2019. Polyethyleneimine functionalized multi-walled carbon nanotubes-based solid phase extraction for selective screening of carboxylic acid compounds in natural products. Chromatographia 82, 1017-1027.Jehli?ka, J., Culka, A., Mana, L., Oren, A., 2019. Comparison of miniaturized Raman spectrometers for discrimination of carotenoids of halophilic microorganisms. Frontiers in Microbiology 10, 1155. doi: 1110.3389/fmicb.2019.01155.Lovatti, B.P.O., Silva, S.R.C., Portela, N.d.A., Sad, C.M.S., Rainha, K.P., Rocha, J.T.C., Rom?o, W., Castro, E.V.R., Filgueiras, P.R., 2019. Identification of petroleum profiles by infrared spectroscopy and chemometrics. Fuel 254, 115670.Nims, C., Cron, B., Wetherington, M., Macalady, J., Cosmidis, J., 2019. Low frequency Raman Spectroscopy for micron-scale and in vivo characterization of elemental sulfur in microbial samples. Scientific Reports 9, Article 7971.Gas Chromatography/GC×GC/GC-MSArslan, F.N., Kolk, A., Janssen, H.G., 2019. Methods for one– and two–dimensional gas chromatography with flame ionization detection for identification of Mycobacterium tuberculosis in sputum. Journal of Chromatography B 1124, 204-217.Decq, L., Abatih, E., Van Keulen, H., Leyman, V., Cattersel, V., Steyaert, D., Van Binnebeke, E., Fremout, W., Saverwyns, S., Lynen, F., 2019. Nontargeted pattern recognition in the search for pyrolysis gas chromatography/mass spectrometry resin markers in historic lacquered objects. Analytical Chemistry 91, 7131-7138.Freije-Carrelo, L., García-Bellido, J., Calderón-Celis, F., Moldovan, M., Encinar, J.R., 2019. GC-ICP-MS/MS instrumental setup for total and speciation sulfur analysis in gasolines using generic standards. Analytical Chemistry 91, 7019-7024.Gough, D.V., Song, D.H., Sch?neich, S., Prebihalo, S.E., Synovec, R.E., 2019. Development of ultrafast separations using negative pulse partial modulation to enable new directions in gas chromatography. Analytical Chemistry 91, 7328-7335.He, J., Yu, L., Huang, X., Qi, M., 2019. Triptycene-based stationary phases for gas chromatographic separations of positional isomers. Journal of Chromatography A 1599, 223-230.Li, G.-S., Fan, X., You, C.-Y., Zhao, Y.-P., Wang, R.-Y., Wei, X.-Y., Ma, F.-Y., Lu, X., Mo, W.-L., Li, X., 2019. Molecular characteristics of the soluble components from three low-rank coals based on the analyses using GC/MS and GC/Q-TOF MS. Fuel 254, 115602.Ma, P., Li, M., Lu, H., Zhang, Z., 2019. MARS 2: A computational tool to resolve and extract features from large-scale GC-MS datasets. Chemometrics and Intelligent Laboratory Systems 191, 12-20.Millan, M., Szopa, C., Buch, A., Cabane, M., Teinturier, S., Mahaffy, P., Johnson, S.S., 2019. Performance of the SAM gas chromatographic columns under simulated flight operating conditions for the analysis of chlorohydrocarbons on Mars. Journal of Chromatography A 1598, 183-195.Palos, R., Kek?l?inen, T., Duodu, F., Gutiérrez, A., Arandes, J.M., J?nis, J., Casta?o, P., 2019. Screening hydrotreating catalysts for the valorization of a light cycle oil/scrap tires oil blend based on a detailed product analysis. Applied Catalysis B: Environmental 256, Article 117863.Schwanz, T.G., Bokowski, L.V.V., Marcelo, M.C.A., Jandrey, A.C., Dias, J.C., Maximiano, D.H., Canova, L.S., Pontes, O.F.S., Sabin, G.P., Kaiser, S., 2019. Analysis of chemosensory markers in cigarette smoke from different tobacco varieties by GC×GC-TOFMS and chemometrics. Talanta 202, 74-89.Sirén, K., Fischer, U., Vestner, J., 2019. Automated supervised learning pipeline for non-targeted GC-MS data analysis. Analytica Chimica Acta: X 1, Article 100005.Swinley, J., de Coning, P., 2019. A Practical Guide to Gas Analysis by Gas Chromatography. Elsevier. 440 pp.Zhang, N., Su, L., Man, S., Lei, X., Huang, T., Zhu, C., Zhang, L., Wu, X., 2019. Task-specific solid-phase microextraction based on ionic liquid/polyhedral oligomeric silsesquioxane hybrid coating for sensitive analysis of polycyclic aromatic hydrocarbons by gas chromatography–mass spectrometry. Journal of Chromatography A 1598, 49-57.Zhu, G., Liu, F., Li, P., He, S., Zhu, S., Gao, Q., Feng, Y., 2019. Profiling free fatty acids in edible oils via magnetic dispersive extraction and comprehensive two-dimensional gas chromatography-mass spectrometry. Food Chemistry 297, Article 124998.Imaging: AFMKaiser, K., Gross, L., Schulz, F., 2019. A single-molecule chemical reaction studied by high-resolution atomic force microscopy and scanning tunneling microscopy induced light emission. ACS Nano 13, 6947-6954.Mittelviefhaus, M., Müller, D.B., Zambelli, T., Vorholt, J.A., 2019. A modular atomic force microscopy approach reveals a large range of hydrophobic adhesion forces among bacterial members of the leaf microbiota. The ISME Journal 13, 1878-1882.Zahl, P., Zhang, Y., 2019. Guide for atomic force microscopy image analysis to discriminate heteroatoms in aromatic molecules. Energy & Fuels 33, 4775-4780.Imaging: SEM, TEM, HIMChen, Z., Song, Y., Jiang, Z., Liu, S., Li, Z., Shi, D., Yang, W., Yang, Y., Song, J., Gao, F., Zhang, K., Guo, X., 2019. Identification of organic matter components and organic pore characteristics of marine shale: A case study of Wufeng-Longmaxi shale in southern Sichuan Basin, China. Marine and Petroleum Geology 109, 56-69.Deirieh, A., Chang, I.Y., Casey, B., Joester, D., Germaine, J.T., 2019. Impact of drying and effective stresses on the pore space and microstructure of mudrocks. Journal of Geophysical Research: Solid Earth 124, 4290-4304.Emslie, S.D., Alderman, A., McKenzie, A., Brasso, R., Taylor, A.R., Molina Moreno, M., Cambra-Moo, O., González Martín, A., Silva, A.M., Valera, A., García Sanjuán, L., Vijande Vila, E., 2019. Mercury in archaeological human bone: biogenic or diagenetic? Journal of Archaeological Science 108, 104969.Hou, Y., Zhang, K., Wang, F., He, S., Dong, T., Wang, C., Qin, W., Xiao, Y., Tang, B., Yu, R., Du, X., 2019. Structural evolution of organic matter and implications for graphitization in over-mature marine shales, south China. Marine and Petroleum Geology 109, 304-316.Kwiecińska, B., Pusz, S., Valentine, B.J., 2019. Application of electron microscopy TEM and SEM for analysis of coals, organic-rich shales and carbonaceous matter. International Journal of Coal Geology 211, Aticle 103203.Song, L., Warner, T., Carr, T., 2019. An efficient, consistent, and trackable method to quantify organic matter–hosted porosity from ion-milled scanning electron microscope images of mudrock gas reservoirs. American Association of Petroleum Geologists Bulletin 103, 1473-1492.Sun, M., Zhang, L., Hu, Q., Pan, Z., Yu, B., Sun, L., Bai, L., Connell, L.D., Zhang, Y., Cheng, G., 2019. Pore connectivity and water accessibility in Upper Permian transitional shales, southern China. Marine and Petroleum Geology 107, 407-422.Turner-Walker, G., 2019. Light at the end of the tunnels? The origins of microbial bioerosion in mineralised collagen. Palaeogeography, Palaeoclimatology, Palaeoecology 529, 24-38.Vishal, V., Chandra, D., Bahadur, J., Sen, D., Hazra, B., Mahanta, B., Mani, D., 2019. Interpreting pore dimensions in gas shales using a combination of SEM imaging, small-angle neutron scattering, and low-pressure gas adsorption. Energy & Fuels 33, 4835-4848.Wu, H., Yao, Y., Zhou, Y., Qiu, F., 2019. Analyses of representative elementary volume for coal using X-ray μ-CT and FIB-SEM and its application in permeability predication model. Fuel 254, Article 115563.Xu, H., Zhou, W., Hu, Q., Xia, X., Zhang, C., Zhang, H., 2019. Fluid distribution and gas adsorption behaviors in over-mature shales in southern China. Marine and Petroleum Geology 109, 223-232.Imaging: X-ray CTBaek, S.-H., Hong, J.-W., Kim, K.Y., Yeom, S., Kwon, T.-H., 2019. X-Ray computed microtomography imaging of abiotic carbonate precipitation in porous media from a supersaturated solution: Insights into effect of CO2 mineral trapping on permeability. Water Resources Research 55, 3835-3855.Chung, T., Wang, Y.D., Armstrong, R.T., Mostaghimi, P., 2019. Approximating permeability of microcomputed-tomography images using elliptic flow equations. SPE-183159-PA 24, 1154-1163.Larmagnat, S., Des Roches, M., Daigle, L.-F., Francus, P., Lavoie, D., Raymond, J., Malo, M., Aubiès-Trouilh, A., 2019. Continuous porosity characterization: Metric-scale intervals in heterogeneous sedimentary rocks using medical CT-scanner. Marine and Petroleum Geology 109, 361-380.Lei, L., Liu, Z., Seol, Y., Boswell, R., Dai, S., 2019. An investigation of hydrate formation in unsaturated sediments using X-ray computed tomography. Journal of Geophysical Research: Solid Earth 124, 3335-3349.Li, T., Li, M., Jing, X., Xiao, W., Cui, Q., 2019. Influence mechanism of pore-scale anisotropy and pore distribution heterogeneity on permeability of porous media. Petroleum Exploration and Development 46, 594-604.Luo, C., Reitner, J., 2019. Three-dimensionally preserved stem-group hexactinellid sponge fossils from lower Cambrian (Stage?2) phosphorites of China. PalZ 93, 187-194.Min, X., Hua, H., Liu, L., Sun, B., Cui, Z., Jiang, T., 2019. Phosphatized Epiphyton from the terminal Neoproterozoic and its significance. Precambrian Research 331, Article 105358.Roslin, A., Pokrajac, D., Zhou, Y., 2019. Cleat structure analysis and permeability simulation of coal samples based on micro-computed tomography (micro-CT) and scan electron microscopy (SEM) technology. Fuel 254, Article 115579.Tonai, S., Kubo, Y., Tsang, M.-Y., Bowden, S., Ide, K., Hirose, T., Kamiya, N., Yamamoto, Y., Yang, K., Yamada, Y., Morono, Y., Heuer, V.B., Inagaki, F., Expedition 370 Scientists, 2019. A new method for quality control of geological cores by X-ray computed tomography: application in IODP Expedition 370. Frontiers in Earth Science 7, 117. doi: 110.3389/feart.2019.00117.Tudisco, E., Etxegarai, M., Hall, S.A., Charalampidou, E.M., Couples, G.D., Lewis, H., Tengattini, A., Kardjilov, N., 2019. Fast 4-D imaging of fluid flow in rock by high-speed neutron tomography. Journal of Geophysical Research: Solid Earth 124, 3557-3569.Wang, Y., Chen, J.-H., Althaus, S.M., Yu, M., Chen, J., 2019. Electrical properties of unconventional source rocks from Micro-CT using numerical mixing law. Fuel 254, Article 115576.Wu, H., Yao, Y., Zhou, Y., Qiu, F., 2019. Analyses of representative elementary volume for coal using X-ray μ-CT and FIB-SEM and its application in permeability predication model. Fuel 254, Article 115563.Wu, Y., Tahmasebi, P., Lin, C., Ren, L., Dong, C., 2019. Multiscale modeling of shale samples based on low- and high-resolution images. Marine and Petroleum Geology 109, 9-21.Yu, T., Kelly, R., Mu, L., Ross, A., Kennedy, J., Broly, P., Xia, F., Zhang, H., Wang, B., Dilcher, D., 2019. An ammonite trapped in Burmese amber. Proceedings of the National Academy of Sciences 116, 11345-11350.Liquid Chromatography/LC-MS/SFCAdamopoulou, T., Nawada, S., Deridder, S., Wouters, B., Desmet, G., Schoenmakers, P.J., 2019. Experimental and numerical study of band-broadening effects associated with analyte transfer in microfluidic devices for spatial two-dimensional liquid chromatography created by additive manufacturing. Journal of Chromatography A 1598, 77-84.Brand?o, P.F., Duarte, A.C., Duarte, R.M.B.O., 2019. Comprehensive multidimensional liquid chromatography for advancing environmental and natural products research. TrAC Trends in Analytical Chemistry 116, 186-197.Daoud, A.B.A., Tremblay, L., 2019. HPLC-SEC-FTIR characterization of the dissolved organic matter produced by the microbial carbon pump. Marine Chemistry 215, 103668.Jin, H., Lao, Y.M., Zhou, J., Zhang, H.J., Cai, Z.H., 2019. Optimization of extraction solvents, solid phase extraction and decoupling for quantitation of free isoprenoid diphosphates in Haematococcus pluvialis by liquid chromatography with tandem mass spectrometry. Journal of Chromatography A 1598, 30-38.Kadokami, K., Ueno, D., 2019. Comprehensive target analysis for 484 organic micropollutants in environmental waters by the combination of tandem solid-phase extraction and quadrupole time-of-flight mass spectrometry with sequential window acquisition of all theoretical fragment-ion spectra acquisition. Analytical Chemistry 91, 7749-7755.Kartsova, L.A., Bessonova, E.A., Somova, V.D., 2019. Hydrophilic interaction chromatography. Journal of Analytical Chemistry 74, 415-424.Kim, D., Kim, S., Son, S., Jung, M.-J., Kim, S., 2019. Application of online liquid chromatography 7 T FT-ICR mass spectrometer equipped with quadrupolar detection for analysis of natural organic matter. Analytical Chemistry 91, 7690-7697.Laaniste, A., Leito, I., Kruve, A., 2019. ESI outcompetes other ion sources in LC/MS trace analysis. Analytical and Bioanalytical Chemistry 411, 3533-3542.Law, K.P., Zhang, C.L., 2019. Current progress and future trends in mass spectrometry-based archaeal lipidomics. Organic Geochemistry 134, 45-61.López-Ruiz, R., Romero-González, R., Garrido Frenich, A., 2019. Ultrahigh-pressure liquid chromatography-mass spectrometry: An overview of the last decade. TrAC Trends in Analytical Chemistry 118, 170-181.Rigano, F., Tranchida, P.Q., Dugo, P., Mondello, L., 2019. High-performance liquid chromatography combined with electron ionization mass spectrometry: A review. TrAC Trends in Analytical Chemistry 118, 112-122.Saowapon, M.T., Thurbide, K.B., 2019. Dehydration of a water stationary phase as a novel separation gradient in capillary supercritical fluid chromatography. Chromatographia 82, 991-1001.Viktor, Z., Farcet, C., Moire, C., Brothier, F., Pfukwa, H., Pasch, H., 2019. Comprehensive two-dimensional liquid chromatography for the characterization of acrylate-modified hyaluronic acid. Analytical and Bioanalytical Chemistry 411, 3321-3330.Yuan, B., Muir, D., MacLeod, M., 2019. Methods for trace analysis of short-, medium-, and long-chain chlorinated paraffins: Critical review and recommendations. Analytica Chimica Acta 1074, 16-32.Mass Spectroscopy/ICR-FTMS/OrbitrapBianco, A., Deguillaume, L., Chaumerliac, N., Va?tilingom, M., Wang, M., Delort, A.-M., Bridoux, M.C., 2019. Effect of endogenous microbiota on the molecular composition of cloud water: a study by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Scientific Reports 9, Article 7663.Dusny, C., Lohse, M., Reemtsma, T., Schmid, A., Lechtenfeld, O.J., 2019. Quantifying a biocatalytic product from a few living microbial cells using microfluidic cultivation coupled to FT-ICR-MS. Analytical Chemistry 91, 7012-7018.Grandy, J.J., Lashgari, M., Heide, H.V., Poole, J., Pawliszyn, J., 2019. Introducing a mechanically robust SPME sampler for the on-site sampling and extraction of a wide range of untargeted pollutants in environmental waters. Environmental Pollution 252. Part A, 825-834.Hoegg, E.D., Godin, S., Szpunar, J., Lobinski, R., Koppenaal, D.W., Marcus, R.K., 2019. Ultra-high resolution elemental/isotopic mass spectrometry (m/Δm?>?1,000,000): Coupling of the liquid sampling-atmospheric pressure glow discharge with an Orbitrap mass spectrometer for applications in biological chemistry and environmental analysis. Journal of The American Society for Mass Spectrometry 30, 1163-1168.Kim, D., Kim, S., Son, S., Jung, M.-J., Kim, S., 2019. Application of online liquid chromatography 7 T FT-ICR mass spectrometer equipped with quadrupolar detection for analysis of natural organic matter. Analytical Chemistry 91, 7690-7697.Kostyukevich, Y., Zherebker, A., Vlaskin, M.S., Roznyatovsky, V.A., Grishin, Y.K., Nikolaev, E., 2019. Speciation of structural fragments in crude oil by means of isotope exchange in near-critical water and Fourier transform mass spectrometry. Analytical and Bioanalytical Chemistry 411, 3331-3339.Krajewski, L.C., Robbins, W.K., Corilo, Y.E., Bota, G., Marshall, A.G., Rodgers, R.P., 2019. Characterization of ketones formed in the open system corrosion test of naphthenic acids by Fourier transform ion cyclotron resonance mass spectrometry. Energy & Fuels 33, 4946-4950.Li, B., Fan, X., Yu, Y.-R., Wang, F., Li, X., Lu, Y., Wei, X.-Y., Ma, F.-Y., Zhao, Y.-P., Zhao, W., 2019. Insight into molecular information of Huolinguole lignite obtained by Fourier transform ion cyclotron resonance mass spectrometry and statistical methods. Rapid Communications in Mass Spectrometry 33, 1107-1113.Neumann, E.K., Ellis, J.F., Triplett, A.E., Rubakhin, S.S., Sweedler, J.V., 2019. Lipid analysis of 30?000 individual rodent cerebellar cells using high-resolution mass spectrometry. Analytical Chemistry 91, 7871-7878.Niles, S.F., Chacón-Pati?o, M.L., Chen, H., McKenna, A.M., Blakney, G.T., Rodgers, R.P., Marshall, A.G., 2019. Molecular-level characterization of oil-soluble ketone/aldehyde photo-oxidation products by Fourier transform ion cyclotron resonance mass spectrometry reveals similarity between microcosm and field samples. Environmental Science & Technology 53, 6887-6894.Niu, X.-Z., Croué, J.-P., 2019. Photochemical production of hydroxyl radical from algal organic matter. Water Research 116, 11-16.Palos, R., Kek?l?inen, T., Duodu, F., Gutiérrez, A., Arandes, J.M., J?nis, J., Casta?o, P., 2019. Screening hydrotreating catalysts for the valorization of a light cycle oil/scrap tires oil blend based on a detailed product analysis. Applied Catalysis B: Environmental 256, Article 117863.Pan, Y., Li, M., Sun, Y., Li, Z., Liu, P., Jiang, B., Liao, Y., 2019. Characterization of free and bound bitumen fractions in a thermal maturation shale sequence. Part 1: Acidic and neutral compounds by negative-ion ESI FT-ICR MS. Organic Geochemistry 134, 1-15.Ridgeway, M.E., Bleiholder, C., Mann, M., Park, M.A., 2019. Trends in trapped ion mobility – Mass spectrometry instrumentation. TrAC Trends in Analytical Chemistry 116, 324-331.Rüger, C.P., Maillard, J., Le Ma?tre, J., Ridgeway, M., Thompson, C.J., Schmitz-Afonso, I., Gautier, T., Carrasco, N., Park, M.A., Giusti, P., Afonso, C., 2019. Structural study of analogues of titan’s haze by trapped ion mobility coupled with a Fourier transform ion cyclotron mass spectrometer. Journal of The American Society for Mass Spectrometry 30, 1169-1173.Wang, K., Zhang, Y., Huang, R.-J., Wang, M., Ni, H., Kampf, C.J., Cheng, Y., Bilde, M., Glasius, M., Hoffmann, T., 2019. Molecular characterization and source identification of atmospheric particulate organosulfates using ultrahigh resolution mass spectrometry. Environmental Science & Technology 53, 6192-6202.Wang, S., Sun, S., Shan, C., Pan, B., 2019. Analysis of trace phosphonates in authentic water samples by pre-methylation and LC-Orbitrap MS/MS. Water Research 161, 78-88.Wu, J., Zhang, W., Ma, C., Wang, F., Zhou, X., Chung, K.H., Hou, D., Zhang, Y., Shi, Q., 2019. Isolation and characterization of sulfur compounds in a lacustrine crude oil. Fuel 253, 1482-1489.Yuan, C., Sleighter, R.L., Weavers, L.K., Hatcher, P.G., Chin, Y.-P., 2019. Fast photomineralization of dissolved organic matter in acid mine drainage impacted waters. Environmental Science & Technology 53, 6273-6281.Zhou, X., Zhao, S., Xu, C., Chung, K.H., Shi, Q., 2019. Molecular structure of heavy petroleum: Revealed by molecular composition of ruthenium-ion-catalyzed oxidation products. Energy & Fuels 33, 4781-4791.Zhu, M., Jiang, B., Li, S., Yu, Q., Yu, X., Zhang, Y., Bi, X., Yu, J., George, C., Yu, Z., Wang, X., 2019. Organosulfur compounds formed from heterogeneous reaction between SO2 and particulate-bound unsaturated fatty acids in ambient air. Environmental Science & Technology Letters 6, 318-322.Zhuo, X., Huang, H., Lan, F., He, C., Pan, Q., Zhang, Y., Shi, Q., 2019. Molecular transformation of dissolved organic matter in high-temperature hydrogen peroxide oxidation of a refinery wastewater. Environmental Chemistry Letters 17, 1117-1123.Mass Spectroscopy/OtherDing, L., Rusinov, A., 2019. High-capacity electrostatic ion trap with mass resolving power boosted by high-order harmonics. Analytical Chemistry 91, 7595-7602.Douchi, D., Liang, F., Cano, M., Xiong, W., Wang, B., Maness, P.-C., Lindblad, P., Yu, J., 2019. Membrane-inlet mass spectrometry enables a quantitative understanding of inorganic carbon uptake flux and carbon concentrating mechanisms in metabolically engineered cyanobacteria. Frontiers in Microbiology 10, 1356. doi: 1310.3389/fmicb.2019.01356.Garimella, S.V.B., Nagy, G., Ibrahim, Y.M., Smith, R.D., 2019. Opening new paths for biological applications of ion mobility - Mass spectrometry using structures for lossless ion manipulations. TrAC Trends in Analytical Chemistry 116, 300-307.Hijazi, H.Y., Bottaro, C.S., 2019. Analysis of thiophenes in seawater: Molecularly imprinted polymer thin-film extraction with desorption electrospray ionization mass spectrometry. International Journal of Mass Spectrometry 443, 9-15.Khare, P., Marcotte, A., Sheu, R., Walsh, A.N., Ditto, J.C., Gentner, D.R., 2019. Advances in offline approaches for trace measurements of complex organic compound mixtures via soft ionization and high-resolution tandem mass spectrometry. Journal of Chromatography A 1598, 163-174.Laaniste, A., Leito, I., Kruve, A., 2019. ESI outcompetes other ion sources in LC/MS trace analysis. Analytical and Bioanalytical Chemistry 411, 3533-3542.Meisenbichler, C., Doppler, C., Bernhard, D., Müller, T., 2019. Improved matrix coating for positive- and negative-ion-mode MALDI-TOF imaging of lipids in blood vessel tissues. Analytical and Bioanalytical Chemistry 411, 3221-3227.Neumann, E.K., Ellis, J.F., Triplett, A.E., Rubakhin, S.S., Sweedler, J.V., 2019. Lipid analysis of 30?000 individual rodent cerebellar cells using high-resolution mass spectrometry. Analytical Chemistry 91, 7871-7878.Nozaki, K., Nakabayashi, Y., Murakami, T., Miyazato, A., Osaka, I., 2019. Novel approach to enhance sensitivity in surface-assisted laser desorption/ionization mass spectrometry imaging using deposited organic-inorganic hybrid matrices. Journal of Mass Spectrometry 54, 612-619.Reinecke, T., Naylor, C.N., Clowers, B.H., 2019. Ion multiplexing: Maximizing throughput and signal to noise ratio for ion mobility spectrometry. TrAC Trends in Analytical Chemistry 116, 340-345.Ridgeway, M.E., Bleiholder, C., Mann, M., Park, M.A., 2019. Trends in trapped ion mobility – Mass spectrometry instrumentation. TrAC Trends in Analytical Chemistry 116, 324-331.Zhai, Y., Xu, Q., Tang, Y., Liu, S., Li, D., Xu, W., 2019. Boosting the sensitivity and selectivity of a miniature mass spectrometer using a hybrid ion funnel. Analytical Chemistry 91, 7911-7919.Zhao, P., Guo, Y., Dewald, H.D., Chen, H., 2019. Improvements for absolute quantitation using electrochemical mass spectrometry. International Journal of Mass Spectrometry 443, 41-45.Metabolomics/LipidomicsBurnum-Johnson, K.E., Zheng, X., Dodds, J.N., Ash, J., Fourches, D., Nicora, C.D., Wendler, J.P., Metz, T.O., Waters, K.M., Jansson, J.K., Smith, R.D., Baker, E.S., 2019. Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples. TrAC Trends in Analytical Chemistry 116, 292-299.Harris, R.A., Leaptrot, K.L., May, J.C., McLean, J.A., 2019. New frontiers in lipidomics analyses using structurally selective ion mobility-mass spectrometry. TrAC Trends in Analytical Chemistry 116, 316-323.Jeanne Dit Fouque, K., Fernandez-Lima, F., 2019. Recent advances in biological separations using trapped ion mobility spectrometry – mass spectrometry. TrAC Trends in Analytical Chemistry 116, 308-315.Jin, H., Lao, Y.M., Zhou, J., Zhang, H.J., Cai, Z.H., 2019. Optimization of extraction solvents, solid phase extraction and decoupling for quantitation of free isoprenoid diphosphates in Haematococcus pluvialis by liquid chromatography with tandem mass spectrometry. Journal of Chromatography A 1598, 30-38.Krummenacker, M., Latendresse, M., Karp, P.D., 2019. Metabolic route computation in organism communities. Microbiome 7, 89.Law, K.P., Zhang, C.L., 2019. Current progress and future trends in mass spectrometry-based archaeal lipidomics. Organic Geochemistry 134, 45-61.Levy, A.J., Oranzi, N.R., Ahmadireskety, A., Kemperman, R.H.J., Wei, M.S., Yost, R.A., 2019. Recent progress in metabolomics using ion mobility-mass spectrometry. TrAC Trends in Analytical Chemistry 116, 274-281.López-Ruiz, R., Romero-González, R., Garrido Frenich, A., 2019. Ultrahigh-pressure liquid chromatography-mass spectrometry: An overview of the last decade. TrAC Trends in Analytical Chemistry 118, 170-181.Meisenbichler, C., Doppler, C., Bernhard, D., Müller, T., 2019. Improved matrix coating for positive- and negative-ion-mode MALDI-TOF imaging of lipids in blood vessel tissues. Analytical and Bioanalytical Chemistry 411, 3221-3227.Moon, M.H., 2019. Flow field-flow fractionation: Recent applications for lipidomic and proteomic analysis. TrAC Trends in Analytical Chemistry 118, 19-28.Paudel, L., Nagana Gowda, G.A., Raftery, D., 2019. Extractive ratio analysis NMR spectroscopy for metabolite identification in complex biological mixtures. Analytical Chemistry 91, 7373-7378.Salama, E.-S., Govindwar, S.P., Khandare, R.V., Roh, H.-S., Jeon, B.-H., Li, X., 2019. Can omics approaches improve microalgal biofuels under abiotic stress? Trends in Plant Science 24, 611-624.Sazanova, K.V., Senik, S.V., Kirtsideli, I.Y., Shavarda, A.L., 2019. Metabolomic profiling and lipid composition of Arctic and Antarctic strains of micromycetes Geomyces pannorum and Thelebolus microsporus Grown at different temperatures. Microbiology 88, 282-291.Sirén, K., Fischer, U., Vestner, J., 2019. Automated supervised learning pipeline for non-targeted GC-MS data analysis. Analytica Chimica Acta: X 1, Article 100005.Tu, J., Zhou, Z., Li, T., Zhu, Z.-J., 2019. The emerging role of ion mobility-mass spectrometry in lipidomics to facilitate lipid separation and identification. TrAC Trends in Analytical Chemistry 116, 332-339.van Outersterp, R.E., Houthuijs, K.J., Berden, G., Engelke, U.F., Kluijtmans, L.A.J., Wevers, R.A., Coene, K.L.M., Oomens, J., Martens, J., 2019. Reference-standard free metabolite identification using infrared ion spectroscopy. International Journal of Mass Spectrometry 443, 77-85.Zang, X., Monge, M.E., Fernández, F.M., 2019. Mass spectrometry-based non-targeted metabolic profiling for disease detection: Recent developments. TrAC Trends in Analytical Chemistry 118, 158-169.Zeng, J., Liu, S., Cai, W., Jiang, H., Lu, X., Li, G., Li, J., Liu, J., 2019. Emerging lipidome patterns associated with marine Emiliania huxleyi-virus model system. Science of The Total Environment 688, 521-528.PuppyomicsLatham, K.J., Losey, R.J., 2019. Spondylosis deformans as an indicator of transport activities in archaeological dogs: A systematic evaluation of current methods for assessing archaeological specimens. PLOS ONE 14, Article e0214575.Archaeological/Art Organic ChemistryAguraiuja-L?tti, ?., L?ugas, L., 2019. Stable isotope evidence for medieval diet in urban and rural northern Estonia. Journal of Archaeological Science: Reports 26, 101901.Barnes, K.M., Whiffin, A.L., Bulling, M.T., 2019. 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Energy & Fuels 33, 5200-5207.Ma, X., Guo, S., Shi, D., Zhou, Z., Liu, G., 2019. Investigation of pore structure and fractal characteristics of marine-continental transitional shales from Longtan Formation using MICP, gas adsorption, and NMR (Guizhou, China). Marine and Petroleum Geology 107, 555-571.Neuzil, C.E., 2019. Permeability of clays and shales. Annual Review of Earth and Planetary Sciences 47, 247-273.Pang, Y., Chen, S., Soliman, M.Y., Morse, S.M., Hu, X., 2019. Evaluation of matrix swelling behavior in shale induced by methane sorption under triaxial stress and strain conditions. Energy & Fuels 33, 4986-5000.Shi, W., Wang, X., Zhang, C., Feng, A., Huang, Z., 2019. Experimental study on gas content of adsorption and desorption in Fuling shale gas field. Journal of Petroleum Science and Engineering 180, 1069-1076.Sobecki, N., Nieto-Draghi, C., Di Lella, A., Ding, D.Y., 2019. Phase behavior of hydrocarbons in nano-pores. Fluid Phase Equilibria 497, 104-121.Song, L., Warner, T., Carr, T., 2019. An efficient, consistent, and trackable method to quantify organic matter–hosted porosity from ion-milled scanning electron microscope images of mudrock gas reservoirs. American Association of Petroleum Geologists Bulletin 103, 1473-1492.Sun, M., Zhang, L., Hu, Q., Pan, Z., Yu, B., Sun, L., Bai, L., Connell, L.D., Zhang, Y., Cheng, G., 2019. Pore connectivity and water accessibility in Upper Permian transitional shales, southern China. Marine and Petroleum Geology 107, 407-422.Tan, S.P., Barsotti, E., Piri, M., 2019. Application of material balance for the phase transition of fluid mixtures confined in nanopores. Fluid Phase Equilibria 496, 31-41.Tang, L., Song, Y., Jiang, Z., Jiang, S., Li, Q., 2019. Pore structure and fractal characteristics of distinct thermally mature shales. Energy & Fuels 33, 5116-5128.Tangirala, S., Sheng, J.J., 2019. Investigation of oil production and flowback in hydraulically-fractured water-wet formations using the Lab-on-a-Chip method. Fuel 254, Article 115543.Vishal, V., Chandra, D., Bahadur, J., Sen, D., Hazra, B., Mahanta, B., Mani, D., 2019. Interpreting pore dimensions in gas shales using a combination of SEM imaging, small-angle neutron scattering, and low-pressure gas adsorption. Energy & Fuels 33, 4835-4848.Wang, K., Wang, G., Jiang, Y., Wang, S., Han, W., Chen, X., 2019. How transport properties of a shale gas reservoir change during extraction: A strain-dependent triple-porosity model. Journal of Petroleum Science and Engineering 180, 1088-1100.Wang, Y., Chen, J.-H., Althaus, S.M., Yu, M., Chen, J., 2019. Electrical properties of unconventional source rocks from Micro-CT using numerical mixing law. Fuel 254, Article 115576.Wei, S., He, S., Pan, Z., Guo, X., Yang, R., Dong, T., Yang, W., Gao, J., 2019. Models of shale gas storage capacity during burial and uplift: Application to Wufeng-Longmaxi shales in the Fuling shale gas field. Marine and Petroleum Geology 109, 233-244.Wen, M., Jiang, Z., Zhang, K., Song, Y., Jiang, S., Jia, C., Liu, W., Huang, Y., Liu, T., Xie, X., Sun, Y., Fan, S., Cao, X., Zhu, L., Zhou, C., 2019. Difference analysis of organic matter enrichment mechanisms in Upper oOdovician-Lower Silurian shale from the Yangtze region of southern China and its geological significance in shale gas exploration. Geofluids 2019, Article 9524507.Wu, S., Zhai, X., Yang, Z., Bale, H., Hong, Y., Cui, J., Pan, S., Lin, S., 2019. Characterization of fracture formation in organic-rich shales - An experimental and real time study of the Permian Lucaogou Formation, Junggar Basin, northwestern China. Marine and Petroleum Geology 107, 397-406.Xu, H., Zhou, W., Hu, Q., Xia, X., Zhang, C., Zhang, H., 2019. Fluid distribution and gas adsorption behaviors in over-mature shales in southern China. Marine and Petroleum Geology 109, 223-232.Yang, R., Hu, Q., Yi, J., Zhang, B., He, S., Guo, X., Hou, Y., Dong, T., 2019. The effects of mineral composition, TOC content and pore structure on spontaneous imbibition in Lower Jurassic Dongyuemiao shale reservoirs. Marine and Petroleum Geology 109, 268-278.Yang, Y., Huang, D., 2019. Geological characteristics and new understandings of exploration and development of Jurassic lacustrine shale oil and gas in the Sichuan Basin. Natural Gas Industry 39, 22-33.Yang, Z., Zou, C., Hou, L., Wu, S., Lin, S., Luo, X., Zhang, L., Zhao, Z., Cui, J., Pan, S., 2019. Division of fine-grained rocks and selection of “sweet sections” in the oldest continental shale in China: Taking the coexisting combination of tight and shale oil in the Permian Junggar Basin. Marine and Petroleum Geology 109, 339-348.Yu, Y., Luo, X., Wang, Z., Cheng, M., Lei, Y., Zhang, L., Yin, J., 2019. A new correction method for mercury injection capillary pressure (MICP) to characterize the pore structure of shale. Journal of Natural Gas Science and Engineering 68, 102896.Zhang, S., Liu, H., Wang, M., Liu, X., Liu, H., Bao, Y., Wang, W., Li, R., Luo, X., Fang, Z., 2019. Shale pore characteristics of Shahejie Formation: Implication for pore evolution of shale oil reservoirs in Dongying sag, north China. Petroleum Research 4, 113-124.Zhang, S., Pu, H., Zhao, J.X., 2019. Experimental and numerical studies of spontaneous imbibition with different boundary conditions: Case studies of Middle Bakken and Berea cores. Energy & Fuels 33, 5135-5146.Zhao, J., Jin, Z., Hu, Q., Liu, K., Liu, G., Gao, B., Liu, Z., Zhang, Y., Wang, R., 2019. Geological controls on the accumulation of shale gas: A case study of the early Cambrian shale in the Upper Yangtze area. Marine and Petroleum Geology 107, 423-437.Zhao, W., Zhang, S., He, K., Zeng, H., Hu, G., Zhang, B., Wang, Z., Li, Y., 2019. Origin of conventional and shale gas in Sinian–lower Paleozoic strata in the Sichuan Basin: Relayed gas generation from liquid hydrocarbon cracking. American Association of Petroleum Geologists Bulletin 103, 1265-1296.Zhao, X., Pu, X., Jin, F., Han, W., Shi, Z., Cai, A., Wang, A., Guan, Q., Jiang, W., Zhang, W., 2019. Geological characteristics and key exploration technologies of continental shale oil sweet spots: A case study of Member 2 of Kongdian Formation in the Cangdong sag in the Huanghua depression, Bohai Bay Basin. Petroleum Research 4, 97-112.Zheng, D., Pang, X., Ma, X., Li, C., Zheng, T., Zhou, L., 2019. Hydrocarbon generation and expulsion characteristics of the source rocks in the third member of the Upper Triassic Xujiahe Formation and its effect on conventional and unconventional hydrocarbon resource potential in the Sichuan Basin. Marine and Petroleum Geology 109, 175-192.Zhou, J., Mao, Q., Luo, K.H., 2019. Effects of moisture and salinity on methane adsorption in kerogen: A molecular simulation study. Energy & Fuels 33, 5368-5376.Zhu, C., Qin, X., Li, Y., Gong, H., Li, Z., Xu, L., Dong, M., 2019. Adsorption and dissolution behaviors of CO2 and n-alkane mixtures in shale: Effects of the alkane type, shale properties and temperature. Fuel 253, 1361-1370.Zou, C., Guo, Q., Yang, Z., Wu, S., Chen, N., Lin, S., Pan, S., 2019. Resource potential and core area prediction of lacustrine tight oil: The Triassic Yanchang Formation in Ordos Basin, China. American Association of Petroleum Geologists Bulletin 103, 1493-1523.AbstractsAbd-Allah, Z.M., Abdullah, W.H., Abdel-Fattah, M.I., 2019. Assessment of Eocene, Paleocene and Cretaceous source rocks in the West Feiran area, offshore Gulf of Suez, Egypt. Journal of Petroleum Science and Engineering 180, 756-772. study area is located in the West Feiran area, offshore Gulf of Suez, Egypt. This gulf is a well-known petroleum prolific basin that was formed from Late-Oligocene to Early Miocene times. This study focuses on evaluating the source rocks of Eocene (Thebes Formation), Paleocene (Esna Formation) and Cretaceous (Sudr, Brown Ls., Matulla, Wata and Raha formations) of GS 197–2 and WFA-1 wells based on total organic carbon (TOC), Rock-Eval pyrolysis, vitrinite reflectance (VR), and seismic data. In this study, Thebes, Sudr and Brown Ls. are considered to have fair to very good TOC (up to 4.05?wt%) that are characterized by Type II kerogen (mainly oil-prone) and mixed Type II/III kerogen (swamp oil and gas-prone), but haven't reach the peak of hydrocarbon generation at present depth of GS 197–2 well. On the other hand, Esna, Matulla, Wata and Raha formations have relatively lower TOC (only up to 1.15?wt%). For these formations the quality of the organic matter is represented by mixed Type II/III and Type III kerogen (mainly gas-prone), but have reached the maturation and generation stages in both wells with the presence of indigenous hydrocarbons detected. Depth-structure maps of these source rocks based on seismic data interpretation indicate that the mature source rocks located in the NW direction are so much deeper than the others in the study area. Understanding regional variations of Eocene, Paleocene and Cretaceous source-rock maturities which largely depend on burial depth will help to reduce the risk for future exploration drilling within the Gulf of Suez.Abedi-Farizhendi, S., Iranshahi, M., Mohammadi, A., Manteghian, M., Mohammadi, A.H., 2019. Kinetic study of methane hydrate formation in the presence of carbon nanostructures. Petroleum Science 16, 657-668. effect of synthesized nanostructures, including graphene oxide, chemically reduced graphene oxide with sodium dodecyl sulfate (SDS), chemically reduced graphene oxide with polyvinylpyrrolidone, and multi-walled carbon nanotubes, on the kinetics of methane hydrate formation was investigated in this work. The experiments were carried out at a pressure of 4.5?MPa and a temperature of 0?°C in a batch reactor. By adding nanostructures, the induction time decreases, and the shortest induction time appeares at certain concentrations of reduced graphene oxide with SDS and graphene oxide, that is, at a concentration of 360?ppm for reduced graphene oxide with SDS and 180?ppm for graphene oxide, with a 98% decrease in induction time compared to that in pure water. Moreover, utilization of carbon nanostructures increases the amount and the rate of methane consumed during the hydrate formation process. Utilization of multi-walled carbon nanotubes with a concentration of 90?ppm showes the highest amount of methane consumption. The amount of methane consumption increases by 173% in comparison with that in pure water. The addition of carbon nanostructures does not change the storage capacity of methane hydrate in the hydrate formation process, while the percentage of water conversion to hydrate in the presence of carbon nanotubes increases considerably, the greatest value of which occurres at a 90?ppm concentration of carbon nanotubes, that is, a 253% increase in the presence of carbon nanotubes compared to that of pure water.Achang, M., Pashin, J.C., Atekwana, E.A., 2019. The influence of moisture on the permeability of crushed shale samples. Petroleum Science 16, 492-501. cuttings and cores recovered from the subsurface and stored for hours to decades tend to dry out and lose moisture and hydrocarbons, leading to an increase in the effective matrix permeability. Moisture loss in shale samples is a fundamental sample preservation problem which can be solved by applying a standard moisture equilibration procedure to restore lost moisture. Our aim was to investigate the relationship between permeability and variable moisture as-received, as-received moisture-equilibrated and saturated moisture-equilibrated samples. Samples were crushed to a series?of?particle sizes (0.6-2.0) mm and moisture equilibrated at 97% relative humidity. Results show that moisture equilibration in the samples was achieved after 72?h. The permeability of the saturated moisture-equilibrated and as-received moisture-equilibrated samples decreased exponentially with increase in moisture content. The high correlation coefficient between permeability and particle size (r?=?0.96 and 0.97) for moisture-equilibrated samples compared to 0.76 for as-received samples indicates that moisture equilibration improves permeability measurements in crushed shale samples. Furthermore, permeability measurements are repeatable for moisture-equilibrated samples compared to samples that were not equilibrated (as-received). We conclude that moisture content affects permeability and moisture equilibration normalizes and improves the repeatability of permeability measurements in crushed shale.Acharya, K., Werner, D., Dolfing, J., Meynet, P., Tabraiz, S., Baluja, M.Q., Petropoulos, E., Mrozik, W., Davenport, R.J., 2019. The experimental determination of reliable biodegradation rates for mono-aromatics towards evaluating QSBR models. Water Research 160, 278-287. Structure Biodegradation Relationships (QSBRs) are a tool to predict the biodegradability of chemicals. The objective of this work was to generate reliable biodegradation data for mono-aromatic chemicals in order to evaluate and verify previously developed QSBRs models. A robust biodegradation test method was developed to estimate specific substrate utilization rates, which were used as a proxy for biodegradation rates of chemicals in pure culture. Five representative mono-aromatic chemicals were selected that spanned a wide range of biodegradability. Aerobic biodegradation experiments were performed for each chemical in batch reactors seeded with known degraders. Chemical removal, degrader growth and CO2 production were monitored over time. Experimental data were interpreted using a full carbon mass balance model, and Monod kinetic parameters (Y, Ks, qmax and μmax) for each chemical were determined. In addition, stoichiometric equations for aerobic mineralization of the test chemicals were developed. The theoretically estimated biomass and CO2 yields were similar to those experimentally observed; 35% (s.d?±?8%) of the recovered substrate carbon was converted to biomass, and 65% (s.d?±?8%) was mineralised to CO2. Significant correlations were observed between the experimentally determined specific substrate utilization rates, as represented by qmax and qmax/Ks, at high and low substrate concentrations, respectively, and the first order biodegradation rate constants predicted by a previous QSBR study. Similarly, the correlation between qmax and selected molecular descriptors characterizing the chemicals structure in a previous QSBR study was also significant. These results suggest that QSBR models can be reliable and robust in prioritising chemical half-lives for regulatory screening purposes.Ackerman, L., Pa?ava, J., ?ípková, A., Martínková, E., Haluzová, E., Rodovská, Z., Chrastn?, V., 2019. Copper, zinc, chromium and osmium isotopic compositions of the Teplá-Barrandian unit black shales and implications for the composition and oxygenation of the Neoproterozoic-Cambrian ocean. Chemical Geology 521, 59-75. Neoproterozoic-Cambrian shale suites that consist of normal (NBS) and metal-rich (HMBS) black shales from the Teplá-Barrandian Unit, Bohemian Massif (Czech Republic) are studied in terms of their Cu, Zn, Cr and Re–Os isotopic compositions to improve our knowledge of elemental and isotopic mass balance of these elements in Earth's oceans in the past and the extent of surface oxygenation at the Neoproterozoic–Cambrian boundary. The rock compositions indicate that the inputs of Cu and Zn have been controlled by variable proportions of metal-rich authigenic and low-metal terrigenous sources, the latter having exceptionally low δ65Cu and partially δ66Zn. In this respect, our data confirm previous studies conclusions that organic-rich sediments with high a terrigenous flux play an important role in the sinking of light Zn in the oceans and provide new evidence that these types of rocks also represent the currently unidentified burial of very light Cu in the ocean. The chromium isotopic composition reveals a complex history of Cr uptake and fractionation through the dominant Cr input from different terrigenous sources with variable δ53Cr followed by Cr fractionation that was controlled by redox states (NBS). On the other hand, mixing and/or continuous equilibrium isotopic exchange between seawater and hydrothermal Cr was the dominant process for the HMBS. The Re–Os contents of the NBS were controlled by hydrogenous components, which yield a poorly defined Re–Os age for the least disturbed samples of 555?±?60?Ma, indicating an open-system behavior, while the HMBS Re–Os composition was largely influenced by hydrothermal fluids during deposition. The calculated authigenic δ65Cu, which is similar to that in the present-day ocean, and highly positive δ53Cr values of the HMBS suggest high levels of surface oxygenation during the Neoproterozoic–Cambrian transition. Furthermore, the authigenic δ66Zn, which is indistinguishable from that in the present-day ocean, may imply a constant Zn isotopic composition of the oceans from the Neoproterozoic because of the well-balanced cycle of phosphates, which were strongly adsorbed by Fe-hydroxides. The radiogenic nature of the initial 187Os/188Os (~0.6), although with a high associated error, seems to not confirm previous indications of an abrupt increase of seawater 187Os/188Os during the late Neoproterozoic due to the large-scale radiogenic Os flux into the ocean.Adamopoulou, T., Nawada, S., Deridder, S., Wouters, B., Desmet, G., Schoenmakers, P.J., 2019. Experimental and numerical study of band-broadening effects associated with analyte transfer in microfluidic devices for spatial two-dimensional liquid chromatography created by additive manufacturing. Journal of Chromatography A 1598, 77-84. one-dimensional column-based liquid chromatographic (LC) systems do not offer sufficient separation power for the analysis of complex mixtures. Column-based comprehensive two-dimensional liquid chromatography offers a higher separation power, yet suffers from instrumental complexity and long analysis times. Spatial two-dimensional liquid chromatography can be considered as an alternative to column-based approaches. The peak capacity of the system is ideally the product of the peak capacities of the two dimensions, yet the analysis time remains relatively short due to parallel second-dimension separations. Aspects affecting the separation efficiency of this type of systems include flow distribution to homogeneously distribute the mobile phase for the second-dimension (2D) separation, flow confinement during the first-dimension (1D) separation, and band-broadening effects during analyte transfer from the 1D separation channel to the 2D separation area.In this study, the synergy between computational fluid dynamics (CFD) simulations and rapid prototyping was exploited to address band broadening during the 2D development and analyte transfer from 1D to 2D. Microfluidic devices for spatial two-dimensional liquid chromatography were designed, simulated, 3D-printed and tested. The effects of presence and thickness of spacers in the 2D separation area were addressed and leaving these out proved to be the most efficient solution regarding band broadening reduction. The presence of a stationary-phase material in the 1D channel had a great effect on the analyte transfer from the 1D to the 2D and the resulting band broadening. Finally, pressure limit of the fabricated devices and printability are discussed.Admakin, L.A., Parada, S.G., 2019. Statistical allocation of the parageneses of minor elements from the associations in fossil coals. Doklady Earth Sciences 485, 260-263. statistical relationships characterizing the concentrations of minor elements in the organic part and mineral impurities in fossil coals are allocated. The confidence ranges for these concentrations are calculated. The concentrations of minor elements within the confidence ranges relate to the clarke distributions; those exceeding the upper boundary of the confidence level, to extremely high values.Aguraiuja-L?tti, ?., L?ugas, L., 2019. Stable isotope evidence for medieval diet in urban and rural northern Estonia. Journal of Archaeological Science: Reports 26, 101901. of stable carbon, nitrogen and sulphur isotope analyses of human bone collagen (n?=?59) from two medieval (12-16th century) populations in coastal northern Estonia are presented. Statistically significant differences between δ15N and δ34S alues from the St Barbara cemetery in the hanseatic town of Tallinn (Reval) and the rural village cemetery of Kaberla suggest that there were likely real differences between urban and rural diets, either in terms of access to certain types of foods or due to different practices regarding farming and food production. While diet at both locations was likely dominated by C3 terrestrial resources, relatively high δ15N values suggest a significant reliance on higher trophic level protein (including fish). However, because of brackish conditions prevalent in the Baltic Sea, local marine, freshwater and terrestrial δ13C and δ34S isotopic ranges in coastal northern Estonia may not be distinct enough to allow for a more detailed palaeodietary reconstruction.Ahamed, M.A.A., Perera, M.S.A., Matthai, S.K., Ranjith, P.G., Li, D.-y., 2019. Coal composition and structural variation with rank and its influence on the coal-moisture interactions under coal seam temperature conditions – A review article. Journal of Petroleum Science and Engineering 180, 901-917. numerous studies were conducted on coal utilisation processes overall, due to the recent expansion of the coal industry, processes which involve within the reservoir bares a significant importance for the effective usage of coal. The key to the effective usage of such processes relies on the understanding of the chemical properties of coal and its changes due to the water interaction as most coal seams are naturally saturated. In this context, this paper provides a fundamental understanding of the coal composition and its structure, water adsorption capacity of coal and the impact on the mechanical characteristics due to the chemical property changes under coal seam temperature conditions. The chemical structure of coal can be separated into three catergories; 1) aromatic structures, 2) aliphatic side chains connecting the aromatic structures, 3) oxygen functional groups. The influence of water on the chemical and physical properties of coal largely depends on the oxygen functional groups, along with expandable minerals and dissolvable minerals. However, the degree of adsorption does not limit only to the concentration of oxygen functional groups, but factors including the amount of exposed hydrophilic material, type of polar functional groups, type of clay minerals and pore fluid conditions also needs to be considered. We also highlight the methods of which the mechanical properties of coal changes due to the coal water interaction.Ahmed, M.A., Hassan, M.M.A., 2019. Hydrocarbon generating-potential and maturity-related changes of the Khatatba Formation, Western Desert, Egypt. Petroleum Research 4, 148-163. petroliferous province of the Western Desert comprises several sedimentary basins with different hydrocarbon potentiality and production capability. The middle Jurassic Khatatba Formation was proved a potential source rock in some basins and active/effective in others. The current study aims to give a comprehensive assessment and evaluation of the potential organic-rich intervals of the Khatatba Formation across JG and JD fields, northeast Abu Gharadig Basin (NEAG). The hydrocarbon generating capability and sourcing of the Khatatba Formation studied through organic geochemistry calibrated with well logging. However, the efficiency of some widely used plots of geochemistry is re-evaluated according to their accuracy and consistency. Forty cuttings, thirteen cores and two oil samples obtained from three wells (JG-2, JG-3 and JD-4) were evaluated. The samples revealed total organic carbon (TOC) values ranging from 1 to 9?wt%, exhibiting a good-excellent potential source rock. A single sample in the JD-4 well attained a TOC value of 21.3?wt% with a generating potential (represented by S2 parameter) exceeding 146 mgHc/g rock required a special evaluation. Most of the samples (mainly in the JD-4 well) attained a sufficient level of thermal maturity for hydrocarbon generation with a Tmax up to 449?°C. The vitrinite reflectance (%Ro) values (a common maturity-related indicator) acquired from the JD-4 well ranging between 0.76% and 0.92%. These values are tediously increasing with depth indicating a uniform geothermal regime. The Khatatba organofacies, with wide variety of kerogen types (I, II, II-S and II/III), contain marine organic matter with a slight terrigenous input, exhibiting anoxic-suboxic environmental conditions. Oil-source correlations define the organic-rich intervals responsible for charging the accumulated hydrocarbon in the NEAG concession.Al-Busaidi, I.K., Al-Maamari, R.S., Karimi, M., Naser, J., 2019. Effect of different polar organic compounds on wettability of calcite surfaces. Journal of Petroleum Science and Engineering 180, 569-583. average oil recovery by conventional water flooding from oil-wet and naturally fractured carbonate reservoirs is often less than 30%. Removal of adsorbed acidic components and/or asphaltene from the carbonate surface results in wettability alteration towards water-wet which is an effective approach to enhance oil recovery. Long chain fatty acids, long chain naphthenic acids and asphaltene are major components in crude oil which are responsible for wettability alteration in carbonate reservoirs while unsaturated acids have minor effect. In this study, a more accurate quantification of the effects of different types and structures of polar components that contribute to the initial oil-wetting extent of the reservoir rocks were used (aliphatic saturated acids, aliphatic unsaturated acids, naphthenic acids, aromatic acids and asphaltene). Different analytical tools (contact angle, zeta potential, Fourier transform infrared spectroscopy and thermal analysis) were utilized for all acids in order to study surface characteristics. The results indicated that polar organic compounds act in different ways according to their structure and properties. Presence of double bond could make the acid molecule more polar, reactive and less hydrophobic. In addition, it can affect the spatial arrangement of the molecule and hence its orientation on the surface. Presence of benzene ring increases the reactivity and polarity of carboxylic group. Moreover, it enhances hydrophilic properties of the acid due to electrons of π double bonds that can resonate over aromatic carbon atoms. The results revealed that, in the presence of water film, combination of acid dissociation in water, surface activity of acid and water solubility controls the acid adsorption and hence wettability alteration of the surface during aging process. Chemisorption of carboxylic acids/asphaltene changes the wettability of calcite surface. In addition to chemical adsorption, some acids adsorb physically on the surface. Physical adsorption of polar compounds may happen via hydrogen bonding between carboxylic groups and carbonate ions on the surface. Although physical adsorption is reversible and forms weak bonds between adsorbate and adsorbent, it may partially contribute to wettability alteration.Ali, M.Y., Lee, J.H., 2019. Petroleum geology of the Nogal Basin and surrounding area, northern Somalia, Part 2: Hydrocarbon potential. Journal of Petroleum Geology 42, 233-260. reflection profiles and well data show that the Nogal Basin, northern Somalia, has a structure and stratigraphy suitable for the generation and trapping of hydrocarbons. However, the data suggest that the Upper Jurassic Bihendula Group, which is the main source rock elsewhere in northern Somalia, is largely absent from the basin or is present only in the western part. The high geothermal gradient (～35–49 °C/km) and rapid increase of vitrinite reflectance with depth in the Upper Cretaceous succession indicate that the Gumburo Formation shales may locally have reached oil window maturity close to plutonic bodies. The Gumburo and Jesomma Formations include high quality reservoir sandstones and are sealed by transgressive mudstones and carbonates.ID petroleum systems modelling was performed at wells Nogal‐1 and Kalis‐1, with 2D modelling along seismic lines CS‐155 and CS‐229 which pass through the wells. Two source rock models (Bihendula and lower Gumburo) were considered at the Nogal‐1 well because the well did not penetrate the sequences below the Gumburo Formation. The two models generated significant hydrocarbon accumulations in tilted fault blocks within the Adigrat and Gumburo Formations. However, the model along the Kalis‐1 well generated only negligible volumes of hydrocarbons, implying that the hydrocarbon potential is higher in the western part of the Nogal Basin than in the east. Potential traps in the basin are rotated fault blocks and roll‐over anticlines which were mainly developed during Oligocene–Miocene rifting.The main exploration risks in the basin are the lack of the Upper Jurassic source and reservoirs rocks, and the uncertain maturity of the Upper Cretaceous Gumburo and Jesomma shales. In addition, Oligocene‐Miocene rift‐related deformation has resulted in trap breaching and the reactivation of Late Cretaceous faults.Allory, V., Cambou, A., Moulin, P., Schwartz, C., Cannavo, P., Vidal-Beaudet, L., Barthès, B.G., 2019. Quantification of soil organic carbon stock in urban soils using visible and near infrared reflectance spectroscopy (VNIRS) in situ or in laboratory conditions. Science of The Total Environment 686, 764-773. soils, like other soils, can be sink or source for atmospheric carbon dioxide, and due to urban expansion, are receiving increasing attention. Studying their highly variable attributes requires high-density sampling, which can hardly be achieved using conventional approaches. The objective of this work was to determine the ability of visible and near infrared reflectance spectroscopy (VNIRS) to quantify soil organic carbon (SOC) concentration (gC kg?1) and stock (gC dm?3, or MgC ha?1 for a given depth layer) in parks and sealed soils of two French cities, Marseille and Nantes, using spectra collected on pit walls or in laboratory conditions (air dried, 2?mm sieved samples).Better VNIRS predictions were achieved using laboratory than in situ spectra (R2?≈?0.8–0.9 vs. 0.7–0.8 in validation), and for sample SOC concentration than stock (R2val up to 0.83 in situ and 0.95 in the laboratory vs. 0.78 and 0.89, respectively). Stock was conventionally calculated according to four methods that variably account for coarse particles (>2?mm); and it was better predicted when coarse particles were not taken into account. This was logical using laboratory spectra, collected on 2?mm sieved samples; but concerning in situ spectra, this suggested the operator tended to put the spectrometer beside the coarsest particles during spectrum acquisition. This point is worth considering for urban soils, often rich in coarse particles.Stocks were then aggregated at the profile level: SOC stock prediction was more accurate at profile than sample level when using laboratory spectra (R2val?=?0.94 vs. 0.89, respectively), probably due to uncertainty compensation; but this was not the case when using in situ spectra, possibly because samples collected for SOC analysis and corresponding VNIRS scans were not at the exact same location.This work demonstrates VNIRS usefulness for quantifying SOC stock time- and cost-effectively, in urban soils especially.AlSofi, A.M., AlKhatib, A.M., Al-Ajwad, H.A., Wang, Q., Zahrani, B.H., 2019. Assessment of enhanced-oil-recovery-chemicals production and its potential effect on upstream facilities. SPE Journal 24, 1037-1056. of past chemical-enhanced-oil-recovery (EOR) projects illustrates that chemical-EOR implementation can result in produced-fluid-handling issues. However, in all projects such issues were resolved, mainly through a combination of improved demulsifiers and oversized vessels. In previous work, we have demonstrated the potential of surfactant/polymer flooding for a high-temperature/high-salinity carbonate. In consideration of future plans to pilot the process, further assessments were conducted to evaluate any side effects of these EOR chemicals on upstream facilities and determine mitigation plans if needed. In this work, we initially conduct a critical review of past experience. Then, we investigate the surfactant/polymer compatibility with the additives used in processing facilities for demulsification and scale and corrosion inhibition as well as the possible effect of surfactant/polymer on oil/water separation, metal corrosion, and scale inhibition. For this purpose, we first perform a sensitivity-based simulation study to estimate the volumes of produced EOR chemicals. Second, a compatibility study is conducted to evaluate EOR chemical compatibility with oilfield additives (i.e., demulsifier, corrosion inhibitor, and scale inhibitor). Third, bottle tests are conducted using surfactant/polymer solutions prepared in both injection and produced water to evaluate the effect of EOR chemicals on oil/water separation. Separated-water qualities are also evaluated using solvent extraction followed by ultraviolet (UV) visibility testing. Fourth, static autoclave and dynamic rotating tests are performed to evaluate the possible side effects of EOR chemicals on corrosion inhibition. Finally, static bottle and dynamic tube tests are performed to evaluate the possible side effects of EOR chemicals on scale inhibition; these observations are supported by characterization of precipitates using environmental scanning electron microscopy (ESEM) and X-ray diffraction (XRD).Depending on simulation, the peak polymer and surfactant concentrations at the separation plant are 83 and 40 ppm, respectively. The sensitivity study suggests a worst-case scenario in which peak polymer and surfactant concentrations of 174 and 128 ppm are produced. Compatibility testing confirms the compatibility of EOR chemicals with the additives used in upstream facilities. In those tests, neither precipitation nor phase separation is observed. Bottle tests indicate an overall negligible effect on oil/water-separation speed. However, analyses of separated-water quality indicated a noteworthy deterioration in separated-water qualities. Oil-in-water concentrations increase from 100 to 750 ppm and from 300 to 450 ppm at injection- and produced-water salinities, respectively. Furthermore, corrosion tests suggest that surfactant/polymer presence results in a significant reduction in corrosion rates by 70 and 86% at static and dynamic conditions, respectively, without any pitting issues. Finally, static and dynamic scale-inhibition studies performed at exacerbated conditions suggest that EOR chemicals can reduce the effectiveness of scale inhibitors. In static scaling tests, the effectiveness of the base polyacrylate inhibitor diminishes completely. However, the same degree of inhibition was achieved by switching to phosphonate inhibitors, but at a slightly higher dosage between 5 and 15 mg/L. In dynamic scaling tests, the base polyacrylate inhibitor failed at all tested dosages up to 100 mg/L. However, the alternative phosphonate inhibitors passed at dosages between 20 and 45 mg/L. Such effects can be attributed to changes in scale morphology and polymorphs, as demonstrated by the XRD and ESEM results.On the basis of those results, we conclude that the selected surfactant/polymer implementation will have a manageable effect on separation facilities. Finally, this work provides an experimental protocol to evaluate the potential side effects of a chemical-EOR process on upstream facilities.Alves, V.E.N., Figueiredo, G.M., 2019. Microplastic in the sediments of a highly eutrophic tropical estuary. Marine Pollution Bulletin 146, 326-335. the implications of microplastics contamination in aquatic ecosystems and information scarcity about microplastic abundances in estuarine sediments, this study aimed to quantify and describe the microplastics in the sublittoral sediments from Guanabara Bay. Sediment samples were collected at four sites and three months, microplastics were separated and classified according to type, color, size, and polymer composition. High abundances of microplastic (160 to 1000 items kg?1 or 4367 to 25,794 items m?2) occurred independent of area or period, indicating microplastics are widely spread in Guanabara Bay. The dominant microplastic in the sediment was the translucent polyester microfiber of <1?mm size; which is a secondary microplastic, possibly coming from washing machines wastes. The extremely high availability of microplastics in Guanabara Bay, compared to the majority of studies around the world, suggests high risk of contamination to benthic organisms and demersal fish, as they may be ingesting microplastics.Ameli, F., Hemmati-Sarapardeh, A., Tatar, A., Zanganeh, A., Ayatollahi, S., 2019. Modeling interfacial tension of normal alkane-supercritical CO2 systems: Application to gas injection processes. Fuel 253, 1436-1445. study the gas injection scenario for successful implementation of enhanced oil recovery (EOR) processes, the prediction of interfacial tension (IFT) between injected gas and the crude oil is of paramount significance. In the present study, some intelligent methods were developed for determining IFT values between supercritical CO2 and normal alkanes. IFT was considered as a function of temperature, pressure, and molecular weight of normal alkanes. The developed methods were Multilayer perceptron (MLP), Genetic Algorithm Radial Basis Function (GA-RBF), and Conjugate Hybrid-PSO ANFIS (CHPSO-ANFIS). The average absolute percent relative errors (AAREs) for the stated techniques were found to be 2.59%, 1.39%, and 1.81%, respectively, showing that GA-RBF is the most efficient technique. This model was then compared to the other previously developed models in literature. It was also found that the current GA-RBF model with AARE of 1.39% surpasses the previously developed models. Finally, the results of the Leverage approach showed that GA-RBF model could be trusted to predict the IFT of the normal alkane- supercritical CO2 systems in the used range of pressure, temperature, and n-alkanes. This study represents the most reliable technique in predicting the IFT value between supercritical CO2 and normal alkanes to be applied in studies on gas injection processes.Aminzadeh, R., Nikazar, M., Dabir, B., 2019. The effect of nonylphenol on asphaltene aggregation: A molecular dynamics approach. Petroleum Science and Technology 37, 1883-1890. dynamics (MD) simulations were performed to study the occurrence time of each stage of asphaltene aggregation from single molecules to a large flocculate with and without nonylphenol (NP) molecules as asphaltene dispersants. NPs reduce the size of asphaltene aggregates, and curb the clustering of nanoaggregates when they are added to the simulation box at nanoaggregation nucleation stage. These dispersants are able to break clusters into their constituent nanoaggregates when they are added at higher concentrations. Moreover, asphaltene–NP interactions change the structure of asphaltene flocculates from globular into filamentary.Amir-Heidari, P., Raie, M., 2019. A new stochastic oil spill risk assessment model for Persian Gulf: Development, application and evaluation. Marine Pollution Bulletin 145, 357-369. Gulf is a semi-enclosed highly saline reverse estuary that is exposed to the risk of oil spills in offshore oil and gas activities. In the early 2000s, a specific version of NOAA's Trajectory Analysis Planner (TAP II) was developed for Persian Gulf to assist regional organizations in preparing oil spill contingency plans. In this research, a new stochastic model is developed to cover the limitations of TAP II. The new model is based on an advanced trajectory model, which is now linked with high resolution spatiotemporal data of the wind and sea current. In a case study, the developed model is compared with TAP II, and evaluated by multiple tests designed for analysis of uncertainty, sensitivity, reliability and variability. The case study proved the applicability of the new model, and the evaluation tests provided useful information for the future development of the model.Amrani, A., Rosenberg, Y.O., Meshoulam, A., Said-Ahmad, W., Turich, C., Luu, N., Jacksier, T., Stankiewicz, A., Feinstein, S., Shurki, A., 2019. Sulfur isotopic composition of gas-phase organic sulfur compounds provides insights into the thermal maturation of organic-rich rocks. Geochimica et Cosmochimica Acta 259, 91-108. and gas phase organic sulfur compounds (VOSCs) are important components in subsurface reservoir fluids and despite their relatively low concentrations, can provide important information about organic matter origin, diagenetic transformation, thermal maturation, and oil and gas generation, expulsion, and migration. We present an approach for the utilization of VOSC concentration and compound specific S isotopes ratio (δ34S) data as a new geochemical tool to study natural gas origin and formation. We studied the formation pathways of VOSCs, their δ34S values, and interaction with an organic-rich sedimentary rock (or ‘source rock’) from the Ghareb Formation (Type II-S kerogen) deposited in an upwelling marine environment. The immature source rock was subjected to laboratory controlled thermal maturation. We used a semi-open, non-isothermal pyrolysis system heated between 200 and 440?°C, and analyzed the molecular composition and compound specific δ34S values of the evolved gases at various thermal maturity stages. Formation of VOSCs commenced at 206?°C, a temperature generally associated with less thermally mature systems, and typically before the onset of oil generation for similar organic-rich source rocks, allowing study of low thermal maturity conditions (～0.3 %Roeq). Overall, the VOSCs obtained had δ34S values similar to the bulk kerogen values (mostly within 4‰). However, thiol (or mercaptan) δ34S values closely followed those of H2S (Δ34Sthiols-H2S?=??1?±?1‰) throughout the experiment. Ab-initio calculations for the S isotopic exchange between H2S and thiols were close to the experimental observations. This suggests that thiols rapidly attained equilibrium with H2S despite their very short residence time in the system (minutes to hours). Furthermore, throughout the experiment, the concentrations of the six different thiols were found to be proportional to the coexisting, concentration ratio of [H2]/[H2S]. The proportionality factors of the 6 different thiols strongly correlate with reported heats of formation (ΔHf°), further supporting the notion that the generation of thiols in the system rapidly reached equilibrium. At pyrolysis temperatures up to 350?°C, δ34S and concentration values of other VOSCs produced in the gas phase, including sulfides and thiophenes, probably represent generation from S-containing moieties in kerogen and bitumen with limited interaction with co-existing H2S. The reaction of hydrocarbons and H2S to produce VOSCs is inversely correlated with thermal stability, i.e. thiols?>?sulfides?>?thiophenes. Therefore, the δ34S values, concentrations and distributions of VOSCs can be utilized as a proxy for reaction extent and formation mechanism of petroleum and H2S, including primary generation by thermal maturation, or potentially other processes such as migration and thermochemical sulfate reduction. This work demonstrates a novel and useful geochemical tool to study the source and fate of natural gas in the subsurface.Antler, G., Mills, J.V., Hutchings, A.M., Redeker, K.R., Turchyn, A.V., 2019. The sedimentary carbon-sulfur-iron interplay – A lesson from east anglian salt marsh sediments. Frontiers in Earth Science 7, 140. doi: 10.3389/feart.2019.00140. explore the dynamics of the subsurface sulfur, iron and carbon cycles in salt marsh sediments from East Anglia, United Kingdom. We report measurements of pore fluid and sediment geochemistry, coupled with results from laboratory sediment incubation experiments, and develop a conceptual model to describe the influence of bioturbation on subsurface redox cycling. In the studied sediments the subsurface environment falls into two broadly defined geochemical patterns – iron-rich sediments or sulfide-rich sediments. Within each sediment type nearly identical pore fluid and solid phase geochemistries (in terms of concentrations of iron, sulfate, sulfide, dissolved inorganic carbon, and the sulfur and oxygen isotope compositions of sulfate) are observed in sediments that are hundreds of kilometres apart. Strictly iron-rich and strictly sulfide-rich sediments, despite their substantive geochemical differences, are observed within spatial distances of less than five meters. We suggest that this bistable system results from a series of feedback reactions that determine ultimately whether sediments will be sulfide-rich or iron-rich. We suggest that an oxidative cycle in the iron-rich sediment, driven by bioirrigation, allows rapid oxidation of organic matter, and that this irrigation impacts the sediment below the immediate physical depth of bioturbation. This oxidative cycle yields iron-rich sediments with low total organic carbon, dominated by microbial iron reduction and no methane production. In the absence of bioirrigation, sediments in the salt marsh become sulfide-rich with high methane concentrations. Our results suggest that the impact of bioirrigation not only drives recycling of sedimentary material but plays a key role in sedimentary interactions among iron, sulfur and carbon.Ardyna, M., Lacour, L., Sergi, S., d’Ovidio, F., Sallée, J.-B., Rembauville, M., Blain, S., Tagliabue, A., Schlitzer, R., Jeandel, C., Arrigo, K.R., Claustre, H., 2019. Hydrothermal vents trigger massive phytoplankton blooms in the Southern Ocean. Nature Communications 10, Article 2451. activity is significant in regulating the dynamics of trace elements in the ocean. Biogeochemical models suggest that hydrothermal iron might play an important role in the iron-depleted Southern Ocean by enhancing the biological pump. However, the ability of this mechanism to affect large-scale biogeochemistry and the pathways by which hydrothermal iron reach the surface layer have not been observationally constrained. Here we present the first observational evidence of upwelled hydrothermally influenced deep waters stimulating massive phytoplankton blooms in the Southern Ocean. Captured by profiling floats, two blooms were observed in the vicinity of the Antarctic Circumpolar Current, downstream of active hydrothermal vents along the Southwest Indian Ridge. These hotspots of biological activity are supported by mixing of hydrothermally sourced iron stimulated by flow-topography interactions. Such findings reveal the important role of hydrothermal vents on surface biogeochemistry, potentially fueling local hotspot sinks for atmospheric CO2 by enhancing the biological pump.Arenas, C.N., Navarro, M.V., Martínez, J.D., 2019. Pyrolysis kinetics of biomass wastes using isoconversional methods and the distributed activation energy model. Bioresource Technology 288, 121485. this work, a thermogravimetric analyser was used to assess the pyrolysis kinetics of pineapple, orange and mango peel wastes and agro-industrial by-products, rice husk and pine wood. Five isoconversional methods (KAS, FWO, Starink, Vyazovkin and Friedman) and one model-fitting method (DAEM) accurately fitted the experimental data at three heating rates (5, 10 and 20?°C/min) between 10% and 90% conversion. These methods agree with the trends shown by the activation energy (Ea) distribution calculated, with fluctuations between 150 and 550?kJ/mol. The fluctuations of Ea in the whole range of conversion, in addition to a higher number of relevant reactions obtained by DAEM for fruit peel samples compared to agro-industrial samples, are associated with a higher extractive content in the peels. Kinetic parameters fitted by DAEM were successfully verified at the highest heating rate studied.Argentino, C., Lugli, F., Cipriani, A., Conti, S., Fontana, D., 2019. A deep fluid source of radiogenic Sr and highly dynamic seepage conditions recorded in Miocene seep carbonates of the northern Apennines (Italy). Chemical Geology 522, 135-147. 87Sr/86Sr, REE and Mo-U systematics were investigated in Miocene seep carbonates formed on accretionary ridges at the front of the northern Apennine wedge. Here we evaluate fluid sources, seepage intensity and redox conditions during carbonate precipitation. Micrite matrix and early calcite cements lining cavities are the main authigenic carbonate phases and show negligible diagenetic alteration. Their AOM-related (anaerobic oxidation of methane) origin is evident from δ13C values ranging from ?38.7‰ to ?25.7‰. The 87Sr/86Sr ratios in carbonates vary between 0.708659 and 0.709132. Most micrite values fall within the range of Middle Miocene seawater (Langhian, MNN5a biozone), in agreement with the biostratigraphy of the host sediments, thus reflecting precipitation of seep carbonates close to the seafloor. Highly radiogenic 87Sr/86Sr ratios, of early calcite cements and micrite from conduit-rich facies at the base of carbonate bodies, likely derived from the interaction of fluids with detrital clays during the fault-controlled upward migration through the underlying terrigenous turbidite successions. Strong Mo and U enrichments in carbonates, with MoEF and UEF up to 233.5 and 86.6 respectively, coupled with (Mo/U)EF ratios ranging between 0.7 and 9.7, indicate dynamic redox conditions, episodically sulfidic and restricted to porewaters. This interpretation is also supported by enrichments in MREE of micrites and a general absence of negative Ce anomalies. These new data provide an indirect indication of rates and temporal variability of AOM at fossil methane seeps developed on a thrust related anticline and help to constrain the complex interaction between fluid migration pathways, seepage intensity and environmental conditions as observed in modern seep analogues.Argiriadis, E., Denniston, R.F., Barbante, C., 2019. Improved polycyclic aromatic hydrocarbon and n-alkane determination in speleothems through cleanroom sample processing. Analytical Chemistry 91, 7007-7011. in paleoenvironmental reconstructions from biomarkers in speleothems is increasing, thanks in part to the capacity of speleothems to grow continuously and to resist postdepositional alteration. In particular, the possibility exists to link high-resolution and accurately dated fire and vegetation records with isotopic data of climatic and paleoenvironmental interactions at the local and regional scale. However, the scarcity of existing methods for the quantification of organic molecules in stalagmites, together with the issues of sample availability, contamination, and low concentrations, complicate this approach. In this work, we developed a novel method for the simultaneous determination of 18 polycyclic aromatic hydrocarbons (PAHs) and 26 n-alkanes (C10–C35) and then tested it on “clean” calcite and aragonite stalagmite samples from cave KNI-51 in the Australian tropics. The method involves subsampling by using a hand-held drill, complete dissolution of the matrix in hydrochloric acid, then liquid–liquid extraction, and GC-MS analysis. Sample preparation was carried out in a 10?000 class clean room built entirely in stainless steel to avoid contamination. Detection limits were 0.3–9 ng for PAHs and 6–44 ng for n-alkanes. Measurable concentrations of fire-derived PAH compounds, namely, phenanthrene, pyrene, benzo(e)pyrene, and indeno(123-cd)pyrene, were detected in only one sample, which dates to the year ～2004 CE, when a fire burned vegetation over the cave; n-alkanes were detected in all samples in the range C23–C35, with no odd–even preference.Armstrong, C.W., Foley, N.S., Slagstad, D., Chierici, M., Ellingsen, I., Reigstad, M., 2019. Valuing blue carbon changes in the Arctic Ocean. Frontiers in Marine Science 6, 331. doi: 10.3389/fmars.2019.00331. ocean capacity to store carbon is crucial, and currently absorbs about 25% CO2 supply to the atmosphere. The ability to store carbon has an economic value, but such estimates are not common for ocean environments, and not yet estimated for the Arctic Ocean. With the severe climatic changes in the Arctic Ocean, impacting sea ice and potentially the vertical carbon transport mechanisms, a projection of future changes in Arctic Ocean carbon storage is also of interest. In order to value present and evolving carbon storage in the changing Arctic marine environment we combine an ocean model with an economic analysis. Placing a value on these changes helps articulate the importance of the carbon storage service to society. The standing stock and fluxes of organic and inorganic carbon from the atmosphere, rivers, shelves and through the gateways linking to lower latitudes, and to the deep of the Arctic Ocean are investigated using the physically-chemically-biologically coupled SINMOD model. To obtain indications of the effect of climate change, trajectories of two IPCC climate scenarios RCP 4.5 and RCP 8.5 from the Max Planck Institute were used for the period 2006-2099. The results show an increase in the net carbon storage in the Arctic Ocean in this time period to be 1.0% and 2.3% in the RCP 4.5 and RCP 8.5 scenarios, respectively. Most of this increase is caused by an increased atmospheric CO2 uptake until 2070. The continued increase in inorganic carbon storage between 2070 and 2099 results from increased horizontal influx from lower latitude marine regions. First estimates of carbon storage values in the Arctic Ocean are calculated using the social cost of carbon and carbon market values as two outer bounds from 2019 to 2099, based on the simulated scenarios. We find the Arctic Ocean will over the time period studied increase its storage of carbon to a value of between €27.6 billion and €1 trillion. This paper clearly neglects a multitude of different negative consequences of climate change in the Arctic, but points to the fact that there are also some positive counterbalancing effects.Arnberg, M., Keitel-Gr?ner, F., Westerlund, S., Ramanand, S., Bechmann, R.K., Baussant, T., 2019. Exposure to chemically-dispersed oil is more harmful to early developmental stages of the northern shrimp Pandalus borealis than mechanically-dispersed oil. Marine Pollution Bulletin 145, 409-417. of key species sensitivity for oil spill response (OSR) options is needed to support decision-making and mitigate impact on sensitive life stages of keystone species. Here, Northern shrimp (Pandalus borealis) larvae were exposed for 24?h to a gradient (H-High, M-Medium: 10 times dilution and L-Low: 100 times dilution) of mechanically- (MDO) (H?<?6?mg/L total hydrocarbon content) and chemically- (CDO) dispersed oil (Slickgone NS, H?<?20?mg/L total hydrocarbon content), followed by a recovery period. Larval mortality, feeding rate and development were evaluated. Overall, the results show that 24?h exposure to field-realistic concentrations of CDO lead to lower survival, reduced feeding rate and slower larval development in P. borealis larvae compared to MDO. These effects persisted during recovery, indicating a higher vulnerability with dispersant use and the need for longer observation periods post-exposure to fully evaluate the consequences for sensitive life-stages from OSR.Arslan, F.N., Kolk, A., Janssen, H.G., 2019. Methods for one– and two–dimensional gas chromatography with flame ionization detection for identification of Mycobacterium tuberculosis in sputum. Journal of Chromatography B 1124, 204-217. simplified methods based on manual thermally–assisted hydrolysis and methylation (THM) GC and GC?×?GC with flame ionization detection (FID) were developed for the detection of mycobacteria and Mycobacterium tuberculosis (MTB) in sputum. A central composite design was employed to optimize the THM derivatization conditions. For the detection of MTB the known mycobacterial markers tuberculostearic acid (TBSA) and hexacosanoic acid (C26), as well as three MTB specific markers, the mycocerosates, were evaluated. We found that the optimum conditions for THM release of TBSA and C26 differ from those for maximum release of the mycocerosates. Higher reagent volumes, higher temperatures and longer incubation increase the mycocerosates yield. Application of these conditions unfortunately resulted in unacceptable safety hazards. A GC?×?GC–FID method was developed that allowed accurate detection of mycocerosates even at poor conversion yields of the derivatization reaction. Using spiked sputum samples from non–TB patients, the detection limit of the method based on TBSA and C26 was found to be comparable to that of microscopy, i.e. 104–105 bacteria/mL sputum. To validate the new test, we compared the results we found for fifteen sputum samples from patients from South Africa suspected of having tuberculosis with those of culture, the gold standard method. Based on the presence of TBSA and C26, all eight microscopy and culture positive samples, and even two microscopy negative but culture positive samples were positive by THM–GC–FID. All five microscopy and culture negative sputum samples were also negative for THM–GC–FID, giving a specificity of 100%. Using GC?×?GC–FID we could detect mycocerosates, the specific markers for MTB in seven out of ten MTB culture positive sputum samples. The five culture negative cases were also negative for mycocerosates in manual THM–GC?×?GC–FID giving again 100% specificity. The results obtained indicate that the new methods hold great potential for the early diagnosis of TB in developing countries.Atkinson, J.W., Wignall, P.B., Morton, J.D., Aze, T., 2019. Body size changes in bivalves of the family Limidae in the aftermath of the end-Triassic mass extinction: the Brobdingnag effect. Palaeontology 62, 561-582. in body size of organisms following mass extinctions is well‐known and often ascribed to the Lilliput effect. This phenomenon is expressed as a temporary body size reduction within surviving species. Despite its wide usage the term is often loosely applied to any small post‐extinction taxa. Here we assess the size of bivalves of the family Limidae (Rafineque) prior to, and in the aftermath of, the end‐Triassic mass extinction event. Of the species studied only one occurs prior to the extinction event, though is too scarce to test for the Lilliput effect. Instead, newly evolved species originate at small body sizes and undergo a within‐species size increase, most dramatically demonstrated by Plagiostoma giganteum (Sowerby) which, over two million years, increases in size by 179%. This trend is seen in both field and museum collections. We term this within‐species size increase of newly originated species in the aftermath of mass extinction, the Brobdingnag effect, after the giants that were contemporary with the Lilliputians in Swift's Gulliver's Travels. The size increase results from greater longevity and faster growth rates. The cause of the effect is unclear, although it probably relates to improved environmental conditions. Oxygen‐poor conditions in the Early Jurassic are associated with populations of smaller body size caused by elevated juvenile mortality but these are local/regional effects that do not alter the long‐term, size increase. Although temperature‐size relationships exist for many organisms (Temperature‐Size Rule and Bergmann's Rule), the importance of this is unclear here because of a poorly known Early Jurassic temperature record.Atwah, I., Sweet, S., Pantano, J., Knap, A., 2019. Light hydrocarbon geochemistry: Insight into Mississippian crude oil sources from the Anadarko Basin, Oklahoma, USA. Geofluids 2019, Article 2795017. Mississippian limestone is a prolific hydrocarbon play in the northern region of Oklahoma and the southern part of Kansas. The Mississippian reservoirs feature variations in produced fluid chemistry usually explained by different possible source rocks. Such chemical variations are regularly obtained from bulk, molecular, and isotopic characteristics. In this study, we present a new geochemical investigation of gasoline range hydrocarbons, biomarkers, phenols, and diamondoids in crude oils produced from Mississippian carbonate and Woodford Shale formations. A set of oil samples was examined for composition using high-performance gas-chromatography and mass-spectrometry techniques. The result shows a distinct geochemical fingerprint reflected in biomarkers such as the abundance of extended tricyclic terpanes, together with heptane star diagrams, and diamantane isomeric distributions. Such compounds are indicative of the organic matter sources and stages of thermal maturity. Phenolic compounds varied dramatically based on geographic location, with some oil samples being depleted of phenols, while others are intact. Based on crude oil compositions, two possible source rocks were identified including the Woodford Shale and Mississippian mudrocks, with a variable degree of mixing reported. Variations in phenol concentrations reflect reservoir fluid dynamic and water interactions, in which oils with intact phenols are least affected by water-washing conversely and crude oils depleted in phenols attributed to reservoir water-washing. These geochemical parameters shed light into petroleum migration within Devonian-Mississippian petroleum systems and mitigate geological risk in exploring and developing petroleum reservoirs.Aubineau, J., El Abani, A., Bekker, A., Somogyi, A., Bankole, O.M., Macchiarelli, R., Meunier, A., Riboulleau, A., Reynaud, J.-Y., Konhauser, K.O., 2019. Microbially induced potassium enrichment in Paleoproterozoic shales and implications for reverse weathering on early Earth. Nature Communications 10, Article 2670. requires potassium incorporation into a smectite precursor, a process akin to reverse weathering. However, it remains unclear whether microbes facilitate K+ uptake to the sediments and whether illitisation was important in the geological past. The 2.1 billion-year-old Francevillian Series of Gabon has been shown to host mat-related structures (MRS) and, in this regard, these rocks offer a unique opportunity to test whether ancient microbes induced illitisation. Here, we show high K content confined to illite particles that are abundant in the facies bearing MRS, but not in the host sandstone and black shale. This observation suggests that microbial biofilms trapped K+ from the seawater and released it into the pore-waters during respiration, resulting in illitisation. The K-rich illite developed exclusively in the fossilized MRS thus provides a new biosignature for metasediments derived from K-feldspar-depleted rocks that were abundant crustal components on ancient Earth.Babarovi?, F., Puttick, M.N., Zaher, M., Learmonth, E., Gallimore, E.-J., Smithwick, F.M., Mayr, G., Vinther, J., 2019. Characterization of melanosomes involved in the production of non-iridescent structural feather colours and their detection in the fossil record. Journal of The Royal Society Interface 16, Article 20180921. structural colour in avian feathers is produced by coherent light scattering through quasi-ordered nanocavities in the keratin cortex of the barbs. To absorb unscattered light, melanosomes form a basal layer underneath the nanocavities. It has been shown that throughout Aves, melanosome morphology reflects broad categories of melanin-based coloration, as well as iridescence, allowing identification of palaeocolours in exceptionally preserved fossils. However, no studies have yet investigated the morphology of melanosomes in non-iridescent structural colour. Here, we analyse a wide sample of melanosomes from feathers that express non-iridescent structural colour from a phylogenetically broad range of extant avians to describe their morphology and compare them with other avian melanosome categories. We find that investigated melanosomes are typically wide (approx. 300 nm) and long (approx. 1400 nm), distinct from melanosomes found in black, brown and iridescent feathers, but overlapping significantly with melanosomes from grey feathers. This may suggest a developmental, and perhaps evolutionary, relationship between grey coloration and non-iridescent structural colours. We show that through analyses of fossil melanosomes, melanosomes indicative of non-iridescent structural colour can be predicted in an Eocene stem group roller (Eocoracias: Coraciiformes) and with phylogenetic comparative methods the likely hue can be surmised. The overlap between melanosomes from grey and non-iridescent structurally coloured feathers complicates their distinction in fossil samples where keratin does not preserve. However, the abundance of grey coloration relative to non-iridescent structural coloration makes the former a more likely occurrence except in phylogenetically bracketed specimens like the specimen of Eocoracias studied here.Bacmann, A., Faure, A., Berteaud, J., 2019. Cold and yet complex: Detection of ethylene oxide in a prestellar core. ACS Earth and Space Chemistry 3, 1000-1013., near-saturated, organic molecules have been detected in a wide range of environments, in harsh photon dominated regions, in protoplanetary disks, in the hot cores of star forming regions, and also in cold prestellar cores. In the latter case, the formation scenarios remain debated. While both gas phase or grain surface mechanisms have been considered, both types of scenarios have difficulties accounting for observed gas-phase abundances but none can be ruled out. The observation of structural isomers can help bring further constraints on molecular formation mechanisms, because their relative ratios should be ruled by kinetics, and not thermodynamics, in these low-density environments. Unfortunately so far no structural isomers of complex organic molecules have been detected. In this paper, we present the detection of ethylene oxide (c-C2H4O) in a prestellar core, using the IRAM 30 m telescope. While this species has previously been detected in hot cores of star forming regions, this represents the first detection in the cold (10 K) interstellar medium. Its more stable structural isomer acetaldehyde (CH3CHO) is also detected but not vinyl alcohol (CH2CHOH). We derive the abundances and abundance ratio of both detected species and compare them with predictions from the literature. We find that neither the previously proposed ion-neutral gas-phase nor the thermal grain surface scenarios can account for the observed abundances, while the radical–radical reaction between C2H5 and O remains a possible formation mechanism for both isomers. In addition, experiments have shown that cosmic ray induced electrons in ices containing CO, CO2, and C2H4 can explain the presence of both acetaldehyde and ethylene oxide in cold regions, but more quantitative data are needed to conclude whether the produced abundances can account for the observations.Baczynski, A.A., McInerney, F.A., Freeman, K.H., Wing, S.L., the Bighorn Basin Coring Project Science Team, 2019. Carbon isotope record of trace n-alkanes in a continental PETM section recovered by the Bighorn Basin Coring Project (BBCP). Paleoceanography and Paleoclimatology 34, 853-865. sedimentary records of early Paleogene hyperthermals are typically limited to weathered, often discontinuous, outcrop exposures. In 2011, the Bighorn Basin Coring Project (BBCP) collected the first continuous terrestrial records of the Paleocene‐Eocene Thermal Maximum (PETM) in the Bighorn Basin, Wyoming. Organic matter preservation was poor during the PETM, even in core material. Concentrations of leaf waxes during the PETM are too low for compound‐specific carbon isotope analysis by conventional means. However, the recent development of picomolar‐scale compound‐specific isotope analyses (pico‐CSIA) has reduced sample requirements and enabled measurements of carbon isotope ratios of n‐alkanes across the PETM in the Basin Substation core. While the prominent, negative carbon isotope excursion in total organic carbon that typically identifies the PETM in the sedimentary record is absent from the core, lithostratigraphic, biostratigraphic, and chemostratigraphic data suggest that the most likely position of the PETM is from ~87.82‐ to ~50‐m composite depth. This ~40‐m interval coincides with the lowest weight percent organic carbon, n‐alkane abundances, and n‐alkane δ13C values and the highest n‐alkane average chain lengths. Comparison of the n‐alkane isotope record from the core with that from organic‐rich rocks exposed in the SE Bighorn Basin suggests that n‐alkanes in the core fail to express the full magnitude of the carbon isotope excursion. We hypothesize that floodplain sediments at Basin Substation contain a mixture of PETM and reworked fossil n‐alkanes. Low total organic carbon suggests that PETM climate accelerated organic matter decay rates and floodplains may have acted as a carbon source during the PETM.Baek, S.-H., Hong, J.-W., Kim, K.Y., Yeom, S., Kwon, T.-H., 2019. X-Ray computed microtomography imaging of abiotic carbonate precipitation in porous media from a supersaturated solution: Insights into effect of CO2 mineral trapping on permeability. Water Resources Research 55, 3835-3855. carbonate precipitation has garnered significant interest as a mechanism for mineral trapping of carbon dioxide (CO2) in geologic carbon storage, as a natural diagenetic process frequently occurring in marine environments, and as an engineering approach for soil improvement. This study explored pore‐scale precipitation of calcium carbonate (CaCO3) and its effect on the permeability of porous media, using X‐ray computed microtomography (CMT). In a column experiment, CaCO3 was precipitated in a sand pack from a supersaturated CaCO3 solution, while porosity, pore volume fraction of carbonate, and permeability were being monitored and X‐ray CMT images were being acquired. Permeability reduction by ~99.94% was observed when precipitated carbonate occupied ~46–47% of pore volume. The X‐ray CMT images showed that carbonate crystals were initially nucleated onto sand grain surfaces, which facilitated subsequent precipitation, indicating a predominantly grain‐coating behavior. The scanning electron microscopy revealed the carbonate crystals of ~1–20 μm in size and the presence of internal pores in the carbonate layers at the submicrometer scale. Variations in carbonate layer thickness and geometric tortuosity, and preferential carbonate precipitation behavior with local clogging were examined through morphological analysis and phase segmentation. Particularly, the pore‐scale precipitation pattern and hence the pore geometry were found to evolve with continued precipitation from a grain‐coating behavior, through a pore‐filling behavior, and finally into a dramatic pore‐throat‐clogging behavior. Our results provide unique experiment data for predictive modeling of long‐term CO2 transport and provide new insights into the changes in physical and transport properties during CO2 mineral trapping.Baek, S., Akkutlu, I.Y., 2019. CO2 stripping of kerogen condensates in source rocks. SPE Journal 24, 1415-1434. research has been conducted on hydrocarbon fluids in the organic materials of source rocks, such as kerogen and bitumen. However, these studies were limited in scope to simple fluids confined in nanopores, while ignoring the multicomponent effects. Recent studies using hydrocarbon mixtures revealed that compositional variation caused by selective adsorption and nanoconfinement significantly alters the phase equilibrium properties of fluids. One important consequence of this behavior is capillary condensation and the trapping of hydrocarbons in organic nanopores. Pressure depletion produces lighter components, which make up a small fraction of the in-situ fluid. Equilibrium molecular simulation of hydrocarbon mixtures was carried out to show the impact of CO2 injection on the hydrocarbon recovery from organic nanopores. CO2 molecules introduced into the nanopore led to an exchange of molecules and a shift in the phase equilibrium properties of the confined fluid. This exchange had a stripping effect and, in turn, enhanced the hydrocarbon recovery. The CO2 injection, however, was not as effective for heavy hydrocarbons as it was for light components in the mixture. The large molecules left behind after the CO2 injection made up the majority of the residual (trapped) hydrocarbon amount. High injection pressure led to a significant increase in recovery from the organic nanopores, but was not critical for the recovery of the bulk fluid in large pores. Diffusing CO2 into the nanopores and the consequential exchange of molecules were the primary drivers that promoted the recovery, whereas pressure depletion was not effective on the recovery. The results for N2 injection were also recorded for comparison.Baek, S., Akkutlu, I.Y., 2019. Produced-fluid composition redistribution in source rocks for hydrocarbon-in-place and thermodynamic recovery calculations. SPE Journal 24, 1395-1414. rocks, such as organic-rich shale, consist of a multiscale pore structure that includes pores with sizes down to the nanoscale, contributing to the storage of hydrocarbons. In this study, we observed hydrocarbons in the source rock partition into fluids with significantly varying physical properties across the nanopore-size distribution of the organic matter. This partitioning is a consequence of the multicomponent hydrocarbon mixture stored in the nanopores, exhibiting a significant compositional variation by pore size—the smaller the pore size, the heavier and more viscous the hydrocarbon mixture becomes. The concept of composition redistribution of the produced fluids uses an equilibrium molecular simulation that considers organic matter to be a graphite membrane in contact with a microcrack that holds bulk-phase produced fluid.A new equation of state (EOS) was proposed to predict the density of the redistributed fluid mixtures in nanopores under the initial reservoir conditions. A new volumetric method was presented to ensure the density variability across the measured pore-size distribution to improve the accuracy of predicting hydrocarbons in place. The approach allowed us to account for the bulk hydrocarbon fluids and the fluids under confinement.Multicomponent fluids with redistributed compositions are capillary condensed in nanopores at the lower end of the pore-size distribution of the matrix (<10 nm). The nanoconfinement effects are responsible for the condensation. During production and pressure depletion, the remaining hydrocarbons become progressively heavier. Hence, hydrocarbon vaporization and desorption develop at extremely low pressures. Consequently, hydrocarbon recovery from these small pores is characteristically low.Balestrin, L.B.d.S., Francisco, R.D., Bertran, C.A., Cardoso, M.B., Loh, W., 2019. Direct assessment of inhibitor and solvent effects on the deposition mechanism of asphaltenes in a Brazilian crude oil. Energy & Fuels 33, 4748-4757. study of the asphaltene deposition mechanism is critical to understand and solve important problems in the petroleum industry. The same is valid for the selection of inhibitors to control or prevent asphaltene flocculation and/or deposition. However, most of the current information on these processes is obtained by experiments performed using model solvent systems. In the present study, we used quartz crystal microbalance (QCM) measurements as well as laser scanning confocal microscopy to characterize the asphaltene deposition directly measured in a Brazilian crude oil at different conditions of flocculant concentration and using inhibitors with different chemical features. Measurements under accelerated sedimentation (LUMiSizer) were also employed to evaluate inhibitor capacity in crude oil systems, in this case using a large excess of n-heptane. Overall, QCM results suggest that the diffusion-limited aggregation (DLA) model can be used to describe systems close to or above the concentration of the onset of asphaltene precipitation. The transition to a behavior that follows the reaction-limited aggregation (RLA) model occurs when an inhibitor added or the flocculant concentration is reduced farther from the onset. Moreover, accelerated sedimentation shows that the inhibitors tested act by preventing aggregate growth. Therefore, these results highlight the importance of performing time-dependent experiments directly in crude oils and support the use of these methodologies to optimize inhibitor selection for different crude oils.Ball, P., 2019. Lessons from cold fusion, 30 years on. Nature 569, 510. revisit long-discredited claims for a source of abundant energy, asks Philip Ball? Because we are still learning how to treat pathological science. In early 1989, chemists Martin Fleischmann and Stanley Pons at the University of Utah, Salt Lake City, made a claim that shocked and galvanized chemists and physicists, and excited society with its potential implications for clean, cheap energy.At a press conference, Fleishmann and Pons announced what would become known as cold fusion — the nuclear fusion of hydrogen at room temperature rather than inside a star. They described a startling process in heavy water (that is, water molecules with deuterium atoms replacing the normal hydrogens) in which the electrolysis of a salt solution could, so they said, make deuterium atoms absorb into a palladium electrode at such a high density that their nuclei merged, producing energy and the neutron and γ-ray emissions that are telltale signs of fusion.The findings didn’t stand up to the storm of scrutiny that followed. As a recent recruit to the physical sciences editorial team at Nature, to which Fleischmann and Pons had submitted their paper, I got a whirlwind introduction to the politics of scientific controversy.This week’s publication of a study funded by Google (C. P. Berlinguette et al. Nature ; 2019) that sought (unsuccessfully) to replicate the claims and to search for deuterium fusion led me to reflect on that past. My conclusion? The sociology is at least as instructive as the science.From the replication crisis of the social and life sciences to the mistaken report of faster-than-light neutrinos in high-energy physics, science is facing ever more claims that both defy conventional wisdom and are based on evidence at the threshold of what analyses or instruments can detect. Adjudicating such claims demands a community of researchers that is united in the spirit of inquiry, despite disagreements about evidence or interpretation. Cold fusion showed us the dangers of polarization, the distorting influence of commercial interests and the importance of being open about methods, data and mistakes.The concept of cold fusion unravelled within weeks of its debut. Even secondary-school students joined the flocks of scientists who were trying to reproduce the findings. A few groups of researchers claimed to have verified the reaction’s excess heat or fusion-related signals, but most experiments revealed nothing unusual. Fleischmann and Pons made their claim in March; by June it had been widely dismissed as illusory — or worse.For some, cold fusion represented a classic example of pathological science. This term was coined in the 1950s to describe a striking claim that conflicts with previous experience, that is based on effects that are difficult to detect and that is defended against criticism by ad hoc excuses. In this view, cold fusion joins an insalubrious list that includes the N-rays of 1903, the polywater affair of the late 1960s and the memory of water episode of the late 1980s.Nature never published the manuscript by Fleischmann and Pons — the authors withdrew it to focus on follow-up work. But a paper reporting similar findings by a group at Brigham Young University in Provo, Utah, was published in April of that year (S. E. Jones et al. Nature 338, 737–740; 1989). The only report at the time from Fleischmann and Pons was a short paper, lacking in detail, in the Journal of Electroanalytical Chemistry (M. Fleischmann & S. Pons J. Electroanal. Chem. 261, 301–308; 1989).Nature did publish follow-up studies by other groups, including one that used the actual equipment of Fleishmann and Pons (M. H. Salamon et al. Nature 344, 401–405; 1990). None observed any hint of cold fusion, and no convincing evidence has since materialized.The small community that insists that cold fusion is a genuine, if elusive, phenomenon is unlikely to be satisfied with the negative findings reported in this issue, in part because these findings suggest that interesting questions remain about the conditions under which fusion might occur.Although often held up as a textbook case of science’s self-correcting capacity, the cold-fusion episode is instructive for how it brought out both the best and worst in scientists.We should not too quickly judge, and thereby alienate, scientists who make controversial claims. The ridicule that was sometimes directed at Fleischmann and Pons was bound to make them double down. When researchers turn out to have been mistaken, they must be allowed a way back without disgrace. Nor should the science under scrutiny be reflexively regarded as being pathological. Some assertions at the time, along the lines of “I knew it was nonsense,” scarcely exhibited the openness to surprise on which science depends.Yet the architects of cold fusion were their own worst enemies. Fleischmann launched ad hominem attacks on his critics; he and Pons were obstructive about their methods. The ill-advised, short-lived attempt by their university to capitalize on cold fusion made matters worse. Some researchers faced unconscionable legal threats for simply trying to do good science. The discipline-led triumphalism — with chemists claiming to have achieved in a cheap test tube what physicists failed to do with high-tech equipment — was trite and divisive. Without a tolerant and collaborative spirit, feelings can rapidly sour.Keeping a handle on such a fast-moving story in the days before the Internet meant that cutting and pasting required scissors and glue, and that sending a fax was the quickest way to share a document. Would the cold-fusion saga play out differently today, with social media, fake news and an even more urgent need for clean energy? Probably — but not necessarily for the better.Banerjee, R., Jones, J.C., Lipscomb, J.D., 2019. Soluble methane monooxygenase. Annual Review of Biochemistry 88, 409-431. life is possible because the molecular structure of oxygen (O2) makes direct reaction with most organic materials at ambient temperatures an exceptionally slow process. Of course, these reactions are inherently very favorable, and they occur rapidly with the release of a great deal of energy at high temperature. Nature has been able to tap this sequestered reservoir of energy with great spatial and temporal selectivity at ambient temperatures through the evolution of oxidase and oxygenase enzymes. One mechanism used by these enzymes for O2 activation has been studied in detail for the soluble form of the enzyme methane monooxygenase. These studies have revealed the step-by-step process of O2 activation and insertion into the ultimately stable C-H bond of methane. Additionally, an elegant regulatory mechanism has been defined that enlists size selection and quantum tunneling to allow methane oxidation to occur specifically in the presence of more easily oxidized substrates.Bangalore Venkatesh, P., D'Entremont, J.H., Meyer, S.E., Bane, S.P.M., Grubelich, M.C., King, D.K., 2019. Bipropellant high energy stimulation for oil and gas applications. Journal of Petroleum Science and Engineering 180, 660-667. extraction of oil and natural gas requires an effective method of generating a high surface area network of fractures, or the stimulation of existing fractures, in a formation in order to increase permeability. Conventional hydraulic fracturing has limited utility in this application. In this work, Sandia National Laboratories is exploring high rate pressurization techniques employing tailored energetic materials systems to control both pressure rise rate and peak pressure in order to optimally stimulate potential rock formations. Rapid pressurization, at rates far exceeding quasi-static conventional hydraulic rates, can generate multiple radial well bore fractures and potentially provide a mechanism to induce shear destabilization within the formation that enables the fractures to be self-propping. Multiple fractures from the well bore allow efficient coupling to the existing formation fracture network and increase near field well bore permeability. Furthermore, these techniques can allow for repeated stimulations and produce energetic events within the fractures thereby allowing fractures to be extended further. Controlled rate pressurization is a useful tool for the efficient generation of fracture networks and has potential application to increase oil and gas production. This paper provides an overview of the concept of controlled rate pressurization, laboratory experiments and field trials that are being conducted. The present work investigates detonations of a stoichiometric mixture of ethylene and nitrous oxide (C2H4?+?6N2O) at high initial pressures ranging from 0.862 to 2.068?MPa as a method of fracturing rock below the ground surface. The experiments investigate the fracture generation as a function of the initial pressure of the mixture. In the current configuration, the combustion reaction is initiated by an electrically fired igniter at the ground surface and quickly transitions to a detonation. The experimental setup accommodates one high pressure (690?MPa) transducer, placed downstream of the igniter, to measure peak pressure. The pressure transducer recorded peak pressures, which are 2.3–2.6 times in excess of the Chapman-Jouguet (CJ) values as a result of pre-compression of the unburned gas mixture during the flame acceleration prior to deflagration-to-detonation transition (DDT). Analysis of the data indicated an increase in rock permeability due to detonations and this was confirmed by the core drilled sections at the test site.Baranov, B.V., Lobkovsky, L.I., Dozorova, K.A., Tsukanov, N.V., 2019. The fault system controlling methane seeps on the shelf of the Laptev Sea. Doklady Earth Sciences 486, 571-574. paper presents data obtained during the 69th and 72nd expeditions of the research vessel Akademik Mstislav Keldysh (2017, 2018). A mechanism of methane discharge that explains the localization of the seep fields in a limited area of the outer shelf and suggesting a system of deep and surface faults is proposed. Along the deep faults, gas fluid is transferred to the upper strata of the sedimentary cover, where it is accumulated below the gas hydrate stability zone and the permafrost horizon. The surface faults of the outer shelf break this caprock, creating conduits for the gas to migrate to the surface and to jet–release into the water column.Barnes, K.M., Whiffin, A.L., Bulling, M.T., 2019. A preliminary study on the antibacterial activity and insect repellent properties of embalming fluids from the 18th Dynasty (1550–1292?BCE) in ancient Egypt. Journal of Archaeological Science: Reports 25, 600-609. ancient Egyptians believed in an afterlife where the body of a dead person would be needed by the spirit. In order to preserve the deceased in as lifelike condition as possible they developed artificial mummification to a high level of sophistication. It is widely believed that natron was the main desiccation agent in the preparation of Egyptian mummified bodies in the 18th Dynasty. Natron is a natural mixture of sodium chloride, sodium sulphate, sodium carbonate and sodium bicarbonate found in the Nile Delta which has significant desiccation properties, but it is currently unclear if natron has further beneficial properties for the mummification process. Previous work indicates that it does not deter insect colonisation in general, although it has been found to act as a killing agent of blow flies. In particular, we are aware of no studies investigating the antibacterial activity of natron nor the wider investigation of the insect repellent nature of ancient Egyptian mummification resins. This study investigated the properties of ancient Egyptian embalming fluids alongside their application in an artificial mummification of a human body at the Medico-legal Centre in Sheffield, UK. Antibacterial assays were used to compare the activity of a modern day antibiotic (Chloramphenicol) to those of key embalming ingredients used in ancient Egypt (natron, palm wine and pine resin). In addition, a field study using rabbit carcasses investigated whether pine resin has insect repellent properties. Results demonstrated that palm wine and natron had higher antibacterial activity than Chlorophemical against the Gram-positive bacteria, Staphylococcus aureus, and that natron had higher antibacterial activity than Chloramphenicol against the Gram-negative bacteria, Escherichia coli. The field study showed a delay in the colonisation of necrophagous insects and a temporal shift in the families of insects present on the carcasses treated with pine resin compared to control carcasses (no pine resin). We found no insect mortality on any of the carcasses during the study, indicating that the pine resin was acting as a repellent only and not as an insecticide. Although this is a preliminary study, the clear results strongly suggest that the embalming fluids used in mummification procedures during the 18th Dynasty had a number of properties which could affect the development of associated bacterial and insect communities.Basheer, C., Kamran, M., Ashraf, M., Lee, H.K., 2019. Enhancing liquid-phase microextraction efficiency through chemical reactions. TrAC Trends in Analytical Chemistry 118, 426-433. microextraction (LPME) is a miniaturized extraction technique with a similar extraction principle to liquid–liquid extraction. In LPME, extraction and preconcentration can be performed in a single step. The basic LPME configuration is that in which extraction involves a single drop of solvent. Another mode of LPME, which entails the use of a porous membrane assisted hollow fiber LPME (HF-LPME) and it is suitable for direct extraction of complex environmental matrices. A more recent LPME development is dispersive liquid-liquid microextraction that has attracted tremendous interest. LPME has the versatility to incorporate chemical reactions in order to enhance extractability and impart compatibility of the final extract with analytical instrumentation. This review focuses on recent developments in LPME involving chemical reactions as part of the extraction process. Reactions that improve the sensitivity of LPME, including ion-pair extraction, complexation, chemical derivatization, phase transfer catalysis, and nanoparticle-assisted chemical reactions are given prominence.Baxter, A.J., Hopmans, E.C., Russell, J.M., Sinninghe Damsté, J.S., 2019. Bacterial GMGTs in East African lake sediments: Their potential as palaeotemperature indicators. Geochimica et Cosmochimica Acta 259, 155-169. monoalkyl glycerol tetraethers (GMGTs) are a group of membrane spanning lipids produced by some species of archaea and bacteria. They differ from the more commonly studied glycerol dialkyl glycerol tetraethers (GDGTs) in having an additional covalent carbon-carbon bond connecting the two alkyl chain. The relative abundance and distribution of bacterial branched GMGTs (brGMGTs) in surface sediments from a set of East African lakes were studied. The abundance of brGMGTs relative to the brGDGTs is positively correlated to measured mean annual air temperature (MAAT), although with a significant amount of scatter. BrGMGT abundance was not correlated to lake water pH. Seven major brGMGTs that vary in degree of methylation were identified, with m/z 1020, 1034 and 1048. Further, the mass chromatograms of the m/z 1020 and 1034 brGMGTs show an interesting distribution of peaks, which likely relates to the occurrence of distinct brGMGT isomers. This structural complexity is higher than previously observed in peats and marine sediments. Principal component analysis of the fractional abundance of bacterial tetraether lipids revealed the brGMGTs behave similarly to one another but differently from both the 5- or 6-methyl brGDGTs. This suggests the brGMGTs are produced by a common source organism and are methylated at a different position. The distribution of the seven brGMGTs showed considerable correlation with MAAT. This variability was captured in a new proxy index (the brGMGTI), which showed a strong positive linear relationship with MAAT. Lacustrine brGMGTs show potential to be applied to ancient settings to provide information about paleoclimate.Bemani, A., Poozesh, A., Bahrami, M., Ashoori, S., 2019. Experimental study of asphaltene deposition: Focus on critical size and temperature effect. Journal of Petroleum Science and Engineering 181, 106186. by far is the most problematic part of crude oil that could separate from oil body as a result of any change in system equilibrium. It can deposit at any point along oil flow path which in turn impose series restrictions, and subsequently create major impact on production from economic perspective. In this study, the influence of oil composition, flow rate, and for the first time, temperature on the intensity of deposition process are experimentally investigated. An in-house deposition unit apparatus was utilized which is based on the measurement of pressure drop across the capillary tube. The results indicate that in overall, temperature and oil composition change toward less soluble asphaltene, accelerate deposition process while flow rate enforces further restriction on process. In addition, by devising novel centrifugal based deposition experiments, critical size concept is more effectively addressed. The concept argues that there is a critical value for asphaltene aggregate size, beyond which the deposition will not occur. This critical size is not necessarily influence by hydrodynamic drag like forces.Berlinguette, C.P., Chiang, Y.-M., Munday, J.N., Schenkel, T., Fork, D.K., Koningstein, R., Trevithick, M.D., 2019. Revisiting the cold case of cold fusion. Nature 570, 45-51. 1989 claim of ‘cold fusion’ was publicly heralded as the future of clean energy generation. However, subsequent failures to reproduce the effect heightened scepticism of this claim in the academic community, and effectively led to the disqualification of the subject from further study. Motivated by the possibility that such judgement might have been premature, we embarked on a multi-institution programme to re-evaluate cold fusion to a high standard of scientific rigour. Here we describe our efforts, which have yet to yield any evidence of such an effect. Nonetheless, a by-product of our investigations has been to provide new insights into highly hydrided metals and low-energy nuclear reactions, and we contend that there remains much interesting science to be done in this underexplored parameter space.Bernstein Ethan, S., Turban, S., 2018. The impact of the ‘open’ workspace on human collaboration. Philosophical Transactions of the Royal Society B: Biological Sciences 373, 20170239.’ pursuit of increased workplace collaboration has led managers to transform traditional office spaces into ‘open’, transparency-enhancing architectures with fewer walls, doors and other spatial boundaries, yet there is scant direct empirical research on how human interaction patterns change as a result of these architectural changes. In two intervention-based field studies of corporate headquarters transitioning to more open office spaces, we empirically examined—using digital data from advanced wearable devices and from electronic communication servers—the effect of open office architectures on employees' face-to-face, email and instant messaging (IM) interaction patterns. Contrary to common belief, the volume of face-to-face interaction decreased significantly (approx. 70%) in both cases, with an associated increase in electronic interaction. In short, rather than prompting increasingly vibrant face-to-face collaboration, open architecture appeared to trigger a natural human response to socially withdraw from officemates and interact instead over email and IM. This is the first study to empirically measure both face-to-face and electronic interaction before and after the adoption of open office architecture. The results inform our understanding of the impact on human behaviour of workspaces that trend towards fewer spatial boundaries.Bhushan, B., 2019. Bioinspired oil–water separation approaches for oil spill clean-up and water purification. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 377, 20190120. contamination is one of the major environmental and natural resource concerns in the twenty-first century. Oil contamination can occur during operation of machinery, oil exploration and transportation, and due to operating environment. Oil spills occasionally occur during oil exploration and transportation. Water contamination with various chemicals is a major concern with growing population and unsafe industrial practices of waste disposal. Commonly used oil–water separation techniques are either time consuming, energy intensive and/or environmentally unfriendly. Bioinspired superhydrophobic/superoleophobic and superoleophobic/superhydrophilic surfaces have been developed which are sustainable and environmentally friendly. Bioinspired oil–water separation techniques can be used to remove oil contaminants from both immiscible oil–water mixtures and oil–water emulsions. Coated porous surfaces with an affinity to water and repellency to oil and vice versa are commonly used. The former combination of affinity to water and repellency to oil is preferred to avoid oil contamination of the porous substrate. Oil–water emulsions require porous materials with a fine pore size. Recommended porous materials include steel mesh and cotton fabric for immiscible oil–water mixtures and cotton for oil–water emulsions. A review of various approaches is presented in this paper.Bianco, A., Deguillaume, L., Chaumerliac, N., Va?tilingom, M., Wang, M., Delort, A.-M., Bridoux, M.C., 2019. Effect of endogenous microbiota on the molecular composition of cloud water: a study by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Scientific Reports 9, Article 7663. cloud water sample collected at the puy de D?me observatory (PUY) has been incubated under dark conditions, with its endogenous microbiota at two different temperatures (5 and 15?°C), and the change in the molecular organic composition of this sample was analyzed by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Microorganisms were metabolically active and strongly modified the dissolved organic matter since they were able to form and consume many compounds. Using Venn diagrams, four fractions of compounds were identified: (1) compounds consumed by microbial activity; (2) compounds not transformed during incubation; (3) compounds resulting from dark chemistry (i.e., hydrolysis and Fenton reactions) and, finally, (4) compounds resulting from microbial metabolic activity. At 15?°C, microorganisms were able to consume 58% of the compounds initially present and produce 266 new compounds. For this cloud sample, the impact of dark chemistry was negligible. Decreasing the temperature to 5?°C led to the more efficient degradation of organic compounds (1716 compounds vs. 1094 at 15?°C) but with the less important production of new ones (173). These transformations were analyzed using a division into classes based on the O/C and H/C ratios: lipid-like compounds, aliphatic/peptide-like compounds, carboxylic-rich alicyclic molecule (CRAM)-like structures, carbohydrate-like compounds, unsaturated hydrocarbons, aromatic structures and highly oxygenated compounds (HOCs). Lipid-like, aliphatic/peptide-like and CRAMs-like compounds were the most impacted since they were consumed to maintain the microbial metabolism. On the contrary, the relative percentages of CRAMs and carbohydrates increased after incubation.Bif, M.B., Hansell, D.A., 2019. Seasonality of dissolved organic carbon in the upper Northeast Pacific Ocean. Global Biogeochemical Cycles 33, 526-539. seasonal cruises in the NE Pacific Ocean during 2017, we (1) determined dissolved organic carbon concentrations; (2) calculated net community production (NCP) from nitrate drawdown; and (3) established relationships between NCP and seasonal dissolved organic carbon (DOC) accumulation in the upper 75 m. The fraction of NCP that accumulated as DOC, hereafter referred to as the net dissolved production ratio, was calculated for several stations during spring and summer. The net dissolved production ratio was about 0.26 at the oceanic station Ocean Station Papa during different seasons and years. Using nitrate concentration profiles obtained from Bio‐Argo floats during 2009–2018 operating near Ocean Station Papa, we calculated NCP at high temporal resolution and then applied the 0.26 constant in order to (4) estimate DOC variability for the 9‐year period. We found strong seasonality near Ocean Station Papa, with NCP maxima during summers ranging from 0.3 to 2.9 mol C/m2 and surface DOC concentrations estimated from 56 μmol/kg in winters to 73 μmol/kg in summers. There was a 10‐fold interannual variability in the seasonally accumulated inventory of DOC, ranging from 0.078 to 0.75 mol C/m2. This study reinforces the value of deploying floats equipped with chemical sensors in order to better understand marine biogeochemical cycles, especially when high resolution data cannot be obtained otherwise. Given that ~26% of NCP accumulates as DOC in the central Gulf of Alaska, the remaining balance of ~74% is available for export as sinking biogenic particles.Boeuf, D., Edwards, B.R., Eppley, J.M., Hu, S.K., Poff, K.E., Romano, A.E., Caron, D.A., Karl, D.M., DeLong, E.F., 2019. Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean. Proceedings of the National Academy of Sciences 116, 11824-11832.: Sinking particles composed of both organic and inorganic material feed the deep-sea ecosystem and contribute centrally to ocean carbon sequestration. Despite their importance, little is known about the biological composition of sinking particles reaching the deep sea. Time-series analyses of sinking particles unexpectedly revealed bacterial assemblages that were simple and homogeneous over time. Particle-associated eukaryote assemblages, however, were more variable and complex. Several modes of export were observed, including summer inputs from the surface, more stochastic export of surface-derived protists and animals, and contributions from midwater animals and deep-sea bacteria. In summary, sinking particles exhibited temporally variable, heterogeneous biological sources and activities that reflected their important roles in the downward transport and transformation of organic matter in the deep sea.Abstract: Sinking particles are a critical conduit for the export of organic material from surface waters to the deep ocean. Despite their importance in oceanic carbon cycling and export, little is known about the biotic composition, origins, and variability of sinking particles reaching abyssal depths. Here, we analyzed particle-associated nucleic acids captured and preserved in sediment traps at 4,000-m depth in the North Pacific Subtropical Gyre. Over the 9-month time-series, Bacteria dominated both the rRNA-gene and rRNA pools, followed by eukaryotes (protists and animals) and trace amounts of Archaea. Deep-sea piezophile-like Gammaproteobacteria, along with Epsilonproteobacteria, comprised >80% of the bacterial inventory. Protists (mostly Rhizaria, Syndinales, and ciliates) and metazoa (predominantly pelagic mollusks and cnidarians) were the most common sinking particle-associated eukaryotes. Some near-surface water-derived eukaryotes, especially Foraminifera, Radiolaria, and pteropods, varied greatly in their abundance patterns, presumably due to sporadic export events. The dominance of piezophile-like Gammaproteobacteria and Epsilonproteobacteria, along with the prevalence of their nitrogen cycling-associated gene transcripts, suggested a central role for these bacteria in the mineralization and biogeochemical transformation of sinking particulate organic matter in the deep ocean. Our data also reflected several different modes of particle export dynamics, including summer export, more stochastic inputs from the upper water column by protists and pteropods, and contributions from sinking mid- and deep-water organisms. In total, our observations revealed the variable and heterogeneous biological origins and microbial activities of sinking particles that connect their downward transport, transformation, and degradation to deep-sea biogeochemical processes.Bonn, B., Magh, R.-K., Rombach, J., Kreuzwieser, J., 2019. Biogenic isoprenoid emissions under drought stress: Different responses for isoprene and terpenes. Biogeosciences Discussions 2019, 1-30. of volatile organic compounds (VOCs) by biogenic sources depend on different environmental conditions. Besides temperature and photosynthetic active radiation (PAR), the available soil water can be a major factor, controlling the emission flux. This factor is expected to become more important under future climate conditions including prolonged drying-wetting cycles. In this paper we use results of available studies on different tree types to set up a parameterization describing the influence of soil water availability (SWA) on different isoprenoid emission rates. Investigating SWA effects on isoprene (C5H8), mono- (C10H16) and sesquiterpene (C15H24) emissions separately, it is obvious that different plant processes seem to control the individual emission fluxes providing a measure of plants to react on stresses and to interact. The SWA impact on isoprene emissions is well described by a biological growth type curve, while the sum of monoterpenes displays a hydraulic conductivity pattern reflecting the plants stomata opening. However, emissions of individual monoterpene structures behave differently to the total sum, i.e. the emissions of some increase whereas of others decline at decreasing SWA. In addition to a rather similar behaviour as of monoterpene emissions, total sesquiterpene fluxes of species adapted to drought stress tend to reveal a rise close to the wilting point protecting against oxidative damages. Considering further VOCs too, the total sum of VOCs tends to increase at the start of severe drought conditions until resources decline. On the contrary, OH and ozone reactivity enhance. Based on these observations a set of plant protection mechanism displays for drought stress and implies notable feedbacks on atmospheric processes such as ozone, aerosol particles and cloud properties. With progressing length of drought periods declining storage pools and plant structure effects yield different emission mixtures and strengths. This drought feedback effect is definitely worth consideration in climate feedback descriptions and for accurate climate predictions.Booker, A.E., Hoyt, D.W., Meulia, T., Eder, E., Nicora, C.D., Purvine, S.O., Daly, R.A., Moore, J.D., Wunch, K., Pfiffner, S.M., Lipton, M.S., Mouser, P.J., Wrighton, K.C., Wilkins, M.J., 2019. Deep-subsurface pressure stimulates metabolic plasticity in shale-colonizing Halanaerobium spp. Applied and Environmental Microbiology 85, Article e00018-19.: Bacterial Halanaerobium strains become the dominant persisting microbial community member in produced fluids across geographically distinct hydraulically fractured shales. Halanaerobium is believed to be inadvertently introduced into this environment during the drilling and fracturing process and must therefore tolerate large changes in pressure, temperature, and salinity. Here, we used a Halanaerobium strain isolated from a natural gas well in the Utica Point Pleasant formation to investigate metabolic and physiological responses to growth under high-pressure subsurface conditions. Laboratory incubations confirmed the ability of Halanaerobium congolense strain WG8 to grow under pressures representative of deep shale formations (21 to 48?MPa). Under these conditions, broad metabolic and physiological shifts were identified, including higher abundances of proteins associated with the production of extracellular polymeric substances. Confocal laser scanning microscopy indicated that extracellular polymeric substance (EPS) production was associated with greater cell aggregation when biomass was cultured at high pressure. Changes in Halanaerobium central carbon metabolism under the same conditions were inferred from nuclear magnetic resonance (NMR) and gas chromatography measurements, revealing large per-cell increases in production of ethanol, acetate, and propanol and cessation of hydrogen production. These metabolic shifts were associated with carbon flux through 1,2-propanediol in response to slower fluxes of carbon through stage 3 of glycolysis. Together, these results reveal the potential for bioclogging and corrosion (via organic acid fermentation products) associated with persistent Halanaerobium growth in deep, hydraulically fractured shale ecosystems, and offer new insights into cellular mechanisms that enable these strains to dominate deep-shale microbiomes.Importance: The hydraulic fracturing of deep-shale formations for hydrocarbon recovery accounts for approximately 60% of U.S. natural gas production. Microbial activity associated with this process is generally considered deleterious due to issues associated with sulfide production, microbially induced corrosion, and bioclogging in the subsurface. Here we demonstrate that a representative Halanaerobium species, frequently the dominant microbial taxon in hydraulically fractured shales, responds to pressures characteristic of the deep subsurface by shifting its metabolism to generate more corrosive organic acids and produce more polymeric substances that cause “clumping” of biomass. While the potential for increased corrosion of steel infrastructure and clogging of pores and fractures in the subsurface may significantly impact hydrocarbon recovery, these data also offer new insights for microbial control in these ecosystems.Booth, J.M., Fusi, M., Marasco, R., Michoud, G., Fodelianakis, S., Merlino, G., Daffonchio, D., 2019. The role of fungi in heterogeneous sediment microbial networks. Scientific Reports 9, Article 7537. prokaryote community diversity and function have been extensively studied in soils and sediments, the functional role of fungi, despite their huge diversity, is widely unexplored. Several studies have, nonetheless, revealed the importance of fungi in provisioning services to prokaryote communities. Here, we hypothesise that the fungal community plays a key role in coordinating entire microbial communities by controlling the structure of functional networks in sediment. We selected a sediment environment with high niche diversity due to prevalent macrofaunal bioturbation, namely intertidal mangrove sediment, and explored the assembly of bacteria, archaea and fungi in different sediment niches, which we characterised by biogeochemical analysis, around the burrow of a herbivorous crab. We detected a high level of heterogeneity in sediment biogeochemical conditions, and diverse niches harboured distinct communities of bacteria, fungi and archaea. Saprotrophic fungi were a pivotal component of microbial networks throughout and we invariably found fungi to act as keystone species in all the examined niches and possibly acting synergistically with other environmental variables to determine the overall microbial community structure. In consideration of the importance of microbial-based nutrient cycling on overall sediment ecosystem functioning, we underline that the fungal microbiome and its role in the functional interactome cannot be overlooked.Borgatti, L., Giovanna, B., Edoardo, B.A., Stefano, C., Gloria, F., Francesca, G., Donato, L., Giuseppe, M., Giovanni, M., Chiara, M.M., Diego, P., 2019. Evidence of Late-Holocene mud-volcanic eruptions in the Modena foothills (northern Italy). The Holocene 29, 975-991. natural hazards, mud volcanoes can damage property and infrastructures and affect hillslope evolution at different spatial and temporal scales. The results of 10-year-long multidisciplinary investigations performed on a Roman-age archaeological site, La Rovina di Montegibbio, are presented, showing a peculiar example of mutual interplay between human settlement and geological forcing in the mud-volcanic environment. The site (350 m a.s.l.) lies at the termination of the upper Secchia River catchment, near the town of Sassuolo (Modena Province). Here, a 4-km-long mud volcano belt borders the Apennines chain front, comprising one of the most prominent mud volcanoes of Italy (Salsa di Montegibbio), and the still-active chain hinge tectonics gives origin to gas and oil seeps. Based on geological, geoarchaeological, palaeobotanical, geochemical, geophysical records and analytical data, we unravel the onset, the evolution and the abandonment of the settlement in relation to the existence of a previously unknown mud volcano, belonging to the larger Montegibbio mud volcano system. The damages affecting the Roman-age buildings record the ground deformations in the context of mud volcano tectonics. In particular, the pattern of faults set buried under the archaeological site is shown and compared with that of the main mud volcano conduit. At least two Roman-age eruptive episodes have been recorded, whose ejected muds are geochemically characterized. The first recorded eruption must be regarded as the reason for the initial location and function of the sacred ancient settlement. The final site abandonment was because of subsequent severe ground deformations affecting the hillslope as a consequence of mud volcano activity.Bortnikov, N.S., Boeva, N.M., Soboleva, S.V., Bocharnikova, Y.I., 2019. Organic complexes in the montmorillonite interlayer space: A unique feature of Sakhalin Island bentonite. Doklady Earth Sciences 486, 558-561. of natural modification with organic complexes was found for the first time in bentonite of the Tikhmenevo deposit on Sakhalin Island. The data obtained permitted us to identify within the interlayer space of the bentonite chain polymethylene, alkylammonium, and other fragments of humic molecules occurring in the humus surrounding the bentonite.Bottoms, B., Potra, A., Samuelsen, J.R., Schutter, S.R., 2019. Geochemical investigations of the Woodford–Chattanooga and Fayetteville Shales: Implications for genesis of the Mississippi Valley–type zinc–lead ores in the southern Ozark Region and hydrocarbon exploration. American Association of Petroleum Geologists Bulletin 103, 1745-1768. relationship between base metal deposits, especially Mississippi Valley–type (MVT) Pb–Zn deposits, and hydrocarbons is not well constrained. This is despite the fact that hydrocarbons generally occur in MVT deposits; the ores are emplaced in the same temperature range as hydrocarbon maturation and migration, and the deposits commonly occur in proximity to metal-rich black shales. Better understanding should lead to better exploration models for both hydrocarbons and MVT deposits. This connection is better understood with the help of Pb isotope patterns. Sphalerite Pb isotope compositions from the northern Arkansas and Tri-State mining districts and Woodford–Chattanooga and Fayetteville Shales were determined to assess the potential of shales as source rocks for the ore metals. The ores in both districts have a broad range of Pb isotope ratios and define linear trends, suggesting mixing of Pb from two distinct end members. Current results and previous depositional environment studies indicate the following: (1) shales deposited mainly under nonsulfidic anoxic conditions represent the less radiogenic end member, or (2) shales are the only source of ore metals. Given the array of organic molecules, each with their own thermochemical range, and the ways metals can be associated with them, the release of metals may cover varying ranges. Thus, the compositions of the released fluids would change through time and not have a single static composition, closely approximating the isotopic composition of the released metals at various times. Mineralization derived from a dynamically evolving fluid may show apparent end members, without the need to call on mixing of fluids from separate sources.Bowers, G.M., Loring, J.S., Schaef, H.T., Cunniff, S.S., Walter, E.D., Burton, S.D., Larsen IV, R.K., Miller, Q.R.S., Bowden, M.E., Ilton, E.S., Kirkpatrick, R.J., 2019. Chemical trapping of CO2 by clay minerals at reservoir conditions: Two mechanisms observed by in situ high-pressure and -temperature experiments. ACS Earth and Space Chemistry 3, 1034-1046. paper presents the results of experiments performed in situ at temperature and pressure relevant to reservoir conditions (T = 323 K and Pfluid = 90 bar) to evaluate whether clay minerals can react with supercritical CO2 to produce carbonate phases by ion exchange–precipitation reactions and dissolution–reprecipitation reactions. The results show that both can occur on a time scale of hours under the conditions of our studies. The dissolution–reprecipitation mechanism was examined using Ca-, Cs-, and tetramethylammonium (TMA+) laponite, a synthetic smectite analogous to hectorite that has small particles (basal dimensions of ～10 × 10 nm2) and a high fraction of edge sites where only two of the usual three bridging oxygen atoms are shared with other tetrahedra in the silicate sheet (Q2 sites), making it an excellent case for examining the role of T–O–T edges. The ion exchange–precipitation mechanism was observed for a Pb-exchanged natural low-Fe smectite (hectorite). Novel X-ray diffraction and NMR and infrared (IR) spectroscopic tools provide in situ observation of these reactions in real time supported by a suite of ex situ analyses. The results demonstrate for the first time that 13C NMR can effectively characterize the amorphous and crystalline products of such reactions. For all three laponites, IR and NMR data show that HCO3– ions form at water content as small as ～5 H2O molecules/exchangeable cation. When the exchangeable cation is Ca2+, the IR data show the formation of carbonate anions at low water content as well, with the NMR spectra showing formation of amorphous calcium carbonate in vacuum-dried samples. For laponites equilibrated at 100% RH at atmospheric conditions and then exposed to scCO2, 13C NMR shows the presence of a greater number of more mobile HCO3– ions and a poorly crystalline or amorphous hydrous magnesium carbonate/bicarbonate phase that forms from Mg2+ released by clay dissolution. The 100% RH sample with exchangeable Ca2+ also forms calcite, vaterite, and aragonite precipitates. Comparison of these and previously published results suggest that a high edge site Q2 fraction is crucial to the dissolution–reprecipitation process occurring on a short time scale. In the Pb-exchanged hectorite exposed to scCO2, once a critical humidity threshold of ～78% is reached, cerussite (PbCO3) forms rapidly concurrent with replacement of interlayer Pb2+ by H3O+ formed by reaction of CO2 with water on the clay surface. This type of reaction is not observed on a similar time scale with Ca- or Na-exchanged natural hectorite and other smectites, and the low solubility of cerussite appears to be the thermodynamic driving force for this process.Brand?o, P.F., Duarte, A.C., Duarte, R.M.B.O., 2019. Comprehensive multidimensional liquid chromatography for advancing environmental and natural products research. TrAC Trends in Analytical Chemistry 116, 186-197. is the separation method of choice in most laboratories worldwide. Nonetheless, the increasing need to decode complex samples has created a demand for better separation skills. The addition of extra separation dimensions to a conventional liquid chromatography system was one of the ways to answer to this demand. Although very common in proteomics and polymer research, the use of Multidimensional Liquid Chromatography (MDLC) coupled to high-resolution detectors for separation and analysis of environmental and natural products samples has yet to receive the deserved attention. This article presents a critical review on the most prominent of these comprehensive MDLC methods for targeted and untargeted analysis of complex environmental and natural products samples. This article also discusses the practical aspects of applying peak capacity and orthogonality concepts in MDLC analysis of complex matrices. It also addresses the limitations and challenges ahead for advancing environmental and natural products research using comprehensive MDLC.Braun, D.R., Aldeias, V., Archer, W., Arrowsmith, J.R., Baraki, N., Campisano, C.J., Deino, A.L., DiMaggio, E.N., Dupont-Nivet, G., Engda, B., Feary, D.A., Garello, D.I., Kerfelew, Z., McPherron, S.P., Patterson, D.B., Reeves, J.S., Thompson, J.C., Reed, K.E., 2019. Earliest known Oldowan artifacts at >2.58 Ma from Ledi-Geraru, Ethiopia, highlight early technological diversity. Proceedings of the National Academy of Sciences 116, 11712-11717.: Humans are distinguished from all other primates by their reliance on tool use. When this uniquely human feature began is debated. Evidence of tool use in human ancestors now extends almost 3.3 Ma and becomes prevalent only after 2.6 Ma with the Oldowan. Here, we report a new Oldowan locality (BD 1) that dates prior to 2.6 Ma. These earliest Oldowan tools are distinctive from the 3.3 Ma assemblage and from materials that modern nonhuman primates produce. So, although tool production and use represent a generalized trait of many primates, including human ancestors, the production of Oldowan stone artifacts appears to mark a systematic shift in tool manufacture that occurs at a time of major environmental changes.Abstract: The manufacture of flaked stone artifacts represents a major milestone in the technology of the human lineage. Although the earliest production of primitive stone tools, predating the genus Homo and emphasizing percussive activities, has been reported at 3.3 million years ago (Ma) from Lomekwi, Kenya, the systematic production of sharp-edged stone tools is unknown before the 2.58–2.55 Ma Oldowan assemblages from Gona, Ethiopia. The organized production of Oldowan stone artifacts is part of a suite of characteristics that is often associated with the adaptive grade shift linked to the genus Homo. Recent discoveries from Ledi-Geraru (LG), Ethiopia, place the first occurrence of Homo ～250 thousand years earlier than the Oldowan at Gona. Here, we describe a substantial assemblage of systematically flaked stone tools excavated in situ from a stratigraphically constrained context [Bokol Dora 1, (BD 1) hereafter] at LG bracketed between 2.61 and 2.58 Ma. Although perhaps more primitive in some respects, quantitative analysis suggests the BD 1 assemblage fits more closely with the variability previously described for the Oldowan than with the earlier Lomekwian or with stone tools produced by modern nonhuman primates. These differences suggest that hominin technology is distinctly different from generalized tool use that may be a shared feature of much of the primate lineage. The BD 1 assemblage, near the origin of our genus, provides a link between behavioral adaptations—in the form of flaked stone artifacts—and the biological evolution of our ancestors.Brislawn, C.J., Graham, E.B., Dana, K., Ihardt, P., Fansler, S.J., Chrisler, W.B., Cliff, J.B., Stegen, J.C., Moran, J.J., Bernstein, H.C., 2019. Forfeiting the priority effect: turnover defines biofilm community succession. The ISME Journal 13, 1865-1877. community succession is a fundamental process that affects underlying functions of almost all ecosystems; yet the roles and fates of the most abundant colonizers are often poorly understood. Does early abundance spur long term persistence? How do deterministic and stochastic processes influence the ecological contribution of colonizers? We performed a succession experiment within a hypersaline ecosystem to investigate how different processes contributed to the turnover of founder species. Bacterial and eukaryotic colonizers were identified during primary succession and tracked through a defined, 79-day biofilm maturation period using 16S and 18S rRNA gene sequencing in combination with high resolution imaging that utilized stable isotope tracers to evaluate successional patterns of primary producers and nitrogen fixers. The majority of the founder species did not maintain high abundance throughout succession. Species replacement (versus loss) was the dominant process shaping community succession. We also asked if different ecological processes acted on bacteria versus Eukaryotes during succession and found deterministic and stochastic forces corresponded more with microeukaryote and bacterial colonization, respectively. Our results show that taxa and functions belonging to different kingdoms, which share habitat in the tight spatial confines of a biofilm, were influenced by different ecological processes and time scales of succession.Brock, O., Kooijman, A., Nierop, K.G.J., Muys, B., Vancampenhout, K., Jansen, B., 2019. Disentangling the effects of parent material and litter input chemistry on molecular soil organic matter composition in converted forests in Western Europe. Organic Geochemistry 134, 66-76. storing carbon in the soil, forests contribute to climate change mitigation. Edaphic (soil-related) factors, such as soil pH, as well as tree species affect forest carbon cycles, but are difficult to disentangle. We studied how conversion of deciduous stands to mono-culture spruce plantations affected the soil organic matter (SOM) composition along a lithological gradient in the Mullerthal (Luxembourg) and Gaume (south-east Belgium) regions. Parent materials in these regions range from decalcified sands to calcareous marls. A twin plot setup of adjacent deciduous and coniferous stands on the same parent material was used to evaluate the effect of edaphic factors versus litter input differences on SOM composition and soil organic carbon (SOC) stocks. Lignin and cutin/suberin molecular proxies were identified with thermally assisted hydrolysis and methylation (THM), to distinguish litter sources (coniferous vs deciduous and leaf litter vs roots) in the studied stands. In this study, SOC stocks were influenced more by parent material than by forest type. Lignin yield, composition and degradation state were influenced both by litter input chemistry and edaphic context. There appear to be important interaction effects between the two, as the relative importance of parent material and litter quality was site specific. We therefore advice that carbon stock models include data on both vegetation history as well as edaphic context.Brown, S.R., Fritz, S.C., 2019. Eukaryotic organisms of continental hydrothermal systems. Extremophiles 23, 367-376. hydrothermal systems are a dynamic component of global thermal and geochemical cycles, exerting a pronounced impact on water chemistry and heat storage. As such, these environments are commonly classified by temperature, thermal fluid ionic concentration, and pH. Terrestrial hydrothermal systems are a refuge for extremophilic organisms, as extremes in temperature, metal concentration, and pH profoundly impact microorganism assemblage composition. While numerous studies focus on Bacteria and Archaea in these environments, few focus on Eukarya—likely due to lower temperature tolerances and because they are not model organisms for understanding the evolution of early life. However, where present, eukaryotic organisms are significant members of continental hydrothermal microorganism communities. Thus, this manuscript focuses on the eukaryotic occupants of terrestrial hydrothermal systems and provides a review of the current status of research, including microbe–eukaryote interactions and suggestions for future directions.Bruggmann, S., Klaebe, R.M., Paulukat, C., Frei, R., 2019. Heterogeneity and incorporation of chromium isotopes in recent marine molluscs (Mytilus). Geobiology 17, 417-435. mollusc genus Mytilus is abundant in various modern marine environments and is an important substrate for palaeo‐proxy work. The redox‐sensitive chromium (Cr) isotope system is emerging as a proxy for changes in the oxidation state of the Earth's atmosphere and oceans. However, potential isotopic offsets between ambient sea water and modern biogenic carbonates have yet to be constrained. We measured Cr concentrations ([Cr]) and isotope variations (δ53Cr) in recent mollusc shells (Mytilus) from open and restricted marine environments and compared these to ambient sea water δ53Cr values. We found a large range in mollusc [Cr] (12–309 ppb) and δ53Cr values (?0.30 to +1.25‰) and in the offset between δ53Cr values of mollusc shells and ambient sea water (Δ53Crbulk Mytilusseawater, ?0.17 to ?0.91‰). Step digestions of cultivated Mytilus edulis specimens indicate that Cr is mainly concentrated in organic components of the shell (periostracum: 407 ppb, n = 2), whereas the mollusc carbonate minerals contain ≤3 ppb Cr. Analyses of individual Cr‐hosting phases (i.e., carbonate minerals and organic matrix) did not reveal significant differences in δ53Cr values, and thus, we suggest that Cr isotope fractionation may likely take place prior to rather than during biomineralisation of Mytilus shells. Heterogeneity of δ53Cr values in mollusc shells depends on sea water chemistry (e.g., salinity, food availability, faeces). The main control for δ53Cr values incorporated into shells, however, is likely vital effects (in particular shell valve closure time) since Cr can be partially or quantitatively reduced in sea water trapped between closed shell valves. The δ53Cr values recorded in Mytilus shells may thus be de‐coupled from the redox conditions of ambient sea water, introducing additional heterogeneity that needs to be better constrained before using δ53Cr values in mollusc shells for palaeo‐reconstructions.Brunswick, P., MacInnis, C.Y., Kim, M., Yan, J., Fieldhouse, B., Brown, C.E., van Aggelen, G., Shang, D., 2019. Improved oil spill dispersant monitoring in seawater using dual tracers: Dioctyl and monoctyl sulfosuccinates sourced from corexit EC9500A. Journal of Chromatography A 1598, 113-121. high resolution mass spectrometry method was developed for the environmental impact monitoring of oil spill dispersants. Previously reported instability of dioctyl sulfosuccinate (DOSS) dispersant tracer was addressed by the new procedure. The method monitors both DOSS and its degradation product, monooctyl sulfosuccinate (MOSS), by liquid chromatography time-of-flight mass spectrometry. The related isomer, 4-(2-ethylhexyl) 2-sulfobutanedioate, was chromatographically resolved from MOSS but was not a product of DOSS degradation. Using this direct injection method (10?μL), the practical lower limit of quantitation was 0.5?nM for each analyte, a concentration equivalent to 0.22?ng?mL?1, or 0.30?ng?mL?1 including initial dilution factor with acetonitrile. The method was shown applicable to analysis of the dispersants Corexit? EC9500?A, Finasol OSR 52, Slickgone NS, and Slickgone EW for which DOSS is an active ingredient. A marine microcosm study of Corexit EC9500A, together with diluted bitumen (dilbit), at 15?±?1?°C, provided evidence of the stoichiometric conversion of DOSS to MOSS under conditions reflecting a western Canadian marine environment. The advantage of the developed method is in its ability to extend environmental seawater sample collection time from 4 days for DOSS alone, to 14 days when both DOSS and MOSS are simultaneously analysed and results combined. The collection time is likely extended beyond the 14 day period with cooler temperatures. Preservation of collected seawater samples using sodium hydroxide, converting DOSS into MOSS in situ, was rejected due to stability issues. Addition of disodium ethylenediaminetetraacetic acid did not improve hold times, thus eliminating the theory of cation induced micelle effects causing DOSS loss.Budsky, A., Scholz, D., Wassenburg, J.A., Mertz-Kraus, R., Sp?tl, C., Riechelmann, D.F.C., Gibert, L., Jochum, K.P., Andreae, M.O., 2019. Speleothem δ13C record suggests enhanced spring/summer drought in south-eastern Spain between 9.7 and 7.8 ka – A circum-Western Mediterranean anomaly? The Holocene 29, 1113-1133. Spain is one of the driest regions in Europe and thus, prone to drought. Terrestrial climate records covering the late Glacial and Holocene from this area are sparse. Here, we present a flowstone record from Cueva Victoria, south-eastern Spain, which covers the late Glacial (15 ka) to the mid-Holocene (7 ka) including the Younger Dryas (YD). Between the onset of the B?lling/Aller?d (B/A) and the early Holocene, flowstone δ18O values progressively decrease in accordance with sea-surface temperatures in the Alboran Sea, indicating an increase in precipitation in south-eastern Spain and a supra-regional signal of North Atlantic temperature change. At the same time, decreasing δ13C values suggest progressively increasing precipitation and vegetation density. This trend is interrupted by both colder and drier conditions during the YD. Between 9.7 ± 0.3 and 7.8 ± 0.2 ka, a large positive excursion of the δ13C values indicates a strong reduction in vegetation density, probably as a consequence of very dry spring/summer conditions. In combination with the continuously low speleothem δ18O values and a nearly unchanged growth rate, this suggests increased seasonality (i.e. drier spring/summer conditions, but not a strong reduction in annual precipitation). This is consistent with several other climate records from the Western Mediterranean region, showing that the Western Mediterranean realm (Spain, Italy) experienced pronounced spring/summer drought during this time interval. Interestingly, the timing of this dry period coincided with the African Humid Period. This may be part of a teleconnection with the North African Monsoon via the Hadley cell circulation.Bulzu, P.-A., Andrei, A.-?., Salcher, M.M., Mehrshad, M., Inoue, K., Kandori, H., Beja, O., Ghai, R., Banciu, H.L., 2019. Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche. Nature Microbiology 4, 1129-1137. advances in phylogenomic analyses and increased genomic sampling of uncultured prokaryotic lineages have brought compelling evidence in support of the emergence of eukaryotes from within the archaeal domain of life (eocyte hypothesis). The discovery of Asgardarchaeota and its supposed position at the base of the eukaryotic tree of life4 provided cues about the long-awaited identity of the eocytic lineage from which the nucleated cells (Eukaryota) emerged. While it is apparent that Asgardarchaeota encode a plethora of eukaryotic-specific proteins (the highest number identified yet in prokaryotes), the lack of genomic information and metabolic characterization has precluded inferences about their lifestyles and the metabolic landscape that favoured the emergence of the protoeukaryote ancestor. Here, we use advanced phylogenetic analyses for inferring the deep ancestry of eukaryotes, and genome-scale metabolic reconstructions for shedding light on the metabolic milieu of Asgardarchaeota. In doing so, we: (1) show that Heimdallarchaeia (the closest eocytic lineage to eukaryotes to date) are likely to have a microoxic niche, based on their genomic potential, with aerobic metabolic pathways that are unique among Archaea (that is, the kynurenine pathway); (2) provide evidence of mixotrophy within Asgardarchaeota; and (3) describe a previously unknown family of rhodopsins encoded within the recovered genomes.Burke, A.J., Lovelock, S.L., Frese, A., Crawshaw, R., Ortmayer, M., Dunstan, M., Levy, C., Green, A.P., 2019. Design and evolution of an enzyme with a non-canonical organocatalytic mechanism. Nature 570, 219-223. combination of computational design and laboratory evolution is a powerful and potentially versatile strategy for the development of enzymes with new functions However, the limited functionality presented by the genetic code restricts the range of catalytic mechanisms that are accessible in designed active sites. Inspired by mechanistic strategies from small-molecule organocatalysis, here we report the generation of a hydrolytic enzyme that uses Nδ-methylhistidine as a non-canonical catalytic nucleophile. Histidine methylation is essential for catalytic function because it prevents the formation of unreactive acyl-enzyme intermediates, which has been a long-standing challenge when using canonical nucleophiles in enzyme design. Enzyme performance was optimized using directed evolution protocols adapted to an expanded genetic code, affording a biocatalyst capable of accelerating ester hydrolysis with greater than 9,000-fold increased efficiency over free Nδ-methylhistidine in solution. Crystallographic snapshots along the evolutionary trajectory highlight the catalytic devices that are responsible for this increase in efficiency. Nδ-methylhistidine can be considered to be a genetically encodable surrogate of the widely employed nucleophilic catalyst dimethylaminopyridine, and its use will create opportunities to design and engineer enzymes for a wealth of valuable chemical transformations.Burnum-Johnson, K.E., Zheng, X., Dodds, J.N., Ash, J., Fourches, D., Nicora, C.D., Wendler, J.P., Metz, T.O., Waters, K.M., Jansson, J.K., Smith, R.D., Baker, E.S., 2019. Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples. TrAC Trends in Analytical Chemistry 116, 292-299. mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), lowering the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.Burton, Z.F.M., Moldowan, J.M., Magoon, L.B., Sykes, R., Graham, S.A., 2019. Correction to: Interpretation of source rock depositional environment and age from seep oil, east coast of New Zealand. International Journal of Earth Sciences 108, 1093-1093.“The authors wish to rescind the speculated correlation of the northern oils with the upper Paleocene Waipawa Formation given that these oils do not match the carbon isotopes or C30?24-propyldiacholestane ratios of Waipawa Formation rocks or Waipawa-sourced oils (Sykes et al. 2012). Instead, we now infer the northern and southern oils to be derived from separate organofacies within a Cretaceous, Whangai-type marine source rock unit, with the northern organofacies being more oxic and having more terrigenous organic matter input than the southern organofacies. The actual source rock unit, however, remains uncertain as none of the known occurrences of Whangai Formation have any significant oil potential.”The original article can be found online at , Z.F.M., Moldowan, J.M., Magoon, L.B., Sykes, R., Graham, S.A., 2019. Interpretation of source rock depositional environment and age from seep oil, east coast of New Zealand. International Journal of Earth Sciences 108, 1079-1091. fingerprints of crude oil samples from four onshore East Coast Basin oil seeps were analyzed to assess source rock characteristics including type of organic matter input, redox conditions, sedimentary facies, and age. Results show that samples generally form two groups, correlating with geographic location: a northern and a southern group. Source rocks associated with all seep samples are interpreted to be marine. However, results suggest northern samples had more terrigenous organic matter input to their source rock(s), while southern samples had more marine input. Results suggest northern sample source rock(s) had more oxic depositional environments, whereas southern sample source rock had more reducing environments. A shale source rock sedimentary facies was indicated for all samples. These observations suggest that southern samples may be derived from slightly higher quality source rocks (higher HI, deposited in more reducing conditions), although source rocks in both regions are oil prone. Biomarker age parameters suggest that the northern oil samples are from a younger (Cenozoic) source rock, whereas the southern oil samples are from an older (Cretaceous) source rock. Source rock characteristics (depositional environment and age) point to the presence of two different source rocks. We postulate that northern oils samples from younger source rock with more terrigenous organic matter input represent the upper Paleocene Waipawa Formation, whereas southern oil samples from older source rock with more marine organic matter input represent the Upper Cretaceous to Paleocene Whangai Formation.Bystrzanowska, M., Tobiszewski, M., 2019. Multi-objective optimization of microextraction procedures. TrAC Trends in Analytical Chemistry 116, 266-273. of extraction process requires finding acceptable conditions for many analytes and good performance in terms of process time or solvent consumption. These optimization criteria are often contradictory to each other, the performance of the system in given conditions is good for some criteria but poor for others. Therefore, such problems require special assessment tools that allow to combine these contradictory criteria into single score to find “the golden mean”. This contribution summarizes the examples of approaches that are used for multi-objective optimization. Derringer's desirability functions are used for large variety of microextraction techniques optimizations. Finding Pareto-optimal solutions allows to easily separate conditions that are definitely not acceptable. Alternative solution is application of multi-criteria decision analysis for microextraction processes optimization.Cabrera Ospino, M., Kojima, H., Fukui, M., 2019. Arsenite oxidation by a newly isolated betaproteobacterium possessing arx genes and diversity of the arx gene cluster in bacterial genomes. Frontiers in Microbiology 10, 1210. doi: 10.3389/fmicb.2019.01210. play essential roles in arsenic transformation in the environment. Microbial arsenite oxidation is catalyzed by either of two distantly related arsenite oxidases, referred to as AIO and ARX. The arx genes encoding ARX and its regulatory proteins were originally defined in the genomes of gammaproteobacteria isolated from an alkaline soda lake. The arx gene cluster has been identified in a limited number of bacteria, predominantly in gammaproteobacteria isolated from lakes characterized by high pH and high salinity. In the present study, a novel arsenite-oxidizing betaproteobacterium, strain M52, was isolated from a hot spring microbial mat. The strain oxidized arsenite under nitrate-reducing conditions at nearly neutral pH. Genome analysis revealed that the strain possesses the arx gene cluster in its genome and lacks genes encoding AIO. Inspection of the bacterial genomes available in the GenBank database revealed that the presence of this gene cluster is restricted to genomes of Proteobacteria, mainly in the classes Gammaproteobacteria and Betaproteobacteria. In these genomes, the structure of the gene cluster was generally well conserved, but genes for regulatory proteins were lacking in genomes of strains belonging to a specific lineage. Phylogenetic analysis suggested that ARX encoded in the genomes can be divided into three groups, and strain M52 belongs to a group specific for organisms living in low-salt environments. The ArxA protein encoded in the genome of strain M52 was characterized by the presence of a long insertion, which was specifically observed in the same group of ARX. In clone library analyses with a newly designed primer pair, a diverse ArxA sequence with a long insertion was detected. Among the isolated bacterial strains whose arsenite oxidation has been demonstrated, strain M52 is the first betaproteobacterium that possesses the arx genes, the first strain encoding ARX of the group specific for low-salt environments, and the first organism possessing the gene encoding ArxA with a long insertion.Cai, L., J?rgensen, B.B., Suttle, C.A., He, M., Cragg, B.A., Jiao, N., Zhang, R., 2019. Active and diverse viruses persist in the deep sub-seafloor sediments over thousands of years. The ISME Journal 13, 1857-1864. are ubiquitous and cause significant mortality in marine bacterial and archaeal communities. Little is known about the role of viruses in the sub-seafloor biosphere, which hosts a large fraction of all microbes on Earth. We quantified and characterized viruses in sediments from the Baltic Sea. The results show that the Baltic Sea sub-seafloor biosphere harbors highly abundant viruses with densities up to 1.8?×?1010 viruses cm?3. High potential viral production down to 37 meters below seafloor in ca. 6000-years-old sediments and infected prokaryotic cells visible by transmission electron microscopy demonstrate active viral infection. Morphological and molecular data indicate that the highly diverse community of viruses includes both allochthonous input from the overlying seawater and autochthonous production. The detection of cyanophage-like sequences showed that viruses of phototrophic hosts may persist in marine sediments for thousands of years. Our results imply that viruses influence sub-seafloor microbial community dynamics and thereby affect biogeochemical processes in the sub-seafloor biosphere.Callieri, C., Slabakova, V., Dzhembekova, N., Slabakova, N., Peneva, E., Cabello-Yeves, P.J., Di Cesare, A., Eckert, E.M., Bertoni, R., Corno, G., Salcher, M.M., Kamburska, L., Bertoni, F., Moncheva, S., 2019. The mesopelagic anoxic Black Sea as an unexpected habitat for Synechococcus challenges our understanding of global “deep red fluorescence”. The ISME Journal 13, 1676-1687. Black Sea is the largest meromictic sea with a reservoir of anoxic water extending from 100 to 1000?m depth. These deeper layers are characterised by a poorly understood fluorescence signal called “deep red fluorescence”, a chlorophyll a- (Chl a) like signal found in deep dark oceanic waters. In two cruises, we repeatedly found up to 103 cells ml?1 of picocyanobacteria at 750?m depth in these waters and isolated two phycoerythrin-rich Synechococcus sp. strains (BS55D and BS56D). Tests on BS56D revealed its high adaptability, involving the accumulation of Chl a in anoxic/dark conditions and its capacity to photosynthesise when re-exposed to light. Whole-genome sequencing of the two strains showed the presence of genes that confirms the putative ability of our strains to survive in harsh mesopelagic environments. This discovery provides new evidence to support early speculations associating the “deep red fluorescence” signal to viable picocyanobacteria populations in the deep oxygen-depleted oceans, suggesting a reconsideration of the ecological role of a viable stock of Synechococcus in dark deep waters.Capelle, D.W., Hallam, S.J., Tortell, P.D., 2019. Time-series CH4 measurements from Saanich Inlet, BC, a seasonally anoxic fjord. Marine Chemistry 215, 103664. present 7?years of water column methane (CH4) measurements from Saanich Inlet, a seasonally anoxic fjord in British Columbia, Canada. Our time-series observations show that CH4 concentrations and sea-air fluxes vary significantly over seasonal cycles, driven primarily by changes in O2-availability throughout the water column. Methane concentrations were always supersaturated in near-surface waters (mean 1160?±?590% saturation at 10?m depth) and remained high between 10 and 85?m depth. We observed a persistent mid-depth CH4 minimum between 85 and 110?m associated with a turbidity maximum near the base of the oxycline. CH4 accumulated steadily below 150?m depth from the onset of anoxia until the subsequent annual renewal, with maximum bottom water values indicative of sedimentary sources. Beyond the strong seasonal cycle in CH4 concentrations, we also observed significant inter-annual variability. Most notably, the moderate 2009–2010 El Ni?o resulted in a weak deep basin renewal, and anomalously high CH4 concentrations in both the deep basin and upper 85?m. Over the time-series, we observed statistically significant shoaling of the hypoxic boundary, associated with declining CH4 concentrations in the upper water column (10–85?m depth). Our results provide insight into the potential effects of expanding hypoxia on CH4 cycling in coastal waters.Cardoso, D.C., Cretoiu, M.S., Stal, L.J., Bolhuis, H., 2019. Seasonal development of a coastal microbial mat. Scientific Reports 9, Article 9035. and activity of coastal microbial mats is strongly seasonal. The development of these mats starts in early spring and fully maturate during late summer, where after growth ceases and subsequently the mat deteriorates by erosion and decomposition in winter. Here, the composition of the microbial community of three different mats developing along the tidal gradient of the North Sea beach of the Dutch barrier island Schiermonnikoog was analysed. The 16S ribosomal RNA molecules and the associated gene were sequenced in order to obtain the active (RNA) and resident (DNA) community members, respectively. Proteobacteria, Cyanobacteria, and Bacteroidetes dominated the mats during the whole year but considerable differences among these groups were found along the tidal gradient and seasonally when observed at a finer taxonomic resolution. Richness and diversity increased during the year starting from a pioneering community that is gradually succeeded by a more diverse climax community. The initial pioneers consisted of the cold-adapted photoautotrophic cyanobacterium Nodularia sp. and potential cold adapted members of the alphaproteobacterial Loktanella genus. These pioneers were succeeded by, amongst others, cyanobacteria belonging to the genera Leptolyngbya, Lyngbya, and Phormidium. At the upper littoral (Dune site), which was characterized by an extensive salt marsh vegetation, the mats contained a distinct bacterial community that potentially contribute to or benefit from plant decay. This study reports in detail on the seasonal changes and succession of these coastal microbial mat communities and discusses the potential forces that drive these changes.Chan-Yam, K., Goordial, J., Greer, C., Davila, A., McKay, C.P., Whyte, L.G., 2019. Microbial activity and habitability of an Antarctic dry valley water track. Astrobiology 19, 757-770. tracks in the Antarctic Dry Valleys are dark linear features of increased soil moisture that flow downslope over the spring and summer, providing a source of moisture in a cold-arid desert. They are typically sourced from melting snow, ground ice, and deliquescence (Levy et al., 2011). This research presents the first in-depth study of the activity potential and diversity of microbial communities of Antarctic water tracks. We investigated whether these water track soils are more habitable to microbial communities by ascertaining the differences in diversity, total and culturable cell counts, and microbial respiratory activity in water track soils compared with the adjacent dry soils in Pearse Valley. Total cell counts ranged from 1.47?×?103 to 4.17?×?105 cells/g dry weight soil. Water track soils had higher total and culturable biomass, in addition to higher microbial activity at 5° and ?5°C, compared with adjacent dry soils. Microbial respiration was positively correlated with soil moisture content, but total cell counts and plate counts were not. Surprisingly, microbial community composition did not differ between wet and dry soil communities, and was not related to soil moisture content. The microbial community composition instead appeared to differ spatially based on location and depth. Overall, the data suggest that cold water tracks are more habitable than the surrounding cold-arid soils. Our results suggest that recurring slope lineae, which are dark linear features that grow downslope on Mars over the spring and summer, where liquid water might be a recurring phenomenon, could be sites of astrobiological potential.Chandrasekar, T., Sabarathinam, C., Nadesan, D., Rajendiran, T., Banajarani Panda, B.R., Keesari, T., Mohan Viswanathan, P., Utharapathi, V., Alagappan, R., 2019. Geochemical (process based) characterization of groundwater along the KT boundary of South India. Geochemistry 79, 62-77. study has been carried out in KT (Cretaceous-Tertiary) boundary along the contact zones of hard rock, limestone and sedimentary formations to discern the geochemical processes governing the groundwater chemistry. A total of sixty-three groundwater samples were collected from the handpumps covering the entire study area and measured for hydrochemical species. Principal component analysis of the hydrochemical data inferred three major processes governing the geochemistry of the groundwater of the region as leaching, ion exchange and weathering. It was also inferred that there are few samples depicting the mixtures of these processes (what are they mention it) and few samples not representing any of these processes with adequate statistical significance. Hence, in order to know the geochemical behaviour of the samples representing each process, their combinations along with the samples which are not- representative samples of these processes were inferred using various standards plots to get an insight into their geochemical characteristics and affinity. This also inferred the samples representing different processes have a significant signature of geochemical facies. The major ions and the stable isotopes of groundwater were used to understand these processes. The carbonate and sulphate saturation states of these samples were calculated by PHREEQC and compared with major variations with the identified three geochemical processes. The state of saturation of Halite, Anhydrite, Gypsum, Aragonite, Dolomite, Calcite, Talc and Chrysolite were determined in all the samples. Inverse modeling was carried out considering the non-representative samples as initial solution and the samples representing each factor as final solution to understand the phase mole transfer in each process. An attempt was also made in this study to compare the geochemical behaviour of groundwaters from different KT boundaries. The samples representing these processes were plotted on an integrated map representing lithology, lineaments, drainage and elevation to determine their interrelationships. The study groups the samples into anthropogenic or geogenic. The leaching process is controlled by lithology and landuse, ion exchange processes is influenced by lithology and drainage patterns whereas weathering processes were controlled by lithology, drainage and lineaments. Non representation of samples (NRS) were mainly controlled by drainage and lineaments of the region.Chang, X., Wang, Y., Shi, B., Xu, Y., 2019. Charging of Carboniferous volcanic reservoirs in the eastern Chepaizi uplift, Junggar Basin (northwestern China) constrained by oil geochemistry and fluid inclusion. American Association of Petroleum Geologists Bulletin 103, 1625-1652. amounts of petroleum were recently discovered in the Carboniferous andesite, tuff, breccia, and basalt reservoirs of the Chepaizi uplift in the western Junggar Basin. However, the charging history of the Carboniferous petroleum reservoir is poorly understood. Oil–oil correlation studies indicate that all of the oils were mainly derived from the middle Permian Wuerhe Formation source rocks, possibly mixed with a small contribution from Carboniferous Baogutu Formation source rocks in the neighboring Changji sag. Based on the petrographic and microthermometry of fluid inclusions, two hydrocarbon charging episodes are defined; these episodes were characterized by a low-peak-range homogenization temperature (Th) distribution (80°C–90°C) and high salinity (13.22–13.42 wt. % NaCl) and a high-peak-range Th distribution (120°C–130°C) and low salinity (4.89–11.72 wt. % NaCl), respectively. Through one-dimensional basin modeling and pressure–volume–temperature–composition simulation, the burial-thermal histories for wells P61, P66, P668, and P663 were reconstructed, and their trapping temperatures of the hydrocarbon inclusions were calculated to be higher than their corresponding highest paleotemperature (i.e., 56.8°C, 53.7°C, 60.9°C, and 58.1°C, respectively), implying fast hydrocarbon charging processes promoted by deep hydrothermal fluids. Associated with the hydrocarbon generation history, sealing process of the Hongche fault, and regional tectonic evolution, these two hydrocarbon charging events were deduced as the adjustments of oils previously accumulated along the Hongche fault zone, because of the tectonic extension in the Paleogene and regional tilting in the Neogene, respectively. The general direction of oil charging was traced from south to north and from east to west, as indicated by the molecular parameters of nitrogen-bearing compounds and C20 + C21 triaromatic steroids/C20 + C21 + C26–C28 triaromatic steroids (TA(I)/TA(I+II)), which roughly coincided with the active fracturing.Chaves Torres, L., Kaur, G., Melbourne, L.A., Pancost, R.D., 2019. Selective chemical degradation of silica sinters of the Taupo Volcanic Zone (New Zealand). Implications for early Earth and Astrobiology. Geobiology 17, 449-464. organic matter (OM) on Earth occurs as kerogen‐like materials, that is naturally formed macromolecules insoluble with standard organic solvents. The formation of this insoluble organic matter (IOM) is a topic of much interest, especially when it limits the detection of compounds of geomicrobiological interest. For example, studies that search for biomarker evidence of life on early Earth or other planets usually use solvent‐based extractions. This leaves behind a pool of OM as unexplored post‐extraction residues, potentially containing diagnostic biomarkers. Since the IOM has an enhanced potential for preservation compared to soluble OM, analysing IOM‐released biomarkers can also provide even deeper insights into the ecology of ancient settings, with implications for early Earth and Astrobiology investigations. Here, we analyse the prokaryotic lipid biosignature within soluble and IOM of the Taupo Volcanic Zone (TVZ) silica sinters, which are key analogues in the search for life. We apply sequential solvent extractions and a selective chemical degradation upon the post‐solvent extraction residue. Moreover, we compare the IOM from TVZ sinters to analogous studies on peat and marine sediments to assess patterns in OM insolubilisation across the geosphere. Consistent with previous work, we find significant but variable proportions—1%–45% of the total prokaryotic lipids recovered—associated with IOM fractions. This occurs even in recently formed silica sinters, likely indicating inherent cell insolubility. Moreover, archaeal lipids seem more prone to insolubilisation as compared to the bacterial analogues, which might enhance their preservation and also bias overall biomarkers interpretation. These observations are similar to those observed in other settings, confirming that even in a setting where the OM derives predominantly from prokaryotic sources, patterns of IOM formation/occurrence are conserved. Differences with other settings, however, such as the occurrence of archaeol in IOM fractions, could be indicative of different mechanisms for IOM formation that merit further exploration.Chen, C.-H., Liu, P.-W.G., Whang, L.-M., 2019. Effects of natural organic matters on bioavailability of petroleum hydrocarbons in soil-water environments. Chemosphere 233, 843-851. bioremediation efficiency of petroleum hydrocarbons in natural soil-water systems is regulated by active microbial populations and other system parameters. Relevant factors include the transfer rate of petroleum contaminants from a medium into microorganisms, the partitioning behavior of contaminants from water into the soil organic matter (SOM), and the influence of the dissolved organic matter (DOM) on the contaminant level in water. The objectives of this study was aimed to determine the correlation among bioavailability of petroleum hydrocarbons, SOM content, and DOM level in soil-water systems. Heptadecane, pristane, and decylcyclohexane were selected as model hydrocarbon contaminants. The bioavailability of target contaminants in soil was examined using soils of different SOM contents (2% and 20%) in slurry bioreactors. In addition, the contaminant bioavailability as affected by various DOM levels (0–100 mgC/L) was also examined. The results showed that the SOM content affected the degrading rate of hydrocarbons significantly, where the rate constant was 4 times higher in 2% SOM microcosm than in the 20% SOM bioreactor for heptadecane degradation. Similarly, the pristane degrading efficiency after 240?h operation was 95% for the 2% SOM microcosm and only 38% for the 20% SOM microcosm. The hydrocarbon degradation rates in water phase were found to be enhanced by the added DOM level. A positive correlation existed between the contaminant bioavailability and the contaminant level in water as impacted by the SOM content in soil and the DOM level in water.Chen, G., Bai, Y., Zeng, R.J., Qin, L., 2019. Effects of different metabolic pathways and environmental parameters on Cr isotope fractionation during Cr(VI) reduction by extremely thermophilic bacteria. Geochimica et Cosmochimica Acta 256, 135-146. isotopes are promising for monitoring and quantifying the extent of microbial Cr(VI) reduction. However, the mechanisms and factors that influence Cr isotope fractionation are not well understood. In the present study, we investigated the effects of different metabolic pathways and various environmental parameters on Cr isotope fractionation during Cr(VI) reduction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. The Cr isotopic compositions were measured on unreacted Cr(VI) in the remaining solution. The reaction product is isotopically lighter than the reactant. The Cr isotope composition for remaining Cr(VI) in the solution followed a Rayleigh fractionation trend and thus became increasingly isotopically heavier as the reduction of Cr(VI) proceeded. Cr(VI) reduction mainly occurs on the cell surface by Ni–Fe hydrogenase; however, in the presence of CuCl2, the activity of Ni–Fe hydrogenase was inhibited, and Cr(VI) was reduced inside the cells. We found that despite different Cr(VI) reduction locations, Cr isotope enrichment factors (ε?=?(α???1)?×?1000, where α is the fractionation factor) were identical within uncertainty for experiments with and without CuCl2 (?2.72?±?0.67‰ and ?2.92?±?0.14‰, respectively). When added to the cell cultures, neutral red (NR) functioned as an electron carrier that enabled bacteria to drive the electron transfer processes. The ε values were also similar for experiments with and without NR (?2.53?±?0.40‰ and ?2.92?±?0.14‰, respectively). We compared these ε values to investigate the effects of different electron transport pathways and cellular Cr(VI) transfer processes, including Cr(VI) transport across the cell envelope and binding to reacting enzymes, on Cr isotope fractionation. Furthermore, the effects of various environmental parameters on Cr isotope fractionation were tested, including temperature (50?°C and 70?°C), hydrogen concentration, and different electron donors (glucose and hydrogen). The ε values were similar at both tested temperatures and stayed within the previously observed range for mesophiles; changes in hydrogen concentration also did not affect the ε values. However, the ε values were slightly higher with hydrogen as the electron donor (?3.64?±?0.24‰) than those with glucose as the electron donor (?2.92?±?0.14‰). In short, the Cr enrichment factors remained unchanged despite of changing microbial Cr (VI) reduction pathways and changing temperature conditions, but may be sensitive to the electron donor type.Chen, G., Lu, S., Liu, K., Xue, Q., Xu, C., Tian, S., Li, J., Zhang, Y., Tong, M., Pang, X., Ni, B., Lu, S., Qi, Q., 2019. Investigation of pore size effects on adsorption behavior of shale gas. Marine and Petroleum Geology 109, 1-8. the effects of pore size on shale gas adsorption behavior is necessary for accurate evaluation of adsorbed gas content under geological conditions. Shale is a porous medium, and the pore structure of the shale reservoir is complicated, with a wide distribution of aperture sizes. Critical parameters for investigating pore size effects on shale gas adsorption behavior were determined, using Grand Canonical Monte Carlo (GCMC) simulations, and the shale gas occurrence state in varying sized kerogen pores was documented, by linking GCMC simulations to the experimental pore size distribution. It was found that using the excess adsorption estimation, in terms of per unit surface area (PUSA), which was obtained from the free gas density calculated by using the GCMC method in a bulk simulation cell, and then derived from the free volume probed by the methane, was a reasonable way of demonstrating pore size effects on shale gas adsorption behavior. The distribution profiles of both the gas density and the interaction energy, rather than their average values, could be used to reflect this pore size effect objectively. Gas density in the adsorption phase rose non-monotonically with reducing pore size, under the combined influence of the interactions’ overlapping effects and the limited pore space, and the overlapping threshold was determined to be 1.24?nm for the experiments. The gas in the pores that were smaller than the overlapping threshold, which was difficult to desorb under geological pressures, accounted for approximately 40.53% of the total adsorbed gas in the kerogen. The adsorbed gas in the kerogen lay mainly (84.97%) in smaller pores (<5?nm), while the free gas was mainly located (77.70%) in larger pores (>5?nm).Chen, J., Wang, X., Ni, Y., Xiang, B., Liao, F., Liao, J., Zhao, C., 2019. Genetic type and source of natural gas in the southern margin of Junggar Basin, NW China. Petroleum Exploration and Development 46, 482-495. gas has been discovered in many anticlines in the southern margin of the Junggar Basin. However, the geochemical characteristics of natural gas in different anticlines haven't been compared systematically, particularly, the type and source of natural gas discovered recently in Well Gaotan-1 at the Gaoquan anticline remain unclear. The gas composition characteristics and carbon and hydrogen isotope compositions in different anticlines were compared and sorted systematically to identify genetic types and source of the natural gas. The results show that most of the gas samples are wet gas, and a few are dry gas; the gas samples from the western and middle parts have relatively heavier carbon isotope composition and lighter hydrogen isotope composition, while the gas samples from the eastern part of southern basin have lighter carbon and hydrogen isotope compositions. The natural gas in the southern margin is thermogenic gas generated by freshwater-brackish water sedimentary organic matter, which can be divided into three types, coal-derived gas, mixed gas and oil-associated gas, in which coal-derived gas and mixed gas take dominance. The Jurassic coal measures is the main natural gas source rock in the southern margin, and the Permian lacustrine and the Upper Triassic lacustrine-limnetic facies source rocks are also important natural gas source rocks. The natural gas in the western part of the southern margin is derived from the Jurassic coal measures and the Permian lacustrine source rock, while the natural gas in the middle part of the southern margin is mainly derived from the Jurassic coal measures, partly from the Permian and/or the Upper Triassic source rocks, and the natural gas in the eastern part of the southern margin is originated from the Permian lacustrine source rock. The natural gas in the Qingshuihe oil and gas reservoir of Well Gaotan-1 is a mixture of coal-derived gas and oil-associated gas, of which the Jurassic and Permian source rocks contribute about half each.Chen, J., Xu, Y.-g., 2019. Establishing the link between Permian volcanism and biodiversity changes: Insights from geochemical proxies. Gondwana Research 75, 68-96. understanding of biodiversity changes in the Permian is presented, especially the consensus and disagreement on the tempo, duration, and pattern of end-Guadalupian and end-Permian mass extinctions. The end-Guadalupian mass extinction (EGME; i.e., pre-Lopingian crisis) is not as severe as previously thought. Moreover, the turnovers of major fossil groups occurred at different temporal levels, therefore the total duration of the end-Guadalupian mass extinction is relatively extended. By comparison, fossil records constrained with high-precision geochronology indicate that the end-Permian mass extinction (EPME) was a single-pulse event and happened geologically instantaneous. Variation of geochemical proxies preserved in the sedimentary records is important evidence in examining potential links between volcanisms and biodiversity changes. Some conventional and non-traditional geochemical proxy records in the Permian show abrupt changes across the Permian-Triassic boundary, reflecting climate change, ocean acidification and anoxia, carbon cycle perturbation, gaseous metal loading, and enhanced continental weathering. These, together with the stratigraphic coincidence between volcanic ashes and the end-Permian mass extinction horizon, point to large-scale volcanism as a potential trigger mechanism. To further define the nature of volcanism which was responsible for global change in biodiversity, main characteristics of four Permian large igneous provinces (LIPs; i.e., Tarim, Panjal, Emeishan, and Siberian) are compared, in terms of timing and tempo, spatial distribution and volume, and magma-wall rock interactions. The comparison indicates that volcanic fluxes (i.e., eruption rates) and gas productions are the key features distinguishing the Siberian Traps from other LIPs, which also are the primary factors in determining the LIP's potential of affecting Earth's surface system. We find that the Siberian Traps volcanism, especially the switch from dominantly extrusive eruptions to widespread sill intrusions, has the strongest potential for destructive impacts, and most likely is the ultimate trigger for profound environmental and biological changes in the latest Permian-earliest Triassic. The role of Palaeotethys subduction-related arc magmatism cannot be fully ruled out, given its temporal coincidence with the end-Permian mass extinction. As for the Emeishan LIP, medium volcanic flux and gas emission probably limited its killing potential, as evident from weak changes in geochemical proxies and biodiversity. Because of its long-lasting but episodic nature, the Early Permian magmatism (e.g., Tarim, and Panjal) may have played a positive role in affecting the contemporaneous environment, as implicated by coeval progressive climate warming, termination of the Late Palaeozoic Ice Age (LPIA), and flourishing of ecosystems.Chen, J., Zhu, Q., Riley, W.J., He, Y., Randerson, J.T., Trumbore, S., 2019. Comparison with global soil radiocarbon observations indicates needed carbon cycle improvements in the E3SM land model. Journal of Geophysical Research: Biogeosciences 124, 1098-1114. evaluated global soil organic carbon (SOC) stocks and turnover time predictions from a global land model (ELMv1‐ECA) integrated in an Earth System Model (E3SM) by comparing them with observed soil bulk and Δ14C values around the world. We analyzed observed and simulated SOC stocks and Δ14C values using machine learning methods at the Earth System Model grid cell scale (~200 km). In grid cells with sufficient observations, the model provided reasonable estimates of soil carbon stocks across soil depth and Δ14C values near the surface but underestimated Δ14C at depth. Among many explanatory variables, soil albedo index, soil order, plant function type, air temperature, and SOC content were major factors affecting predicted SOC Δ14C values. The influences of soil albedo index, soil order, and air temperature were primarily important in the shallow subsurface (≤30 cm). We also performed sensitivity studies using different vertical root distributions and decomposition turnover times and compared to observed SOC stock and Δ14C profiles. The analyses support the role of vegetation in affecting soil carbon turnover, particularly in deep soil, possibly through supplying fresh carbon and degrading physical‐chemical protection of SOC via root activities. Allowing for grid cell‐specific rooting and decomposition rates substantially reduced discrepancies between observed and predicted Δ14C values and SOC content. Our results highlight the need for more explicit representation of roots, microbes, and soil physical protection in land models.Chen, L., Wei, Y., Shi, M., Li, Z., Zhang, S.-H., 2019. An archaeal chitinase with a secondary capacity for catalyzing cellulose and its biotechnological applications in shell and straw degradation. Frontiers in Microbiology 10, 1253. doi: 10.3389/fmicb.2019.01253. thermostable enzymes have been reported from the hyperthermophilic archaeon Thermococcus kodakarensis KOD1, which made it an attractive resource for gene cloning. This research reported a glycosyl hydrolase (Tk-ChiA) form T. Kodakarensis with dual hydrolytic activity due to the presence of three binding domains with affinity toward chitin and cellulose. The Tk-ChiA gene was cloned and expressed on Pichia pastoris GS115. The molecular weight of the purified Tk-ChiA is about 130.0 kDa. By using chitosan, CMC-Na and other polysaccharides as substrates, we confirmed that Tk-ChiA with dual hydrolysis activity preferably hydrolyzes both chitosan and CMC-Na. Purified Tk-ChiA showed maximal activity for hydrolyzing CMC-Na at temperature 65°C and pH 7.0. It showed thermal stability on incubation for 4 h at temperatures ranging from 70 to 80°C and remained more than 40% of its maximum activity after pre-incubation at 100°C for 4 h. Particularly, Tk-ChiA is capable of degrading shrimp shell and rice straw through scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR) analysis. The main factors affecting shell and straw degradation were determined to be reaction time and temperature; and both factors were optimized by central composite design (CCD) of response surface methodology (RSM) to enhance the efficiency of degradation. Our findings suggest that Tk-ChiA with dual thermostable hydrolytic activities maybe a promising hydrolase for shell and straw waste treatment, conversion, and utilization.Chen, M., Jung, J., Lee, Y.K., Kim, T.-W., Hur, J., 2019. Production of tyrosine-like fluorescence and labile chromophoric dissolved organic matter (DOM) and low surface accumulation of low molecular weight-dominated DOM in a productive Antarctic sea. Marine Chemistry 213, 40-48. Antarctic seas play critical roles in global carbon cycling. Yet, little is known about the dissolved organic matter (DOM) characteristics and the dynamics there. Here, we conducted an extensive study on the seawater DOM in the Amundsen Sea in the Pacific sector of the Southern Ocean. We found that low molecular weight fractions quantitatively dominated the DOM composition at the surface of the highly productive Amundsen Sea Polynya with the relative abundance reaching up to ~89%. Moreover, CDOM and tyrosine-like fluorescence generation were observed, with the average values of~2.4–2.6?m?1 (a254) and ~0.3 RU, respectively. While there is a net positive accumulation of dissolved organic carbon (DOC) at the ocean's surface, the net accumulation was negative for the chromophoric DOM (CDOM), which suggests a labile nature for the freshly produced CDOM. The estimated net DOC production ratio was only ~9?±?6%, which was less than the global level (~17%). This finding signified a low surface accumulation of DOM in the austral summer, which is potentially explained by its nonlimiting nutrients, photo- and/or bio-labile nature of produced DOM, and long water residence time.Chen, R., Liu, G., Shang, F., Cao, Y., 2019. Nitrogen isotope compositions of the Upper Triassic Chang 7 Shale, Ordos Basin, North China: Implications for depositional redox conditions. Marine and Petroleum Geology 109, 279-290. isotope (δ15N) analysis has been used to evaluate depositional redox conditions in well-preserved sedimentary systems; however, fewer N-isotope studies have been performed to reconstruct the redox conditions in lacustrine shales. In this paper, we report the δ15N data from the Upper Triassic Chang 7 Shale of the Ordos Basin, North China. Sedimentary δ15N values are significantly higher in the Chang 73 and the lower part of the Chang 72 submembers (Zone A; average?=?9.4?±?1.3‰) than in the upper part of the Chang 72 and the Chang 71 submembers (Zone B; average?=?5.4?±?1.5‰). Previous geochemical measurements (i.e., U and TOC/P) of both zones show wide redox variation, however, the average values of these redox proxies are relatively higher in Zone A than those of Zone B. Combined with lithological aspects of the Chang 7 Shale, our study suggest that Zone A was mainly deposited under suboxic bottom water conditions, whereas Zone B deposits accumulated within an oxygenated water column. Stable organic carbon isotopes (δ13Corg) and total nitrogen (TN) values of the two zones display little variation that could be attributed to changing organic matter sources and/or post-depositional alteration of δ15N. Thus, we suggest that variations in δ15N throughout the Chang 7 Shale primarily reflect differences in depositional redox conditions and δ15N values of the shale that can provide important details regarding the depositional history of unconventional resource plays.Chen, S., Ryb, U., Piasecki, A.M., Lloyd, M.K., Baker, M.B., Eiler, J.M., 2019. Mechanism of solid-state clumped isotope reordering in carbonate minerals from aragonite heating experiments. Geochimica et Cosmochimica Acta 258, 156-173. clumped isotope compositions of carbonate minerals are subject to alteration at elevated temperatures. Understanding the mechanism of solid-state reordering in carbonate minerals is important in our interpretations of past climates and the thermal history of rocks. The kinetics of solid-state isotope reordering has been previously studied through controlled heating experiments of calcite, dolomite and apatite. Here we further explore this issue through controlled heating experiments on aragonite. We find that Δ47 values generally decrease during heating of aragonite, but increase by 0.05–0.15‰ as aragonite starts to transform into calcite. We argue that this finding is consistent with the presence of an intermediate pool of immediately adjacent singly-substituted carbonate ion isotopologues (‘pairs’), which back-react to form clumped isotopologues during aragonite to calcite transformation, revealing the existence of kinetically preferred isotope exchange pathways. Our results reinforce the ‘reaction-diffusion’ model as the mechanism for solid-state clumped isotope reordering in carbonate minerals. Our experiments also reveal that the reordering kinetics in aragonite is faster than in calcite and dolomite, making its clumped isotope composition highly susceptible to alteration during early diagenesis, even before conversion to calcite.Chen, S., Xu, Y., Sun, S., Chen, F., Liu, J., 2019. Halalkalicoccus subterraneus sp. nov., an extremely halophilic archaeon isolated from a subterranean halite deposit. Antonie van Leeuwenhoek 112, 1067-1075. extremely halophilic archaeon, designated strain GSM28T, was isolated from a subterranean halite deposit in a Yunnan salt mine, China. Cells of the strain were observed to be cocci, non-motile and Gram-variable, and to require at least 15% (w/v) NaCl for growth (optimum 20%). Growth was found to occur in the ranges of 20–45 °C (optimum 42 °C) and pH 6.0–8.5 (optimum 7.5). Cells did not lyse in distilled water. Phylogenetic analysis based on 16S rRNA gene sequences indicated that this strain belongs to the genus Halalkalicoccus and shows 99.1% similarities with its close phylogenetic relative Halalkalicoccus paucihalophilus DSM 24557T. Genomic ANI analysis showed that the DNA–DNA relatedness between strain GSM28T and the closely related species Hac. paucihalophilus DSM 24557T and Halalkalicoccus jeotgali B3T was 83.7% and 83.1%, respectively. The major polar lipids were determined to be phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate, sulfated mannosyl-glucosyl-glycerol diether-1 and two unidentified glycolipids. The DNA G?+?C content was determined to be 61.8 mol %. On the basis of physiological, biochemical tests and phylogenetic differentiations, strain GSM28T is concluded to represent a novel species in the genus Halalkalicoccus, for which the name Halalkalicoccus subterraneus sp. nov. is proposed. The type strain is GSM28T (=?CGMCC 1.16344T?=?NBRC 113432T).Chen, Z., Chai, Z., Cao, Y., Liu, Q., Zhang, S., Yuan, G., 2019. Suppression of thermal maturity indicators in lacustrine source rocks: A case study of Dongying Depression, eastern China. Marine and Petroleum Geology 109, 108-127. Paleogene Shahejie formation of the Dongying Depression in eastern China is a unique region and can offer insights into the suppression of thermal maturity in a large set of successive lacustrine shales. This study focuses on the Paleogene Shahejie formation of N-38 Well in the Dongying Depression. The unusual distribution of thermal maturity indicators, such as vitrinite reflectance (VRO) and C29 sterane thermal parameters was investigated through geochemical analysis. The research interval (2770–3376?m) was divided into three parts: the upper part of Es32 (2770–2990?m), the lower part of Es32 (2990–3190?m), and the Es31 (3190–3376?m). The Es31 mainly contained organic matter type I and some type II, which included mostly good and excellent source rocks. Meanwhile, the upper Es32 mainly contained organic matter type III, which included mostly poor and moderate source rocks. The parameters G/C30H, C35H/C31-35H, C31M/C31H, C29-20S/(20S + 20R), C31-22S/(22S + 22R), and C32-22S/(22S + 22R) showed a different distribution corresponding to the different lake sedimentary environments. Various organic facies were developed at the different evolution stages of the lake basin, which showed a noticeable influence on the parameters. The thermal maturity indicator VRO and molecular thermal parameters, such as C29-20S/(20S + 20R), C31-22S/(22S + 22R), C32-22S/(22S + 22R), and C31M/C31H, presented abnormal distributions in the large set of lacustrine shales, especially in the Es31. This observation suggested suppression of several thermal maturity indicators. VRO suppression positively correlated well with the corrected hydrogen index and alginite content in maceral composition. The high content of alginite group was considered to be the primary reason behind the evident negative VRO anomaly.Chen, Z., Song, Y., Jiang, Z., Liu, S., Li, Z., Shi, D., Yang, W., Yang, Y., Song, J., Gao, F., Zhang, K., Guo, X., 2019. Identification of organic matter components and organic pore characteristics of marine shale: A case study of Wufeng-Longmaxi shale in southern Sichuan Basin, China. Marine and Petroleum Geology 109, 56-69. the global success of the commercial exploration and development of shale oil and gas, research interest in the structure of shale pore, the gas and oil storage carrier, is increasing. However, current studies on shale organic pore are insufficient. Based on this, the basic parameters of Wufeng-Longmaxi shale in Sichuan Basin were tested and shale samples were observed using optical and electron microscopes. In the Changning and Weiyuan areas, CO2, N2 adsorption and mercury intrusion porosimetry (MIP) experiments were conducted on shale samples with different total organic carbon (TOC) content. In this study, we termed the organic matter (OM) with fixed form as formed OM, and the OM without fixed form as amorphous OM, rather than the amorphous OM in the conventional context, which only exists when the maturity of shale is less than 1.0%. The results showed that: (1) formed and amorphous OM can be distinguished under optical and electron microscopes. The formed OM was mainly graptolite, while the amorphous OM could be subdivided into bitumen and micrinite. Under reflected light, bitumen appeared gray-black, while micrinite exhibited certain fluorescence. Under the electron microscope, bitumen showed larger particles than micrinite; (2) there were abundant organic pores in graptolite and bitumen. The organic pores in graptolites were significantly smaller than those in bitumen. Due to the limitation associated with the scanning electron microscope (SEM) resolution, we did not observe organic pores in micrinite, which indicated that the organic pore size in micrinite is smaller than that in bitumen; (3) there were obvious differences in the development of organic pore. In different areas, the relationship between shale porosity and TOC content varied greatly, which was related to the shale gas preservation conditions. Microscopically, there were also several reasons for the developmental differences of organic pore. Among them, inorganic minerals contribute to the preservation of organic pore by filling these pores or forming rigid spatial skeletons, which is an important reason for the micro-difference of organic pore development; (4) The SEM image processing results showed that the organic pore of Wufeng-Longmaxi shale in the Sichuan Basin mainly occurs in the range of mesopore. By comparing the pore size distribution curves of shale samples in the Changning and Weiyuan areas, it is concluded that the organic pore size of shale in the Changning area is primarily 4–10?nm and that in the Weiyuan area it is primarily 2–20?nm.Cheng, P., Tian, H., Xiao, X., Liu, D., Zhang, Y., Huang, B., Zhou, Q., Gai, H., Li, T., 2019. Fluorescence lifetimes of crude oils and oil inclusions: A preliminary study in the Western Pearl River Mouth Basin, South China Sea. Organic Geochemistry 134, 16-31. fluorescence lifetimes were measured for crude oils and oil inclusions in the Western Pearl River Mouth Basin, South China Sea. The results show that the fluorescence lifetimes are long for crude oils in the WC-A sag, short for those in the WC-B sag and moderate for those in the Qionghai and Shenhu uplifts. Two types of oil inclusions were identified in the reservoirs. The fluorescence lifetimes of type I oil inclusions are longer than those of the crude oils in the same reservoir; however, the fluorescence lifetimes of type II oil inclusions are slightly shorter than those of the crude oils in the same reservoir. The fluorescence lifetimes of crude oils have negative correlations with oil density, viscosity, sulfur content, and polar component content, including aromatics, resins and asphaltenes; however, they have a positive correlation with the saturates content of the crude oils. According to these correlations, the physical properties and gross chemical compositions of the two types of inclusion oils were inferred. The characteristics of the type I inclusion oils differ from those of the type II inclusion oils and reservoir crude oils, indicating that two oil charge events occurred in the reservoirs. The reservoirs in this area are inferred to have been first charged by high maturity oils sourced from the Wenchang Formation mudstones deeply buried in the WC-A sag, and then the reservoirs were charged by low maturity to high maturity oils sourced from the Enping Formation mudstones in the WC-A sag and partially mature oils sourced from the Wenchang Formation mudstones in the WC-B sag.Cheng, P., Xiao, X., Wang, X., Sun, J., Wei, Q., 2019. Evolution of water content in organic-rich shales with increasing maturity and its controlling factors: Implications from a pyrolysis experiment on a water-saturated shale core sample. Marine and Petroleum Geology 109, 291-303. the present study, a pyrolysis experiment was performed on an immature water-saturated shale core sample, and a set of artificially matured subsamples (maturity with equivalent vitrinite reflectance values of 0.67–3.20%, i.e., EqVRo values) with initial water phases was obtained. The water content of these shale samples and its influencing factors were investigated. The results show that the water content significantly varies with maturity and is closely related to the hydrocarbon generation and expulsion, clay mineral transformation, and pore structure evolution of shales. According to the changes of water content with maturity and the main influencing factors, the evolution of the water content in shales is approximately divided into three stages. At the low maturity stage (0.67%?<?EqVRo?<?0.90%), the water content decreases with increasing maturity, which is mainly controlled by the displacement drainage of liquid hydrocarbons. At the moderately mature stage (0.90%?<?EqVRo?<?1.36%), the water content remarkably increases with increasing maturity, which is mainly due to the generation of clay-associated water. At the high maturity stage (EqVRo?>?1.36%), with increasing maturity, the water content remarkably decreases at the wet gas window (1.36%?<?EqVRo?<?1.90%) and slightly decreases at the dry gas window (EqVRo?>?1.90%), which is mainly controlled by the displacement drainage of gaseous hydrocarbons. In addition, the pore structure evolution of shale, which changes its water-storage capacity, also has an influence on the water content evolution.Cheung, A., Fox-Kemper, B., Herbert, T., 2019. Can we use sea surface temperature and productivity proxy records to reconstruct Ekman Upwelling? Climate of the Past Discussions 2019, 1-19. sediments have greatly improved our understanding of the climate system, but their interpretation often assumes that certain climate mechanisms operate consistently over all timescales of interest and that variability at one or few sample sites is representative of an oceanographic province. In this study, we test these assumptions using modern observations in an idealized manner mimicking paleo-reconstruction to investigate whether sea surface temperature and productivity proxy records in the Southern California Current System can be used to reconstruct Ekman upwelling. The method uses Extended Empirical Orthogonal Function (EEOF) analysis of covariation of alongshore windstress, chlorophyll and sea surface temperature as measured by satellites from 2002 to 2009. We find that EEOF1 does not reflect an Ekman upwelling pattern, but instead much broader California Current processes. EEOF2 and 3 reflect upwelling patterns, but these patterns are timescale dependent and are regional. Thus, the skill of using one site to reconstruct the large scale dominant patterns is spatially dependent. Lastly, we show that using multiple sites and/or multiple variables generally improve field reconstruction. These results together suggest caution is needed when attempting to extrapolate mechanisms that may be important on seasonal time scales (e.g. Ekman upwelling) to deeper time, but also the advantage of having multiple proxy records.Chung, T., Wang, Y.D., Armstrong, R.T., Mostaghimi, P., 2019. Approximating permeability of microcomputed-tomography images using elliptic flow equations. SPE Journal 24, 1154-1163. simulation of flow on microcomputed-tomography (micro-CT) images of rocks is widely used for the calculation of permeability. However, direct numerical methods are computationally demanding. A rapid and robust method is proposed to solve the elliptic flow equation. Segmented micro-CT images are used for the calculation of local conductivity in each voxel. The elliptic flow equation is then solved on the images using the finite-volume method. The numerical method is optimized in terms of memory usage using sparse matrix modules to eliminate memory overhead associated with both the inherent sparsity of the finite-volume two-point flux-approximation (TPFA) method, and the presence of zero conductivity for impermeable grain cells. The estimated permeabilities for a number of sandstone and carbonate micro-CT images are compared against estimation of other solvers, and results show a difference of approximately 11%. However, the computational time is 80% lower. Local conductivity can furthermore be assigned directly into matrix voxels without a loss in generality, hence allowing the pore-scale finite-volume solver (PFVS) to be able to solve for flow in a permeable matrix as well as open pore space. This has been developed to include the effect of microporosity in flow simulation.Clapham, M.E., Renne, P.R., 2019. Flood basalts and mass extinctions. Annual Review of Earth and Planetary Sciences 47, 275-303. basalts were Earth's largest volcanic episodes that, along with related intrusions, were often emplaced rapidly and coincided with environmental disruption: oceanic anoxic events, hyperthermals, and mass extinction events. Volatile emissions, both from magmatic degassing and vaporized from surrounding rock, triggered short-term cooling and longer-term warming, ocean acidification, and deoxygenation. The magnitude of biological extinction varied considerably, from small events affecting only select groups to the largest extinction of the Phanerozoic, with less-active organisms and those with less-developed respiratory physiology faring especially poorly. The disparate environmental and biological outcomes of different flood basalt events may at first order be explained by variations in the rate of volatile release modulated by longer trends in ocean carbon cycle buffering and the composition of marine ecosystems. Assessing volatile release, environmental change, and biological extinction at finer temporal resolution should be a top priority to refine ancient hyperthermals as analogs for anthropogenic climate change.Clark, C.D., Bowen, J.C., de Bruyn, W.J., Keller, J.K., 2019. Optical characterization of chromophoric dissolved organic matter (CDOM) and Fe(II) concentrations in soil porewaters along a channel-bank transect in a salt marsh. Estuaries and Coasts 42, 1297-1307. dissolved organic matter (CDOM) optical properties were measured in surface and porewaters as a function of depth and distance from the channel in a transect up the bank in a southern California salt marsh. Higher absorbance coefficients and fluorescence intensities in porewaters at depth vs. surface waters and shallower porewaters suggest soil porewater is a reservoir of CDOM in the marsh. Higher values were observed at the marsh sites compared to the channel site, suggesting increased production and storage in the marsh sites, and reduced leaching into overlying surface waters, is occurring. Spectral slope ratios decreased with depth, consistent with more aromatic, higher molecular weight material in the deeper porewaters, possibly due to different bacterial processing in the anaerobic vs. aerobic zones. Fe(II) concentrations, indicative of anaerobic bacterial processing, increased significantly at depth to values >?1000?μM, consistent with active anaerobic microbial processing occurring at depth. The transitions to higher reduced iron concentrations correlated with increased absorbance and fluorescence, suggesting processing by anaerobic iron-reducing bacteria in these deeper zones may not mineralize as much carbon as in the shallower aerobic zones. Alternatively, this may be due to reduction of solid iron oxides coated with organic matter releasing both DOM and Fe(II). The ratio of humic-like fluorescence to the absorption coefficient decreased with increasing iron concentration, possibly due to optical interference by iron species. Taken together, the data indicate that marsh sites in the salt marsh act as a reservoir for higher molecular weight, more aromatic organic matter.Cleland, C.E., 2019. Moving beyond definitions in the search for extraterrestrial life. Astrobiology 19, 722-729. to the 2015 Astrobiology Strategy, a central goal of astrobiology is to provide a definition of life. A similar claim is made in the 2018 CRC Handbook of Astrobiology. Yet despite efforts, there remains no consensus on a definition of life. This essay explores an alternative strategy for searching for extraterrestrial life: Search for potentially biological anomalies (as opposed to life per se) using tentative (vs. defining) criteria. The function of tentative criteria is not, like that of defining criteria, to provide an estimate (via a decision procedure) of the likelihood that an extraterrestrial phenomenon is the product of life. Instead, it is to identify phenomena that resist classification as living or nonliving as worthy of further investigation for novel life. For as the history of science reveals, anomalies are a driving force behind scientific discovery and yet (when encountered) are rarely recognized for what they represent because they violate core theoretical beliefs about the phenomena concerned. While the proposed strategy resembles that of current life-detection missions, insofar as it advocates the use of a variety of lines of evidence (biosignatures), it differs from these approaches in ways that increase the likelihood of noticing truly novel forms of life, as opposed to dismissing them as just another poorly understood abiological phenomenon. Moreover, the strategy under consideration would be just as effective at detecting forms of life closely resembling our own as a definition of life. Clementi, V.J., Sikes, E.L., 2019. Southwest Pacific vertical structure influences on oceanic carbon storage since the Last Glacial Maximum. Paleoceanography and Paleoclimatology 34, 734-754. atmospheric CO2 concentrations during the Last Glacial Maximum (LGM; 23.0–18.0 ka) have been attributed to the sequestration of respired carbon in the ocean interior, yet the mechanism responsible for the release of this CO2 during the deglaciation remains uncertain. Here we present calculations of vertical differences in oxygen and carbon isotopes (?δ18O and ?δ13C, respectively) from a depth transect of southwest Pacific Ocean sediment cores to reconstruct changes in water mass structure and CO2 storage. During the Last Glacial Maximum, ?δ18O indicates a more homogenous deep Pacific below 1,100 m, whereas regional ?δ13C elucidates greater sequestration of CO2 in two distinct layers: enhanced CO2 storage at intermediate depths between ~940 and 1,400 m, and significantly more CO2 at 1,600 m and below. This highlights an isolated glacial intermediate water mass and places the main geochemical divide at least 500 m shallower than the Holocene. During the initial stages of the deglaciation in Heinrich Stadial 1 (17.5–14.5 ka), restructuring of the upper ~2,000 m of the southwest Pacific water column coincided with sea‐ice retreat and rapid CO2 release from intermediate depths, while CO2 release from the deep ocean was earlier and more gradual than waters above it. These changes suggest that sea‐ice retreat and shifts in Southern Ocean frontal locations contributed to rapid CO2 ventilation from the Southern Ocean's intermediate depths and gradual ventilation from the deep ocean during the early deglaciation.Clomburg, J.M., Qian, S., Tan, Z., Cheong, S., Gonzalez, R., 2019. The isoprenoid alcohol pathway, a synthetic route for isoprenoid biosynthesis. Proceedings of the National Academy of Sciences 116, 12810-12815.: We have demonstrated the design, prototyping, and implementation of a non-natural route to isoprenoid biosynthesis, termed the isoprenoid alcohol (IPA) pathway. Opposed to working within the confines of native metabolic pathways, our approach of utilizing all available biochemical reactions identified a synthetic route to isoprenoid compounds that is both different and provides a more energy-efficient pathway compared with native isoprenoid biosynthesis. By improving the overall pathway design, the IPA pathway has the potential to facilitate the synthesis of a diverse range of isoprenoid compounds at high product titers and yields.Abstract: The more than 50,000 isoprenoids found in nature are all derived from the 5-carbon diphosphates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Natively, IPP and DMAPP are generated by the mevalonate (MVA) and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, which have been engineered to produce compounds with numerous applications. However, as these pathways are inherently constrained by carbon, energy inefficiencies, and their roles in native metabolism, engineering for isoprenoid biosynthesis at high flux, titer, and yield remains a challenge. To overcome these limitations, here we develop an alternative synthetic pathway termed the isoprenoid alcohol (IPA) pathway that centers around the synthesis and subsequent phosphorylation of IPAs. We first established a lower IPA pathway for the conversion of IPAs to isoprenoid pyrophosphate intermediates that enabled the production of greater than 2 g/L geraniol from prenol as well as limonene, farnesol, diaponeurosporene, and lycopene. We then designed upper IPA pathways for the generation of (iso)prenol from central carbon metabolites with the development of a route to prenol enabling its synthesis at more than 2 g/L. Using prenol as the linking intermediate further facilitated an integrated IPA pathway that resulted in the production of nearly 0.6 g/L total monoterpenoids from glycerol as the sole carbon source. The IPA pathway provides an alternative route to isoprenoids that is more energy efficient than native pathways and can serve as a platform for targeting a repertoire of isoprenoid compounds with application as high-value pharmaceuticals, commodity chemicals, and fuels.Cook, J.C., Dalle Ore, C.M., Protopapa, S., Binzel, R.P., Cruikshank, D.P., Earle, A., Grundy, W.M., Ennico, K., Howett, C., Jennings, D.E., Lunsford, A.W., Olkin, C.B., Parker, A.H., Philippe, S., Reuter, D., Schmitt, B., Singer, K., Stansberry, J.A., Stern, S.A., Verbiscer, A., Weaver, H.A., Young, L.A., Hanley, J., Alketbi, F., Thompson, G.L., Pearce, L.A., Lindberg, G.E., Tegler, S.C., 2019. The distribution of H2O, CH3OH, and hydrocarbon-ices on Pluto: Analysis of New Horizons spectral images. Icarus 331, 148-169. July 14, 2015, the New Horizons spacecraft made its closest approach to Pluto at about 12,000 km from its surface (Stern et al., 2015). Using the LEISA (Linear Etalon Imaging Spectral Array) near-IR imaging spectrometer we obtained two scans across the encounter hemisphere of Pluto at 6–7?km/pixel resolution. By correlating each spectrum with a crystalline H2O-ice model, we find several sites on Pluto’s surface that exhibit the 1.5, 1.65 and 2.0 ?m absorption bands characteristic of H2O-ice in the crystalline phase. These sites tend to be isolated and small (??? 5000 km2 per site). We note a distinct near-IR blue slope over the LEISA wavelength range and asymmetries in the shape of the 2.0 ?m H2O-ice band in spectra with weak CH4-ice bands and strong H2O-ice bands. These characteristics are indicative of fine-grain (grain diameters ?<? wavelength or ?～?1 ?m) H2O-ice, like that seen in the spectra of Saturnian rings and satellites. However, the best-fit Hapke models require small mass fractions (?10?3) of fine-grained H2O-ice that we can exchange for other refractory materials in the models with little change in χ2, which may mean that the observed blue slope is possibly not due to a fine-grained material but an unidentified material with a similar spectral characteristic. We use these spectra to test for the presence of amorphous H2O-ice and estimate crystalline-to-amorphous H2O-ice fractions between 30 and 100%, depending on the location. We also see evidence for heavy hydrocarbons via strong absorption at λ?>?2.3? ?m. Such heavy hydrocarbons are much less volatile than N2, CH4, and CO at Pluto temperatures. We test for CH3OH, C2H6, C2H4, and C3H8-ices because they have known optical constants and these ices are likely to arise from UV and energetic particle bombardment of the N2, CH4, CO-rich surface and atmosphere. Finally, we attempt to estimate the surface temperature using optical constants of pure CH4, and H2O-ice and best-fit Hapke models. Our standard model gives temperature estimates between 40 and 90 K, while our models including amorphous H2O-ice give lower temperature estimates between 30 and 65 K.Cooper, R.E., DiChristina, T.J., 2019. Fe(III) oxide reduction by anaerobic biofilm formation-deficientS-ribosylhomocysteine lyase (LuxS) mutant of Shewanella oneidensis. Geomicrobiology Journal 36, 639-650. oneidensis respires a variety of terminal electron acceptors, including solid phase Fe(III) oxides. S. oneidensis transfers electrons to Fe(III) oxides via direct (outer membrane- or nanowire-localized c-type cytochromes) and indirect (electron shuttling and Fe(III) solubilization) pathways. In the present study, the influence of anaerobic biofilm formation on Fe(III) oxide reduction by S. oneidensis was determined. The gene encoding the activated methyl cycle (AMC) enzyme S-ribosylhomocysteine lyase (LuxS) was deleted in-frame to generate the corresponding mutant ΔluxS. Conventional biofilm assays and visual inspection via confocal laser scanning microscopy indicated that the wild-type strain formed anaerobic biofilms on Fe(III) oxide-coated silica surfaces, while the ΔluxS mutant was severely impaired in anaerobic biofilm formation on such surfaces. Cell-hematite attachment isotherms demonstrated that the ΔluxS mutant was also severely impaired in attachment to hematite surfaces under anaerobic conditions. The S. oneidensis ΔluxS mutant, however, reduced Fe(III) at wild-type rates during anaerobic incubation with Fe(III) oxide-coated silica surfaces or in batch cultures with Fe(III) oxide or hematite as a terminal electron acceptor. Anaerobic biofilm formation by the ΔluxS mutant was restored to wild-type rates by providing a wild-type copy of luxS in trans or by the addition of AMC or transsulfurylation pathway metabolites involved in organic sulfur metabolism. LuxS is thus required for wild-type anaerobic biofilm formation on Fe(III) oxide surfaces, yet the inability to form wild-type anaerobic biofilms on Fe(III) oxide surfaces does not alter Fe(III) oxide reduction activity.Cordiner, M.A., Linnartz, H., Cox, N.L.J., Cami, J., Najarro, F., Proffitt, C.R., Lallement, R., Ehrenfreund, P., Foing, B.H., Gull, T.R., Sarre, P.J., Charnley, S.B., 2019. Confirming interstellar C60+ using the Hubble Space Telescope. The Astrophysical Journal 875, Article L28. advances in laboratory spectroscopy lead to the claim of ionized Buckminsterfullerene (C60+) as the carrier of two diffuse interstellar bands (DIBs) in the near-infrared. However, irrefutable identification of interstellar C60+ requires a match between the wavelengths and the expected strengths of all absorption features detectable in the laboratory and in space. Here we present Hubble Space Telescope (HST) spectra of the region covering the C60+ 9348, 9365, 9428, and 9577 ? absorption bands toward seven heavily reddened stars. We focus in particular on searching for the weaker laboratory C60+ bands, the very presence of which has been a matter for recent debate. Using the novel STIS-scanning technique to obtain ultra-high signal-to-noise spectra without contamination from telluric absorption that afflicted previous ground-based observations, we obtained reliable detections of the (weak) 9365, 9428 ? and (strong) 9577 ? C60+ bands. The band wavelengths and strength ratios are sufficiently similar to those determined in the latest laboratory experiments that we consider this the first robust identification of the 9428 ? band, and a conclusive confirmation of interstellar C60+.Costin, G., G?tz, A.E., Ruckwied, K., 2019. Sedimentary organic matter characterization of the Whitehill shales (Karoo Basin, South Africa): An integrated quantitative approach using FE-EPMA and LA-ICP-MS. Review of Palaeobotany and Palynology 268, 29-42. black shales of South Africa's Karoo Basin have been classified as potential unconventional gas resources, the Whitehill Formation of the southern basin parts being the main target for future shale gas exploration and production. Here, we present a novel approach of SOM characterization integrating routine palynofacies analysis and high-resolution BSE imaging, modal mineral analysis, quantitative carbon analysis, EPMA trace element analysis, WDS mapping of carbon particles and carbon peak shift method using field emission microprobe as well as LA-ICP-MS trace element analysis. Black shales of the Whitehill Formation intersected in two deep boreholes of the southern Karoo Basin were studied: (1) massive carbonaceous siltstone (borehole KZF-1, southwestern basin) and (2) laminated shale made of alternating silty and clayey–silty laminae (borehole KWV-1, southeastern basin). Palynofacies indicates an outer shelf setting in the southwestern part (KZF-1) and a stratified basin in the southeastern part (KWV-1). The two shale types reveal striking differences in mineralogy, major and trace element concentrations, and shape and texture of organic particles. The EPMA trace element data of SOM show that the concentration of the elements in the organic particles does not correlate with the chemistry of the black shale when SOM is thermally untransformed. However, in the case of thermally affected and mobilized SOM, the organic acid-rich fluids liberated during the transformation and deformation of SOM can differentially dissolve chemical elements from the surrounding minerals. The LA-ICP-MS data show that the Whitehill shales are enriched in S, Mn, Mo, Ag, Cd, Re, Bi and U relative to the standard marine mud MAG-1. Shales from the southeastern basin (KWV-1) are strongly depleted in Cu, Zn, As and Ba. The granulometric and mineralogical properties of the shales suggest an outer shelf setting with low-energy sediment fallout and sediment reworking, consistent with the paleoenvironmental interpretation based on palynofacies analysis. Different burial depths are inferred from different organic textures: KZF-1 shales show organic particles which preserve organic textures, randomly distributed throughout the siltstone, whereas KWV-1 shales show deformed, thermally transformed and mobilized organic particles, located in between distinct laminae. WDS quantitative element mapping allows for identifying various carbon concentrations within the organic particles. This variability of carbon at grain scale may indicate different carbon–hydrogen molecule speciations. The observed peak shift of carbon in EPMA on different textural types of SOM allowed a correlation between the peak shift and the degree of SOM maturation, indicating that this method potentially works as a vitrinite reflectance proxy. Ultimately, the evaluation of the diagenetic conditions of organic-rich shales from different parts of the basin based on textural criteria of the detrital material and organic particles combined with the carbon peak shift in different organic particles contributes to the assessment of the hydrocarbon potential.Couradeau, E., Sasse, J., Goudeau, D., Nath, N., Hazen, T.C., Bowen, B.P., Chakraborty, R., Malmstrom, R.R., Northen, T.R., 2019. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature Communications 10, Article 2770. ability to link soil microbial diversity to soil processes requires technologies that differentiate active microbes from extracellular DNA and dormant cells. Here, we use BONCAT (bioorthogonal non-canonical amino acid tagging) to measure translationally active cells in soils. We compare the active population of two soil depths from Oak Ridge (Tennessee, USA) and find that a maximum of 25–70% of the extractable cells are active. Analysis of 16S rRNA sequences from BONCAT-positive cells recovered by fluorescence-activated cell sorting (FACS) reveals that the phylogenetic composition of the active fraction is distinct from the total population of extractable cells. Some members of the community are found to be active at both depths independently of their abundance rank, suggesting that the incubation conditions favor the activity of similar organisms. We conclude that BONCAT-FACS is effective for interrogating the active fraction of soil microbiomes in situ and provides a new approach for uncovering the links between soil processes and specific microbial groups.Crósta, A.P., Reimold, W.U., Vasconcelos, M.A.R., Hauser, N., Oliveira, G.J.G., Maziviero, M.V., Góes, A.M., 2019. Impact cratering: The South American record—Part 2. Geochemistry 79, 191-220. the first part of this review of the impact record of South America, we have presented an up-to-date introduction to impact processes and to the criteria to identify/confirm an impact structure and related deposits, as well as a comprehensive examination of Brazilian impact structures. The current paper complements the previous one, by reviewing the impact record of other countries of South America and providing current information on a number of proposed impact structures. Here, we also review those structures that have already been discarded as not being formed by meteorite impact. In addition, current information on impact-related deposits is presented, focusing on impact glasses and tektites known from this continent, as well as on the rare K–Pg boundary occurrences revealed to date and on reports of possible large airbursts. We expect that this article will not only provide systematic and up-to-date information on the subject, but also encourage members of the South American geoscientific community to be aware of the importance of impact cratering and make use of the criteria and tools to identify impact structures and impact deposits, thus potentially contributing to expansion and improvement of the South American impact record.Crósta, A.P., Reimold, W.U., Vasconcelos, M.A.R., Hauser, N., Oliveira, G.J.G., Maziviero, M.V., Góes, A.M., 2019. Impact cratering: The South American record – Part 1. Geochemistry 79, 1-61. Earth’s impact record is known to be rather limited in both time and space. There are ca. 190 impact structures currently known on Earth, representing a minor fraction of all the impact events that contributed to the initial formation of our protoplanet, and then to formation and modification of the surface of the planet. Moreover, the distribution of impact structures on Earth is manifestly uneven. One continent that stands out for its relatively small number of confirmed impact structures and impact ejecta occurrences is South America. The limited impact record for this large continent makes a robust case that there is a significant potential for further discoveries. Significant information on the impact record of South America is dispersed in different types of publications (journal articles, books, conferences abstracts, etc.), and in several languages, making it difficult to access and disseminate it among the geoscientific community. We aim to present a summary of the current knowledge of the impact record of this continent, encompassing the existing literature on the subject. It is published in two parts, with the first one covering an up-to-date introduction to impact cratering processes and to the criteria to identify/confirm an impact structure and related deposits. This is followed by a comprehensive analysis of the Brazilian impact structures. The Brazilian impact record accounts for the totality of the large structures of this kind currently confirmed in South America. The second part will examine the impact record of other countries in South America, provide information about a number of proposed impact structures, and review those that already have been discarded as not being formed by impact.Cui, T., Green, H.S., Selleck, P.W., Zhang, Z., O’Brien, R.E., Gold, A., Keywood, M., Kroll, J.H., Surratt, J.D., 2019. Chemical characterization of isoprene- and monoterpene-derived secondary organic aerosol tracers in remote marine aerosols over a quarter century. ACS Earth and Space Chemistry 3, 935-946. and monoterpenes are ubiquitous precursors of biogenic secondary organic aerosol (SOA) over continental regions; however, their contributions to organic aerosol (OA) mass and chemical processes in remote marine atmospheres remain uncertain. Determining exact sources of organics in marine aerosol is needed to more accurately assess aerosol climate effects in remote locations through coupled atmospheric chemistry–climate simulations. Over 200 archived ocean-originated particulate samples collected from 1991 to 2015 at Cape Grim, Australia, were analyzed using a suite of chromatographic and mass spectrometric techniques. To our knowledge, this is one of the longest running continual archives of marine aerosol samples collected under remote background conditions. Up to 6.75 and 1.11 ng m–3 of isoprene- and monoterpene-derived SOA, respectively, were quantified using authentic standards. Although there was no clear temporal trend over the decades, consistent seasonal variations were observed, with higher biogenic SOA in summer, which was moderately to strongly correlated (r = 0.61–0.85) with marine bioactivity indicators, such as methanesulfonic acid and chlorophyll a. These correlations indicate that marine biota likely emit biogenic SOA precursors that are able to contribute to remote background OA levels. On the basis of historical observations of OA mass estimated in the marine baseline samples, these biogenic SOA tracers contributed up to 0.71% (0.26 ± 0.24% on average) of the total OA mass fraction. Our data suggest that larger sources of OA exist in remote marine atmospheres, such as primary OA produced from bubble-bursting processes or SOA precursors derived from photosensitized reactions of dissolved organic matter present in the sea surface microlayer.Cukur, D., Kong, G.-S., Chun, J.-H., Kang, M.-H., Um, I.-K., Kwon, T., Johnson, S.Y., Kim, K.-O., 2019. Morphology and genesis of giant seafloor depressions on the southeastern continental shelf of the Korean Peninsula. Marine Geology 415, 105966. identify and describe five giant seafloor depressions from the southeastern continental shelf of the Korean Peninsula using multibeam bathymetry, sub-bottom profiler, and multi-channel seismic reflection data, supplemented by piston cores. Multibeam bathymetry data from the shelf show four crescent-shaped depressions (SD1 to SD4) and one near-circular depression (SD5) within a group of NW-SE trending depressions, the largest covering an area of about 7?km2 on the seafloor. The depressions reach up to ~4.5?km in width and ~2?km in length and have asymmetric cross-sections. Some have depths as large as 40?m below the surrounding seafloor with walls as steep as 45°. The depressions are confined to water depths between 130 and 170?m and bounded on the north by a large submarine channel that was plausibly formed by fluvial or tidal processes during the Last Glacial Maximum (LGM) sea-level lowstand. Multi-channel seismic and sub-bottom profiler data reveal truncated depression walls and the presence of sediment drift deposits within the depressions, indicating that both erosion and deposition are active processes. Flaser and lenticular bedding in the cored drift deposits along with variable grain size (ranging between ~2.6 phi and ~4.3 phi) are diagnostic features of the bottom currents influenced by tidal forces. Depressions SD1 to SD4 lack evidence of fluid or gas escape. In contrast, many features of depression SD5 are characteristic of gas escapes and blowouts, including acoustic anomalies, a 20-m-high carbonate mound or carbonate-encrusted mound, and mud dikes and mud patches in cores. Based on the SD5 example, we think it is likely that the other crescent-shaped seafloor depressions formed originally as pockmarks by gas/fluid venting, and have since become inactive. The pockmarks represent zones of weakened sediment that were eroded, expanded, and merged by bottom currents to form larger seafloor depressions. Modern currents are strong enough to transport shelf sediments, and these currents were probably much stronger at lower sea levels when the Korea Strait was a more restricted passage between the East China Sea and East Sea.Cumming, L., Hawkins, J., Sminchak, J., Valluri, M., Gupta, N., 2019. Researching candidate sites for a carbon storage complex in the Central Appalachian Basin, USA. International Journal of Greenhouse Gas Control 88, 168-181. purpose of the Central Appalachian Basin-Carbon Storage Assurance Facility Enterprise Integrated Prefeasibility Project was to identify candidate sites in eastern Ohio for a storage complex capable of storing 50 million tonnes. Carbon capture and storage (CCS) will be essential in the Appalachian Basin, which includes coal-fired power plants, natural gas processing, refineries, chemical plants, and natural gas power. The project team investigated Cambrian-Ordovician Age sandstones and carbonates collocated near depleted oilfields, where enhanced oil recovery could provide a stepping stone for developing a storage hub. Feasible routes for linking sources to sinks via regional pipelines were assessed. The sub-basinal analysis demonstrated significant potential storage capacity in both deep saline reservoirs and depleted oil and gas fields. The project definition analysis revealed the project footprint would be reasonable and only two wells would be needed for injection of CO2. Project economics illustrated a need for both government and private investment in the absence of a regulatory mandate. Ohio also lacks a comprehensive policy for long-term liability and subsurface storage rights, which could be addressed during pilot testing. Developing qualified sites within two selected areas for large-scale deployment of CCS appears feasible and the study helped to define future research needs.Dai, J., Ni, Y., Liao, F., Hong, F., Yao, L., 2019. The significance of coal-derived gas in major gas producing countries. Petroleum Exploration and Development 46, 435-450. core of coal-derived gas theory is that coal measure is the gas source, and the hydrocarbon generation of coal measure is dominated by gas and supplemented by oil, so discoveries in related basins are dominated by gas fields. Discovering and developing giant gas fields, especially those super giant gas fields with recoverable reserves more than 1×1012 m3, plays a key role in determining whether a country can be a major gas producing country with annual output over 500×108 m3. The coal resource and coal-derived gas reserves are abundant and widespread in the world, and coal-derived gas makes a major contribution to the gas reserves and gas production in the world. By the end of 2017, 13 super giant coal-derived gas fields have been discovered in the world. The total initial recoverable reserves were 49.995 28×1012 m3, accounting for 25.8% of the total remaining recoverable reserves (193.5×1012 m3) in that year in the world. In 2017, there were 15 giant gas producing countries in the world, with a total gas yield of 28 567×108 m3. Among them, six major coal-derived gas producing countries had a total gas yield of 11 369×108 m3, accounting for 39.8% of total gas yield of major gas producing countries. The Urengoi gas field is a super giant coal-derived gas field with the most cumulative gas production in the world. By the end of 2015, the Urengoi gas field had cumulative gas production of 63 043.96×108 m3, with the highest annual gas yield in the world. Its gas output was 3 300×108 m3 in 1989, accounting for 41.4% and 15.7% of the gas output of Russia and the world, respectively. This study introduces the gas source rocks of the basins with super giant coal-derived gas fields in Russia, Turkmenistan, Netherlands, Mozambique and China, and their significances for these countries becoming giant gas producing countries in the world.Dalcin Martins, P., Frank, J., Mitchell, H., Markillie, L.M., Wilkins, M.J., 2019. Wetland sediments host diverse microbial taxa capable of cycling alcohols. Applied and Environmental Microbiology 85, Article e00189-19.: Alcohols are commonly derived from the degradation of organic matter and yet are rarely measured in environmental samples. Wetlands in the Prairie Pothole Region (PPR) support extremely high methane emissions and the highest sulfate reduction rates reported to date, likely contributing to a significant proportion of organic matter mineralization in this system. While ethanol and isopropanol concentrations up to 4 to 5?mM in PPR wetland pore fluids have been implicated in sustaining these high rates of microbial activity, the mechanisms that support alcohol cycling in this ecosystem are poorly understood. We leveraged metagenomic and transcriptomic tools to identify genes, pathways, and microorganisms potentially accounting for alcohol cycling in PPR wetlands. Phylogenetic analyses revealed diverse alcohol dehydrogenases and putative substrates. Alcohol dehydrogenase and aldehyde dehydrogenase genes were included in 62 metagenome-assembled genomes (MAGs) affiliated with 16 phyla. The most frequently encoded pathway (in 30 MAGs) potentially accounting for alcohol production was a Pyrococcus furiosus-like fermentation which can involve pyruvate:ferredoxin oxidoreductase (PFOR). Transcripts for 93 of 137 PFOR genes in these MAGs were detected, as well as for 158 of 243 alcohol dehydrogenase genes retrieved from these same MAGs. Mixed acid fermentation and heterofermentative lactate fermentation were also frequently encoded. Finally, we identified 19 novel putative isopropanol dehydrogenases in 15 MAGs affiliated with Proteobacteria, Acidobacteria, Chloroflexi, Planctomycetes, Ignavibacteriae, Thaumarchaeota, and the candidate divisions KSB1 and Rokubacteria. We conclude that diverse microorganisms may use uncommon and potentially novel pathways to produce ethanol and isopropanol in PPR wetland sediments.Importance: Understanding patterns of organic matter degradation in wetlands is essential for identifying the substrates and mechanisms supporting greenhouse gas production and emissions from wetlands, the main natural source of methane in the atmosphere. Alcohols are common fermentation products but are poorly studied as key intermediates in organic matter degradation in wetlands. By investigating genes, pathways, and microorganisms potentially accounting for the high concentrations of ethanol and isopropanol measured in Prairie Pothole wetland sediments, this work advanced our understanding of alcohol fermentations in wetlands linked to extremely high greenhouse gas emissions. Moreover, the novel alcohol dehydrogenases and microbial taxa potentially involved in alcohol metabolism may serve biotechnological efforts in bioengineering commercially valuable alcohol production and in the discovery of novel isopropanol producers or isopropanol fermentation pathways.Daly, P., Sieh, K., Seng, T.Y., Edwards McKinnon, E., Parnell, A.C., Ardiansyah, Feener, R.M., Ismail, N., Nizamuddin, Majewski, J., 2019. Archaeological evidence that a late 14th-century tsunami devastated the coast of northern Sumatra and redirected history. Proceedings of the National Academy of Sciences 116, 11679-11686.: We demonstrate that a tsunami in the late 14th century CE destroyed coastal sites along a critical part of the maritime Silk Road and set in motion profound changes in the political economy of Southeast Asia. Our results provide a precise chronology of settlement and trade along a historically strategic section of the Sumatran coast and are robust physical evidence for the rise of the Aceh Sultanate. Tragically, coastal areas impacted by the late 14th century tsunami were devastated by the 2004 Indian Ocean tsunami. This makes our findings relevant to debates about hazard mitigation and risk reduction. This example shows that archaeological, historical, and geological data are relevant in discussions about the long-term sustainability of communities exposed to geological hazards.Abstract: Archaeological evidence shows that a predecessor of the 2004 Indian Ocean tsunami devastated nine distinct communities along a 40-km section of the northern coast of Sumatra in about 1394 CE. Our evidence is the spatial and temporal distribution of tens of thousands of medieval ceramic sherds and over 5,000 carved gravestones, collected and recorded during a systematic landscape archaeology survey near the modern city of Banda Aceh. Only the trading settlement of Lamri, perched on a headland above the reach of the tsunami, survived into and through the subsequent 15th century. It is of historical and political interest that by the 16th century, however, Lamri was abandoned, while low-lying coastal sites destroyed by the 1394 tsunami were resettled as the population center of the new economically and politically ascendant Aceh Sultanate. Our evidence implies that the 1394 tsunami was large enough to impact severely many of the areas inundated by the 2004 tsunami and to provoke a significant reconfiguration of the region’s political and economic landscape that shaped the history of the region in subsequent centuries.Daoud, A.B.A., Tremblay, L., 2019. HPLC-SEC-FTIR characterization of the dissolved organic matter produced by the microbial carbon pump. Marine Chemistry 215, 103668. microbial carbon pump (MCP) concept regroups different processes that contribute to the formation of refractory dissolved organic matter (DOM) from labile substrates. In this study, long-term (1?yr) incubation experiments in fresh- and sea-waters were done with glucose as the only source of carbon for microorganisms. Bulk carbon, glucose and amino acid enantiomers analyses confirmed that glucose was transformed into microbial biomass and complex non-labile DOM. Dissolved organic carbon concentrations decreased during the first four months and then remained constant at ~20% of the initial level. After one year, the microbial DOM and DOM from natural waters were concentrated by evaporation and a low volume solid-phase extraction (SPE) that resulted in a very high (70 to 85%) extraction efficiency. These SPE-DOM samples were characterized by size-exclusion chromatography (HPLC-SEC) coupled with Fourier transform infrared spectroscopy (FTIR). These are the first HPLC-SEC-FTIR analyses of microbial DOM and of such high proportions of natural DOM. Results revealed that microbial DOM showed all the FTIR absorption bands seen in the DOM from natural waters. However, amino acids, carbohydrates, and aliphatic CH were more abundant in the microbial DOM, whereas phenols and esters were more visible in DOM from natural waters. It was difficult to identify consistent (in all samples) compositional trends according to molecular weight (MW). Cluster analyses showed that 72% of the variability in the relative absorbance for all the bands was explained by the origin and the type of the DOM extracts. The microbial DOM from freshwater had the most unique bulk composition while the microbial DOM from seawater was more similar to the DOM from natural waters. The DOM from natural fresh- and sea-waters exhibited the most similar composition when all the bands and MW are considered. The lack of consistent trends in the composition of the samples having the same origin (e.g., the two microbial DOM or the two freshwater DOM) shows the high heterogeneity and complexity of DOM, including the microbial non-labile DOM produced by the MCP. This suggests that the MCP contributes to the heterogeneity and complexity of the DOM found in natural waters.Dasan, Y.K., Lam, M.K., Yusup, S., Lim, J.W., Lee, K.T., 2019. Life cycle evaluation of microalgae biofuels production: Effect of cultivation system on energy, carbon emission and cost balance analysis. Science of The Total Environment 688, 112-128. rapid depletion of fossil fuels and ever-increasing environmental pollution have forced humankind to look for a renewable energy source. Microalgae, a renewable biomass source, has been proposed as a promising feedstock to generate biofuels due to their fast growth rate with high lipid content. However, literatures have indicated that sustainable production of microalgae biofuels are only viable with a highly optimized production system. In the present study, a cradle-to-gate approach was used to provide expedient insights on the effect of different cultivation systems and biomass productivity toward life cycle energy (LCEA), carbon balance (LCCO2) and economic (LCC) of microalgae biodiesel production pathways. In addition, a co-production of bioethanol from microalgae residue was proposed in order to improve the economic sustainability of the overall system. The results attained in the present work indicated that traditional microalgae biofuels processing pathways resulted to several shortcomings, such as dehydration and lipid extraction of microalgae biomass required high energy input and contributed nearly 21 to 30% and 39 to 57% of the total energy requirement, respectively. Besides, the microalgae biofuels production system also required a high capital investment, which accounted for 47 to 86% of total production costs that subsequently resulted to poor techno-economic performances. Moreover, current analysis of environmental aspects of microalgae biorefinery had revealed negative CO2 balance in producing microalgae biofuels.Davies, A., Hunter, S.J., Gréselle, B., Haywood, A.M., Robson, C., 2019. Evidence for seasonality in early Eocene high latitude sea-surface temperatures. Earth and Planetary Science Letters 519, 274-283. challenges still exist in our understanding of past greenhouse climate states. Whilst climate model simulations using atmospheric CO2 concentrations consistent with proxy estimates broadly align with lower latitude proxy temperature estimates, they struggle to reproduce the warming implied by proxies at higher latitudes, especially in the marine realm. This inconsistency has often led to the conclusion that climate models are insufficiently sensitive. Here, we analyse the distribution of photozoan and heterozoan carbonates, which provide important constraints for latitudinal sea surface temperature (SST) gradients, to assess data/model mismatches for the early Eocene Climatic Optimum. The carbonate facies distribution is compared against quantitative geochemical proxy temperature estimates (δ18O, Mg/Ca, clumped isotopes and TEX86) and a new HadCM3L climate simulation. Good correspondence exists between the simulated cold-month SSTs and photozoan carbonates, indicating HadCM3L is effectively reconstructing meridional temperature gradients into mid-latitudes. Whilst there is good agreement between simulated mean annual SSTs and geochemical proxy estimates in low latitudes, the δ18O, Mg/Ca and TEX86 estimates instead align with warm-month SSTs at higher latitudes. In light of the carbonate facies evidence, and consistency between our simulation and available terrestrial proxy temperature estimates, this study supports previous claims that a warm season bias exists in many middle and high latitude SST estimates. This helps resolve the discrepancy between climate simulations and marine proxies and shows that climate models and data might be more closely aligned than is appreciated. Further, we demonstrate that simple, and widely available, proxies can play a fundamental role in contextualising wider paleoclimate uncertainties.de Araujo, L.L.G.C., Sodré, L.G.P., Brasil, L.R., Domingos, D.F., de Oliveira, V.M., da Cruz, G.F., 2019. Microbial enhanced oil recovery using a biosurfactant produced by Bacillus safensis isolated from mangrove microbiota - Part I biosurfactant characterization and oil displacement test. Journal of Petroleum Science and Engineering 180, 950-957. primary and secondary recovery operations, the majority of the original oil in place remains in the reservoir due to physical and geological limitations. Thus, increasing oil recovery yields and reducing operational costs are major goals of the oil industry and efforts are being made to develop economic methods of enhanced oil recovery. One alternative method is the use of the microbiological enhanced oil recovery method (MEOR), which uses microorganisms or their metabolites, including biosurfactants, to mobilize the oil trapped in reservoirs and increase the oil recovery factor. This study aimed to evaluate the potential of a pumilacidin produced by Bacillus safensis CCMA-560 to increase oil recovery in a laboratory scale MEOR process. This bioactive molecule was previously isolated from a mangrove, increasing its potential to contribute to a more sustainable economy and to the environment. The critical micelle concentration (CMC) of the biosurfactant was determined by surface tension and thermal gravimetric analysis (TGA) was performed to evaluate if its thermal stability is consistent with the average reservoir temperature. Surface and interfacial tension measurements were performed to investigate the interfacial activity behaviors of the biosurfactant with oil and brine. Core flood experiments showed that this biosurfactant has a great potential for chemical EOR flooding applications. The results demonstrated that an alternate injection of a 1.3 CMC biosurfactant solution and 3?wt% brine should be able to permeate through the porous media, migrate to the water/oil interface, reduce the interfacial tension (IFT), and increase the oil recovery factor by 13%. In additional, a core flood experiment was performed to study the impact of this MEOR injection on the rock properties.de Morais, M.G., de Morais, E.G., Duarte, J.H., Deamici, K.M., Mitchell, B.G., Costa, J.A.V., 2019. Biological CO2 mitigation by microalgae: technological trends, future prospects and challenges. World Journal of Microbiology and Biotechnology 35, 78. increase in the CO2 concentration in the Earth's atmosphere has been a topic of worldwide concern since anthropogenic emissions of greenhouse gases began increasing considerably during the industrial period. The effects of these mass emissions are probably the main cause of global warming, which has been observed over recent decades. Among the various techniques of CO2 capture, microalgal biofixation by photosynthesis is considered a promising technology due to the efficiency of these microorganisms in converting this gas into organic compounds through its use as a nutrient in the culture medium. Over the years, several research centers have developed studies on this subject, which have focused on mainly the development of bioreactors, the growth conditions that increase the efficiency of the process and the production of biomass with applicability in several areas. The biological mitigation of CO2 by microalgae has many advantages, including reductions in the concentration of an industrially sourced greenhouse gas and the energy or food obtained from the produced photosynthetic biomass. This versatility allows for the cultivation of economically useful biomass while reducing the environmental impacts of industrial facilities. In this context, this mini-review aims to discuss new technologies and strategies along with the main challenges and future prospects in the field and the ecological and economic impacts of CO2 biofixation by microalgae.Decq, L., Abatih, E., Van Keulen, H., Leyman, V., Cattersel, V., Steyaert, D., Van Binnebeke, E., Fremout, W., Saverwyns, S., Lynen, F., 2019. Nontargeted pattern recognition in the search for pyrolysis gas chromatography/mass spectrometry resin markers in historic lacquered objects. Analytical Chemistry 91, 7131-7138. differential expression analysis technology developed for linear modeling of gene expression data was used in combination with thermally assisted hydrolysis and methylation gas chromatography/mass spectrometry (THM-GC/MS) to support the analysis of lacquers and varnishes on historical objects. Exudates from tropical trees, such as Manila copal, sandarac, South American copal, and Congo copal, which were frequently used in finishing layers on decorative objects up to the early 20th century, were compared through this approach. Highly discriminating features indicate biomarkers that can help to identify copals in resinous lacquers. The approach allows new, more systematic ways for finding biomarkers in the analysis of lacquered objects of art and varnishes.Dehaghani, A.H.S., Daneshfar, R., 2019. How much would silica nanoparticles enhance the performance of low-salinity water flooding? Petroleum Science 16, 591-605. and low-salinity water (LSW) flooding are two novel techniques for enhanced oil recovery. Despite some efforts on investigating benefits of each method, the pros and cons of their combined application need to be evaluated. This work sheds light on performance of LSW augmented with nanoparticles through examining wettability alteration and the amount of incremental oil recovery during the displacement process. To this end, nanofluids were prepared by dispersing silica nanoparticles (0.1 wt%, 0.25 wt%, 0.5 wt% and 0.75 wt%) in 2, 10, 20 and 100 times diluted samples of Persian Gulf seawater. Contact angle measurements revealed a crucial role of temperature, where no wettability alteration occurred up to 80?°C. Also, an optimum wettability state (with contact angle 22°) was detected with a 20 times diluted sample of seawater augmented with 0.25 wt% silica nanoparticles. Also, extreme dilution (herein 100 times) will be of no significance. Throughout micromodel flooding, it was found that in an oil-wet condition, a combination of silica nanoparticles dispersed in 20 times diluted brine had the highest displacement efficiency compared to silica nanofluids prepared with deionized water. Finally, by comparing oil recoveries in both water- and oil-wet micromodels, it was concluded that nanoparticles could enhance applicability of LSW via strengthening wettability alteration toward a favorable state and improving the sweep efficiency.Deirieh, A., Chang, I.Y., Casey, B., Joester, D., Germaine, J.T., 2019. Impact of drying and effective stresses on the pore space and microstructure of mudrocks. Journal of Geophysical Research: Solid Earth 124, 4290-4304. evolution of the pore space of mudrocks induced by drying shrinkage and effective stresses is of importance to several areas of research. Drying is a prerequisite for most mudrock characterization methods, while effective stresses have a direct impact on mudrocks properties such as permeability, compressibility, and strength. Mercury porosimetry intrusion has been widely utilized to show that drying shrinkage and effective stresses lead to the collapse of large pores only (~?>?50?nm), while small pores (~?<?50?nm) remain unaffected. However, the validity of mercury porosimetry intrusion-derived pore size distributions is greatly doubted in the literature due to the fact that most pores in mudrocks are not directly accessible to the surrounding mercury. This study follows a different approach by utilizing a suite of methods including imaging by transmission electron microscopy and scanning electron microscopy at cryogenic temperature after high-pressure freezing (cryoSEM), and gravimetric porosity measurements to investigate the influence of volumetric changes on the pore space of mudrocks. Contrary to previously published results, we show that volumetric changes induced by drying and effective stresses lead to the collapse of pores of all sizes. Furthermore, we show that porosity measured from SEM images is dependent on SEM resolution and reveals only a fraction of the actual porosity. These results provide valuable insights used to interpret the results of characterization methods requiring drying and modeling of effective stress influence on the properties of mudrocks.Demopoulos, A.W.J., McClain-Counts, J.P., Bourque, J.R., Prouty, N.G., Smith, B.J., Brooke, S., Ross, S.W., Ruppel, C.D., 2019. Examination of Bathymodiolus childressi nutritional sources, isotopic niches, and food-web linkages at two seeps in the US Atlantic margin using stable isotope analysis and mixing models. Deep Sea Research Part I: Oceanographic Research Papers 148, 53-66. environments support distinct benthic communities capable of utilizing reduced chemical compounds for nutrition. Hundreds of methane seeps have been documented along the U.S. Atlantic margin (USAM), and detailed investigations at a few seeps have revealed distinct environments containing mussels, microbial mats, authigenic carbonates, and soft sediments. The dominant mussel, Bathymodiolus childressi, contains methanotrophic endosymbionts but is also capable of filter feeding, and stable isotope analysis (SIA) of mussel-shell periostracum suggests that these mussels are mixotrophic, assimilating multiple food resources. However, it is unknown whether mixotrophy is widespread or varies spatially and temporally. We used SIA (δ13C, δ15N, and δ34S) and an isotope mixing model (MixSIAR) to estimate resource contribution to B. childressi and characterize food webs at two seep sites (Baltimore Seep; 400?m and Norfolk Seep; 1500?m depths) along the USAM, and applied a linear mixed-effects model to explore the role of mussel population density and tissue type in influencing SIA variance. After controlling for location and temporal variation, isotopic variability was a function of proportion of live mussels present and tissue type. Isotopic differences were also spatially discrete, possibly reflecting variations in the underlying carbon source at the two sites. Low mussel δ13C values (～?63‰) are consistent with a dependence on microbial methane. However, MixSIAR results revealed mixotrophy for mussels at both sites, implying a reliance on a mixture of methane and phytoplankton-derived particulate organic material. The mixing model results also reveal population density-driven patterns, suggesting that resource use is a function of live mussel abundance. Mussel isotopes differed by tissue type, with gill having the lowest δ15N values relative to muscle and mantle tissues. Based on mass balance equations, up to 79% of the dissolved inorganic carbon (DIC) of the pore fluids within the anaerobic oxidation of the methane zone is derived from methane and available to fuel upper slope deep-sea communities, such as fishes (Dysommina rugosa and Symphurus nebulosus), echinoderms (Odontaster robustus, Echinus wallisi, and Gracilechinus affinis), and shrimp, (Alvinocaris markensis). The presence of these seeps thereby increases the overall trophic and community diversity of the USAM continental slope. Given the presence of hundreds of seeps within the region, primary production at seeps may serve as an important, yet unquantified, energy source to the USAM deep-sea environment.Deng, R., Chen, C., Shi, S., Wang, Y., 2019. Fluid phase simulation and evolution of a condensate gas reservoir in the Tazhong Uplift, Tarim Basin. Geofluids 2019, Article 8627698. fluid phase and the evolution of the condensate gas reservoir in the Lianglitage Formation (O3), Well ZG7-5, Tazhong Uplift, were studied by integrating the PVTsim and the PetroMod software. The fluid phase was successfully simulated, and the burial, temperature, pressure, and pressure coefficient histories were reconstructed. The evolution of the fluid phase and its properties (density, viscosity, and gas-oil ratio) under the ideal and gas washing conditions was also explored. The simulated pressure-temperature (P-T) phase diagram confirms that the reservoir fluid is in the condensate gas phase at present, with an order of critical point-cricondenbar-cricondentherm (CP-Pm-Tm). The temperature and pressure show an overall increasing trend considering the entirety of geological evolution. Under ideal conditions, fluid transition from coexisting gas and liquid phases to a single condensate gas phase occurred during the Late Cretaceous (80?Ma, T =135.7°C, and P = 58.19 MPa). The density and viscosity of the liquid phase decreased gradually while the density and viscosity of the gas phase and the solution gas-oil ratio increased during geological processes. With the consideration of gas washing, the critical phase transition time points for 100% and 50% gas washing fluid are 394?Ma, 383?Ma, 331?Ma, and 23?Ma, as well as 266?Ma and 23?Ma, respectively. The average liquid phase density, gas phase density, and liquid phase viscosity under 100% gas washing are larger than those under 50% gas washing before 23?Ma (Miocene), while the gas phase viscosity values are similar for both cases. This study visually suggests that the temperature and pressure histories, which are controlled by the burial history and heat flow evolution, and gas washing have significant impacts on the formation of the condensate gas reservoirs and evolution of the fluid phase and its features in the Tazhong Uplift.DeVries, T., Le Quéré, C., Andrews, O., Berthet, S., Hauck, J., Ilyina, T., Landschützer, P., Lenton, A., Lima, I.D., Nowicki, M., Schwinger, J., Séférian, R., 2019. Decadal trends in the ocean carbon sink. Proceedings of the National Academy of Sciences 116, 11646-11651. ocean and land absorb anthropogenic CO2 from industrial fossil-fuel emissions and land-use changes, helping to buffer climate change. Here, we compare decadal variability of ocean CO2 uptake using three independent methods and find that the ocean could be responsible for as much as 40% of the observed decadal variability of CO2 accumulation in the atmosphere. The remaining variability is due to variability in the accumulation of carbon in the terrestrial biosphere. Models capture these variations, but not as strongly as the observations, implying that CO2 uptake by the land and ocean is more sensitive to climate variability than currently thought. Models must capture this sensitivity to provide accurate climate predictions.Abstract: Measurements show large decadal variability in the rate of CO2 accumulation in the atmosphere that is not driven by CO2 emissions. The decade of the 1990s experienced enhanced carbon accumulation in the atmosphere relative to emissions, while in the 2000s, the atmospheric growth rate slowed, even though emissions grew rapidly. These variations are driven by natural sources and sinks of CO2 due to the ocean and the terrestrial biosphere. In this study, we compare three independent methods for estimating oceanic CO2 uptake and find that the ocean carbon sink could be responsible for up to 40% of the observed decadal variability in atmospheric CO2 accumulation. Data-based estimates of the ocean carbon sink from CO2 mapping methods and decadal ocean inverse models generally agree on the magnitude and sign of decadal variability in the ocean CO2 sink at both global and regional scales. Simulations with ocean biogeochemical models confirm that climate variability drove the observed decadal trends in ocean CO2 uptake, but also demonstrate that the sensitivity of ocean CO2 uptake to climate variability may be too weak in models. Furthermore, all estimates point toward coherent decadal variability in the oceanic and terrestrial CO2 sinks, and this variability is not well-matched by current global vegetation models. Reconciling these differences will help to constrain the sensitivity of oceanic and terrestrial CO2 uptake to climate variability and lead to improved climate projections and decadal climate predictions.Diasty, W.S.E., El Beialy, S.Y., El Attar, R.M., Khairy, A., Peters, K.E., Batten, D.J., 2019. Oil-source correlation in the West Esh El Mellaha, southwestern margin of the Gulf of Suez rift, Egypt. Journal of Petroleum Science and Engineering 180, 844-860. are several source rock units in the Gulf of Suez graben, but the Upper Cretaceous–Miocene sequence has probably produced most of the commercial hydrocarbons in this petroleum province. One hundred and nine shale, marl and marly shale samples collected from five wells in the West Esh El Mellaha Concession and surrounding area were studied by petrographic and organic geochemical methods to determine organic facies, depositional paleoenvironment, and thermal maturity. We also investigated the molecular and stable carbon isotopic compositions of nine oil samples to establish genetic relationships with the source rock samples.Pyrolysis data for samples from the Cenomanian–Santonian Matulla, Paleocene Esna, Eocene Thebes, Oligo-Miocene Nukhul and Lower–Middle Miocene Rudeis formations contain hydrogen-poor terrigenous Type-III to II/III kerogen. However, the Campanian–Maastrichtian Brown Limestone samples contain Type-II and Type-II/III kerogens indicating very good to excellent generation potential. The acyclic isoprenoids and normal alkane distributions and biomarkers in the source rock extracts indicate derivation from bacteria and algae, with varying contributions from land plants, deposited under suboxic to anoxic conditions in normal marine to higher salinity waters.The oil samples have high sulfur content and low to moderately high API gravity, typical of mature oils from pre-rift marine carbonate or calcareous shale lithofacies. Hierarchical cluster analysis (HCA) of 18 source-related biomarker ratios revealed four genetic families of oil samples. The two South Malak-1 oils (Family-4) are substantially different from the Rabeh E?8 and Rabeh E?10 (Family-1), Rabeh-1 and Hurghada-1 (Family-2) and Abu Marwa-1 and Wadi El Sahl-1 (Family-3) oil families, which are more closely related. Principal component analysis (PCA) and HCA based on the 18 ratios for the total data from extracts and oils indicate three groups. The South Malak-1 oils seem to be most closely related to the two Brown Limestone extracts. Group-1 oils appear to represent mixtures with one end member consisting of the South Malak-1 oils and the Brown Limestone source rock, but the other end member is not in the dataset.Ding, L., Rusinov, A., 2019. High-capacity electrostatic ion trap with mass resolving power boosted by high-order harmonics. Analytical Chemistry 91, 7595-7602. form of electrostatic ion trap mass analyzer, named the orbital frequency analyzer (OFA), has been developed. The ions in the analyzer are trapped around the middle plane and orbit around the central axis perpendicular to the middle plane with high-ellipticity and precessing trajectories. The orbital frequency of the ions in this device has been optimized to be independent of ions’ energy so that the image charge signal picked up by some of the field-forming circular/ring electrodes can be used to produce a mass spectrum after Fourier transform data processing. Spectra acquired by the OFA are rich of high-order harmonics, which offer higher mass resolving power than that for fundamental frequency components. The experiment shows that the resolving power is proportional to the harmonic order and exceeds 150 k for mass-to-charge ratio (m/z) of 526 Th and the transient length of 500 ms. Using high-order harmonics, an isotopic cluster of a heavy protein was resolved with a shorter transient length. The transient signals from different pick-up electrodes give different waveform shapes, and therefore, their harmonic peak distributions in a frequency spectrum are different, thus allowing the removal of unwanted harmonic peaks. The preliminary results also show a wide dynamic range of the analyzer.Dirksen, J.P., Hennekam, R., Geerken, E., Reichart, G.-J., 2019. A novel approach using time-depth distortions to assess multicentennial variability in deep-sea oxygen deficiency in the Eastern Mediterranean Sea during sapropel S5. Paleoceanography and Paleoclimatology 34, 774-786. millennial‐ to centennial‐scale climate variability for the Eemian—an interval with estimated sea surface temperatures ~0.5 °C warmer than “preindustrial”—requires records with high temporal resolution. Sapropel S5 sediments, deposited under anoxic conditions in the Eastern Mediterranean Sea, offer the rare opportunity to assess multicentennial climate variability during this time. Here we present high‐resolution S5 piston core data from the Nile delta region. Specifically, we focus on Ba/Ti, Br/Ti, and Mo/Ti, as they are proxies for paleo‐productivity, marine organic carbon, and sediment anoxia, respectively. A high correlation between our Ba/Ti values in core 64PE‐406‐E1 and well‐dated Ba records of nearby cores (LC21 and ODP967) was found. We, therefore, tuned our data to these cores obtaining an initial age model. A time‐frequency analyses indicated significant frequency content in the multicentennial band, although the frequency components drifted over time. Assuming spectral simplicity, we corrected for sedimentation rate changes on a multicentennial time scale. This novel approach grants a higher‐resolution age model. The resulting variability in sedimentation rate is similar to records of monsoon variability, indicating a possible link between sedimentation at the core location and low‐latitude monsoon variability, linked via the River Nile. Moreover, the periodicities found in the sapropel time series are similar to the frequency content of total solar irradiance and sunspot records known for the Holocene, at least at high frequencies (~50–150 years). Hence, our data suggest cyclic intrasapropel variability, at least during the deposition of sapropel S5, may be linked to solar cycles.Dominy, N.J., Calsbeek, R., 2019. A movie monster evolves, fed by fear. Science 364, 840-841. would be a mistake to dismiss Godzilla: King of the Monsters as mindless pap or escapist fantasy. It is the 35th film in a series stretching to 1954, easily the longest in world cinema history. This fact alone invites scholarly attention, for icons are always a reflection of their times, and few have enjoyed such longevity.The franchise began in direct response to “Castle Bravo,” a U.S. thermonuclear weapon test conducted on 1 March 1954 at Bikini Atoll in the Marshall Islands. The Bravo shot yielded 15 megatons of TNT—some 2.5 times more than expected—and produced dangerous levels of radioactive fallout for hundreds of miles. As a result, tainted tuna (and the idiom genshi maguro, “atomic tuna”) entered Japanese households, and 23 crewmembers of the Japanese tuna trawler Daigo Fukuryu Marū suffered acute radiation sickness.In Japan, the incident was viewed as yet another U.S. nuclear attack on civilians, and strident antinuclear peace movements sprouted across the country. It was in this fraught context, and amid substantial anti-American sentiment, that Godzilla was introduced in October 1954.The film, Gojira—a portmanteau of the Japanese words gorira (“gorilla”) and kujira (“whale”)—portrays Godzilla as both the victim and embodiment of American H-bomb testing. The tests destroyed the creature's deep-water ecosystem, and in turn, the creature destroys the urban infrastructure of Tokyo. The indiscriminate nature of this destruction at night is a stark and unmistakable reference to the “saturation bombing” of Japanese cities during the spring and summer of 1945 (1).In her landmark essay, “The imagination of disaster” (2), the cultural critic Susan Sontag attributes the success of Gojira to the aesthetics of this destruction, the peculiar beauty of Godzilla wreaking havoc and making a mess. Yet Godzilla has endured in our collective imaginations even as other oversized movie monsters from the 1950s have faded from memory.The cultural historian William Tsutsui (3) attributes this lasting success to the ever-shifting metaphor behind Godzilla and his proclivity for toppling buildings and destroying cities. What began as a pointed antinuclear fable has since evolved into a broader allegory for human folly and our reckless disregard for the natural environment.Tellingly, it is left to the films' dour paleobiologists—from Kyohei Yamane (Takashi Shimura) in Gojira to Emma Russell (Vera Farmiga) in the upcoming film—to deliver the bad news. “Our world is changing,” warns Russell in a trailer for King of the Monsters. “The mass extinction we feared has already begun, and we are the cause, we are the infection.” This elegy to pre-Anthropocene biodiversity speaks to the deep time perspective that informs our understanding of Godzilla, and it warrants further interrogation.THE “EVOLUTIONARY BIOLOGY” OF GODZILLA. is a topic of enduring interest among devotees, with numerous fan pages and forums dedicated to the subject. If we accept Godzilla as a ceratosaurid dinosaur (4) and Lazarus taxon (5)—a species thought to have gone extinct, only to be rediscovered later—then it represents a sensational example of evolutionary stasis, second only to coelacanths among vertebrates. Yet, the creature's recent morphological change has been dramatic.Godzilla has doubled in size since 1954. This rate of increase far exceeds that of ceratosaurids during the Jurassic, which was exceptional (6). The rate of change rules out genetic drift as the primary cause. It is more consistent with strong natural selection.The strength of this selective pressure can be estimated by using the breeder's equation, where the response to selection “R” is the product of the heritability (h2) of a given trait and the strength of selection. If we assume that h2 = 0.55 for body size—a reasonable estimate according to quantitative genetic studies of lizards (7, 8)—then the observed increase in Godzilla's body size would require a total strength of selection of 4.89 SD. To put this number in context, the median value of natural selection documented in a review of more than 2500 estimates in the wild was 0.16 (9). Godzilla, it seems, has been subject to a selective pressure 30 times greater than that of typical natural systems.All of this is silly conjecture, of course—Godzilla is a commercial enterprise, and the films are responding to market forces. Yet still we wondered, what agent of natural selection could act so swiftly and at such high intensity?SONTAG ARGUED that our taste for disaster films is constant and unchanging. On the contrary, we suggest that Godzilla is evolving in response to a spike in humanity's collective anxiety. Whether reacting to geopolitical instability, a perceived threat from terrorists, or simply fear of “the other,” many democracies are electing nationalist leaders, strengthening borders, and bolstering their military presence around the world.Making matters worse, a 2003 Pentagon report that forecasted the effects of climate change on water and food security predicted raised tensions and international conflict because of forced migrations (10). The idea that climate change is now the “mother of all security problems” (11) has scarcely dissipated since. Today, the U.S. Department of Defense views climate change as both an “accelerant of instability” and a “threat multiplier” (12). If U.S. military spending is used as a proxy for humanity's collective anxieties, it is perhaps unsurprising to see that there is a positive and robust correlation between the growth of Godzilla and that of the American military [coefficient of determination (r2) = 0.74].In 1965, Sontag asserted that a great enough disaster cancels all enmities and calls for collective action in the service of self-preservation. Indeed, Godzilla's near invincibility almost always eventually leads humanity to the realization that they must work together to defeat it (except, of course, when the creature becomes an unlikely ally, but that is another story). The monster is thus more than a metaphor; it is a fable with a lesson for our times.Now is the time for cooperation—across countries, across disciplines, and across party lines. It is our only hope of mitigating the dire existential threats we face today.Dong, H., Lu, X., Elzinga, E., 2019. Preface to recent research advances in biogeochemical cycles in China. Geochimica et Cosmochimica Acta 256, 1-5. play an important role in many biogeochemical cycles in various terrestrial and aquatic ecosystems (Rousk and Bengtson, 2014). Studies of microbially-driven geochemical cycles emphasize the mutual interactions between organisms and their environments, on both the modern and ancient Earth. Carbon, nitrogen, sulfur, metals, and metalloids undergo biogeochemical cycling between various oxidation and coordination states, and these processes control nutrient availability and transport as well as regulate microbial population size and activity. Microbially induced dissolution, precipitation and transformation of minerals can be recorded in the form of bio-signatures, which can be used to infer past microbial activity. The study of biogeochemical cycles enriches our understanding of how the spatial and temporal distributions of nutrients and other elements have evolved through time and their environmental consequences.In China, biogeochemical cycling has become a major research topic over the last two decades. For example, the first symposium on Microbe-Mineral Interaction and Geochemical Cycles was held in 2003, and since then microbial geochemistry in China has been studied in the context of Earth critical zone processes and mineral-microbe interactions. Of specific relevance is a China-US Geomicrobiology workshop that was held in Beijing in October 2008, which was co-sponsored by the National Natural Science Foundations of China (NNSFC) and the National Science Foundation (NSF) of the United States. Over 70 scientists from both countries attended the meeting. They reviewed past achievements and evaluated future opportunities and challenges in the field of life in extreme environments, including submarine sediments, natural gas hydrate, hot springs, deep earth, saline lakes, and acid mining drainage. The workshop greatly facilitated the collaboration between Chinese and American scholars in the field of Microbial Geochemistry and Geomicrobiology, and several international projects and programs were subsequently funded and/or created.In the past decade, such international workshops have been held on a regular basis and have served as a major platform to promote the field of Geomicrobiology, with each meeting focusing on a special topic, such as critical zone processes and microbial extracellular electron transfer (Shi et al., 2016). As a result of these workshops and increased funding in China, more scientists, especially post-doctoral researchers and graduate students, have been heavily engaged in research of biogeochemical cycles, some of whom have become widely recognized contributors in the field. One major outcome is that people with different backgrounds (in geochemistry, microbiology, mineralogy, bioinformatics, and environment science) have come together under the umbrella of biogeochemical cycling of elements, and these efforts have greatly improved our understanding of the microbial role in catalyzing geochemical reactions in a variety of environments.Most recently, the NNSFC launched one of its most ambitious “Major Research Plans”, namely the “Mechanisms of Microbially-driven Geochemical Cycles in the Hydrosphere” with the total amount of ?200 million in funding for the next 8?years. Co-funded by several directorates within the NNSFC including Bioscience, Earth Science, Chemistry, and Informatics, a major goal of this research initiative is to study biogeochemical cycles of life-essential elements including C, N, S, P and transition metals, and to advance our understanding of the biosphere-geosphere interaction and co-evolution. A secondary objective of this initiative is to protect water resources in the context of global climate change, and to develop a sustainable economy. At this critical junction of biogeochemical research, a special issue in Geochimica et Cosmochimica Acta not only showcases the past achievements in China but also further promotes international collaboration between China and the broader international geochemical community. Although specific topics vary in scope, the common thread connecting all these contributions is “Biogeochemical Cycles”. This special issue includes 9 papers on various topics including biogeochemical cycles of carbon, nitrogen, sulfur, biomineralization, microbial interactions, and environmental remediation of heavy metal contaminants.Douchi, D., Liang, F., Cano, M., Xiong, W., Wang, B., Maness, P.-C., Lindblad, P., Yu, J., 2019. Membrane-inlet mass spectrometry enables a quantitative understanding of inorganic carbon uptake flux and carbon concentrating mechanisms in metabolically engineered cyanobacteria. Frontiers in Microbiology 10, 1356. doi: 10.3389/fmicb.2019.01356. uses solar energy to drive inorganic carbon (Ci) uptake, fixation, and biomass formation. In cyanobacteria Ci uptake is assisted by carbon concentrating mechanisms (CCM), and CO2 fixation is catalyzed by RubisCO in Calvin-Benson-Bassham (CBB) cycle. Understanding the regulation that governs CCM and CBB cycle activities in natural and engineered strains requires methods and parameters that quantify these activities. Here we used membrane-inlet mass spectrometry (MIMS) to simultaneously quantify Ci concentrating and fixation processes in the cyanobacterium Synechocystis 6803. By comparing cultures acclimated to ambient air conditions to cultures transitioning to high Ci conditions, we show that acclimation to high Ci involves a concurrent decline of Ci uptake and fixation parameters. By varying light input, we show that both CCM and CBB reactions become energy limited under low light conditions. A strain over-expressing the gene for the CBB cycle enzyme fructose-biphosphate aldolase showed higher CCM and carbon fixation capabilities, suggesting a regulatory link between CBB metabolites and CCM capacity. While an engineered ethanol production pathway had no effect on CCM or carbon fixation parameters, additional fructose-biphosphate aldolase gene over-expression enhanced both activities while simultaneously increasing ethanol productivity. These observations show that MIMS can be a useful tool to study the extracellular Ci flux and how CBB metabolites regulate Ci uptake and fixation.Druffel, E.R.M., Griffin, S., Wang, N., Garcia, N.G., McNichol, A.P., Key, R.M., Walker, B.D., 2019. Dissolved organic radiocarbon in the central Pacific Ocean. Geophysical Research Letters 46, 5396-5403.: We report marine dissolved organic carbon (DOC) concentrations, and DOC ?14C and δ13C values in seawater collected from the central Pacific. Surface ?14C values are low in equatorial and polar regions where upwelling occurs and high in subtropical regions dominated by downwelling. A core feature of these data is that 14C aging of DOC (682 ± 86 14C years) and dissolved inorganic carbon (643 ± 40 14C years) in Antarctic Bottom Water between 54.0°S and 53.5°N are similar. These estimates of aging are minimum values due to mixing with deep waters. We also observe minimum ?14C values (?550‰ to ?570‰) between the depths of 2,000 and 3,500 m in the North Pacific, though the source of the low values cannot be determined at this time.Plain Language Summary: Most of the organic carbon in ocean water is in the dissolved form, like the broth in chicken soup. Even though it is believed that dissolved organic carbon (DOC) is formed during photosynthesis in the surface ocean using modern carbon, its radiocarbon age is surprisingly thousands of years old. We present the first transect of radiocarbon in DOC for the Pacific Ocean. We find that the radiocarbon age of DOC in the bottom waters decreases similarly to that found in the more abundant dissolved inorganic carbon. We conclude that DOC ages in the bottom water as it flows northward toward AlaskaDu, J., Zhao, Y., Wang, Q., Yu, Y., Xiao, H., Xie, X., Du, Y., Su, Z., 2019. Geochemical characteristics and resource potential analysis of Chang 7 organic-rich black shale in the Ordos Basin. Geological Magazine 156, 1131-1140. Ordos Basin is the largest and most important intracontinental sedimentary depression in China, and a significant amount of crude oil resources has developed within this Mesozoic formation. High-grade organic-rich shale is prevalent in the large-scale areas of the Chang 7 sedimentary stage and provides essential hydrocarbon resources for abundant oil enrichment in the Mesozoic. This research investigated the geochemical characteristics of Chang 7 shale using core samples and well logs and via laboratory tests. In addition, the microscopic components of the shale organic matter (OM), biological marker compounds, carbon isotopes, enrichment grade of trace elements, and elemental ratio were analysed systematically. Moreover, the aspects related to the shale OM source, sedimentary environment and resource potential were evaluated. Our results revealed that spherical alginate and calcium spherical alginate were predominant in the micropetrological components of the shale. Many biomarkers, including n-alkanes, steranes and terpanes, were detected in the gas chromatography – mass spectrometry spectra. An analysis of n-alkanes, regular sterane shapes (C21?/C22? and C26+C27/C28+C29), odd–even predominance index (OEP) and carbon preference index (CPI) values and carbon isotope distributions showed that OM was produced from aquatic organisms. The indicators of trace elements, such as Sr/Ba and V/V+Ni, combined with the biomarker compound in Pr/Ph and the gammacerane index showed the presence of a semi-deep – deep lake environment containing fresh–brackish water. In addition, the hydrocarbon conversion rate index and shale rock pyrolysis parameters revealed that Chang 7 has a high hydrocarbon generation ability and hydrocarbon expulsion efficiency.Du, X., Gu, M., Liu, Z., Zhao, Y., Sun, F., Wu, T., 2019. Enhanced shale gas recovery by the injections of CO2, N2, and CO2/N2 mixture gases. Energy & Fuels 33, 5091-5101. this paper, the experiments of enhanced shale gas recovery by the injections of CO2, N2, and CO2/N2 mixture gases were carried out in a fixed bed setup to investigate the influence of the types of displacing fluid on CH4 recovery and gas flow dynamics. Investigation results show that when taking CO2 or N2 as displacement agent, the Coats–Smith dispersion–capacitance model can give an excellent simulated result to the breakthrough curves of CO2 and N2. The injection of N2 leads to the shortest breakthrough time (tb) of injected gas and the lowest recovery of CH4 product (RCH4-product), while injecting CO2 into shale formations results in the longest tb of injected gas and the highest RCH4-product with a relatively sharp displacement front. The differences of dispersion coefficient (KD) and the flowing fraction of pore space (Fv) in the Coats–Smith dispersion–capacitance model are the underlying reasons for the distinct behaviors of CO2 injection and N2 injection. With increasing CO2 mole fraction in CO2/N2 mixture gases, RCH4-product rises. The injection of 50:50/N2:CO2 mixture gases exhibits the biggest enhancement degree of N2 concentration during the displacement process. The injection of a N2-rich mixture can significantly prolong tb of CO2 and help to sequestrate injected CO2 over a long-term. For the transport of CO2 in reservoir, Fv increases and KD and the mass transfer coefficient between mobile and immobile regions (Km) decreases with increasing N2 concentration in binary gas mixture, revealing that N2 can hinder the diffusion of CO2 into the micropore system to displace CH4. The fluctuation range of flow rate of injected gas (Finjected-gas) and the CO2 storage amount (Vstorage-CO2) enhance as CO2 mole fraction in mixture raises. In order to optimize RCH4-product, Vstorage-CO2, and CO2 sequestration time, the selection of displacing fluid and the ratio of CO2/N2 mixture gases should be taken into consideration.Duan, Y., Wu, Y., Yao, J., He, J., Zhang, X., Xu, L., Ma, L., 2019. Hydrogen isotopic composition of n-alkanes in sediments from freshwater Fuxian Lake in subtropical, China: Implications for the ecological environment. GEOCHEMICAL JOURNAL 53, 181-193. normal alkanes (n-alkanes) and their hydrogen isotopic (δD) values in sediments and aquatic and terrestrial plants from Fuxian Lake area of China were analyzed by gas chromatography-mass spectrometry (GC-MS) and GC-isotope ratio mass spectrometry (GC-IRMS), respectively. According to the δD values of the odd carbon-numbered n-alkanes, the sediment samples were divided into types I and II. The type I samples had a heavier hydrogen isotopic composition (–161 to –155‰ on average) compared to that of the type II samples (–208 to –173‰ on average). This isotopic difference is likely a result of their different biological sources. Similarity in the average n-alkane δD values in the sediments and plants indicated that C17 and C21 to C25 were mainly derived from aquatic submerged plants in the lake, C27 and C29 mainly from woody plants from the surrounding area, and C31 and C33 principally from a mixture of terrestrial herbaceous and woody plants. The results further demonstrate that n-alkane hydrogen isotopic composition can be used as an useful source indicator. The study also suggests that the ecological environment of the lake area is an important factor controlling the hydrogen isotopic composition of lake sedimentary n-alkanes. This study also found that the plots of the sedimentary n-alkane δD values and the average n-alkane chain length (ACL values), and the sedimentary n-alkane δD values and relative contribution of n-alkanes from woody and terrestrial herbaceous plants (Qw values) can distinguish sediment samples from the two different ecological environments of Fuxian Lake and Gahai Lake. Our results also show that the effect of the ecological environment on hydrogen isotopic composition of sedimentary n-alkanes should be considered when reconstructing paleoclimatic and hydrologic conditions using sedimentary n-alkane δD values.Dusny, C., Lohse, M., Reemtsma, T., Schmid, A., Lechtenfeld, O.J., 2019. Quantifying a biocatalytic product from a few living microbial cells using microfluidic cultivation coupled to FT-ICR-MS. Analytical Chemistry 91, 7012-7018. in vivo quantification of metabolic products from microbial single cells is one of the last grand challenges in (bio)analytical chemistry. To date, no label-free analytical concept exists that is powerful enough to detect or even quantify the minute amounts of secreted low molecular weight compounds produced by living and isolated single bacteria or yeast cells. Coupling microfluidic cultivation systems with ultrahigh resolution electrospray-ionization mass spectrometry with its exquisite sensitivity and specificity offers the prospect of single-cell product analysis and quantification, but has not been successfully implemented yet. We report an analytical framework that interfaces noninvasive microfluidic trapping and cultivation of a few bacterial single cells with the analysis of their catalytic products by Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). Cell trapping was performed with the microfluidic Envirostat platform for cultivating bacterial cells under continuous perfusion via negative dielectrophoresis (nDEP). A total of 1.5 μL of product-containing cell supernatant was sampled into microcapillaries using a dead volume-reduced world-to-chip interface. The samples were analyzed with a nanoESI ion source coupled to a FT-ICR-MS (limit of detection for lysine: 0.5 pg). As a biocatalytic model system, we analyzed few Corynebacterium glutamicum DM 1919 pSenLys cells that synthesized l-lysine from d-glucose. Secreted lysine was quantified from a few cells (down to 19). Single-cell specific lysine productivities were 2 and 10 fmol/cell/h. This demonstrates that coupling microfluidics and mass spectrometry (SIC-MS) now enables the quantification of catalytic products and extracellular metabolites from only a few living microbial cells.Dutta, A., Peoples, L.M., Gupta, A., Bartlett, D.H., Sar, P., 2019. Exploring the piezotolerant/piezophilic microbial community and genomic basis of piezotolerance within the deep subsurface Deccan traps. Extremophiles 23, 421-433. deep biosphere is often characterized by multiple extreme physical–chemical conditions, of which pressure is an important parameter that influences life but remains less studied. This geomicrobiology study was designed to understand the response of a subterranean microbial community of the Deccan traps to high-pressure conditions and to elucidate their genomic properties. Groundwater from a deep basaltic aquifer of the Deccan traps was used to ascertain the community response to 25 MPa and 50 MPa pressure following enrichment in high-salt and low-salt organic media. Quantitative PCR data indicated a decrease in bacterial and archaeal cell numbers with increasing pressure. 16S rRNA gene sequencing displayed substantial changes in the microbial community in which Acidovorax appeared to be the most dominant genus in the low-salt medium and Microbacteriaceae emerged as the major family in the high-salt medium under both pressure conditions. Genes present in metagenome-associated genomes which have previously been associated with piezotolerance include those related to nutrient uptake and extracytoplasmic stress (omp, rseC), protein folding and unfolding (dnaK, groEL and others), and DNA repair mechanisms (mutT, uvr and others). We hypothesize that these genes facilitate tolerance to high pressure by certain groups of microbes residing in subsurface Deccan traps.Edgcomb, V., 2019. Symbiotic magnetic motility. Nature Microbiology 4, 1066-1067. and genomic analyses reveal an intriguing symbiosis between eukaryotic protists and Deltaproteobacteria in anoxic marine sediments that involves division of labour and interspecies hydrogen transfer, and enables collective magnetotactic motility by the consortium.Elder, C.D., Schweiger, M., Lam, B., Crook, E.D., Xu, X., Walker, J., Walter Anthony, K.M., Czimczik, C.I., 2019. Seasonal sources of whole-lake CH4 and CO2 emissions from interior Alaskan thermokarst lakes. Journal of Geophysical Research: Biogeosciences 124, 1209-1229. lakes that form via ice‐rich permafrost thaw emit CH4 and CO2 to the atmosphere from previously frozen ancient permafrost sources. Despite this potential to positively feedback to climate change, lake carbon emission sources are not well understood on whole‐lake scales, complicating upscaling. In this study, we used observations of radiocarbon (14C) and stable carbon (13C) isotopes in the summer and winter dissolved CH4 and CO2 pools, ebullition‐CH4, and multiple independent mass balance approaches to characterize whole‐lake emission sources and apportion annual emission pathways. Observations focused on five lakes with variable thermokarst in interior Alaska. The 14C age of discrete ebullition‐CH4 seeps ranged from 395 ± 15 to 28,240 ± 150 YBP across all study lakes; however, dissolved 14CH4 was younger than 4,730 YBP. In the primary study lake, Goldstream L., the integrated whole‐lake 14C age of ebullition‐CH4, as determined by three different approaches, ranged from 3,290 to 6,740 YBP. A new dissolved‐14C‐CH4‐based approach to estimating ebullition 14C age and flux showed close agreement to previous ice‐bubble surveys and bubble‐trap flux estimates. Differences in open water versus ice‐covered dissolved gas concentrations and their 14C and 13C isotopes revealed the influence of winter ice trapping and forcing ebullition‐CH4 into the underlying water column, where it comprised 50% of the total dissolved CH4 pool by the end of winter. Across the study lakes, we found a relationship between the whole‐lake 14C age of dissolved CH4 and CO2 and the extent of active thermokarst, representing a positive feedback system that is sensitive to climate warming.Plain Language Summary: Lakes that form as a result of thawing permafrost (perennially frozen ground) can release new greenhouse gases from ancient carbon reservoirs, which further warm the atmosphere and promote more permafrost thaw. Existing observations of this phenomenon are insufficient to fully understand the impact that thaw lakes have on the current atmosphere, let alone the atmosphere of a future warmer world. In this study, we used a novel approach and made open water and ice‐covered measurements of rare carbon isotopes in methane and carbon dioxide dissolved in lake water and in bubbles emitted from sediments to determine the whole‐lake‐scale environmental drivers that regulate gas emissions from thawing permafrost. We learned that despite highly variable carbon source ages within single lakes, the presence of winter‐ice traps and mixes all lake sources proportionally into the dissolved gas pool during winter and allows the stronger greenhouse gas, methane, to be oxidized to carbon dioxide before emission to the atmosphere in spring. This study also confirmed that higher levels of permafrost thaw within a lake are related to older carbon sources fueling whole‐lake gas emissions, which, if consistent with lakes across northern permafrost regions, is evidence of a potential positive feedback to further climate warming.Eley, Y.L., Thompson, W., Greene, S.E., Mandel, I., Edgar, K., Bendle, J.A., Dunkley Jones, T., 2019. OPTiMAL: A new machine learning approach for GDGT-based palaeothermometry. Climate of the Past Discussions 2019, 1-39. the modern oceans, the relative abundances of Glycerol dialkyl glycerol tetraether (GDGTs) compounds produced by marine archaeal communities show a significant dependence on the local sea surface temperature at the site of formation. When preserved in ancient marine sediments, the measured abundances of these fossil lipid biomarkers thus have the potential to provide a geological record of long-term variability in planetary surface temperatures. Several empirical calibrations have been made between observed GDGT relative abundances in late Holocene core top sediments and modern upper ocean temperatures. These calibrations form the basis of the widely used TEX86 palaeothermometer. There are, however, two outstanding problems with this approach, first the appropriate assignment of uncertainty to estimates of ancient sea surface temperatures based on the relationship of the ancient GDGT assemblage to the modern calibration data set; and second, the problem of making temperature estimates beyond the range of the modern empirical calibrations (>?30??C). Here we apply modern machine-learning tools, including Gaussian Process Emulators and forward modelling, to develop a new mathematical approach we call OPTiMAL (Optimised Palaeothermometry from Tetraethers via MAchine Learning) to improve temperature estimation and the representation of uncertainty based on the relationship between ancient GDGT assemblage data and the structure of the modern calibration data set. We reduce the root mean square uncertainty on temperature predictions (validated using the modern data set) from ~?±6??C using TEX86 based estimators to ±3.6??C using Gaussian Process estimators for temperatures below 30??C. We also provide a new but simple quantitative measure of the distance between an ancient GDGT assemblage and the nearest neighbour within the modern calibration dataset, as a test for significant non-analogue behaviour. Finally, we advocate against the use of temperature estimates beyond the range of the modern empirical calibration dataset, given the absence – to date – of a robust predictive biological model or extensive and reproducible mesocosm experimental data in this elevated temperature range.Elwegaa, K., Emadi, H., Soliman, M., Gamadi, T., Elsharafi, M., 2019. Improving oil recovery from shale oil reservoirs using cyclic cold carbon dioxide injection – An experimental study. Fuel 254, Article 115586. this study, effects of injecting gas temperature and pressure on oil recovery factor (RF) of shale oil reservoirs were investigated by implementing cyclic cold carbon dioxide (CO2) injection on Eagle Ford Shale Oil core samples. Also, effects of injecting gas temperature on porosity, permeability, and brittleness indices of these core samples were assessed.An experimental setup was designed and built to implement CO2 cyclic gas injection and thermal shock tests. Four Eagle Ford Shale outcrop core samples were used in this study. The saturated samples were heated to 180°F and carbon dioxide at various combinations of pressure (1000 psi, 2000 psi, 3000 psi, and 4000 psi) and temperature (?15°F, 0°F, 32°F, and 74°F) was injected into them. Oil RF for each experiment was measured after five days of production period. Additionally, porosity, permeability and ultrasonic velocity of each core sample were measured both prior to and after conducting the experiment.The results indicate that injecting CO2 at low temperature results in higher oil recovery factor (up to 7%) than injecting carbon dioxide at ambient temperature. It was also observed that injecting cold CO2 enhanced both porosities and permeabilities of the core samples. The porosities and the permeabilities of the core samples enhanced by up to 3.5% and 8.8%, respectively. Also, a noticeable reduction (between 100?ft/s and 400?ft/s) in P-wave velocity was observed after injecting the cold gas into the core samples, which is an indication of creating induced fractures. The results also revealed that injecting the cold gas increased the brittleness indices of the core samples by up to 8. Hence, cyclic cold carbon dioxide injection could be potentially implemented in the shale oil fields to improve the efficiency of the current industry practice of cyclic gas injection technique.Emmings, J.F., Hennissen, J.A.I., Stephenson, M.H., Poulton, S.W., Vane, C.H., Davies, S.J., Leng, M.J., Lamb, A., Moss-Hayes, V., 2019. Controls on amorphous organic matter type and sulphurization in a Mississippian black shale. Review of Palaeobotany and Palynology 268, 1-18. proxies (Fe speciation, trace element and δ34Spy) integrated with sedimentological and palynological observations link the distribution and type of particulate organic matter (OM) preserved to hydrocarbon source rock potential. In the Mississippian Bowland Shale Formation (Lancashire, UK), particulate OM is dominated by “heterogeneous” amorphous OM (AOM), primarily “sharp-edged, pellet-like” (AOMpel) and “heterogeneous, granular” (AOMgr) types. AOMpel is abundant in muds deposited under anoxic and moderately to highly sulphidic conditions and most likely represents the fecal minipellets of zooplankton and/or pellets of macro-zooplankters. We recognize two intervals, “A” and “B,” which exhibit Sorg/TOC?>?0.04, suggesting a bulk Type II-S kerogen composition. The Interval A palynofacies is typified by pyritized AOMpel (AOMpyr) particles that contain high-relief organic spheres surrounding individual pyrite framboids, within each AOMpyr particle. These textures are interpreted as sulphurized OM local to pyrite framboids (Sorg-PF). Sorg-PF is rarely observed in Interval B, and absent in all other samples. Redox oscillation between ferruginous and euxinic conditions during early diagenesis of Interval A likely promoted S cycling in microenvironments surrounding pyrite framboids, which generated reactive S species and reactive OM required for sulphurization. Early diagenetic redox oscillation processes were apparently triggered by relative sea level fall, associated with an increased supply of FeHR from adjacent shelves into the basin. Interval B represents deposition during the late stages of basin infill and transition from anoxic to (sub)oxic bottom waters, where AOMpel is replaced by AOMgr as the dominant type of AOM. A large particle diameter at the limit of the mesh size (500?μm), sheet-like, fragmented character, and presence of candidate organic sheaths suggests AOMgr at least partially represent fragments of benthic microbial mats, probably as sulphide-oxidizers. A ternary plot of AOMpel?+?AOMpyr versus AOMgr versus spores?+?phytoclasts links the observed palynofacies to bottom and pore water redox conditions, water column productivity and proximity to fluvial (deltaic) supply of spores and phytoclasts. These variables were moderated by changing basin accommodation, driven primarily by eustatic sea level fluctuation. A sequence-stratigraphic control on AOM type and sulphurization is important for understanding the link between source rock heterogeneity and the timing of hydrocarbon generation and expulsion from this source rock.Emslie, S.D., Alderman, A., McKenzie, A., Brasso, R., Taylor, A.R., Molina Moreno, M., Cambra-Moo, O., González Martín, A., Silva, A.M., Valera, A., García Sanjuán, L., Vijande Vila, E., 2019. Mercury in archaeological human bone: biogenic or diagenetic? Journal of Archaeological Science 108, 104969. investigated mercury (Hg) in human bone from archaeological sites in the Iberian Peninsula where the cultural use of cinnabar (HgS) as a pigment, offering or preservative in burial practices has been documented from the 4th to 2nd millennia cal B.C. (Late Neolithic, Copper Age and Bronze Age). Previous analyses have shown high levels of total mercury (THg) in human bone at numerous Neolithic and Chalcolithic sites in this region, but the question remains if this mercury entered the bones via diagenetic processes in the soil, especially where cinnabar powder and paint was found associated with the burials, or if it entered the bone via biogenic pathways from exposure to mercury from using cinnabar in life. We analyzed the humerus, femur, and tibia from a total of 30 individual burials from four Neolithic to Bronze Age sites in Iberia and found low to high values of THg in these bones, with the humerus showing significantly more THg concentrations than other skeletal elements when the THg was greater than 1?ppm. This pattern of Hg deposition in skeletal material from different sites and ages strongly suggests a biogenic origin for the mercury. In addition, absence of detectable Hg in bones with high to low values of THg using SEM EDS analysis further discounts diagenetic intrusion of Hg or cinnabar particles into the bone from the soil. It is likely that greater stress and bone remodeling rates from use of heavy tools and other activities in life are responsible for higher THg in the humerus than other skeletal elements, but additional research is needed to verify this.Erikstad, H.-A., Ceballos, R.M., Smestad, N.B., Birkeland, N.-K., 2019. Global biogeographic distribution patterns of thermoacidophilic Verrucomicrobia methanotrophs suggest allopatric evolution. Frontiers in Microbiology 10, 1129. doi: 10.3389/fmicb.2019.01129. methane-oxidizing Verrucomicrobia of candidate genus Methylacidiphilum represent a bacterial taxon adapted to highly acidic (pH 1-4) and moderate temperature (~65°C) methane-containing geothermal environments. Their apparent ubiquitous presence in acidic terrestrial volcanic areas makes them ideal model organisms to study prokaryotic biogeography. Three Methylacidiphilum species isolated from distantly-separated geothermal regions in Russia, New Zealand, and Italy were previously described. We have explored the intra-taxon phylogenetic patterns of these organisms based on comparative genome analyses and phenotypic comparisons with six new Verrucomicrobia methanotroph isolates from other globally-separated acidic geothermal locations. Comparison of rRNA and particulate methane monooxygenase (pmoCAB) operon sequences indicates a close phylogenetic relationship among the new isolates as well as with the previously characterized strains. All share similar cell morphology including the presence of extensive intracellular inclusion bodies and lack of intracellular membrane systems, which is typical for proteobacterial methanotrophs. However, genome sequence comparisons and concatenated MLST-based phylogenetic analyses separate the new isolates into three distinct species. Three recently processed isolates from the Azores (each from geographically-separate hot springs within the region) and a single isolate from Iceland are highly similar, sharing more than 88% in silico genome homology with each other as well as with the previous isolate, Methylacidiphilum fumariolicum strain SolV, from Italy. This appears to constitute a distinct European/Atlantic clade. However, two of the new isolates - one from the Yellowstone National Park (USA) and another sampled from The Philippines - constitute separate and novel Methylacidiphilum species. There is no clear correlation between fatty acid profiles and geographic distance between origins, or any phylogenetic relationship. Serological analysis using antiserum raised against M. kamchatkense strain Kam1 revealed large differences in the degree of cross-reactivity with no correlation with other factors. However, the genetic distance between the strains does correlate to the distance between their geographic origins and suggests a global biogeographic pattern shaped by an isolation-by-distance mechanism. These results further confirm terrestrial geothermal springs as isolated islands featuring allopatric prokaryotic speciation.Eshelman, E.J., Malaska, M.J., Manatt, K.S., Doloboff, I.J., Wanger, G., Willis, M.C., Abbey, W.J., Beegle, L.W., Priscu, J.C., Bhartia, R., 2019. WATSON: In situ organic detection in subsurface ice using deep-UV fluorescence spectroscopy. Astrobiology 19, 771-784. icy environments have been found to preserve organic material and contain habitable niches for microbial life. The cryosphere of other planetary bodies may therefore also serve as an accessible location to search for signs of life. The Wireline Analysis Tool for the Subsurface Observation of Northern ice sheets (WATSON) is a compact deep-UV fluorescence spectrometer for nondestructive ice borehole analysis and spatial mapping of organics and microbes, intended to address the heterogeneity and low bulk densities of organics and microbial cells in ice. WATSON can be either operated standalone or integrated into a wireline drilling system. We present an overview of the WATSON instrument and results from laboratory experiments intended to determine (i) the sensitivity of WATSON to organic material in a water ice matrix and (ii) the ability to detect organic material under various thicknesses of ice. The results of these experiments show that in bubbled ice the instrument has a depth of penetration of 10?mm and a detection limit of fewer than 300 cells. WATSON incorporates a scanning system that can map the distribution of organics and microbes over a 75 by 25?mm area. WATSON demonstrates a sensitive fluorescence mapping technique for organic and microbial detection in icy environments including terrestrial glaciers and ice sheets, and planetary surfaces including Europa, Enceladus, or the martian polar caps.Feng, X., D'Andrea, W.J., Zhao, C., Xin, S., Zhang, C., Liu, W., 2019. Evaluation of leaf wax δD and soil brGDGTs as tools for paleoaltimetry on the southeastern Tibetan Plateau. Chemical Geology 523, 95-106. orogenic history of the Tibetan Plateau (TP) and surrounding mountain ranges continues to be a major source of disagreement among geologists, particularly concerning the uplift models for the Cenozoic evolution of the TP and estimates for when the highest and largest plateau on Earth reached its current elevation. Quantitative reconstructions of past elevation from geologic samples are necessary to document the uplift history of TP and examine the interactions between tectonic-relief and climate over geological time-scales. Several studies establishing lipid biomarker-based paleoaltimetry based on leaf wax δD values and brGDGTs have been reported in recent years for the TP and surrounding regions, but have yet to be synthesized into a regional framework for paleoelevation determination and uncertainty analysis. Here we report new leaf wax δD and brGDGTs data developed from surface soil samples along an elevation transect spanning ~1250–3900?m.a.s.l in the Hengduan Mountains on the southeastern edge of the TP. We find that the abundance-weighted mean leaf wax δD (n-C27, n-C29 and n-C31) values (δDwax) lapse rates determined for the Hengduan Mountains and for five other nearby study locations are statistically indistinguishable, and can be combined to provide a regional δDwax lapse rate of ?1.97?±?0.04‰ (1σ)/100?m for use in regional paleoelevation studies across the southeastern TP. We also find a strong correlation (R2?=?0.71) between brGDGTs and elevation-dependent mean annual air temperature, which contributes to a number of studies in the region that support the use of fossil brGDGTs as a paleoelevation proxy. Our results reveal that δDwax and brGDGTs for the Hengduan Mountains provide similar empirical uncertainty in paleoelevation reconstruction, with standard errors of elevation estimation (SE) of ±483?m (±1σ) and?±?394?m (±1σ), respectively. We propose a paleoaltimetric approach that combines δDwax and brGDGT data, in order to derive paleoelevation estimates with lower uncertainties. In the Hengduan Mountains data set, the approach yields a SE (±286?m; ±1σ) that is 27–40% lower than when δDwax values and brGDGTs are applied separately.Fennell, J., Arciszewski, T.J., 2019. Current knowledge of seepage from oil sands tailings ponds and its environmental influence in northeastern Alberta. Science of The Total Environment 686, 968-985. of oil sand process-affected waters (OSPW) from tailings ponds into surface waters is a common concern in the minable oil sands region of northeast Alberta. Research on seepage has been extensive, but few comprehensive treatments evaluating all aspects relevant to the phenomenon are available. In this work, the current information relevant for understanding the state of seepage from tailings ponds was reviewed. The information suggests the infiltration of OSPW into groundwater occurs near some ponds. OSPW may also be present in sediments beneath the Athabasca River adjacent to one pond, but there are no clear observations of OSPW in the river water. Similarly, most water samples from tributaries also show no evidence of OSPW, but these observations are limited by the lack of systematic, systemic, and repeated surveys, missing baseline data, standard analytical approaches, and reference materials. Waters naturally influenced by bitumen, discharge of saline groundwaters, and dilution also potentially affect the consolidation of information and certainty of any conclusions. Despite these challenges, some data suggest OSPW may be present in two tributaries of the Athabasca River adjacent to tailings ponds: McLean Creek and Lower Beaver River. Irrespective of the possible source(s), constituents of OSPW often affect organisms exposed in laboratories, but research in all but one study suggests the concentrations of organics in the surface water bodies assessed are below the standard toxicological effect thresholds for these compounds. In contrast, many samples of groundwater, irrespective of source, likely affect biota. Biomonitoring of surface waters suggests generic responses to stressors, but the influence of natural phenomena and occasionally nutrient enrichment are often suggested by data. In summary, valuable research has been done on seepage. The data suggest infiltration into groundwater is common, seepage into surface waters is not, and anthropogenic biological impacts are not likely.Fiebig, J., Bajnai, D., L?ffler, N., Methner, K., Krsnik, E., Mulch, A., Hofmann, S., 2019. Combined high-precision ?48 and ?47 analysis of carbonates. Chemical Geology 522, 186-191. analysis of the excess abundance (relative to the stochastic distribution) of mass 48 isotopologues in CO2 evolved from acid digestion of carbonates (?48) has not been possible until recently due to the relatively low natural abundance of 18O. Here we show that the 253 Plus? gas source mass spectrometer equipped with Faraday cups and 1013 Ω resistors can perform combined ?47 and ?48 analyses on carbonates with external reproducibilities (1SD) of 0.010 ‰ and 0.030 ‰, respectively.~10 mg aliquots of five carbonate reference materials (ETH 1, ETH 2, ETH 3, ETH 4, and Carrara) are digested with phosphoric acid at 90 °C using a common acid bath. The evolved CO2 is purified using an automated gas preparation system (including cryotraps and a GC) and analyzed for its ?47 and ?48 compositions using the dual inlet system of a 253 Plus? gas source mass spectrometer. Raw ?47 and ?48 values are finally normalized to the Carbon Dioxide Equilibrium Scale (CDES).In ?47, CDES 90°C vs. ?48, CDES 90°C space, calcite reference materials Carrara, ETH 3 and ETH 4 agree with the equilibrium curve for calcite after adding semi-empirically determined 90?°C acid fractionation factors of 0.196 ‰ (for ?47) and 0.136 ‰ (for ?48) to theoretical ?63 and ?64 data. Agreement between measured and theoretically expected ?48, CDES 90°C highlights the accuracy of our high-precision clumped isotope analytical setup. Combined analysis of the abundances of mass 47 and mass 48 isotopologues in CO2 evolved from acid digestion of natural carbonates has excellent potential for the determination of accurate and highly precise paleotemperatures as well as for the identification of rate-limiting kinetic processes involved in biomineralization. A formation temperature of 15(±2) °C is obtained on the 95 % confidence level for the Upper Cretaceous chalk sample ETH 3.Field, M.C., 2019. The kinetochore and the origin of eukaryotic chromosome segregation. Proceedings of the National Academy of Sciences 116, 12596-12598. organisms must faithfully segregate their DNA during cell division to safeguard complete inheritance of the genome. In eukaryotes, mechanisms of cell and nuclear division are highly variable, and while these usually involve the use of a mitotic microtubule-based spindle and a kinetochore (KT) that physically links the chromatin and spindle, beyond this, the arrangement and manner in which mitosis is completed can adopt one of a vast number of disparate pathways (1, 2). Each of these pathways requires the participation of multiple cellular functions, including the nucleoskeleton, centromeres (chromatin-marked KT assembly sites), the nuclear envelope, and the nuclear pore complex (NPC), to achieve the ultimate goal of partitioning a complete genome to both daughter cells. Because the eukaryotic genome is contained on multiple DNA elements and is frequently diploid makes this task even more challenging. In PNAS, Tromer et al. (3) revisit the origin of a key component, the KT, using highly sensitive sequence and architectural search methods to provide a possible evolutionary history.Variability in mitotic mechanisms stretches back to our prokaryotic ancestors, where chromosomes exhibit distinct physical arrangements within cells from different bacterial linages and which then necessitates an accommodating organization (4, 5). The parABS system, which is used for segregation of chromosomes in a large number of bacterial lineages, including Caulobacter crescentus, is far from universal, however (6, 7), and is not used by Escherichia coli, for example, where the mukBEF SMC complex operates (8, 9). There is considerable interest into how these prokaryotic and eukaryotic mechanisms evolved, including their origins and the relationships between these disparate solutions for essentially the same problem. For eukaryotes, the configuration of the system in the last eukaryotic common ancestor (LECA) is an important facet of reconstructions of eukaryote evolutionary history (Fig. 1A). Most importantly, there is no evidence for common descent between known bacterial chromosome segregation systems and the eukaryotic KT, suggesting an evolutionary discontinuity in the inheritance of a fundamental and universal cellular process. The LECA stands as the root for most paneukaryotic phylogenetic reconstructions and represents a conceptual organism or, as some have suggested, population (10, 11). The LECA existed some 1.5 billion years ago, and most reconstructions suggest a surprisingly complex cellular state and plan that is essentially modern (12). Indeed, LECA compartmental complexity exceeds many extant organisms, including Saccharomyces cerevisiae. Regardless, the LECA cell(s) possessed a set of structures that indicate a nucleus with pretty much the same organization as in modern eukaryotes and which needed to faithfully separate chromosomes (13).The KT consists of at least 3 subcomplexes: several variant histones and distinct inner and outer KT complexes (Fig. 1B). The sheer complexity of the KT, the widely disparate architectures of known KT components, and the components’ apparent interdependence have made understanding how the KT arose difficult to reconstruct, and stands in contrast to other cellular structures of similar complexity, such as the NPC and intraflagellar transport (IFT) systems in which a considerable number of subunits have obvious shared architecture. The NPC, IFT, and other systems are united in possessing multiple β?α coatomer subunits (13, 14) and have provided a framework for reconstructing the evolution of multiple endomembrane systems. In brief, these models have reached a consensus that much eukaryotic cellular architecture arose by the paralogous expansion of β?α coatomer family proteins (together with several other protein families), which diversified and led to the establishment of the NPC and IFT systems as well as antero- and retrograde vesicular transport. Critically, all of this occurred during the transition between the first eukaryotic common ancestor (FECA) and the LECA, and was complete before the LECA. Moreover, some of these factors, such as guanine nucleotide-binding proteins and proteins ancestral to the β?α architecture, may have been present in the Asgard archaea (15), considered by some as the nearest prokaryotic ancestors to the eukaryotic lineage. While the status of Asgardian genomes, which are based solely on metagenomic analysis at present, has become somewhat controversial of late, such a pathway is probably the most parsimonious interpretation of the origins of the FECA (16?–18). Regardless of these events, several cellular systems, including the KT, do not obviously fit within this schema and, consequently, KT origins have been cryptic.In PNAS, Tromer et al. (3) suggest a complex mosaic origin for the KT and posit connections with several additional cellular systems. The authors used methods that are highly sensitive for the detection of even distant relationships and which included identification of possible common protein folds that are frequently more conserved than sequence alone. Perhaps most significant is that these data suggest a mechanism by which the KT became so complex. The authors also establish that a modern KT was present in the LECA and thus must have arisen during the transition between the FECA and the LECA (Fig. 1C).The KT reconstruction in Tromer et al. (3) leads to a complex containing at least 52 distinct proteins. The KT contains a cohort of proteins with relationships to other eukaryotic protein families; for example, the RWD-like family is related to E2 ubiquitin ligases as well as 5 variant histones that provide the link between the KT and chromatin. For the former family, there are potential links to the mediator complex, and several subdomains may also have a structural relationship with coatomer and TATA box-binding proteins (albeit rather limited in scope), providing links to vesicular transport and transcriptional systems. Further, there are a number of HORMA domain proteins, including the Mad2 and p31 KT components; significantly, the HORMA domain is also present in the Archaea, not only providing a prokaryotic component to the KT but also, as the HORMA KT components are monophyletic, indicating expansion of a single archaeal HORMA domain-containing gene that gives rise to the entire KT HORMA complement. Such paralog expansions are also clear for the RWD proteins and histones and provide a mechanism for generating over half of the LECA KT protein complement. One further family of proteins, the calponin homology proteins Ndc80 and Nuf2 (important in microtubule interactions), are likely eukaryotic specific, while a final group of proteins, including CenpK, CenpH, and Shugosin, have no obvious homology to other sequences in the databases (although, of course, they must have some ancestor and are perhaps also as likely to have simply diverged beyond the point of recognition). Overall, Tromer et al. (3) suggest that the KT has been assembled from a mixture of ancient, prokaryotic progenitors, with possible components from other nascent eukaryotic cellular systems, together with the presence of highly divergent or unique proteins, and is all tied together and integrated by the inevitable cohort of kinases, including the central mitotic regulator Aurora kinase.A complement of 52 proteins means that, in terms of subunit diversity, the KT rivals the NPC and IFT systems, which also achieved their present state in the FECA-to-LECA transition and likely derived, at least in part, from Archaeal ancestral genes. Hence, the KT and other cellular systems conform to a similar overall mechanism of evolutionary origin, with paralog expansions and neofunctionalization providing much of the increased complexity. The KT does stand out from these other complexes in the heterogeneity of the architectures of its components and thus their origins. This is an important advance and provides a framework for further investigation, but it should be noted that KT diversity may well exceed the KT diversity Tromer et al. (3) report. Specifically, the searches are based around animal and fungal sequences such that any lineage-specific components that are not present in these taxa cannot have been sampled, and the overall architecture of the KT in many lineages remains unknown. For example, the recent demonstration of divergent structures for the NPCs among mammals, fungi, and plants are based around an altered copy number of components, but not changes in the complement of components themselves. This mode of highly significant change in architecture is completely silent to in silico analysis. Further, we have a highly diverse example of KT structure in the trypanosomes, a group of protozoa that likely branched from the main eukaryotic lineage quite rapidly after the LECA (19?–21). Here, the entire KT bears little or no obvious resemblance to the LECA structure Tromer et al. (3) describe, which begs the question of how the LECA KT was replaced by the trypanosome form. More surprises certainly await in uncovering the origins and modifications of KTs—an exciting challenge to understanding fundamental mechanisms of genome inheritance and origins of the eukaryotic cell.References1. S. Sazer, M. Lynch, D. Needleman, Deciphering the evolutionary history of open and closed mitosis. Curr. Biol. 24, R1099–R1103 (2014).2. S. Suresh, S. A. Osmani, Poring over chromosomes: Mitotic nuclear pore complex segregation. Curr. Opin. Cell Biol. 58, 42–49 (2019).3.. E. C. Tromer, J. J. E. van Hooff, G. J. P. L. Kops, B. Snel, Mosaic origin of the eukaryotic kinetochore. Proc. Natl. Acad. Sci. U.S.A., doi:10.1073/pnas.1821945116.4. S. Nolivos, D. Sherratt, The bacterial chromosome: Architecture and action of bacterial SMC and SMC-like complexes. FEMS Microbiol. Rev. 38, 380–392 (2014).5. G. T. Marczynski, K. Petit, P. Patel, Crosstalk regulation between bacterial chromosome replication and chromosome partitioning. Front. Microbiol. 10, 279 (2019).6. N. Kleckner et al., The bacterial nucleoid: Nature, dynamics and sister segregation. Curr. Opin. Microbiol. 22, 127–137 (2014).7. C. W. Shebelut, J. M. Guberman, S. van Teeffelen, A. A. Yakhnina, Z. Gitai, Caulobacter chromosome segregation is an ordered multistep process. Proc. Natl. Acad. Sci. U.S.A. 107, 14194–14198 (2010).8. V. V. Rybenkov, V. Herrera, Z. M. Petrushenko, H. Zhao, MukBEF, a chromosomal organizer. J. Mol. Microbiol. Biotechnol. 24, 371–383 (2014).9. S. Nolivos et al., MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation. Nat. Commun. 7, 10466 (2016).r10. J. B. Dacks et al., The changing view of eukaryogenesis—fossils, cells, lineages and how they all come together. J. Cell Sci. 129, 3695–3703 (2016).11. M. A. O’Malley, M. M. Leger, J. G. Wideman, I. Ruiz-Trillo, Concepts of the last eukaryotic common ancestor. Nat. Ecol. Evol. 3, 338–344 (2019).12. V. L. Koumandou et al., Molecular paleontology and complexity in the last eukaryotic common ancestor. Crit. Rev. Biochem. Mol. Biol. 48, 373–396 (2013).13. M. P. Rout, M. C. Field, The evolution of organellar coat complexes and organization of the eukaryotic cell. Annu. Rev. Biochem. 86, 637–657 (2017).14. D. Devos et al., Components of coated vesicles and nuclear pore complexes share a common molecular architecture. PLoS Biol. 2, e380 (2004).15. K. Zaremba-Niedzwiedzka et al., Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).16. G. P. Fournier, A. M. Poole, A briefly argued case that Asgard archaea are part of the eukaryote tree. Front. Microbiol. 9, 1896 (2018).17. V. Da Cunha, M. Gaia, D. Gadelle, A. Nasir, P. Forterre, Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genet. 13, e1006810 (2017).18. V. Da Cunha, M. Gaia, A. Nasir, P. Forterre, Asgard archaea do not close the debate about the universal tree of life topology. PLoS Genet. 14, e1007215 (2018).19. B. Akiyoshi, K. Gull, Discovery of unconventional kinetochores in kinetoplastids. Cell 156, 1247–1258 (2014).20. S. D’Archivio, B. Wickstead, Trypanosome outer kinetochore proteins suggest conservation of chromosome segregation machinery across eukaryotes. J. Cell Biol. 216, 379–391 (2017).21. O. O. Nerusheva, B. Akiyoshi, Divergent polo box domains underpin the unique kinetoplastid kinetochore. Open Biol. 6, 150206 (2016).Figueirido, B., Palmqvist, P., Pérez-Claros, J.A., Janis, C.M., 2019. Sixty-six million years along the road of mammalian ecomorphological specialization. Proceedings of the National Academy of Sciences 116, 12698-12703.: The six “evolutionary faunas” of large mammal taxonomic diversity described for the North American Cenozoic have a nonrandom ecomorphological spectrum and show a long-term trend toward greater ecological specialization over the past 66 My. We show here that each successive fauna was characterized by a change toward more specialized ecotypes; these changes were correlated with vegetation shifts caused by major climatic changes, which may have promoted the appearance of new ecological opportunities and morphological innovations.Abstract: The fossil record of the large terrestrial mammals of the North American Cenozoic has previously been quantitatively summarized in six sequential episodes of faunal associations—“evolutionary faunas”—that correspond well with previously proposed qualitative “Chronofaunas.” Here, we investigate the ecological spectrum of these faunas by classifying their major taxonomic components into discrete ecomorphological categories of diet, locomotion, and body size. To specifically address the potential influence of long-term climatic shifts on the ecomorphological composition of these faunas, we analyze via contingency tables and detrended correspondence analyses the frequency distribution of ecomorph types within faunas. We show that each evolutionary fauna has a unique, nonrandom association of ecomorphs, and we identify a long-term trend toward greater ecomorphological specialization over successive faunas during the past 66 My. Major vegetation shifts induced by climatic changes appear to underlie the ecomorphological dynamics of these six temporal associations that summarize Cenozoic North American mammalian evolutionary history.Fletcher, S.E.M., Schaefer, H., 2019. Rising methane: A new climate challenge. Science 364, 932-933. 2007, the amount of methane in the atmosphere (CH4) began to rise after a 7-year period of near-zero growth (1). Recent research shows that a second step change occurred in 2014 (2). From 2014 to at least the end of 2018, the amount of CH4 in the atmosphere increased at nearly double the rate observed since 2007 (see the figure). Because CH4 is a potent greenhouse gas, rising atmospheric CH4 presents a major challenge to achieving the goals set out in the Paris Agreement, an international consensus to limit temperature increase to 2°C or, if possible, to 1.5°C above preindustrial levels.The causes for the recent rise in atmospheric CH4 remain a subject of scientific debate, even for the initial period of increase from 2007 to 2014 (1–8). Process-based estimates of CH4 emissions from inventory data, wetland models, and other information offer conflicting explanations, but measurements of the distribution of CH4 in the atmosphere and its 13C/12C isotopic ratio at a global network of stations hold clues.Although CH4 has been rising across the globe, this growth has been largest in the midlatitudes and tropics of the Northern Hemisphere (2, 3). Further, the proportion of 13C in atmospheric CH4 has declined as atmospheric CH4 has risen (see the figure) (1, 2). The 13C/12C ratio in CH4 depends on the sources of the CH4 emissions. Release from biogenic sources (such as wetlands and agriculture) reduces the proportion of 13C in atmospheric CH4, whereas fossil emissions slightly increase this proportion and biomass burning emissions increase it strongly (1, 2). On the basis of selected CH4 and 13C/12C time series from four latitudinal bands, a multibox atmospheric model, and a running-budget analysis, Nisbet et al. (2) identified three potential pathways consistent with both the CH4 and isotope data: a surge in biogenic emissions, a decrease in the amount of CH4 destroyed in the atmosphere through CH4 oxidation, and an increase in fossil fuel emissions if balanced by a decrease in biomass burning.Recent studies have identified source and sink processes that can explain part of the rise, but no single process can simultaneously account for the sudden onset of the rise and the steadiness of the increase, while remaining consistent with other available data. The most likely scenario is a combination of processes.Biogenic emissions mainly come from wetlands and agriculture, particularly ruminant livestock. Multimodel wetland studies do not confirm an emission increase since 2007 (3, 9). However, livestock inventories show that ruminant emissions began to rise steeply around 2002 and can account for about half of the CH4 increase since 2007 (4).CH4 is destroyed in the atmosphere by reaction with hydroxyl radicals (OH) and other atmospheric constituents. Reduced chemical destruction of CH4 could both increase atmospheric CH4 and decrease its proportion of 13C. Actual OH changes over the past years are controversial (5, 6), as is the role of sinks in global inversion studies (7, 8). Only extreme changes in all major sinks can cause the observed CH4 rise and still do not explain observed short-term variability (2), limiting the contribution that sinks are likely to make.Increasing fossil emissions could explain the change, but a simultaneous reduction in 13C-rich emissions from biomass burning is required to balance the 13C/12C trends. Fire reconstructions using satellite observations support such a decline with an emissions drop around 2006 (10). The resulting 13C/12C balance restricts fossil fuels to half of total additional emissions since 2007. Coal mining in East Asia is universally recognized to contribute to the CH4 increase (2, 7, 8), whereas fossil CH4 emissions from North America remained flat despite a nearly 50% increase in natural gas production (11).Coincident with the 2014 acceleration, Nisbet et al. find a source shift to the southern tropics, where wetlands are concentrated (2). They hypothesize that record high temperatures in 2014 and the following years spiked wetland CH4 production. Such a wetland climate feedback challenges the commonly held view that wetland area rather than temperature is the main control of wetland CH4 emissions (although some wetland CH4 models are more temperature driven) (10). If natural wetlands, or changes in atmospheric chemistry, indeed accelerated the CH4 rise, it may be a climate feedback that humans have little hope of slowing. Although studies have demonstrated the potential for substantial CH4-climate feedbacks, they were expected to occur gradually, not reaching the magnitude observed by Nisbet et al. for decades (12).While the scientific community continues to debate the causes of the CH4 surge, the consequences are clear. The latest Intergovernmental Panel on Climate Change (IPCC) emission scenarios that limit warming to 1.5°C assume that the amount of CH4 in the atmosphere will decrease by 35% between 2010 and 2050 (13). Yet, between 2007 and 2014, the amount has risen by an average of 5.7 parts per billion (ppb) per year, and by an average of 9.7 ppb per year since 2014. If this rise continues unabated, cuts to carbon dioxide and other greenhouse gases will need to be even steeper to achieve the Paris goal.Atmospheric greenhouse gas measurements remain the fastest way to assess progress toward slowing climate change. More atmospheric observations are essential to understand the sources of rising CH4, particularly in the tropics, which appear to be the engines of this change. Atmospheric models informed by CH4 data will incorrectly attribute emission changes to regions poorly constrained by data, like equatorial ones (3).Together with satellite observations and time series of additional tracers (14), a comprehensive global measurements network will be crucial to understand changes in CH4. Ascension Island in the South Atlantic is currently the only tropical site with observations of CH4, its 13C/12C ratio, and column CH4 measurements, which are indispensable for validating satellite observations. Yet, this site is in danger of being discontinued. Ongoing support for vitally important sites like Ascension Island, and establishing similar ones in other parts of the tropics, will be crucial for studies of CH4 trends.Close integration between atmospheric observations, process-based studies, and policy is urgently needed to provide meaningful answers about the real emission reductions needed to meet the climate goals of the Paris Agreement. The World Meteorological Organization established the Integrated Global Greenhouse Gas Information System (IG3IS) to address this issue. IG3IS provides a bridge between the atmospheric greenhouse gas community and decisionmakers. Timely dialogue between these groups has never been more essential, as the window for achieving the goals of the Paris Agreement is rapidly closing.References1. H. Schaefer et al, Science 352, 80 (2016).2. E. G. Nisbet et al., Global Biogeochem. Cycles 33, 318 (2019)3. M. Saunois et al., Atmos. Chem. Phys. 17, 11135 (2017)4. J. Wolf, G. R. Asrar, T. O. West, Carbon Balance Manag. 12, 16 (2017).5. M. Rigby et al., Proc. Natl. Acad. Sci. U.S.A. 114, 5373 (2017).6. S. Naus et al., Atmos. Chem. Phys. 19, 407 (2019).7. J. McNorton et al., Atmos. Chem. Phys. 18, 18149 (2018).8. R. L. Thompson et al., Geophys. Res. Lett. 45, 11499 (2018).9. B. Poulter et al., Environ. Res. Lett. 12, 094013 (2017).10. J. R. Worden et al., Nat. Commun. 8, 2227 (2017).11. X. Lan et al., Geophys. Res. Lett. 46, 4991 (2019).12. J. F. Dean et al., Rev. Geophys. 56, 207 (2018)13. V. Masson-Delmotte et al., Eds., “Global Warming of 1.5°C. An IPCC special report on the impacts of global warming of 1.5°C above pre-industrial amounts and related global greenhouse gas emission pathways, in the context of strengthening the global response to the threat of climate change, sustainable development, and efforts to eradicate poverty” (World Meteorological Organization, 2018).14. A. J. Turner, C. Frankenberg, E. A. Kort, Proc. Natl. Acad. Sci. U.S.A. 116, 2805 (2019).Fones, E.M., Colman, D.R., Kraus, E.A., Nothaft, D.B., Poudel, S., Rempfert, K.R., Spear, J.R., Templeton, A.S., Boyd, E.S., 2019. Physiological adaptations to serpentinization in the Samail Ophiolite, Oman. The ISME Journal 13, 1750-1762. of ultramafic rock during the geologic process of serpentinization can generate reduced substrates that microorganisms may use to fuel their carbon and energy metabolisms. However, serpentinizing environments also place multiple constraints on microbial life by generating highly reduced hyperalkaline waters that are limited in dissolved inorganic carbon. To better understand how microbial life persists under these conditions, we performed geochemical measurements on waters from a serpentinizing environment and subjected planktonic microbial cells to metagenomic and physiological analyses. Metabolic potential inferred from metagenomes correlated with fluid type, and genes involved in anaerobic metabolisms were enriched in hyperalkaline waters. The abundance of planktonic cells and their rates of utilization of select single-carbon compounds were lower in hyperalkaline waters than alkaline waters. However, the ratios of substrate assimilation to dissimilation were higher in hyperalkaline waters than alkaline waters, which may represent adaptation to minimize energetic and physiologic stress imposed by highly reducing, carbon-limited conditions. Consistent with this hypothesis, estimated genome sizes and average oxidation states of carbon in inferred proteomes were lower in hyperalkaline waters than in alkaline waters. These data suggest that microorganisms inhabiting serpentinized waters exhibit a unique suite of physiological adaptations that allow for their persistence under these polyextremophilic conditions.Foster, K.R., Davidson, C., Tanna, R.N., Spink, D., 2019. Introduction to the virtual special issue monitoring ecological responses to air quality and atmospheric deposition in the Athabasca Oil Sands region the wood Buffalo environmental Association's Forest health monitoring program. Science of The Total Environment 686, 345-359. expansion of oil sands resource development in the Athabasca Oil Sands Region in the early 1990's led to concerns regarding the potential ecological and health effects of increased emissions and deposition of acidic substances. Conditions attached to a 1994 approval for an oil sands facility expansion led to the creation of the Wood Buffalo Environmental Association, and its Terrestrial Environmental Effects Monitoring committee. This multi-stakeholder body was tasked with development and operation of an environmental (forest health) monitoring program for the detection of ecological responses to atmospheric emissions and deposition. Initially focused on acid deposition monitoring, jack pine forest, growing on sandy soils with limited acid buffering capacity, was selected as the receptor system. An initial set of 10 monitoring locations was established using the Canadian Acid Rain Network Early Warning System methodology (since increased to 27, with three lost to development). Ecological monitoring is on a 6-year?cycle, with concurrent measures of soil, needle and lichen chemistry, and tree and understory condition, together with ongoing measurements of air quality and atmospheric deposition. Because jack pine forest edges facing the emissions sources were expected to be more exposed to acidic emissions, evaluation of stand edge monitoring locations began in 2008. Monitoring of a targeted suite of indicators began in 2012 at 25 jack pine stand edge monitoring sites. This special issue presents the results derived from biophysical sampling campaigns (1998 to 2013), coupled with ongoing ambient atmospheric, deposition and epiphytic lichen monitoring (data through 2017) and source apportionment studies, as well as papers contributed by others engaged in regional research and monitoring programs. The Forest Health Monitoring Program provides data supportive of regulatory and stakeholder evaluations of environmental quality, and is adaptive to new needs, extreme environmental events and technological development while providing continuity of monitoring.Fox-Powell, M.G., Osinski, G.R., Applin, D., Stromberg, J.M., Gázquez, F., Cloutis, E., Allender, E., Cousins, C.R., 2019. Natural analogue constraints on Europa's non-ice surface material. Geophysical Research Letters 46, 5759-5767.: Non‐icy material on the surface of Jupiter's moon Europa is hypothesized to have originated from its subsurface ocean and thus provide a record of ocean composition and habitability. The nature of this material is debated, but observations suggest that it comprises hydrated sulfate and chloride salts. Analogue spectroscopic studies have previously focused on single‐phase salts under controlled laboratory conditions. We investigated natural salts from perennially cold (<0 °C) hypersaline springs and characterized their reflectance properties at 100, 253, and 293 K. Despite similar major ion chemistry, these springs form mineralogically diverse deposits, which when measured at 100 K closely match reflectance spectra from Europa. In the most sulfate‐rich samples, we find that spectral features predicted from laboratory salts are obscured. Our data are consistent with sulfate‐dominated europan non‐icy material and further show that the emplacement of endogenic sulfates on Europa's surface would not preclude a chloride‐dominated ocean.Plain Language Summary: Europa, a moon of Jupiter, has become a priority target in the search for life off the Earth, due to the presence of a liquid water ocean under its icy shell. Salts on the moon's surface might originate from this ocean and therefore offer a way of studying the ocean without requiring direct access. Our knowledge of these salts comes from comparing spacecraft measurements to pure salts produced in laboratories. We have studied natural salts from hypersaline springs in the Canadian Arctic as an alternative, complementary approach. Measuring samples from these deposits at europan surface temperatures, several unexpected properties were observed, including the absence of spectral details predicted by previous laboratory studies. This challenges some of the estimates of europan surface composition. Natural analogues such as these will form part of an integrative approach to understanding data from upcoming missions, such as the National Aeronautics and Space Administration's (NASA) Europa Clipper and the European Space Agency's JUpiter ICy moons Explorer.Frank, A.B., Klaebe, R.M., Frei, R., 2019. Fractionation behavior of chromium isotopes during the sorption of Cr (VI) on kaolin and its implications for using black shales as a paleoredox archive. Geochemistry, Geophysics, Geosystems 20, 2290-2302. stable isotope variations in marine black shales are increasingly used to constrain redox changes though time. However, how well black shale δ53Cr values represent ambient seawater δ53Cr values is difficult to assess as black shales contain both detrital and authigenic mineral phases, of which only authigenic phases are expected to mirror seawater, while detrital silicate phases are expected to show igneous δ53Cr values. In order to correct for detrital contamination, it is thus imperative to know whether detrital minerals are in fact characterized by igneous δ53Cr values. To investigate this further, three sets of Cr (VI) batch sorption experiments were conducted, reacting kaolin with (1) with a synthetic Cr (VI) solution, (2) with Cr (VI) doped river water, and (3) with Cr (VI) doped seawater. Further, sequential leaches were applied to reacted kaolin to evaluate how well sorbed Cr (VI) can be leached. The experiments revealed that Cr (VI) readily sorbs on kaolin, changing its Cr concentration and isotopic composition. In river water, kaolin sorbed up to 36 μg of Cr (VI) per gram of kaolin and recorded a negative offset in bulk δ53Cr of up to 0.26‰ relative to unreacted kaolin, while no sorption was observed in seawater. Our leaching experiments revealed that already a weak acid leach (0.5M HCl) readily mobilizes some of the sorbed Cr from kaolin, which when applied to black shales will likely contaminate leachates designed to release authigenic Cr. This has major implications for the application of Cr stable isotopes in black shales as marine paleoredox archives.Freije-Carrelo, L., García-Bellido, J., Calderón-Celis, F., Moldovan, M., Encinar, J.R., 2019. GC-ICP-MS/MS instrumental setup for total and speciation sulfur analysis in gasolines using generic standards. Analytical Chemistry 91, 7019-7024. characterization of sulfur-containing petroleum derivatives is mainly limited by the large number of potential targets present and the matrix effects suffered due to the high-carbon-containing matrices. Herein we describe the instrumental modifications required in a commercial GC-ICP-MS/MS instrument, and their corresponding optimization, for turning it into a compound-independent quantitative technique for both total and speciation sulfur analysis in gasolines. Additionally, carbon-derived matrix effects were made negligible for direct and fast total S analysis, making the use of relatively complex isotope-dilution strategies not necessary anymore. An absolute detection limit of 0.3 pg of S was achieved, which is, to the best of our knowledge, more than 1 order of magnitude below the ones reported for other sulfur GC selective detectors. The precision was below 3% RSD. Total analysis was performed by flow-injection analysis through a transfer line and external calibration, whereas speciation analysis was carried out by chromatographic separation and internal standardization. In both cases, simple generic standards were used, which enabled us to get rid of specific S-containing standards, which were sometimes not available or unstable. The proposed method was successfully applied to total and speciation sulfur analysis of a commercial gasoline sample and validated with a certified-reference-material (ERM-EF213) gasoline. The approach has proved to be simple, fast, robust, and convenient for implementation in routine laboratories, as demonstrated by the successive analyses of 50 gasoline samples in 3 h without any instrumental drift.French, K.E., Terry, N., 2019. A high-throughput fluorescence-based assay for rapid identification of petroleum-degrading bacteria. Frontiers in Microbiology 10, 1318. doi: 10.3389/fmicb.2019.01318. the past 100 years, oil spills and long-term waste deposition from oil refineries have significantly polluted the environment. These contaminants have widespread negative effects on human health and ecosystem functioning. Natural attenuation of long chain and polyaromatic hydrocarbons is slow and often incomplete. Bioaugmentation of polluted soils with indigenous bacteria that naturally consume petroleum hydrocarbons could speed up this process. However, the characterization of bacterial crude oil degradation efficiency—which often relies upon expensive, highly specialized gas-chromatography mass spectrometry analyses--can present a substantial bottleneck in developing and implementing these bioremediation strategies. Here, we develop a low-cost, rapid, high-throughput fluorescence-based assay for identifying wild-type bacteria that degrade crude oil using the dye Nile Red. We show that Nile Red fluoresces when in contact with crude oil and developed a robust linear model to calculate crude oil content in liquid cell cultures based on fluorescence intensity (FI). To test whether this assay could identify bacteria with enhanced metabolic capacities to break down crude oil, we screened bacteria isolated from a former Shell Oil refinery in Bay Point, CA and identified one strain (Cupriavidus sp. OPK) with superior crude oil depletion efficiencies (up to 83%) in only three days. We further illustrate that this assay can be combined with fluorescence microscopy to study how bacteria interact with crude oil and the strategies they use to degrade this complex substance. We show for the first time that bacteria use three key strategies for degrading crude oil: biofilm formation, direct adherence to oil droplets, and vesicle encapsulation of oil. We propose that the quantitative and qualitative data from this assay can be used to develop new bioremediation strategies based on bioaugmentation and/or biomimetic materials that imitate the natural ability of bacteria to degrade crude oil.Fu, Q., Liu, B., Niu, C., Zhao, S., 2019. The geochemical evidences of sulphur oil sources in the BZ35/36 structures of the Huanghekou Sag, Bohai Bay Basin, China. Petroleum Research 4, 164-172. oils in the BZ35/BZ36 fields found within the Paleogene Dongying and Shahejie formations in the Huanghekou Sag of the Bohai Bay Basin, China have generally high density, viscosity, and sulfur content. Their physical properties and geochemical features have obvious differences when compared with crude oils from other structures within the Huanghekou Sag. The comparison and analysis of biomarkers(e.g., pristine/phytane, gammacerane, C24Te/C26TT, C2920S/(20S?+?20R), C29ββ/(ββ+αα), etc.) show that sour crude oil from the BZ35/BZ36 fields is similar to the sour oil in the Miaoxi Sag adjacent to the eastern of Huanghekou Sag. Sour, low maturity oils in the Miaoxi Sag have likely migrated southwest, while the sweet, higher maturity oils in the Huanghekou Sag have migrated northeast. Crude oils generated from these two sags have focused in the BZ35/BZ36 structures. The source rock of the sour crude oil was most likely formed in a dry climate and strong reducing saline lake.Fu, W., Nelson, D.R., Mystikou, A., Daakour, S., Salehi-Ashtiani, K., 2019. Advances in microalgal research and engineering development. Current Opinion in Biotechnology 59, 157-164. have been investigated for the photosynthetic production of natural products with industrial and biomedical applications. Their rapid growth offers an advantage over higher plants, while their complex metabolic capacities allow for the production of various molecules. Despite their potentials, molecular techniques are underdeveloped in microalgae compared to higher plants, fungi, and bacteria. However, recent advances in genome sequencing, strain development, and genome editing technologies, are providing thrust to enhance research on microalgal species that have branched out from several focal model organisms to encompass a great diversity of species. In this review, we highlight the recent, significant advances in microalgal research, with a focus on the development of new resources that can enhance work on model and non-model species.Fuchs, M., Lenz, J., Jock, S., Nitze, I., Jones, B.M., Strauss, J., Günther, F., Grosse, G., 2019. Organic carbon and nitrogen stocks along a thermokarst lake sequence in Arctic Alaska. Journal of Geophysical Research: Biogeosciences 124, 1230-1247.: Thermokarst lake landscapes are permafrost regions, which are prone to rapid (on seasonal to decadal time scales) changes, affecting carbon and nitrogen cycles. However, there is a high degree of uncertainty related to the balance between carbon and nitrogen cycling and storage. We collected 12 permafrost soil cores from six drained thermokarst lake basins (DTLBs) along a chronosequence north of Teshekpuk Lake in northern Alaska and analyzed them for carbon and nitrogen contents. For comparison, we included three lacustrine cores from an adjacent thermokarst lake and one soil core from a non thermokarst affected remnant upland. This allowed to calculate the carbon and nitrogen stocks of the three primary landscape units (DTLB, lake, and upland), to reconstruct the landscape history, and to analyze the effect of thermokarst lake formation and drainage on carbon and nitrogen stocks. We show that carbon and nitrogen contents and the carbon‐nitrogen ratio are considerably lower in sediments of extant lakes than in the DTLB or upland cores indicating degradation of carbon during thermokarst lake formation. However, we found similar amounts of total carbon and nitrogen stocks due to the higher density of lacustrine sediments caused by the lack of ground ice compared to DTLB sediments. In addition, the radiocarbon‐based landscape chronology for the past 7,000 years reveals five successive lake stages of partially, spatially overlapping DTLBs in the study region, reflecting the dynamic nature of ice‐rich permafrost deposits. With this study, we highlight the importance to include these dynamic landscapes in future permafrost carbon feedback models.Plain Language Summary: When permanently frozen soils (permafrost) contain ice‐rich sediments, the thawing of this permafrost causes the surface to sink, which may result in lake formation. This process, the thaw of ice‐rich permafrost and melting of ground ice leads to characteristic landforms—known as thermokarst. Once such a thaw process is initiated in ice‐rich sediments, a thaw lake forms and grows by shoreline erosion, eventually expanding until a drainage pathway is encountered and the lake eventually drains, resulting in a drained thermokarst lake basin. In our study, we show that such a thermokarst‐affected landscape north of Teshekpuk Lake in northern Alaska is shaped by repeated thaw lake formation and lake drainage events during the past 7,000 years, highlighting the dynamic nature of these landscapes. These landscape‐scale processes have a big effect on the carbon and nitrogen stored in permafrost soils. We show that large amounts of carbon (>45 kg C/m2) and nitrogen (>2.6 kg N/m2) are stored in unfrozen lake sediments and in frozen soil sediments. The findings are important when considering the potential effect that permafrost thaw has for the global climate through releasing carbon and nitrogen, which was frozen and therefore locked away for millennia, from the active carbon cycle.Gafurov, M., Mamin, G., Gracheva, I., Murzakhanov, F., Ganeeva, Y., Yusupova, T., Orlinskii, S., 2019. High-Field (3.4 T) ENDOR investigation of asphaltenes in native oil and vanadyl complexes by asphaltene adsorption on alumina surface. Geofluids 2019, Article 3812875. porphyrin complexes in asphaltenes from heavy (Karmalinskoye) oil and in asphaltene films obtained as a result of adsorption on the surface of aluminum oxide were studied by electron paramagnetic resonance (EPR) and double electron-nuclear resonance (ENDOR) in the W-band frequency range (microwave frequency of 95?GHz, magnetic field of 3.4?T). Mims ENDOR spectra from 1H and 27Al nuclei are observed. ENDOR spectra are different for native oil and asphaltenes from one side and the adsorbed samples from the other side while no significant changes in X- (microwave frequency of 9?GHz) or W-band EPR spectra are found. The results allow supposing that vanadyl porphyrin complexes (at least in the studied asphaltene films) participate in the formation of asphaltene aggregates through the functional groups rather than π–π interactions. The data show the feasibility of the commercial pulsed ENDOR approaches for the investigation of crude oils and their constituents under external influence.Gal, F., Proust, E., Kloppmann, W., 2019. Towards a better knowledge of natural methane releases in the French Alps: A field approach. Geofluids 2019, Article 6487162. report investigations performed at some hydrocarbon gas seeps located in the French Subalpine Chains in zones of outcropping Jurassic black shales, increasing the reported number of such occurrences in this part of the Alps. We present the characteristics of each of the seeps, based on soil flux measurements and soil gas measurements. Gases emitted are CH4-rich (87–94%) with the exception of one site (78.5% CH4 + 8.2% CO2) where an active landslide may induce dilution by atmospheric air. CO2 is generally measured at low levels (<1.6%). Concentrations in C2H6 are more variable, from less than 1% to more than 2.3%. Gas is emitted over areas of various sizes. The smallest gas emission area measures only , characterized by a strong hydrocarbon flux (release of about 100?kg of CH4 per year). At a second site, hydrocarbon emissions are measured over a surface of 12?m2. For this site, methane emission is evaluated at 235?kg per year and CO2 emission is 600?kg per year, 210?kg being related to gas seepage. At the third site, hydrocarbons are released over a 60?m2 area but strong gas venting is restricted to localized seeps. Methane emission is evaluated at 5.1 tons per year and CO2 emission at 1.58 tons per year, out of which 0.53 tons are attributed to gas seepage. Several historical locations remain uninvestigated at present, and numerous others may still be unknown. We outline strategies to search for such unrecorded sites. Considering the topography of the potential alpine and perialpine emission areas, the possibilities to detect gas emissions appear of the size recorded so far seem to be restricted to ground-based methods or to methods offering the possibility to point orthogonally to the soil towards the seep maximum. If such sites are to be investigated in the future in the frame of Environmental Baseline Assessment (EBA), even establishing appropriate monitoring protocols will be challenging.Ganti, V., Whittaker, A.C., Lamb, M.P., Fischer, W.W., 2019. Low-gradient, single-threaded rivers prior to greening of the continents. Proceedings of the National Academy of Sciences 116, 11652-11657.: The origin of low-gradient meandering rivers—the primary conduits of water, carbon, and nutrients in present-day terrestrial landscapes—is considered coeval with Silurian-age plant evolution. It was hypothesized that pre-Silurian rivers lacked bank strength and were dominantly steep and braided, implying vastly different transport capacities of water and sediment. This idea, however, is inconsistent with the supercontinental-scale drainage of Neoproterozoic rivers, which requires unrealistically high mountains to achieve the necessary river gradients. Using geologic observations and paleohydraulic analyses, we show that pre-Silurian rivers were low-gradient, deep, and single-threaded—similar to modern meandering rivers. Results demonstrate uniformity of fluvial morphology despite a global revolution in Earth’s terrestrial biota, with ramifications for the topographic signature of life on Earth and other planets.Abstract: The Silurian-age rise of land plants is hypothesized to have caused a global revolution in the mechanics of rivers. In the absence of vegetation-controlled bank stabilization effects, pre-Silurian rivers are thought to be characterized by shallow, multithreaded flows, and steep river gradients. This hypothesis, however, is at odds with the pancontinental scale of early Neoproterozoic river systems that would have necessitated extraordinarily high mountains if such river gradients were commonplace at continental scale, which is inconsistent with constraints on lithospheric thickness. To reconcile these observations, we generated estimates of paleogradients and morphologies of pre-Silurian rivers using a well-developed quantitative framework based on the formation of river bars and dunes. We combined data from previous work with original field measurements of the scale, texture, and structure of fluvial deposits in Proterozoic-age Torridonian Group, Scotland—a type-example of pancontinental, prevegetation fluvial systems. Results showed that these rivers were low sloping (gradients 10?5 to 10?4), relatively deep (4 to 15 m), and had morphology similar to modern, lowland rivers. Our results provide mechanistic evidence for the abundance of low gradient, single-threaded rivers in the Proterozoic eon, at a time well before the evolution and radiation of land plants—despite the absence of muddy and vegetated floodplains. Single-threaded rivers with stable floodplains appear to have been a persistent feature of our planet despite singular changes in its terrestrial biota.Gao, S., Yang, J., 2019. Exploration of tight oil resources based on stratigraphic paleo-tectonics during hydrocarbon generation in the Ordos Basin, China. Arabian Journal of Geosciences 12, Article 387. many years, oil resource exploration has emphasized the current structural characteristics of potential oil-bearing formations. The traditional view of the Ordos Basin has been that the slope in northern Shaanxi is a gentle westward-dipping monocline that lacks structural traps, such as anticlines. Therefore, it was assumed that structural factors could exert no control over the formation and distribution of the oil reservoirs in the Yanchang Formation. By modeling the evolution and structure of a target layer in the Chang-8 reservoir during its hydrocarbon accumulation period, combined with a comprehensive analysis of the distributional characteristics of the Chang-8 oil reservoir, we found a strong link between paleo-slopes and paleo-highs in the target layer and the modern distribution of tight oils. The paleo-structural characteristics of the target layer clearly exhibit control over the Chang-8 reservoir. We have proposed a new understanding and method for tight oil exploration, which is based on the recovery of the paleo-geomorphology of the target layer during the hydrocarbon generation period. It incorporates a number of key controls over tight oil accumulation and represents an evolution in the mindset suggested for tight oil exploration in the Ordos Basin.Garcias-Bonet, N., Delgado-Huertas, A., Carrillo-de-Albornoz, P., Anton, A., Almahasheer, H., Marbà, N., Hendriks, I.E., Krause-Jensen, D., Duarte, C.M., 2019. Carbon and nitrogen concentrations, stocks, and isotopic compositions in Red Sea seagrass and mangrove sediments. Frontiers in Marine Science 6, 267. doi: 10.3389/fmars.2019.00267. vegetated ecosystems are intense global carbon (C) sinks; however, seagrasses and mangroves in the Central Red Sea are depleted in organic C (Corg). Here, we tested whether Corg depletion prevails across the whole Red Sea, or if sediment Corg and nitrogen (N) stocks reflect the latitudinal productivity gradient of the Red Sea. We assessed Corg and N concentrations, stocks, isotopic compositions (δ13C and δ15N), and the potential contribution of primary producers to the organic matter accumulation in seagrass and mangrove sediments along the Eastern coast of the Red Sea. Sediment Corg concentration was higher in mangroves than seagrasses, while N concentrations were similar, resulting in higher C/N ratios in mangrove than seagrass sediments. Mangrove Corg stocks (integrated over the top 10 cm) were two-fold higher than those of seagrasses, respectively. N concentrations and stocks decreased from south to north in seagrass sediments matching the productivity gradient while Corg concentrations and stocks were uniform. The δ15N decreased from south to north in seagrass and mangrove sediments, reflecting a shift from nitrate and nitrite as N sources in the south, to N2 fixation towards the north. Stable isotope mixing models showed that seagrass leaves and macroalgae blades were the major contributors to the organic matter accumulation in seagrass sediments; while mangrove leaves were the major contributors in mangrove sediments. Overall, vegetated sediments in the Red Sea tend to be carbonate-rich and depleted in Corg and N, compared to coastal habitats elsewhere. Specifically, mean Corg stocks in Red Sea seagrass and mangrove sediments (7.2 ± 0.4 and 14.5 ± 1.4 Mg C ha-1, respectively) are lower than previously reported mean global values. This new information of Blue Carbon resources in the Red Sea provides a background for Blue Carbon programs in the region while also helping to balance global estimates.Garimella, S.V.B., Nagy, G., Ibrahim, Y.M., Smith, R.D., 2019. Opening new paths for biological applications of ion mobility - Mass spectrometry using structures for lossless ion manipulations. TrAC Trends in Analytical Chemistry 116, 300-307. mobility separations coupled to mass spectrometry (IM-MS) have received much attention for their ability to provide complementary structural information to solution-phase-based separations, as well as to aid in the identification of unknown compounds. While IM-MS is an increasingly powerful analytical technique, significant bottlenecks related to the resolution of measurements have kept it from becoming broadly applied for biological analyses. Presently, IM-MS-based measurements also remain limited in terms of their sensitivity as compared to state of the art MS-based approaches alone. Structures for Lossless Ion Manipulations (SLIM)-based IM separations provide a basis for overcoming these bottlenecks, addressing issues associated with resolution and sensitivity in the omics, and potentially opening the door to much broader application.Georgiev, S.V., Stein, H.J., Hannah, J.L., Yang, G., Markey, R.J., Dons, C.E., Pedersen, J.H., di Primio, R., 2019. Comprehensive evolution of a petroleum system in absolute time: The example of Brynhild, Norwegian North Sea. Chemical Geology 522, 260-282. systems are inherently complex, comprising multiple components and processes, which variably interact in space and time to form petroleum accumulations. Improved understanding of these complex systems requires a holistic approach of integrating diverse geological, geophysical and organic and inorganic geochemical data. Here, we present an applied and comprehensive Re-Os geochronological and geochemical study on the Brynhild petroleum system from the Norwegian North Sea. Essential components of this system include shale source rocks of the Mandal and Farsund Formations, reservoir sandstones of the Ula Formation and their bitumen extracts, and produced Brynhild crude oil.Rock-Eval, trace metal and Re-Os data reveal the excellent oil-generation potential of the shaley source rocks (high contents of organic matter containing large amounts of type I kerogens) and constrain their depositional conditions (anoxic bottom waters in a high-productivity regime driven by enhanced supply of land-derived nutrients). Seven Re-Os shale ages between ~146 and ~134?Ma are consistent with existing Volgian–Ryazanian age estimates and constrain the initial 187Os/188Os of the shales to ~0.52 in the lowermost Farsund Formation and ~0.75 in the uppermost Mandal Formation. Solvent-extracted reservoir rocks of the Ula Formation contain insoluble organic matter with type III–type IV kerogens likely supplied by erosion of older (a precise 179?Ma Re-Os age with unrealistically low initial 187Os/188Os) coal-bearing sediments or organic-rich shales.The Brynhild crude oil has relatively low 187Os/188Os and a generation age of ~44?Ma based on an asphaltene-only Re-Os isochron. Maltenes from the Brynhild crude oil are isotopically affected by interaction with organic-rich source rocks that represent the seal for the Brynhild oil field. Compared with the crude oil, bitumen from Ula Formation sandstones have contrasting Re-Os properties: high 187Os/188Os ratios and young generation ages between 8 and 0?Ma based on asphaltene-bitumen-maltene Re-Os triplets, asphaltene-only Re-Os regressions, and ReOs model ages for components with extremely high 187Os/188Os. The 44?Ma and 8–0?Ma Re-Os ages agree well with regional burial models that indicate oil generation from ~44?Ma to present day. A genetic link between crude oil and bitumen is indicated by their similar alkane patterns, V and Ni contents, and V/Ni and pristane/phytane ratios. Modeling of 187Os/188Os for individual organic components through time shows that shales of the Mandal Formation developed 187Os/188Os ratios that match those of the crude oil and bitumen at ~44?Ma and ~8?Ma, respectively, and therefore confirm the source for both hydrocarbon phases. We suggest that bitumen formed during in-reservoir mixing of a ~44?Ma old early mature, asphaltene-poor oil (Brynhild crude oil) with an ~8?Ma old asphaltene-rich oil.Ghashghavi, M., Belova, S.E., Bodelier, P.L.E., Dedysh, S.N., Kox, M.A.R., Speth, D.R., Frenzel, P., Jetten, M.S.M., Lücker, S., Lüke, C., 2019. Methylotetracoccus oryzae strain C50C1 is a novel type ib gammaproteobacterial methanotroph adapted to freshwater environments. mSphere 4, e00631-18.: Methane-oxidizing microorganisms perform an important role in reducing emissions of the greenhouse gas methane to the atmosphere. To date, known bacterial methanotrophs belong to the Proteobacteria, Verrucomicrobia, and NC10 phyla. Within the Proteobacteria phylum, they can be divided into type Ia, type Ib, and type II methanotrophs. Type Ia and type II are well represented by isolates. Contrastingly, the vast majority of type Ib methanotrophs have not been able to be cultivated so far. Here, we compared the distributions of type Ib lineages in different environments. Whereas the cultivated type Ib methanotrophs (Methylococcus and Methylocaldum) are found in landfill and upland soils, lineages that are not represented by isolates are mostly dominant in freshwater environments, such as paddy fields and lake sediments. Thus, we observed a clear niche differentiation within type Ib methanotrophs. Our subsequent isolation attempts resulted in obtaining a pure culture of a novel type Ib methanotroph, tentatively named “Methylotetracoccus oryzae” C50C1. Strain C50C1 was further characterized to be an obligate methanotroph, containing C16:1ω9c as the major membrane phospholipid fatty acid, which has not been found in other methanotrophs. Genome analysis of strain C50C1 showed the presence of two pmoCAB operon copies and XoxF5-type methanol dehydrogenase in addition to MxaFI. The genome also contained genes involved in nitrogen and sulfur cycling, but it remains to be demonstrated if and how these help this type Ib methanotroph to adapt to fluctuating environmental conditions in freshwater ecosystems.Importance: Most of the methane produced on our planet gets naturally oxidized by a group of methanotrophic microorganisms before it reaches the atmosphere. These microorganisms are able to oxidize methane, both aerobically and anaerobically, and use it as their sole energy source. Although methanotrophs have been studied for more than a century, there are still many unknown and uncultivated groups prevalent in various ecosystems. This study focused on the diversity and adaptation of aerobic methane-oxidizing bacteria in different environments by comparing their phenotypic and genotypic properties. We used lab-scale microcosms to create a countergradient of oxygen and methane for preenrichment, followed by classical isolation techniques to obtain methane-oxidizing bacteria from a freshwater environment. This resulted in the discovery and isolation of a novel methanotroph with interesting physiological and genomic properties that could possibly make this bacterium able to cope with fluctuating environmental conditions.Ghayyem, M.A., Ghanavati Nasab, A., Zare Khormizi, M., Rostami, M., 2019. Predicting the conditions for gas hydrate formation. Petroleum Science and Technology 37, 1855-1860. hydrate is a crystalline mixture obtained from gas molecules trapped in the cavity of hydrogen bonding water. To date, an essential step in the development of natural gas industry has been the acquisition of knowledge in the operation and handling of gas under high pressure without hydrate formation. Since there are several ways to predict hydrate formation, this study investigates predicting hydrate formation using the Katz method. In addition, several new models for accurate estimation of gas hydrate formation conditions will be provided. These models are based on artificial neural network (ANN) requirements. To create the model, predictive experimental data published in books and journals, as well as data extracted from Katz graph (Katz chart), estimate the formation conditions of gas hydrate. We validate the model created with the use of various statistical parameters such as mean squared error (MSE) and R2-value. The result of these parameters in models created to predict the formation of hydrates accurately and efficiently is evaluated. In this study, our goals are to use an artificial intelligence neural network to predict the formation of gas hydrates.Ghosh, B., Sulemana, N., Banat, F., Mathew, N., 2019. Ionic liquid in stabilizing asphaltenes during miscible CO2 injection in high pressure oil reservoir. Journal of Petroleum Science and Engineering 180, 1046-1057. potential of ionic liquids to prevent asphaltene precipitation during miscible Carbon dioxide (CO2) flooding was investigated. Asphaltene dispersion tests were performed to compare the effectiveness of commercial inhibitors and the ionic liquids at ambient conditions. Based on the results 1-Butyl-3-methyl-imidazolium bromide [BMIM][Br], Ionic Liquid was selected and asphaltene onset pressure (AOP) was determined at high-temperature high-pressure conditions through isothermal depressurization experiments in PVT cell. The effect of CO2, organic solvents and [BMIM][Br] on AOP were documented and correlated with nodal pressure analysis of the reservoir/wells. The results show a 21% decrease in AOP compared to the untreated oil and about 46% decrease when 35?mol% of CO2 is solubilized in oil. [BMIM][Br] is seen to have higher activity when injected in solution with isopropanol-n-heptane compared to direct addition. The application of [BMIM][Br]in miscible CO2 flooded reservoir is found to have good potential in inhibiting asphaltene deposition within the reservoir and near wellbore nodal conditions.Gibney, E., 2019. A Google programme failed to detect cold fusion — but is still a success. Nature 569, 599-600.. Major project to reproduce controversial claims of bench-top nuclear fusion kindles debate about when high-risk research is worthwhile. Thirty years ago, claims of ‘cold fusion’ hit the headlines, promising a solution to the apparently impossible dream of producing cheap and clean energy using little more than standard bench-top apparatus. From the outset, it sounded too good to be true.Fusion of atomic nuclei is typically associated with high-energy astrophysical environments (the Sun, for example). So when researchers at the University of Utah in Salt Lake City asserted in early 1989 that they had induced the process by passing an electric current through a simple electrochemical cell, it drew scepticism straight away. The phenomenon — even if real — seemed ephemeral and had little to no theoretical basis. Many groups failed to repeat the findings. The episode is now largely remembered as a case study in confirmation bias. Discussions of the phenomenon are relegated to the fringes of mainstream scientific discourse, and for years it has received little serious attention.Until 2015, that is, when Google convened and funded a group of around 30 researchers spanning several laboratories to take another look. After all, absence of evidence is not the same as evidence of absence. Society’s need for cheaper and cleaner sources of energy is more pressing than ever, and, if cold fusion were possible, it could be a disruptive technology with a world-changing pay-off.The goals of the Google team were simple to state, but challenging to execute: to develop a series of rigorous experiments and reproducible protocols that would tightly constrain the conditions under which cold fusion can be realized; and, if the team could detect the phenomenon, to develop a definitive reference experiment that would benchmark it for the wider academic community to scrutinize and verify. The programme is described for the first time in a Perspective, a technical opinion piece.The team found no evidence whatsoever of cold fusion.Is that the final nail in the cold-fusion coffin? Not quite. The group was unable to attain the material conditions speculated to be most conducive to cold fusion. Indeed, it seems extremely difficult to do so using current experimental set-ups — although the team hasn’t excluded such a possibility. So the fusion trail, although cooling, is not yet cold, leaving a few straws for optimists to clutch on to.The question now is whether it is even worth continuing this research. Here, the message is more nuanced. The project has produced materials, tools and insights — such as calorimeters that operate reliably under extreme conditions, and techniques for producing and characterizing highly hydrided metals — that could benefit other areas of energy and fusion research. But whether the spin-off benefits alone justify continued efforts and investment in pursuit of a probable pipe dream is another matter. Opinions are split.So what do we take home from a multi-year failed experiment? First, that the programme has been conducted with rigour and attention to detail — we can have confidence in the results. Second, although the work provides no support for fringe groups that continue to insist that cold fusion exists, it does bring this research area back into the light of harsh scientific scrutiny. And, by doing so, the project might help responsible research in this general area to become less taboo, even if the chances of achieving cold fusion still look extremely remote.Gibney, E., 2019. Google revives controversial cold-fusion experiments. Nature 569, 611. tested? mechanisms linked to nuclear fusion at room temperature — but found no evidence for the phenomenon. Since 2015, Google has been funding experiments into the controversial science of cold fusion — the theory that nuclear fusion, the process that powers the Sun, can produce energy in a table-top experiment at room temperature. Two scientists first made sensational claims about achieving the phenomenon — promising endless, cheap energy — 30 years ago, but their results were quickly debunked and the topic is now considered a scientific taboo.Google’s project — revealed in a peer-reviewed Nature Perspective1 this week — found no evidence that cold fusion is possible, but made some advances in measurement and materials-science techniques that the researchers say could benefit energy research. The team also hopes that its work will inspire others to revisit cold-fusion experiments, even if the phenomenon still fails to materialize.“This is not just a chase for cold fusion,” says Matthew Trevithick, a research programme manager at Google in Mountain View, California. “If it were, I don’t think we would have maintained an interest of this calibre of team for so long.”The Google team explored three experimental set-ups that have been proposed to generate cold fusion — two involving palladium and hydrogen, and one involving metallic powders and hydrogen. None found? evidence of fusion. The results have been published across 12 papers over the past 2 years: 9 in peer-reviewed journals and 3? on the arXiv preprint server.Some scientists welcomed the scrutiny brought by the Google project. But Frank Close, a theoretical physicist at the University of Oxford, UK, says that the scientific mainstream has shunned the topic for good reason: no one has managed to independently reproduce the finding and more worthwhile topics have emerged, he says. “There is no theoretical reason to expect cold fusion to be possible, and a vast amount of well-established science that says it should be impossible,” says Close, who was involved in efforts to replicate the original 1989 experiment. Notorious claimsIn March 1989, two US-based chemists Stanley Pons and Martin Fleischmann announced that they had seen excess heat and fusion-reaction products — signs of nuclear fusion — when they ran a current across two palladium plates in water laden with deuterium, a heavy isotope of hydrogen. Others quickly pointed out errors in their experimental procedure. Since then, two US Department of Energy reviews have found no evidence of the phenomenon .But cold fusion — now commonly referred to as low-energy nuclear reactions — has retained a persistent following that continues to claim evidence of success.Google’s US$10-million project aimed to test the cold-fusion claims rigorously in a field that lacked credible scientific data, says Trevithick. Another goal was also to push methods in challenging experimental conditions. But, he adds: “The fact that the pay-out could be huge is definitely a component of our interest.Energy sinkNuclear fusion is thought to happen only in extreme environments such as the Sun, where high temperatures and pressures can cause hydrogen atoms to overcome their mutual repulsion and fuse into helium, releasing enormous amounts of energy. Some experiments on Earth are trying to replicate the phenomenon, but haven’t yet proved that they can generate enough energy to make up for the vast amounts they need to run.The probability of atoms fusing at much lower temperatures is thought to be vanishingly small. But, if possible, this phenomenon would bring enormous benefits by doing away with fusion’s vast energy requirements.Google’s team was made up of 30 researchers who had no strong opinions on cold fusion. All had access to each other’s data and apparatus, and could review each other’s work.The researchers pursued the three experimental strands that they deemed sufficiently credible. In one, they tried to load palladium with amounts of deuterium hypothesized to be necessary to trigger fusion. But at high concentrations the team was unable to create stable samples.A second strand followed up on 1990s work by US physicists who claimed to have generated anomalous levels of tritium — another heavy hydrogen isotope, created only through nuclear reactions — by bombarding palladium with pulses of hot deuterium ions. Google’s analysis of nuclear signatures showed no tritium production from this experiment.A final strand involved heating up metallic powders in a hydrogen-rich environment. Some current proponents of cold fusion claim that the process produces excess and unexplained heat, which they theorize is the result of fusing elements. But across 420 tests, the Google-funded team found no such heat excess.But the researchers say that both palladium experiments warrant further study. The hypothesized effects in the tritium experiment could be too small to measure with current equipment, they suggest. The team also says that further work could produce stable samples at extremely high deuterium concentrations, where interesting effects might occur.All the projects pushed the frontier of experimental methods, says Trevithick, including developing “the best calorimeters in the world” to detect even slight excesses of heat under extreme experimental conditions. These could potentially be used to test future claims.Pushing the envelope“I think that the authors have done a really good job,” says David Williams, an electrochemist at the University of Auckland in New Zealand — especially in how they have navigated the controversial topic. Pushing the envelope of measurement science is also important, says Williams, whose team did some of the first failed replication studies of the original claim.The techniques the team developed to load palladium may also help researchers to boost the hydrogen storage capacity of materials being studied for use in batteries and fuel cells, says George Chen, an electrochemist at the University of Nottingham’s China campus in Ningbo. Trevithick notes that in one case his team has not been able to reach even the hypothesized starting conditions for fusion, so have not fully eliminated the possibility that it occurs.But Close says that being unable to rule an idea out completely does not mean there is good reason to pursue it. “You cannot prove a negative in science,” he says. If Google wants to invest in cold fusion — that’s up to them, he says. But “if somebody I was investing my money in started doing this, I would withdraw my money”, says Close.Curtis Berlinguette, a chemist at the University of British Columbia in Vancouver and one of the project’s principal investigators, is sceptical of the “classic” cold-fusion experiments. But he was excited to do the work and thinks that a new generation of creative scientists could develop methods that drive fusion reactions at low temperatures. Some might judge the team harshly but the project simply explored an underexplored space — which was off limits because of prejudice, he says. “This is what we are supposed to do as scientists.”Gibson, B.M., Rahman, I.A., Maloney, K.M., Racicot, R.A., Mocke, H., Laflamme, M., Darroch, S.A.F., 2019. Gregarious suspension feeding in a modular Ediacaran organism. Science Advances 5, Artical eaaw0260. Precambrian eukaryotic paleoecology is pivotal to understanding the origins of the modern, animal-dominated biosphere. Here, we combine new fossil data from southern Namibia with computational fluid dynamics (CFD) to test between competing feeding models for the Ediacaran taxon Ernietta. In addition, we perform simulations for multiple individuals, allowing us to analyze hydrodynamics of living communities. We show that Ernietta lived gregariously, forming shallow marine aggregations in the latest Ediacaran, 548 to 541 million years (Ma) ago. We demonstrate enhanced vertical mixing of the water column above aggregations and preferential redirection of current into body cavities of downstream individuals. These results support the reconstruction of Ernietta as a macroscopic suspension feeder and also provide a convincing paleoecological advantage to feeding in aggregations analogous to those recognized in many extant marine metazoans. These results provide some of the oldest evidence of commensal facilitation by macroscopic eukaryotes yet recognized in the fossil record.Gielnik, A., Pechaud, Y., Huguenot, D., Cébron, A., Esposito, G., van Hullebusch, E.D., 2019. Bacterial seeding potential of digestate in bioremediation of diesel contaminated soil. International Biodeterioration & Biodegradation 143, 104715. contaminated soils constitute an environmental problem which may be solved with the help of bioremediation. Soil bioaugmentation with petroleum degrading bacteria is an efficient clean-up strategy. Currently scientific interest focuses on finding sources of microbial agents able to degrade hydrocarbons which may serve as species pools for enrichments during inoculum preparation. Seven microbial enrichments were obtained from various digestates, from a petroleum contaminated soil and from mix of both: soil and digestate. Diesel degrading capacities of microorganisms from digestates, which may serve as inoculum and nutrient source for bioremediation, were assessed. Additionally, the presence and abundance of alkane monooxygenase encoding genes (alkB) was estimated in enrichments. The highest proportion of alkB genes was found for enrichments originating from composted digestate of organic fraction of municipal solid waste and petroleum contaminated soil having the most efficient diesel removal rates (78 and 77% diesel removal, respectively). Enrichments obtained from digestate mixed with soil have a lower performance than single source enrichments. Strains belonging to Rhodococcus and Achromobacter genus were found in all enrichments, and Rhodococcus dominated in enrichment with the higher diesel degradation potential. All those results indicate a great potential of digestate as a source of diesel degraders for soil bioremediation.Glombitza, C., Egger, M., R?y, H., J?rgensen, B.B., 2019. Controls on volatile fatty acid concentrations in marine sediments (Baltic Sea). Geochimica et Cosmochimica Acta 258, 226-241. fatty acids (VFA) are key intermediates in the degradation pathway of organic matter (OM) in marine sediments. They are products of fermentation and are utilized as substrates in the terminal steps of microbial OM mineralization, such as sulfate reduction and methanogenesis. We studied the distribution of formate, acetate, propionate and butyrate concentrations in the pore water throughout 100-m deep sedimentary sequences in the Baltic Sea. The sediments included both sulfate and methane zones and were retrieved during the Integrated Ocean Drilling Program Expedition 347. VFA concentrations were consistently low throughout the sulfate and methane zones, ranging from few hundred nanomolar to about hundred micromolar, thus pointing to efficient microbial utilization in the terminal OM mineralization steps in both zones. Concentrations of formate followed a different depth trend than the other three VFAs suggesting a different mechanistical control of the formate turnover. Calculations of the Gibbs energy reveal that acetoclastic methanogenesis is exergonic (up to ?30?kJ (mol CH4)?1) throughout the sulfate zone and suggest that methanogens can potentially coexist with sulfate reducers in the sulfate zone while sharing acetate as a substrate. In the deeper methane-rich sediments, the energy yield of acetoclastic methanogenesis is generally very low (less negative than ?10?kJ (mol CH4)?1). The uniformly low acetate concentrations in the methane zone suggest its active microbial turnover but the pathway from acetate to methane still remains unclear. Interestingly, acetoclastic sulfate reduction still yields at least ?20?kJ (mol sulfate)?1 in the methane zone and, thus, sulfate reducers may utilize acetate as electron donor in the methane zone, which is in agreement with the earlier findings of sulfate reducers in methanogenic sediments.G?llner, P.L., Wüstemann, T., Bendschneider, L., Reimers, S., Clark, M.D., Gibson, L., Lightfoot, P.C., Riller, U., 2019. Thermo-mechanical interaction of a large impact melt sheet with adjacent target rock, Sudbury impact structure, Canada. Meteoritics & Planetary Science 54, 1228-1245. 1.85?Ga Sudbury Igneous Complex (SIC) and its thermal aureole are unique on Earth with regard to unraveling the effects of a large impact melt sheet on adjacent target rocks. Notably, the formation of Footwall Breccia, lining the basal SIC, remains controversial and has been attributed to impact, cratering, and postcratering processes. Based on detailed field mapping and microstructural analysis of thermal aureole rocks, we identified three distinct zones characterized by static recrystallization, incipient melting, and crystallization textures. The temperature gradient in the thermal aureole increases toward the SIC and culminates in a zone of partial melting, which correlates spatially with the Footwall Breccia. We therefore conclude that assimilation of target rock into initially superheated impact melt and simultaneous deformation after cratering strongly contributed to breccia formation. Estimated melt fractions of the Footwall Breccia amount to 80 vol% and attest to an extreme loss in mechanical strength and, thus, high mobility of the Breccia during assimilation. Transport of highly mobile Footwall Breccia material into the overlying Sublayer Norite of the SIC and vice versa can be attributed to Raleigh?Taylor instability of both units, long-term crater modification caused by viscous relaxation of crust underlying the Sudbury impact structure, or both.Gomez-Bolivar, J., Mikheenko, I.P., Orozco, R.L., Sharma, S., Banerjee, D., Walker, M., Hand, R.A., Merroun, M.L., Macaskie, L.E., 2019. Synthesis of Pd/Ru bimetallic nanoparticles by Escherichia coli and potential as a catalyst for upgrading 5-hydroxymethyl furfural into liquid fuel precursors. Frontiers in Microbiology 10, 1276. doi: 10.3389/fmicb.2019.01276. coli cells support the nucleation and growth of ruthenium and ruthenium-palladium nanoparticles (Bio-Ru and Bio-Pd/Ru NPs). We report a method for the synthesis of these monometallic and bimetallic NPs and their application in the catalytic upgrading of 5-hydroxymethyl furfural (5-HMF) to 2,5 dimethylfuran (DMF). Examination using high resolution transmission electron microscopy with energy dispersive X-ray microanalysis (EDX) and high angle annular dark field (HAADF) showed Ru NPs located mainly at the cell surface using Ru(III) alone but small intracellular Ru-NPs (size ~ 1-2 nm) were visible only in cells that had been pre-‘seeded’ with Pd(0) (5 wt%) and loaded with equimolar Ru. Pd(0) NPs were distributed between the cytoplasm and cell surface. Cells bearing 5%Pd/5%Ru showed some co-localization of Pd and Ru but chance associations were not ruled out. Cells loaded to 5 wt% Pd/20wt% Ru showed evidence of core-shell structures (Ru core, Pd shell) at the cell surface. Examination of the cell surface material using X-ray photoelectron spectroscopy (XPS) showed Pd(0) and Pd(II) and Ru(IV) and Ru(III), with confirmation by XANES and EXAFS analysis of bulk material. Both Bio-Ru NPs and Bio-Pd/Ru NPs were active in the conversion of 5-HMF into 2,5-DMF but commercial Ru on carbon catalyst outperformed 5 wt% bio-Ru by 4-fold. While 5wt%Pd/20wt%Ru achieved 20% yield of DMF the performance of the 5wt%Pd/5wt%Ru bio-catalyst was higher and comparable to the commercial 5wt% Ru/C catalyst in a test reaction using commercial 5-HMF (> 50% selectivity). 5-HMF was prepared by thermochemical hydrolysis of starch and cellulose with solvent extraction of 5-HMF into methyltetrahydrofuran (MTHF). Under these conditions and with MTHF as the reaction solvent the commercial Ru/C catalyst had little activity (100 conversion, negligible selectivity to DMF) whereas the 5wt%Pd/5wt%Ru bio-bimetallic gave 100% conversion and 14% selectivity to DMF from material extracted the hydrolyzates. The results indicate a potential green method for realising increased energy potential from biomass wastes as well as showing a novel bio-based pathway to manufacturing a scarcely-described bimetallic material.Gómez-Consarnau, L., Needham, D.M., Weber, P.K., Fuhrman, J.A., Mayali, X., 2019. Influence of light on particulate organic matter utilization by attached and free-living marine bacteria. Frontiers in Microbiology 10, 1204. doi: 10.3389/fmicb.2019.01204. plays a central role on primary productivity of aquatic systems. Yet, its potential impact on the degradation of photosynthetically produced biomass is not well understood. We investigated the patterns of light-induced particle breakdown and bacterial assimilation of detrital C and N using 13C and 15N labeled freeze-thawed diatom cells incubated in laboratory microcosms with a marine microbial community freshly collected from the Pacific Ocean. Particles incubated in the dark resulted in increased bacterial counts and dissolved organic carbon concentrations compared to those incubated in the light. Light also influenced the attached and free-living microbial community structure as detected by 16S rRNA gene amplicon sequencing. For example, Sphingobacteriia were enriched on dark-incubated particles and taxa from the family Flavobacteriaceae and the genus Pseudoalteromonas were numerically enriched on particles in the light. Isotope incorporation analysis by phylogenetic microarray and NanoSIMS (a method called Chip-SIP) identified free-living and attached microbial taxa able to incorporate N and C from the particles. Some taxa, including members of the Flavobacteriaceae and Cryomorphaceae, exhibited increased isotope incorporation in the light, suggesting the use of photoheterotrophic metabolisms. In contrast, some members of Oceanospirillales and Rhodospirillales showed decreased isotope incorporation in the light, suggesting that their heterotrophic metabolism, particularly when occurring on particles, might increase at night or may be inhibited by sunlight. These results show that light influences particle degradation and C and N incorporation by attached bacteria, suggesting that the transfer between particulate and free-living phases are likely affected by external factors that change with the light regime, such as time of day, water column depth and season.Gómez, F., Cavalazzi, B., Rodríguez, N., Amils, R., Ori, G.G., Olsson-Francis, K., Escudero, C., Martínez, J.M., Miruts, H., 2019. Ultra-small microorganisms in the polyextreme conditions of the Dallol volcano, Northern Afar, Ethiopia. Scientific Reports 9, Article 7907. Dallol geothermal area in the northern part of the Danakil Depression (up to 124–155 meter below sea level) is deemed one of the most extreme environments on Earth. The area is notable for being part of the Afar Depression, an incipient seafloor-spreading center located at the triple junction, between Nubian, Somali and Arabian plates, and for hosting environments at the very edge of natural physical-chemical extremities. The northern part of the Danakil Depression is dominated by the Assale salt plain (an accumulation of marine evaporite deposits) and hosts the Dallol volcano. Here, the interaction between the evaporitic deposit and the volcanisms have created the unique Dallol hot springs, which are highly acidic (pH?~?0) and saline (saturation) with maximum temperatures ranging between 90 and 109?°C. Here we report for the first time evidence of life existing with these hot springs using a combination of morphological and molecular analyses. Ultra-small structures are shown to be entombed within mineral deposits, which are identified as members of the Order Nanohaloarchaea. The results from this study suggest the microorganisms can survive, and potential live, within this extreme environment, which has implications for understanding the limits of habitability on Earth and on (early) Mars.Gopalsamy, K., Thripati, S., Ramabhadran, R.O., 2019. Weak interactions in interstellar chemistry: How do open shell molecules interact with closed shell molecules? ACS Earth and Space Chemistry 3, 1080-1095. interstellar medium (ISM) is home to several open shell and closed shell molecules considered to be unusual or highly unstable on Earth. The chemistry of these molecules in the ISM has been widely studied over many decades. However, the concept of weak chemical interactions, which is terrestrially well-studied, has not been highlighted much in interstellar chemistry. In this study, we illustrate the wide variety of possible weak interactions in the ISM occurring between a carefully chosen set of open shell (OH, SH, CN, NO, NH2, and HO2) and closed shell (H2O, H2S, HF, HCl, NH3, PH3,HCN, HNC, HCP, CH3OH, and CH3SH) molecules, which are important in interstellar chemistry. We expound upon the structural and energetic features of the weak interactions by employing electronic structure calculations [CCSD(T) and density functional theory]. The nature of the weak interactions is further probed by three different techniques, viz., the atoms-in-molecules (AIM) method, the transfer of spin densities, and the natural bond orbital (NBO) method. The astrochemical implications of the weak interactions are subsequently discussed, and it is suggested that the weak interactions could impact the molecular abundances in the ISM.Gorce, J.S., Caddick, M.J., Bodnar, R.J., 2019. Thermodynamic constraints on carbonate stability and carbon volatility during subduction. Earth and Planetary Science Letters 519, 213-222. breakdown of carbonate minerals at high pressure is frequently cited as an important mechanism that leads to carbon release from subducted rocks. However, carbonate minerals in the subducting slab are predicted to be stable to depths that are greater than arc-generating magma depths of approximately 150 km, implying that breakdown of carbonate phases in dehydrated MORB may not be a major contributor to arc volcano carbon budgets. To account for this discrepancy, previous studies have suggested that addition of H2O-rich fluids promotes the breakdown of carbonate-rich lithologies, thus generating volatile C species that could be incorporated into arc magmas. Here, we explore the feasibility of H2O-mediated decarbonation with a simple thermodynamic model. We calculate equilibrium mineral assemblages and accompanying fluid H2O/CO2 ratios for typical subducted lithologies, assuming a range of subduction zone geotherms, and explore the implications of addition of external fluids that are generated from deserpentinization of ultramafic lithologies at various stages. Results suggest that the liberation of C along volcanic arcs is facilitated by either the breakdown of carbonate minerals due to thermodynamically favorable conditions in hotter subduction systems, or by the breakdown of carbonate minerals during periods of higher fluid productivity associated with deserpentinization at appropriate depths along colder subduction geotherms. A comparison of C fluxes measured at volcanic arcs shows that colder subduction zones generate higher C fluxes, implying that the depth at which deserpentinization reactions occur strongly controls the availability of aqueous fluids for slab decarbonation, and that fluid availability represents the dominant control on carbon volatility during subduction.Gou, Q., Xu, S., 2019. Quantitative evaluation of free gas and adsorbed gas content of Wufeng-Longmaxi shales in the Jiaoshiba area, Sichuan Basin, China. Advances in Geo-Energy Research 3, 258-267. analysis of free gas and adsorbed gas contents in shale reservoirs are great significance for efficient exploration and development of shale gas. Based on the isothermal adsorption experiment of shale samples from Wufeng-Longmaxi Formation of JYA well in Jiaoshiba area and Langmuir volume model, the relationship between shale adsorption capacity and temperature, pressure, organic carbon content, quartz and clay mineral content is analyzed. Besides, the key parameters such as Langmuir volume and Langmuir pressure are dynamically calibrated by combining grey correlation method. A new model for calculating adsorbed gas and free gas is established, which takes fully into account the formation temperature, pressure, total organic carbon and shale mineral components. The results showed that the gas content of shale calculated by the new dynamic modified model is in good agreement with the actual gas content characteristics of shale reservoirs. The new model fully takes into account the vertical and horizontal heterogeneity of mineral components and its influence on shale adsorption capacity. That is not only suitable for the tectonic stability area but also for the gas content analysis in the area with strong tectonic movement. It is concluded that the modified calculation model can effectively predict the adsorbed gas, free gas and total gas content of shale reservoirs under formation conditions, which can be used as an indicator for the analysis and prediction of the exploration and development potential of shale gas wells.Gough, D.V., Song, D.H., Sch?neich, S., Prebihalo, S.E., Synovec, R.E., 2019. Development of ultrafast separations using negative pulse partial modulation to enable new directions in gas chromatography. Analytical Chemistry 91, 7328-7335. modulation via a pulse flow valve operated in the negative pulse mode is developed for high-speed one-dimensional gas chromatography (1D-GC), comprehensive two-dimensional (2D) gas chromatography (GC × GC), and comprehensive three-dimensional gas chromatography (GC3). The pulse flow valve readily provides very short modulation periods, PM, demonstrated herein at 100, 200, and 300 ms, and holds significant promise to increase the scope and applicability of GC instrumentation. The negative pulse mode creates an extremely narrow, local analyte concentration pulse. The reproducibility of the negative pulse mode is validated in a 1D-GC mode, where a pseudosteady-state analyte stream is modulated, and 8 analytes are baseline resolved (resolution, Rs ≥ 1.5) in a 200 ms window, providing a peak capacity, nc, of 14 at unit resolution (Rs = 1.0). Additionally, the pulse width, pw, of the pulse flow valve “injection” relationship to peak width-at-base, wb, resolution between peaks and detection sensitivity are studied. To demonstrate the applicability to GC × GC, a high-speed separation of a 20-component test mixture of similar, volatile analytes is shown. Analytes were separated on the second-dimension column, 2D, with 2wb ranging from 7 to 12 ms, providing an exceptional 2D peak capacity, 2nc, of ～12 using a modulation period (PM) of 100 ms. Next, a 12 min separation of a diesel sample using a PM of 300 ms is presented. The 1wb is ～4 s, resulting in a 1nc of ～180, and 2wb is ～18 ms, resulting in a 2nc of ～17, thus achieving a nc,2D of ～3000 in this rapid GC × GC diesel separation. Finally, GC3 with time-of-flight mass spectrometry (TOFMS) detection using a PM of 100 ms applied between the 2D and 3D columns is reported. Narrow third dimension, 3D, peaks with 3wb of ～15 ms were obtained, resulting in a GC3 peak capacity, nc,3D, of ～35?000 in a 45 min separation.Gourier, D., Binet, L., Calligaro, T., Cappelli, S., Vezin, H., Bréhéret, J., Hickman-Lewis, K., Gautret, P., Foucher, F., Campbell, K., Westall, F., 2019. Extraterrestrial organic matter preserved in 3.33?Ga sediments from Barberton, South Africa. Geochimica et Cosmochimica Acta 258, 207-225. paramagnetic resonance (EPR) analysis of carbonaceous, volcanic, tidal sediments from the 3.33?Ga-old Josefsdal Chert (Kromberg Formation, Barberton Greenstone Belt), documents the presence of two types of insoluble organic matter (IOM): (1) IOM similar to that previously found in Archean cherts from numerous other sedimentary rocks in the world and of purported biogenic origin; (2) anomalous IOM localized in a 2?mm-thick sedimentary horizon. Detailed analysis by continuous-wave-EPR and pulse-EPR reveals that IOM in this layer is similar to the insoluble component of the hydrogenated organic matter in carbonaceous chondrites, suggesting that this narrow sedimentary horizon has preserved organic matter of extraterrestrial origin. This conclusion is supported by the presence in this thin layer of another anomalous EPR signal at g?=?3 attributed to Ni-Cr-Al ferrite spinel nanoparticles, which are known to form during atmospheric entry of cosmic objects. From this EPR analysis, it was deduced that the anomalous sedimentary layer originates from deposition, in a nearshore environment, of a cloud of tiny dust particles originating from a flux of micrometeorites falling through the oxygen-poor Archean atmosphere.Grandy, J.J., Lashgari, M., Heide, H.V., Poole, J., Pawliszyn, J., 2019. Introducing a mechanically robust SPME sampler for the on-site sampling and extraction of a wide range of untargeted pollutants in environmental waters. Environmental Pollution 252. Part A, 825-834. present study introduces a mechanically robust, sealable SPME sampler for the on-site sampling and extraction of a wide range of untargeted pollutants in environmental waters. Spray-coating and dip coating methodologies were used to coat the surfaces of six stainless steel bolts with a layer of HLB/PAN particles, which served as the extractive substrate in the proposed device. In addition, this sampler was designed to withstand rough handling, long storage times, and various environmental conditions. In order to identify whether the sampler was able to stabilize extracted compounds for long periods of time, the effects of storage time and temperature were evaluated. The results of these tests showed no significant differences in the quantity and quality of the extracted chemicals following 12 days storage at room temperature, thus confirming the device's suitability for use at sampling sites that are far away from the laboratory facilities. The proposed device was also used to perform extraction and untargeted analyses of river waters in five different geographical locations. The constituent chemicals in the samplers were analyzed and determined using high-resolution HPLC-Orbitrap MS. Toxin and Toxin-Target Database was used as a reference database for toxins and environmental contaminants. Ultimately, over 80 tentative chemicals with widely varying hydrophobicities ranging within ?2.43?<?logP <11.9—including drugs, metabolites, wide ranges of toxins, pesticide, and insecticides—were identified in the samplers used in the different rivers. The log P values for the tentative analytes confirmed that the introduced device is suitable for the extraction and trace analysis of wide ranges of targeted and untargeted pollutants.Gregory, D., Mukherjee, I., Olson, S.L., Large, R.R., Danyushevsky, L.V., Stepanov, A.S., Avila, J.N., Cliff, J., Ireland, T.R., Raiswell, R., Olin, P.H., Maslennikov, V.V., Lyons, T.W., 2019. The formation mechanisms of sedimentary pyrite nodules determined by trace element and sulfur isotope microanalysis. Geochimica et Cosmochimica Acta 259, 53-68. sensitive trace elements in pyrite, including nodules, are increasingly used to infer the chemical conditions of ancient oceans—but considerable uncertainty remains regarding the mechanism and timing of nodule formation. Resolving these uncertainties is important because pyrite nodules must form in connection with the overlying water column, rather than during late diagenesis, to reflect the composition of the global ocean. Existing models for pyrite nodule formation have been specific to pyrite textures from individual sites, and we lack a unified model that can explain the compositional and textural diversity observed in nodules from different localities. In this study we examine ten pyrite nodules from several geological periods (Neoarchean to Carboniferous) using in situ LA-ICP-MS and SHRIMP-SI analyses. We present transects of spot analyses of trace elements (As, Ag, Cu, Co, Ni, Sb and Se) and S isotope ratios for each nodule. The pyrite nodules can be classified according to three main categories: those with (1) little to no trace element or isotopic zonation of the nodule from core to margin, (2) strong zonation from core to margin, and (3) minor zonation near the core but more significant zonation near the margin of the nodule. We further illustrate this zonation with a NanoSIMS element map from an additional pyrite nodule. These results are interpreted to indicate nodule formation along a spectrum between two end-member mechanisms. We suggest that the absence of trace element or isotopic zonation reflects nodule growth by a pathway that is analogous to the pervasive growth mechanism for carbonate nodules. This model involves the production of many nucleation sites that are evenly distributed within the volume that the nodule eventually occupies. Consequently, this mechanism results in a chemically homogenous nodule. Pyrites formed this way are suitable for paleoceanographic reconstruction. The other end-member mechanism is analogous to the concentric growth model for carbonate concretions. In this scenario, the core of the nodule forms first and is followed by the addition of concentric layers—each with a progressively different trace element content and δ34S signature as diagenesis progresses. Despite having limited utility for reconstructing ancient seawater, these late forming nodules may track the evolving availability of bioessential trace elements for the subsurface biosphere with important implications for global biogeochemical cycles. Spatial trends in trace elements and S isotopes thus speak to the mechanisms of pyrite nodule formation and provide a framework for evaluating nodule suitability for a range of paleoenvironmental studies.Groeneveld, J., Ho, S.L., Mackensen, A., Mohtadi, M., Laepple, T., 2019. Deciphering the cariability in Mg/Ca and stable oxygen isotopes of individual foraminifera. Paleoceanography and Paleoclimatology 34, 755-773. are commonly used in paleoclimate reconstructions as they occur throughout the world's oceans and are often abundantly preserved in the sediments. Traditionally, foraminifera‐based proxies like δ18O and Mg/Ca are analyzed on pooled specimens of a single species. Analysis of single specimens of foraminifera allows reconstructing climate variability on timescales related to El Ni?o–Southern Oscillation or seasonality. However, quantitative calibrations between the statistics of individual foraminifera analyses (IFA) and climate variability are still missing. We performed Mg/Ca and δ18O measurements on single specimens from core top sediments from different settings to better understand the signal recorded by individual foraminifera. We used three species of planktic foraminifera (Globigerinoides ruber (s.s.), T. sacculifer, and N. dutertrei) from the Indo‐Pacific Warm Pool and one species (G. ruber (pink)) from the Gulf of Mexico. Mean values for the different species of Mg/Ca versus calculated δ18O temperatures agree with published calibration equations. IFA statistics (both mean and standard deviation) of Mg/Ca and δ18O between the different sites show a strong relationship indicating that both proxies are influenced by a common factor, most likely temperature variations during calcification. This strongly supports the use of IFA to reconstruct climate variability. However, our combined IFA data for the different species only show a weak relationship to seasonal and interannual temperature changes, especially when seasonal variability increases at a location. This suggests that the season and depth habitat of the foraminifera strongly affect IFA variability, such that ecology needs to be considered when reconstructing past climate variability.Guitreau, M., Flahaut, J., 2019. Record of low-temperature aqueous alteration of Martian zircon during the late Amazonian. Nature Communications 10, Article 2457. lines of evidence support the presence of liquid water on Mars at different times. Among those, hydrated minerals testify to past aqueous weathering processes that can be precisely studied in Martian meteorites such as NWA 7533/7034. Bringing constraints on the timing of weathering of the Martian crust would help understand its evolution, the availability of liquid water, and the habitability of Mars. Here we present a new method based on U–Th–Pb isotope systems to assess if zircon crystals underwent low-temperature aqueous alteration, such as exemplified by Hadean-aged detrital crystals from Western Australia. Data for NWA 7533 zircons show evidence for aqueous alteration and modeling of U–Th–Pb isotope system evolution indicates that the latest alteration event occurred during the late Amazonian (227–56 Ma). This finding largely expands the time duration over which liquid water was available near the Martian surface, thereby suggesting that Mars might still be habitable.Guo, C., Nisancioglu, K.H., Bentsen, M., Bethke, I., Zhang, Z., 2019. Equilibrium simulations of Marine Isotope Stage 3 climate. Climate of the Past 15, 1133-1151. equilibrium simulation of Marine Isotope Stage 3 (MIS3) climate with boundary conditions characteristic of Greenland Interstadial 8 (GI-8; 38?kyr?BP) is carried out with the Norwegian Earth System Model (NorESM). A computationally efficient configuration of the model enables long integrations at relatively high resolution, with the simulations reaching a quasi-equilibrium state after 2500 years. We assess the characteristics of the simulated large-scale atmosphere and ocean circulation, precipitation, ocean hydrography, sea ice distribution, and internal variability. The simulated MIS3 interstadial near-surface air temperature is 2.9?°C cooler than the pre-industrial (PI). The Atlantic meridional overturning circulation (AMOC) is deeper and intensified by ～13?%. There is a decrease in the volume of Antarctic Bottom Water (AABW) reaching the Atlantic. At the same time, there is an increase in ventilation of the Southern Ocean, associated with a significant expansion of Antarctic sea ice and concomitant intensified brine rejection, invigorating ocean convection. In the central Arctic, sea ice is ～2?m thicker, with an expansion of sea ice in the Nordic Seas during winter. Attempts at triggering a non-linear transition to a cold stadial climate state, by varying atmospheric CO2 concentrations and Laurentide Ice Sheet height, suggest that the simulated MIS3 interstadial state in the NorESM is relatively stable, thus underscoring the role of model dependency, and questioning the existence of unforced abrupt transitions in Greenland climate in the absence of interactive ice sheet–meltwater dynamics.Guo, W., Zhang, S., Wu, G., 2019. Quantitative oil spill risk from offshore fields in the Bohai Sea, China. Science of The Total Environment 688, 494-504. oil spill risk in the environments surrounding the Bohai Sea is aggravated by increasing marine petroleum exploitation. There is a growing need to assess the risk of oil pollution in sensitive marine areas and coastlines. Both the recurrence frequency of spill accidents and the duration of exposure in marine areas and coastal shorelines are considered in our statistical model, which consists of a probabilistic oil spill model used to simulate various oil spill scenarios at twenty oil fields in the Bohai Sea based on high-resolution oceanographic, meteorological, and geomorphological data. The statistical results of the risk to marine areas integrate the probability of pollution in marine areas, oil slick thickness, and duration of water surface covered by a floating slick. The coastal risk index includes the probability of a shoreline hit, average mass of stranding oil, and time of oil beaching. The spatial distributions of environmental triggering factors and coastal/marine vulnerability are merged, and a map of the oil spill risk in the Bohai Sea is presented, which is useful for contingency planning and the assessment of environmental risk of marine petroleum exploitation.Guo, X., He, S., Liu, K., Yang, Z., Yuan, S., Liu, M., 2019. Generation and evolution of overpressure caused by hydrocarbon generation in the Jurassic source rocks of the central Junggar Basin, northwestern China. American Association of Petroleum Geologists Bulletin 103, 1553-1574. Jurassic black mudstone and coal beds in the central Junggar Basin, northwestern China, are the major source rocks for the basin with type II2 and type III (gas-prone) kerogens. Widespread overpressures are developed in the Jurassic stratigraphic interval. Sonic and resistivity logs display strong characteristic responses of overpressure in the mudstones, with anomalously high acoustic traveltimes and low resistivity compared with the normally pressured mudstones. The overpressured Jurassic sediment sequences appear to have undergone normal compaction because the mudstones exhibit no anomalously low bulk density. The overpressured mudstones deviate from the normally pressured mudstones in density–effective vertical stress space. The overpressure in the Jurassic source rocks is, therefore, not caused by disequilibrium compaction. The overpressured Jurassic sandstone reservoirs are predominantly oil and gas saturated or oil bearing. The well-log responses of the overpressured mudstones and seismic velocity characteristics indicate that the top depth of the overpressure zone ranges from 3800 to 4600 m (12,500 to 15,100 ft), corresponding to formation temperatures of approximately 94°C to 111°C (～201°F to 232°F), with estimated vitrinite reflectance values of 0.6% to 0.75%. The Jurassic source rocks with overpressure are capable of generating hydrocarban at present and are currently overpressured. All the evidence suggests that the overpressure in the Jurassic source rocks in the central Junggar Basin is caused by hydrocarbon (HC) generation. The overpressure evolution was modeled quantitatively in response to pressure changes caused by HC generation during basin evolution. The results indicate that multiple episodes of overpressure development and release occurred within the Jurassic source rocks, suggesting multiple episodes of HC expulsion. The timing and numbers of these episodes of HC expulsion were thus determined from the modeled overpressure evolution.Guo, X., Hu, D., Li, Y., Duan, J., Zhang, X., Fan, X., Duan, H., Li, W., 2019. Theoretical progress and key technologies of onshore ultra-deep oil/gas exploration. Engineering 5, 458-470. exploration around the world has extended into deep and ultra-deep strata because it is increasingly difficult to find new large-scale oil/gas reservoirs in shallow to middle buried strata. In recent years, China has made remarkable achievements in oil/gas exploration in ultra-deep areas including carbonate and clastic reservoirs. Some (ultra) large-scale oil and gas fields have been discovered. The oil/gas accumulation mechanisms and key technologies of oil/gas reservoir exploration and development are summarized in this study in order to share China’s experiences. Ultra-deep oil/gas originates from numerous sources of hydrocarbons and multiphase charging. Liquid hydrocarbons can form in ultra-deep layers due to low geothermal gradients or overpressures, and the natural gas composition in ultra-deep areas is complicated by the reactions between deep hydrocarbons, water, and rock or by the addition of mantle or crust-sourced gases. These oils/gases are mainly stored in the original high-energy reef shoal complexes or in sand body sediments. They usually have high original porosity. Secondary pores are often developed by dissolution, dolomitization, and fracturing in the late stage. The early pores have been preserved by retentive diagenesis such as the early charging of hydrocarbons. Oil/gas accumulation in ultra-deep areas generally has the characteristics of near-source accumulation and sustained preservation. The effective exploration and development of ultra-deep oil/gas reservoirs depend on the support of key technologies. Use of the latest technologies such as seismic signal acquisition and processing, low porosity and permeability zone prediction, and gas-water identification has enabled the discovery of ultra-deep oil/gas resources. In addition, advanced technologies for drilling, completion, and oil/gas testing have ensured the effective development of these fields.Guo, X., Hu, D., Liu, R., Wei, X., Wei, F., 2019. Geological conditions and exploration potential of Permian marine–continent transitional facies shale gas in the Sichuan Basin. Natural Gas Industry B 6, 198-204.–continent transitional facies shale of the Longtan Fm, Upper Permian is an important source rock stratum in the Sichuan Basin. The previous researches on it mainly focus more on source rock evaluation, but less on shale gas accumulation. In this paper, the test and analysis results of Well DYS1, the coring well of Longtan Fm were dissected. Combined with the drilling results of its adjacent area, the organic rich shale in the Longtan Fm were studied from the aspects of distribution, geochemical, reservoir, gas-bearing characteristics and roof and floor conditions, and then compared with the shale strata with similar sedimentary background and good shale gas shows. And accordingly, its geological conditions for the formation of Longtan shale gas and its exploration potential were made clear. And the following research results were obtained. First, in the southeastern Sichuan Basin, the organic rich shale of transitional facies of Longtan Fm is developed with a thickness of more than 40?m. It is characterized by high brittle mineral content, high porosity, high total organic carbon (TOC), moderate thermal evolution (Ro) and good gas-bearing property. Therefore, it is geologically favorable for the formation of shale gas. Second, compared with the existing transitional facies shales at home and abroad, the Longtan shale is better in terms of porosity, TOC, Ro, gas content and other key parameters. Third, the type of organic matters is the main reason for the low development degree of organic pores in the Longtan shale. And during its shale gas exploration and selection, the coal seam enriched sections shall be avoided. In conclusion, considering the development degree, interlayer thickness, depth and preservation conditions of organic rich shale comprehensively, the Qijiang–Chishui area is the best exploration area for the transitional facies shale gas of Longtan Fm in the Sichuan Basin.Gupta, N., Skinner, K.A., Summers, Z.M., Edirisinghe, J.N., Faria, J.P., Marshall, C.W., Sharma, A., Gottel, N.R., Gilbert, J.A., Henry, C.S., O’Loughlin, E.J., 2019. Draft genome sequence of Rhodococcus sp. strain ATCC 49988, a quinoline-degrading bacterium. Microbiology Resource Announcements 8, Article e00403-19. report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation.Gurven, M.D., Davison, R.J., 2019. Periodic catastrophes over human evolutionary history are necessary to explain the forager population paradox. Proceedings of the National Academy of Sciences 116, 12758-12766.: Much of what is known about human life histories is based on studying modern hunter-gatherers experiencing rapid population growth. Yet, if populations are near-stationary over most of their evolutionary history, the positive growth of contemporary foragers is puzzling and potentially unrepresentative. Investigating multiple demographic scenarios in a large sample of human and chimpanzee populations, we find that periodic catastrophes combined with plausible fertility or mortality reductions can reasonably generate zero population growth. Our findings bolster arguments about the role of intergenerational cooperation and cumulative culture in supporting the colonizing potential of human populations once released from catastrophes.Abstract: The rapid growth of contemporary human foragers and steady decline of chimpanzees represent puzzling population paradoxes, as any species must exhibit near-stationary growth over much of their evolutionary history. We evaluate the conditions favoring zero population growth (ZPG) among 10 small-scale subsistence human populations and five wild chimpanzee groups according to four demographic scenarios: altered mean vital rates (i.e., fertility and mortality), vital rate stochasticity, vital rate covariance, and periodic catastrophes. Among most human populations, changing mean fertility or survivorship alone requires unprecedented alterations. Stochastic variance and covariance would similarly require major adjustment to achieve ZPG in most populations. Crashes could maintain ZPG in slow-growing populations but must be frequent and severe in fast-growing populations—more extreme than observed in the ethnographic record. A combination of vital rate alteration with catastrophes is the most realistic solution to the forager population paradox. ZPG in declining chimpanzees is more readily obtainable through reducing mortality and altering covariance. While some human populations may have hovered near ZPG under harsher conditions (e.g., violence or food shortage), modern Homo sapiens were equipped with the potential to rapidly colonize new habitats and likely experienced population fluctuations and local extinctions over evolutionary history.Haalboom, S., Price, D.M., Mienis, F., van Bleijswijk, J.D.L., de Stigter, H.C., Witte, H.J., Reichart, G.-J., Duineveld, G.C.A., 2019. Successional patterns of (trace) metals and microorganisms in the Rainbow hydrothermal vent plume at the Mid-Atlantic Ridge. Biogeosciences Discussions 2019, 1-44. vent fields found at mid-ocean ridges emit hydrothermal fluids which disperse as neutrally buoyant plumes. From these fluids seafloor massive sulfides (SMS) deposits are formed which are being explored as possible new mining sites for (trace) metals and rare earth elements (REE). It has been suggested that during mining activities large amounts of suspended matter will appear in the water column due to excavation processes, and due to discharge of mining waste from the surface vessel. Understanding how natural hydrothermal plumes evolve as they spread away from their source and how they affect their surrounding environment may provide some analogies for the behaviour of the dilute distal part of chemically enriched mining plumes.This study on the extensive Rainbow hydrothermal plume, observed up to 25 km downstream from the vent site, enabled us to investigate how microbial communities change in the presence of a natural plume. The (trace) metal and REE content of suspended particulate matter (SPM) was determined using HR-ICP mass spectrometry and the microbial communities of the neutrally buoyant plume, above plume-, below plume-, and near-bottom water and sediment were characterised by using 16S rRNA amplicon sequencing methods. Both vertically in the water column and horizontally along the neutrally buoyant plume, geochemical and biological changes were evident as the neutrally buoyant plume stood out by its enrichments in (trace) metals and REEs, of which the concentrations changed as the plume aged. This was also reflected in the background pelagic system as Epsilonproteobacteria started to dominate and the biodiversity appeared to reduce with distance away from the Rainbow hydrothermal vent field. The Rainbow hydrothermal plume provides a geochemically enriched natural environment, which is a heterogeneous, dynamic habitat that is conducive to ecological changes in a short time span.Han, Y., Horsfield, B., LaReau, H., Mahlstedt, N., 2019. Intraformational migration of petroleum: Insights into the development of sweet spot in the Cretaceous Niobrara shale-oil system, Denver Basin. Marine and Petroleum Geology 107, 301-309. Cretaceous Niobrara Formation is one of the latest unconventional exploration targets in North America. In this paper, an overall Type-II marine organofacies with some variability is present within a core which consists of alternating marls and chalks, covering a maturity range of 0.8–1.0 %Rc (calculated vitrinite reflectance). Enhanced oil saturation index (OSI) values have previously been reported for the chalk, and here a positive trend (R2?=?0.92) between the OSI and the percentage of saturates in gross fractions is present. Thus, the saturate fraction gradually increases from 40% to above 60% as the OSI increases from 40 to 550?mg HC/g TOC (total organic carbon). Extremely high OSI values (>300?mg HC/g TOC) are characteristic of Niobrara chalks. Therefore, the chalk intervals represent primary sweet spots. Using a combined analytical approach, petroleum has been shown to migrate from the organic-rich marls into juxtaposed chalks, and that this has fractionated oils into higher quality liquids. Extractable organic matter in the chalks is clearly enriched in saturate hydrocarbons, while the NSO-containing polar compounds are preferentially retained in the shale and marl units. Compared with the significant fractionation effects between these gross fractions, fractionation within a given compound class is nevertheless indistinct.Hao, N., Alper, K., Tekin, K., Karagoz, S., Ragauskas, A.J., 2019. One-pot transformation of lignocellulosic biomass into crude bio-oil with metal chlorides via hydrothermal and supercritical ethanol processing. Bioresource Technology 288, Article 121500. seeds were deconstructed in both hydrothermal and supercritical ethanol media with a combination of two metal chlorides (TiCl4:MgCl2) to produce bio-oils. The use of metal chloride additives in supercritical ethanol achieved the highest bio-oil yield of 49.2?wt% (300?°C, 30?min). Both the hydrothermal and supercritical ethanol deconstruction with the additives (TiCl4:MgCl2?=?4?mmol:4mmol) produced the bio-oils with a higher heating value (HHV) of 35?MJ/Kg. Gas chromatography-mass spectrometry (GC-MS) analysis of the bio-oils showed that the major products in bio-oils from the hydrothermal deconstruction were acids while the majority products in bio-oils form the supercritical ethanol deconstruction were esters. Nuclear magnetic resonance (NMR) data of the bio-oils suggested that both hydrothermal and supercritical ethanol deconstruction with metal chlorides significantly reduced the non-condensed OH and oxygenated lignin sub-units in bio-oils; while only supercritical ethanol deconstruction with metal chlorides reduced the aliphatic OH and O-alkylated structures in bio-oils.Harris, R.A., Leaptrot, K.L., May, J.C., McLean, J.A., 2019. New frontiers in lipidomics analyses using structurally selective ion mobility-mass spectrometry. TrAC Trends in Analytical Chemistry 116, 316-323. growth of lipidomics and the high isomeric complexity of the lipidome has revealed a need for analytical techniques capable of structurally characterizing lipids with a high degree of specificity. Lipids are morphologically diverse molecules that can exist as any one of a large number of isomeric species, and as such are often indistinguishable by mass spectrometry without a complementary separation method. Recent developments in the field of lipidomics aim to address these challenges by utilizing a combination of multiple analytical techniques which are selective to lipid primary structure. This review summarizes two emerging strategies for lipidomic analysis, namely, ion mobility-mass spectrometry and ion fragmentation via ozonolysis.Hasiotis, S.T., Brake, S.S., 2019. Macroscopic and microscopic morphological features of stromatolites related to activity of eukaryote-dominated biofilms in an acid mine drainage environment: Biosignatures and understanding preservation of stromatolites as trace fossils. Geomicrobiology Journal 36, 651-671., diatom-, and algae-dominated biofilms are the principal producers of iron-rich biolaminates that result in biosedimentary structures, or stromatolites, in an acid mine drainage (AMD) environment in Indiana. These structures are considered trace fossils because they are produced by organism-sediment interactions and record physicochemical conditions of the environment. Our purpose was to link the biofilm types to specific micro- and micromorphological features and the physicochemical conditions under which they were formed. Analyses revealed that Euglena-dominated biofilm produced thin, porous microlaminae by trapping, binding, and relocating AMD precipitates as the biofilm kept pace with chemical sedimentation. More massive microlaminae were produced by high rates of chemical sedimentation brought on by increased discharge and dilution of acidity. Diatom- and algae-dominated biofilms produced thick, mm–cm-scale, porous, spongelike micro- to macrolaminae through oxygenic photosynthesis and/or metal uptake in extracellular polymeric substances, which promoted mineral precipitation on cell walls to create a rigid, porous structure. The variations in biolaminate textures within the stromatolites record seasonal changes in the microbial populations and physicochemical conditions of the AMD environment. These iron-rich stromatolites represent trace fossils that record morphological biosignatures of eukaryote-dominated microbial biofilms and may serve as appropriate proxies in the search for similar evidence of eukaryotic life in other iron-rich paleoenvironments, such as those on early Earth and Mars.Hassan, K.M., 2019. Stable isotope ratios of carbonate and organic carbon from silicified tree trunks, petrified forest, new Cairo, Egypt – possible interpretations of palaeoenvironment. Geochemistry International 57, 564-574. silicified tree trunks of the New Cairo Petrified Forest – evidence of fossilized remains of Paleogene angiosperms also abundant in other sites in Egypt – are found in horizontal positions on the surface and buried completely or partly by Oligocene sand and gravel underlain by late Eocene sediments. Differences in petrographic characteristics allowed for grouping these silicified woods into two types: (1) Type A composed of microgranular quartz ± some goethite ± minor moganite and (2) Type B composed of chalcedony or a mixture of chalcedony and cryptograined quartz ± some goethite ± minor gypsum. The two type groups contain traces of carbonate and organic matter: 0.004 to 0.35 wt % CaCO3 and 0.004 to 0.16 wt % organic carbon. The carbonate of each type has characteristic δ13C and δ18O values: –3.2 ± 5.7‰ VPDB and –0.88 ± 5‰ VPDB for silicified wood Type A and –10.9 ± 6.8‰ VPDB and –7.64 ± 3.3‰ VPDB for silicified wood Type B, respectively. Covariation between carbonate δ13C and δ18O values of both silicified wood Type A and B samples indicate a hydrologically closed system with different inorganic carbon and meteoric water signatures. These interpretations are supported by mineralogical and chemical data from the samples. Various factors likely influenced the carbonate δ13C and δ18O values of the silicified wood samples during the time they formed, including biogenic CO2, water residence effect, salinity, and evaporation. The δ13C values of bulk organic matter of silicified wood Type A and B samples ranging from –24.04 to –26.89‰ VPDB are within a characteristic range of C3-type biomass. The shift to a less negative bulk organic matter δ13C value in these samples (particularly those of the silicified wood Type B) has been attributed to post-depositional changes.He, C., Mu, L., Xu, A., Zhao, L., He, J., Zhang, A., Shan, F., Luo, E., 2019. Phase behavior and miscible mechanism in the displacement of crude oil with associated sour gas. Oil & Gas Science and Technology – Revue d’IFP Energies nouvelles 74, Article 54. re-injection of associated sour gas, with high H2S and CO2 content, into the reservoir is proposed to be an effective development method due to its low investment cost and high oil recovery. The aim of this work is to present the phase behavior and miscible mechanism of crude oil displaced by associated sour gas. Based on the equation of state and the phase equilibrium theory, the phase behavior of crude oil mixed with various gases (associated sour gas, H2S, CO2 and CH4) have been analyzed. Then, the miscibility of associated sour gas was determined by calculating its Minimum Miscible Pressure (MMP) and the effect of sour component fraction on miscibility was evaluated. Moreover, a series of numerical simulations modeling 1D slim-tube were conducted using a compositional simulator to study the miscible mechanism in the displacement of crude oil with associated sour gas. The results show that the injection of H2S can reduce the bubble point pressure of crude oil and therefore is beneficial to prevent the crude oil degassing; nevertheless, the injection of CO2 has little effect on it. The miscible ability of associated sour gas decreases as its sour component fraction decreases. It is observed that the crude oil displaced by associated sour gas and sweet gas both show a combined condensing/vaporizing mechanism, with miscible zone in the middle of transition zone. However, the vaporizing-gas drive mechanism is slightly stronger than the condensing-gas drive mechanism during the displacement by associated sour gas while is significantly stronger during the displacement by sweet gas.He, J., Yu, L., Huang, X., Qi, M., 2019. Triptycene-based stationary phases for gas chromatographic separations of positional isomers. Journal of Chromatography A 1599, 223-230. work presents the investigation of two triptycene-based materials (TP-3OB and TP-3Im) as the stationary phases for gas chromatographic (GC) separations. The TP-3OB and TP-3Im capillary columns fabricated by static coating exhibited column efficiency of 3000–3500 plates/m for n-dodecane at 120?°C. Also, their McReynolds constants and Abraham system constants were determined to characterize their polarity and molecular interactions with analytes. On the basis of the unique 3D TP architecture, the TP-3OB and TP-3Im stationary phases exhibited complementary high-resolution performance for analytes of a wide ranging polarity, including alkylbenzenes, alkylnaphthalenes, halobenzenes, phenols and anilines, respectively. Moreover, the TP-based columns exhibited good repeatability and reproducibility on the retention times of analytes with the relative standard deviation (RSD) values in the range of 0.01–0.14% for run-to-run, 0.11–0.47% for day-to-day and 0.68–4.7% for column-to-column, respectively. Additionally, their applications for the determination of isomer impurities in the commercial reagents of o-dichlorobenzene, p-/m-diethylbenzene, o-toluidine and 2,3-/3,5-xylidine proved their good potential for practical analysis. This work demonstrates the promising future of the triptycene-based stationary phases for chromatographic separations.He, Z., Cui, M., Qian, Q., Zhang, J., Liu, H., Han, B., 2019. Synthesis of liquid fuel via direct hydrogenation of CO2. Proceedings of the National Academy of Sciences 116, 12654-12659.: CO2 is a greenhouse gas. Synthesis of liquid fuel using CO2 and H2 is promising for the sustainability of mankind. The reported technologies usually proceed via CO intermediate, which needs high temperature, and tend to cause low selectivity. Direct hydrogenation of CO2 to liquid fuel, not via CO, is a challenging issue. In this work, we designed a Co6/MnOx nanocatalyst that could successfully avoid the CO route. The reaction could proceed at 200 °C, which is much lower than those reported so far. The selectivity of the liquid fuel in total products reached 53.2 C-mol%, which is among the highest reported to date.Abstract: Synthesis of liquid fuels (C5+ hydrocarbons) via CO2 hydrogenation is very promising. Hydrogenation of CO2 to liquid hydrocarbons usually proceeds through tandem catalysis of reverse water gas shift (RWGS) reaction to produce CO, and subsequent CO hydrogenation to hydrocarbons via Fischer–Tropsch synthesis (FTS). CO2 is a thermodynamically stable and chemically inert molecule, and RWGS reaction is endothermic and needs a higher temperature, whereas FTS reaction is exothermic and is thermodynamically favored at a lower temperature. Therefore, the reported technologies have some obvious drawbacks, such as high temperature, low selectivity, and use of complex catalysts. Herein we discovered that a simple Co6/MnOx nanocatalyst could efficiently catalyze CO2 hydrogenation. The reaction proceeded at 200 °C, which is much lower than those reported so far. The selectivity of liquid hydrocarbon (C5 to C26, mostly n-paraffin) in total product could reach 53.2 C-mol%, which is among the highest reported to date. Interestingly, CO was hardly detectable during the reaction. The in situ Fourier transform infrared characterization and 13CO labeling test confirmed that the reaction was not via CO, accounting for the eminent catalytic results. This report represents significant progress in CO2 chemistry and CO2 transformation.Heidke, I., Scholz, D., Hoffmann, T., 2019. Lignin oxidation products as a potential proxy for vegetation and environmental changes in speleothems and cave drip water – a first record from the Herbstlabyrinth, central Germany. Climate of the Past 15, 1025-1037., we present the first quantitative speleothem record of lignin oxidation products (LOPs), which has been determined in a Holocene stalagmite from the Herbstlabyrinth Cave in central Germany. In addition, we present LOP results from 16 months of drip water monitoring. Lignin is only produced by vascular plants and therefore has the potential to be an unambiguous vegetation proxy and to complement other vegetation and climate proxies in speleothems. We compare our results with stable isotope and trace element data from the same sample. In the stalagmite, LOP concentrations show a similar behavior to P, Ba and U concentrations, which have previously been interpreted as vegetation proxies. The LOP S∕V and C∕V ratios, which are usually used to differentiate between angiosperm and gymnosperm and woody and non-woody vegetation, show complex patterns suggesting additional influencing factors, such as transport and microbiological effects. The drip water from a fast drip site shows a seasonal pattern of LOPs with low LOP concentrations in winter and higher LOP concentrations in summer. These results indicate the potential of LOPs as a new proxy for vegetational and environmental changes in speleothems but also demonstrate the complexity and the current limitations of our understanding of the transport of lignin from the soil into the cave and the speleothems.Hendrix, K., Bleyen, N., Mennecart, T., Bruggeman, C., Valcke, E., 2019. Sodium azide used as microbial inhibitor caused unwanted by-products in anaerobic geochemical studies. Applied Geochemistry 107, 120-130. azide, applied as microbial inhibitor, has caused unwanted by-products in environmental samples during anaerobic, long-term (2–3 year) experiments. When ignored, this can lead to the misinterpretation of observed phenomena. Sodium azide was indeed found to react with several components of environmental samples. Azide reacted with dissolved organic matter present in clay pore water, causing a lowered reducing capacity of the system. It also reacted with pyrite, forming thiosulfate and with ferrous iron, lowering its concentration in solution. When nitrite was added to the environmental samples, nitrous oxide and nitrogen gas were formed through reaction with azide. Azide could act both as an oxidant and reductant. Some of these reactions showed slow kinetics but nonetheless gave rise to significant amounts of by-products during these long-term experiments. When working with environmental samples, sodium azide can affect the chemical composition significantly, especially for long incubation periods. Other sterilization techniques such as filter sterilization are therefore advised.Henkel, J.V., Dellwig, O., Pollehne, F., Herlemann, D.P.R., Leipe, T., Schulz-Vogt, H.N., 2019. A bacterial isolate from the Black Sea oxidizes sulfide with manganese(IV) oxide. Proceedings of the National Academy of Sciences 116, 12153-12155. is one of the most abundant redox-sensitive metals on earth. Some microorganisms are known to use Mn(IV) oxide (MnO2) as electron acceptor for the oxidation of organic compounds or hydrogen (H2), but so far the use of sulfide (H2S) has been suggested but not proven. Here we report on a bacterial isolate which grows autotrophically and couples the reduction of MnO2 to the oxidation of H2S or thiosulfate (S2O32?) for energy generation. The isolate, originating from the Black Sea, is a species within the genus Sulfurimonas, which typically occurs with high cell numbers in the vicinity of sulfidic environments [Y. Han, M. Perner, Front. Microbiol. 6, 989 (2015)]. H2S and S2O32? are oxidized completely to sulfate (SO42?) without the accumulation of intermediates. In the culture, Mn(IV) reduction proceeds via Mn(III) and finally precipitation of Ca-rich Mn(II) carbonate [Mn(Ca)CO3]. In contrast to Mn-reducing bacteria, which use organic electron donors or H2, Fe oxides are not observed to support growth, which may either indicate an incomplete gene set or a different pathway for extracellular electron transfer.Hepp, J., Sch?fer, I.K., Lanny, V., Franke, J., Bliedtner, M., Rozanski, K., Glaser, B., Zech, M., Eglinton, T.I., Zech, R., 2019. Evaluation of bacterial glycerol dialkyl glycerol tetraether and 2H-18O biomarker proxies along a Central European topsoil transect. Biogeosciences Discussions 2019, 1-27. fossils, like bacterial branched glycerol dialkyl glycerol tetraethers (brGDGTs), and the stable isotopic composition of biomarkers, such as δ2H of leaf wax-derived n-alkanes (δ2Hn-alkane) or δ18O of hemicellulose-derived sugars (δ18Osugar) are increasingly used for the reconstruction of past climate and environmental conditions. Plant-derived δ2Hn-alkane and δ18Osugar values record the isotopic composition of plant source water (δ2H/δ18Osource-water), which usually reflects mean annual precipitation (δ2H/δ18Oprecipiation), modulated by evapotranspirative leaf water enrichment and biosynthetic fractionation. Accuracy and precision of respective proxies should be ideally evaluated at a regional scale. For this study, we analysed topsoils below coniferous and deciduous forests, as well as grassland soils along a Central European transect in order to investigate the variability and robustness of various proxies, and to identify effects related to vegetation. Soil pH-values derived from brGDGTs correlate reasonably well with measured soil pH-values, but systematically overestimate them (ΔpH?=?0.6?±?0.6). The branched vs. isoprenoid tetraether index (BIT) can give some indication whether the pH reconstruction is reliable. Temperatures derived from brGDGTs overestimate mean annual air temperatures slightly (?TMA?=?0.5?°C?±?2.4). Apparent isotopic fractionation (εn-alkane/precipitation and εsugar/precipitation) is lower for grassland sites than for forest sites due to "signal damping", i.e. grass biomarkers do not record the full evapotranspirative leaf water enrichment. Coupling δ2Hn-alkane with δ18Osugar allows to reconstruct the stable isotopic composition of the source water more accurately than without the coupled approach (Δδ2H?=?~-21?‰?±?22 and Δδ18O?=?~-2.9?‰?±?2.8). Similarly, relative humidity during daytime and vegetation period (RHMDV) can be reconstructed using the coupled isotope approach (ΔRHMDV?=?~-17?±?12). Especially for coniferous sites, reconstructed RHMDV values as well as source water isotope composition underestimate the measured values. This can be likely explained by understory grass vegetation at the coniferous sites contributing significantly to the n-alkane pool but only marginally to the sugar pool in the topsoil. The large uncertainty likely reflect the fact that biosynthetic fractionation is not constant, as well as microclimate variability. Overall, GDGTs and the coupled δ2Hn-alkane-δ18Osugar approach have great potential for more quantitative paleoclimate reconstructions.Herrmann, A.J., Gehringer, M.M., 2019. An investigation into the effects of increasing salinity on photosynthesis in freshwater unicellular cyanobacteria during the late Archaean. Geobiology 17, 343-359. oldest species of bacteria capable of oxygenic photosynthesis today are the freshwater Cyanobacteria Gloeobacter spp., belonging to the class Oxyphotobacteria. Several modern molecular evolutionary studies support the freshwater origin of cyanobacteria during the Archaean and their subsequent acquisition of salt tolerance mechanisms necessary for their expansion into the marine environment. This study investigated the effect of a sudden washout event from a freshwater location into either a brackish or marine environment on the photosynthetic efficiency of two unicellular freshwater cyanobacteria: the salt‐tolerant Chroococcidiopsis thermalis PCC7203 and the cyanobacterial phylogenetic root species, Gloeobacter violaceus PCC7421. Strains were cultured under present atmospheric levels (PAL) of CO2 or an atmosphere containing elevated levels of CO2 and reduced O2 (eCO2rO2) in simulated shallow water or terrestrial environmental conditions. Both strains exhibited a reduction in growth rates and gross photosynthesis, accompanied by significant reductions in chlorophyll a content, in brackish water, with only C. thermalis able to grow at marine salinity levels. While the experimental atmosphere caused a significant increase in gross photosynthesis rates in both strains, it did not increase their growth rates, nor the amount of O2 released. The differences in growth responses to increasing salinities could be attributed to genetic differences, with C. thermalis carrying additional genes for trehalose synthesis. This study demonstrates that, if cyanobacteria did evolve in a freshwater environment, they would have been capable of withstanding a sudden washout into increasingly saline environments. Both C. thermalis and G. violaceus continued to grow and photosynthesise, albeit at diminished rates, in brackish water, thereby providing a route for the evolution of open ocean‐dwelling strains, necessary for the oxygenation of the Earth's atmosphere.Hijazi, H.Y., Bottaro, C.S., 2019. Analysis of thiophenes in seawater: Molecularly imprinted polymer thin-film extraction with desorption electrospray ionization mass spectrometry. International Journal of Mass Spectrometry 443, 9-15. new method coupling molecularly imprinted polymer thin-films (MIP thin-films) with desorption electrospray ionization mass spectrometry (DESI-MS) has been developed for indirect analysis of thiophene compounds in water. MIP thin-films were prepared on non-porous glass slides using a simple drop-casting fabrication method. The resulting films were used for indirect quantitative analysis of thiophene compounds in water by sorbing thiophene oxidation products (sulfones) to MIP films, then interrogating the MIP surface by DESI-MS. Oxidation of thiophenes to sulfones in water was achieved by reaction with a mixture of H2O2/formic acid at 65?°C for 2?h. DESI source parameters were optimized, and the optimal spray solvent composition was found to be MeOH:H2O (95:5 v/v) containing 0.5?mM NaCl. Among all sulfones formed, the protonated ion and sodium adduct signals were observed only for dibenzothiophene sulfone. The method was applied to dibenzothiophene in seawater, yielding a limit of detection at 3?ng?L?1 and relative standard deviations (RSDs) below 8.0%. DESI-MS response was linear (R2?=?0.9841) over the range studied 0.1–10?μg?L?1. With limited sample handling and ease of sample processing, many samples can be processed simultaneously making the method suitable for high throughput of screening environmental waters for dibenzothiophene and has the potential for detection its sulfone-metabolite.Hippertt, J.P., Caxito, F.A., Uhlein, G.J., Nalini, H.A., Sial, A.N., Abreu, A.T., Nogueira, L.B., 2019. The fate of a Neoproterozoic intracratonic marine basin: Trace elements, TOC and iron speciation geochemistry of the Bambuí Basin, Brazil. Precambrian Research 330, 101-120. marine systems are associated with major paleoecological changes that took place in the Ediacaran and during the Ediacaran-Cambrian transition. During this timespan, the Bambuí basin located on east Brazil held a peculiar paleoenvironmental scenario. Due to its intracratonic evolution, the basin was partially disconnected from neighboring open marine systems. This setting raises a very interesting opportunity to understand how an isolated Neoproterozoic marine system evolved in contrast with typical (globally connected) open marine systems. To understand the paleoenvironmental changes that took place in the Bambuí basin, we investigate the pre-glaciogenic deposits of the Carrancas Fm and the post-glaciogenic mixed (shale-carbonate) successions of the Bambuí Group. Through the analysis of iron speciation, TOC, trace element and C-O isotope systematics, our study suggests a very complex environmental evolution. Firstly, our samples are marked by strong contamination of detrital continental material that can be related to an increased bioproductivity on both the Carrancas Fm. and lower Bambuí group stratigraphic units, and provenance data show that all studied sediments probably shared common source areas. Iron speciation data, Ce anomalies and RSE enrichments shows that lower Bambuí Group stratigraphic units were likely deposited in an open marine scenario featuring high bioproductivity in shallow waters and euxinic incursions in predominant anoxic/ferruginous bottom waters. On the other hand, upper Bambuí stratigraphic units register a marine evolution in a restricted scenario, where anoxic ferruginous conditions probably reached surface waters. Finally, our data show that the lack of oceanic connection prevented the re-supply of marine sulfate, RSE, bionutrients and ultimately of dissolved oxygen which may have decreased biological activity and probably hindered biological evolution, preventing the rise of a typical modern-like Cambrian ecosystem. In this sense, our data suggest that oceanic connectivity and proper re-supply of inorganic marine input were important features in the development of complex life in the Ediacaran-Cambrian environment.Hirave, P., Wiesenberg, G.L.B., Birkholz, A., Alewell, C., 2019. Understanding the effects of early degradation on isotopic tracers: implications for sediment source attribution using compound-specific isotope analysis (CSIA). Biogeosciences Discussions 2019, 1-18. of compound-specific isotope analysis (CSIA) in sediment fingerprinting source apportionment studies is becoming more frequent, as it can potentially provide robust land-use based source attribution of suspended sediments in a freshwater system. Isotopic tracers such as δ13C values of vegetation-derived organic compounds are considered to be suitable for CSIA based fingerprinting method. However, a rigorous evaluation of tracer conservativeness in terms of the stability of isotopic signature during detachment and transport of soil during erosion process is essential for the suitability of the method. With the aim to identify potential fractionation and shifts in tracer signature during early degradation of organic matter in surface soils, we measured concentrations and δ13C values of long-chain fatty acids and n-alkanes from fresh plant biomass (as vegetation is a direct source of these compounds to the soils), degraded organic horizon (O horizon) as well as mineral soil (A horizon) from various forest types with different humus forms (five sites). The bulk δ13C values showed continuous 13C enrichment through the degradation stages from fresh plant material to the O and A horizon, ranging between 3.5 and 5.6?‰. Compound-specific δ13C values showed a general 13C enrichment for both, long-chain fatty acids (up to 5?‰) as well as n-alkanes (up to 3.9?‰) from fresh plant biomass to the O horizon overlying the A horizon. However, only slight or no further changes occurred from the O to the A horizon. We also compared compound-specific δ13C values between two soil particle-size classes (<?2?mm and <?63??m) from four sites and found no significant differences of tracer values between them, with even less fractionation for the long-chain n-alkanes within the soil particle fractions, which points to the conclusion that sampling and analysing bulk soil material might be valid for the isotopic tracer applications. We further conclude, that our results support the suitability of studied isotopic tracers as representative source soil signature in CSIA based sediment source attribution, as they demonstrated necessary stability in plant-soil system during organic matter degradation.Hodgskiss, M.S.W., Dagnaud, O.M.J., Frost, J.L., Halverson, G.P., Schmitz, M.D., Swanson-Hysell, N.L., Sperling, E.A., 2019. New insights on the Orosirian carbon cycle, early Cyanobacteria, and the assembly of Laurentia from the Paleoproterozoic Belcher Group. Earth and Planetary Science Letters 520, 141-152. Orosirian Period (2050–1800 Ma) of the Paleoproterozoic Era represents an interval between the Great Oxidation Event and Lomagundi-Jatuli Excursion, and the apparent environmental stability of the late Paleoproterozoic to mid-Mesoproterozoic (1800–1300 Ma). Here, we present stratigraphic data, carbon isotope chemostratigraphy, element abundances, and U–Pb zircon depositional ages from the Belcher Group in subarctic Canada, providing an unparallelled global reference section for the Orosirian Period. U–Pb dates of 2018.5 ± 1.0 Ma and 2015.4 ± 1.8 Ma for two tuffs in the Kasegalik Formation (lowest Belcher Group) provide the first robust age constraints for Earth's earliest unambiguous cyanobacterial fossil, Eoentophysalis belcherensis. A tuffaceous shale ～4 km stratigraphically higher, at the contact of the Flaherty and Omarolluk formations (1854.2 ± 1.6 Ma), provides an age for foreland basin development associated with the collision of the Superior and Hearne cratons. Carbonate carbon isotope data show smooth fluctuations ranging from ?2.3 to +3.6‰, reaching a maximum near ca. 1.88 Ga. This trend toward heavier carbon isotope values is interpreted as the result of global orogenesis during Nuna assembly that elevated nutrient supply and sedimentation rates, leading to an increase in the proportion of organic carbon burial relative to carbonate carbon burial.Hoegg, E.D., Godin, S., Szpunar, J., Lobinski, R., Koppenaal, D.W., Marcus, R.K., 2019. Ultra-high resolution elemental/isotopic mass spectrometry (m/Δm?>?1,000,000): Coupling of the liquid sampling-atmospheric pressure glow discharge with an Orbitrap mass spectrometer for applications in biological chemistry and environmental analysis. Journal of The American Society for Mass Spectrometry 30, 1163-1168. fundamental questions of astrophysics, biochemistry, and geology rely on the ability to accurately and precisely measure the mass and abundance of isotopes. Taken a step further, the capacity to perform such measurements on intact molecules provides insights into processes in diverse biological systems. Described here is the coupling of a combined atomic and molecular (CAM) ionization source, the liquid sampling-atmospheric pressure glow discharge (LS-APGD) microplasma, with a commercially available ThermoScientific Fusion Lumos mass spectrometer. Demonstrated for the first time is the ionization and isotopically resolved fingerprinting of a long-postulated, but never mass-spectrometrically observed, bi-metallic complex Hg:Se-cysteine. Such a complex has been implicated as having a role in observations of Hg detoxification by selenoproteins/amino acids. Demonstrated as well is the ability to mass spectrometrically-resolve the geochronologically important isobaric 87Sr and 87Rb species (Δm?~?0.3?mDa, mass resolution m/Δm?≈?1,700,000). The mass difference in this case reflects the beta-decay of the 87Rb to the stable Sr isotope. These two demonstrations highlight what may be a significant change in bioinorganic and atomic mass spectrometry, with impact expected across a broad spectrum of the physical, biological, and geological sciences.Hou, Y., Zhang, K., Wang, F., He, S., Dong, T., Wang, C., Qin, W., Xiao, Y., Tang, B., Yu, R., Du, X., 2019. Structural evolution of organic matter and implications for graphitization in over-mature marine shales, south China. Marine and Petroleum Geology 109, 304-316. characterize the degree of organic matter graphitization in the over mature lower Paleozoic marine shales from South China, a suite of kerogen samples covering different maturity (Ro% ranging from 1.2% to 4.2%) were analyzed by Laser Raman microprobe (LRM), Transmission electron microscope (TEM) and Fourier transform infrared spectroscopy (FTIR) techniques. Chemical structures and related major changes caused by thermal evolution history were systematically discussed. The results indicate that with the thermal maturity increasing, the aliphatic side chains fall off gradually, and the aromatic rings increase continuously. The ordered structure of shales continues to enhance, leading to the increasing of graphitization degree. The parameters of LRM (i.e. position of G and D bands, peak position difference (RBS), full width at half maximum (FWHM) and intensity ratio (ID/IG)) highlight the “turning point” at maturity level around RmcRo%?=?3.5%, which represents the chemical structure jump of the kerogen. This chemical structure jump can be characterized by the continuous decreasing of amorphous carbon before the RmcRo% exceeded 3.5% and the sharp increasing degree of aromatic conjugation after that point. TEM analysis indicates that the carbon layers of shale samples with RmcRo% exceeds 3.5% show better ordering and continuity than that of low maturity shale samples. The FTIR analysis suggests that there are relatively high aromatics CC chains and very few aromatic C-H chains in the high maturity samples. This critical chemical structure jump at RmcRo%?=?3.5% could be interpreted as the structure of organic matter begins to transform from amorphous carbon to crystalline graphite in shales. Due to the increasing degree of graphitization, graphitized shale is characterized by stable chemical structure, condensed and orderly carbon layer constructure, and ultra-low resistivity.Hu, D., Wei, Z., Liu, R., Fan, Z., Han, J., 2019. Development characteristics and exploration potential of the Lower Carboniferous black shale in the Guizhong Depression. Natural Gas Industry B 6, 205-214. Carboniferous shale in the Guizhong Depression of central Guangxi presents good exploration potential of shale gas, but its exploration effectiveness is restricted by the unclear distribution, quality and potential of high-quality shale. In this paper, the Lower Carboniferous Luzhai shale was taken as the research object in order to guide the exploration of Carboniferous shale gas in the Guizhong Depression. Based on the field outcrops, well drilling, well logging and test data of the Guizhong Depression and its surrounding areas, the shale formation was studied systematically based on the characteristics of distribution, organic geochemistry and reservoir, and the preservation conditions. Then, the development characteristics of black shale were confirmed and the distribution laws of high-quality shale were summarized. Finally, shale gas exploration was analyzed and the favorable exploration areas were defined. And the following research results were obtained. First, the Luzhai shale in the Guizhong Depression is mainly carbonaceous shale and siliceous shale of deepwater continental shelf facies. Second, the high-quality Luzhai shale is 20–60?m thick and it is characterized by high total organic carbon, good type of organic matters, moderate maturity of organic matter, high content of brittle minerals, good reservoir property and developed pores of organic matters. Third, regional caprocks and roofs & floors are well developed in the Liucheng Slope and the Yishan Sag. They are weakly deformed, suffer from less uplift and denudation, and are far away from the strong strike–slip reverse fault, so they have good preservation conditions. Fourth, shallow wells which were drilled in the surface structures of the Guizhong Depression in the early stage present abundant gas shows, and most of them produce gas flow, which reveals a promising prospect of shale gas exploration in this area. In conclusion, the wide and gentle synclines with large burial depth in the Liucheng Slope and the Yishan Sag are the favorable areas for shale gas exploration in the Guizhong Depression.Hu, L., Andrews, A.E., Thoning, K.W., Sweeney, C., Miller, J.B., Michalak, A.M., Dlugokencky, E., Tans, P.P., Shiga, Y.P., Mountain, M., Nehrkorn, T., Montzka, S.A., McKain, K., Kofler, J., Trudeau, M., Michel, S.E., Biraud, S.C., Fischer, M.L., Worthy, D.E.J., Vaughn, B.H., White, J.W.C., Yadav, V., Basu, S., van der Velde, I.R., 2019. Enhanced North American carbon uptake associated with El Ni?o. Science Advances 5, Article eaaw0076. atmospheric CO2 mole fraction and δ13CO2 observations over North America document persistent responses to the El Ni?o–Southern Oscillation. We estimate these responses corresponded to 0.61 (0.45 to 0.79) PgC year?1 more North American carbon uptake during El Ni?o than during La Ni?a between 2007 and 2015, partially offsetting increases of net tropical biosphere-to-atmosphere carbon flux around El Ni?o. Anomalies in derived North American net ecosystem exchange (NEE) display strong but opposite correlations with surface air temperature between seasons, while their correlation with water availability was more constant throughout the year, such that water availability is the dominant control on annual NEE variability over North America. These results suggest that increased water availability and favorable temperature conditions (warmer spring and cooler summer) caused enhanced carbon uptake over North America near and during El Ni?o.Huang, J., Guo, X., Xu, T., Fan, L., Zhou, X., Wu, S., 2019. Ionic deep eutectic solvents for the extraction and separation of natural products. Journal of Chromatography A 1598, 1-19. ionic liquids (ILs) used as green solvents have received considerable attention and wide application in different research and industrial fields, such as chemistry, biology, catalysis, energy, and even environmental sciences. Recently, a new class of sustainable solvents named deep eutectic solvents (DESs) have been developed, which share the promising solvent characteristics of ILs, such as thermal and chemical stability, low vapor pressure and design ability. In addition, the major advantages of DESs over ILs are their lower prices and easier preparation. Therefore, DESs have been considered to be a potential alternative to replace conventional organic solvents and ILs. Currently, the developed DESs may be classified into ionic and nonionic liquids. Typically, choline chloride (ChCl)/urea (1:2) is an ionic DES, while glucose/sucrose (1:1) is a nonionic DES. Although several reviews have covered advancements in DESs, in this review, we aim to provide a general insight into DESs, particularly ionic DESs, like choline-based DES, in terms of their preparation and application in the extraction of natural products (NPs) mainly from traditional Chinese medicines and the recovery of extracted compounds from their extracts. Additionally, various factors affecting the extraction efficiency of DESs are discussed.Huang, L., Ning, Z., Wang, Q., Qi, R., Cheng, Z., Wu, X., Zhang, W., Qin, H., 2019. Molecular insights into kerogen deformation induced by CO2/CH4 sorption: Effect of maturity and moisture. Energy & Fuels 33, 4792-4805. is the source of hydrocarbons in shale. As a soft nanoporous matter, kerogen constantly experiences mechanical deformation induced by subsurface stress environment and interplay with geofluid, significantly affecting the percolation and production of hydrocarbons. However, the associated coupling deformation of kerogen in reservoir conditions remains poorly understood. Here we quantify the kerogen coupling deformation induced by moisture uptake, CH4 and CO2 sorption, and mechanical compression using the combination of molecular simulations and poromechanics theory. The effects of kerogen maturity and preloaded moisture are discussed in detail. Our results show that moisture induced deformation is governed by the dynamic distribution of water molecules and the physicochemical characteristics of kerogen. Moisture induced volumetric strain increases with decreasing kerogen maturity or rising moisture content. The porosity of kerogen skeleton increases upon moisture uptake, although the residual porosity accessible for fluid presents a linearly decreasing trend. The coupling deformation upon gas sorption results from the combined effect of sorption swelling and mechanical compression. The coupling volumetric strain increases with rising kerogen maturity or declining moisture content, contrary to results for moisture uptake. The total deformation, coupling sorption–pressure–moisture effect, rises with increasing kerogen maturity. The evolution the total deformation follows with moisture content depends on the kerogen maturity. Results of this work can help improve the estimation of fluid-in-place in a shale gas reservoir and the understanding of the chemomechanical coupling associated with CO2 sequestration and CO2 fracturing.Huang, S., Duan, S., Wang, Z., Jiang, Q., Jiang, H., Su, W., Qingfu, F., Huang, T., Yuan, M., Ren, M., Chen, X., 2019. Affecting factors and application of the stable hydrogen isotopes of alkane gases. Petroleum Exploration and Development 46, 518-530. study the composition, affecting factors of the stable hydrogen isotopes of alkane gases and their application to identification of the natural gas origin and maturities, the chemical and isotopic compositions of 118 gas samples of Carboniferous- Permian in the Ordos Basin, and of Triassic in the Sichuan Basin, combined with 68 gas samples from the Sinian and Cambrian reservoirs in the Sichuan Basin, and Ordovician and Siliurian reservoirs of Tarim Basin, are analyzed comprehensively. The following conclusions are obtained: (1) Natural gases in the study area and strata of the Ordos and Sichuan basins are dominated by alkane gases, and the dryness coefficients and maturities of the Carboniferous-Permian gases in the Ordos Basin are higher than the gases in the Triassic Xujiahe Formation of the Sichuan Basin, while the hydrogen isotopes of the latter ones are much enriched in 2H than the former. (2) The δ2HCH4-C1/C2+3 genetic identification diagram of natural gas was drawn, and the diagrams of hydrogen isotopic differences between the heavy alkane gases and methane vs. hydrogen isotopes of alkane gases can also be used in natural gas genetic identification. (3) The δ2HCH4-Ro formulas of coal-formed gas in different areas of the two basins are given, and the δ2HC2H6-δ2HCH4 is a new index for maturity, and the (δ2HC2H6—δ2HCH4)-Ro formula of the coal-formed gas can be used to calculate the maturity of the natural gas. (4) The stable hydrogen isotopes of alkane gases are affected by parent materials in source rocks, maturity, mixing and the aqueous medium conditions, among which the aqueous paleo-salinity is the key factor. To sum up, the hydrogen isotopes of alkane gases are affected by multiple factors, and they are significant to the identification of the origin, and maturity of natural gas, and the water environment during the deposition of source rocks.Huang, S., Yang, L., Xia, Y., Du, M., Yang, Y., 2019. An experimental and numerical study of a steam chamber and production characteristics of SAGD considering multiple barrier layers. Journal of Petroleum Science and Engineering 180, 716-726. gravity drainage (SAGD) is an efficient technology that has been used to develop oil sand resources, and it has been successfully and maturely applied in Canada. However, oilfield production has demonstrated that reservoir heterogeneity has a serious impact on SAGD development, among which the most drastic impact is caused by multiple barrier layers in the reservoir. These barrier layers can severely impede the development of a steam chamber and the drainage of oil. Hence, it is important to investigate their influence mechanism. In this study, oil samples from the Long Lake oil field were used in laboratory experiments to study the development of the steam chamber and the residual oil distribution under the effect of multiple barrier layers. Then, a theoretical numerical simulation model was established to describe the fluid flow more precisely. In addition, the production characteristics of SAGD under the influence of different numbers of barrier layers were analyzed by comparing the development of the steam chamber. Finally, the impacts of multiple barrier layers with different modes of combinations were studied for their effects on SAGD production. The results indicated that for impermeable barrier layers of the same length, the steam primarily developed upward after flowing around the first barrier layer. After the steam chamber reached the top of the reservoir, the steam began to enter into the interbedded zone. Based on an unchanged first barrier layer, the number of barrier layers had little influence on the overall shape of the steam chamber and SAGD production, which confirmed that the first barrier layer played a dominant role in the influence of multiple barrier layers. In addition, characteristic points (P1, P2, P3), which corresponded to changes in the stage of steam chamber development, were established and used to evaluate the effect of the barrier layers. Different combinations of barrier layers were realized by changing the relative properties of the first barrier layer. The results showed that the longer the length of the first barrier layer, the closer it was to the steam injection well and the lower the permeability; hence, the more obvious its hysteresis effect on the SAGD process.Huang, X., Liu, M., Liu, X., Liu, Q., Chen, X., 2019. Polyethyleneimine functionalized multi-walled carbon nanotubes-based solid phase extraction for selective screening of carboxylic acid compounds in natural products. Chromatographia 82, 1017-1027. this work, by adopting polyethyleneimine functionalized multi-walled carbon nanotubes as the absorbent, a solid phase extraction based method for fast and selective screening of carboxylic acid compounds was developed. The structure and morphology of the polyethyleneimine functionalized multi-walled carbon nanotubes were confirmed via scanning electron micrograph, transmission electron microscopy, Fourier transform infrared spectra and X-ray photoelectron spectroscopy. And the proposed approach was successfully applied to screen carboxylic compounds from the crude extract of Perilla frutescens. As a result, seven polyhydric compounds with carboxyl including caffeic acid, luteolin-7-O-diglucuronide, apigenin-7-O-diglucuronide, sagerinic acid, scutellarein-7-O-glucuronide, rosmarinic acid, and apigenin-7-O-glucuronide were favorably?screened?out from compounds without carboxyl?group. Similar screening results were also obtained via generalizing the method to the crude extract of Chrysanthemum. This strategy could serve as a rapid and efficient pathway for preliminary screening of certain types of compounds from complex natural products.Huang, Y.-R., Yao, Q.-Z., Li, H., Wang, F.-P., Zhou, G.-T., Fu, S.-Q., 2019. Aerobically incubated bacterial biomass-promoted formation of disordered dolomite and implication for dolomite formation. Chemical Geology 523, 19-30. the realization that the formation of low-temperature dolomite could involve the microbial activity, a new pathway to understand the origin and mechanism of dolomite is emerging. Although microbially mediated Ca-Mg carbonates and dolomite occur in some aerobic and high-salinity conditions, little information about the exact role of aerobic microbes is available. Herein, a strain of moderately halophilic bacteria, Shewanella piezotolerans WP3, was selected to study the involvement of aerobically incubated bacterial biomass in the Ca-Mg carbonate mineralization. Different biomass components were isolated from the bacterial cultures by a set of separation techniques, and used to mediate Ca-Mg carbonate mineralization under a carbon dioxide diffused system. The experimental results showed that bacterial cells play a dominant role in the formation of disordered dolomite. And the mineralization of the disordered dolomite can be attributed to the bare cells and bound extracellular polymeric substances (bound EPS) isolated from the bacterial cells, most likely due to the promotion of high concentration and density of carboxyl and phosphoryl groups on the bacterial biomass (i.e., bare cells and bound EPS). Hence, it does imply that bacterial biomass, even without the active microbial activities, can also play an important role in the formation of dolomite. Current results can not only extend the insight into the biologically influenced mineralization of Ca-Mg carbonates, but also shed light on the precipitation of disordered dolomite/dolomite in modern settings and geological records.Huang, Y., Zhang, K., Jiang, Z., Song, Y., Jiang, S., Jia, C., Liu, W., Wen, M., Xie, X., Liu, T., Li, X., Wang, X., Liu, X., Zhang, Y., Tang, L., 2019. A cause analysis of the high-content nitrogen and low-content hydrocarbon in shale gas: A case study of the Early Cambrian in Xiuwu Basin, Yangtze region. Geofluids 2019, Article 1435892. are successes and failures in the exploration of marine shale gas in South China. In some shale gas plays with great basis for hydrocarbon generation, a phenomenon exists that gas loggings reflect low gas bearing in some of the wells and the gas is dominated by nitrogen rather than hydrocarbon gas. The study of nitrogen concentration in shale gas contributes to solve the question that how shale gas diffuses in complex tectonic areas, which helps to figure out the preservation requirements and accumulation mechanisms of shale gas and avoid exploration crisis. This study focused on the lower Cambrian shale in Xiuwu Basin, Lower Yangtze Region, with emphasis on the well Jiangye-1, using gas component analysis, stable nitrogen isotope analysis, overburden permeability tests in parallel and perpendicular directions, and FIB-HIM experiments, also combining with core description, outcrop observation, and seismic interpretation to explore the causes of the high-content nitrogen and low-content hydrocarbon in the lower Cambrian shale gas. The results show that the nitrogen of the lower Cambrian shale in Xiuwu Basin is derived from the atmosphere and the deep crust-upper mantle. The bedding planes and the detachment layer at the bottom of the lower Cambrian compose the lateral pathways, and the widespread deep faults are the vertical pathways for shale gas migration and diffusion. Combining these two, an effective pathway network was built, favorable to gas exchange between the shale gas interval and the atmosphere, partly leading to the concentration of nitrogen and the diffusion of hydrocarbon gas. In the Jurassic, the magmatic activities occurred frequently in the surrounding areas, which not only brought nitrogen from the deep crust-upper mantle but also increased the value of paleo-heat flow even though the basin began to uplift, which promoted the graphitization of organic matter and the collapse of organic pores and accelerated the loss of shale gas. Based on the study above, an explanation model was summarized to expound the causes of high-content nitrogen and low-content hydrocarbon in shale gas plays near the plate-active region in Xiuwu Basin, Lower Yangtze Region.Hull, K.L., Jacobi, D., Abousleiman, Y.N., 2019. Oxidative kerogen degradation: A potential approach to hydraulic fracturing in unconventionals. Energy & Fuels 33, 4758-4766. and gas production from shale formations has proven to be economical because of advances in hydraulic fracturing but remains very challenging in part because of the presence of the ductile, polymer nature of the hydrocarbon source material, kerogen. This organic matter is intertwined among silicates, aluminosilicates, and other minerals as fine laminae that weave among the shale rock fabric, adding soft mechanical cohesion to the material. A potential solution has been developed, a new type of reactive fracturing fluid composed of strong oxidizers such as bromate (BrO3–), which could mitigate the adverse effects of the polymeric nature of kerogen on the hydraulic conductivity of the fractured shale formation. High-resolution scanning electron microscopy of kerogen-rich shale samples before and after fluid treatment demonstrates notable porosity enhancement evident by cracks forming in the macerals and augmenting the volumetric porosity. The stability of the reactive components at elevated reservoir temperatures in addition to the demonstrated results suggest the potential for measureable improvements in hydraulic conductivity and hence in the ultimate recovery of oil and gas from future hydraulic fracturing operations.Imam, A., Suman, S.K., Ghosh, D., Kanaujia, P.K., 2019. Analytical approaches used in monitoring the bioremediation of hydrocarbons in petroleum-contaminated soil and sludge. TrAC Trends in Analytical Chemistry 118, 50-64. is a familiar process involving actions of microorganisms on the pollutants present in environmental matrices. Monitoring the fate of petroleum hydrocarbons present as contaminants in environmental samples is a retrospective approach to assess the progress of biodegradation process. Chemical analysis is essential in the determination of hydrocarbons at various stages of the experiment. Pervasive research in this area has involved the use of popular analytical tools such as chromatography and spectroscopy. This review focuses on the significance of analytical chemistry in monitoring of bioremediation experiments. The discussions present a comprehensive account of the analysis plan, deviations and critical description of the involved approaches for determination of different hydrocarbons present in petroleum-contaminated soils. Various sample pre-treatment methods such as liquid-liquid, solid-phase, Soxhlet, pressurized fluid extraction etc. have been discussed. Use of chromatography, spectroscopy and other hyphenated platforms is also discussed to expand the prevalent scenario of analysis in bioremediation studies.Imperiali, B., 2019. Bacterial carbohydrate diversity — a Brave New World. Current Opinion in Chemical Biology 53, 1-8. and glycoconjugates feature on the ‘front line’ of bacterial cells, playing critical roles in the mechanical and chemical stability of the microorganisms, and orchestrating interactions with the environment and all other living organisms. To negotiate such central tasks, bacterial glycomes incorporate a dizzying array of carbohydrate building blocks and non-carbohydrate modifications, which create opportunities for infinite structural variation. This review highlights some of the challenges and opportunities for the chemical biology community in the field of bacterial glycobiology.Irfan, M., Bai, Y., Zhou, L., Kazmi, M., Yuan, S., Mbadinga, S.M., Yang, S.-Z., Liu, J.F., Sand, W., Gu, J.-D., Mu, B.-Z., 2019. Direct microbial transformation of carbon dioxide to value-added chemicals: A comprehensive analysis and application potentials. Bioresource Technology 288, 121401. dioxide storage in petroleum and other geological reservoirs is an economical option for long-term separation of this gas from the atmosphere. Other options include applications through conversion to valuable chemicals. Microalgae and plants perform direct fixation of carbon dioxide to biomass, which is then used as raw material for further microbial transformation (MT). The approach by microbial transformation can achieve reduction of carbon dioxide and production of biofuels. This review addresses the research and technological processes related to direct MT of carbon dioxide, factors affecting their efficiency in operation and the review of economic feasibility. Additionally, some commercial plants making utilization of CO2 around the globe are also summarized along with different value-added chemicals (methane, acetate, fatty acids and alcohols) as reported in literature. Further information is also provided for a better understanding of direct CO2 MT and its future prospects leading to a sustainable and clean environment.Isaji, Y., Yoshimura, T., Araoka, D., Kuroda, J., Ogawa, N.O., Kawahata, H., Ohkouchi, N., 2019. Magnesium isotope fractionation during synthesis of chlorophyll a and bacteriochlorophyll a of benthic phototrophs in hypersaline environments. ACS Earth and Space Chemistry 3, 1073-1079. is a major divalent cation in the cell and is vital for maintaining cellular function. The magnesium isotopic composition (δ26Mg) of chloropigments potentially provides detailed information on cellular physical and biochemical reactions that involve Mg; however, existing data are scarce, and its controlling factors remain unresolved. Here, we report δ26Mg of chlorophyll a and bacteriochlorophyll a derived from cyanobacteria and purple sulfur bacteria that inhabit benthic microbial mats and gypsum crusts formed under shallow hypersaline environments. There was substantial Mg isotope fractionation in both positive and negative directions from source Mg2+ in the brine (δ26Mg, from ?1.05 to ?0.78‰) to chloropigments (chlorophyll a, from ?1.77 to ?0.39‰; bacteriochlorophyll a, from ?2.13 to ?0.12‰), suggesting that multiple processes are involved in the fractionation of Mg during chlorophyll biosynthesis. The relationship between δ26Mg and δ15N of bacteriochlorophyll a indicates a correlation between δ26Mg values and the growth rate of phototrophs. We suggest that the extent of kinetic isotopic fractionation during the Mg-insertion step changes in response to the amounts of cellular chloropigments, resulting in the large variability in δ26Mg of chloropigments observed in natural environments.Islam, Z.F., Cordero, P.R.F., Feng, J., Chen, Y.-J., Bay, S.K., Jirapanjawat, T., Gleadow, R.M., Carere, C.R., Stott, M.B., Chiri, E., Greening, C., 2019. Two Chloroflexi classes independently evolved the ability to persist on atmospheric hydrogen and carbon monoxide. The ISME Journal 13, 1801-1813. aerobic bacteria exist in dormant states within natural environments. In these states, they endure adverse environmental conditions such as nutrient starvation by decreasing metabolic expenditure and using alternative energy sources. In this study, we investigated the energy sources that support persistence of two aerobic thermophilic strains of the environmentally widespread but understudied phylum Chloroflexi. A transcriptome study revealed that Thermomicrobium roseum (class Chloroflexia) extensively remodels its respiratory chain upon entry into stationary phase due to nutrient limitation. Whereas primary dehydrogenases associated with heterotrophic respiration were downregulated, putative operons encoding enzymes involved in molecular hydrogen (H2), carbon monoxide (CO), and sulfur compound oxidation were significantly upregulated. Gas chromatography and microsensor experiments showed that T. roseum aerobically respires H2 and CO at a range of environmentally relevant concentrations to sub-atmospheric levels. Phylogenetic analysis suggests that the hydrogenases and carbon monoxide dehydrogenases mediating these processes are widely distributed in Chloroflexi genomes and have probably been horizontally acquired on more than one occasion. Consistently, we confirmed that the sporulating isolate Thermogemmatispora sp. T81 (class Ktedonobacteria) also oxidises atmospheric H2 and CO during persistence, though further studies are required to determine if these findings extend to mesophilic strains. This study provides axenic culture evidence that atmospheric CO supports bacterial persistence and reports the third phylum, following Actinobacteria and Acidobacteria, to be experimentally shown to mediate the biogeochemically and ecologically important process of atmospheric H2 oxidation. This adds to the growing body of evidence that atmospheric trace gases are dependable energy sources for bacterial persistence.Ivanov, K.S., Kostrov, N.P., Koroteev, V.A., 2019. The relationship among geodynamics, heat flow, deep structure, and the oil and gas potential of Yamal. Doklady Earth Sciences 486, 490-493. amount of hydrocarbon deposits per unit area of Yamal Peninsula is more than 100 times as much as the global average. The hydrocarbon deposits are generally situated in areas with high current geodynamic activity. According to the data of seismic tomography, in the Yamal area, the mantle structure is abnormal. The southern part of the Kara Sea, the Yamal Peninsula, and the western part of the Gydan Peninsula are involved into the large positive anomaly of the heat flow density, the epicenter of which occurs in the vicinity of the Rusanovskoye deposit. Almost all hydrocarbon deposits of Yamal are situated on the flanks of the West Siberian rift system and, simultaneously, in the gradient zones of the heat flow density.Ivanova, A.E., Kanat’eva, A.Y., Kurganov, A.A., 2019. Aerobic biodegradation of liquid motor fuels under extreme acidic conditions. Microbiology 88, 300-308. of liquid petroleum motor fuels and fuel mixtures containing biodiesel fuel (methyl ethers of rapeseed fatty acids) by aerobic acidophilic actinobacteria Mycobacterium sp. AGS10 was studied. Strain AGS10 was found to be able to grow on aviation kerosene Jet A-1 as the sole carbon and energy source under highly acidic conditions. After 21 days of cultivation at 30°C and pH 2.5, bacterial numbers increased from 4.2 × 106 to 7.0 × 108 cells/mL, while the hexane-soluble part of the fuel was degraded by 90.4%. The strain also utilized components of the winter diesel fuel, including С8–С20 n-alkanes, iso-alkanes, and aromatic compounds. Overall hydrocarbon consumption under the same conditions was 99.4%. The ratio of (iso-С19 (pristane) + iso-С20 (phytane))/(n-С17 + n-С18) changed from 1.21 in the control to 2.39 in the experiment with bacterial degradation, which indicated preferable utilization of n-alkanes, rather than isoprenoids. Over 90% of diesel fuel hydrocarbons were consumed from day 4 to day 12 of cultivation, while abundance of the bacterial population increased by three orders of magnitude. Strain AGS10 consumed both hydrocarbons and oxygen-containing (plant-derived) components of the fuel mixtures with biodiesel fuel. Bacteria preferentially consumed hydrocarbons, and the ratio between oil diesel fuel and biodiesel fuel in the mixture changed in the course of incubation.Izawa, M.R.M., Dynes, J.J., Banerjee, N.R., Flemming, R.L., MacLean, L.C.W., Hetherington, C.J., Matveev, S., Southam, G., 2019. Organic matter preservation and incipient mineralization of microtubules in 120 Ma basaltic glass. Frontiers in Earth Science 7, 149. doi: 10.3389/feart.2019.00149. tubular structures in subaqueously-emplaced basaltic glass may represent trace fossils caused by microbially-mediated glass dissolution. Mineralized structures of similar morphology and spatial distribution in ancient, metamorphosed basaltic rocks have widely been interpreted as ichnofossils, possibly dating to ~3.5 Ga or greater. Doubts have been raised, however, regarding the biogenicity of the original hollow tubules and granules in basaltic glass. In particular, although elevated levels of biologically-important elements such as C, S, N and P as well as organic compounds have been detected in association with these structures, a direct detection of unambiguously biogenic organic molecules has not been accomplished. In this study, we describe the direct detection of proteins associated with tubular textures in basaltic glass using synchrotron X-ray spectromicroscopy. Protein-rich organic matter is shown to be associated with the margins of hollow and partly-mineralized tubules. Furthermore, a variety of tubule-infilling secondary minerals, including Ti-rich oxide phases, were observed filling and preserving the microtextures, demonstrating a mechanism whereby cellular materials may be preserved through geologic time.Jahanbani Veshareh, M., Nick, H.M., 2019. A sulfur and nitrogen cycle informed model to simulate nitrate treatment of reservoir souring. Scientific Reports 9, Article 7546. treatment has been widely used in various seawater injection projects to treat biologic sulfate reduction or reservoir souring. To design a promising nitrate treatment plan, it is essential to have a comprehensive understanding of reactions that represent the microbial communities of the reservoir and mechanisms through which the souring process is inhibited. We employ a new approach of evaluating different reaction pathways to design reaction models that reflect governing microbial processes in a set of batch and flow experiments. Utilizing the designed models, we suggest dissimilatory nitrate reduction to ammonium is the main reaction pathway. Additionally, we illustrate nitrite inhibition is the major mechanism of nitrate treatment process; independent of nitrate reduction being autotrophic or heterotrophic. We introduce an inhibitory nitrate injection concentration that can inhibit souring regardless of nitrite inhibition effect and the distance between injection and production wells. Furthermore, we demonstrate that the ratio of the nitrite-nitrate reduction rate can be used to estimate nitrate treatment effectiveness. Our findings in regard to importance of nitrite inhibition mechanism and the inhibitory nitrate concentration are in accordance with the field observations.James, P.B., Smith, D.E., Byrne, P.K., Kendall, J.D., Melosh, H.J., Zuber, M.T., 2019. Deep structure of the lunar South Pole-Aitken Basin. Geophysical Research Letters 46, 5100-5106. South Pole‐Aitken basin is a gigantic impact structure on the far side of the Moon, with an inner rim extending approximately 2,000 km in the long axis dimension. The structure and history of this basin are illuminated by gravity and topography data, which constrain the subsurface distribution of mass. These data point to the existence of a large excess of mass in the Moon's mantle under the South Pole‐Aitken basin. This anomaly has a minimum mass of 2.18?×?1018 kg and likely extends to depths of more than 300 km. Plausible sources for this anomaly include metal from the core of a differentiated impactor or oxides from the last stage of magma ocean crystallization. Although the basin‐forming impact event likely excavated the vast majority of the preexisting crust, the present‐day crust of the basin interior is at least 16 km thick in undisturbed regions.Jarrett, A.J.M., Cox, G.M., Brocks, J.J., Grosjean, E., Boreham, C.J., Edwards, D.S., 2019. Microbial assemblage and palaeoenvironmental reconstruction of the 1.38?Ga Velkerri Formation, McArthur Basin, northern Australia. Geobiology 17, 360-380. ca. 1.38 billion years (Ga) old Roper Group of the McArthur Basin, northern Australia, is one of the most extensive Proterozoic hydrocarbon‐bearing units. Organic‐rich black siltstones from the Velkerri Formation were deposited in a deep‐water sequence and were analysed to determine their organic geochemical (biomarker) signatures, which were used to interpret the microbial diversity and palaeoenvironment of the Roper Seaway. The indigenous hydrocarbon biomarker assemblages describe a water column dominated by bacteria with large‐scale heterotrophic reworking of the organic matter in the water column or bottom sediment. Possible evidence for microbial reworking includes a large unresolved complex mixture (UCM), high ratios of mid‐chained and terminally branched monomethyl alkanes relative to n‐alkanes—features characteristic of indigenous Proterozoic bitumen. Steranes, biomarkers for single‐celled and multicellular eukaryotes, were below detection limits in all extracts analysed, despite eukaryotic microfossils having been previously identified in the Roper Group, albeit largely in organically lean shallower water facies. These data suggest that eukaryotes, while present in the Roper Seaway, were ecologically restricted and contributed little to export production. The 2,3,4‐ and 2,3,6‐trimethyl aryl isoprenoids (TMAI) were absent or in very low concentration in the Velkerri Formation. The low abundance is primary and not caused by thermal destruction. The combination of increased dibenzothiophene in the Amungee Member of the Velkerri Formation and trace metal redox geochemistry suggests that degradation of carotenoids occurred during intermittent oxygen exposure at the sediment–water interface and/or the water column was rarely euxinic in the photic zone and likely only transiently euxinic at depth. A comparison of this work with recently published biomarker and trace elemental studies from other mid‐Proterozoic basins demonstrates that microbial environments, water column geochemistry and basin redox were heterogeneous.Jasmine, J., Mukherji, S., 2019. Impact of bioremediation strategies on slurry phase treatment of aged oily sludge from a refinery. Journal of Environmental Management 246, 625-635. oily sludge was subjected to long term (90 day) slurry phase treatment (10% w/v oily sludge) using various biodegradation strategies involving intermittent spiking with nutrients (N), surfactant (S) and microorganisms (M), employed singly or in combination. The strategy involving simultaneous addition of N, S, and M (BNMS) resulted in the highest rate (0.0126 day?1) and extent of oil degradation (68.4%). However, oil degradation rate from aged sludge was almost half that observed for freshly procured sludge. In addition to removal of maltenes (85.7%), removal of asphaltenes (53.6%) was also achieved during BNMS treatment. Two-dimensional gas chromatograph equipped with time of flight mass spectrometer could resolve the unresolved complex mixture hump observed in both degraded and un-degraded samples and could provide greater insights on compositional changes in residual oil due to biodegradation. Although the BNMS strategy significantly enhanced oil degradation from aged sludge, treatment of fresh sludge would be faster and more cost effective.Jeanne Dit Fouque, K., Fernandez-Lima, F., 2019. Recent advances in biological separations using trapped ion mobility spectrometry – mass spectrometry. TrAC Trends in Analytical Chemistry 116, 308-315. Mobility Spectrometry (IMS) is a widely used technique for the post-ionization separation and structural characterization of biomolecules. Trapped IMS (TIMS) is a relatively recent advance in the field of linear IMS that has shown advantages for the study of biological problems when in tandem with mass spectrometry (TIMS-MS). TIMS's unique nature of holding ions using an electric field against a moving buffer gas allows for the tuning of the mobility separation by defining the scan rate as a function of the analytical challenge. TIMS can provide accurate CCS values (<0.2% RSD) and a high mobility resolving power (R up to 470). This recently commercialized technology has distinct analytical and structural biology applications. The present review focuses on advances in biological separations using TIMS-MS instrumentation for the case of isomer separations (e.g., lipids, epimers, topoisomers, positional PTMs), conformational states (e.g., peptides and proteins) and native macromolecular assemblies.Jehli?ka, J., Culka, A., Mana, L., Oren, A., 2019. Comparison of miniaturized Raman spectrometers for discrimination of carotenoids of halophilic microorganisms. Frontiers in Microbiology 10, 1155. doi: 10.3389/fmicb.2019.01155. present a comparison of the performance of four miniature portable Raman spectrometers for the discrimination of carotenoids in samples of carotene-producing microorganisms. Two spectrometers using a green laser allowing to obtain Resonance Raman (or pre-Resonance Raman) signals, one instrument with a 785 nm laser, and a recently developed Portable Sequentially Shifted Excitation Raman spectrometer (PSSERS) were used for identifying major pigments of different halophilic (genera Halobacterium, Halorubrum, Haloarcula, Salinibacter, Ectothiorhodospira, Dunaliella) and non-halophilic microorganisms (Micrococcus luteus, Corynebacterium glutamicum). Using all the tested instruments including the PSSERS, strong carotenoids signals corresponding to the stretching vibrations in the polyene chain and in-plane rocking modes of the attached CH3 groups were found at the correct positions. Raman spectra of carotenoids can be obtained from different types of microbiological samples (wet pellets, lyophilized cultur biomass and pigment extracts in organic solvents), and can be collected fast and without time-consuming procedures.Ji, L., Fu, X., Wang, M., Xu, C., Chen, G., Song, F., Guo, S., Zhang, Q., 2019. Enzyme cocktail containing NADH regeneration system for efficient bioremediation of oil sludge contamination. Chemosphere 233, 132-139. sludge is one kind of toxic and persistent contamination to ecology system from petroleum industry. In order to recycle contaminated sands and reduce environmental impacts at a lower operating cost, enzyme cocktail 21/CbFDH including NADH regeneration system for oily sludge bioremediation was constructed for the first time. The intracellular enzymes of oil-degrading strain Acinetobacter calcoaceticus 21 were prepared and the formate dehydrogenase gene Cbfdh from Candida boidinii was cloned and functionally expressed in E.coli BL21 induced by lactose. The activity and stability of CbFDH was enhanced through self-induction medium optimization using Box-Behnken design. The CbFDH activity was 12.2 times increased and was only decreased 3.9% upon storage at 30?°C for 5?d. The CbFDH increased the degradation rate of oil in high concentration. For the sludge with 10% oil (w/w), the degradation rate achieved 35.6% after 12?h using enzyme 21/CbFDH with the protein ratio of 1:4. The results will provide novel perspectives for creation and operation of petroleum-degrading enzymes involving formate dehydrogenase with higher efficiency and lower cost comparing to current microbial strains or consortium.Jiang, B., Zhang, R., Yang, N., Zhang, L., Sun, Y., Jian, C., Liu, L., Xu, Z., 2019. Molecular mechanisms of suppressing asphaltene aggregation and flocculation by dodecylbenzenesulfonic acid probed by molecular dynamics simulations. Energy & Fuels 33, 5067-5080. behaviors of an asphaltene model compound, N-(1-undecyldodecyl)-N′-(5-carboxylicpentyl)-perylene-3,4,9,10-tetracarboxylbisimide (C5PeC11), in the absence and presence of an asphaltene inhibitor, dodecylbenzenesulfonic acid (DBSA), in n-heptane and toluene solutions were studied using molecular dynamics simulation. The presence of DBSA was found to reduce both the rate and degree of C5PeC11 aggregation while increasing the solvation of C5PeC11 molecules in the solvents studied. A higher concentration of DBSA molecules exhibited better dispersion of C5PeC11 molecules. Core–core stacking between polyaromatic cores was found to be the major driving force for C5PeC11 aggregation, while the association among the polar groups was a contributing factor for enhancing aggregation. DBSA molecules added after C5PeC11 aggregation were able to weaken the C5PeC11 aggregates by breaking the hydrogen bonds between C5PeC11 molecules within the aggregates. A protective shell of DBSA molecules around C5PeC11 aggregates was formed due to the interactions between DBSA and C5PeC11 and the self-association of DBSA molecules. The protective shell was beneficial for hindering the flocculation of C5PeC11 aggregates. The results provided a scientific basis for manipulating asphaltenes precipitation as often occurred in oil production wells and transport pipelines.Jiang, C., Niu, B., Yin, G., Zhang, D., Yu, T., Wang, P., 2019. CT-based 3D reconstruction of the geometry and propagation of hydraulic fracturing in shale. Journal of Petroleum Science and Engineering 179, 899-911. fracturing is one of the primary techniques which has been widely implemented in order to allow for the stimulation of shale gas reservoirs. To accurately distinguish the extension characteristics and the spatial distribution of fractures during the hydraulic fracturing of the Longmaxi shale reservoirs in Changning, a self-developed, multifunctional, true triaxial experimental process (utilizing a fluid-solid coupling testing system) was used to simulate the horizontal well hydraulic fracturing. The CT technique was used to scan the samples prior to and following the conduction of the experiments; the CT scanning images of internal fractures were reconstructed and visualized via 3D reconstruction. The influence of in-situ stress, the displacement of the fracturing fluid upon the fracture morphology and the resultant fractural extensions caused by hydraulic fracturing were discussed. The study shows that the reconstructed 3D model based on the different CT values corresponding to the shale matrix, minerals and fractures can accurately characterize the internal structure and fracture distribution of shale. Shale hydraulic fracturing fractures can be divided into 3 categories: single transverse fractures, main arc fractures and complex fractures. The “fluctuation phenomenon” of a water pressure curve is related to the formation and extension of reservoir fractures, and is a discernible characteristic of complex fractures formed by the volume fracturing of shale. Stress differences and the stress difference coefficient are the governing factors in terms of the complexity of shale hydraulic fracturing networks. Displacement has a particular range of influence on the manifestation of fracture complexity; a low displacement may not result in a complete fracture, but too high a displacement tends to culminate a single fracture in the formation, which to a certain extent reduces fractural complexity.Jiménez-Moreno, G., Pérez-Asensio, J.N., Larrasoa?a, J.C., Sierro, F.J., Garcia-Castellanos, D., Salazar, ?., Salvany, J.M., Ledesma, S., Mata, M.P., Mediavilla, C., 2019. Early Pliocene climatic optimum, cooling and early glaciation deduced by terrestrial and marine environmental changes in SW Spain. Global and Planetary Change 180, 89-99. Pliocene is a key period in Earth's climate evolution, as it records the transition from warm and stable conditions to the colder and more variable glaciated climate of the Pleistocene. Simultaneously, climate became more seasonal in the Mediterranean area, and Mediterranean-type seasonal precipitation rhythm with summer drought established. These climatic changes presumably had significant impacts on terrestrial environments. However, the response of terrestrial environments to such climate changes is still not fully understood due to the lack of detailed studies dealing with this period of time. In this study, multiproxy analyses of continuous core sampling from La Matilla (SW Spain) shows detailed and continuous record of pollen, sand content and abundance of benthic foraminifer Bolivina spathulata to describe paleoenvironmental and paleoclimate trends during the early Pliocene. This record shows warmest, most humid climate conditions and highest riverine nutrient supply at ~ 4.35?Ma, coinciding with the Pliocene climatic optimum and high global sea level. A climate cooling and aridity trend occurred subsequently and a significant glaciation occurred at ~ 4.1–4.0?Ma, during a period known by very little terrestrial evidence of glaciation. Our multiproxy data thus indicate that terrestrial and marine environments were significantly variable during the early Pliocene and that major glaciation-like cooling occurred before the intensification of northern hemisphere glaciation at the beginning of the Pleistocene (~2.7?Ma). This major climate cooling and aridity maxima between 4.1 and 4.0?Ma is independently validated by a coeval sea-level drop (third order Za2 sequence boundary). This sea level drawdown is supported by enhanced coarse sedimentation and minima in riverine nutrient supply, showing paired vegetation and sea-level changes and thus a strong land-ocean relationship. This study also shows that long-term climatic trends were interrupted by orbital-scale cyclic climatic variability, with eccentricity, obliquity and precession acting as the main triggers controlling climate and environmental change in the area.Jin, F., Wang, X., Li, H., Wu, X., Fu, L., Lou, D., Zhang, J., Feng, J., 2019. Formation of the primary petroleum reservoir in Wumaying inner buried-hill of Huanghua Depression, Bohai Bay Basin, China. Petroleum Exploration and Development 46, 543-552. Yinggu 1 drilled on the tectonic belt of the Wumaying buried-hill in Huanghua Depression obtained non-H2S high-yield oil and gas flow from the Permian Lower Shihezi Formation sandstone. The oil and gas are derived from the Upper Paleozoic coal source rock, the petroleum reservoir is an inner buried-hill primary oil and gas accumulation, showing a good prospect of the Paleozoic inner buried-hill primary reservoir exploration. The formation and accumulation of the primary petroleum reservoir in the Wumaying inner buried-hill are discussed by studying the primary source conditions, the inner buried-hill reservoir-cap combinations and the hydrocarbon accumulation period. The primary petroleum reservoir has three preponderant characteristics of accumulation: secondary large-scale gas generation of coal source rock, multi reservoir-cap combinations and mainly late hydrocarbon charging, which formed the compound hydrocarbon accumulation of the above-source sandstone and under-source carbonate rock in the Paleozoic inner buried-hill. Along with the Mesozoic and Cenozoic tectonic activities, the formation of the primary reservoir in Wumaying inner buried-hill is characterized by “mixed oil and gas charge in local parts in early stage, adjustment accumulation due to structural high migration in middle stage, and large-scale natural gas charge and compound accumulation in late stage”.Jin, G., Lei, H., Xu, T., Liu, L., Xin, X., Zhai, H., Liu, C., 2019. Seafloor subsidence induced by gas recovery from a hydrate-bearing sediment using multiple well system. Marine and Petroleum Geology 107, 438-450. response behavior of the methane exploitation from natural gas hydrate (NGH) using multiple well system is complex and needs to be investigated, as gas production from a single vertical well generally cannot meet commercial demand. This study numerically investigates the production performance and geomechanical response of an unconfined hydrate deposit in Shenhu area, South China Sea, under single and multiple vertical well conditions. For a single vertical well with a mild constant bottom-hole pressure, gas production is relatively stable. However, seafloor subsidence exhibits an initial rapid drop and a subsequent mild drop stage. The vertical displacement is highly developed at the top and bottom of the production zone. The results from doublet and triplet vertical wells indicate that both the gas and water production and seafloor subsidence increase with the increase in number of production wells. The superimposition of subsidence leads to a deterioration in subsidence and the change in location for the largest subsidence, which may affect the risk location of well instability. The interference of pore pressure and subsidence increases with the decrease in well spacing. However, gas production decreases and water production changes insignificantly. Furthermore, a same subsidence at seafloor cannot indicate the same evolution of subsidence in the vertical and lateral direction. The results presented in this study help in balancing the production and subsidence of the NGH exploitation in complex well configurations.Jin, H., Lao, Y.M., Zhou, J., Zhang, H.J., Cai, Z.H., 2019. Optimization of extraction solvents, solid phase extraction and decoupling for quantitation of free isoprenoid diphosphates in Haematococcus pluvialis by liquid chromatography with tandem mass spectrometry. Journal of Chromatography A 1598, 30-38. diphosphates are important precursors actively participating in many downstream metabolisms; they are often in modified forms, e.g., protein-coupled or esterified form. Therefore, in vivo level of free isoprenoid diphosphates is quite low, ?0.07?nmol/g fresh weight in plants. In order to directly measure the isoprenoid diphosphate pool during stress-induced accumulation of astaxanthin in Haematococcus pluvialis, the present study optimized several pretreatment procedures to enrich free isoprenoid diphosphates for high-pressure liquid chromatography with tandem mass spectrometry (HPLC-MS/MS) detection. Specifically, different extraction solvents, e.g., water, methanol, chloroform, and mixture of water, methanol, and chloroform (1:1:1, V/V/V), and solid phase extraction (SPE) columns (OASIS@ WAX and HLB Cartridges) were compared; and gentle decoupling by NaOH or trifluoroacetic acid (TFA) was introduced to release free isoprenoid diphosphates. Results found that solvent mixture of water, methanol and chloroform (1:1:1, V/V/V) showed the highest extraction efficiency (RE) for five isoprenoid diphosphates, ranging from 76.83% to 92.43%; HLB column showed the balanced recoveries ranging from 75.29% to 87.54%; and incubation with low NaOH (?4.7?mmol/L) at 4?°C significantly increased detectable isoprenoid diphosphates in algal cells, some of which were undetectable or in trace level before NaOH decoupling. The method was applied to H. pluvialis cells under various stresses. Low levels of isoprenoid diphosphates were determined in most of the stresses used, e.g., 0.19?±?0.09 to 0.98?±?0.06?mg/g fresh weight (FW) for IPP/DMAPP, 0.35?±?0.07?mg/g FW for GGPP and undetectable for FPP and GPP; while isoprenoid diphosphates were significantly accumulated in the dark to 3.27?±?0.05, 0.17?±?0.09, 1.81?±?0.16 and 0.58?±?0.07?mg/g FW for IPP/DMAPP, GPP, FPP and GGPP, respectively. These results implied that isoprenoid diphosphates were exhausted by downstream carotenogenesis under stress. Our work emphasizes NaOH decoupling for exact quantitation of in vivo isoprenoid diphosphates.Jing, J., Tang, Z., Yang, Y., Ma, L., 2019. Impact of formation slope and fault on CO2 storage efficiency and containment at the Shenhua CO2 geological storage site in the Ordos Basin, China. International Journal of Greenhouse Gas Control 88, 209-225. dioxide (CO2) storage security is a key issue in CO2 geological storage (CGS). A three-dimensional (3D) conceptual reservoir model of the Shenhua CO2 geological storage site in the Ordos Basin has been used to investigate the impact of reservoir formation dip and the influence of enhanced permeability fault zones on CO2 storage and migration security. A total of 8 simulations were carried out using the TOUGH2 integral finite difference modelling code with the ECO2N fluid property module. The simulation results showed that the dip of the reservoir formation and fault had a significant impact on CO2 migration and storage security. Increasing the dip of the reservoir increased CO2 migration distance, decreased the total volume of CO2 safely stored in the formation and resulted in increased maximum gas saturation and liquid mass fraction of dissolved CO2. The presence of fault provided a channel for CO2 leakage and caused an irregular distribution of formation pressure. The onset time of leakage through the fault proved to be a function of formation dip, occurring at 465, 230, and 160?years following commencement of CO2 injection for dips of 5°, 10°, and 15° respectively. The lateral extent of both the high saturation CO2 plume and the plume of dissolved CO2 was greater in the steeply dipping faulted reservoir model, suggesting that gently dipping un-faulted reservoir formations should be selected for future CGS projects in the Ordos Basin.Jirman, P., Ger?lová, E., Bubík, M., Sachsenhofer, R.F., Bechtel, A., Wi?c?aw, D., 2019. Depositional environment and hydrocarbon potential of the Oligocene Menilite Formation in the Western Carpathians: A case study from the Lou?ka section (Czech Republic). Marine and Petroleum Geology 107, 334-350. Eocene-Oligocene boundary in the Paratethys area represents a period associated with a major extinction event followed by anoxic events. A good understanding of the factors controlling the formation of organic-rich layers is a key for prediction of source rock distributions. An excellent opportunity to study these factors is provided by the Lou?ka section situated in the Silesian Unit of the Czech Republic.The Menilite Formation is subdivided into the Subchert Member, Chert Member, Dynów Marlstone and ?itbo?ice Member and comprises non-calcareous shales, marlstones and cherts. The lithological variations reflect strongly depositional environment, which caused strong changes in geochemical parameters and source rock potential. The ratio of total organic carbon to total sulphur (TOC/TS) and methylated 2-methyl-2 (trimethyltridecyl) chroman (MTTC) ratios supported by paleontological evidence show normal marine to brackish water conditions. Pr/Ph ratios indicate strictly anoxic conditions during deposition of the upper part of the Subchert Member and the lower part of the Chert Member. Very low steranes/hopanes ratios reflect strong bacterial activity during deposition of the Chert Member. Very high HI values (>600?mg HC/g TOC) and the apparent absence of terrestrial macerals suggest that high amounts of C29 steranes and long-chain n-alkanes in this member result from the input of algal material.The Menilite Formation contains mainly type II kerogen and typically holds a “good” source rock potential. HI values?>?600?mg HC/g TOC are observed in the Chert Member, while values?<?250?mg HC/g TOC occur in some low TOC samples from the base of the Subchert Member. Tmax and low homohopane ratios confirm that the organic matter is immature.The source potential index (SPI) of the entire succession of the Menilite Formation is about 1.25?t HC/m2, which is significantly lower than SPI determined for the Polish and Ukrainian Carpathians, but mainly due to the lower thickness.Johnson, G.M., Sutherland, D.A., Roering, J.J., Mathabane, N., Gavin, D.G., 2019. Estuarine dissolved oxygen history inferred from sedimentary trace metal and organic matter preservation. Estuaries and Coasts 42, 1211-1225. history recorded in estuarine sediment describes water quality regimes through the use of geochemical and biological proxies. We collected sediment cores from two locations in the Coos Estuary, Oregon, at South Slough and Haynes Inlet, spanning from ~?1680?AD to the present. To reconstruct the historical water column oxygen in the estuary, we measured geochemical proxies including organic matter, magnetic susceptibility, and elemental composition, and we constructed sediment chronologies using the Pb210 profile and radiocarbon dates. Correlation of geochemical proxies and a detailed 15-year record of dissolved oxygen observations supports the inference of dissolved oxygen (DO) history from these sediment cores: a novel finding for small, seasonal Pacific Northwest estuaries. Geochemical evidence suggests that over the last 300?years, annually or semi-annually averaged dissolved oxygen stress has been increasing at South Slough, while remaining stable or even decreasing at Haynes inlet. This history was explained by changing climatic and land-use effects on erosion and organic matter as well as the role of shipping channel maintenance in providing a dissolved oxygen reservoir at Haynes Inlet relative to the more isolated South Slough.Jones, D.S., Walker, G.M., Johnson, N.W., Mitchell, C.P.J., Coleman Wasik, J.K., Bailey, J.V., 2019. Molecular evidence for novel mercury methylating microorganisms in sulfate-impacted lakes. The ISME Journal 13, 1659-1675. (MeHg) is a bioaccumulative neurotoxin that is produced by certain anaerobic microorganisms, but the abundance and importance of different methylating populations in the environment is not well understood. We combined mercury geochemistry, hgcA gene cloning, rRNA methods, and metagenomics to compare microbial communities associated with MeHg production in two sulfate-impacted lakes on Minnesota’s Mesabi Iron Range. The two lakes represent regional endmembers among sulfate-impacted sites in terms of their dissolved sulfide concentrations and MeHg production potential. rRNA amplicon sequencing indicates that sediments and anoxic bottom waters from both lakes contained diverse communities with multiple clades of sulfate reducing Deltaproteobacteria and Clostridia. In hgcA gene clone libraries, however, hgcA sequences were from taxa associated with methanogenesis and iron reduction in addition to sulfate reduction, and the most abundant clones were from unknown groups. We therefore applied metagenomics to identify the unknown populations in the lakes with the capability to methylate mercury, and reconstructed 27 genomic bins with hgcA. Some of the most abundant potential methylating populations were from phyla that are not typically associated with MeHg production, including a relative of the Aminicenantes (formerly candidate phylum OP8) and members of the Kiritimatiellaeota (PVC superphylum) and Spirochaetes that, together, were more than 50% of the potential methylators in some samples. These populations do not have genes for sulfate reduction, and likely degrade organic compounds by fermentation or other anaerobic processes. Our results indicate that previously unrecognized populations with hgcAB are abundant and may be important for MeHg production in some freshwater ecosystems.Josh, M., Delle Piane, C., Esteban, L., Bourdet, J., Mayo, S., Pejcic, B., Burgar, I., Luzin, V., Clennell, M.B., Dewhurst, D.N., 2019. Advanced laboratory techniques characterising solids, fluids and pores in shales. Journal of Petroleum Science and Engineering 180, 932-949. are of significant interest as reservoirs, seals and overburden in petroleum exploration and production, geological storage of CO2 and in the nuclear waste industry. Their properties and microstructure are difficult to measure and image and as such, there are still considerable gaps in our understanding of shale behaviour. The advent of more advanced and quantitative imaging methods along with novel sample preparation techniques including synchrotron imaging and K-edge subtraction with a contrast fluid, scanning (SEM) and transmission electron microscopy (TEM), have combined to allow the resolution of pores in the matrix and the organic matter in gas shales down to the nanometre scale. Textural quantification methods include neutron diffraction to quantify clay fabric alignment in siliciclastic shales as well as stress-dependent calcite c-axis orientation in carbonate-rich gas shales. The contents of the pores are also critical to the assessment of the preservation state of shales as well as the degree of water/gas saturation in resource shales. Combinations of dielectric analysis and 2 and 23?MHz nuclear magnetic resonance (NMR) measurements in siliciclastic and carbonate-rich gas shales can resolve not only the location of water, but also the interaction between water and mineral/organic surfaces in addition to the water and oil content. The organic content of shales is of particular interest in unconventional resources and this has driven application of Fourier transform infra-red (FTIR), to distinguish both mineral and organic maceral components in gas shales and Raman spectroscopy, which is increasingly used for organic matter characterisation in high maturity shales. Ultimately, shales are extremely complex nano-composite materials which require the application of multiple techniques to help determine their bulk physical and flow properties as well as factors controlling fabric and pore orientations and structure.Joung, D., Leonte, M., Kessler, J.D., 2019. Methane sources in the waters of Lake Michigan and Lake Superior as revealed by natural radiocarbon measurements. Geophysical Research Letters 46, 5436-5444.: The methane dynamics in the waters of Lakes Michigan and Superior, components of the North American Great Lake system, were investigated using measurements of methane concentration and natural radiocarbon (14C‐CH4) dissolved in these lake waters. All 14C‐CH4 measurements were above modern levels regardless of location and depth with a range of 117‐145% modern carbon (pMC). Methane concentrations in the deep basin of both lakes were low, ranging from 3.3 to 4.3 nM, with minimal vertical variation. However, the concentrations of CH4 increased toward coastal areas in both lakes, possibly due to higher groundwater inputs and aerobic methanogenesis associated with primary productivity. Except for one site, 14C‐CH4 dissolved in the waters of Lake Michigan was greater than in Lake Superior by ~12 pMC, a difference that was likely due to inputs of excess 14CH4 from nuclear power plants along the coast of Lake Michigan.Plain Language Summary: Methane is a greenhouse gas whose concentration is increasing rapidly in the modern atmosphere, and freshwater lakes globally provide a significant source to the atmosphere. Here we investigate the dynamics of methane dissolved in waters of the North American Great Lakes, one of the largest liquid freshwater environments on Earth. We found that methane dynamics in both Lakes Michigan and Superior are impacted by atmospheric input, in situ aerobic methanogenesis, groundwater, and nuclear power plants, as well as rapid vertical mixing in the water column.Kaal, J., Gianotti, C., del Puerto, L., Criado-Boado, F., Rivas, M., 2019. Molecular features of organic matter in anthropogenic earthen mounds, canals and lagoons in the Pago Lindo archaeological complex (Tacuarembó, Uruguayan lowlands) are controlled by pedogenetic processes and fire practices. Journal of Archaeological Science: Reports 26, 101900. Pago Lindo site in the River Plate basin (Uruguay) is an important pre-hispanic mound settlement (ca. 3000–600?BP), of which the technologically and socially advanced nature have only recently been revealed. Different angles of pedogenetic and palaeo-ecological science are rapidly improving our understanding of the history of the site and the relationships between human activity and habitat alteration. Here we add to this progress by molecular characterization of soil organic matter (SOM) in anthropogenic earthen mounds, canals and lagoons from Pago Lindo, by pyrolysis-GC–MS. The results showed that the SOM in the earthen mound and the archaeological lagoon are composed of microbial (partially chitin), aliphatic (partially root-derived) and pyrogenic (from fireplaces or wildfires) materials, whereas the canal and younger lagoon contained SOM with larger proportions of relatively intact plant remains (lignin and polysaccharides from herbaceous species). In most systems, a clear degradation trend can be observed with increasing depth –either from intact plant remains to microbial tissues (canal, young lagoon), or from microbial tissues to recalcitrant aliphatic and pyrogenic sources (earthen mound, ancient lagoon)– which is indicative of a strong control of decay intensity on SOM composition. Multivariate statistics confirmed that most variability in pyrolysis fingerprints can be attributed to degradation/preservation dynamics, which probably erased most of the molecular information on habitat development under the influence of past societies, including nearby maize cultivation.Kadnikov, V.V., Mardanov, A.V., Beletsky, A.V., Frank, Y.A., Karnachuk, O.V., Ravin, N.V., 2019. Genome of a member of the candidate archaeal phylum Verstraetearchaeota from a subsurface thermal aquifer revealed pathways of methyl-reducing methanogenesis and fermentative metabolism. Microbiology 88, 316-323. is the main source of biogenic methane in the atmosphere and therefore plays an important role in climate change. While all methanogens known until recently belonged to the phylum Euryarchaeota, potential methanogens were recently found among two uncultured archaeal phyla, Bathyarchaeota and Verstraetearchaeota. Analysis of the genomes of several members of Verstraetearchaeota revealed their ability to use methylated compounds for methanogenesis; however, all these genomes were incomplete, which prevents an unequivocal reconstruction of their metabolic pathways. The present work reports the complete genome of a new member of Verstraetearchaeota from the metagenome of the microbial community of a deep subsurface reservoir of thermal waters in Western Siberia. Phylogenetic analysis revealed the new archaeon to belong to a new species of the genus ‘Candidatus Methanosuratus’, for which the name ‘Candidatus Methanosuratus subterraneum’ was proposed. The possibility of methyl-reducing methanogenesis was indicated by the presence of the methyl coenzyme M reductase complex and of the genes required for methane production using methanol as the methyl group donor, while the genes required for the oxidation of methyl group to CO2 were missing. Genome analysis showed that ‘Ca. Methanosuratus subterraneum’ has the metabolic pathways required for growth by fermentation of proteinaceous substrates. Analysis of the global distribution of ‘Ca. Methanosuratus’ revealed the 16S rRNA gene sequences assigned to this genus in hot springs, underground waters, and oil reservoirs, which makes it possible to consider this genus as a representative of the subsurface biosphere.Kadokami, K., Ueno, D., 2019. Comprehensive target analysis for 484 organic micropollutants in environmental waters by the combination of tandem solid-phase extraction and quadrupole time-of-flight mass spectrometry with sequential window acquisition of all theoretical fragment-ion spectra acquisition. Analytical Chemistry 91, 7749-7755. are many thousands of chemicals in use for a wide range of purposes, and highly efficient analytical methods are required to monitor them for protection of the environment. In order to cope with this difficult task we developed a novel, comprehensive method for 484 substances in water samples. In this method target chemicals were extracted by tandem SPE and then determined by LC-QTOF-MS-SWATH. Targets were unambiguously identified using retention times, accurate masses of a precursor and two product ions, their ion ratios, and accurate MS/MS spectrum. Quantitation was achieved by the internal standard method using a precursor ion. Results of recovery tests at two concentrations (50 and 500 ng L–1) showed average recoveries of 87.5% and 87.0% (RSD, 9.1% and 9.4%), respectively. Limits of detection of one-half of the targets were below 1.0 ng L–1. The method was applied to the influent and effluent of a sewage treatment plant, and around 100 chemicals were detected. Results of examination on matrix effects using their extracts spiked with 209 pesticides showed that the ratios of detected amounts between the extracts and the standard solution were 89.8% (influent) and 91.7% (effluent), respectively. In addition, investigation on the stability of calibration curves by injecting the same standards for 1 year showed that their quantitative results did not change; average accuracy was 103.3% (RSD, 10.0%), indicating that the calibration curves can be used for an extended period of time without calibration, and quantitative retrospective analysis can be done after creating calibration curves for new targets.Kahkashan, S., Wang, X., Ya, M., Chen, J., Wu, Y., Cai, Y., Saleem, M., Inam, A., Aftab, J., 2019. Evaluation of marine sediment contamination by polycyclic aromatic hydrocarbons along the Karachi coast, Pakistan, 11 years after the Tasman Spirit oil spill. Chemosphere 233, 652-659. July 27, 2003, a spill of approximately 31,000 tons of Iranian light crude oil affected the coast of Karachi, Pakistan. Approximately 11 years after the spill, we analyzed polycyclic aromatic hydrocarbons (PAHs) and their alkylated homologues (alkyl-PAHs) as the indicators to evaluate the residual effect of oil spill to the sediment along the Karachi coast. The total concentrations (dry weight) of parent PAHs and alkyl-PAHs ranged from 121.9 to 735.4 and 42.3–1149.9?ng/g, respectively. The estuary and harbor were the two regions with the highest levels of PAHs in the sediment. Conversely, sedimentary PAHs in the oil spill areas and remote coastal areas showed significantly lower levels. Although the results of the source identification indicated the up to 75.2% of the contribution from petroleum and its derivatives, this could only reflect the direct impact of the Karachi city on the presence of PAHs in the coastal sedimentary environment and did not indicated that the oil spill continues to stay 11 years later. Compared with 11 years ago, the sharply reduced PAH content, great changed composition, and the degradation driven trend of diagnostic ratios all indicated a sharp decrease in the influence of PAHs caused by the oil spill. Finally, the ecological risk caused by the PAH residual in the marine sedimentary ecosystem had disappeared along the Karachi coasts, Pakistan.Kai, N., Naiang, W., Xiaonan, L., Zhuolun, L., Jiaqi, S., Ran, A., Lvlv, Z., 2019. A grain size and n-alkanes record of Holocene environmental evolution from a groundwater recharge lake in Badain Jaran Desert, Northwestern China. The Holocene 29, 1045-1058. water transport plays an important role in the development and maintenance of lakes in arid zones. However, previous study of this phenomenon has focused mainly on the effects of regional precipitation, rather than effects of groundwater recharge, on arid-zone environmental change. We selected a sedimentary profile from a seasonal lake basin located in the hinterland of the Badain Jaran Desert, northwestern China, to assess the Holocene environmental evolution of this region and its response to climate change. Our results show that peat deposition from 11 to 10 ka indicates humidification after Younger Dryas (YD) event; the lake sediment and lower EM2 and lower principal component analysis (PCA)-1 scores indicate relative more humid environment from 10 to 7.8 ka; the lake sediment and higher EM2 and higher PCA-1 scores indicate most humid environment from 7.8 to 5.8 ka; the transition from lacustrine facies to limnetic facies and increasing salinity indicate drying trend from 5.8 to 2.5 ka; the aeolian sand sediment and lowest EM2 and lowest PCA-1 scores indicate driest environment from 2.5 to 0.8 ka; and lacustrine facies and finest grain size indicate relative humid environment during the ?Little Ice Age? period. The environment was relative humid in early Holocene, most Humid in mid-Holocene, and dry in mid-late Holocene. The moisture pattern in the hinterland of the Badain Jaran Desert was synchronous with that in the northeastern of Tibetan Plateau, which implies that the groundwater recharge lake was dominated by the intensity of groundwater recharge from monsoon margin area, especially the northeastern of Tibetan Plateau. As a record from groundwater recharge lake without runoff, our study provides the groundwater output quantity record from northeastern of Tibetan Plateau and would benefit the environment change research and regional water resources allocation around the Tibetan Plateau.Kaiser, K., Gross, L., Schulz, F., 2019. A Single-Molecule Chemical Reaction Studied by High-Resolution Atomic Force Microscopy and Scanning Tunneling Microscopy Induced Light Emission. ACS Nano 13, 6947-6954. force microscopy (AFM) as well as scanning tunneling microscopy induced light emission (STM-LE) are, each on their own, powerful tools used to investigate a large variety of properties of single molecules adsorbed on a surface. However, accessing both structural information by AFM as well as optical information by STM-LE on the same molecule so far remains elusive. We present a combined high-resolution AFM and STM-LE study on single metal-oxide phthalocyanines. Using atomic manipulation, the molecules can be deliberately reduced. We demonstrate structure elucidation and adsorption geometry determination of single molecules with atomic resolution combined with optical characterization by STM-LE and the possibility of investigating the change in a molecule?s exciton emission intensity by a chemical reaction.Kalanat, B., Vaziri-Moghaddam, H., 2019. The Cenomanian/Turonian boundary interval deep-sea deposits in the Zagros Basin (SW Iran): Bioevents, carbon isotope record and palaeoceanographic model. Palaeogeography, Palaeoclimatology, Palaeoecology 533, 109238. Cenomanian/Turonian (C/T) boundary interval, spanning the upper part of the Sarvak Formation in the Zagros Basin (Izeh Zone), has been studied to determine the timing and the possible cause of biotic turnovers, coinciding with the intense environmental perturbations during the Oceanic Anoxic Event 2 (OAE2). The upper Cenomanian strata in the study section, composed of light-colour marlstone/organic-rich marlstone and shale bedding couplets, record fluctuations in microfossil assemblages and organic carbon contents. We suggest that the organic-poor layers, characterized by high abundance of radiolarians, were deposited during cold periods under surface water eutrophication (upwelling) and ventilated seafloor. In contrast, water column stratification during warm periods enhanced organic matter preservation and allowed deposition of organic-rich strata. Continued stratification and also increased runoff and primary productivity during warm intervals of OAE2 led to expansion of oxygen minimum zone (OMZ), which may have caused extinctions of deep followed by intermediate water planktic foraminifera. Such conditions may have led to significant decreases in the abundance and diversity of planktic foraminifera and dominance of the biserial genus Planoheterohelix (“Heterohelix” shift event). The δ13C curve in the study interval reveals the diagnostic features of global C/T boundary carbon isotope record, including three positive peaks (A, B and C) within the Whiteinella archaeocretacea Biozone. These carbon isotope features and the most important bioevents in the study section are stratigraphically listed below: 1- Highest occurrences (HOs) of Th. greenhornensis and Th. deeckei, 2- HO of R. cushmani and δ13C peak A, 3- HO of “G”. bentonensis, 4- Onset of “Heterohelix” shift event, 5- δ13C peak B, 6- δ13C peak C, 7- Filament event, 8- Lowest occurrence (LO) of H. helvetica, and 9- Holywell event.Kardani, M.N., Baghban, A., Hamzehie, M.E., Baghban, M., 2019. Phase behavior modeling of asphaltene precipitation utilizing RBF-ANN approach. Petroleum Science and Technology 37, 1861-1867. of heavy hydrocarbons, particularly asphaltenes, is the reason for numerous operational and production problems in the petroleum industry. Hence, knowing the amount of asphaltene precipitation is a critical commission for petroleum engineers to overcome its problems. The aim of this study was to predict the amount of asphaltene precipitation as a function of temperature, dilution ratio, and molecular weight of different n-alkanes utilizing radial basis function artificial neural network (RBF-ANN). Additionally, this model has been compared with previous correlations, and its great accuracy was proved to predict the precipitated asphaltene. The values of R-squared and mean squared error obtained were 0.998 and 0.007, respectively. The efforts confirmed brilliant forecasting skill of RBF-ANN for the approximation of the precipitated asphaltene as a function of temperature, dilution ratio, and molecular weight of different n-alkanes.Karolyt?, R., Johnson, G., Gy?re, D., Serno, S., Flude, S., Stuart, F.M., Chivas, A.R., Boyce, A., Gilfillan, S.M.V., 2019. Tracing the migration of mantle CO2 in gas fields and mineral water springs in south-east Australia using noble gas and stable isotopes. Geochimica et Cosmochimica Acta 259, 109-128. monitoring of CO2 storage requires understanding of both innate and introduced fluids in the crust as well as the subsurface processes that can change the geochemical fingerprint of CO2 during injection, storage and any subsequent migration. Here, we analyse a natural analogue of CO2 storage, migration and leakage to the atmosphere, using noble gas and stable isotopes to constrain the effect of these processes on the geochemical fingerprint of the CO2. We present the most comprehensive evidence to date for mantle-sourced CO2 in south-east Australia, including well gas and CO2-rich mineral spring samples from the Otway Basin and Central Victorian Highlands (CVH). 3He/4He ratios in well gases and CO2 springs range from 1.21 to 3.07 RA and 1.23–3.65 RC/RA, respectively. We present chemical fractionation models to explain the observed range of 3He/4He ratios, He, Ne, Ar, Kr, Xe concentrations and δ13C(CO2) values in the springs and the well gases. The variability of 3He/4He in the well gases is controlled by the gas residence time in the reservoir and associated radiogenic 4He accumulation. 3He/4He in CO2 springs decrease away from the main mantle fluid supply conduit. We identify one main pathway for CO2 supply to the surface in the CVH, located near a major fault zone. Solubility fractionation during phase separation is proposed to explain the range in noble gas concentrations and δ13C(CO2) values measured in the mineral spring samples. This process is also responsible for low 3He concentrations and associated high CO2/3He, which are commonly interpreted as evidence for mixing with crustal CO2. The elevated CO2/3He can be explained solely by solubility fractionation without the need to invoke other CO2 sources. The noble gases in the springs and well gases can be traced back to a single end-member which has suffered varying degrees of radiogenic helium accumulation and late stage degassing. This work shows that combined stable and noble gas isotopes in natural gases provide a robust tool for identifying the migration of injected CO2 to the shallow subsurface.Kartsova, L.A., Bessonova, E.A., Somova, V.D., 2019. Hydrophilic interaction chromatography. Journal of Analytical Chemistry 74, 415-424. interaction liquid chromatography (HILIC), which includes the distribution, adsorption, ion exchange, and exclusion of analytes, has gained active development recently. The review covers the principles of the method, types of stationary and mobile phases, mechanisms of retention of highly polar compounds under HILIC conditions, implementation of 2D chromatography, and also fields of application of the method.K?telh?n, A., Meys, R., Deutz, S., Suh, S., Bardow, A., 2019. Climate change mitigation potential of carbon capture and utilization in the chemical industry. Proceedings of the National Academy of Sciences 116, 11187-11194.: Carbon dioxide (CO2) drives climate change when released to the atmosphere. Alternatively, CO2 could be captured and utilized as carbon source for chemicals. Here, we provide a global assessment of the technical climate change mitigation potential of carbon capture and utilization (CCU) in the chemical industry. We develop an engineering-level model of the global chemical industry representing 75% of current greenhouse gas (GHG) emissions. The model allows us to analyze the potential disruptive changes through large-scale CO2 utilization and resulting emission reductions. Our study shows that CCU has the technical potential to lead to a carbon-neutral chemical industry and decouple chemical production from fossil resources. This transition, however, would cause largely increased mass flows and demand for low-carbon electricity.Abstract: Chemical production is set to become the single largest driver of global oil consumption by 2030. To reduce oil consumption and resulting greenhouse gas (GHG) emissions, carbon dioxide can be captured from stacks or air and utilized as alternative carbon source for chemicals. Here, we show that carbon capture and utilization (CCU) has the technical potential to decouple chemical production from fossil resources, reducing annual GHG emissions by up to 3.5 Gt CO2-eq in 2030. Exploiting this potential, however, requires more than 18.1 PWh of low-carbon electricity, corresponding to 55% of the projected global electricity production in 2030. Most large-scale CCU technologies are found to be less efficient in reducing GHG emissions per unit low-carbon electricity when benchmarked to power-to-X efficiencies reported for other large-scale applications including electro-mobility (e-mobility) and heat pumps. Once and where these other demands are satisfied, CCU in the chemical industry could efficiently contribute to climate change mitigation.Kawai, S., Nishihara, A., Matsuura, K., Haruta, S., 2019. Hydrogen-dependent autotrophic growth in phototrophic and chemolithotrophic cultures of thermophilic bacteria, Chloroflexus aggregans and Chloroflexus aurantiacus, isolated from Nakabusa hot springs. FEMS Microbiology Letters 366, Artricle fnz122. genus Chloroflexus is a deeply branching group of thermophilic filamentous anoxygenic phototrophic bacteria. The bacteria in this genus have been shown to grow well heterotrophically under anaerobic photosynthetic and aerobic respiratory conditions. We examined autotrophic growth in new isolates of Chloroflexus strains from hot springs in Nakabusa, Japan. The isolates belonging to Chloroflexus aggregans (98.7% identity of 16S rRNA gene sequence to the respective type strain) and Chloroflexus aurantiacus (99.9% identity to the respective type strain) grew photoautotrophically under a 24% H2 atmosphere. We also observed chemolithotrophic growth of these isolates under 80% H2 and 5% O2 conditions in the dark. This is the first report showing that Chloroflexus grew under both photoautotrophic and chemolithotrophic conditions in addition to photoheterotrophic and aerobic chemoheterotrophic conditions.Kayler, Z.E., Premke, K., Gessler, A., Gessner, M.O., Griebler, C., Hilt, S., Klemedtsson, L., Kuzyakov, Y., Reichstein, M., Siemens, J., Totsche, K.-U., Tranvik, L., Wagner, A., Weitere, M., Grossart, H.-P., 2019. Integrating aquatic and terrestrial perspectives to improve insights into organic matter cycling at the landscape scale. Frontiers in Earth Science 7, 127. doi: 10.3389/feart.2019.00127. a landscape, aquatic-terrestrial interfaces within and between ecosystems are hotspots of organic matter (OM) mineralization. These interfaces are characterized by sharp spatio-temporal changes in environmental conditions, which affect OM properties and thus control OM mineralization and other transformation processes. Consequently, the extent of OM movement at and across aquatic-terrestrial interfaces is crucial in determining OM turnover and carbon (C) cycling at the landscape scale. Here, we propose expanding current concepts in aquatic and terrestrial ecosystem sciences to comprehensively evaluate OM turnover at the landscape scale. We focus on three main concepts toward explaining OM turnover at the landscape scale: the landscape spatio-temporal context, OM turnover described by priming and ecological stoichiometry, and anthropogenic effects as a disruptor of natural OM transfer magnitudes and pathways. A conceptual framework is introduced that allows for discussing the disparities in spatial and temporal scales of OM transfer, changes in environmental conditions, ecosystem connectivity, and microbial–substrate interactions. The potential relevance of priming effects in both terrestrial and aquatic systems is addressed. For terrestrial systems, we hypothesize that the interplay between the influx of OM and its corresponding elemental composition and the elemental demand of the microbial communities – stoichiometric question – may alleviate spatial and metabolic thresholds. In comparison, substrate level OM dynamics may be substantially different in aquatic systems due to matrix effects that accentuate the role of abiotic conditions, substrate quality, and microbial community dynamics. We highlight the disproportionate impact anthropogenic activities can have on OM cycling across the landscape including reversing natural OM flows through the landscape, disrupting ecosystem connectivity, and nutrient additions that cascade across the landscape. This knowledge is crucial for a better understanding of OM cycling in a landscape context, in particular since terrestrial and aquatic compartments may respond differently to the ongoing changes in climate, land use, and other anthropogenic interferences.Kazemzadeh, Y., Dehdari, B., Etemadan, Z., Riazi, M., Sharifi, M., 2019. Experimental investigation into Fe3O4/SiO2 nanoparticle performance and comparison with other nanofluids in enhanced oil recovery. Petroleum Science 16, 578-590. because of their surface characteristics improve the oil production from reservoirs by enabling different enhanced recovery mechanisms such as wettability alteration, interfacial tension (IFT) reduction, oil viscosity reduction, formation and stabilization of colloidal systems and the decrease in the asphaltene precipitation. To the best of the authors’ knowledge, the synthesis of a new nanocomposite has been studied in this paper for the first time. It consists of nanoparticles of both SiO2 and Fe3O4. Each nanoparticle has its individual surface property and has its distinct effect on the oil production of reservoirs. According to the previous studies, Fe3O4 has been used in the prevention or reduction of asphaltene precipitation and SiO2 has been considered for wettability alteration and/or reducing IFTs in enhanced oil recovery. According to the experimental results, the novel synthesized nanoparticles have increased the oil recovery by the synergistic effects of the formed particles markedly by activating the various mechanisms relative to the use of each of the nanoparticles in the micromodel individually. According to the results obtained for the use of this nanocomposite, understanding reservoir conditions plays an important role in the ultimate goal of enhancing oil recovery and the formation of stable emulsions plays an important role in oil recovery using this method.Ka?mierczak, J., Kremer, B., 2019. Pattern of cell division in ～3.4?Ga-old microbes from South Africa. Precambrian Research 331, Article 105357. cell division, most microbes rely on binary fission. Some, however, show less common division patterns, such as multiple fission or budding. Little is known about the nature of cell division in the Earth’s earliest fossil microbes, largely because of their poor preservation, but such details could be key in establishing the biogenicity of putative Archean fossils and their relationships to modern microbes. In this report we describe cellularly preserved microfossils from Paleoarchean (～3.4-Ga-old) deposits of South Africa (Kromberg Formation). Their cellularity is revealed by well-preserved reproduction patterns exemplified by binary (symmetrical and asymmetrical) and multiple (coupled and/or sequential) cell fission. Although no clues concerning physiology or affinity of the studied cells can be drawn basing on their division mode, the identified reproductive patterns link them particularly closely with coccoidal microbes classified within the cyanobacterial group Pleurocapsales.Ke, C.-Y., Lu, G.-M., Wei, Y.-L., Sun, W.-J., Hui, J.-F., Zheng, X.-Y., Zhang, Q.-Z., Zhang, X.-L., 2019. Biodegradation of crude oil by Chelatococcus daeguensis HB-4 and its potential for microbial enhanced oil recovery (MEOR) in heavy oil reservoirs. Bioresource Technology 287, 121442. of crude heavy oil was investigated with Chelatococcus daeguensis HB-4 that was isolated from the produced fluid of Baolige Oilfield in China. Batch growth characterization and crude oil degradation tests confirmed HB-4 to be facultative anaerobic and able to degrade heavy oil. The oil degradation was found to occur through degrading long hydrocarbons chains to shorter ones, resulting in oil viscosity reduction. By mixing crude oil with glucose, or using sole crude oil as carbon source, the content of light fractions (C8-C22) increased by 4.97% while heavy fractions (C23-C37) decreased by 7.98%. It was also found that bioemulsifiers were produced rather than commonly observed biosurfactants in the fermentation process, which was attributed to the extracellular degradation of hydrocarbons. Core flooding tests demonstrated 20.5% oil recovery by microbial enhancement, and 59.8% viscosity reduction, showing potential of strain HB-4 for application in the oil industry, especially in enhanced heavy oil recovery.Kedzierski, M., Falcou-Préfol, M., Kerros, M.E., Henry, M., Pedrotti, M.L., Bruzaud, S., 2019. A machine learning algorithm for high throughput identification of FTIR spectra: Application on microplastics collected in the Mediterranean Sea. Chemosphere 234, 242-251. development of methods to automatically determine the chemical nature of microplastics by FTIR-ATR spectra is an important challenge. A machine learning method, named k-nearest neighbors classification, has been applied on spectra of microplastics collected during Tara Expedition in the Mediterranean Sea (2014). To realize these tests, a learning database composed of 969 microplastic spectra has been created. Results show that the machine learning process is very efficient to identify spectra of classical polymers such as poly(ethylene), but also that the learning database must be enhanced with less common microplastic spectra. Finally, this method has been applied on more than 4000 spectra of unidentified microplastics. The verification protocol showed less than 10% difference in the results between the proposed automated method and a human expertise, 75% of which can be very easily corrected.K?dzior, S., Dreger, M., 2019. Methane occurrence, emissions and hazards in the Upper Silesian Coal Basin, Poland. International Journal of Coal Geology 211, 103226. paper presents the variability of methane emissions into mining excavations and the atmosphere in the Upper Silesian Coal Basin (USCB) (Poland) against the background of natural and mining factors. Emissions of methane from exploited coal seams have become a serious problem in the USCB due to the growing methane hazard in coal mines and emissions of methane into the atmosphere. In the mid-nineties 753 million m3 of methane was emitted annually from the USCB mines. Despite a significant drop in coal production over the next 20?years, methane emissions have not decreased sharply; on the contrary, in recent years they have begun to grow, and, in 2016, reached the level of 933 million m3 per year. This represents an increase of 180 million m3 per year since the mid-nineties. One of the important reasons for this phenomenon is the constantly increasing depth of coal exploitation, which in many mines now exceeds 1000?m; this is the depth corresponding to the deep methane zone, where the volume of accumulated methane in the coal seams is particularly high. Factors influencing the volume of methane emissions in relation to mine workings can be divided roughly into two groups: natural (geological) and anthropogenic (mining-related). Natural factors include methane content in coal seams, gas pressure, the presence of free gas in fault zones, related fissures and porous sandstone, the migration of methane through faults and fissures, and the presence of a continuous and impermeable Miocene overburden. Mining factors include the depth of exploitation and the concentration of coal production as expressed in terms of the length, height, and advance of walls. The interdependence of these factors means that, despite the decline in coal production, methane emissions, both total and specific, are increasing. This problem cannot be neglected, especially since it may grow worse in future. One measure to prevent the growth of methane emissions and the associated hazard may be the intensification of mine methane drainage and the economic use of captured mining gas, which is already done in the USCB.Kehe, J., Kulesa, A., Ortiz, A., Ackerman, C.M., Thakku, S.G., Sellers, D., Kuehn, S., Gore, J., Friedman, J., Blainey, P.C., 2019. Massively parallel screening of synthetic microbial communities. Proceedings of the National Academy of Sciences 116, 12804-12809.: Microbial communities have many applications, but current experimental strategies to investigate their behavior are limited by the combinatorial complexity of interactions between species. Here, we introduce a platform to automatically construct and test synthetic communities of microbes from a set of input species at a scale of ～100,000 communities per day. As a first demonstration, we discovered specific compositions of bacteria isolated from local soil that promote the growth of a model plant symbiont. More broadly, our platform can be adopted for the discovery of microbial consortia with many useful properties, such as suppression of pathogens or degradation of recalcitrant substrates for use in biofuel production or environmental remediation.Abstract: Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ～100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.Keller, M., Spyrou, M.A., Scheib, C.L., Neumann, G.U., Kr?pelin, A., Haas-Gebhard, B., P?ffgen, B., Haberstroh, J., Ribera i Lacomba, A., Raynaud, C., Cessford, C., Durand, R., Stadler, P., N?gele, K., Bates, J.S., Trautmann, B., Inskip, S.A., Peters, J., Robb, J.E., Kivisild, T., Castex, D., McCormick, M., Bos, K.I., Harbeck, M., Herbig, A., Krause, J., 2019. Ancient Yersinia pestis genomes from across Western Europe reveal early diversification during the First Pandemic (541–750). Proceedings of the National Academy of Sciences 116, 12363-12372.: The first historically reported pandemic attributed to Yersinia pestis started with the Justinianic Plague (541–544) and continued for around 200 y as the so-called First Pandemic. To date, only one Y. pestis strain from this pandemic has been reconstructed using ancient DNA. In this study, we present eight genomes from Britain, France, Germany, and Spain, demonstrating the geographic range of plague during the First Pandemic and showing microdiversity in the Early Medieval Period. Moreover, we detect similar genome decay during the First and Second Pandemics (14th to 18th century) that includes the same two virulence factors, thus providing an example of potential convergent evolution of Y. pestis during large-scale epidemics.Abstract: The first historically documented pandemic caused by Yersinia pestis began as the Justinianic Plague in 541 within the Roman Empire and continued as the so-called First Pandemic until 750. Although paleogenomic studies have previously identified the causative agent as Y. pestis, little is known about the bacterium’s spread, diversity, and genetic history over the course of the pandemic. To elucidate the microevolution of the bacterium during this time period, we screened human remains from 21 sites in Austria, Britain, Germany, France, and Spain for Y. pestis DNA and reconstructed eight genomes. We present a methodological approach assessing single-nucleotide polymorphisms (SNPs) in ancient bacterial genomes, facilitating qualitative analyses of low coverage genomes from a metagenomic background. Phylogenetic analysis on the eight reconstructed genomes reveals the existence of previously undocumented Y. pestis diversity during the sixth to eighth centuries, and provides evidence for the presence of multiple distinct Y. pestis strains in Europe. We offer genetic evidence for the presence of the Justinianic Plague in the British Isles, previously only hypothesized from ambiguous documentary accounts, as well as the parallel occurrence of multiple derived strains in central and southern France, Spain, and southern Germany. Four of the reported strains form a polytomy similar to others seen across the Y. pestis phylogeny, associated with the Second and Third Pandemics. We identified a deletion of a 45-kb genomic region in the most recent First Pandemic strains affecting two virulence factors, intriguingly overlapping with a deletion found in 17th- to 18th-century genomes of the Second Pandemic.Kemp, D.B., Baranyi, V., Izumi, K., Burgess, R.D., 2019. Organic matter variations and links to climate across the early Toarcian oceanic anoxic event (T-OAE) in Toyora area, southwest Japan. Palaeogeography, Palaeoclimatology, Palaeoecology 530, 90-102. climate warming during the early Toarcian oceanic anoxic event (T-OAE, ~182?Ma) has been shown to have had a significant effect on the global carbon cycle and biosphere. There is also emerging evidence that a primary short-term consequence of this warming was a marked increase in hydrological cycling. In this study, we have investigated local environmental responses to T-OAE climate change by conducting a palynofacies analysis through an expanded Panthalassic margin record of the event exposed in southwestern Japan (Nishinakayama Formation, Toyora area). Palynomorphs are poorly preserved and rare in the studied interval. A pronounced increase in terrestrial phytoclast abundance coeval with the peak of the T-OAE can be linked to increased fluvial supply driven by enhanced hydrological cycling that occurred in response to early Toarcian warming. Broader scale trends in phytoclast abundance through the studied interval may be linked to longer-term sea-level changes. Nitrogen-isotopes, commonly used to elucidate basin redox changes, are found to correlate with changes in the relative abundance of phytoclasts. In contrast, carbon-isotope data are probably not significantly influenced by changes in organic matter type through the succession. However, thermal maturity indicators demonstrate that the succession is overmature, and this likely suppresses the magnitude of the well-known T-OAE carbon-isotope excursion in this succession.Khare, P., Marcotte, A., Sheu, R., Walsh, A.N., Ditto, J.C., Gentner, D.R., 2019. Advances in offline approaches for trace measurements of complex organic compound mixtures via soft ionization and high-resolution tandem mass spectrometry. Journal of Chromatography A 1598, 163-174. airborne mixtures of organic compounds can contain 10,000′s of diverse compounds at trace concentrations. Here, we incorporate high-resolution mass spectrometry into our integrated offline sampling-to-analysis measurement system for routine molecular-level speciation of complex mixtures in gas- or particle-phase samples with detection limits of 2–20?pg L?1 (i.e. 0.2–1.9 ppt in 6?L samples). Analytes desorbed from custom adsorbent tubes (or filter extracts) were separated via gas chromatography (GC) and simultaneously analyzed by an electron ionization quadrupole mass spectrometer (EI-MS), and by atmospheric pressure chemical ionization (APCI) combined with a high-resolution quadrupole time-of-flight mass spectrometer (Q-TOF) with a resolution of 25,000–40,000?M/ΔM in HR-TOF and MS/MS modes. We demonstrated our system with simple standards, a Macondo crude oil standard as a reference for complex mixtures of common airborne compounds, and ambient samples using GC-TOF and GC–MS/MS. We speciated complex mixtures at mass accuracy error (i.e. mass tolerance) down to 8?±?2?ppm (e.g. resolving analytes of mass 270.000?u with 0.003?u accuracy) using a targeted approach with 3000 molecular formulas, including hydrocarbons and functionalized analytes containing oxygen, sulfur, nitrogen, or phosphorous. This extended from compounds with 10 to 32 carbon atoms and up to 16 hydrocarbon formulas per carbon number, and a similar range for functionalized compound classes. We also demonstrated our MS/MS capabilities to differentiate structural isomers and determine the presence of specific functional groups; and our direct-TOF capability, which bypasses high-temperature chromatographic separation to preserve functionalized analytes.Khatiwala, S., Schmittner, A., Muglia, J., 2019. Air-sea disequilibrium enhances ocean carbon storage during glacial periods. Science Advances 5, Article eaaw4981. prevailing hypothesis for lower atmospheric carbon dioxide (CO2) concentrations during glacial periods is an increased efficiency of the ocean’s biological pump. However, tests of this and other hypotheses have been hampered by the difficulty to accurately quantify ocean carbon components. Here, we use an observationally constrained earth system model to precisely quantify these components and the role that different processes play in simulated glacial-interglacial CO2 variations. We find that air-sea disequilibrium greatly amplifies the effects of cooler temperatures and iron fertilization on glacial ocean carbon storage even as the efficiency of the soft-tissue biological pump decreases. These two processes, which have previously been regarded as minor, explain most of our simulated glacial CO2 drawdown, while ocean circulation and sea ice extent, hitherto considered dominant, emerge as relatively small contributors.Kim, D., Kim, S., Son, S., Jung, M.-J., Kim, S., 2019. Application of online liquid chromatography 7 T FT-ICR mass spectrometer equipped with quadrupolar detection for analysis of natural organic matter. Analytical Chemistry 91, 7690-7697. this study, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), combined with quadrupolar detection (QPD), was applied for online liquid chromatography (LC) MS analysis of natural organic matter (NOM). Although FT-ICR MS has emerged as an important analytical technique to study NOM, there are few previous reports on online LC FT-ICR MS analysis of NOM due to the long acquisition time (2–8 s) required to obtain high-resolution mass spectra. The QPD technique provides a critical advantage over the conventional dipolar detection (DPD) technique for LC-MS analysis because a spectrum with the same resolving power can be obtained in approximately half the acquisition time. QPD FT-ICR MS provides resolving powers (m/Δm50%) of ～300000 and 170000 at m/z 400 with acquisition times per scan of 1.2 and 0.8 s, respectively. The reduced acquisition time per scan allows increased number of acquisitions in a given LC analysis time, resulting in improved signal to noise (S/N) ratio and dynamic range in comparison to conventional methods. For example, 40% and 100% increases in the number of detected peaks were obtained with LC QPD FT-ICR MS, in comparison to conventional LC DPD FT-ICR MS and direct-injection FT-ICR MS. It is also possible to perform more quantitative comparison and molecular level investigation of NOMs with 2 μg of a NOM sample. The data presented herein demonstrate a proof of principle that QPD combined with LC FT-ICR MS is a sensitive analytical technique that can provide comprehensive information about NOM.Kim, H.-S., Dong, K., Kim, J., Lee, S.-S., 2019. Characteristics of crude oil-degrading bacteria Gordonia iterans isolated from marine coastal in Taean sediment. MicrobiologyOpen 8, Article e00754. oil is a major pollutant of marine and coastal ecosystems, and it causes environmental problems more seriously. It is believed ultimate and complete degradation is accomplished mainly by microorganisms. In this study, we aim to search out for bacterial strains with high ability in degrading crude oil. From sediments contaminated by the petroleum spilled in 2007, an accident in Taean, South Korea, we isolated thirty-one bacterial strains in total with potential application in crude oil contamination remediation. In terms of removal percentage after 7?days, one of the strains, Co17, showed the highest removal efficiency with 84.2% of crude oil in Bushnell-Haas media. The Co17 strain even exhibited outstanding ability removing crude oil at a high salt concentration. Through the whole genome sequencing annotation results, many genes related with n-alkane degradation in the genome of Gordonia sp. Co17, revealed alkane-1-monooxygenase, alcohol dehydrogenase, and Baeyer?Villiger monooxygenase. Specially, for confirmation of gene-level, alkB gene encoding alkane hydroxylase (alkane-1-monooxygenase) was found in the strain Co17. The expression of alkB upregulated 125-fold after 18?hr accompany with the removal of n-alkanes of 48.9%. We therefore propose the strain Gordonia iterans Co17, isolated from crude oil-contaminated marine sediment, could be used to offer a new strategy for bioremediation with high efficiency.Knebl, A., Domes, R., Yan, D., Popp, J., Trumbore, S., Frosch, T., 2019. Fiber-enhanced Raman gas spectroscopy for 18O–13C-labeling experiments. Analytical Chemistry 91, 7562-7569. isotopes are used in ecology to track and disentangle different processes and pathways. Especially for studies focused on the gas exchange of plants, sensing techniques that offer oxygen (O2) and carbon dioxide (CO2) sensitivity with isotopic discrimination are highly sought after. Addressing this challenge, fiber-enhanced Raman gas spectroscopy is introduced as a fast optical technique directly combining 13CO2 and 12CO2 as well as 18O2 and 16O2 measurements in one instrument. We demonstrate how a new type of optical hollow-core fiber, the so-called revolver fiber, is utilized for enhanced Raman gas sensing. Carbon dioxide and oxygen isotopologues were measured at concentrations expected when using 13C- and 18O-labeled gases in plant experiments. Limits of detection have been determined to be 25 ppm for CO2 and 150 ppm for O2. The combination of measurements with different integration times allows the creation of highly resolved broadband spectra. With the help of calculations based on density functional theory, the line at 1512 cm–1 occurring in the oxygen spectrum is assigned to 18O16O. The relative abundances of the isotopologues 18O16O and nitrogen 15N14N were in good agreement with typical values. For CO2, fiber-enhanced Raman spectra show the Fermi diad and hotbands of 12C16O2, 13C16O2, and 12C18O16O. Several weak lines were observed, and the line at 1426 cm–1 was identified as originating from the (0 4 0 2) → (0 2 0 2) transition of 12C16O2. With the demonstrated sensitivity and discriminatory power, fiber-enhanced Raman spectroscopy is a possible alternative means to investigate plant metabolism, directly combining 13CO2 and 12CO2 measurements with 18O2 and 16O2 measurements in one instrument. The presented method thus has large potential for basic analytical investigations as well as for applications in the environmental sciences.Kong, W., Liu, J., Ji, M., Yue, L., Kang, S., Morgan-Kiss, R.M., 2019. Autotrophic microbial community succession from glacier terminus to downstream waters on the Tibetan Plateau. FEMS Microbiology Ecology 95, Article fiz074. harbour diverse microbes and autotrophic microbes play a key role in sustaining the glacial ecosystems by providing organic carbon. The succession of glacier-originated autotrophic microbes and their effects on downstream aquatic ecosystems remain unknown. We herein investigated the shift of autotrophic microbial communities in waters (not biofilms) along a glacier meltwater transect consisting of a glacier terminus outflow (subglacial), a glacial stream, two glacier-fed lakes (upper and lower) and their outflow on the Tibetan Plateau. The autotrophic community was characterized by cbbL gene using qPCR, T-RFLP and clone library/sequencing methods. The results demonstrated that form IC and ID autotrophic microbes exhibited a much higher abundance than form IAB in all waters along the transect. Form IAB autotrophic abundance in waters gradually decreased, while the form IC exhibited a substantial increase in the upper lake waters, and ID exhibited a substantial increase in the lower lake waters. The water form IC autotrophic community structure exhibited a distinguished shift from the glacier terminus outflow to the stream, while the form ID showed a dramatic shift from the stream to the lower lake. Our results revealed the succession patterns of glacier-originated autotrophic microbial communities and possible effects on downstream aquatic ecosystems.Kontorovich, A.E., Bogorodskaya, L.I., Borisova, L.S., Burshtein, L.M., Ismagilov, Z.P., Efimova, O.S., Kostyreva, E.A., Lemina, N.M., Ryzhkova, S.V., Sozinov, S.A., Fomin, A.N., 2019. Geochemistry and catagenetic transformations of kerogen from the Bazhenov horizon. Geochemistry International 57, 621-634. representative suite of 276 samples was used to study the isotopic and elemental geochemistry of kerogens from the Bazhenov horizon (Bazhenov Formation and its age equivalents) of the western Siberian sedimentary basin and to map the variations in the elemental composition of kerogen in the area. The elemental composition of the kerogen was used to determine the types of organic matter (H and C contents), the initial components of the living matter that were the source of the kerogen (H and N contents), the diagenetic history of organic matter (S content), and the level of catagenetic transformation of the kerogen (C and O contents). Kerogen from the central, western, and southern parts of the western Siberian basin, up to the pinch-out boundary of the Bazhenov horizon, shows strong enrichment in hydrogen (up to 8–9%) and 12С (δ13С‰ from –35 to –29), suggesting its derivation from polymer lipids of aquatic origin. Kerogen from the Bazhenov horizon (catagenetic grade MC1) in the northeast of the basin contains much lower hydrogen concentrations (2–4%). A map of the types of organic matter in the Bazhenov horizon is constructed.Kostyukevich, Y., Zherebker, A., Vlaskin, M.S., Roznyatovsky, V.A., Grishin, Y.K., Nikolaev, E., 2019. Speciation of structural fragments in crude oil by means of isotope exchange in near-critical water and Fourier transform mass spectrometry. Analytical and Bioanalytical Chemistry 411, 3331-3339. structures of individual molecules in crude oil remain largely unknown despite the considerable amount of research dedicated to this topic. The extreme complexity of crude oil (recently Marshall reported the observation of more than 400,000 unique compounds in one sample) makes it impossible to separate crude oil into individual compounds and determine their structure by NMR or X-ray spectroscopy. Recently, isotope exchange, performed both in solution and in the gas phase, combined with high-resolution mass spectrometry was used for speciation of certain structural fragments of individual molecules in crude oil and humic substances. 16O/18O exchange allows enumeration of =O groups and speciation of furans, whereas H/D exchange allows enumeration of –OH groups, –NH groups, aromatic hydrogens, alpha hydrogens, etc. Unfortunately, crude oil is insoluble in water (the most available and cleanest source of isotopes), so performance of the exchange in solution requires harsh conditions, such as concentrated acids or bases, which could considerably modify the sample. Here we describe the use of a cheap and simple analytical approach for performing both H/D and 16O/18O exchange in crude oil using only water as the source of the isotopes. Crude oil was incubated in near-critical water and the reaction was monitored by high-resolution Fourier transform mass spectrometry. Although isotope exchange results in complication of the spectrum, the resolving power of modern mass spectrometers is sufficient to determine the number of exchanges for each molecule simultaneously. We determined the number of 16O/18O exchanges in 276 species and the number of H/D exchanges in 150 species. Our results allow deeper investigation of crude oil and other nonpolar samples on the molecular level.Krajewski, L.C., Robbins, W.K., Corilo, Y.E., Bota, G., Marshall, A.G., Rodgers, R.P., 2019. Characterization of ketones formed in the open system corrosion test of naphthenic acids by Fourier transform ion cyclotron resonance mass spectrometry. Energy & Fuels 33, 4946-4950. the rate of naphthenic acid corrosion does not correlate with the concentration of acids, it has been proposed that a subset of naphthenic acids in petroleum fractions may be more corrosive than others. The primary corrosion products (iron naphthenates) decompose to form ketones at corrosion temperatures (250–400 °C), so characterization of ketones in corrosion fluids could potentially be used to identify the reactive acids that generated the iron naphthenate. Previous work with model acids has reported the development of a method to characterize such ketones by isolation with strong anion exchange separation and detection, with the assistance of ketone targeting derivatization reagent, by Fourier transform ion cyclotron resonance mass spectrometry. Here, we extend that method to characterize the ketones formed in a corrosion test by use of commercially available naphthenic acids (NAP) in a flow-through reactor. The NAP corrosion test yields a single O1 ketones/aldehydes distribution close to that predicted from the O2 acids distribution before corrosion, with no bias in the carbon number and a slight bias toward lower double bond equivalents in the reactive acids detected. Ketone distributions did not appear to change over the 24 h test. With a fluid residence time of only ～30 min at reactor temperature, the results suggest that the ketones were formed rapidly beneath an FeS scale.Krim, L., Mencos, A., 2019. Determination of [CH3NC]/[H2C═C═NH] abundance ratios from N + CH3CN solid phase reaction in the temperature range from 10 to 40 K: Application to the complex chemistry in star-forming regions. ACS Earth and Space Chemistry 3, 973-979. interstellar detection of CH3CN metastable isomers would suggest that CH3NC and H2C═C═NH formed in star-forming regions through energetic processing provoked by shocks or others energy sources. In this context, laboratory simulations have been carried out to investigate the chemical transformation of CH3CN into CH3NC and H2C═C═NH induced by UV photolysis and high energy particle irradiation. In the present study, we have carried out the CH3CN + N solid state reaction in the 10–40 K temperature range in order to examine the behavior of acetonitrile interacting with nitrogen atoms in icy interstellar grains. We show that CH3CN + N is efficient in the solid phase but only in a very specific temperature range, which combines high mobility and relatively long surface residence time of N atoms to allow the CH3CN activation. By focusing on the behavior of [CH3NC]/[H2C═C═NH] abundance ratios versus temperature, we have measured abundance ratios around 10.4 at 10 K, which decreases to 6.8 when the temperature of the reaction increases. These ratios are of the same order of magnitude as those reported from acetonitrile isomers detection toward Sagittarius B2(N). In contrast, previous studies involving energetic processing of solid CH3CN, CH3NC and CH2CNH have found that they have been formed with [CH3NC]/[CH2CNH] ratios ranging between 0.3 and 1.7. Additionally, the analysis of CH3NC and H2C═C═NH column densities shows that at low temperatures, the less stable isomer is favored against the most stable one. These results are compared to the puzzling behavior of CN-containing isomers such as HNC, HCN, HCNO, and HOCN in molecular clouds.Krings, M., Sergeev, V.N., 2019. A coccoid, colony-forming cyanobacterium from the Lower Devonian Rhynie chert that resembles Eucapsis (Synechococcales) and Entophysalis (Chroococcales). Review of Palaeobotany and Palynology 268, 65-71. Rhynie chert provides sublime fossils of cyanobacteria from an Early Devonian hot spring ecosystem. However, only a small fraction of the diversity has been documented. Rhyniotaxillus devonicus nov. gen. et sp., a minute coccoid cyanobacterium from the Rhynie chert, is characterized by cuboid to somewhat irregular colonies of up to 64 cells (cell diameter: 2.5–3.5?μm) arranged into sarcinoid packages, and held together by prominent gelatinous envelopes. Colony morphology parallels that seen in certain present-day species of Eucapsis (Synechococcales) and Entophysalis (Chroococcales), as well as Eoentophysalis belcherensis, a Precambrian fossil equivalent of Entophysalis. The systematic affinities of R. devonicus remain unresolved. Nevertheless, this discovery expands our knowledge of cyanobacterial diversity in early non-marine ecosystems.Kroepsch, A.C., Maniloff, P.T., Adgate, J.L., McKenzie, L.M., Dickinson, K.L., 2019. Environmental justice in unconventional oil and natural gas drilling and production: A critical review and research agenda. Environmental Science & Technology 53, 6601-6615. drilling phase of oil and natural gas development is a growing area of environmental justice (EJ) research, particularly in the United States. Its emergence complements the longstanding EJ scholarship on later phases of the oil and gas commodity chain, such as pipeline transport, refining, and consumption. The growing scholarly attention to the EJ implications of drilling has been prompted by the surge in development of unconventional oil and gas resources in recent decades. More specifically, the oil and gas industry’s adoption of horizontal drilling and hydraulic fracturing (a.k.a., “fracking” or “fracing”) as methods for extracting oil and gas from a wider range of geologic formations has simultaneously heightened oil and gas production, brought extractive activities closer to more people, intensified them, and made well pad siting more flexible. Here, we provide a critical review of the novel EJ research questions that are being prompted by these on-the-ground changes in extractive techniques and patterns, propose an interdisciplinary conceptual framework for guiding EJ inquiry in this context, discuss key methodological considerations, and propose a research agenda to motivate future inquiry.Krummenacker, M., Latendresse, M., Karp, P.D., 2019. Metabolic route computation in organism communities. Microbiome 7, 89.: Microbiomes are complex aggregates of organisms, each of which has its own extensive metabolic network. A variety of metabolites are exchanged between the microbes. The challenge we address is understanding the overall metabolic capabilities of a microbiome: through what series of metabolic transformations can a microbiome convert a starting compound to an ending compound?Results: We developed an efficient software tool to search for metabolic routes that include metabolic reactions from multiple organisms. The metabolic network for each organism is obtained from BioCyc, where the network was inferred from the annotated genome. The tool searches for optimal metabolic routes that minimize the number of reactions in each route, maximize the number of atoms conserved between the starting and ending compounds, and minimize the number of organism switches. The tool pre-computes the reaction sets found in each organism from BioCyc to facilitate fast computation of the reactions defined in a researcher-specified organism set. The generated routes are depicted graphically, and for each reaction in a route, the tool lists the organisms that can catalyze that reaction.We present solutions for three route-finding problems in the human gut microbiome: (1) production of indoxyl sulfate, (2) production of trimethylamine N-oxide (TMAO), and (3) synthesis and degradation of autoinducers. The optimal routes computed by our multi-organism route-search (MORS) tool for indoxyl sulfate and TMAO were the same as routes reported in the literature.Conclusions: Our tool quickly found plausible routes for the discussed multi-organism route-finding problems. The routes shed light on how diverse organisms cooperate to perform multi-step metabolic transformations. Our tool enables scientists to consider multiple alternative routes and identifies the organisms responsible for each reaction.KeywordsKuang, Y., Yang, L., Li, Q., Lv, X., Li, Y., Yu, B., Leng, S., Song, Y., Zhao, J., 2019. Physical characteristic analysis of unconsolidated sediments containing gas hydrate recovered from the Shenhu Area of the South China sea. Journal of Petroleum Science and Engineering 181, 106173. research based on the physical characteristics of unconsolidated sediments containing gas hydrate was carried out on hydrate-bearing sediment samples recovered from China National Offshore Oil Corporation (CNOOC) drilling expeditions in 2015 and 2017?at the station of LW3 in the northern part of the South China Sea. We herein have measured the gas composition, index properties, surface characteristics, thermal properties, and mechanical properties of these sediment cores drilled at different seafloor depths. Based on the measurement results, more than 99% of the gas composition is methane gas. The hydrate-bearing sediments recovered from Shenhu Area are non-diagenetic rock, the fraction of grain size which less than 40 μm was more than 90%. The results could provide useful guidance for potential sand-control system operations. Such small and consolidated particles indicated that the application of a novel solid fluidization mining method is viable and promising. The fine-grained layers were found to be mostly self-filtering and internally stable for the seepage flow during production. Gas hydrate mostly occurs in vein-type, and bioclastics consisting of marine planktonic diatoms and foraminifera were also found. The mineral components of the sediments were mostly quartz, clay minerals like illite and some feldspar like albite. The thermal conductivities changed from 1.4 to 1.77?W/(mK), which suggests that the isolated depressurization methods could exacerbate the problem of gas hydrate reformation or ice generation; thus, heat injection in wellbores should be combined for gas hydrate production strategies. The low liquid limit (38%) and plastic limit (24%) imply that stability of the production platform should be taken into account for avoiding submarine landslide impacts. The results of mechanical property analyses indicated that hydrate-bearing sediments at deeper sites have a relatively higher strength at hydrate layer of 120–133?mbsf in the Shenhu Area of the South China Sea.Kumar, S.S., Ghosh, A.R., 2019. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology 165, 593-610. bacterial contamination in environmental samples is critical in determining threats to public health. The classical methods are time-consuming and only recognize species that grow easily on culture media. Viable but non-culturable (VBNC) bacteria are a possible threat that may resuscitate and cause infections. Recent dye-based screening techniques employ nucleic acid dyes such as ethidium monoazide (EMA) and propidium monoazide (PMA), along with many fluorescent dyes, which are an effective alternative for viability assessment. The measurement of cellular metabolism, heat flow and ATP production has also been widely applied in detection approaches. In addition, RNA-based detection methods, including nucleic acid sequence-based amplification (NASBA), have been applied for bacterial pathogen determination. Stable isotope probing using 13C, 15N and 18O, which are mobilized by microbes, can also be used for effective viability assessment. Future detection tools, such as microarrays, BioNEMS and BioMEMS, which are currently being validated, might offer better microbial viability detection.Kurganova, I.N., Lopes de Gerenyu, V.O., Zhiengaliyev, A.T., Kudeyarov, V.N., 2019. Carbon budgets in the steppe ecosystems of Russia. Doklady Earth Sciences 485, 450-452. lands formed in the place of former arable lands occupy considerable areas in the steppe zone and are a basic reserve for the restoration of the steppe biome in Russia. Taking into account the secondary steppe ecosystems developed in the place of the abandoned lands, the total carbon dioxide sink in the steppe zone of Russia can reach 92–121 Mt С per year. This is comparable to the СО2 sink in the managed forests of the Russian Federarion (96 Mt/yr) and accounts for 10–20% of the total sink of СО2 in the terrestrial ecosystems of Russia. To increase the sink potential on the territory of the Russian Federation, the natural and restored steppe ecosystems should be preserved.Kurth, J.M., Smit, N.T., Berger, S., Schouten, S., Jetten, M.S.M., Welte, C.U., 2019. Anaerobic methanotrophic archaea of the ANME-2d clade feature lipid composition that differs from other ANME archaea. FEMS Microbiology Ecology 95, Article fiz082. anaerobic oxidation of methane (AOM) is a microbial process present in marine and freshwater environments. AOM is important for reducing the emission of the second most important greenhouse gas methane. In marine environments anaerobic methanotrophic archaea (ANME) are involved in sulfate-reducing AOM. In contrast, Ca. Methanoperedens of the ANME-2d cluster carries out nitrate AOM in freshwater ecosystems. Despite the importance of those organisms for AOM in non-marine environments little is known about their lipid composition or carbon sources. To close this gap, we analysed the lipid composition of ANME-2d archaea and found that they mainly synthesise archaeol and hydroxyarchaeol as well as different (hydroxy-) glycerol dialkyl glycerol tetraethers, albeit in much lower amounts. Abundant lipid headgroups were dihexose, monomethyl-phosphatidyl ethanolamine and phosphatidyl hexose. Moreover, a monopentose was detected as a lipid headgroup that is rare among microorganisms. Batch incubations with 13C labelled bicarbonate and methane showed that methane is the main carbon source of ANME-2d archaea varying from ANME-1 archaea that primarily assimilate dissolved inorganic carbon (DIC). ANME-2d archaea also assimilate DIC, but to a lower extent than methane. The lipid characterisation and analysis of the carbon source of Ca. Methanoperedens facilitates distinction between ANME-2d and other ANMEs.Kwiecińska, B., Pusz, S., Valentine, B.J., 2019. Application of electron microscopy TEM and SEM for analysis of coals, organic-rich shales and carbonaceous matter. International Journal of Coal Geology 211, Aticle 103203. paper provides a brief summary of the history, development and variety of applications of electron microscopy techniques to analyze coals, organic-rich shales, and carbonaceous materials. General construction and principles of operation of transmitted (TEM) and scanning electron microscope (SEM) are outlined, along with guidance on specimen preparation, and a brief overview of published TEM and SEM applications related to coal, shales, and carbonaceous materials. This work was accepted as the chapter 18.2 of International Committee for Coal and Organic Petrology Methods Handbook at the ICCP Plenary Session on September 27, 2018 in Brisbane (Australia).Laaniste, A., Leito, I., Kruve, A., 2019. ESI outcompetes other ion sources in LC/MS trace analysis. Analytical and Bioanalytical Chemistry 411, 3533-3542. an appropriate ion source is a crucial step in liquid chromatography mass spectrometry (LC/MS) method development. In this paper, we compare four ion sources for LC/MS analysis of 40 pesticides in tomato and garlic matrices. We compare electrospray ionisation (ESI) source, thermally focused/heated electrospray (HESI), atmospheric pressure photoionisation (APPI) source with and without dopant, and multimode source in ESI mode, atmospheric pressure chemical ionisation (APCI) mode, and combined mode using both ESI and APCI, i.e. altogether seven different ionisation modes. The lowest limits of detection (LoDs) were obtained by ESI and HESI. Widest linear ranges were observed with the conventional ESI source without heated nebuliser gas. In comparison to HESI, ESI source was significantly less affected by matrix effect. APPI ranked second (after ESI) by not being influenced by matrix effect; therefore, it would be a good alternative to ESI if low LoDs are not required.Labonté, J.M., Pachiadaki, M., Fergusson, E., McNichol, J., Grosche, A., Gulmann, L.K., Vetriani, C., Sievert, S.M., Stepanauskas, R., 2019. Single cell genomics-based analysis of gene content and expression of prophages in a diffuse-flow deep-sea hydrothermal system. Frontiers in Microbiology 10, 1262. doi: 10.3389/fmicb.2019.01262. interactions likely play a major role in the composition and functioning of many microbiomes, yet remain poorly understood. Here we employed single cell genomics to investigate phage–host interactions in a diffuse-flow, low-temperature hydrothermal vent that may be reflective of a broadly distributed biosphere in the subseafloor. We identified putative prophages in 10% of 126 sequenced single amplified genomes (SAGs), with no evidence for lytic infections, which is in stark contrast to findings in the surface ocean. Most were distantly related to known prophages, while their hosts included bacterial phyla Bacteroidetes, Chlorobi, Proteobacteria, Lentisphaerae, Spirochaetes, and Thermotogae. Our results suggest the predominance of lysogeny over lytic interaction in diffuse-flow, deep-sea hydrothermal vents, despite the high productivity of the dominant Campylobacteria (formerly Epsilonproteobacteria). We show that some of the identified lysogens have co-evolved with their host over geological time scales and that their genes are transcribed in the environment. Functional annotations of lysogeny-related genes suggest involvement in horizontal gene transfer and in host’s protection against toxic metals and antibacterial compounds.Lackey, G., Vasylkivska, V.S., Huerta, N.J., King, S., Dilmore, R.M., 2019. Managing well leakage risks at a geologic carbon storage site with many wells. International Journal of Greenhouse Gas Control 88, 182-194. geologic carbon storage (GCS) sites with a history of oil and gas production have well-characterized injectivity and storage capacity, but the presence of legacy wells increases leakage risk. Thus, the success of GCS operations at sites with many wells will require a thorough leakage risk assessment and a robust strategy for managing well leakage risk over the lifetime of the project. In this study, we demonstrate a workflow that uses the National Risk Assessment Partnership’s open-source Integrated Assessment Model to quantify well leakage risks and test the performance of various leakage risk management strategies at a heavily drilled GCS site. Our model simulates a 50-year basin-scale injection of CO2 at a hypothetical site based on the Kimberlina Project Site in the Southern San Joaquin Valley of California. Brine and CO2 leakage through 1000 legacy wells into a USDW are stochastically simulated as a proxy for risk. We consider multiple scenarios that explore the efficacy of various well leakage risk management strategies with changes in well leakage behavior, reservoir behavior, and post-injection site care (PISC) length. Predicted leakage at the site after 100 years was small with a maximum CO2 leakage of 102.1?tonnes (4.08?×?10?5% of the 250?Mt injected) and a maximum brine leakage of 2.4?tonnes. Leakage risk management strategies based on accurate prior information about well leak probability reduced leakage risks more effectively at the modeled site and were more robust with respect to reservoir uncertainty than strategies based on the distance of the legacy well from the injector. The importance of the PISC period length was not clear as it had a negligible impact on CO2 leakage risk but a sizable impact on brine leakage risk in our model.Lamb, D.C., Follmer, A.H., Goldstone, J.V., Nelson, D.R., Warrilow, A.G., Price, C.L., True, M.Y., Kelly, S.L., Poulos, T.L., Stegeman, J.J., 2019. On the occurrence of cytochrome P450 in viruses. Proceedings of the National Academy of Sciences 116, 12343-12352.: Cytochrome P450 monooxygenase enzymes metabolize drugs, carcinogens, and endogenous molecules in the Eukarya, the Bacteria, and the Archaea. The notion that viral genomes contain P450 genes was not considered until discovery of the giant viruses. We have uncovered multiple and unique P450 genes in giant viruses from the deep ocean, terrestrial sources, and human patients. P450s were also found in a herpesvirus and a mycobacteriophage, and we report a crystal structure of the phage P450. Our findings herald an era of research regarding the evolution of this important gene family, with implications for understanding the biology and the origin of the giant viruses themselves. The findings also present potential drug targets for giant viruses that may be human pathogens.Abstract: Genes encoding cytochrome P450 (CYP; P450) enzymes occur widely in the Archaea, Bacteria, and Eukarya, where they play important roles in metabolism of endogenous regulatory molecules and exogenous chemicals. We now report that genes for multiple and unique P450s occur commonly in giant viruses in the Mimiviridae, Pandoraviridae, and other families in the proposed order Megavirales. P450 genes were also identified in a herpesvirus (Ranid herpesvirus 3) and a phage (Mycobacterium phage Adler). The Adler phage P450 was classified as CYP102L1, and the crystal structure of the open form was solved at 2.5 ?. Genes encoding known redox partners for P450s (cytochrome P450 reductase, ferredoxin and ferredoxin reductase, and flavodoxin and flavodoxin reductase) were not found in any viral genome so far described, implying that host redox partners may drive viral P450 activities. Giant virus P450 proteins share no more than 25% identity with the P450 gene products we identified in Acanthamoeba castellanii, an amoeba host for many giant viruses. Thus, the origin of the unique P450 genes in giant viruses remains unknown. If giant virus P450 genes were acquired from a host, we suggest it could have been from an as yet unknown and possibly ancient host. These studies expand the horizon in the evolution and diversity of the enormously important P450 superfamily. Determining the origin and function of P450s in giant viruses may help to discern the origin of the giant viruses themselves.Lamberts, T., Markmeyer, M.N., Kolb, F.J., K?stner, J., 2019. Formation of acetaldehyde on CO-rich ices. ACS Earth and Space Chemistry 3, 958-963. radicals HCO and CH3 on carbon monoxide ice surfaces were simulated using the density functional theory. Their binding energy on amorphous CO ice shows broad distributions, with approximative average values of 500 K for HCO and 200 K for CH3. If they are located on the surface close to each other (3–4 ?), molecular dynamics calculations based on the density functional theory show that they can form acetaldehyde (CH3CHO) or CH4 + CO in barrier-less reactions, depending upon the initial orientation of the molecules with respect to each other. In some orientations, no spontaneous reactions were found and the products remained bound to the surface. Sufficient configurational sampling, inclusion of the vibrational zero-point energy, and a thorough benchmark of the applied electronic structure method are important to predict reliable binding energies for such weakly interacting systems. From these results, it is clear that complex organic molecules, such as acetaldehyde, can be formed by recombination reactions of radicals on CO surfaces.Langner, M., Mulitza, S., 2019. Technical Note: PaleoDataView - A software toolbox for the collection, homogenization and visualization of marine proxy data. Climate of the Past Discussions 2019, 1-9. present a software toolbox that allows the efficient collection, management and maintenance of larger paleoceanographic data sets. The program combines a graphical user interface (GUI) with a simple document-based database and functionality for visualization, stratigraphy (visual alignment and radiocarbon calibration), age modelling and efficient ensemble time series generation to create larger homogenous data compilations. Data can be imported from Excel or text files, are stored locally in netCDF format and can be easily exchanged between collaborating scientists. Within a data collection, data can either be imported to proxy-specific sub-collections or to a multi-proxy (miscellaneous) sub-collection that allows to import and manage any downcore data. A single age model is shared among all proxies of a core within a collection. The stand-alone software can be used with Windows and macOS and does not require web access.Larmagnat, S., Des Roches, M., Daigle, L.-F., Francus, P., Lavoie, D., Raymond, J., Malo, M., Aubiès-Trouilh, A., 2019. Continuous porosity characterization: Metric-scale intervals in heterogeneous sedimentary rocks using medical CT-scanner. Marine and Petroleum Geology 109, 361-380. computed tomography (CT-Scanning) has been regularly applied to core analyses in petroleum geology, there is still a need to improve our ways to document porosity and porosity distribution in the entire pore scale spectrum, from the tens of nanometer to the meter-scale. Porosity imaging is particularly crucial for complex and heterogeneous rocks such as hydrothermally altered and fractured carbonates. The present work proposes an improved method using medical-CT to reliably estimate reservoir porosity. An in-house core-flooding setup allowed to analyse several individual core samples, scanned simultaneously (dry and saturated), as well as continuous core sections up to 1.5?m long. Without any prior knowledge of samples, three-dimensional alignment and subtraction of the two data sets (dry and saturated states) results in the generation of 3D porosity matrices. The methodology tested on a large set of reference core material shows a strong correlation between conventional gas porosimetry techniques and porosity from CT-scan. The added value of the porosity measurements by CT-scan is, first of all, the generation of 3D images of pore network, allowing to assess spatial attributes of macropores, their distribution and connectivity. Secondly, the CT-scan method also provides continuous porosity profile at the millimetric scale. Both developments are crucial for the understanding of reservoir rock properties.Larour, E., Seroussi, H., Adhikari, S., Ivins, E., Caron, L., Morlighem, M., Schlegel, N., 2019. Slowdown in Antarctic mass loss from solid Earth and sea-level feedbacks. Science 364, Article eaav7908. uplifting effect. The rise in sea level that is occurring from the melting of Antarctica is only going to accelerate as climate warms. However, Larour et al. report that crustal uplift in the Amundsen Sea sector is helping to reduce grounding line retreat, thereby stabilizing the ice sheet and slowing its rate of mass loss (see the Perspective by Steig). This effect will not stop or reverse ice sheet loss, but it could delay the progress of dynamic mass loss of Thwaites Glacier by approximately 20 years.Structured AbstractIntroduction: Geodetic investigations of crustal motions in the Amundsen Sea sector of West Antarctica and models of ice-sheet evolution in the past 10,000 years have recently highlighted the stabilizing role of solid-Earth uplift on polar ice sheets. One critical aspect, however, that has not been assessed is the impact of short-wavelength uplift generated by the solid-Earth response to unloading over short time scales close to ice-sheet grounding lines (areas where the ice becomes afloat). Here, we present a new global simulation of Antarctic evolution at high spatiotemporal resolution that captures solid-Earth processes stabilizing and destabilizing ice sheets. These include interactions with global eustatic sea-level rise (SLR), self-attraction and loading (SAL) of the oceans, Earth’s rotational feedback to SAL, and elastic uplift of the solid Earth.Rationale: In Antarctica, dynamic thinning and retreat of ice streams has been the main driver of mass loss over the past decades, largely controlled by how grounding lines migrate and interact with bedrock pinning points. Studies have shown that the physical representation of grounding-line dynamics (GLD) can only be captured through simulations with a horizontal resolution higher than 1 km. Current models of SLR that incorporate solid-Earth processes with viscoelastic response tend to involve GLD that is resolved at much coarser resolutions (25 to 100 km) and involve time steps on the order of decades. Such resolution bounds are incompatible with capturing the complex bed topography of the ice streams of West Antarctica that are vulnerable to rapid retreat. In addition, a resolution of 25 to 100 km is inherently too coarse to capture short-wavelength elastic uplift generated by fast GLD. Elastic uplift generated by a 2-km grounding-line retreat, modeled as loss of 100-m-thick ice from a disk of 2-km radius, can reach 52 mm near the grounding line (centroid of the equivalent disk). At coarser resolutions (say, 16 km), the same model generates uplift one order of magnitude lower. This implies that uplift generated in simulations at coarse resolutions might underestimate how much uplift is generated during ungrounding of active areas of Antarctica such as Thwaites Glacier (TG), where highly complex grounding-line geometries and associated retreat are observed over short time scales on the order of years. Our goal was therefore to carry out a sensitivity study of sea level– and ice flow–related processes that incorporate kilometer-scale resolutions and global processes involving solid-Earth dynamics.Results: Our sensitivity study spans 500 years and demonstrates how in Antarctica, TG is particularly prone to negative feedback from SAL and elastic uplift. At year 2350, including these feedbacks leads to a ~20-year delay in dynamic mass loss of TG, corresponding to a 26.8% reduction in sea-level contribution, along with a reduction in grounding-line retreat of 38% and elastic uplift rates reaching ~0.25 m/year. At year 2100, though, this negative feedback is considerably lower, with a 1.34% reduction in sea-level contribution only. Not including a kilometer-scale resolution representation of such processes will lead to projections of SLR that will significantly overestimate Antarctic Ice Sheet contribution over several centuries.Conclusion: For 21st-century projections, the effects we have modeled here remain negligible. However, for the period starting 2250 and after, SLR projections that would not account for such dynamic geodetic effects run the risk of consistently overestimating (by 20 to 40%) relative sea-level estimates. Our approach shows that significant stabilization in grounding-line migration occurs when uplift rates start approaching 10 cm/year. This has strong implications for late Quaternary reconstructions of SLR, for example, in which the inclusion of these solid-Earth processes will allow SLR modelers to gain a better grasp of the time scales involved in reaching maximum coastal inundation levels during extended warm periods.Larsen, C.S., Knüsel, C.J., Haddow, S.D., Pilloud, M.A., Milella, M., Sadvari, J.W., Pearson, J., Ruff, C.B., Garofalo, E.M., Bocaege, E., Betz, B.J., Dori, I., Glencross, B., 2019. Bioarchaeology of Neolithic ?atalh?yük reveals fundamental transitions in health, mobility, and lifestyle in early farmers. Proceedings of the National Academy of Sciences 116, 12615-12623.: Bioarchaeological investigation of human remains from Neolithic ?atalh?yük, Turkey, contributes to a growing body of data documenting population dynamics, health, and lifestyle of early farmers in Holocene settings in the Near East and globally. The extensive archaeological context of foodways, material culture, housing, environment, ecology, population structure and size, social interaction, and community living informs interpretation of the bioarchaeological record representing nearly 1,200 continuous years of community life. This record presents biological outcomes and comprehensive understanding of the challenges associated with dependence on domesticated plants and animals, the labor involved in acquiring food and other resources, impacts of settled community life on health and well-being, and evolving lifeways to the present day.Abstract: The transition from a human diet based exclusively on wild plants and animals to one involving dependence on domesticated plants and animals beginning 10,000 to 11,000 y ago in Southwest Asia set into motion a series of profound health, lifestyle, social, and economic changes affecting human populations throughout most of the world. However, the social, cultural, behavioral, and other factors surrounding health and lifestyle associated with the foraging-to-farming transition are vague, owing to an incomplete or poorly understood contextual archaeological record of living conditions. Bioarchaeological investigation of the extraordinary record of human remains and their context from Neolithic ?atalh?yük (7100–5950 cal BCE), a massive archaeological site in south-central Anatolia (Turkey), provides important perspectives on population dynamics, health outcomes, behavioral adaptations, interpersonal conflict, and a record of community resilience over the life of this single early farming settlement having the attributes of a protocity. Study of ?atalh?yük human biology reveals increasing costs to members of the settlement, including elevated exposure to disease and labor demands in response to community dependence on and production of domesticated plant carbohydrates, growing population size and density fueled by elevated fertility, and increasing stresses due to heightened workload and greater mobility required for caprine herding and other resource acquisition activities over the nearly 12 centuries of settlement occupation. These changes in life conditions foreshadow developments that would take place worldwide over the millennia following the abandonment of Neolithic ?atalh?yük, including health challenges, adaptive patterns, physical activity, and emerging social behaviors involving interpersonal violence.Latham, K.J., Losey, R.J., 2019. Spondylosis deformans as an indicator of transport activities in archaeological dogs: A systematic evaluation of current methods for assessing archaeological specimens. PLOS ONE 14, Article e0214575. the past several decades archaeologists have used the spinal pathology spondylosis deformans as an indicator that archaeological dogs were used to pull or carry loads. This interpretive approach is largely based upon observations of prehistoric dog remains and archaeologist’s interpretations of veterinary literature on recent sled dogs and other draft animals. However, no comparative large-scale studies of the occurrence of spondylosis deformans in wild canids, transport dogs, and dogs never involved in pulling or carrying loads have been published. To evaluate the reliability of spondylosis deformans in archaeological dogs as an indicator of participation in transport activities, 136 modern non-transport dogs, 19 sled dogs, and 241 wolves were systematically analyzed for the occurrence of spondylosis deformans. Our results indicate this pathology is not a reliable skeletal indicator of dog transport because the disease is prevalent in both dogs and wolves, regardless of their occupational histories. Numerous factors correlate with the occurrence and manifestation of this disease in canids, including age, body size, sex, and inbreeding. As such, it remains extremely challenging to identify specific etiologies for spondylosis deformans in archaeological specimens.Law, K.P., Zhang, C.L., 2019. Current progress and future trends in mass spectrometry-based archaeal lipidomics. Organic Geochemistry 134, 45-61. play pivotal roles in geochemical cycles in global ecosystems, but little is known about the membrane functions of these organisms under different environmental conditions. Mass spectrometry (MS) is an indispensable tool for the study of the Archaea and their unique isoprenoidal ether-linked lipids. A variety of techniques, including GC–MS, UHPLC-MS, MALDI-MS, and shotgun lipidomics, have been employed for studying archaeal lipids and significant progress has been made in the last two decades. These developments often make use of high-mass resolution systems to perform untargeted fingerprinting of archaeal lipids from complex cellular and environmental samples. As a result, these methods generate a large volume of data that cannot be easily processed, analyzed, and interpreted manually. Recent progress in bioinformatics has thus become an important factor for the development of this research field. Still, there are challenges associated with complications in sample preparation, differentiating closely or co-eluted isomeric and isobaric lipids, and elucidation of compounds with unknown structures. Furthermore, while a collection of archaeal lipids has been reported, only a limited number of chemical structures are currently available in freely accessible databases, and little progress has been made to amalgamate the experimental data and construct an archaeal lipid-specific structural and spectral library. This article describes the progress and evaluates the benefits and drawbacks of MS-based techniques and contemplates potential solutions to overcome current challenges for future lipidomic research in organic geochemistry and environmental sciences.Lee, C.-T., Dee, S., 2019. Does volcanism cause warming or cooling? Geology 47, 687-688. million-year time scales, Earth’s climate fluctuates between warm and cool baselines. For example, the past 40 m.y. has been relatively cool and characterized by a permanent ice sheet on Antarctica, while the interval between 150 and 50 m.y. ago was characterized by warm temperatures and no permanent ice sheets (Royer et al., 2004; Zachos et al., 2008). What controls these fluctuations is debated, but to first order, the average surface temperature of Earth reflects the balance of incoming solar insolation (energy in) versus planetary albedo and greenhouse gas concentrations (energy out). It is generally thought that over the past billion years, the most important control on long-term climate is variations in greenhouse gases in the atmosphere, namely CO2 (Berner, 1991). What controls long-term CO2 are variations in geologic inputs and the efficiency of CO2 sequestration, the former through volcanic and metamorphic degassing and oxidative weathering of organic carbon, and the latter through silicate weathering (and eventual carbonate precipitation) and organic carbon burial. Importantly, the efficiency of silicate weathering and organic carbon burial is widely thought to scale directly and indirectly with atmospheric pCO2; CO2’s impact on global temperature and the hydrologic cycle serves as a negative feedback, enhancing (mitigating) carbon sequestration mechanisms given increased (decreased) inputs of CO2. As the residence time of CO2 in the exogenic system (ocean-atmosphere-biosphere) is on the order of 10–100 k.y., exogenic carbon contents on million-year time scales are at steady state, where inputs equal outputs (Berner and Caldeira, 1997). Changes in exogenic cabon over greater than million-year time scales thus reflect secular changes in the steady-state baseline, driven by changes in inputs and/or the kinetics of carbon sequestration (Fig. 1).The current debate is centered around the relative importance of changes in inputs and output efficiencies. Input-driven scenarios mostly invoke changes in volcanic activity, such as changes in production of oceanic crust or arc magmatism. Output-driven scenarios have focused primarily on collisional orogens in increasing the global efficiency of chemical weathering. For example, Cenozoic cooling is often attributed to enhanced erosion associated with the India-Eurasia collision (Raymo and Ruddiman, 1992). Another sink-driven hypothesis invokes changes in the efficiency of organic carbon sequestration. The rise of land plants has been suggested to have amplified terrestrial carbon sequestration during the Paleozoic, possibly triggering the Late Paleozoic Ice Age (LPIA), a 100 m.y. interval of icehouse conditions (Ibarra et al., 2019).So far, none of these scenarios alone is sufficient to explain the paleoclimatic record over the Phanerozoic, but this should not be surprising. Tectonics drives both degassing and carbon sequestration, which means that tectonics can warm or cool Earth’s surface. In particular, there is a growing appreciation that magmatism and weathering are intimately connected (Jiang and Lee, 2017). Magmatic orogens, such as continental arcs, output vast quantities of CO2, but after magmatism ends, these magmatic arcs become regional sinks due to continued weathering, enhancing the global efficiency of weathering and CO2 drawdown (Lee et al., 2015; Macdonald et al., 2019). To what extent are magmatic outgassing and weathering in phase? Do flare-ups in orogenic magmatism drive greenhouses? Does weathering of these magmatic orogens, after they die, drive icehouses?Recently, an evaluation of the radiative impacts of explosive volcanism has offered a fresh twist on the debate. Soreghan et al. (2019, p. 600 in this issue of Geology) propose that explosive volcanism may trigger and sustain long icehouse intervals. They show that there may be a temporal coincidence between enhanced explosive volcanism and the extent of glaciations during the late Paleozoic, hypothesizing that a sustained increase in sulfate aerosols shading the stratosphere would increase planetary albedo, cooling the planet (Fig. 1). They also suggest that the greater reactivity of volcanic ash fertilizes the oceans and enhances biological productivity and organic carbon burial, cooling the planet further. If Soreghan et al. are correct, then our assumption that volcanism strictly increases atmospheric CO2, leading to warming, may need revisiting. However, important questions remain. First, the residence time of aerosols in the stratosphere is on the order of a few years (Robock, 2000). While Soreghan et al. cite relevant work highlighting the attenuation of volcanic cooling via ocean heat transfer, the enhanced glaciation during the LPIA would require tropopause-penetrating volcanic eruptions to occur every few years over tens of millions of years to sustain a long-term icehouse. Detailed studies of ash layers in the Cretaceous Interior Seaway of western North America, a time of a global flareup in arc magmatism, indeed show numerous eruptive events, but even in a 10-m.y.-long sedimentary record, there are only ～200 events (20/m.y.) (Minisini et al., 2017), with only a few large enough to have injected significant amounts of ash and/or aerosols into the stratosphere. Unless the Earth system was already precariously poised to tip into an icehouse mean-state, it is difficult to envision a world where volcanism could sustain long-term icehouse conditions from increasing albedo alone.As for the effects of ash, there is growing evidence that ashfall events might lead to enhanced organic carbon burial (Lee et al., 2018). However, recurrence intervals of 10–50 k.y. would be required to maintain long-term low pCO2 levels. While this may not be unreasonable during a global magmatic flareup, what remains to be seen is whether the effects of ash on organic carbon burial can offset the added CO2 inputs from volcanism. On million-year time scales, it is unlikely that volcanism can cause a long-term decrease in atmospheric CO2 because ash represents a small component of the total magmatic flux (<1%?). On long time scales, CO2 inputs likely play a larger role than ash because degassing comes from the overall magmatic flux, which mostly does not erupt (Aiuppa et al., 2017). However, the episodic nature of ash generation may generate interesting behavior on short time scales. That is, it may be possible for individual eruptions to perturb the carbon cycle on time scales of 1–10 k.y., where ash-driven organic carbon burial is unsupported by CO2 inputs from the same volcanic event. These effects would be manifested as short-term cooling events superimposed upon on an otherwise warmer baseline. It would be difficult for volcanic eruptions to sustain long-term continuous icehouse conditions in the late Paleozoic or any other time. On the other hand, if the late Paleozoic ice age was characterized by numerous but short-lived icehouse conditions, volcanic eruptions could have played a key role in their initiation.More broadly, the nature by which volatiles are exchanged between planetary interiors and their surfaces is rich with complexity. The magnitude and style of magmatism not only controls volatile degassing but also erosion, weathering, radiative balance, and biological productivity. How magmatic processes change through time and with geodynamic states is an area ripe for interdisciplinary research and new discoveries. Soreghan et al.’s work is an example of how investigating these processes from deep time to the present, as well as on Earth and other planets, will force us to rethink how planetary systems operate.ReferencesAiuppa, A., Fischer, T.P., Plank, T., Robidoux, P., and Di Napoli, R., 2017, Along-arc, inter-arc and arc-to-arc variations in volcanic gas CO2/ST ratios reveal dual source of carbon in arc volcanism: Earth-Science Reviews , v. 168, p. 24–47,Berner, R.A., 1991, A model for atmospheric CO2 over Phanerozoic time: American Journal of Science , v. 291, p. 339–376Berner, R.A., and Caldeira, K., 1997, The need for mass balance and feedback in the geochemical carbon cycle: Geology , v. 25, p. 955–956,Ibarra, D.E., Rugenstein, J.K.C., Bachan, A., Baresch, A., Lau, K.V., Thomas, D.L., Lee, J.-E., Boyce, C.K., and Chamberlain, C.P., 2019, Modeling the consequences of land plant evolution on silicate weathering: American Journal of Science , v. 319, p. 1–43,Jiang, H., and Lee, C.-T.A., 2017, Coupled magmatism-erosion in continental arcs: Reconstructing the history of the Cretaceous Peninsular Ranges batholith, southern California through detrital hornblende barometry in forearc sediments: Earth and Planetary Science Letters , v. 472, p. 69–81,Lee, C.-T.A., Jiang, H., Ronay, E., Minisini, D., Stiles, J., and Neal, M., 2018, Volcanic ash as a driver of enhanced organic carbon burial in the Cretaceous: Scientific Reports , v. 8, p. 4197, Lee, C.-T.A., Thurner, S., Paterson, S.R., and Cao, W., 2015, The rise and fall of continental arcs: Interplays between magmatism, uplift, weathering and climate: Earth and Planetary Science Letters , v. 425, p. 105–119, Macdonald, F.A., Swanson-Hysell, N.L., Park, Y., Lisiecki, L., and Jagoutz, O., 2019, Arc-continent collisions in the tropics set Earth’s climate state: Science , p. eaav5300.Minisini, D., Eldrett, J., Bergman, S.C., and Forkner, R., 2017, Chronostratigraphic framework and depositional environments in the organic-rich, mudstone-dominated Eagle Ford Group, Texas, USA: Sedimentology , v. 65, p. 1520-1557,Raymo, M.E., and Ruddiman, W.F., 1992, Tectonic forcing of late Cenozoic climate: Nature , v. 359, p. 117–122Robock, A., 2000, Volcanic eruptions and climate: Reviews of Geophysics , v. 38, p. 191–219Royer, D.L., Berner, R.A., Montanez, I.P., Tabor, N.J., and Beerling, D.J., 2004, CO2 as a primary driver of Phanerozoic climate: GSA Today , v. 14, p. 4–10Soreghan, G.S., Soreghan, M.J., and Heavens, N.G., 2019, Explosive volcanism as a key driver of the late Paleozoic ice age: Geology , v 47, p. 600–604Zachos, J.C., Dickens, G.R., and Zeebe, R.E., 2008, An early Cenozoic perspective on greenhouse warming and carbon-cycle dynamics: Nature , v. 451, p. 279–283Léger, A., Defrère, D., García Mu?oz, A., Godolt, M., Grenfell, J.L., Rauer, H., Tian, F., 2019. Searching for atmospheric bioindicators in planets around the two nearby stars, Proxima Centauri and Epsilon Eridani—Test cases for retrieval of atmospheric gases with infrared spectroscopy. Astrobiology 19, 797–810. tested the ability of thermal infrared spectroscopy to retrieve assumed atmospheric compositions for different types of planets orbiting Proxima Centauri and Epsilon Eridani. Six cases are considered, covering a range of atmospheric compositions and some diversity in the bulk composition (rocky, water ocean, hydrogen rich) and the spectral type of the parent star (M and K stars). For some cases, we applied coupled climate chemistry, or climate-only calculations; for other cases, we assumed the atmospheric composition, ground temperature, and surface reflectivity. The IR emission was then calculated from line-by-line radiative transfer models and used to investigate retrieval of input atmospheric species. For the six cases considered, no false positive of the triple bioindicator (H2O, CO2, and O2, in specified conditions) was found. In some cases, results show that the simultaneous acquisition of a visible spectrum would be valuable, for example, when CO2 is very abundant and its 9.4?μm satellite band hides the 9.6?μm O3 band in the IR. In each case, determining the mass appears mandatory to identify the planet's nature and have an idea of surface conditions, which are necessary when testing for the presence of life.Lei, L., Liu, Z., Seol, Y., Boswell, R., Dai, S., 2019. An investigation of hydrate formation in unsaturated sediments using X-ray computed tomography. Journal of Geophysical Research: Solid Earth 124, 3335-3349. properties of hydrate‐bearing sediments are often correlated with hydrate saturation with little or no information on hydrate distribution uniformity in the specimens. This study focuses on water redistribution and sediment skeleton shift depending on various hydrate formation conditions in unsaturated systems, as well as on the resulting hydrate distribution patterns. Using X‐ray computed tomography, we investigate the factors such as fines content and the pressure‐temperature path on mass migration during carbon dioxide hydrate formation. The experiments show water migration, preferential hydrate formation toward the core periphery, localized patchy hydrate distribution, and sediment particle movement toward the core center. Sediment particle movement can be impeded in densely packed specimens. The overall mass migration due to hydrate formation can be significantly suppressed by adding 5% by mass of kaolinite. Hydrate formation initiated by pressurization and then cooling causes less mass migration than the cases where hydrate is formed using cooling followed by pressurization or pressurizing frozen cores followed by heating methods. Freezing can induce water migration and particle pushing in a similar manner as hydrate formation. Image analyses show that the pressure‐temperature path and the rates of heat transfer during hydrate nucleation and growth govern the uniformity of hydrate distribution in sediments.Leitenmüller, V., Rupprecht, B.J., 2019. A multidisciplinary approach for chemical EOR screening: Understanding alkali-oil interaction by the use of petroleum geochemistry. Journal of Petroleum Science and Engineering 180, 967-981. chemical enhanced oil recovery is used to increase the incremental oil production and relies on the interaction of alkali lye with crude oil. Optimizing the chemical formulation depends on screening multiple alkali concentration ranges to maximize the generated emulsion volume. However, the strong chemical variation of the crude oil, caused by biodegradation within the reservoirs, and its influence on generating in-situ soaps has never been studied in detail. In this paper, organic geochemical oil characterization was combined with phase screening data. Thereby, differences in terms of initial crude oil composition (slightly degraded, moderate degraded, and heavy degraded oils), but also regarding the excess alkali-equilibrated oil phase, and the hydrocarbons which are included in the in-situ soap (emulsion phase) were worked out.Different alkalis, concentration ranges, and water-oil-ratios were studied, to understand the control mechanism for the in-situ soap generation. The formed emulsions were observed over time (emulsion stability) and classified into possible emulsion types. Alterations caused by the alkali-oil interaction were quantified by the use of organic geochemistry.The degree of biodegradation seems to be an important control mechanism. Slightly degraded oils do not interact with the alkali lye due to a high content of non-polar compounds such as alkanes and isoprenoids. Moderately and heavily degraded oils show varying interactions with the alkali solution. The degree of interaction depends on the used degradation type, the alkali type as well as on the used concentration. Moderately degraded oils interact in a lower concentration range compared to heavily degraded oils, which show an increased non-soap forming acid content. Phase experiments conducted over a long period of time (100 days) were used to determine which emulsion types (micro or macro) were formed. Stable micro emulsions were preferably generated over time in formulations prepared with potassium carbonate (K2CO3). In contrast, formulations containing sodium carbonate (Na2CO3) hardly did not generate stable micro emulsions.The composition of alkali-equilibrated oil differs from the initial oil composition and shows a strong dependency of the used alkali type. Potassium carbonate caused mild alterations of the moderately and heavily degraded oils, whereas the impact of sodium carbonate was more severe. In addition, dissolution of naphthalenes, steranes, hopanes, and parts of the generated in-situ soap into the aqueous phase, was observed during the performed phase experiments of the moderately degraded oils (at the elevated pH values).Lelchat, F., Mocaer, P.Y., Ojima, T., Michel, G., Sarthou, G., Bucciarelli, E., Cérantola, S., Colliec-Jouault, S., Boisset, C., Baudoux, A.-C., 2019. Viral degradation of marine bacterial exopolysaccharides. FEMS Microbiology Ecology 95, Article fnz122. identification of the mechanisms by which marine dissolved organic matter (DOM) is produced and regenerated is critical to develop robust prediction of ocean carbon cycling. Polysaccharides represent one of the main constituents of marine DOM and their degradation is mainly attributed to polysaccharidases derived from bacteria. Here, we report that marine viruses can depolymerize the exopolysaccharides (EPS) excreted by their hosts using five bacteriophages that infect the notable EPS producer, Cobetia marina DSMZ 4741. Degradation monitorings as assessed by gel electrophoresis and size exclusion chromatography showed that four out of five phages carry structural enzymes that depolymerize purified solution of Cobetia marina EPS. The depolymerization patterns suggest that these putative polysaccharidases are constitutive, endo-acting and functionally diverse. Viral adsorption kinetics indicate that the presence of these enzymes provides a significant advantage for phages to adsorb onto their hosts upon intense EPS production conditions. The experimental demonstration that marine phages can display polysaccharidases active on bacterial EPS lead us to question whether viruses could also contribute to the degradation of marine DOM and modify its bioavailability. Considering the prominence of phages in the ocean, such studies may unveil an important microbial process that affects the marine carbon cycle.León-Zayas, R., Roberts, C., Vague, M., Mellies, J.L., 2019. Draft genome sequences of five environmental bacterial isolates that degrade polyethylene terephthalate plastic. Microbiology Resource Announcements 8, Article e00237-19., we report the annotated draft genome sequences of three Pseudomonas spp. and two Bacillus spp. that, as consortia, degrade polyethylene terephthalate plastic. Improved microbial degradation of plastic waste could help reduce the billions of metric tons of these materials that currently exist in our environment.LeRoy, M.A., Gill, B.C., 2019. Evidence for the development of local anoxia during the Cambrian SPICE event in eastern North America. Geobiology 17, 381-400. later Cambrian Steptoean Positive Carbon Isotope Excursion (SPICE) event was an episode marked by pronounced changes to the global biogeochemical cycles of carbon and sulfur and significant extinctions on several paleocontinents including Laurentia (North America). While the exact cause(s) of these events remains debated, various lines of evidence suggest an increase in the areal extent of anoxia at the seafloor was a likely feature. Here, we explore whether changes in local oxygenation accompanied the onset of the SPICE in southern Laurentia using cores of the Nolichucky and Eau Claire Formations from Ohio and Kentucky, USA, that represent a transect into the Rome Trough/Conasauga intrashelf basin. At our study locations, the initial positive δ13C shift of the SPICE occurs in conjunction with increases in the abundance and δ34S of sedimentary pyrite. Further local redox conditions, tracked using iron speciation analysis, indicate anoxic conditions developed at the two proximal locations after the start of the paired isotopic excursions. However, the location near the basin center shows no indication for anoxia before or during the onset of the SPICE. While this signal may reflect the structure of local redox conditions within the basin, with the development of anoxia limited to the basin margins, we argue that authigenic iron enrichments were muted by sedimentary dilution and/or the enhanced authigenesis of iron‐bearing sheet silicates near the basin center, masking the signal for anoxia there. Regardless of the areal extent of anoxia within the basin, in either scenario the timing of the development of anoxic bottom waters was concurrent with local faunal turnover, features broadly consistent with a global expansion of anoxia playing a role in driving the isotopic trends and extinctions observed during the event.Leutert, T.J., Sexton, P.F., Tripati, A., Piasecki, A., Ho, S.L., Meckler, A.N., 2019. Sensitivity of clumped isotope temperatures in fossil benthic and planktic foraminifera to diagenetic alteration. Geochimica et Cosmochimica Acta 257, 354-372. the clumped isotope (Δ47) thermometer to foraminifer microfossils offers the potential to significantly improve paleoclimate reconstructions, owing to its insensitivity to the isotopic composition of seawater (unlike traditional oxygen isotope (δ18O) analyses). However, the extent to which primary Δ47 signatures of foraminiferal calcites can be altered during diagenesis is not well known. Here, we present Δ47 data as well as high-resolution (～10 kyr) δ18O and δ13C middle Eocene time series, measured on benthic and planktic foraminifera from ODP/IODP Sites 1408, 1409, 1410, 1050, 1260 and 1263 in the Atlantic Ocean. The sites examined span various oceanographic regimes, including the western tropical to mid-latitude North Atlantic, and the eastern mid-latitude South Atlantic. Comparing data from contemporaneous foraminifera with different preservation states, we test the effects of diagenetic alteration on paleotemperature reconstructions for the deep and surface ocean. We find that overall, primary Δ47 signatures appear similarly sensitive to diagenetic overprinting as δ18O, with differences in sensitivity depending on pore fluid chemistry and the amount of secondary calcite. Where planktic foraminifera are significantly altered, sea surface temperatures derived from Δ47 and δ18O values are biased towards cool temperatures. In comparison, Δ47 and δ18O values of benthic and well preserved planktic foraminifera are less affected by diagenesis and thus likely to yield robust foraminiferal calcification temperatures. With independent estimates of diagenetic calcite fractions, secondary overprints could be corrected for, using end-member modeling and Δ47-based temperatures from benthic foraminifera.Levy, A.J., Oranzi, N.R., Ahmadireskety, A., Kemperman, R.H.J., Wei, M.S., Yost, R.A., 2019. Recent progress in metabolomics using ion mobility-mass spectrometry. TrAC Trends in Analytical Chemistry 116, 274-281. recent years, metabolomics and lipidomics approaches have become increasingly popular for use in the analysis of human heath, molecular mechanisms, and disease progression. Despite the growth in applications and advances in instrumentation, metabolomics and lipidomics are limited by factors including interference from matrix effects, the need for lengthy for chromatographic analysis, and structural diversity of metabolites and lipids creating interference of isomers and isobars, which can confound identification. Ion mobility spectrometry (IMS) provides a method to enhance throughput, enhance isomeric separation, and reduce chemical noise. This review focuses on (i) the use of IMS and subsequent advancements in global metabolomics and lipidomics, (ii) the application and benefits of IMS in targeted metabolomics studies, and (iii) the use of IMS for non-chromatographic methods such as direct analysis, desorption ionization methods, and imaging.Li, B., Fan, X., Yu, Y.-R., Wang, F., Li, X., Lu, Y., Wei, X.-Y., Ma, F.-Y., Zhao, Y.-P., Zhao, W., 2019. Insight into molecular information of Huolinguole lignite obtained by Fourier transform ion cyclotron resonance mass spectrometry and statistical methods. Rapid Communications in Mass Spectrometry 33, 1107-1113.: Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) was applied to the characterization of organic compounds in coal extracts at the molecular level. Large volumes of data obtained by FT‐ICR MS were processed via statistical methods to extract valuable information on the molecular structures and compositions of organic compounds in coal.Methods: A low‐rank coal was subjected to ultrasonic extraction sequentially with six solvents to separate and enrich species with different molecular characteristics. Complex mass spectra of the six extracts were obtained by a FT‐ICR MS system equipped with two ionization sources. Two multivariate statistical methods, hierarchical clustering analysis (HCA) and principle component analysis (PCA), were introduced to mine useful information from the complex MS data and visually exhibit comprehensive molecular details in coal extracts.Results: Similarities and differences between the 17 MS data sets from six coal extracts ionized by different ion sources were visually exhibited in plots via data processing using HCA and PCA. For HCA, all of the identified compounds were divided into seven classes (CH, O, N, S, ON, OS, and NS), and detailed differences in the relative abundance were revealed. In addition, PCA discriminated the differences in molecular composition for organic compounds from the six extracts.Conclusions: Multivariate statistical analysis is a promising methodology which can interpret the chemical composition of coals and coal derivatives at the molecular level, especially for the analysis of multiple complex samples presenting in a single plot.Li, G.-S., Fan, X., You, C.-Y., Zhao, Y.-P., Wang, R.-Y., Wei, X.-Y., Ma, F.-Y., Lu, X., Mo, W.-L., Li, X., 2019. Molecular characteristics of the soluble components from three low-rank coals based on the analyses using GC/MS and GC/Q-TOF MS. Fuel 254, 115602. low-rank coals were subjected to a thermal dissolution (TD) process sequentially using cyclohexane (CYH) and methanol (MeOH) solvent to obtain six TD extracts. The six TD extracts were analyzed by Fourier transform infrared spectroscopy (FTIR), gas chromatograph/mass spectrometry (GC/MS) and gas chromotography/quadrupole time-of-flight MS (GC/Q-TOF MS) to understand the compositional features of three low-rank coals. Hierarchical clustering analysis (HCA) and principle component analysis (PCA) were applied to show the relationships among 10 classes in the six TD extracts. Compared with GC/MS, a routine analytical method, more species with relative high molecular mass and more oxygen-containing organic compounds (OCOCs) were determined using GC/Q-TOF MS. In addition, HCA dendrogram and heatmap reveal the difference among 10 classes in the TD extracts. Meanwhile, the distributional and compositional features of six TD extracts were also exhibited in the score plot and loading plot of PCA.Li, H., Yao, Q.-Z., Wang, F.-P., Huang, Y.-R., Fu, S.-Q., Zhou, G.-T., 2019. Insights into the formation mechanism of vaterite mediated by a deep-sea bacterium Shewanella piezotolerans WP3. Geochimica et Cosmochimica Acta 256, 35-48. mediated carbonate mineralization plays a crucial role in biogeochemical cycling of carbon, as microbes can efficiently transform atmospheric CO2 and organic carbon into carbonate cements which represent a significant sink in the global carbon cycle. It is well established that diverse bacteria from various natural habitats can induce the precipitation of calcium carbonate, and an increasing number of bacteria were found to be able to mediate the mineralization of vaterite. However, the precise mechanisms for the formation of bacterial vaterite are not fully understood. To better understand the effect of bacterial activity on vaterite formation, Shewanella piezotolerans WP3 was selected as a model microbe to induce calcium carbonate mineralization. A combination of bacterial and biomimetic mineralization experiments was adopted. Different bacterial components including native cells, EPS-free cells, cell-bound EPS, soluble EPS, and small molecule organics were isolated from the cultures and used to influence calcium carbonate crystallization and growth. The identification and characterization of the mineralized products were done using field emission scanning electron microscopy (FESEM), X-ray powder diffraction (XRD), Raman spectroscopy, Fourier transform infrared spectroscopy (FT-IR), thermogravimetry and differential thermal analysis (TG-DTA), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) and selected area electron diffraction (SAED). Bacterial in situ mineralization experiments demonstrate that S. piezotolerans WP3 can not only promote the mineralization of calcium carbonate, but also mediate polymorph selection of vaterite. Biomimetic mineralization experiments involving individual bacterial components reveal that different bacterial components have different effects on calcium carbonate polymorphism, and low molecular-weight amino acids secreted by the bacteria play a dominant role on vaterite formation and stabilization. Our observations also suggest that soluble EPS can induce the formation of aragonite while bound EPS facilitate calcite erosion. Current results can provide a deeper insight into bacterially mediated mineralization of vaterite and calcium carbonate polymorphism problem, and help evaluate the significance of biogenic carbonate in the diagenetic carbonate sinks.Li, J., Han, Z., Yan, Q., Wang, S., Ge, S., 2019. Distribution and genesis of mercury in natural gas of large coal derived gas fields in China. Petroleum Exploration and Development 46, 463-470. mercury content in natural gas samples from more than 500 gas wells in eight large gas bearing basins of China was tested, mercury release experiments on two coal samples from different areas were conducted, and the mercury content of 11 coal samples from different gas wells of Ordos Basin was tested. The mercury distribution of the coal derived gas has three features: The first is that mercury content of coal derived gas is generally much higher than that of oil derived gas, the second is that the coal derived gases from different fields vary widely in mercury content, the third is that the mercury content in coal derived gas increases with the increase of production layer depth. Mercury in coal derived natural gas mainly originates from the source rock. Besides three evidences, namely, coal derived gas mercury content is much higher than that of oil derived gas, mercury content of gas with high carbon dioxide content decreases with the increase of carbon dioxide content, and the coal bearing strata have the material base to generate natural gas with high mercury content, the pyrolysis experiment of two coal samples show that coal can produce natural gas with high mercury content during the process of thermal evolution. The mercury content of coal derived natural gas is controlled mainly by the temperature of source rock and the sulfur environment of reservoir. According to lithospheric material cycling process and oil-gas formation process, the formation of mercury in coal derived gas can be divided into four stages, transportation and deposition, shallow burial, deep burial, and preservation and destruction.Li, L., Li, C., Kang, T., 2019. Adsorption/desorption behavior of CH4 on shale during the CO2 huff-and-puff process. Energy & Fuels 33, 5147-5152. CO2 huff-and-puff method has been widely adopted for enhancing CH4 recovery in shale reservoirs. Revealing the behavior of CH4 adsorption/desorption in shale during the CO2 huff-and-puff process clarifies the recovery mechanisms of CH4 from shale reservoirs. In our work, the question of how CO2 plays a role in affecting the adsorption/desorption of CH4 is investigated using the low-field nuclear magnetic resonance technique. In addition, phase transition of CH4 is also analyzed to investigate how the existing states of CH4 transform in shale during this process. Specifically, the states in which CH4 resides in shale are first recognized by analyzing the measured T2 spectrum of shale after injecting CH4. CO2 huff-and-puff tests are then conducted to investigate how CO2 impacts the adsorption/desorption behavior of CH4 on shale samples. Furthermore, the T2 signals of shale during depressurization are measured to investigate the state transformation of CH4 in shale during the CO2 huff-and-puff process. Test results show that three states are observed for CH4 storage in shale samples, that is, bulk CH4, free CH4 at the pore center, and adsorbed CH4 on the pore surface. After injecting CO2, the adsorbed CH4 will be desorbed from the shale surface, which thus increases the free CH4 at the pore center. During depressurization, the free CH4 is more readily produced from the shale samples, whereas the adsorbed CH4 is hard to be recovered; more advanced technology should thereby be proposed for enhancing the adsorbed CH4 from shale reservoirs. This work is expected to inspire new understanding of the mechanisms of CH4 recovery using CO2 huff-and-puff methods.Li, L., Liu, Z., George, S.C., Sun, P., Xu, Y., Meng, Q., Wang, K., Wang, J., 2019. Lake evolution and its influence on the formation of oil shales in the Middle Jurassic Shimengou Formation in the Tuanyushan area, Qaidam Basin, NW China. Geochemistry 79, 162-177. non-marine Qaidam Basin is a petroliferous basin in northwest China. The Tuanyushan area is located in the Saishiteng Depression in the northern Qaidam Basin. Coal and oil shales are widely developed in the Middle Jurassic Dameigou and Shimengou formations in this area where the sedimentary sequence and controls on coal accumulation have already been well documented. However, the geochemical characteristics of lacustrine fine-grained sediments, including lacustrine oil shales, in the shale member of the Shimengou Formation and the main controlling factors of the formation of the oil shales are ambiguous. This paper aims to reconstruct the lake evolution history during the Middle Jurassic period and reveal its influence on the formation of the oil shales in this area. Oil shales and fine-grained sediments were systematically sampled to determine their mineralogical and geochemical characteristics (major, trace and rare earth elements; stable carbon and oxygen isotopes). Based on lithological variations and total organic carbon (TOC) contents, a complete third-order sequence is identified and can be further divided into four system tracts (lowstand system tract, LST; transgressive system tract, TST; highstand system tract, HST and regressive system tract, RST) that correspond to four lake evolution stages (A–D). Changes in the lake level show an initial shallow lake, followed by a continuous upward deepening trend, followed by a shallowing trend. Shallow lake facies developed in the LST, TST and RST, whereas semi-deep to deep lake facies developed in the HST. Stable carbon and oxygen isotopes indicate that the Shimengou Lake was semi-closed to closed in the Middle Jurassic. Therefore, the water properties responded strongly to climate changes. According to elemental and mineralogical analyses, a moist climate prevailed, except during the early stages of the TST (stage B1) and HST (stage C1) when there was a semiarid climate. The semiarid climate influenced the water properties and detrital input and was the major controlling factor for the formation of the higher quality oil shales within a saline water environment. In comparison, under the moist climatic condition in the HST, the stable semi-deep to deep-water environment was the major controlling factor for the formation of lower quality oil shales within a fresh water environment.Li, T., Li, M., Jing, X., Xiao, W., Cui, Q., 2019. Influence mechanism of pore-scale anisotropy and pore distribution heterogeneity on permeability of porous media. Petroleum Exploration and Development 46, 594-604. on micro-CT scanning experiments, three-dimensional digital cores of tight sandstones were established to quantitatively evaluate pore-scale anisotropy and pore-distribution heterogeneity. The quartet structure generation set method was used to generate three-dimensional anisotropic, heterogeneous porous media models. A multi-relaxation-time lattice Boltzmann model was applied to analyze relationships of permeability with pore-scale anisotropy and pore distribution heterogeneity, and the microscopic influence mechanism was also investigated. The tight sandstones are of complex pore morphology, strong anisotropy and pore distribution heterogeneity, while anisotropy factor has obvious directivity. The obvious anisotropy influences the orientation of long axis of pores and fluid flow path, making tortuosity smaller and flowing energy loss less in the direction with the greater anisotropy factor. The strong correlation of tortuosity and anisotropy is the inherent reason of anisotropy acting on permeability. The influence of pore distribution heterogeneity on permeability is the combined effects of specific surface area and tortuosity, while the product of specific surface area and tortuosity shows significantly negative correlation with heterogeneity. The stronger the pore distribution heterogeneity, the smaller the product and the greater the permeability. In addition, the permeability and tortuosity of complex porous media satisfy a power relation with a high fitting precision, which can be applied for approximate estimation of core permeability.Li, W., Kuang, Y., Lu, S., Cheng, Z., Xue, H., Shi, L., 2019. Porosity enhancement potential through dolomite mineral dissolution in the shale reservoir: A case study of an argillaceous dolomite reservoir in the Jianghan Basin. Energy & Fuels 33, 4857-4864., X., Chi, P., Guo, X., Sun, Q., 2019. CO2-induced asphaltene deposition and wettability alteration on a pore interior surface. Fuel 254, Article 115595. enhanced oil recovery has a great potential to improve the rate of oil production and store carbon dioxide emission. However, CO2 injection can destabilize the asphaltene-oil colloidal system and thus favor severe asphaltene particle deposition in porous reservoir formation. These block reservoir pores and change pore wetting condition, finally damage the porous reservoir formation and significantly reduce oil production. A good understanding on CO2-induced asphaltene deposition at a pore scale is of significance for CO2-EOR processes. Few studies have directly investigated the asphaltene deposition behavior and asphaltene-induced pore wetting alteration on a pore interior surface in a confined pore. In this study, we directly measured the CO2-induced asphaltene deposition behavior on the interior surface of a single pore under high pressure and temperature. The particle size and particle size distribution of CO2-induced asphaltene deposition on pore interior surfaces were directly measured and analyzed, by considering the influences of aging time and temperature. The results indicate that long aging period and elevated temperature could favor CO2-induced asphaltene flocculation and deposition on pore interior surfaces. Finally, the pore-scale wetting alteration caused by asphaltene deposition was quantified by direct pore contact angle measurements.Li, Y., Blois, G., Kazemifar, F., Christensen, K.T., 2019. High-speed quantification of pore-scale multiphase flow of water and supercritical CO2 in 2-D heterogeneous porous micromodels: Flow regimes and interface dynamics. Water Resources Research 55, 3758-3779. pore‐scale flow of CO2 and water in 2‐D heterogeneous porous micromodels over a Ca range of nearly three orders of magnitude was explored experimentally. The porous geometry is a close reprint of real sandstone, and the experiments were performed under reservoir‐relevant conditions (i.e., 8?MPa and 21?°C), thus ensuring relevance to practical CO2 operations. High‐speed fluorescent microscopy and image processing were employed to achieve temporally and spatially resolved data, providing a unique view of the dynamics underlying this multiphase flow scenario. Under conditions relevant to CO2 sequestration, final CO2 saturation was found to decrease and increase logarithmically with Ca within the capillary and viscous‐fingering regimes, respectively, with a minimum occurring during regime crossover. Specific interfacial length generally scales linearly with CO2 saturation, with higher slopes noted at high Ca due to stronger viscous and inertial forces, as supported by direct pore‐scale observations. Statistical analysis of the interfacial movements revealed that pore‐scale events are controlled by their intrinsic dynamics at low Ca, but overrun by the bulk flow at high Ca. During postfront flow, while permeability is typically correlated with total CO2 saturation in the porous domain (regardless of its mobility), the saturation of active CO2 pathways in the current study correlated very well with permeability. This alternate approach to characterize relative permeability could serve to mitigate hysteresis in relative permeability curves. Taken together, these results provide unique insights that address inconsistent observations in the literature and previously unanswered questions about the underlying flow dynamics of this important multiphase flow scenario.Li, Y., Liu, F., Xu, X., Liu, Y., Li, Y., Ding, H., Chen, N., Yin, H., Lin, H., Wang, C., Lu, A., 2019. Influence of heavy metal sorption pathway on the structure of biogenic birnessite: Insight from the band structure and photostability. Geochimica et Cosmochimica Acta 256, 116-134., primarily formed by biooxidation, is a common semiconducting Mn oxide in nature and a major controller of heavy metals cycling processes. In turn, the heavy metal sorption pathway alters its structural chemistry and thus the electronic structure. We synthesize three kinds of birnessite, namely biogenic (bio-birnessite), Cu coprecipitated (co-birnessite) and Cu adsorbed birnessite (ad-birnessite), to investigate the influence of Cu(II) occupancy on the structure, semiconducting property and photostability of birnessite. XRD show co-birnessite holds the same hexagonal symmetry as bio-birnessite, whereas ad-birnessite transforms to triclinic symmetry as reflected by the splitting reflections at 2.44 and 1.42??. The adsorption process is accompanied by a more intense releasing of Mn(II) (156.88?μM/L) from a bio-birnessite analog δ-MnO2 in light than in dark (19.55?μM/L), suggesting the photoreductive releasing of Mn(II) promotes structure transformation. Conformably, both the Mn average oxidation state (AOS) (3.32) and mole ratio of Cu/Mn (0.08) in ad-birnessite is lower than those in co-birnessite (AOS: 3.47, Cu/Mn ratio: 0.17). EXAFS demonstrate different Cu complexing features in ad- and co-birnessite that the ratio of Cu incorporated (INC) into vacancies is 1.16 and 0.45 for ad- and co-birnessite, respectively. UV–vis diffuse reflection spectra (DRS) and photoelectron spectrometer (PS) exhibit the band gap (Eg) and valence band (VB) of bio-birnessite are 2.05 and ?5.58?eV, while there is 0.1 and 0.05?eV decrease of Eg, and 0.08 and 0.16?eV lowering of VB in co- and ad-birnessite, respectively. The reduced Eg guarantee them to generate photoelectron-hole pairs under mild indoor visible light, and the lower energy level of VB in ad-birnessite makes its VB holes more reactive to accept electrons from electron donors. Further density functional theory (DFT) calculations focus on interpreting the fine structures brought by different Cu sorption pathways on the electronic structure of birnessite. A Mn vacancy in a 2?×?2?×?1 hexagonal birnessite cell significantly reduces Eg from 1.60 to 0.28?eV by hybridizing Mn 3d and O 2p states in VB. The doped Cu reduces Eg mainly through incorporating Cu 3d orbital in VB. The INC Cu in hexagonal birnessite contributes more to reduce Eg (1.60–0.34?eV) than TCS Cu (1.60–1.20?eV), while in triclinic birnessite cell, TCS Cu causes more obvious reduction of Eg (1.68–0.28?eV) than INC Cu (1.68–1.55?eV). Thus, we conclude the vacancy imposes more effect on the electronic structure of hexagonal co-birnessite than doped Cu in TCS or INC sites; and the band structure of co-birnessite is more sensitive to INC Cu, in contrast to TCS Cu affecting more in ad-birnessite. Overall, the crystal structure differs according to Cu fixation pathway, which imposes a comprehensive effect on band structure and photostability contributed by vacancies, Cu occupancy sites and structural symmetry. Cu coprecipitating with birnessite is suggested as a preferred method in practical clean-up of metals such as Cu, due to the higher adsorption capacity for Cu, better stability of TCS Cu and better photostability influenced by Cu.Li, Y., Wang, X., Li, Y., Duan, J., Jia, H., Ding, H., Lu, A., Wang, C., Nie, Y., Wu, X., 2019. Coupled anaerobic and aerobic microbial processes for Mn-carbonate precipitation: A realistic model of inorganic carbon pool formation. Geochimica et Cosmochimica Acta 256, 49-65. carbonate is the main MnII mineral phase that precipitates in suboxic to anoxic environments. The coupled processes of MnIV oxide bioreduction and organic oxidation serve as dominant factors leading to Mn carbonate precipitation. This study examined the simultaneous respiration of oxygen and birnessite by a facultatively anaerobic bacterium, the Dietzia strain DQ12-45-1b (45-1b), and discussed the possible mechanism of rhodochrosite precipitation under general oxic environments. Compared to anaerobic experiments, the more rapid growth of 45-1b under aerobic conditions caused faster oxidation of acetate (1.0?×?103?μM?h?1) and accumulation of HCO3? (5.5?×?102?μM?h?1) within 72?h, which was coupled to a dramatic increase in pH from 7.0 to more than 9.2. By virtue of the higher biomass and bioactivity in the aerobic condition, the bioreduction of MnIV was accelerated and it caused a higher accumulating rate of soluble reduced Mn (4.0?μΜ?h?1) than that in the anaerobic condition (2.0?μΜ?h?1). Those rates indicated that an anaerobic-aerobic sub-interface was present in the aerobic system, in which anaerobic and aerobic respiration co-occurred to give rise to sufficient Mn(II) and alkalinity, thus, increased the supersaturation index (SI) for rhodochrosite. The mineral intermediates and products were identified by time-course XRD, SEM, and Raman spectra. Manganite (MnOOH) was found as the transient intermediate, which suggested the stepwise one-electron transfer mechanism of birnessite reduction. The dialysis tube, lysed cells, dead cells and two-compartment experiments suggested that the living 45-1b not only carried out a direct extracellular electron transfer for birnessite reduction but also provided necessary nucleation sites for rhodochrosite precipitation. Furthermore, both the isotope experiments and Raman analysis showed that the carbon source in rhodochrosite was mainly 13C isotope-labeled acetate, which corresponded well with the geological isotopic records. Finally, a conceptual model of Mn carbonate precipitation at oxic-suboxic/anoxic interfaces that could be possibly present in soil and sedimentary environments was proposed based on three prerequisites: (i) sufficient Mn(II) produced on an aerobic-anaerobic sub-interface, (ii) adequate alkalinity, and (iii) nucleation sites provided by cell surfaces. This model highlights the role of aerobic respiration in Mn(IV) reduction and Mn-carbonate formation, and may suggest a realistic way for inorganic carbon storage.Li, Y., Zhang, J., Liu, Y., Shen, W., Chang, X., Sun, Z., Xu, G., 2019. Organic geochemistry, distribution and hydrocarbon potential of source rocks in the Paleocene, Lishui Sag, East China Sea Shelf Basin. Marine and Petroleum Geology 107, 382-396. Lishui Sag, one of the most promising hydrocarbon exploration areas in the East China Sea Shelf Basin, has had no major breakthroughs after its exploration and development. Therefore, it is crucial to carry out a comprehensive assessment of this basin to illustrate the potential and distribution of source rocks in the Lishui Sag. Based on organic petrographic examinations, Rock-Eval pyrolysis, gas chromatography (GC) and gas chromatography–mass spectrometry (GC–MS) analysis, the organic geochemical characteristics and paleoenvironment of the source rocks were investigated. The results imply that the kerogen type of the source rocks in the Lishui Sag is dominated by Type III, with a small amount of Type II kerogen. Biomarkers show that the source rocks are characterized by a mixed origin of organic matter in a transitional environment. The lower Mingyuefeng (E1ml), lower Lingfeng (E1ll) and Yueguifeng (E1y) Formations show higher inputs of aquatic organic matter. The base limits of the total organic carbon (TOC) values of effective source rocks were determined to be 0.9?wt % in the E1m Formation, 1.0?wt % in the E1l Formation and 0.7?wt % in the E1y Formation. Based on an artificial neural network (ANN) model and the Δlog R method, the distribution of effective source rocks in the Lishui Sag was illustrated. Source rocks in the E1ml and Lingfeng (E1l) Formations can be expected to generate mixed liquid hydrocarbons, while samples from E1y Formation are oil prone source rocks with normal oil and light oil potentials. Additionally, the post mature source rocks of the E1y Formation may be the origin of natural gas. Upon full consideration of the potential and distribution of source rocks, the North part of the Lingfeng Uplift is the most favorable exploration zone.Li, Z.-b., Lu, X., Teng, H.H., Chen, Y., Zhao, L., Ji, J., Chen, J., Liu, L., 2019. Specificity of low molecular weight organic acids on the release of elements from lizardite during fungal weathering. Geochimica et Cosmochimica Acta 256, 20-34. solubilization and mobilization of elements from silicate minerals during fungal weathering are predominantly promoted by acidification and complexation reactions. However, stark differences exist in the release rates of different elements driven by fungal-derived low molecular weight organic compounds (LMWOCs) when acidity maintains constant, raising the question of whether the release of individual element during dissolution is ligand-specific. In this work, we investigate this question by characterizing the release of Mg, Si, Fe, and Ni from lizardite [(Mg, Fe, Ni)3Si2O5(OH)4]. Miniaturized batch reactors (microplate wells of 250??L) were used in dissolution experiments in the presence and absence of the indigenous fungus Talaromyces flavus. Abiotic chemical weathering experiments with metabolically relevant organics and HCl were also carried out to isolate the vital effects of elemental releases. The initial release rates of Mg, Si, Fe, and Ni were obtained from determining the dissolved elemental concentrations. The results show that T. flavus enhances the release of Mg and Si by a factor of ～2, but that of Fe and Ni by a factor of >10, relative to the rates measured in the control experiment. Additionally, the measurements show an overexcretion of siderophores and oxalic acid, as well as acidification of bulk solution, during bioweathering. Abiotic chemical dissolution of lizardite confirms the release of Fe and Ni proceeds mainly via a ligand-promoted pathway. In addition, the results indicate that siderophores and oxalic acid are responsible for the solubilization of Fe and Ni, respectively. These findings provide direct evidence that the rate and mechanism of elemental release from silicate during bioweathering are ligand-specific, and both synergistic and inhibitory effects may be involved. Given that siderophore- and oxalic acid-producing fungi are highly active in soils, these results may have the potential to advance our understanding of the critical roles of fungi in rhizosphere geochemistry and ecology.Lian, D., Yang, J., 2019. Ophiolite-hosted diamond: A new window for probing carbon cycling in the deep mantle. Engineering 5, 406-420. reported in our prior work, we have recovered microdiamonds and other unusual minerals, including pseudomorph stishovite, moissanite, qingsongite, native elements, metallic alloys, and some crustal minerals (i.e., zircon, quartz, amphibole, and rutile) from ophiolitic peridotites and chromitites. These ophiolite-hosted microdiamonds display different features than kimberlitic, metamorphic, and meteoritic diamonds in terms of isotopic values and mineral inclusions. The characteristic of their light carbon isotopic composition implies that the material source of ophiolite-hosted diamonds is surface-derived organic matter. Coesite inclusions coexisting with kyanite rimming an FeTi alloy from the Luobusa ophiolite show a polycrystalline nature and a prismatic habit, indicating their origin as a replacement of stishovite. The occurrence in kyanite and coesite with inclusions of qingsongite, a cubic boron nitride mineral, and a high-pressure polymorph of rutile (TiO2 II) point to formation pressures of 10–15 GPa at temperatures ～1300 °C, consistent with depths greater than 380 km, near the mantle transition zone (MTZ). Minerals such as moissanite, native elements, and metallic alloys in chromite grains indicate a highly reduced environment for ophiolitic peridotites and chromitites. Widespread occurrence of diamonds in ophiolitic peridotites and chromitites suggests that the oceanic mantle may be a more significant carbon reservoir than previously thought. These ophiolite-hosted diamonds have proved that surface carbon can be subducted into the deep mantle, and have provided us with a new window for probing deep carbon cycling.Liang, X., Zhuang, J., L?ffler, F.E., Zhang, Y., DeBruyn, J.M., Wilhelm, S.W., Schaeffer, S.M., Radosevich, M., 2019. Viral and bacterial community responses to stimulated Fe(III)-bioreduction during simulated subsurface bioremediation. Environmental Microbiology 21, 2043-2055. The delivery of fermentable substrate(s) to subsurface environments stimulates Fe(III)-bioreduction and achieves detoxification of organic/inorganic contaminants. Although, much research has been conducted on the microbiology of such engineered systems at lab and field scales, little attention has been given to the phage-host interactions and virus community dynamics in these environments. The objective was to determine the responses of soil bacterial communities and viral assemblages to stimulated anaerobic Fe(III)-bioreduction following electron donor (e.g. acetate) addition. Microbial communities, including viral assemblages, were investigated after 60?days of Fe(III)-bioreduction in laboratory-scale columns continuously fed with acetate-amended artificial groundwater. Viral abundances were greatest in the influent section and decreased along the flow path. Acetate availability was important in influencing bacterial diversity, microbial interactions and viral abundance and community composition. The impact of acetate addition was most evident in the influent section of the columns. The increased relative abundance of Fe(III)-reducing bacteria coincided with an increase in viral abundance in areas of the columns exhibiting the most Fe(III) reduction. The genetic composition of viruses in these column sections also differed from the control column and distal sections of acetate-treated columns suggesting viral communities responded to biostimulated Fe(III)-bioreduction.Liduino, V.S., Cravo-Laureau, C., Noel, C., Carbon, A., Duran, R., Lutterbach, M.T., Camporese Sérvulo, E.F., 2019. Comparison of flow regimes on biocorrosion of steel pipe weldments: Community composition and diversity of biofilms. International Biodeterioration & Biodegradation 143, 104717., the corrosion of petroleum pipelines is the cause of severe operational failures and damages to the environment, and the majority of them may have been intensified by microbial activities. However, few scientific publications have investigated the influence of seawater with indigenous microorganisms in internal corrosion of welded joints in long-distance pipelines, which has motivated this study. Here, a combination of culture-based and molecular microbiological methods was applied to measure the microbial abundance, diversity and composition of biofilms formed on two corroded weldments (gas tungsten arc - GTAW and shielded metal arc - SMAW) of an API 5L X65 microalloyed steel under laminar and turbulent flow regimes using seawater from Guanabara Bay (Rio de Janeiro, Brazil). Overall, turbulent flow did not reduce the biomass of sessile microorganisms on welded joints compared to laminar flow. Phylogenetic analysis revealed that the Proteobacteria, Firmicutes and Bacteroidetes were the dominant phyla in biofilms attached to GTAW and SMAW joints. At the genus level, all samples showed similar microbial composition with dominance of Desulfovibrio. However, analysis at OTU level revealed that there were specific microorganisms in each corrosive sample, even though they were affiliated to sulfate-reducers. Thus, microbial community compositions were influenced by type of weld, flow regime and biofilm age. The results of our study will be of benefit to the further studies of weld biocorrosion and biofilm ecology within pipelines.Lin, Y., Li, Y., Zheng, B., Yin, X., Wang, L., He, J., Shu, F., Qiao, L., 2019. Evolution of sedimentary organic matter in a small river estuary after the typhoon process: A case study of Quanzhou Bay. Science of The Total Environment 686, 290-300. weather events occur frequently under global warming scenarios and have an important impact on the global carbon cycle. Compared to large rivers, small rivers are more sensitive to extreme weather events (such as typhoons). This paper reports the results of a study carried out in the Quanzhou Bay to explore the evolution of small river estuarine sedimentary organic matter after typhoon process using measurements of the grain-size, total organic carbon (TOC), total nitrogen (TN) and δ13C of surface sediment samples collected 2–3?days and a month, respectively, after typhoon Matmo landing in 2014. The results show that the contents of TOC and TN in the sediments, which gradually decrease from the estuary to the outer sea of Quanzhou Bay, decreased approximately 13% and 16%, respectively, a month later compared with 2–3?days after typhoon landing. The significant decrease occurred in the Jinjiang River estuary and along the South Channel of Quanzhou Bay, while the North Channel and Luoyangjiang River estuary retained high levels of TOC and TN. The results of δ13C values and TOC/TN ratios show that the organic matter in the sediment of the Quanzhou Bay was a mixture derived from C3 terrestrial plants and marine algae. The terrestrial organic matter was mainly deposited in the Jinjiang River estuary 2–3?days after typhoon landing and then spread along the tidal channel to the outer sea a month later. It indicates that the hydrodynamic forces stirred sedimentary organic matters that were input and settled during typhoon, and transported later along the North and South Channel to the outer sea. Some of those organic matters were accumulated in the North Channel during the transport process. The results provide significant meaning for the carbon cycle and material flux study on the coastal and margin seas.Lingam, M., Ginsburg, I., Bialy, S., 2019. Active galactic nuclei: Boon or bane for biota? The Astrophysical Journal 877, Article 62. galactic nuclei (AGNs) emit substantial fluxes of high-energy electromagnetic radiation, and have therefore attracted some recent attention for their negative impact on galactic habitability. In this paper, we propose that AGNs may also engender the following beneficial effects: (i) prebiotic synthesis of biomolecular building blocks mediated by ultraviolet (UV) radiation, and (ii) powering photosynthesis on certain free-floating planets and moons. We also reassess the harmful biological impact of UV radiation originating from AGNs, and find that their significance could have been overestimated. Our calculations suggest that neither the positive nor negative ramifications stemming from a hypothetical AGN in the Milky Way are likely to affect putative biospheres in most of our Galaxy. On the other hand, we find that a sizable fraction of all planetary systems in galaxies with either disproportionately massive black holes (～109–10 M ⊙) or high stellar densities (e.g., compact dwarf galaxies) might be susceptible to both the beneficial and detrimental consequences of AGNs, with the former potentially encompassing a greater spatial extent than the latter.Lipus, D., Vikram, A., Hammack, R., Bibby, K., Gulliver, D., 2019. The effects of sample storage conditions on the microbial community composition in hydraulic fracturing produced water. Geomicrobiology Journal 36, 630-638. petroleum industry has an increasing interest in understanding the microbial communities driving biofouling and biocorrosion in reservoirs, wells, and infrastructure. However, sampling of the relevant produced fluids from subsurface environments for microbiological analyses is often challenged by high liquid pressures, workplace regulations, operator liability concerns, and remote sampling locations. These challenges result in infrequent sampling opportunities and the need to store and preserve the collected samples for several days or weeks. Maintaining a representative microbial community structure from produced fluid samples throughout storage and handling is essential for accurate results of downstream microbial analyses. Currently, no sample handling or storage recommendations exist for microbiological analyses of produced fluid samples. We used 16S rRNA gene sequencing to monitor the changes in microbial communities in hypersaline produced water stored at room temperature or at 4?°C for up to 7 days. We also analyzed storage at ?80?°C across a 3-week period. The results suggest ideal handling methods would include placing the collected sample on ice as soon as possible, but at least within 24?h, followed by shipping the samples on ice over 2–3?days, and finally, long-term storage in the ?20?°C or ?80?°C freezer.Litasov, K.D., Inerbaev, T.M., Abuova, F.U., Chanyshev, A.D., Dauletbekova, A.K., Akilbekov, A.T., 2019. High-pressure elastic properties of polycyclic aromatic hydrocarbons obtained by first-principles calculations. Geochemistry International 57, 499-508. crystal structures and compressibility parameters of benzene and a number of polycyclic aromatic hydrocarbons (PAHs) were calculated by the methods of the first-principles density functional theory with the gradient approximation of exchange and correlation potentials in the PBE form accounting for van der Waals interactions (optPBE–vdWB) at pressures of 0–20 GPa. A comparison with experimental data for benzene, naphthalene, tetracene, and pentacene demonstrated the high accuracy of our calculations. All the compounds have similar compressibilities, bulk moduli (8–12 GPa), and their pressure derivatives (6.9–7.5). The similarity of the calculated parameters indicates the main role of a decrease in interatomic distances during PAH compression and weak deformation of the molecules and benzene rings. The compressibility is weakly dependent on the number of atoms (benzene rings) in the molecule or crystal structure type (most of the PAHs have the space group P21/a). Compounds with many benzene rings and with a denser structure of rings (cyclic pyrene and coronene) are less compressible than less dense PAHs (tetracene and hexacene). Some PAHs (benzene, phenanthrene, pyrene, coronene) have high-pressure modifications, but a correct description of their structures allowing calculation of their elastic moduli has not been made so far. The obtained data on PAH compressibility can be used to develop high-temperature equations of state and calculation of the equilibrium composition of liquid and solid components of the C–O–H system.Liu, B., Yuan, L., Shi, X., Li, Y., Jiang, C., Ren, B., Sun, Q., 2019. Variations in microbiota communities with the ranks of coals from three Permian mining areas. Energy & Fuels 33, 5243-5252. play vital roles in the biogeochemical processes, such as biomethane production, which is an important source of coal bed methane (CBM), that occur in coal beds. However, little information is available regarding the microbial communities in in situ coal beds of different ranks from Permian mining areas. In this study, anaerobic Biolog ECO microplates were used to determine the microbial metabolic activity, and high-throughput sequencing was used to investigate the bacteria and archaea communities in three typical mining areas. Anaerobic Biolog ECO microplates showed that the peak value of average well color development (AWCD) in low-rank coal seams from Anhui Province (A-L) was 0.46 higher than that of medium-rank coal from Shanxi Province (S-M). Phylogenetic analysis indicated that the bacterial phyla Proteobacteria, Firmicutes, and Actinobacteria were the predominant lineages in all samples, in particular, the family Oxalobacteraceae accounted for the overwhelming majority of the bacterial sequences (from 47.20 to 92.67%). Most of the identified genera, Herbaspirillum, Pseudomonas, and Acinetobacter, were fermentative bacteria that can convert coal macromolecules into methanol, acetic acid, and CO2. In addition, the archaea in A-L were dominated by the phyla Euryarchaeota, Thaumarchaeota, and Woesearchaeota. Additionally, Euryarchaeota was the dominant archaeal lineage in S-M, and Thaumarchaeota was predominant in the Guizhou Province group of high-rank coals (G-H). Canonical correspondence analysis (CCA) showed that there were significant correlations between the microbial community and porosity, hydrogen content, and oxygen content (p < 0.05). The KEGG pathway analysis indicated that biomethane production mainly depended on archaea and that the methane metabolism capacity of A-L coals was the highest. Overall, the results suggest that the diversities of the microbial communities were related to the porosity and chemical elements of the different ranks of coal.Liu, C., Yin, G., Li, M., Deng, B., Song, Z., Liu, Y., Yin, S., 2019. Shale permeability model considering bedding effect under true triaxial stress conditions. Journal of Natural Gas Science and Engineering 68, 102908. permeability anisotropy of shales can be attributed largely to bedding planes. It is critical to study the bedding effect on permeability evolution for shales. We conducted an experiment on shale permeability anisotropy under true triaxial stress conditions. Even though the mean stress of shales was different, the permeability still exhibits obvious bedding dependent. In this study, we present a new permeability model considering bedding planes. The introduction of characteristic functions and parameters characterizes the transformation process from bedding to non-bedding during compression. Compared with the experimental data, we obtained a good fitting result. Owing to the increase in the resistance of the pressurized gas into the fracture system, Biot's coefficient α decreases with increasing mean stress. The porosity sensitivity exponent s parallel to the bedding planes are larger than those perpendicular to the bedding planes. In our opinion, owing to the smaller stiffness of the bedding plane, the relatively large amount of pore deformation is caused by the loading on the vertical bedding planes. Furthermore, we introduce η to characterize the effect of non-bedding and bedding on permeability. The permeability of shale or bedding is more sensitive at lower stress than at higher stress and the fluid flow through the non-bedding in shales cannot be ignored.Liu, H., Meng, G., Li, W., Gu, T., Liu, H., 2019. Microbiologically influenced corrosion of carbon steel beneath a deposit in CO2-saturated formation water containing Desulfotomaculum nigrificans. Frontiers in Microbiology 10, 1298. doi: 10.3389/fmicb.2019.01298. corrosion mechanism of carbon steel under deposit in the presence of sulfate reducing bacterium (SRB) Desulfotomaculum nigrificans was studied using surface analysis, weight loss and electrochemical measurements. Results showed that both the general corrosion and localized corrosion were considerably promoted by SRB under deposit. The uniform corrosion rate of steel in the presence of SRB was approximately 6 times of that for the control according to the weight loss measurements. The maximum corrosion pit depth in the presence of SRB was approximately 7.7 times of that of the control. Both the anodic and cathodic reactions were significantly accelerated by SRB. A galvanic effect in the presence of SRB due to the heterogeneous biofilm led to serious localized corrosion.Liu, J.-F., Zhang, K., Liang, B., Zhou, Z.-C., Yang, S.-Z., Li, W., Hou, Z.-W., Wu, X.-L., Gu, J.-D., Mu, B.-Z., 2019. Key players in the methanogenic biodegradation of n-hexadecane identified by DNA-Stable isotope probing. International Biodeterioration & Biodegradation 143, 104709. biodegradation of n-alkanes is an important process in the biogeochemical carbon cycles. The key players in this biochemical processes were investigated for a 920-day of culturing with universally labelled (UL)-13C-hexadecane and 1, 2-13C-hexadecane as the sources of carbon and energy, using stable isotope probing combined with 16S rRNA gene amplification. Results show that the relative abundance of Anaerolineaceae and Tepidiphilus phylotypes increased significantly in the heavy fractions of DNA obtained from the cultures amended with UL-13C-hexadecane and 1, 2-13C-hexadecane, indicating their actively involvement in the transformation and biodegradation of the alkanes by the microbial community. This study provides insights into the active members of the microbial community members in hydrocarbon degradation and is of significant scientific value in further research and relative technology to methanogenic degradation of n-alkanes.Liu, J., Haeckel, M., Rutqvist, J., Wang, S., Yan, W., 2019. The mechanism of methane gas migration through the gas hydrate stability zone: Insights from numerical simulations. Journal of Geophysical Research: Solid Earth 124, 4399-4427. gas migration through the gas hydrate stability zone (GHSZ) and subsequent gas seepage at the seabed are characteristic features in marine gas hydrate provinces worldwide. The biogenic or thermogenic gas is typically transported along faults from deeper sediment strata to the GHSZ. Several mechanisms have been proposed to explain free gas transport through the GHSZ. While inhibition of hydrate formation by elevated salinities and temperatures have been addressed previously in studies simulating unfocused, area-wide upward advection of gas, which is not adequately supported by field observations, the role of focused gas flow through chimney-like structures has been underappreciated in this context. Our simulations suggest that gas migration through the GHSZ is, fundamentally, a result of methane gas supply in excess of its consumption by hydrate formation. The required high gas flux is driven by local overpressure, built up from gas accumulating below the base of the GHSZ that fractures the overburden when exceeding a critical pressure, thereby creating the chimney-like migration pathway. Initially rapid hydrate formation raises the temperature in the chimney structure, thereby facilitating further gas transport through the GHSZ. As a consequence, high hydrate saturations form preferentially close to the seafloor, where temperatures drop to bottom water values, producing a prominent subsurface salinity peak. Over time, hydrates form at a lower rate throughout the chimney structure, while initial temperature elevation and salinity peak dissipate. Thus, our simulations suggest that the near-surface salinity peak and elevated temperatures are a result of transient high-flux gas migration through the GHSZ.Liu, J., Lu, D., Li, P., 2019. Nano-scale dual-pore-shape structure and fractal characteristics of transitional facies shale matrix. Journal of Natural Gas Science and Engineering 68, 102907. pore structure and fractal characteristics are significant information to understand shale gas reservoirs. Therefore, seventeen marine-continental transitional shale samples of Leping Formation in Qingjiang Basin, southeast China were investigated to study the potential relationship between pore structure and fractal characteristics. In this work, a dual-pore-shape method was firstly applied to construct pore structure in the shapes of cylinder and slit, which is closer to reality. Meanwhile, non-local density function theory method and Barrett-Joyner-Halenda method were employed for comparison as well. Fractal dimensions obtained from nitrogen isotherms via Frenkel-Halsey-Hill method were divided into two parts, one characterizes larger pores and the other characterizes smaller pores. Geochemical index, pore structure information, and fractal characteristics showed different correlated behaviors with each other. Total organic carbon content strongly affects pore structure of transitional shale, but clay and quartz content have no clear influence. Correlations between fractal dimensions and geochemical parameters were affected by the degree of isotropy. Pore parameters have conspicuous relationships with the fractal dimension of larger pores but not with that of smaller pores. It is found that slit pores play a significant role in pore space in shale matrix. Moreover, the connections between different shapes of pores and fractal dimensions are displayed. Pore volume of cylindrical pores positively correlates with fractal dimension of larger pores, whereas pore volume of slit pores negatively correlates with fractal dimension of smaller pores. The comparison of all pore parameters obtained by different methods shows that dual-pore-shape method could better construct real pore structure and obtain the pore volume distributions more accurately.Liu, L., Wang, J., Levin, M.J., Sinnott-Armstrong, N., Zhao, H., Zhao, Y., Shao, J., Di, N., Zhang, T.e., 2019. The origins of specialized pottery and diverse alcohol fermentation techniques in Early Neolithic China. Proceedings of the National Academy of Sciences 116, 12767-12774.: China is well-known for its distinctive techniques in alcohol fermentation. Here we present archaeological evidence of alcohol making based on analyses of starch granules, phytoliths, and fungi in food residues adhering to 8,000- to 7,000-y-old Neolithic pottery vessels. We demonstrate the earliest association between the wide occurrences of globular jars as liquid storage vessels and the development of two methods of alcohol making: use of cereal malts and use of moldy grain and herbs as starters. The latter method was arguably a unique invention initiated in China. Neolithic people made low-alcohol beverages with broomcorn millet, Triticeae grasses, Job’s tears, rice, beans, snake gourd root, ginger, yam, lily, and so forth. Such fermented beverages may have served social, spiritual, and medicinal functions.Abstract: In China, pottery containers first appeared about 20000 cal. BP, and became diverse in form during the Early Neolithic (9000–7000 cal. BP), signaling the emergence of functionally specialized vessels. China is also well-known for its early development of alcohol production. However, few studies have focused on the connections between the two technologies. Based on the analysis of residues (starch, phytolith, and fungus) adhering to pottery from two Early Neolithic sites in north China, here we demonstrate that three material changes occurring in the Early Neolithic signal innovation of specialized alcoholic making known in north China: (i) the spread of cereal domestication (millet and rice), (ii) the emergence of dedicated pottery types, particularly globular jars as liquid storage vessels, and (iii) the development of cereal-based alcohol production with at least two fermentation methods: the use of cereal malts and the use of moldy grain and herbs (qu and caoqu) as starters. The latter method was arguably a unique invention initiated in China, and our findings account for the earliest known examples of this technique. The major ingredients include broomcorn millet, Triticeae grasses, Job’s tears, rice, beans, snake gourd root, ginger, possible yam and lily, and other plants, some probably with medicinal properties (e.g., ginger). Alcoholic beverages made with these methods were named li, jiu, and chang in ancient texts, first recorded in the Shang oracle-bone inscriptions (ca. 3200 cal. BP); our findings have revealed a much deeper history of these diverse fermentation technologies in China.Liu, S.-A., Li, S.-G., 2019. Tracing the deep carbon cycle using metal stable isotopes: Opportunities and challenges. Engineering 5, 448-457. subduction of marine carbonates and carbonated oceanic crust to the Earth’s interior and the return of recycled carbon to the surface via volcanism may play a pivotal role in governing Earth’s atmosphere, climate, and biosphere over geologic time. Identifying recycled marine carbonates and evaluating their fluxes in Earth’s mantle are essential in order to obtain a complete understanding of the global deep carbon cycle (DCC). Here, we review recent advances in tracing the DCC using stable isotopes of divalent metals such as calcium (Ca), magnesium (Mg), and zinc (Zn). The three isotope systematics show great capability as tracers due to appreciable isotope differences between marine carbonate and the terrestrial mantle. Recent studies have observed anomalies of Ca, Mg, and Zn isotopes in basalts worldwide, which have been interpreted as evidence for the recycling of carbonates into the mantle, even into the mantle transition zone (410–660 km). Nevertheless, considerable challenges in determining the DCC remain because other processes can potentially fractionate isotopes in the same direction as expected for carbonate recycling; these processes include partial melting, recycling of carbonated eclogite, separation of metals and carbon, and diffusion. Discriminating between these effects has become a key issue in the study of the DCC and must be considered when interpreting any isotope anomaly of mantle-derived rocks. An ongoing evaluation on the plausibility of potential mechanisms and possible solutions for these challenges is discussed in detail in this work. Based on a comprehensive evaluation, we conclude that the large-scale Mg and Zn isotope anomalies of the Eastern China basalts were produced by recycling of Mg- and Zn-rich carbonates into their mantle source.Liu, T., Chen, D., Luo, X., Li, X., Li, F., 2019. Microbially mediated nitrate-reducing Fe(II) oxidation: Quantification of chemodenitrification and biological reactions. Geochimica et Cosmochimica Acta 256, 97-115. reactions between iron and nitrogen drive the global biogeochemical cycles of these two elements and, concomitantly, change the fate of nutrients in and the mineralogy of the cycles. The microbially mediated NO3? -reducing Fe(II) oxidation process (NRFO) plays a key role in Fe/N interactions under neutral-anoxic conditions. Microbially mediated NRFO was considered a biological process, yet recently it has been documented that chemical mechanisms are also at play. However, the relative contributions of biological processes and chemical processes to Fe(II) oxidation remain largely unquantified owing to the co-occurrence of the reactions. Herein, the kinetics and secondary minerals of microbially mediated NRFO by Pseudogulbenkiania sp. strain 2002 and Acidovorax sp. strain BoFeN1 were investigated with acetate as electron donor unless otherwise stated. The results of Cells?+?NO3? suggested the two strains could biologically reduce NO3? to NO3?/NOx/N2O/N2 and concomitantly oxidize acetate and result in cell growth. Fe(II) oxidation and NO3? reduction occurred simultaneously in the presence of Fe(II) (Cells?+?Fe(II)?+?NO3?). For strain BoFeN1, the presence of Fe(II) slightly enhanced the NO3?reduction, acetate consumption, and cell growth, all of which were substantially retarded by Fe(II) for strain 2002. When compared with the microbial nitrite reduction, the relatively higher rate of chemical reaction between NO2? and dissolved Fe(II) confirmed the occurrence of chemodenitrification in the microbially mediated NRFO processes. After 5?days’ incubation, no green rust was observed, and lepidocrocite, goethite, and magnetite were observed with the Cells?+?Fe(II)?+?NO3? treatment, but only goethite was found with the Fe(II)?+?NO2? . The spectra for the EPSs?+?Fe(II) treatment suggested that the oxidized c-Cyts in the EPSs could oxidize Fe(II), which show the theoretical capability of taking electrons from Fe(II) into the cells via c-Cyts. A brief model was established by combining the verified reactions of (1) biological reduction of NO3? to NO2?/NOx/N2O/N2, (2) Fe(II) oxidation by NO2?, and (3) Fe(II) oxidation by c-Cyts in EPSs. Based on the model, the rate constant of Fe(II) oxidation by c-Cyts in EPSs was derived. For nitrite reduction, the relative contribution of biological processes to the nitrite reduction was higher than that of chemodenitrification. For Fe(II) oxidation, the relative contribution of the chemical process via nitrite to Fe(II) oxidation was higher than that of biological processes. These findings provide a quantitative interpretation of the chemodenitrification and biological reactions in the microbially mediated NRFO processes, which could assist the mechanistic understanding of the global biogeochemical cycles of iron and nitrogen in subsurface environments.Liu, X., Zhang, D., 2019. A review of phase behavior simulation of hydrocarbons in confined space: Implications for shale oil and shale gas. Journal of Natural Gas Science and Engineering 68, 102901. oil field development, phase behavior would influence fluid components and mobility, thus affecting production. As a fine-grained sedimentary rock, shale brings difficulties to observing and modelling fluid behavior in similar ways to conventional reservoir experiments and simulations due to the abundance of nanometer-sized pores. Confined in nanopores, hydrocarbons exhibit largely different phase behavior in shale reservoirs. Limited experiments showed the shifts of phase envelopes, heterogeneous density profiles, and decreasing fluid viscosity. There exist controversies concerning bubblepoint deviation and critical density shift. Based on experimental observations, various computational methods are proposed to simulate phase behavior in confined spaces. These methods can be classified as either molecular simulation methods or varieties of equation of state. This article presents a review of the deviated phase behaviors of hydrocarbons in confined space and approaches to modelling them. Comparisons are made among different models. This article also proposes some promising research directions for future simulation models of shale oil and shale gas reservoirs.Liu, Y., Ma, X., Hou, J., 2019. Comparing the effectiveness of SO2 with CO2 for replacing hydrocarbons from nanopores. Energy & Fuels 33, 5200-5207. dynamic simulation is employed to investigate the fluid distribution of pure hydrocarbons, i.e., C1, C2, nC3, nC4, and nC5, in a hydrocarbon-wetting nanopore. SO2 and CO2 are then introduced into this nanopore to explore how SO2 and CO2 affect the hydrocarbon adsorption in an organic pore. Adsorption selectivity and replacement efficiency of SO2 over hydrocarbons are subsequently calculated and compared with those of CO2. The performance of SO2 and CO2 in enhancing hydrocarbon recovery from nanopores is thus evaluated. After introducing SO2 or CO2 into the “hydrocarbon-saturated” pore, the density of hydrocarbons in the adsorption layer decreases, while the density in the pore center increases. It suggests that both SO2 and CO2 can replace the adsorbed hydrocarbons from the pore surface. In addition, higher adsorption capacity is observed for CO2 than that for C1 but smaller than those of the heavier hydrocarbons, i.e., 2, nC3, nC4, and nC5,5. Comparatively, SO2 exhibits a stronger adsorption capacity than C1, C2, nC3 and nC4,, suggesting its potential for enhancing the recovery of heavier hydrocarbons from organic pores. We expect this strategy will inspire new perspectives for flue-gas treatment and recovery of shale resources using flue-gas injection.Liu, Y., Nielsen, J., 2019. Recent trends in metabolic engineering of microbial chemical factories. Current Opinion in Biotechnology 60, 188-197. chemical production can replace traditional fossil-dependent production and hereby ensure sustainable production of chemicals that are important for our society. Significant success in economical chemical bioproduction has been accomplished by improving the cellular properties of microbial cells through metabolic engineering. The emergence of new techniques and strategies has led to a significant reduction in the turnaround time in the classic design-build-test-learn (DBTL) cycle in metabolic engineering. Here, we summarize the recent achievements and trends in microbial production of chemicals, with a focus on biofuels and high-value natural compounds. In addition, we offer perspectives on the challenges and opportunities for the successful establishment of future microbial chemical factories.Liu, Y., Qiu, N., Hu, W., Li, H., Shen, F., Yao, Q., 2019. Temperature and pressure characteristics of Ordovician gas condensate reservoirs in the Tazhong area, Tarim Basin, northwestern China. American Association of Petroleum Geologists Bulletin 103, 1351-1381. paper investigates the temperature and pressure distribution characteristics and their evolution in the Upper Ordovician strata in the Tazhong area, Tarim Basin, northwestern China. Based on hundreds of temperature data from boreholes, the present-day temperature ranges from 100°C to 130°C, increasing from the southeast to the northwest and having a “cool” belt in the central fault horst. Pore pressures in the Upper Ordovician reservoirs range from 35 to 62 MPa (5076 to 8992 psi). Overpressures developed in the southwestern region and along the eastern segment of the central fault horst to the northern slope. The Lower Ordovician reservoirs in the east reached 140°C during the Late Ordovician, but those in the west heated continuously and reached the maximum temperature (>130°C) during present day. Paleopressures reconstructed from fluid inclusion data indicate that overpressures caused by hydrocarbon generation were formed in the areas away from fault belts but were absent in the area around the no. 1 fault belt. The temperature evolution indicates that the middle?lower Cambrian source rocks reached gas generation stage (vitrinite reflectance [Ro] > 2.0%) at the end of the Ordovician, whereas the Middle?Upper Ordovician source rocks are still in the high-maturity stage (Ro < 1.3%) at the present day. Deep oil and gas migration is driven by overpressure, and commercial reservoirs are predominantly distributed in the normally pressured zones along the no. 1 fault belt. The formation of gas condensate is controlled by specific temperature and pressure characteristics.Liu, Z., Song, Y., Liu, W., Lang, C., Zhao, J., Li, Y., 2019. Formation of methane hydrate in oil–water emulsion governed by the hydrophilic and hydrophobic properties of non-ionic surfactants. Energy & Fuels 33, 5777-5784. oil and gas production moves into deep water, the formation of gas hydrate has been a primary flow assurance challenge in the deep water pipelines. Because of the complex composition of crude oil and various additives, the objective of this work is to study the effect of additive hydrophilic–hydrophobic property on hydrate formation in the emulsion, which usually occurs in pipelines. The formation experiments of methane hydrate in emulsion with the same water cut but surfactants of different hydrophilic lipophilic balance (HLB) values were conducted. The emulsion was prepared with mineral oil, deionized water, and two types of non-ionic surfactants (Span 80 and Tween 80). The experimental results indicate that with the HLB value increasing, the emulsion was divided into relatively stable water-in-oil, the phase transition region, and stable oil-in-water; meanwhile, the effect of the hydrophobic surfactant on hydrate formation also changed from inhibition to promotion to inhibition. In addition, hydrate formation is closely related to pressure, temperature, and stirring speed. The higher the pressure and the lower the temperature, the easier the methane hydrate formation. The increase of stirring speed within a certain range (less than 300 rpm) could significantly shorten the induction time of methane hydrate formation and accelerate the formation rate. As the stirring speed continued to rise to 500 rpm, the induction time of methane hydrate formation became longer, but the formation rate had a significant acceleration.Llanos, E.J., Leal, W., Luu, D.H., Jost, J., Stadler, P.F., Restrepo, G., 2019. Exploration of the chemical space and its three historical regimes. Proceedings of the National Academy of Sciences 116, 12660-12665.: We found that the number of new chemical compounds has grown exponentially with a 4.4% annual production rate from 1800 to 2015 not even affected by World Wars. There are three distinct growth regimes: proto-organic, organic, and organometallic, with decreasing variability in the production of compounds over time. Contrary to the belief that organic synthesis developed only after 1828, synthesis had been a key provider of new compounds already at the beginning of the 19th century. By 1900, it became the established tool to report new compounds. We found that chemists are conservative when selecting starting materials and that despite the growing production of new compounds, most of them belong to a restricted set of chemical compositions.Abstract: Chemical research unveils the structure of chemical space, spanned by all chemical species, as documented in more than 200 y of scientific literature, now available in electronic databases. Very little is known, however, about the large-scale patterns of this exploration. Here we show, by analyzing millions of reactions stored in the Reaxys database, that chemists have reported new compounds in an exponential fashion from 1800 to 2015 with a stable 4.4% annual growth rate, in the long run neither affected by World Wars nor affected by the introduction of new theories. Contrary to general belief, synthesis has been the means to provide new compounds since the early 19th century, well before W?hler’s synthesis of urea. The exploration of chemical space has followed three statistically distinguishable regimes. The first one included uncertain year-to-year output of organic and inorganic compounds and ended about 1860, when structural theory gave way to a century of more regular and guided production, the organic regime. The current organometallic regime is the most regular one. Analyzing the details of the synthesis process, we found that chemists have had preferences in the selection of substrates and we identified the workings of such a selection. Regarding reaction products, the discovery of new compounds has been dominated by very few elemental compositions. We anticipate that the present work serves as a starting point for more sophisticated and detailed studies of the history of chemistry.Loh, A., Shankar, R., Ha, S.Y., An, J.G., Yim, U.H., 2019. Suspended particles enhance biodegradation of oil in sea. Science of The Total Environment 685, 324-331. patterns of oil in four distinct phases were compared over a 14-day series of exposures. The dispersibility and stability of oil droplets in the water column were important factors affecting oil biodegradation. Due to the stability of oil droplets with particle interactions, oil-suspended particulate matter aggregates (OSA) showed a five-fold enhancement in biodegradation compared to non-dispersed oil. The reduction of total petroleum hydrocarbons was highest in OSA (51.45%), followed by chemically dispersed oil (33.5%), oil film (21.6%), and water-accommodated fractions (WAF, 14.3%). Polycyclic aromatic hydrocarbon (PAH) profiles and percentage weathering plots showed that reductions in PAHs in WAF, oil film, and chemically dispersed oil were mainly due to evaporation (41.5–69.5%) and only partially due to biodegradation (7.4–16.3%). However, the reduction of PAHs in OSA was driven more by biodegradation (36.8%) than evaporation (29.7%). The strong PAH–particle interactions in OSA inhibited evaporation of PAHs and enhanced microorganism biodegradation in the water column.López-García, P., Moreira, D., 2019. Eukaryogenesis, a syntrophy affair. Nature Microbiology 4, 1068-1070. evolved from a symbiosis involving Alphaproteobacteria and archaea phylogenetically nested within the Asgard clade. Two recent studies explore the metabolic capabilities of Asgard lineages, supporting refined symbiotic metabolic interactions that might have operated at the dawn of eukaryogenesis.López-Ruiz, R., Romero-González, R., Garrido Frenich, A., 2019. Ultrahigh-pressure liquid chromatography-mass spectrometry: An overview of the last decade. TrAC Trends in Analytical Chemistry 118, 170-181. the last years, advances in ultra-high performance liquid chromatography (UHPLC) coupled to mass spectrometry (MS) have been increased exponentially. This technique has been widely used by both research and routine laboratories, decreasing the cost and time of analysis, and increasing sample throughput. This review is focused on the main advances of UHPLC-MS in the last decade, describing the pros and cons of its use coupled to both Low Resolution Mass Spectrometry (LRMS) and High Resolution Mass Spectrometry (HRMS), and the main applications. Targeted analyses have been carried out by UHPLC-LRMS, but other approaches, screening or unknown analyses, have also been performed with HRMS. New advances in UHPLC-MS are also discussed, introducing techniques as two dimensional chromatography (2D-LC), ion mobility separation (IMS) and supercritical fluid chromatography (SFC). The coupling of LC with automated extraction techniques ,as on-line solid phase extraction (SPE) and turbulent flow chromatography (TurboFlow?), has also been evaluated.López, L., Lo Mónaco, S., Kalkreuth, W., Peralba, M.d.C.R., 2019. Assessment of the depositional environment and source rock potential of Permian shales, siltstones and coal seams from the Santa Terezinha Coalfield, Paraná Basin, Brazil. Journal of South American Earth Sciences 94, 102227., shale and siltstone samples from the Serra Alta, Irati, Palermo and Rio Bonito formations (Early Permian: Kungarian, Artinskian and Sakmarian) were collected from borehole CBM001-ST-RS (core ST) over a depth range from 496.40 to 637.75?m. This core was evaluated by geochemical parameters to identify organic matter type, depositional environment and hydrocarbon generation potential. The effects of igneous intrusion on the maturity parameters from the shale and carbonaceous shale from Rio Bonito Formation between 605.45 and 610.90?m were also evaluated. Regardless the geological formation, the mineralogical composition along the ST core shows few variations in quartz, Na-plagioclase, illite, kaolinite, carbonates such as calcite and ankerite and some contributions of pyrite. Samples are characterized by a predominance of terrigenous organic matter and the evaluation of the depositional environment indicates two types: fluvial-deltaic environment, where the organic matter was subjected to suboxic or periodically dysoxic conditions, and marine environment related to source rocks deposited under anoxic conditions. All samples are at present time at a maturity near the peak of the oil window (except samples in contact or near igneous intrusions), and have poor to fair hydrocarbon generative potential. In the stratigraphic interval of the Rio Bonito Formation, specifically in samples close to diabase intrusions (coal seam ST-5 and shale ST-6), TOC, bitumen, and SARA composition showed significant variations that are probably caused by the contact with igneous intrusions. In this interval, saturated biomarkers did not represent values indicating an advanced maturity degree. They seem not having reached their equilibrium or endpoint values of maturity. This behavior is attributed to the development of rapid heating rates probably caused by high temperatures associated with the diabase intrusions. However, aromatic hydrocarbon ratios such as the methylphenanthrene index (MPI-1 and MPI-1(modified)) and methyldibenzothiophene ratio (MDR) did show maturity trends that agree with reported vitrinite reflectance determinations in the contact zones with igneous rocks. As a result, these parameters may be used to identify maturity levels in areas with igneous activity.Loron, C.C., Fran?ois, C., Rainbird, R.H., Turner, E.C., Borensztajn, S., Javaux, E.J., 2019. Early fungi from the Proterozoic era in Arctic Canada. Nature 570, 232–235. are crucial components of modern ecosystems. They may have had an important role in the colonization of land by eukaryotes, and in the appearance and success of land plants and metazoans. Nevertheless, fossils that can unambiguously be identified as fungi are absent from the fossil record until the middle of the Palaeozoic era. Here we show, using morphological, ultrastructural and spectroscopic analyses, that multicellular organic-walled microfossils preserved in shale of the Grassy Bay Formation (Shaler Supergroup, Arctic Canada), which dates to approximately 1,010–890?million years ago, have a fungal affinity. These microfossils are more than half a billion years older than previously reported unambiguous occurrences of fungi, a date which is consistent with data from molecular clocks for the emergence of this clade. In extending the fossil record of the fungi, this finding also pushes back the minimum date for the appearance of eukaryotic crown group Opisthokonta, which comprises metazoans, fungi and their protist relatives8,9.Louca, S., Scranton, M.I., Taylor, G.T., Astor, Y.M., Crowe, S.A., Doebeli, M., 2019. Circumventing kinetics in biogeochemical modeling. Proceedings of the National Academy of Sciences 116, 11329-11338.: Predicting biochemical processes driven by microbes in the environment remains challenging, because the “kinetic” parameters conventionally used to predict reaction rates are usually poorly known. Here we mathematically show that in poorly mixed systems, such as stagnant waters, bulk biochemical reaction rates can become limited by the slow transport of substrates across space and essentially independent of kinetic parameters. We demonstrate our arguments for a large and heavily studied ocean basin, where we accurately predict the microbially driven fluxes of various substances, across a depth range of hundreds of meters. Our work opens up avenues for predicting ecosystem processes without knowledge of kinetic parameters and without laborious chemical profile measurements.Abstract: Predicting biochemical processes driven by microbes in the environment remains challenging, because the “kinetic” parameters conventionally used to predict reaction rates are usually poorly known. Here we mathematically show that in poorly mixed systems, such as stagnant waters, bulk biochemical reaction rates can become limited by the slow transport of substrates across space and essentially independent of kinetic parameters. We demonstrate our arguments for a large and heavily studied ocean basin, where we accurately predict the microbially driven fluxes of various substances, across a depth range of hundreds of meters. Our work opens up avenues for predicting ecosystem processes without knowledge of kinetic parameters and without laborious chemical profile measurements.Microbial metabolism drives biogeochemical fluxes in virtually every ecosystem. Modeling these fluxes is challenged by the incredible diversity of microorganisms, whose kinetic parameters are largely unknown. In poorly mixed systems, such as stagnant water columns or sediments, however, long-term bulk microbial metabolism may become limited by physical transport rates of substrates across space. Here we mathematically show that under these conditions, biogeochemical fluxes are largely predictable based on the system’s transport properties, chemical boundary conditions, and the stoichiometry of metabolic pathways, regardless of the precise kinetics of the resident microorganisms. We formalize these considerations into a predictive modeling framework and demonstrate its use for the Cariaco Basin subeuphotic zone, one of the largest anoxic marine basins worldwide. Using chemical concentration data solely from the upper boundary (depth 180 m) and lower boundary (depth 900 m), but without a priori knowledge of metabolite fluxes, chemical depth profiles, kinetic parameters, or microbial species composition, we predict the concentrations and vertical fluxes of biologically important substances, including oxygen, nitrate, hydrogen sulfide, and ammonium, across the entire considered depth range (180–900 m). Our predictions largely agree with concentration measurements over a period of 14 years (R2 = 0.78–0.92) and become particularly accurate during a period where the system was near biogeochemical steady state (years 2007–2009, R2 = 0.86–0.95). Our work enables geobiological predictions for a large class of ecosystems without knowledge of kinetic parameters or geochemical depth profiles. Conceptually, our work provides a possible explanation for the decoupling between microbial species composition and bulk metabolic function, observed in various ecosystems.Louvado, A., Coelho, F.J.R.C., Oliveira, V., Gomes, H., Cleary, D.F.R., Sim?es, M.M.Q., Cunha, A., Gomes, N.C.M., 2019. Microcosm evaluation of the impact of oil contamination and chemical dispersant addition on bacterial communities and sediment remediation of an estuarine port environment. Journal of Applied Microbiology 127, 134-149.: To evaluate the interactive effects of oil contamination and chemical dispersant application on bacterial composition and sediment remediation of an estuarine port environment.Methods and Results: A multifactorial controlled microcosm experiment was set up using sediment cores retrieved from an estuarine port area located at Ria de Aveiro lagoon (Aveiro, Portugal). An oil spill with and without chemical dispersant addition was simulated. Sediment oil hydrocarbon concentrations and benthic bacterial community structure were evaluated by GC‐MS and 16S rRNA high‐throughput sequencing respectively. Although initially (first 10 days) chemical dispersion of oil enhanced the concentrations of the heavier polycyclic aromatic hydrocarbons and of the C22‐C30 alkane group, with time (21 days), no significant differences in hydrocarbon concentrations were detected among treatments. Moreover, no significant changes were detected in the structure of sediment bacterial communities, which mainly consisted of operational taxonomic units related to hydrocarbon‐contaminated marine environments. We hypothesize that the environmental background of the sampling site preconditioned the communities’ response to additional contamination. Conclusion: This experimental microcosm study showed that the chemical dispersion of oil did not influence sediment remediation or bacterial community composition.Significance and Impact of the Study: Our study showed that chemical dispersion of oil may not improve the remediation of port sediments. Further studies are needed to investigate the impact of chemical dispersants in combination with bioremediation strategies on the process of sediment remediation in port areas.Lovatti, B.P.O., Silva, S.R.C., Portela, N.d.A., Sad, C.M.S., Rainha, K.P., Rocha, J.T.C., Rom?o, W., Castro, E.V.R., Filgueiras, P.R., 2019. Identification of petroleum profiles by infrared spectroscopy and chemometrics. Fuel 254, 115670. petroleum industry has the interest to know the physicochemical properties of the crude oil before its exploration in order to estimate its costs with processing, transportation, storage and refining. The profile of the recovered oil is determined by the analysis of some physicochemical properties, which may require a long time or a large volume of the sample, delaying decision-making on production and refining. Spectroscopic techniques allow the acquisition of a large amount of information about the sample at a molecular level, in a short time, and with a small amount of sample. This paper aims to identify petroleum profiles using a spectroscopy technique in the middle infrared region associated with methods of standards recognition PCA and kNN. We used 81 oils, divided into two groups: 69 samples of the training set (model construction) and 12 samples of the test set (model performance verification). For all samples, MIR spectra were acquired and measurements of 13 physicochemical properties were obtained. The results show that the methodology using MIR spectroscopy with chemometrics makes it possible to obtain equivalent conclusions about the most similar crude oils, that is, with similar behaviors, when we analyze a database with 13 physicochemical properties of the crude oils.Lowery, C.M., Fraass, A.J., 2019. Morphospace expansion paces taxonomic diversification after end Cretaceous mass extinction. Nature Ecology & Evolution 3, 900-904. resolved palaeontological records can address a key question about our current climate crisis: how long will it be before the biosphere rebounds from our actions? There are many ways to conceptualize the recovery of the biosphere; here, we focus on the global recovery of species diversity. Mass extinction may be expected to be followed by rapid speciation, but the fossil record contains many instances where speciation is delayed—a phenomenon about which we have a poor understanding. A probable explanation for this delay is that extinctions eliminate morphospace as they curtail diversity, and the delay in diversification is a result of the time needed for new innovations to rebuild morphospace, which can then be filled out by new species. Here, we test this morphospace reconstruction hypothesis using the morphological complexity of planktic foraminifer tests after the Cretaceous–Palaeogene mass extinction. We show that increases in complexity precede changes in diversity, indicating that plankton are colonizing new morphospace, then slowly filling it in. Preliminary diversification is associated with a rapid increase in the complexity of groups refilling relict Cretaceous ecospace. Subsequent jumps in complexity are driven by evolutionary innovations (development of spines and photosymbionts), which open new niche space. The recovery of diversity is paced by the construction of new morphospace, implying a fundamental speed limit on diversification after an extinction event.Lu, Y., Jiang, S., Lu, Y., Xu, S., Shu, Y., Wang, Y., 2019. Productivity or preservation? The factors controlling the organic matter accumulation in the late Katian through Hirnantian Wufeng organic-rich shale, South China. Marine and Petroleum Geology 109, 22-35. Wufeng organic-rich shale is widespread in the Upper Yangtze platform, and it is one of the most advantageous shale gas producers in China. Its deposition commenced with the onset of the Boda warming event in the late Katian and terminated at the Hirnantian glacial maximum. The depositional mechanism of the Wufeng Formation was poorly understood owing to its relatively thin thickness, being interpreted as the result of organic matter (OM) accumulation in a shelf setting under anoxic conditions. This study integrated detailed geochemical analyses based on the core samples from three boreholes which are located in the outer-, middle- and inner-shelf of the Upper Yangtze platform, in order to investigate the depositional environments during the deposition of the Wufeng Formation. Geochemical redox proxies (Mo-EF, U-EF, and V/Cr) and productivity proxies (P, Baxs, Sixs) indicate that the deposition of the Wufeng Formation was associated with four intervals (WF1 to WF4), each characterized by its unique geochemical features related to sea-level fluctuations. Black siliceous mudstones deposited during WF1 and WF2 are relatively organic-lean due to low productivity, less favorable preservation conditions, and terrestrial dilution. Whereas black siliceous mudstone deposited during WF3 and WF4 is organic-rich due to high paleoproductivity and conducive preservation conditions. The geochemical proxies (Cd/Mo, Co x Mn) associated with the modern upwelling settings were replicated in the Wufeng Formation, revealing that the outer-shelf of the Upper Yangtze platform was dominated by persistent upwelling. The upwelling-driven primary productivity is considered as the first-order control for the OM enrichment at the outer-shelf of the Upper Yangtze platform. Seasonal upwelling may influence the middle-shelf of the Upper Yangtze Platform, where both primary productivity and preservation played essential roles in the OM accumulation. In contrast, the OM accumulation at the inner-shelf was fundamentally driven by good preservation conditions.Lubecki, L., Kowalewska, G., 2019. Plastic-derived contaminants in sediments from the coastal zone of the southern Baltic Sea. Marine Pollution Bulletin 146, 255-262. may leach out harmful chemicals, such as plastic additives and monomers, to the environment. This study focused on three intrinsic plastic-derived contaminants, viz. bis(2-ethylhexyl) phthalate (DEHP), bisphenol A (BPA), and styrene, based on surface (0–5?cm) sediment samples taken from transition areas located in the human-impacted coastal zone of the southern Baltic Sea. The concentrations of DEHP in the sediments from the Gulf of Gdańsk and the Szczecin Lagoon ranged from 38 to 228?ng/g d.w. and from 494 to 807?ng/g d.w., respectively. The levels of sedimentary BPA varied from <1 to 32?ng/g d.w., whereas styrene was not detected in any of the samples studied. Compared to worldwide data, the levels of plastic-derived contaminants in the sediments from the Gulf of Gdańsk and the Szczecin Lagoon were generally not high. However, according to sediment quality guidelines, some adverse environmental effects are probable.Lugli, F., Cipriani, A., Capecchi, G., Ricci, S., Boschin, F., Boscato, P., Iacumin, P., Badino, F., Mannino, M.A., Talamo, S., Richards, M.P., Benazzi, S., Ronchitelli, A., 2019. Strontium and stable isotope evidence of human mobility strategies across the Last Glacial Maximum in southern Italy. Nature Ecology & Evolution 3, 905-911. the reason(s) behind changes in human mobility strategies through space and time is a major challenge in palaeoanthropology. Most of the time this is due to the lack of suitable temporal sequences of human skeletal specimens during critical climatic or cultural shifts. Here, we present temporal variations in the Sr isotope composition of 14 human deciduous teeth and the N and C stable isotope ratios of four human remains from the Grotta Paglicci site (Apulia, southern Italy). The specimens were recovered from the Gravettian and Epigravettian layers, across the Last Glacial Maximum, and dated between 31210–33103 and 18334–19860 yr cal bp (2σ). The two groups of individuals exhibit different 87Sr/86Sr ratios and, while the Gravettians are similar to the local macro-fauna in terms of Sr isotopic signal, the Epigravettians are shifted towards higher radiogenic Sr ratios. These data, together with stable isotopes, can be explained by the adoption of different mobility strategies between the two groups, with the Gravettians exploiting logistical mobility strategies and the Epigravettians applying residential mobility.Luo, C., Reitner, J., 2019. Three-dimensionally preserved stem-group hexactinellid sponge fossils from lower Cambrian (Stage?2) phosphorites of China. PalZ 93, 187-194., in situ preserved sponge fossils were collected from the phosphorites at the basal Niutitang Formation (Cambrian Stage 2) in Hunan Province, China. These fossils are preserved as nodular bodies in authigenic carbonaceous cherty Ca-phosphorites. Spicules are either completely embedded in cryptocrystalline phosphate or immediately overgrown by early isopachous phosphate cements, leaving the remaining interspace filled by other deposits. Two specimens are described in detail as examples. One is composed of hexactins of at least three size-hierarchies, the small spicules in which may be interpreted as microscleres. The other, investigated using grinding tomography, shows a skeletal frame composed of pentactins, hexactins, and diactins. These spicules exhibit a weak pattern of perpendicular orientation in 3D space and a possible differentiation of hypodermalia and parenchymalia. These skeletal architectures belong to new taxonomic groups and seem to represent very basic forms of hexactinellids. Disarticulated spicules scattered in other parts of the investigated phosphorites indicate a still unexplored diversity of the fossil community, and some show combined features, which were regarded characteristic and mutually exclusive in living hexactinellids and demosponges. This work suggests that the lower Cambrian phosphorite Lagerst?tten have a great potential to preserve details of the early evolutionary history of sponges.Lupoi, J.S., Hackley, P.C., Birsic, E., Fritz, L.P., Solotky, L., Weislogel, A., Schlaegle, S., 2019. Quantitative evaluation of vitrinite reflectance in shale using Raman spectroscopy and multivariate analysis. Fuel 254, Article 115573. current research builds upon a previously published study that demonstrated the combination of Raman spectroscopy coupled with multivariate analysis (MVA) for the prediction of thermal maturity in coal by evaluating the efficacy of this method for the prediction of thermal maturity in shale. MVA techniques eliminate analyst bias in peak-fitting methods by using the full Raman spectrum, and then extricating the important spectral regions for distinguishing samples and building accurate, robust models. Partial least squares (PLS) regression models were developed using Raman spectra and VRo values (0.58–4.59%) for 53 geographically diverse shale chip samples, and 43 shale powder samples. Separate PLS models were built using Raman spectra from shale chips or powders. The calibration sets were validated using approximately one-third of the samples to rigorously assess the predictive accuracy of the models. The root mean standard error of prediction was 0.24 for the shale chip model, and 0.28 for the shale powder model. The coefficients of determination (R2) for the cross-validated data sets were identical (0.90, chips; 0.90, powders), revealing a strong linearity despite the geographic and age diversity of the samples. This study demonstrates the validity of using PLS models for the prediction of shale VRo from Raman spectra. The MVA method described herein presents a Raman alternative to the VRo industry benchmark for assessing thermal maturity in shale that is not imperiled by the shortcomings and subjectivity of peak-fitting methods.Lusa, M., Knuutinen, J., Lindgren, M., Virkanen, J., Bomberg, M., 2019. Microbial communities in a former pilot-scale uranium mine in Eastern Finland – Association with radium immobilization. Science of The Total Environment 686, 619-640. bacterial, fungal and archaeal communities were characterized in 17 top soil organic and mineral layer samples and in top sediment samples of the Paukkajanvaara area, a former pilot-scale uranium mine, located in Eno, Eastern Finland, using amplicon sequencing and qPCR. Soil and sediment samples were in addition analyzed for radium (226Ra), sulfate (SO42?), nitrate (NO3?) and phosphate (PO43?) concentrations. New bacterial strains, representing Pseudomonas spp., were isolated from the mine and reference area and used in laboratory experiments on uptake and leaching of radium (Ra). The effect of these strains on the sulfate leaching from the soil samples was also tested in vitro. Between 6?×?106 and 5?×?108 copies g?1 DW (dry weight) of bacterial 16S rRNA genes, 5?×?105–1?×?108 copies g?1 DW archaeal 16S rRNA genes and 1?×?105–1?×?108 copies g?1 DW fungal 5.8S rRNA genes were detected in the samples. A total of 814, 54 and 167 bacterial, archaeal and fungal genera, respectively, were identified. Proteobacteria, Euryarchaeota and Mortiriella were the dominant bacterial, archaeal and fungal phyla, respectively. All tested Pseudomonas spp. strains isolates from Paukkajanvaara removed Ra from the solution, but the amount of removed Ra depended on incubation conditions (temperature, time and nutrient broth). The highest removal of Ra (5320?L/kg DW) was observed by the Pseudomonas sp. strain T5-6-I at 37?°C. All Pseudomonas spp. strains decreased the release of Ra from soil with an average of 23% while simultaneously increasing the concentration of SO42? in the solution by 11%. As Pseudomonas spp. were frequent in both the sequence data and the cultures, these bacteria may play an important role in the immobilization of Ra in the Paukkajanvaara mine area.Lüskow, F., Kl?ve-Mogensen, K., Toph?j, J., Pedersen, L.H., Riisg?rd, H.U., Eriksen, N.T., 2019. Seasonality in lipid content of the demosponges Halichondria panicea and H. bowerbanki at two study sites in temperate Danish waters. Frontiers in Marine Science 6, 328. doi: 10.3389/fmars.2019.00328. study relates the lipid content of two marine filter-feeding demosponges, Halichondria panicea and H. bowerbanki to the seasonal availability of their suspended food, mainly free-living bacteria and phytoplankton at two study sites in Danish waters. The aim was to investigate if the lipid content of sponges is linked to food availability and season, and to what extend free-living bacteria are available in starvation periods where the phytoplankton biomass is low. The highest concentrations of bacteria were observed during summer when also chlorophyll a concentrations were high, and therefore bacteria and phytoplankton were available in similar ratio at all seasons. Bacterial cell carbon was estimated to contribute 2.9 and 4.6% compared to phytoplankton cell carbon in the food at the two sites, respectively, and free-living bacteria were available only as a minor food source at all seasons. Highest lipid contents (29.5% of sponge dry weight) were seen in H. panicea at the site with lowest food availability, while the lipid content of H. bowerbanki was 11.5% of dry weight. No seasonal variations in lipid content as fraction of sponge dry weight were observed, and the lipid content was not affected by food availability or starvation. It remains unclear why the lipid-content levels at the two study sites were conspicuously different.Ma, P., Li, M., Lu, H., Zhang, Z., 2019. MARS 2: A computational tool to resolve and extract features from large-scale GC-MS datasets. Chemometrics and Intelligent Laboratory Systems 191, 12-20. (MS-Assisted Resolution of Signal) is a computational tool for feature extraction using multivariate curve resolution approaches. However, it is time-consuming for large-scale GC-MS datasets and sensitive to the component number estimation. Here we introduce MARS 2 with substantial improvements to overcome these limitations. Reverse matching (RM) and principal component optimization-iterative transformation target factor analysis (PCO-ITTFA) are developed to reduce the time for locating peak regions and determine the correct component number for resolving optimal features. The greatest strength of MARS 2 is “resolve once, extract anywhere”. It means that mass spectra of each component were needed to resolve from only one profile. Then, chromatographic features can be extracted automatically from hundreds of other profiles with the assistance from the resolved mass spectra. To evaluate its performance, plasma datasets and fatty acid standard mixtures were processed by MARS 2, AMDIS, ADAP-GC 3.0, eRah and MS-DIAL. Amino acid standard mixtures were analyzed by MARS 2 for calibration. Results show that MARS 2 can achieve better performance in both qualitative and quantitative analysis. It is implemented in Python programming language and open-sourced at , X., Guo, S., Shi, D., Zhou, Z., Liu, G., 2019. Investigation of pore structure and fractal characteristics of marine-continental transitional shales from Longtan Formation using MICP, gas adsorption, and NMR (Guizhou, China). Marine and Petroleum Geology 107, 555-571. shale samples from marine-continental transitional facies of the Late Permian Longtan Formation in southwestern Guizhou were investigated using organic petrography analysis, X-ray diffraction analysis, mercury intrusion capillary pressure experiments, gas adsorption experiments, nuclear magnetic resonance, scanning electron microscopy image analysis, and multi-fractal theory to quantitatively and qualitatively investigate the full-size pore structure and fractal characteristics of the shale. The correlations among the total organic carbon (TOC) content, mineral composition, and pore structure were discussed. The fractal dimension was used to evaluate the production potential of a shale reservoir. Results show that samples have a high TOC content (4.38?wt % on average), low permeability (less than 0.001 mD), and complex pore structure. The pore volume (PV) varies from 0.001997?cm3/g to 0.03653?cm3/g, with an average of 0.02864?cm3/g, and the specific surface area (SSA) varies from 14.144?m2/g to 29.740?m2/g, with an average of 21.533?m2/g. Mesopores (diameter between 2 and 50?nm according to IUPAC) are the predominant contributors to the pore volume, while mesopores and micropores (diameter less than 2?nm) are the main contributors to the specific surface area. The shale samples with higher TOC and clay mineral content have larger PVs and SSAs and higher fractal dimensions than those that do not. A high fractal dimension indicates a rough pore surface and complicated pore structure. Shale with higher D1 and DA (representing the pore surface roughness and the adsorption space, respectively) has high adsorption capacity and favors gas accumulation, while shale with higher D2 and DS (representing the pore structure complexity and the seepage space, respectively) has greater flow capability and favors gas diffusion.Ma, X., Zheng, G., Liang, M., Xie, D., Martinelli, G., Sajjad, W., Xu, W., Fan, Q., Li, L., Du, L., Zhao, Y., 2019. Occurrence and origin of H2S from volcanic reservoirs in Niudong area of the Santanghu Basin, NW China. Geofluids 2019, Article 1279658. series of samples including natural gas, formation water, and rocks were collected from volcanic rock reservoirs in the Niudong area of the Santanghu Oilfields and analyzed for their mineral and/or chemical compositions and sulfur and carbon isotopes in order to investigate the occurrence and origin of hydrogen sulfide (H2S). H2S was mostly dissolved in the formation water along with petroleum production in the study area. The δ34S values of on-well H2S samples varied in a range of 9.2‰ to 20.5‰, probably indicating thermochemical sulfate reduction (TSR) and/or thermal decomposition of organic sulfur-bearing compounds (TDS) as the genetic process for H2S. However, the chemical composition of formation waters from the Kalagang Formation (C2k) and their coefficient of desulfurization also revealed that TSR could be the main principle for H2S formation. Considering the regional geological background, especially the tectonic structures and thermal evolution features of the basin, it was concluded that H2S in the study area was dominantly produced by thermal genesis with TSR as a domain through interactions between hydrocarbons and aqueous sulfate dissolved from sulfate minerals.MacKay, K., Risk, D., Atherton, E., Fougére, C., Bourlon, E., O’Connell, E., Baillie, J., 2019. Fugitive and vented methane emissions surveying on the Weyburn CO2-EOR field in southeastern Saskatchewan, Canada. International Journal of Greenhouse Gas Control 88, 118-123. oil and gas related methane (CH4) emissions being the largest anthropogenic source of CH4 in Canada, there are few measurement studies on such emissions to date. That being said, understanding the emissions footprint of different development types is becoming increasingly important in Canada, as the oil and gas sector faces new aggressive regulations to reduce CH4 emissions to 45% below 2014 levels by 2025. In this study, a vehicle-based measurement technique was used to quantify fugitive and vented CH4 emissions from the Weyburn CO2 Enhanced Oil Recovery (EOR) field in southeastern Saskatchewan, Canada. In total, 162 infrastructure sites consisting of 211 active wells and 13 facilities were sampled two or more times. Emission occurrences were substantially low in comparison to other recent emission studies in Canada and the United States, with only 1.85% of sampled sites emitting CH4. We estimated the average emission rate of CH4 at these sites to be ～0.5?m3/day, which is small compared to the proposed 2020 federal venting cap of ～110?m3/day. As expected, the low levels of emissions are likely a result of the field's unitized (closed-loop) design, coupled with the operators ongoing commitment to best practice, and the in-depth understanding of the field's characteristics from historical research.MacKenzie, S.M., Barnes, J.W., Hofgartner, J.D., Birch, S.P.D., Hedman, M.M., Lucas, A., Rodriguez, S., Turtle, E.P., Sotin, C., 2019. The case for seasonal surface changes at Titan’s lake district. Nature Astronomy 3, 506-510., Saturn’s largest moon, hosts lakes and seas of liquid hydrocarbons at its poles. General circulation models demonstrate that regional evaporation and precipitation rates of methane are likely to change with the seasons (Titan’s year is 29.5?Earth years) and evolve on a geological timescale (~105?Earth years). Cassini observations suggest shoreline recession at a few south polar lakes during local summer, but similar seasonal changes have yet to be observed at the north pole where lakes are larger and more numerous. We present three ‘phantom lakes’ that appear to be north polar surface liquids in winter observations by Cassini RADAR but that are inconsistent with lakes in infrared images obtained up to seven?years later, after vernal equinox, suggesting that the liquids were removed in between. If this were the case, the phantom lakes could be interpreted as shallow ponds, with either a pure methane composition or a regolith porous enough to remove the less volatile ethane. These phantom lakes provide observational constraints on removal timescales for surface liquids at Titan’s north pole. The location, size and longevity of surface liquid reservoirs affect sediment processing7, seasonal weather, climate evolution, and even, perhaps, their habitability. As solubility of the possible non-polar mixtures is generally low, short-lived lakes might be nutrient-poor10 and thus have low astrobiological potential.Macreadie, P.I., Atwood, T.B., Seymour, J.R., Fontes, M.L.S., Sanderman, J., Nielsen, D.A., Connolly, R.M., 2019. Vulnerability of seagrass blue carbon to microbial attack following exposure to warming and oxygen. Science of The Total Environment 686, 264-275. meadows store globally-significant quantities of organic ‘blue’ carbon. These blue carbon stocks are potentially vulnerable to anthropogenic stressors (e.g. coastal development, climate change). Here, we tested the impact of oxygen exposure and warming (major consequences of human disturbance) on rates of microbial carbon break-down in seagrass sediments. Active microbes occurred throughout seagrass sediment profiles, but deep, ancient sediments (~5000?yrs. old) contained only 3% of the abundance of active microbes as young, surface sediments (<2?yrs. old). Metagenomic analysis revealed that microbial community structure and function changed with depth, with a shift from proteobacteria and high levels of genes involved in sulfur cycling in the near surface samples, to a higher proportion of firmicutes and euraracheota and genes involved in methanogenesis at depth. Ancient carbon consisted almost entirely (97%) of carbon considered ‘thermally recalcitrant’, and therefore presumably inaccessible to microbial attack. Experimental warming had little impact on carbon; however, exposure of ancient sediments to oxygen increased microbial abundance, carbon uptake and sediment carbon turnover (34–38 fold). Overall, this study provides detailed characterization of seagrass blue carbon (chemical stability, age, associated microbes) and suggests that environmental disturbances that expose coastal sediments to oxygen (e.g. dredging) have the capacity to diminish seagrass sediment carbon stocks by facilitating microbial remineralisation.Maegaard, K., Garcia-Robledo, E., Kofoed, M.V.W., Agneessens, L.M., de Jonge, N., Nielsen, J.L., Ottosen, L.D.M., Nielsen, L.P., Revsbech, N.P., 2019. Biogas upgrading with hydrogenotrophic methanogenic biofilms. Bioresource Technology 287, 121422. produced from periodic excess of electrical energy may be added to biogas reactors where it is converted to CH4 that can be utilized in the existing energy grid. The major challenge with this technology is gas-to-liquid mass transfer limitation. The microbial conversions in reactors designed for hydrogenotrophic methanogenesis were studied with microsensors for H2, pH, and CO2. The H2 consumption potential was dependent on the CO2 concentration, but could partially recover after CO2 depletion. Reactors with 3-dimensional biofilm carrier material and a large gas headspace allowed for a methanogenic biofilm in direct contact with the gas phase. A high density of Methanoculleus sp. in the biofilm mediated a high rate of CH4 production, and it was calculated that a reactor filled with 75% carrier material could mediate a biogas upgrading from 50 to 95% CH4 within 24?h when an equivalent amount of H2 was added.Maity, J.P., Chen, G.-S., Huang, Y.-H., Sun, A.-C., Chen, C.-Y., 2019. Ecofriendly heavy metal stabilization: Microbial induced mineral precipitation (mimp) and biomineralization for heavy metals within the contaminated soil by indigenous bacteria. Geomicrobiology Journal 36, 612-623. metals (HMs) pollution is a serious problem, worldwide. The present study focuses on HMs removal (HMs mobility restricted within soil) by microbial induced mineral precipitation (MIMP) using indigenous isolates. Indigenous isolates were identified as Bacillus subtilis C(225)(MK334652), Oceanobacillus indicireducens 5(225)(MK334653), and Bacillus pumilus 7(225)(MK334654) by 16S-rRNA from HMs polluted industrial-soil (soil-225) that is used for bioremediation. The studied soil contained high level (mg/kg) of Cr(307.41?±?1.02), Cu(576.35?±?1.02), and Zn(708.81?±?1.50) as per Taiwan permissible limit (TPL) and/or Canadian Soil Quality Guidelines (CSQG). Minimum inhibitory concentration (MIC) of Bacillus species were higher compare to Oceanobacillus. Bioavailable-fraction (F1) of HMs (Cr/Cu/Zn) in untreated 225-soil was noticed to be higher compared to F2–F5 fraction. Bacillus subtilis C(225) are more efficient for HMs-mineralization, compared to other isolates where Cr/Cu/Zn immobilized within soil, transforming from bioavailable-fraction (F1) (high-mobility) (60–90% reduction) to residual-fraction F5 (low-mobility) (50–80% increment). Organic-bound-fraction (F4) (medium-mobility) of Cr increased (42.66?±?2.1%), compared to Cu/Zn, by Bacillus subtilis C(225). Urease (40.8%) and dehydrogenase (8.3%) activity increased in bio-remediated soil, compared to control. MIMP of HMs by ingenious bacteria reflects the transformation-pathway from F1 to F5 of HMs to fix strongly within soils with inadequate mobility. Thus, MIMP by indigenous microbe can be applicable for HMs stabilization/removal in contaminated soil for ecofriendly environmental cleanup.Makk, J., Enyedi, N.T., Tóth, E., Anda, D., Szabó, A., Felf?ldi, T., Schumann, P., Mádl-Sz?nyi, J., Borsodi, A.K., 2019. Deinococcus fonticola sp. nov., isolated from a radioactive thermal spring in Hungary. International Journal of Systematic and Evolutionary Microbiology 69, 1724-1730. Gram-stain-negative, aerobic, non-motile and coccus-shaped bacterium, designated strain FeSDHB5-19T, was isolated from a biofilm sample collected from a radioactive thermal spring (Budapest, Hungary), after exposure to 5 kGy gamma radiation. A polyphasic approach was used to study the taxonomic properties of strain FeSDHB5-19T, which had highest 16S rRNA gene sequence similarity to Deinococcus antarcticus G3-6-20T (96.5?%). The 16S rRNA gene sequence similarity to type strains of other Deinococcus species were 93.0?% or lower. The DNA G+C?content of the draft genome sequence, consisting of 3.9?Mb, was 63.9?mol%. Strain FeSHDB5-19T was found to grow at temperatures of 10–32?°C (optimum, 28?°C) and pH 5–10 (pH 6.5–7.5) and tolerated up to 1.5?% NaCl (w/v) with optimum growth at 0–0.5?%?NaCl. The predominant fatty acids (>10?%) were C16?:?0 and C16?:?1ω7c. The cell-wall peptidoglycan type was A3β l-Orn–Gly1-2. The whole-cell sugars were glucose and low amounts of galactose. Strain FeSDHB5-19T possessed MK-8 as the predominant respiratory quinone, typical of the genus Deinococcus . The polar lipid profile contained unidentified phosphoglycolipids and unidentified glycolipids. The isolate was found to be highly resistant to gamma (D10<8?kGy) and UV (D10~800 J?m?2) radiation. According to its genotypic, phenotypic and chemotaxonomic characteristics, strain FeSDHB5-19T represents a novel species in the genus Deinococcus , for which the name Deinococcus fonticola sp. nov. is proposed. The type strain is FeSDHB5-19T (=NCAIM B.02639T=DSM 106917T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain FeSDHB5-19T is LT853728. The whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession SMMH00000000. The version described in this paper is SMMH01000000.Manning, P.L., Edwards, N.P., Bergmann, U., Anné, J., Sellers, W.I., van Veelen, A., Sokaras, D., Egerton, V.M., Alonso-Mori, R., Ignatyev, K., van Dongen, B.E., Wakamatsu, K., Ito, S., Knoll, F., Wogelius, R.A., 2019. Pheomelanin pigment remnants mapped in fossils of an extinct mammal. Nature Communications 10, Article 2250. progress has been made in paleontology with respect to resolving pigmentation in fossil material. Morphological identification of fossilized melanosomes has been one approach, while a second methodology using chemical imaging and spectroscopy has also provided critical information particularly concerning eumelanin (black pigment) residue. In this work we develop the chemical imaging methodology to show that organosulfur-Zn complexes are indicators of pheomelanin (red pigment) in extant and fossil soft tissue and that the mapping of these residual biochemical compounds can be used to restore melanin pigment distribution in a 3 million year old extinct mammal species (Apodemus atavus). Synchotron Rapid Scanning X-ray Fluorescence imaging showed that the distributions of Zn and organic S are correlated within this fossil fur just as in pheomelanin-rich modern integument. Furthermore, Zn coordination chemistry within this fossil fur is closely comparable to that determined from pheomelanin-rich fur and hair standards. The non-destructive methods presented here provide a protocol for detecting residual pheomelanin in precious specimens.M?nnist?, E., Korrensalo, A., Alekseychik, P., Mammarella, I., Peltola, O., Vesala, T., Tuittila, E.-S., 2019. Multi-year methane ebullition measurements from water and bare peat surfaces of a patterned boreal bog. Biogeosciences 16, 2409-2421. measured methane ebullition from a patterned boreal bog situated in the Siikaneva wetland complex in southern Finland. Measurements were conducted on water (W) and bare peat surfaces (BP) in three growing seasons (2014–2016) using floating gas traps. The volume of the trapped gas was measured weekly, and methane and carbon dioxide (CO2) concentrations of bubbles were analysed from fresh bubble samples that were collected separately. We applied a mixed-effect model to quantify the effect of the environmental controlling factors on the ebullition.Ebullition was higher from W than from BP, and more bubbles were released from open water (OW) than from the water's edge (EW). On average, ebullition rate was the highest in the wettest year (2016) and ranged between 0 and 253?mg?m?2?d?1 with a median of 2?mg m?2?d?1, 0 and 147?mg?m?2?d?1 with a median of 3?mg?m?2?d?1, and 0 and 186?mg?m?2?d?1 with a median of 28?mg?m?2?d?1 in 2014, 2015, and 2016, respectively. Ebullition increased together with increasing peat temperature, weekly air temperature sum and atmospheric pressure, and decreasing water table (WT). Methane concentration in the bubbles released from W was 15–20 times higher than the CO2 concentration, and from BP it was 10 times higher. The proportion of ebullition fluxes upscaled to ecosystem level for the peak season was 2?%–8?% and 2?%–5?% of the total flux measured with eddy covariance technique and with chambers and gas traps, respectively. Thus, the contribution of methane ebullition from wet non-vegetated surfaces of the bog to the total ecosystem-scale methane emission appeared to be small.Marron, A., Cassarino, L., Hatton, J., Curnow, P., Hendry, K.R., 2019. The silicon isotopic composition of choanoflagellates: implications for a mechanistic understanding of isotopic fractionation during biosilicification. Biogeosciences Discussions 2019, 1-14. marine silicon cycle is intrinsically linked with carbon cycling in the oceans via biological production of silica by a wide range of organisms. The stable silicon isotopic composition (denoted by δ30Si) of siliceous microfossils extracted from sediment cores can be used as an archive of past oceanic silicon cycling. However, the silicon isotopic composition of biogenic silica has only been measured in diatoms, sponges and radiolarians, and isotopic fractionation relative to seawater is entirely unknown for many other silicifiers. Furthermore, the biochemical pathways and mechanisms that determine isotopic fractionation during biosilicification remain poorly understood. Here, we present the first measurements of the silicon isotopic fractionation during biosilicification by loricate choanoflagellates, a group of protists closely related to animals. We cultured two species of choanoflagellates, Diaphanoeca grandis and Stephanoeca diplocostata, which showed consistently greater isotopic fractionation (approximately ?5 to ?7?‰) than cultured diatoms (?0.5 to ?2?‰). Instead, choanoflagellate silicon isotopic fractionation appears to be more similar to sponges grown under similar DSi concentrations. Our results highlight that there is a taxonomic component to silicon isotope fractionation during biosilicification, possibly via a shared or related biochemical transport pathway. These findings have implications for the use of biogenic silica δ30Si produced by different silicifiers as proxies for past oceanic change.Marshall, B.D., 2019. A PC-SAFT model for hydrocarbons IV: Water-hydrocarbon phase behavior including petroleum pseudo-components. Fluid Phase Equilibria 497, 79-86. paper is the fourth installment of a series which develops a new generalized treatment of hydrocarbon molecules based on the PC-SAFT equation of state. In this paper, a generalized approach to water/hydrocarbon phase behavior is developed. The model accurately predicts mutual solubilities (partitioning in LLE) of saturates, aromatics and alkenes with water. The generality is a result of incorporating hydrogen bonding interactions between unsaturated bonds and water in a general/scalable way. Further, we extend our PC-SAFT hydrocarbon characterization model EMPETRO to allow for aromatics to receive hydrogen bonds from hydrogen bond donors (water, ethanol, etc.). We demonstrate the model can accurately predict mutual solubilities for hydrocarbons with water when the hydrocarbon is parameterized solely from petroleum variables boiling point, specific gravity and molecular weight.Martin-Bello, L., Arenas, C., Andrews, J.E., Alonso-Zarza, A.M., Marca, A., 2019. Lacustrine stromatolites as multi-scale recorders of climate change: Insights from the Miocene Ebro Basin. Palaeogeography, Palaeoclimatology, Palaeoecology 530, 312-329., δ13C and δ18O data from stromatolites in a lower and middle Miocene sequence from the Ebro Basin (N Spain) are used to assess the potential of ancient lacustrine stromatolite lamination as an archive of palaeoenvironmental and palaeoclimatic change. The isotopic evolution through the studied sequence supports a general trend toward less saline conditions with time. Stromatolites and muddy-grainy laminated limestones developed in lake water that underwent little renewal, compared with other carbonate facies. The palaeoclimatic value of the stable-isotope changes and concurrent textural variations in calcite stromatolite lamination is studied at different orders of cyclicity. Stromatolite lamination consists of simple laminae (dark dense, light dense and light porous) grouped into alternating composite light and dark laminae. δ13C and δ18O analyses in consecutive composite laminae (bulk sampling) yielded a cyclic pattern that mimics textural variations. Light laminae, with lower δ13C and δ18O values, reflect higher precipitation/evaporation ratio (P/E) and more influence of biogenic 12C. Dark laminae, with higher δ13C and δ18O values, reflect drier conditions, more complete atmospheric CO2 exchange with water and photosynthetic 12CO2 uptake. Textural features of laminae support these results: the dark laminae are related to higher calcite saturation in lake water during drier periods. Isotopic values from high-resolution sampling through a 2.1-cm thick stromatolite reveal palaeoclimate variations at different temporal scales. Isotopic variation in 3rd order cyclicity of alternating light/dark simple laminae is recording seasonal P/E variations. Light and dark composite laminae (2nd order cyclicity) correspond to pluriannual dominantly-humid or -dry conditions, respectively. A gradual succession from light to dark composite laminae forms the 1st order cycles driven by decreasing P/E through longer pluriannual periods, resulting in lake level lowering. The stromatolites are thus recording lake level changes of centennial to millennial scale.Maruyama, S., Kurokawa, K., Ebisuzaki, T., Sawaki, Y., Suda, K., Santosh, M., 2019. Nine requirements for the origin of Earth's life: Not at the hydrothermal vent, but in a nuclear geyser system. Geoscience Frontiers 10, 1337-1357. origin of life on Earth remains enigmatic with diverse models and debates. Here we discuss essential requirements for the first emergence of life on our planet and propose the following nine requirements: (1) an energy source (ionizing radiation and thermal energy); (2) a supply of nutrients (P, K, REE, etc.); (3) a supply of life-constituting major elements; (4) a high concentration of reduced gases such as CH4, HCN and NH3; (5) dry-wet cycles to create membranes and polymerize RNA; (6) a non-toxic aqueous environment; (7) Na-poor water; (8) highly diversified environments, and (9) cyclic conditions, such as day-to-night, hot-to-cold etc.Based on these nine requirements, we evaluate previously proposed locations for the origin of Earth's life, including: (1) Darwin's “warm little pond”, leading to a “prebiotic soup” for life; (2) panspermia or Neo-panspermia (succession model of panspermia); (3) transportation from/through Mars; (4) a deep-sea hydrothermal system; (5) an on-land subduction-zone hot spring, and (6) a geyser systems driven by a natural nuclear reactor. We conclude that location (6) is the most ideal candidate for the origin point for Earth's life because of its efficiency in continuously supplying both the energy and the necessary materials for life, thereby maintaining the essential “cradle” for its initial development. We also emphasize that falsifiable working hypothesis provides an important tool to evaluate one of the biggest mysteries of the universe – the origin of life.Ma?mig, M., Lüdke, J., Krahmann, G., Engel, A., 2019. High bacterial organic carbon uptake in the Eastern Tropical South Pacific oxygen minimum zone. Biogeosciences Discussions 2019, 1-26. minimum zones (OMZs) show distinct biogeochemical processes that relate to microorganisms being able to thrive under low or even absent oxygen. Microbial degradation of organic matter is expected to be reduced in OMZs, although quantitative evidence is low. Here, we present heterotrophic bacterial production (3H leucine-incorporation), extracellular enzyme rates (leucine aminopeptidase/?-glucosidase) and bacterial cell abundance for various in situ oxygen concentrations in the water column of the Eastern Tropical South Pacific off Peru. Bacterial heterotrophic activity in the suboxic core of the OMZ (at in situ ≤?5??mol O2?kg?1) ranged from 0.6 to 160??mol?C?m?3?d?1 and was not significantly lower than in waters of 5–60??mol?O2?kg?1. Moreover, bacterial abundance in the OMZ was slightly and leucine aminopeptidase activity even significantly higher in suboxic waters compared to the upper oxycline suggesting no impairment of bacterial organic matter degradation in the core of the OMZ. Nevertheless, high cell-specific bacterial production and extracellular enzyme rates were observed in samples from the upper or lower oxyclines corroborating earlier findings of highly active and distinct micro-aerobic bacterial communities. To assess the impact of bacterial degradation of dissolved organic matter for oxygen loss in the Peruvian OMZ, we compared diapycnal fluxes of oxygen and dissolved organic carbon (DOC) and their microbial uptake within the upper 60?m of the water column. Our data indicate bacterial growth efficiencies of 0.5–8.6?% at the upper oxycline, resulting in a high bacterial oxygen demand that can explain up to 33?% of the observed average oxygen loss over depth. Our study therewith shows that microbial degradation of DOM has a considerable share in sustaining the OMZ off PeruMastrogiuseppe, M., Poggiali, V., Hayes, A.G., Lunine, J.I., Seu, R., Mitri, G., Lorenz, R.D., 2019. Deep and methane-rich lakes on Titan. Nature Astronomy 3, 535-542.’s largest moon, Titan, hosts liquid hydrocarbon lakes and seas on its surface. During the last close encounter with Titan (22 April 2017), the Cassini spacecraft used its RADAR as a sounder to probe the depth of several lakes in the north polar terrain. This was the first time that Titan’s lakes, as opposed to its seas, have been viewed in a sounding configuration. Here, we show that these lakes can exceed 100?m depth and their transparency at the 2.17?cm radar wavelength indicates that they have a methane-dominated composition. This composition differs significantly from that of Ontario Lacus, the only major lake in Titan’s southern hemisphere, which is more ethane rich. If the methane-rich north polar lakes, perched hundreds of metres above the major seas, are formed by a karstic-type process, then they may drain by subsurface flow at rates between 0.001 and 1?m?yr?1 (Titan year). Subsurface reservoirs and flows therefore may be an important element of the Titan geochemical system.McDougall, K., John, C.M., 2019. Benthic foraminiferal biotic events related to the Paleocene–Eocene Thermal Maximum along the California margin. Marine Micropaleontology 150, 101745. faunal expression of the Paleocene-Eocene Thermal Maximum (PETM) is well documented in deep-sea sediments. However, few studies have examined continental margin sections, especially active margins. The Moreno and Lodo formations, Central California, were deposited along the eastern margin of a north-south trending forearc basin on the convergent margin of California during the Cretaceous through Late Cenozoic. The Tumey Gulch section which includes the Moreno and Lodo formations, is 80?m thick, contains the Paleocene-Eocene boundary and Carbon Isotope Excursion (CIE), and was deposited at abyssal to lower bathyal depths along an active continental margin. Benthic foraminiferal assemblages from this section record faunal changes related to the PETM and a younger hyperthermal, ETM3 which include a disruption of the gradual shallowing of water depths and fluctuation of the CCD. Associated with the onset of the hyperthermals in this section is a red clay-siltstone layer (low calcium carbonate content) and an increase in smoothly finished dissolution resistant agglutinated benthic foraminiferal species which corresponds with a rapid shoaling of the CCD. The subsequent overcompensation is identified by a rapid change to shallower benthic biofacies faunas, increased sediment rate, current activity, and terrestrial organic matter which is associated with increased weathering. Further analysis of the foraminiferal faunas identified the benthic foraminiferal extinction event (BEE), deep water agglutinated faunal acmes, and fluctuations in the calcareous foraminiferal assemblages which indicate changes in the paleoenvironmental conditions (e.g., dissolved oxygen, sedimentation rates and current activity, and the influx of organic carbon) during the PETM and ETM3. The Ynezian, Bulitian, and Penutian California benthic foraminiferal stages are recognized in the Tumey Gulch section as well as the benthic foraminiferal extinction event (BEE) which occurs at the onset of the PETM and is distinguished by the last appearance of Paleocene species and the first appearance of many Eocene species. Agglutinated foraminiferal species dominate the late Paleocene through early Eocene part of the section indicating deposition occurred at abyssal depths and/or below the CCD and that the environment was oligotrophic with moderate to low organic flux. The Glomospira acme zone is recognized at the base of the CIE and just above the top of red clay-siltstone layer and suggests increased terrestrial organic matter and elevated sedimentation rates. The abundance of calcareous species, specifically Bulimina alazanensis, followed by the appearance of opportunistic taxa (Tappanina and Quadrimorphina) in the PETM interval indicates deposition within the lower bathyal biofacies and/or a drop in the depth of the CCD. Eocene species characteristic of the Survivor faunal group (Anomalinoides, Bulimina, Cibicidoides, and Pleurostomella) appear above this event. Foraminiferal assemblages dominated by agglutinated foraminifera appear in sediments overlying the PETM interval and indicate deposition occurred at abyssal depths and below the CCD. Calcareous foraminiferal assemblages appear higher in the section as water depths decrease. The presence of a second red clay-siltstone layer associated with a second isotope excursion and faunal changes in the upper part of the section indicate the presence of another hyperthermal, ETM3.McLennan, S.M., Grotzinger, J.P., Hurowitz, J.A., Tosca, N.J., 2019. The sedimentary cycle on early Mars. Annual Review of Earth and Planetary Sciences 47, 91-118. decades of intensive research have demonstrated that early Mars (>2 Gyr) had an active sedimentary cycle, including well-preserved stratigraphic records, understandable within a source-to-sink framework with remarkable fidelity. This early cycle exhibits first-order similarities to (e.g., facies relationships, groundwater diagenesis, recycling) and first-order differences from (e.g., greater aeolian versus subaqueous processes, basaltic versus granitic provenance, absence of plate tectonics) Earth's record. Mars' sedimentary record preserves evidence for progressive desiccation and oxidation of the surface over time, but simple models for the nature and evolution of paleoenvironments (e.g., acid Mars, early warm and wet versus late cold and dry) have given way to the view that, similar to Earth, different climate regimes on Mars coexisted on regional scales and evolved on variable timescales, and redox chemistry played a pivotal role. A major accomplishment of Mars exploration has been to demonstrate that surface and subsurface sedimentary environments were both habitable and capable of preserving any biological record. Mehana, M., Fahes, M., Huang, L., 2019. Asphaltene aggregation in oil and gas mixtures: Insights from molecular simulation. Energy & Fuels 33, 4721-4730. dynamics of asphaltene molecules is highly impacted by both the nature of the solvent and the physical conditions of the system. We performed molecular simulation to investigate the dynamic behavior of asphaltene during gas flooding. We also consulted the experimental observations for validation purposes when available. Two structures representing the archipelago and continental types are used, whose aggregation and interactions are studied in methane (C1), propane (C3), carbon dioxide (CO2), heptane (C7), and toluene as pure solvents, binary mixtures of toluene and either C1, C3, or CO2, and a representative oil composition. The continental structure is used afterward to evaluate the impact of temperature, pressure, and resin content on the aggregation dynamics in CO2 mixtures. Interestingly, the solvating power of CO2 is dependent on the asphaltene structure where inhibitor-like behavior is observed for the continental structure and precipitator-like behavior is observed for the archipelago structure. The solvent quality is highly correlated with the solvent s ability to replace the interactions among asphaltene molecules with interactions between asphaltene and solvent. The aggregate size is reduced by temperature and enhanced by pressure in CO2. However, limited effect is reported for resins on asphaltene dynamics in CO2. The aggregation of asphaltene is impacted by the physical state of CO2 as its solvating power to asphaltene is significantly enhanced in its supercritical state. Nonetheless, this impact is limited when CO2 is introduced to a representative oil mixture.Meisenbichler, C., Doppler, C., Bernhard, D., Müller, T., 2019. Improved matrix coating for positive- and negative-ion-mode MALDI-TOF imaging of lipids in blood vessel tissues. Analytical and Bioanalytical Chemistry 411, 3221-3227. matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) of lipids in biological tissue relies on the fabrication of a homogeneous matrix coating featuring best possible analyte integration. This communication addresses a matrix vapor deposition/recrystallization process for the application of 1,5-diaminonaphthalene (1,5-DAN) onto slices of human aortic tissue. The matrix coating is compatible with both positive- as well as negative-ion-mode MALDI MSI facilitating a significantly enhanced detection of lipid-related signals in different cell layers of blood vessel walls.Melott, A.L., Marinho, F., Paulucci, L., 2019. Hypothesis: Muon radiation dose and marine megafaunal extinction at the end-Pliocene supernova. Astrobiology 19, 825–830. data and analysis support the detection of one or more supernovae (SNe) at a distance of about 50?pc, ～2.6 million years ago. This is possibly related to the extinction event around that time and is a member of a series of explosions that formed the Local Bubble in the interstellar medium. We build on previous work, and propagate the muon flux from SN-initiated cosmic rays from the surface to the depths of the ocean. We find that the radiation dose from the muons will exceed the total present surface dose from all sources at depths up to 1?km and will persist for at least the lifetime of marine megafauna. It is reasonable to hypothesize that this increase in radiation load may have contributed to a newly documented marine megafaunal extinction at that time.Menotti, T., Hosford Scheirer, A., Meisling, K., Graham, S.A., 2019. Integrating strike-slip tectonism with three-dimensional basin and petroleum system analysis of the Salinas Basin, California. American Association of Petroleum Geologists Bulletin 103, 1443-1472. Salinas Basin is a strike-slip basin in central California with stratigraphy dominantly composed of Miocene Monterey Formation. Despite a long history of oil production, aspects of petroleum system development in the basin remain poorly understood. Of the seven main oil fields, one—San Ardo field—has produced more than 500 million bbl of oil or 99% of all oil found in the basin. The evolution of this basin was profoundly influenced by strike-slip movement on the Rinconada Fault, which bisected the depocenter beginning circa 15 Ma. To address the influence of strike-slip motion on petroleum system development, we constructed a three-dimensional (3-D) basin and petroleum system model that incorporates strike-slip displacement. Seismic reflection profiles from a 3-D survey reveal four main tectonic stages that correspond to events in petroleum system evolution. Petroleum generation from type II kerogen source rock began circa 11 Ma, approximately 4 m.y. after strike-slip faulting began to offset a once-contiguous sedimentary depocenter. Two separate petroleum provinces—an eastern one and a western one—developed, and the fault zone likely was a conduit for petroleum, if nonsealing. Most accumulated petroleum was derived from the eastern pod of active source rock because of greater sedimentary burial east of the fault. Our model roughly replicates the skewed distribution in oil-field size. Factors controlling field size distribution include trap size and connectivity to source.Mhatre, S.S., Kaufmann, S., Marshall, I.P.G., Obrochta, S., Andrèn, T., J?rgensen, B.B., Lomstein, B.A., 2019. Microbial biomass turnover times and clues to cellular protein repair in energy-limited deep Baltic Sea sediments. FEMS Microbiology Ecology 95, Article fiz068. discovery of active microbial life deeply buried beneath the seafloor has opened important questions: how do microorganisms cope with extreme energy limitation, what is their metabolic activity, and how do they repair damages to essential biomolecules? We used a D:L-amino acid model to calculate microbial biomass turnover times. We used a metagenome and metatranscriptome analysis to investigate the distribution of the gene that encodes Protein-L-iso aspartate(D-aspartate) O-methyltransferase (PCMT), an enzyme which recognizes damaged L-isoapartyl and D-aspartyl residues in proteins and catalyzes their repair. Sediment was retrieved during the Integrated Ocean Drilling Program (IODP) Expedition 347 from Landsort Deep and the Little Belt in the Baltic Sea. The study covers the period from the Baltic Ice Lake ca. 13?000 years ago to the present. Our results provide new knowledge on microbial biomass turnover times and protein repair in relation to different regimes of organic matter input. For the first time, we show that the PCMT gene was widely distributed and expressed among phylogenetically diverse groups of microorganisms. Our findings suggest that microbial communities are capable of repairing D-amino acids within proteins using energy obtained from the degradation of a mixture of labile compounds in microbial necromass and more recalcitrant organic matter.Mi, Z., Wang, F., Yang, Z., Li, X., Diao, Y., Ma, X., Tian, H., 2019. Numerical simulation of the influence of geological CO2 storage on the hydrodynamic field of a reservoir. Geofluids 2019, Article 1853274. geological storage in deep saline aquifers is an effective way to reduce CO2 emissions. The injection of CO2 inevitably causes a significant pressure increase in reservoirs. When there exist faults which cut through a deep reservoir and shallow aquifer system, there is a risk of the shallow aquifer being impacted by the changes in reservoir hydrodynamic fields. In this paper, a radial model and a 3D model are established by TOUGH2-ECO2N for the reservoir system in the CO2 geological storage demonstration site in the Junggar Basin to analyze the impact of the CO2 injection on the deep reservoir pressure field and the possible influence on the surrounding shallow groundwater sources. According to the results, the influence of CO2 injection on the reservoir pressure field in different periods and different numbers of well is analyzed. The result shows that the number of injection wells has a significant impact on the reservoir pressure field changes. The greater the number of injection wells is, the greater the pressure field changes. However, after the cessation of CO2 injection, the number of injection wells has little impact on the reservoir pressure recovery time. Under the geological conditions of the site and the constant injection pressure, although the CO2 injection has a significant influence on the pressure field in the deep reservoir, the impact on the shallow groundwater source area is minimal and can be neglected and the existing shallow groundwater sources are safe in the given project scenarios.Miersch, T., Czech, H., Hartikainen, A., Ihalainen, M., Orasche, J., Abbaszade, G., Tissari, J., Streibel, T., Jokiniemi, J., Sippula, O., Zimmermann, R., 2019. Impact of photochemical ageing on Polycyclic Aromatic Hydrocarbons (PAH) and oxygenated PAH (Oxy-PAH/OH-PAH) in logwood stove emissions. Science of The Total Environment 686, 382-392. combustion of spruce logwood in a modern residential stove was found to emit polycyclic aromatic hydrocarbons (PAH) and oxygenated polycyclic aromatic hydrocarbons (OPAH) with emission factors of 404?μg?MJ?1 of 35 analysed PAH, 317?μg?MJ?1 of 11 analysed Oxy-PAH and 12.5?μg?MJ?1 of 5 analysed OH-PAH, most of which are known as potential mutagens and carcinogens. Photochemical ageing in an oxidation flow reactor (OFR) degraded particle-bound PAH, which was also reflected in declining PAH toxicity equivalent (PAH-TEQ) values by 45 to 80% per equivalent day of photochemical ageing in the atmosphere. OPAH concentrations decreased less than PAH concentrations during photochemical ageing, supposedly due to their secondary formation, while 1-hydroxynaphthalene, 1,5-dihydroxynaphthalene and 1,8-naphthalaldehydic acid were significantly increased after ageing. Furthermore, secondary organic aerosol (SOA) formation and aromatic compounds not included in targeted analysis were investigated by thermal-optical carbon analysis (TOCA) hyphenate to resonance-enhanced multi-photon ionisation time-of-flight mass spectrometry (REMPI-TOFMS).The commonly used PAH-source indicators phenanthrene/anthracene, fluoranthene/pyrene, retene/chrysene, and indeno[cd]pyrene/benzo[ghi]perylene remained stable during photochemical ageing, enabling identification of wood combustion emissions in ambient air. On the other hand, benz[a]pyrene/benz[e]pyrene and benz[a]anthracene/chrysene were found to decrease with increasing photochemical age. Retene/chrysene was not a proper classifier for the wood combustion emissions of this study, possibly due to more efficient combustion than in open wood burning, from which this diagnostic ratio was initially derived.This study motivates in-depth investigation of degradation kinetics of particle-bound species on different combustion aerosol as well as the consequences of photochemical ageing on toxicity and identification of wood combustion emissions in ambient air.Mignon, P., Navarro-Ruiz, J., Rimola, A., Sodupe, M., 2019. Nucleobase stacking at clay edges, a favorable interaction for RNA/DNA oligomerization. ACS Earth and Space Chemistry 3, 1023-1033. density functional theory (DFT) calculations have been performed to model the adsorption of nucleobases at clay edges as potential adsorption sites for DNA/RNA oligomerization. According to the accessibility and availability of hydroxyl groups and water molecules at clay edges, numerous adsorption conformations via H-bonding, in a similar way to the Watson–Crick base pairing in DNA strands, have been considered. It is found that guanine and cytosine are mainly adsorbed through three H-bonds with edge’s hydroxyls and water molecules, while adenine and thymine do generally engage two H-bonds. As a result, the largest adsorption energies were found for guanine and cytosine (?32 to ?35 kcal mol–1) in comparison to most adsorbed modes with adenine and thymine (?22 to ?24 kcal mol–1). For thymine, a three H-bond tilted adsorption mode has also been observed with an exceptionally large adsorption energy of ?35 kcal mol–1. Significant stabilizing dispersive forces with the surface are present in all the explored adducts, around 30% of the total adsorption energy (?6 to ?10 kcal mol–1). The stacking of an additional nucleobase and its adsorption via H-bonding on the edge surface has also been studied. The large stabilizing interactions of the complexes, arising from both H-bonding and stacking interactions, range between ?44 and ?66 kcal mol–1, the dispersion component accounting for around ?20 kcal mol–1, while no cooperative effects are observed. A significant number of strong H-bonds (<1.6 ?) is observed in the most stable complexes. Obtained results show that a side by side nucleobase adsorption is possible at clay edges due to the availability of hydroxyl and water motifs. Finally, the adsorption of a thymine dinucleotide unit (TpT) is simulated, showing that its adsorption occurs also via H-bonding with the edges. This adsorption mechanism may be considered as a probable adsorption mode allowing for the phosphodiester bond formation leading to RNA oligomerization.Mikhailov, N.N., Ermilov, O.M., Sechina, L.S., 2019. Effect of asphaltenes on wettability of gas and oil saturated reservoir rocks. Doklady Earth Sciences 486, 465-467. wettability by asphaltenes of siliciclastic and carbonate drill–cores from oil and gas condensate fields extracted with n-hexane and chloroform was studied. The values obtained for the drill–cores of wetting by asphaltenes indicate the effect of asphaltenes on the wettability change for various rocks.Milano, S., Szymanek, M., 2019. Lacustrine molluscan carbonates: An interspecific approach toward the understanding of palaeoenvironmental conditions during the Holsteinian Interglacial (MIS 11) using δ18O and δ13C. Palaeogeography, Palaeoclimatology, Palaeoecology 530, 49-58. isotope geochemistry is a well-known tool for the investigation of palaeoclimate. The application of this methodology to molluscan carbonate materials has increasingly receiving more attention in recent decades, stimulating the development of numerous environmental reconstructions. Among the different habitats and shell species investigated so far, the freshwater are the ones that have received least attention. The scarcity of systematic studies on lacustrine and riverine molluscan species considerably limits the use of these remains to reconstruct the environmental conditions of inland palaeontological and archaeological sequences. The present study focuses on Bithynia tentaculata, a freshwater species abundant in the European Quaternary fossil record. The aim of the research is to validate the use of oxygen (δ18O) and carbon stable isotopes (δ13C) of this species as palaeoenvironmental proxies. For this purpose, shells and opercula from stratigraphic sequences of three palaeolakes in eastern Poland, formed during the Holsteinian Interglacial (MIS 11), are analysed. The intercorrelation between B. tentaculata and two other molluscan species, together with good agreement with the pollen record, reveal that δ18O and δ13C are suitable indicators of water temperature and humidity levels for lacustrine environments. These results pave the way for using B. tentaculata in further palaeoclimatic reconstructions.Millan, M., Szopa, C., Buch, A., Cabane, M., Teinturier, S., Mahaffy, P., Johnson, S.S., 2019. Performance of the SAM gas chromatographic columns under simulated flight operating conditions for the analysis of chlorohydrocarbons on Mars. Journal of Chromatography A 1598, 183-195. Sample Analysis at Mars (SAM) instrument is a gas chromatograph-mass spectrometer onboard the NASA Curiosity rover, currently operating on the surface of Mars. Organic compounds are of major importance with regard to questions of habitability and the potential presence of life on Mars, and one of the mission’s main objectives is to analyze the organic content of soil and rock samples. In SAM’s first chromatographic measurements, however, unexpected chlorine-bearing organic molecules were detected. These molecules have different origins but the presence of perchlorates and chlorates detected at the surface of Mars suggests that reactivity between organic molecules and thermal decomposition products from oxychlorines is one of the major sources of the chlorinated organic molecules. Here we perform a comprehensive and systematic study of the separation of volatile chlorohydrocarbons with the chromatographic columns used in the SAM instrument. Despite the constrained operating conditions of the flight instrument, we demonstrate that SAM’s capillary chromatographic columns allow for effective separation and identification of a wide range of chlorine-bearing species. We also show that instrumental limitations prevent the detection of certain molecules, obscuring our ability to make definitive conclusions about the origin of these organic materials.Miller, M.J., Albarracin-Jordan, J., Moore, C., Capriles, J.M., 2019. Chemical evidence for the use of multiple psychotropic plants in a 1,000-year-old ritual bundle from South America. Proceedings of the National Academy of Sciences 116, 11207-11212.: Humans have a long history of using natural resources, especially plants, to induce nonordinary states of consciousness. Imbibing substances derived from plants have been linked to ancient and elaborate knowledge systems and rituals. While archaeological evidence of the consumption of psychotropics, such as alcohol or caffeine, dates back thousands of years, evidence of the use of other psychoactive substances has been more difficult to document. This article presents the results of chemical analyses of organic residues found in a 1,000-year-old ritual bundle recovered from the highland Andes. The analyses provide evidence of the use of multiple psychoactive plants associated with a sophisticated botanical knowledge system among ritual specialists (shamans) during pre-Columbian times.Abstract: Over several millennia, various native plant species in South America have been used for their healing and psychoactive properties. Chemical analysis of archaeological artifacts provides an opportunity to study the use of psychoactive plants in the past and to better understand ancient botanical knowledge systems. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to analyze organic residues from a ritual bundle, radiocarbon dated to approximately 1,000 C.E., recovered from archaeological excavations in a rock shelter located in the Lípez Altiplano of southwestern Bolivia. The site is located at an elevation of ～3,900 m above sea level and contains evidence of intermittent human occupations during the last 4,000 years. Chemical traces of bufotenine, dimethyltryptamine, harmine, and cocaine, including its degradation product benzoylecgonine, were identified, suggesting that at least three plants containing these compounds were part of the shamanic paraphernalia dating back 1,000 years ago, the largest number of compounds recovered from a single artifact from this area of the world, to date. This is also a documented case of a ritual bundle containing both harmine and dimethyltryptamine, the two primary ingredients of ayahuasca. The presence of multiple plants that come from disparate and distant ecological areas in South America suggests that hallucinogenic plants moved across significant distances and that an intricate botanical knowledge was intrinsic to pre-Columbian ritual practices.Min, X., Hua, H., Liu, L., Sun, B., Cui, Z., Jiang, T., 2019. Phosphatized Epiphyton from the terminal Neoproterozoic and its significance. Precambrian Research 331, Article 105358. fossil record of calcified cyanobacteria in the Precambrian is scarce, especially for fossils with dichotomous filaments. Epiphyton, which have complex branching structures like cyanobacteria and are usually regarded as calcimicrobe with uncertain affinity, and are widely considered to appear at the beginning of the Cambrian. Exceptional phosphatized three-dimensional Epiphyton are reported from the Gaojiashan Member, Dengying Formation of the terminal Neoproterozoic, Lijiagou section, southern Shaanxi Province of China. Based on data from scanning electron microscopy and X-ray tomographic microscopy, two preservational modes of Epiphyton, namely tubular and solid branches, and their corresponding phosphatic processes are proposed. Branching forms of the thallus, sizes, and outer surface ornamentations of the filaments are characteristic of Phanerozoic Epiphyton, and has allowed us to give a possible interpretation of this genus, and to recognize its similarity to cyanobacteria. The finding enhances our understanding of the diversity of cyanobacteria in the terminal Neoproterozoic, give us an opportunity to reassess the theories involving the coevolution of calcification of microbes and metazoans.Misch, D., Riedl, F., Liu, B., Horsfield, B., Ziegs, V., Mendez-Martin, F., Vranjes-Wessely, S., Sachsenhofer, R.F., 2019. Petrographic and sorption-based characterization of bituminous organic matter in the Mandal Formation, Central Graben (Norway). International Journal of Coal Geology 211, 103229. Upper Jurassic Mandal Fm. of the Central Graben, Norway represents an important source rock that charged major petroleum accumulations in the North Sea, including the giant Ekofisk field. Nevertheless, exploration to date has been less successful than expected in marginal basin position such as the Cod Terrace, the Mandal High or the S?gne Basin, probably due to higher proportions of thermally stable (type III) kerogen. In an attempt to delineate changes in initial kerogen composition from later effects such as delayed expulsion of hydrocarbons, traditional organic petrography and scanning electron microscopy were combined with organic geochemical proxies and gas adsorption tests. The kerogen composition of the Mandal Fm. shows considerable variation. Samples hosting autochthonous coaly layers were found in wells from the S?gne Basin and the Cod Terrace, for which less generative potential was previously postulated. Nevertheless, samples hosting mainly vitrodetrinite were also found in basinal wells. A correlation of total organic carbon contents with liptinite percentages highlights enhanced bioproductivity or preservation efficiency for samples with abundant algal organic matter, that were likely deposited under deeper water and possibly oxygen-depleted conditions. By combining organic geochemical proxies with nitrogen sorption data, it could be proven that in case of the Mandal Fm., the (bituminous) organic matter fraction represents the controlling factor on abundance of micro- and mesopores and hence adsorptive gas retention. The amount of bitumen extractable from the Rock-Eval S2 peak (S2bitumen) shows a strong correlation with the total inner surface area, suggesting that small mesopores (<10–15?nm) are mainly associated with the high-molecular bituminous fraction represented by the S2bitumen, which appears non-porous at SEM-scale. Furthermore, the total inner surface area decreases strongly with thermal maturity, documenting a change in pore characteristics of the organic matter fraction (growth of mesopores and occurrence of macropores) by advancing hydrocarbon generation. Pyrobitumen-rich Upper Visean reference samples at peak oil and early wet gas window maturity show intense sponge-like pyrobitumen-hosted porosity coinciding with a low relative proportion of S2bitumen (high petroleum quality). Pyrobitumen is not affected by solvent extraction, thus not contributing high-molecular weight compounds to the extracted fraction. Such inert meso- to macroporous residues might contribute only relatively little to gas sorption capacity, but might represent important storage space for free gas, as well as flow pathways during expulsion.Mittelviefhaus, M., Müller, D.B., Zambelli, T., Vorholt, J.A., 2019. A modular atomic force microscopy approach reveals a large range of hydrophobic adhesion forces among bacterial members of the leaf microbiota. The ISME Journal 13, 1878-1882. adhesion is the initial step in surface colonization and community formation. At the single-cell level, atomic force microscopy (AFM) techniques have enabled the quantification of adhesive forces between bacteria and substrata. However, conventional techniques depend on the irreversible immobilization of cells onto cantilevers, thus hampering throughput. Here, we developed a modular AFM method to reversibly immobilize functionalized beads as surface mimic and to probe adhesion of individual bacteria. We performed single-cell force spectroscopies with phylogenetically diverse leaf isolates of various size and morphology. Adhesion measurement of 28 bacterial strains revealed large differences in hydrophobic interactions of about three orders of magnitude. The highest adhesion forces of up to 50?nN were recorded for members of the Gammaproteobacteria. The hydrophobicity of the different isolates correlated positively with the retention of bacteria observed in planta and might provide a basis for successful leaf colonization and potentially disease outbreaks of pathogens.Monteil, C.L., Vallenet, D., Menguy, N., Benzerara, K., Barbe, V., Fouteau, S., Cruaud, C., Floriani, M., Viollier, E., Adryanczyk, G., Leonhardt, N., Faivre, D., Pignol, D., López-García, P., Weld, R.J., Lefevre, C.T., 2019. Ectosymbiotic bacteria at the origin of magnetoreception in a marine protist. Nature Microbiology 4, 1088-1095. symbioses are often a source of evolutionary innovation and drivers of biological diversification. Widely distributed in the microbial world, particularly in anoxic settings, they often rely on metabolic exchanges and syntrophy. Here, we report a mutualistic symbiosis observed in marine anoxic sediments between excavate protists (Symbiontida, Euglenozoa) and ectosymbiotic Deltaproteobacteria biomineralizing ferrimagnetic nanoparticles. Light and electron microscopy observations as well as genomic data support a multi-layered mutualism based on collective magnetotactic motility with division of labour and interspecies hydrogen-transfer-based syntrophy. The guided motility of the consortia along the geomagnetic field is allowed by the magnetic moment of the non-motile ectosymbiotic bacteria combined with the protist motor activity, which is a unique example of eukaryotic magnetoreception acquired by symbiosis. The nearly complete deltaproteobacterial genome assembled from a single consortium contains a full magnetosome gene set, but shows signs of reduction, with the probable loss of flagellar genes. Based on the metabolic gene content, the ectosymbiotic bacteria are anaerobic sulfate-reducing chemolithoautotrophs that likely reduce sulfate with hydrogen produced by hydrogenosome-like organelles underlying the plasma membrane of the protist. In addition to being necessary hydrogen sinks, ectosymbionts may provide organics to the protist by diffusion and predation, as shown by magnetosome-containing digestive vacuoles. Phylogenetic analyses of 16S and 18S ribosomal RNA genes from magnetotactic consortia in marine sediments across the Northern and Southern hemispheres indicate a host–ectosymbiont specificity and co-evolution. This suggests a historical acquisition of magnetoreception by a euglenozoan ancestor from Deltaproteobacteria followed by subsequent diversification. It also supports the cosmopolitan nature of this type of symbiosis in marine anoxic sediments.Montgomery, W., Jaramillo, E.A., Royle, S.H., Kounaves, S.P., Schulze-Makuch, D., Sephton, M.A., 2019. Effects of oxygen-containing salts on the detection of organic biomarkers on Mars and in terrestrial analog soils. Astrobiology 19, 722-729. detection of chlorinated hydrocarbons by Curiosity on Mars has been attributed to the presence of unidentified indigenous organic matter. Similarly, oxychlorines on Earth have been proposed to be responsible for the apparent lack of organics in the Atacama Desert. The presence of perchlorate (ClO4?) poses a unique challenge to the measurement of organic matter due to the oxidizing power of oxychlorines during commonly used pyrolysis–gas chromatography–mass spectrometry (py-GC-MS) methods. Here, we show that perchlorates and other oxyanion salts inhibit the detection of organic compounds but that removing these problematic species prior to pyrolysis by using an optimal sample extraction duration and suitable ratios of water to sample mass enables analysis. We have characterized leached and unleached samples containing perchlorates from the Atacama Desert and have found that after leaching, the py-GC-MS chromatograms of the dried mineral residues show identifiable biomarkers associated with indigenous cyanobacteria. Samples which were pyrolyzed without leaching showed no detectable organic matter other than background siloxane and very weak or no trace of detectable polychlorinated benzenes. Dried sample residues remaining after leaching, the mineral matrix and water-insoluble organic matter, showed a strong organic response in all cases when analyzed by py-GC-MS. These residues are most likely the product of the pyrolysis of water-insoluble organics originally present in the samples. In addition, our results imply that previous soil analyses which contained high levels of oxyanions and concluded that organics were either not present or were present at extremely low levels should be reexamined. Moon, M.H., 2019. Flow field-flow fractionation: Recent applications for lipidomic and proteomic analysis. TrAC Trends in Analytical Chemistry 118, 19-28. field-flow fractionation (FlFFF) is a versatile size-based separation method suitable for biological macromolecules including proteins/protein aggregates, DNA, subcellular organelles, extracellular species, and whole cells. This review introduces briefly the basic principles of FlFFF and its recent applications for proteomic and lipidomic analysis, which are described in two parts: (1) off-line coupling of FlFFF with MS and other bioanalytical methods, and (2) on-line FlFFF with MS. The first part includes applications for lipoproteins, exosomes, and subcellular organelles for the size-dependent analysis of proteins and lipids in narrow size-fractions collected during FlFFF, followed by independent analysis including western blotting and nanoflow liquid chromatography-electrospray ionisation-tandem mass spectrometry (nLC-ESI-MS/MS). The second part highlights the on-line FlFFF-MS, in which a miniaturised FlFFF channel is coupled to ESI-MS/MS for the high-speed lipid analysis of lipoproteins and to inductively-coupled plasma MS for the direct analysis of metals in metalloproteins from blood plasma.More, K.D., Giosan, L., Grice, K., Coolen, M.J.L., 2019. Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea. Geobiology 17, 436-448. microbial communities are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors and porosity, but recent studies suggest that the vertical distribution of a subset of subseafloor microbial taxa, which were present at the time of deposition, were selected by the paleodepositional environment. However, additional highly resolved temporal records of subsurface microbiomes and paired paleoenvironmental reconstructions are needed to justify this claim. Here, we performed a highly resolved shotgun metagenomics survey to study the taxonomic and functional diversity of the subsurface microbiome in Holocene sediments underlying the permanently stratified and anoxic Black Sea. Obligate aerobic bacteria made the largest contribution to the observed shifts in microbial communities associated with known Holocene climate stages and transitions. This suggests that the aerobic fraction of the subseafloor microbiome was seeded from the water column and did not undergo post‐depositional selection. In contrast, obligate and facultative anaerobic bacteria showed the most significant response to the establishment of modern‐day environmental conditions 5.2 ka ago that led to a major shift in planktonic communities and in the type of sequestered organic matter available for microbial degradation. No significant shift in the subseafloor microbiome was observed as a result of environmental changes that occurred shortly after the marine reconnection, 9 ka ago. This supports the general view that the marine reconnection was a gradual process. We conclude that a high‐resolution analysis of downcore changes in the subseafloor microbiome can provide detailed insights into paleoenvironmental conditions and biogeochemical processes that occurred at the time of deposition.Mu, C., Zhang, F., Chen, X., Ge, S., Mu, M., Jia, L., Wu, Q., Zhang, T., 2019. Carbon and mercury export from the Arctic rivers and response to permafrost degradation. Water Research 161, 54-60. rivers export a large amount of organic carbon (OC) and mercury (Hg) to Arctic oceans. Because there are only a few direct calculations of OC and Hg exports from these large rivers, very little is known about their response to changes in the active layer in northern permafrost-dominated areas. In this study, multiyear data sets from the Arctic Great Rivers Observatory (ArcticGRO) are used to estimate the export of dissolved organic carbon (DOC), particulate organic carbon (POC), total mercury (THg) and methylmercury (MeHg) from the six largest rivers (Yenisey, Lena, Ob, Mackenzie, Yukon and Kolyma) draining to the Arctic Ocean. From 2003 to 2017, annual DOC and POC export to the Arctic Ocean was approximately 21612?Gg and 2728?Gg, and the exports of Hg and MeHg to the Arctic Ocean were approximately 20090?kg and 110?kg (0.002% of the total Hg stored in the northern hemisphere active layer). There were great variations in seasonal OC and Hg concentrations and chemical characteristics, with higher fluxes in spring and lower fluxes in winter (baseline). DOC and Hg concentrations are significantly positively correlated to discharge, as discharge continues to increase in response to a deepening active layer thickness during recent past decades. This study shows that previous results likely underestimated DOC exports from rivers in the circum-Arctic regions, and both OC and Hg exports will increase under predicted climate warming scenarios.Nemirovskaya, I.A., Redzhepova, Z.Y., Lisitzin, A.P., 2019. Hydrocarbons of surface waters in the Transantarctic section. Doklady Earth Sciences 486, 562-567. data obtained for 2015–2017 on the content and composition of aliphatic hydrocarbons (HCs) in particulate matter at the river–sea geochemical barriers (the Ob, Yenisei, Lena, Khatanga, Indigirka, and Kolyma rivers–the Kara, Laptev, and East Siberian seas) are presented. It was shown that the HC distribution coincided roughly with the content of particulate matter. The losses of the HC concentrations in mixing zones of riverine and marine waters in some cases exceeded 90% of the riverine supply. The HC concentrations in the pelagic zones of the seas were about the background values (2–7 ?g/L). The behavior and composition of HCs are determined by the features of riverine drainage areas, sampling seasons, and time (high or low tide). The influence of anthropogenic supply was registered exclusively in the Gulf of Ob where the composition of alkanes was close to that of oil, with a HC concentration of 86 ?g per mg of particulate matter. In other samples, natural HCs prevailed.Neumann, E.K., Ellis, J.F., Triplett, A.E., Rubakhin, S.S., Sweedler, J.V., 2019. Lipid analysis of 30?000 individual rodent cerebellar cells using high-resolution mass spectrometry. Analytical Chemistry 91, 7871-7878. measurements aid our understanding of chemically heterogeneous systems such as the brain. Lipids are one of the least studied chemical classes, and their cell-to-cell heterogeneity remains largely unexplored. We adapted microscopy-guided single-cell profiling using matrix-assisted laser desorption/ionization ion cyclotron resonance mass spectrometry to profile the lipid composition of over 30?000 individual rat cerebellar cells. We detected 520 lipid features, many of which were found in subsets of cells; Louvain clustering identified 101 distinct groups that can be correlated to neuronal and astrocytic classifications and lipid classes. Overall, the two most common lipids found were [PC(32:0)+H]+ and [PC(34:1)+H]+, which were present within 98.9 and 89.5% of cells, respectively; lipid signals present in <1% of cells were also detected, including [PC(34:1)+K]+ and [PG(40:2(OH))+Na]+. These results illustrate the vast lipid heterogeneity found within rodent cerebellar cells and hint at the distinct functional consequences of this heterogeneity.Neuzil, C.E., 2019. Permeability of clays and shales. Annual Review of Earth and Planetary Sciences 47, 247-273. low permeability of clays, shales, and other argillaceous lithologies makes them key controls of transport and deformation processes in the crust but is known for being challenging to characterize. As muds are modified by compaction and diagenesis to low-porosity shales, permeability can decrease by six or more orders of magnitude, but at large scales it is often dramatically and unpredictably increased by fractures, faults, and other features. Testing and inverse modeling show that petrophysical properties and the geological environment are dominant controls of clay and shale matrix permeability and its scale dependence. Active sedimentation and tectonism on continental margins cause large-scale permeability to vary with time, but in stable continent interiors it is unclear how regional permeability of argillaceous formations changes over time or, in most cases, what controls it. Although rarely considered, it is also unknown whether Darcian permeability adequately describes flow in clay-rich materials. Ni, Y., Liao, F., Gong, D., Jiao, L., Gao, J., Yao, L., 2019. Stable carbon and hydrogen isotopic characteristics of natural gas from Taibei sag, Turpan-Hami Basin, NW China. Petroleum Exploration and Development 46, 531-542. Basin is a major petroliferous basin in China. To date the natural gas exploration is concentrated in the Taibei sag. The origin and source of natural gas in the Taibei sag has long been controversial. To further investigate the origin and source of the natural gas in the Taibei sag, combined with previous studies and the local geological backgrounds, this study collected 23 gas samples from the Baka, Qiuling, Shanshan and Wenmi oil fields in the Taibei sag and analyzed the sample composition, stable carbon and hydrogen isotopes of all the gas samples. The results show that, gases from the four oil fields in the Taibei sag are dominated by hydrocarbon gas and belong to wet gas. Methane accounts for 65.84% to 97.94%, the content of heavy hydrocarbon (C2-5) can be up to 34.98%, while the content of nonhydrocarbon (CO2, N2) is trace. The δ13C1 value is –44.9‰ to –40.4‰, δ13C2 is –28.2‰ to –24.9‰, δ13C3 is –27.1‰ to –18.0‰ and δ13C4 is –26.7‰ to –22.1; while the variation of δD1 is not significant from –272‰ to –252‰, δD2 is –236‰ to –200‰ and δD3 is –222‰ to –174‰. Methane and its homologues (C2-5) are characterized by normal stable carbon and hydrogen isotopic distribution pattern, i.e., with the increase of carbon number, methane and its homologues become more and more enriched in 13C or D (δ13C1<δ13C2<δ13C3<δ13C4<δ13C5, δD1<δD2<δD3), which is consistent with the carbon and hydrogen isotopic features of typical thermogenic gas. All these results show that the natural gases in the four oil fields are coal-derived gas with low maturity (Ro averaged at 0.7%), and are sourced from the Middle-Lower Jurassic coal measure. The hydrogen isotopic data of natural gas are affected by both thermal maturity and the water medium of the environment where source rocks are formed. The hydrogen isotopic data indicate that the source rocks are formed in terrestrial limnetic facies with freshwater. Natural gases from Well Ba23 and Well Ke19 experienced biodegradation in the late stage.Niles, S.F., Chacón-Pati?o, M.L., Chen, H., McKenna, A.M., Blakney, G.T., Rodgers, R.P., Marshall, A.G., 2019. Molecular-level characterization of oil-soluble ketone/aldehyde photo-oxidation products by Fourier transform ion cyclotron resonance mass spectrometry reveals similarity between microcosm and field samples. Environmental Science & Technology 53, 6887-6894. present a solid-phase extraction method followed by derivatization with a charged tag to characterize ketone/aldehyde-containing functionalities (proposed photo-oxidation transformation products) in weathered petroleum by Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). A photo-oxidation-only microcosm mimics solar irradiation of crude oil in the environment after an oil spill. A biodegradation-only microcosm enables independent determination as to which of the two weathering processes contributes to the formation of oil-soluble ketone/aldehyde species. Results confirm that photo-oxidation produces ketones/aldehydes in crude oil when exposed to solar radiation in laboratory experiments, whereas biodegraded oil samples do not produce ketone/aldehyde compounds. Field samples collected after different time periods and locations after the Deepwater Horizon oil spill are also shown to contain ketones/aldehydes, and comparison of field and photo-oxidation-only microcosm transformation products reveal remarkable similarity. These results indicate that the photo-oxidation microcosm comprehensively represents ketone/aldehyde-formation products in the field, whereas the biodegradation microcosm does not. Solid-phase extraction coupled with derivatization leads to selective identification of ketone/aldehyde species by MS. Although improved dynamic range and slightly reduced mass spectral complexity is achieved by separation/derivatization, comprehensive molecular characterization still requires mass resolving power and mass accuracy provided by FT-ICR MS.Nims, C., Cron, B., Wetherington, M., Macalady, J., Cosmidis, J., 2019. Low frequency Raman Spectroscopy for micron-scale and in vivo characterization of elemental sulfur in microbial samples. Scientific Reports 9, Article 7971. sulfur (S(0)) is an important intermediate of the sulfur cycle and is generated by chemical and biological sulfide oxidation. Raman spectromicroscopy can be applied to environmental samples for the detection of S(0), as a practical non-destructive micron-scale method for use on wet material and living cells. Technical advances in filter materials enable the acquisition of ultra-low frequency (ULF) Raman measurements in the 10–100?cm?1 range using a single-stage spectrometer. Here we demonstrate the potency of ULF Raman spectromicroscopy to harness the external vibrational modes of previously unrecognized S(0) structures present in environmental samples. We investigate the chemical and structural nature of intracellular S(0) granules stored within environmental mats of sulfur-oxidizing γ-Proteobacteria (Thiothrix). In vivo intracellular ULF scans indicate the presence of amorphous cyclooctasulfur (S8), clarifying enduring uncertainties regarding the content of microbial sulfur storage globules. Raman scattering of extracellular sulfur clusters in Thiothrix mats furthermore reveals an unexpected abundance of metastable β-S8 and γ-S8, in addition to the stable α-S8 allotrope. We propose ULF Raman spectroscopy as a powerful method for the micron-scale determination of S(0) structure in natural and laboratory systems, with a promising potential to shine new light on environmental microbial and chemical sulfur cycling mechanisms.Ning, Z., Li, R., Lian, K., Liao, P., Liao, H., Liu, C., 2019. Transport and retention of Shewanella oneidensis strain MR1 in water-saturated porous media with different grain-surface properties. Chemosphere 233, 57-66. Shewanella oneidensis strain (MR1), a facultative microorganism that plays critical role in contaminant transformation and degradation, was used as an example to decipher the transport and retention of microorganisms in water-saturated porous media with different grain-surface properties and under different ionic compositions (i.e. Na+, Ca2+, and Mg2+). Dolomite and quartz sands, which contained different surface charge properties, were used as the representative minerals. Dolomite was selected because its surface charges are significantly affected by solution composition. The mobility of MR1 in the dolomite column was lower than that in the quartz column, because the lower energy barrier between MR1 and dolomite than that between MR1 and quartz, resulting in the larger retention of MR1 in the dolomite column. The breakthrough curves were well simulated by the two sites kinetic model with HYDRUS-1D. The maximum concentration of attached bacteria (Smax) were positively correlated to the ionic strength regardless of mineral types. The values of Smax were about 1.1–4.0 times larger in the MR1-dolomite system than that in the MR1-quartz system under different ionic strength conditions. The retention of the MR1 on dolomite surfaces in the presence of divalent cations Ca2+ is significantly higher than that on quartz surfaces primarily due to the larger electrostatic attraction energy between the MR1 and dolomite grains. The findings demonstrate that the porous media with the lower negative charge has the higher capacity for the retention and deposition of MR1, potentially affecting the transport of MR1 and other bacteria in the subsurface.Niu, X.-Z., Croué, J.-P., 2019. Photochemical production of hydroxyl radical from algal organic matter. Water Research 116, 11-16. production of hydroxyl radical (·OH) from algal organic matter (AOM) collected from Lake Torrens in South Australia was examined using a sunlight simulator. The two AOM isolates featured lower molecular weight, lower chromophoric content, and lower SUVA254 (0.7 and 0.9, L mgC?1 m?1) than the reference Suwannee River hydrophobic acid (SR-HPO), they had considerably higher apparent quantum yields (?NOMOH, 3.03?×?10?5 and 2.18?×?10?5) than SR-HPO (0.84?×?10?5). Fluorescence excitation-emission matrix (FEEM) showed that the major components in the AOM were aromatic protein-like and soluble microbial substances. Unique formulas of the two AOM isolates as compared to SR-HPO were revealed using FTICR-MS and classified into four areas, namely protein-like molecules with low O/C (H/C?>?1.5, O/C: 0.2–0.4), lignin-derived moieties with low O/C (H/C:1.0–1.5, O/C: 0.1–0.3), protein-like molecules with high O/C (H/C?>?1.5, O/C: 0.5–0.7), and carbohydrate derivatives (H/C?>?1.5, O/C?>?0.7). These unique AOM moieties characterised utilizing FEEM and FTICR-MS were tentatively postulated to contribute to the high ?NOMOH. To the best of our knowledge, this is the first study performed to both evaluate natural AOM as an efficient photosensitiser of ·OH and propose AOM moieties responsible for the high ?NOMOH.Niu, Z., Yue, T., He, X., Manica, R., 2019. Changing the interface between an asphaltene model compound and water by addition of an EO–PO demulsifier through adsorption competition or adsorption replacement. Energy & Fuels 33, 5035-5042. adding an EO–PO demulsifier, the interface between the asphaltene model compounds and water was changed. The adsorption replacement of C5Pe or C5PeC11 molecules by an EO–PO demulsifier and the competitive adsorption between them were compared. A reduction of the interfacial tension of the C5Pe or C5PeC11–water interface by EO–PO demulsifier addition for the water-in-oil (W/O) and oil-in-water (O/W) systems was observed, suggesting higher interfacial activities of the EO–PO demulsifier, especially at high EO–PO demulsifier concentrations. Crumpling ratios of the flat C5Pe–water interfacial film for W/O and O/W systems were also measured, and the results showed that the EO–PO demulsifier was capable of softening and weakening the interfacial films for both systems. The EO–PO demulsifier showed similar performance on changing the C5Pe interfacial film through both diffusion (simulating the W/O system) and spreading (simulating the O/W system) protocols. By investigating the Langmuir interfacial-area isotherms, it was found that the C5Pe–water interfacial film became much more compressible with the addition of the EO–PO demulsifier. The EO–PO demulsifier could also destroy the integrity of the C5Pe interfacial film or avoid a networked film formation as indicated by atomic force microscopy images. In addition, shear rheology measurements showed that the rigidity of the C5Pe interfacial film was dramatically reduced or even absent in the presence of the EO–PO demulsifier. Moreover, the changes in the C5Pe–water interface by the EO–PO demulsifier were similar to those of the EO–PO/asphaltene system, providing further justification for using C5Pe as the asphaltene model compound.Nixon, F.C., Chand, S., Thorsnes, T., Bjarnadóttir, L.R., 2019. A modified gas hydrate-geomorphological model for a new discovery of enigmatic craters and seabed mounds in the Central Barents Sea, Norway. Geo-Marine Letters 39, 191-203. of newly discovered gas seeps, craters, and mounds are presented from the central Barents Sea, Norway. Where they occur together, the crater-mound pairs have a preferred orientation towards the southeast. According to complex cross-cutting relationships with iceberg ploughmarks, both the craters and mounds formed during deglaciation (ca. 11–13 ka BP). Free gas, trapped beneath shallow gas hydrates in discrete areas, deformed or displaced overlying bedrock and sediment, forming mounds. Over-steepened slopes, weak layers, fractured bedrock, and unstable sediment resulted in small landslides towards the southeast: the direction of regional slope. In some cases, the highly buoyant, hydrate-cored sediment mounds may have instead, detached and floated with bottom currents before being re-deposited, either locally or distally. In this scenario, southeasterly flowing bottom currents would also explain the preferred orientation of the observed crater-mound pairs. Crater collapse would have occurred simultaneously or subsequently to landslide or detachment and floating due to the rapid dissociation of any remaining gas hydrates; a result of attendant regional changes in temperature and pressure following deglaciation and local removal of overlying sediment. The model of formation developed in this study explains the southeasterly trend in crater-mound orientation, but differs from other studies that interpret modern mounds, located elsewhere in the Barents Sea, as gas hydrate-cored.Nozaki, K., Nakabayashi, Y., Murakami, T., Miyazato, A., Osaka, I., 2019. Novel approach to enhance sensitivity in surface-assisted laser desorption/ionization mass spectrometry imaging using deposited organic-inorganic hybrid matrices. Journal of Mass Spectrometry 54, 612-619. Sample pretreatment is key to obtaining good data in matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Although sublimation is one of the best methods for obtaining homogenously fine organic matrix crystals, its sensitivity can be low due to the lack of a solvent extraction effect. We investigated the effect of incorporating a thin film of metal formed by zirconium (Zr) sputtering into the sublimation process for MALDI matrix deposition for improving the detection sensitivity in mouse liver tissue sections treated with olanzapine. The matrix-enhanced surface-assisted laser desorption/ionization (ME-SALDI) method, where a matrix was formed by sputtering Zr to form a thin nanoparticle layer before depositing MALDI organic matrix comprising α-cyano-4-hydroxycinnamic acid (CHCA) by sublimation, resulted in a significant improvement in sensitivity, with the ion intensity of olanzapine being about 1800 times that observed using the MALDI method, comprising CHCA sublimation alone. When Zr sputtering was performed after CHCA deposition, however, no such enhancement in sensitivity was observed. The enhanced sensitivity due to Zr sputtering was also observed when the CHCA solution was applied by spraying, being about twice as high as that observed by CHCA spraying alone. In addition, the detection sensitivity of these various pretreatment methods was similar for endogenous glutathione. Given that sample preparation using the ME-SALDI-MSI method, which combines Zr sputtering with the sublimation method for depositing an organic matrix, does not involve a solvent, delocalization problems such as migration of analytes observed after matrix spraying and washing with aqueous solutions as sample pretreatment are not expected. Therefore, ME-Zr-SALDI-MSI is a novel sample pretreatment method that can improve the sensitivity of analytes while maintaining high spatial resolution in MALDI-MSI.Nutman, A.P., Bennett, V.C., Friend, C.R.L., Van Kranendonk, M.J., Rothacker, L., Chivas, A.R., 2019. Cross-examining Earth’s oldest stromatolites: Seeing through the effects of heterogeneous deformation, metamorphism and metasomatism affecting Isua (Greenland)?～3700?Ma sedimentary rocks. Precambrian Research 331, Article 105347.?～3700?Ma and 3800?Ma meta-volcanic and -sedimentary rocks in the Isua supracrustal belt (Greenland) were affected by heterogeneous ductile deformation under amphibolite facies conditions (～500–650?°C), and variably modified by secondary silica and carbonate mineralisation deposited from diagenetic and metasomatic fluids. Rare low-deformation areas preserve original volcanic features – submarine basaltic pillows and sedimentary features – including bedding. These are best-preserved in two dimensions on flat- to moderately-inclined outcrop surfaces, but invariably are tectonically-stretched along a steeply-plunging third dimension, through stretching in the direction of fold axes; a style of deformation found throughout Earth’s history. There is a debate about whether rare relicts of?～3700?Ma stromatolites preserved in metadolomites that formed in a shallow marine setting (Nutman et al., 2016) represent bona fide biogenic primary structures fortuitously preserved in low deformation, or whether these structures are manifestations of deformation combined with non-biogenic deposition of secondary carbonate (Allwood et al., 2018). Here, we critically test the primary nature of the sedimentary rocks hosting the proposed stromatolites and also the veracity of the proposed stromatolites, by addressing the following questions: (i) Are the rocks an in situ outcrop of known age, or displaced blocks of unknown age or origin?; (ii) How much of the carbonate is of an originally sedimentary versus a secondary (i.e., metasomatic – introduced) origin?; (iii) Is the seawater-like REE?+?Y (rare earth element and yttrium) trace element signature carried definitely by carbonate minerals and therefore diagnostic of a cool, surficial sedimentary system?; (iv) Are the proposed stromatolites consistent with biogenicity in terms of their geometry and fine-scale layering, or could they be the product of soft sediment or structural deformation (compression in folding)? The answers to these questions, which combine diverse observations from geologic context, geochemistry and stromatolite morphology show that the weight of evidence is consistent with a biogenic origin for the stromatolites formed in a shallow water setting and are inconsistent with formation entirely through inorganic processes.Offord, C., 2019. Quantum biology may help solve some of life’s greatest mysteries. The Scientist 2019, the remarkable speed of enzyme-catalyzed reactions to the workings of the human brain, numerous biological puzzles are now being explored for evidence of quantum effects.In one of the University of Sheffield’s physics labs, a few hundred photosynthetic bacteria were nestled between two mirrors positioned less than a micrometer apart. Physicist David Coles and his colleagues were zapping the microbe-filled cavity with white light, which bounced around the cells in a way the team could tune by adjusting the distance between the mirrors. According to results published in 2017, this intricate setup caused photons of light to physically interact with the photosynthetic machinery in a handful of those cells, in a way the team could modify by tweaking the experimental setup.1That the researchers could control a cell’s interaction with light like this was an achievement in itself. But a more surprising interpretation of the findings came the following year. When Coles and several collaborators reanalyzed the data, they found evidence that the nature of the interaction between the bacteria and the photons of light was much weirder than the original analysis had suggested. “It seemed an inescapable conclusion to us that indirectly what [we were] really witnessing was quantum entanglement,” says University of Oxford physicist Vlatko Vedral, a coauthor on both papers.Quantum entanglement refers to the states of two or more particles being interdependent, regardless of the distance separating them. It’s one of many counterintuitive features of the subatomic landscape, in which particles such as electrons and photons behave as both particles and waves simultaneously, occupy multiple positions and states at once, and traverse apparently impermeable barriers. Processes at this scale are captured in the complex mathematical language of quantum mechanics, and frequently produce effects that appear to defy common sense. (See Glossary: Quantum Terminology infographic.) It was using this language that Vedral and colleagues had detected signatures of entanglement between photons and bacteria in data from the Sheffield experiment.Researchers have demonstrated entanglement many times in inanimate objects—in 2017, scientists reported they’d managed to maintain this interdependence between pairs of photons separated by 1,200 kilometers. But if Vedral and colleagues’ proposal that the phenomenon was taking place in bacteria is correct, the study could mark the first time entanglement has been observed inside a living organism, and add to a growing body of evidence that quantum effects are not as unusual in biology as once believed.2That quantum phenomena might be observable in the messy world of living systems is historically a fringe idea. While quantum theories accurately describe the behavior of the individual particles making up all matter, scientists have long presumed that the mass action of billions of particles jostling around at ambient temperature drowns out any weird quantum effects and is better explained by the more familiar rules of classical mechanics formulated by Isaac Newton and others. Indeed, researchers studying quantum phenomena often isolate particles at temperatures approaching absolute zero—at which almost all particle motion grinds to a halt—just to quash the background noise.“The warmer the environment is, the more busy and noisy it is, the quicker these quantum effects disappear,” says University of Surrey theoretical physicist Jim Al-Khalili, who coauthored a 2014 book called Life on the Edge that brought so-called quantum biology to a lay audience. “So it’s almost ridiculous, counterintuitive, that they should persist inside cells. And yet, if they do—and there’s a lot of evidence suggesting that in certain phenomena they do—then life must be doing something special.”Al-Khalili and Vedral are part of an expanding group of scientists now arguing that effects of the quantum world may be central to explaining some of biology’s greatest puzzles—from the efficiency of enzyme catalysis to avian navigation to human consciousness—and could even be subject to natural selection.“The whole field is trying to prove a point,” says Chiara Marletto, a University of Oxford physicist who collaborated with Coles and Vedral on the bacteria-entanglement paper. “That is to say, not only does quantum theory apply to these [biological systems], but it’s possible to test whether these [systems] are harnessing quantum physics to perform their functions.”Quantum effects in biology’s fundamental reactionsBy the mid-1980s, University of California, Berkeley, biochemist Judith Klinman was convinced that the traditional explanation of enzyme catalysis was incomplete. Contemporary theories held that enzymes interact with substrates on the basis of shape and classical mechanics, physically bringing together substrates at their active sites and stabilizing transition states of molecular structure to accelerate reaction rates up to a trillionfold or more. But Klinman had been getting odd results from in vitro experiments with an enzyme extracted from yeast.In catalyzing the oxidation of benzyl alcohol to benzaldehyde, the alcohol dehydrogenase enzyme shifts a hydrogen atom from one position to another. Unexpectedly, when Klinman and her colleagues replaced specific hydrogen atoms in the substrate with the heavier isotopes deuterium and tritium, the reaction drastically slowed down. Although classical explanations of enzyme catalysis allowed for modest isotope effects, they couldn’t account for the large drop in rate Klinman observed. “What we saw were deviations from the existing theories,” she says.Her team kept investigating, and, in 1989, published an explanation building on ideas already circulating among enzyme researchers: that catalysis involves a quantum trick called tunneling.3 Quantum tunneling is like kicking a football through a hill, explains Al-Khalili—where the football is an electron or another particle, and the hill is an energy barrier preventing a reaction from happening. “In the classical world you have to kick it hard enough to get it up the hill and down the other side,” he says. “In the quantum world, you don’t have to. It can go halfway up, disappear, and reappear on the other side.”Klinman’s team posited in this and later papers that, during the catalysis of benzyl alcohol oxidation and many other reactions, hydrogen transfer takes place with assistance from tunneling. This helps explain why deuterium and tritium often hold reactions up—heavier particles are worse at tunneling, and can make tunneling harder for other particles in the same molecule. The effects observed by Klinman’s group have since been replicated by other labs for multiple enzymes and provide some of the strongest evidence for quantum effects in biological systems, Al-Khalili says. (See infographic.)But while it’s now generally accepted that tunneling occurs in biological catalysis, researchers are divided on how much it matters—and whether it might be subject to natural selection. Chemist Richard Finke at Colorado State University, for example, showed that some reactions exhibit isotope effects to a similar degree whether or not an enzyme is present, suggesting that it’s unlikely that enzymes are particularly adapted to enhance tunneling effects in the reactions they catalyze.4 It’s also unclear how much tunneling speeds up reactions; some researchers argue that the effect generally contributes no more than a small boost to processes governed primarily by classical mechanics.Klinman says she thinks that tunneling in enzymes is far more fundamental. “Our view is that enzymes create very precise and compact active site structures” that promote tunneling, she says. During catalysis, for example, enzymes change conformation in a way that can bring hydrogen donor and acceptor sites close enough—within about 0.27 nanometers of each other—to facilitate tunneling, she notes.Her group has pursued the idea by mutating enzymes’ active sites and observing how reaction rates and isotope effects change in vitro. Earlier this year, for example, the team created a version of soybean lipoxygenase that slightly mispositions its substrates in a way that should make hydrogen tunneling unfavorable. Compared with the wild type, the mutant enzyme’s catalytic power is four orders of magnitude lower, and it’s much more sensitive to the replacement of hydrogen with deuterium.5Researchers are still quantifying tunneling’s role in catalysis, and Klinman emphasizes the importance of using multiple methods, including mutagenesis and computational modeling, to understand exactly how proteins speed up reactions. Experimental evolution of enzymes, in which researchers repeatedly select proteins to increase their catalytic power, could also offer insight into tunneling’s contribution—although at least one recent attempt to do this was inconclusive. Last year, a team that evolved an enzyme catalyzing a reaction involving hydrogen transfer reported that quantum tunneling was “not observed to significantly change” across the evolutionary process.6The debate mirrors an ongoing conversation about the functional importance of quantum phenomena in another of Earth’s critical biological processes, photosynthesis. While Vedral and colleagues are investigating whether bacteria’s photosynthetic machinery becomes entangled with photons, other groups have been studying how another quantum effect could help maximize the efficiency of photosynthetic energy transfer.During the light-harvesting reaction in plants and some microbes, photons excite electrons contained in chlorophyll molecules to create entities called excitons. These excitons are then transferred from chlorophyll molecule to chlorophyll molecule until they reach the reaction center—a cluster of proteins where their energy can be captured and stored.Excitons can lose energy as they’re transferred, meaning that the more roundabout their routes are among the chlorophyll molecules, the less energy reaches the reaction center. Physicists suggested decades ago that this wastefulness could be averted if the transfer process was quantum coherent. That is, if excitons could travel like waves rather than particles, they could simultaneously try out all paths to the reaction center and take only the most efficient route. (See illustration.)In 2007, a team led by chemists Graham Fleming of the University of California, Berkeley, and Robert Blankenship of Washington University in St. Louis claimed to have observed quantum coherence in complexes of chlorophyll molecules extracted from green sulfur bacteria, photosynthetic microbes often found in the deep ocean where light availability is low. The researchers used a technique that analyzes the energy absorbed and emitted by a sample, and detected a signal called quantum beating—oscillations they interpreted as evidence of coherence—in complexes cooled to 77 Kelvin. Over the next few years, they and other groups replicated the results at ambient temperatures,8 and extended the findings to chlorophyll complexes from marine algae9 and spinach.10Whether these results reflect a meaningful quantum contribution to energy transfer in photosynthesis is up for debate. In 2017, for example, researchers in Germany took another look at green sulfur bacteria and reported that the coherence effect lasted less than 60 femtoseconds (0.00006 nanoseconds)—too brief to aid energy transfer to the reaction center.11 But last year, another group argued that there are multiple types of coherence in chlorophyll complexes, and some do appear to last long enough to be useful in photosynthesis.12 Other scientists point to hints that some bacteria can switch coherence effects on or off by producing different forms of a key light-harvesting protein.13 Such findings have reignited speculation that, like enzymes, photosynthetic machinery might have evolved to exploit quantum phenomena.Coherence effects in photosynthesis are now a well-accepted phenomenon, says Blankenship. As is the case for tunneling in enzymes, “the most relevant discussion at this point is whether they really have an effect on [the] efficiency of the system or some other aspect of it that gives a real biological benefit. I think the jury’s still out.”Quantum explanations for puzzles in animal biologyEvery winter, European robins in the northern part of the continent migrate hundreds of kilometers south to the Mediterranean. It’s a navigational feat made possible by magnetoreception—specifically, the birds’ ability to detect the direction of the Earth’s magnetic field. But early attempts to explain this sixth sense, including the proposal that birds rely on internal magnetite crystals, failed to garner experimental support.By the late 1990s, the problem had caught the eye of Thorsten Ritz, then a graduate student working on quantum effects in photosynthesis under the supervision of the late biophysicist Klaus Schulten at the University of Illinois at Urbana-Champaign. He became particularly interested in cryptochrome, a light-sensitive protein found in the retinas of birds for which there’s now “good evidence” of a role in magnetoreception, says Ritz, who has since moved to the University of California, Irvine. So in 2000, focusing on this protein and building on Schulten’s earlier theoretical work, Ritz, Schulten, and another Illinois colleague published what would come to be known as the radical-pair model to explain how magnetoreception might operate.14The researchers proposed that reactions in the cryptochrome protein generate a pair of radicals—molecules that each have a lone electron. The behavior of those electrons, which can be quantumly entangled with each other, is sensitive to the alignment of weak magnetic fields such as the Earth’s. Changes in the alignment of this pair relative to the magnetic field could theoretically trigger downstream chemical reactions, allowing the information to be somehow transmitted to the brain. (See illustration.)The hypothesis generated a handful of predictions that Ritz went on to test in collaboration with the biologists who first described magnetoreception in robins, Roswitha and Wolfgang Wiltschko. In a study published in 2004, for example, the team exposed robins to magnetic fields oscillating at frequencies and angles that the model predicted would disrupt the radical pair’s sensitivity to the Earth’s magnetic field—and effectively knocked out the birds’ ability to navigate.15The idea has taken off since then, with growing theoretical support. And two 2018 studies of the molecular properties and expression patterns of one version of cryptochrome, Cry4, point to the protein as a likely candidate magnetoreceptor in zebra finches16 and European robins.17More work is needed to determine whether or not avian magnetoreception really works this way, and to reveal if entanglement between the electrons of the radical pair is important. Scientists also don’t fully understand how cryptochrome could communicate magnetic field information to the brain, says Ritz. Meanwhile, his group is focused on mutagenesis experiments, which could help unravel cryptochrome’s magnetosensitivity. Last fall, University of Oxford chemist Peter Hore and biologist Henrik Mouritsen of the University of Oldenburg in Germany won European funding for QuantumBirds, a project with similar aims.Magnetoreception isn’t the only puzzle in animal sensory biology that’s generated interest among quantum physicists; another scientifically mysterious sense that researchers hope to help crack is olfaction. The traditional theory—that odorant molecules fit into protein receptors on olfactory neurons to trigger smells—faces the challenge that some molecules with almost identical shapes have completely different odors, while others with different stereochemistry smell alike.In the mid-1990s, University College London (UCL) biophysicist Luca Turin, now a respected perfume critic, proposed that olfactory receptors might be sensitive not just to shape, but to the frequencies of vibrating bonds in odorant molecules.18 He argued that when an odorant binds to a receptor, if its bonds are vibrating at a certain frequency they can facilitate the quantum tunneling of electrons within that receptor. This transfer of electrons, according to his model, triggers a signaling cascade in the olfactory neuron that ultimately sends an impulse to the brain.Experimental evidence for the idea is still elusive, says Jenny Brookes, a UCL physicist who has formulated the problem mathematically to show that it’s theoretically feasible. “But that’s partly why it’s quite exciting.” In recent years, researchers have looked for isotope effects similar to the ones found in enzyme function. If tunneling plays a substantial role, odorant molecules containing heavier hydrogen isotopes should smell different from normal versions due to the lower vibration frequencies of their bonds.The findings are mixed. In 2013, Turin’s group reported that humans can distinguish between odorants containing different isotopes.19 Two years later, other researchers failed to reproduce the results and called the theory “implausible.”20 But the idea didn’t go out of fashion. In 2016, another team reported that honey bees can differentiate odors with different isotopes,21 while a recent theoretical study presents a suite of new predictions to help test the model’s validity.22Theoretical work is also driving interest in quantum biological explanations with far less experimental support. For example, some researchers have speculated that the coherence effects posited to play a role in photosynthesis could also contribute to such widespread biological phenomena as vision and cellular respiration. Others have suggested that proton tunneling could promote spontaneous mutations in DNA, although theoretical work by Al-Khalili and colleagues suggest this isn’t terribly likely, at least for the adenine-thymine base pairs they modeled.23Perhaps the most extreme extension of quantum physics to the animal kingdom is the idea that weird quantum effects might play a role in the human brain. University of California, Santa Barbara, physicist Matthew Fisher has argued that neurons possess molecular machinery capable of behaving like a quantum computer, which instead of using bits of 0s or 1s operates with qubits, units of information that can have states of both 0 and 1 simultaneously.24The brain’s qubits, Fisher proposed, are encoded in the states of phosphate ions inside Posner molecules, clusters of phosphate and calcium found in bone and possibly within certain cells’ mitochondria. Recent theoretical work by his team argues that the states of phosphate ions in different Posner molecules could be entangled with one another for hours or even days, and may therefore be able to perform rapid and complex computations.25 Fisher recently received funding to set up an international collaboration, called QuBrain, to look for these effects experimentally. Many neuroscientists have expressed skepticism that the project will turn up positive results.Putting quantum biology to workMost ideas in quantum biology are still driven more by theory than by experimental support, but a number of researchers are now trying to close the gap. Vedral’s team plans to collect more data on bacterial entanglement later this year, and physicist Simon Gr?blacher of Delft University of Technology in the Netherlands has proposed carrying out entanglement experiments with tardigrades. In 2017, Al-Khalili and his Life on the Edge coauthor, University of Surrey biologist Johnjoe McFadden, helped establish a doctoral training center for quantum biology to encourage interdisciplinary crosstalk and advance research efforts. Among the wider community of scientists and research funders, “now you’re not considered completely mad if you say you’re studying quantum mechanics in biology,” McFadden says. “It’s just considered a little bit wacky.”Researchers who spoke to The Scientist also emphasize that, whether or not the theorized mechanisms garner experimental support, the speculation in quantum biology is itself valuable. “As we miniaturize our technology, we have a wealth of information in the biological world from which to draw inspiration,” says theoretical physicist and quantum computing researcher Adriana Marais, head of innovation at tech company SAP Africa. “This is a fantastic opportunity to investigate what life is, but also to learn lessons on how to engineer processes at this microscale in an optimal way.”Real-world applications encompass technologies from more-efficient solar cells to new classes of biosensors. Last year, one group proposed a design for a “biomimetic nose,” based partly on the quantum theory of olfaction, to detect tiny concentrations of odorants.26 And Hore and others have highlighted the radical-pair mechanism that may underlie magnetoreception for use in devices to sense weak magnetic fields.“We can use the information we gain to design systems on these principles,” says Ritz, “even if it turns out that that’s not how birds do it.”References1.D. Coles et al., “A nanophotonic structure containing living photosynthetic bacteria,” Small, doi:10.1002/smll.201701777, 2017.2.C. Marletto et al., “Entanglement between living bacteria and quantized light witnessed by Rabi splitting,” J Phys Commun, 2:101001, 2018. 3.Y. Cha et al., “Hydrogen tunneling in enzyme reactions,” Science, 243:1325–30, 1989.4.K.M. Doll et al., “The first experimental test of the hypothesis that enzymes have evolved to enhance hydrogen tunneling,” J Am Chem Soc, 125:10877–84, 2003. 5.S. Hu et al., “Biophysical characterization of a disabled double mutant of soybean lipoxygenase: The ‘undoing’ of precise substrate positioning relative to metal cofactor and an identified dynamical network,” J Am Chem Soc, 141:1555–67, 2019. 6.N.-S. Hong et al., “The evolution of multiple active site configurations in a designed enzyme,” Nat Commun, 9:3900, 2018. 7.G.S. Engel et al., “Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems,” Nature, 446:782–86, 2007. 8.G. Panitchayangkoon et al., “Long-lived quantum coherence in photosynthetic complexes at physiological temperature,” PNAS, 107:12766–70, 2010.9.E. Collini et al., “Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature,” Nature, 463:644–47, 2010.10.T.R. Calhoun et al., “Quantum coherence enabled determination of the energy landscape in light-harvesting complex II,” J Phys Chem B, 113:16291–95, 2009.11.H.-G. Duan et al., “Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer,” PNAS, 114:8493–98, 2017. 12.E. Thyrhaug et al., “Identification and characterization of diverse coherences in the Fenna–Matthews–Olson complex,” Nat Chem, 10:780–86, 2018. 13.S.J. Harrop et al., “Single-residue insertion switches the quaternary structure and exciton states of cryptophyte light-harvesting proteins,” PNAS, 111:E2666–75, 2014.14.T. Ritz et al., “A model for photoreceptor-based magnetoreception in birds,” Biophys J, 78:707–18, 2000. 15.T. Ritz et al., “Resonance effects indicate a radical-pair mechanism for avian magnetic compass,” Nature, 429:177–80, 2004. 16.A. Pinzon-Rodriguez et al., “Expression patterns of cryptochrome genes in avian retina suggest involvement of Cry4 in light-dependent magnetoreception,” J Roy Soc Int, doi:10.1098/rsif.2018.0058, 2018.17.A. Günther et al., “Double-cone localization and seasonal expression pattern suggest a role in magnetoreception for European robin cryptochrome 4,” Curr Biol, 28: 211–23.E4, 2018.18.L. Turin, “A spectroscopic mechanism for primary olfactory reception,” Chem Senses, 21:773–91, 1996.19.S. Gane et al., “Molecular vibration-sensing component in human olfaction,” PLOS ONE, 8:e55780, 2013.20.E. Block et al., “Implausibility of the vibrational theory of olfaction,” PNAS, 112:E2766–74, 2015.21.M. Paoli et al., “Differential odour coding of isotopomers in the honeybee brain,” Sci Rep, 6:21893, 2016.22.A. Tirandaz et al., “Validity examination of the dissipative quantum model of olfaction,” Sci Rep, 7:4432, 2017.23.A.D. Godbeer et al., “Modelling proton tunnelling in the adenine–thymine base pair,” Phys Chem Chem Phys, 17:13034–44, 2015. 24.M.P.A. Fisher, “Quantum cognition: The possibility of processing with nuclear spins in the brain,” Ann Phys, 362:593–602, 2015.25.M.W. Swift et al., “Posner molecules: from atomic structure to nuclear spins,” Phys Chem Chem Phys, 20:12373–80, 2018.26.A. Patil et al., “A quantum biomimetic electronic nose sensor,” Sci Rep, 8:128, 2018.Ogawa, N., Kato, H., Kishida, K., Ichihashi, E., Ishige, T., Yoshikawa, H., Nagata, Y., Ohtsubo, Y., Tsuda, M., 2019. Suppression of substrate inhibition in phenanthrene-degrading Mycobacterium by co-cultivation with a non-degrading Burkholderia strain. Microbiology 165, 625-637. natural environments contaminated by recalcitrant organic pollutants, efficient biodegradation of such pollutants has been suggested to occur through the cooperation of different bacterial species. A phenanthrene-degrading bacterial consortium, MixEPa4, from polluted soil was previously shown to include a phenanthrene-degrading strain, Mycobacterium sp. EPa45, and a non-polycyclic aromatic hydrocarbon (PAH)-degrading strain, Burkholderia sp. Bcrs1W. In this study, we show that addition of phenanthrene to rich liquid medium resulted in the transient growth arrest of EPa45 during its degradation of phenanthrene. RNA-sequencing analysis of the growth-arrested cells showed the phenanthrene-dependent induction of genes that were predicted to be involved in the catabolism of this compound, and many other cell systems, such as a ferric iron-uptake, were up-regulated, implying iron deficiency of the cells. This negative effect of phenanthrene became much more apparent when using phenanthrene-containing minimal agar medium; colony formation of EPa45 on such agar was significantly inhibited in the presence of phenanthrene and its intermediate degradation products. However, growth inhibition was suppressed by the co-residence of viable Bcrs1W cells. Various Gram-negative bacterial strains, including the three other strains from MixEPa4, also exhibited varying degrees of suppression of the growth inhibition effect on EPa45, strongly suggesting that this effect is not strain-specific. Growth inhibition of EPa45 was also observed by other PAHs, biphenyl and naphthalene, and these two compounds and phenanthrene also inhibited the growth of another mycobacterial strain, M. vanbaalenii PYR-1, that can use them as carbon sources. These phenomena of growth inhibition were also suppressed by Bcrs1W. Our findings suggest that, in natural environments, various non-PAH-degrading bacterial strains play potentially important roles in the facilitation of PAH degradation by the co-residing mycobacteria.?ksenv?g, J.H.C., Fossen, M., Farooq, U., 2019. Study on how oil type and weathering of crude oils affect interaction with sea ice and polyethylene skimmer material. Marine Pollution Bulletin 145, 306-315. the fate of spilled oil in cold environments is essential for oil spill response in Arctic areas. The potential for oils to adhere to sea ice and mechanical skimmers can significantly impact the success of oil spill response and influence the fate of oil in the marine environment. Therefore, the affinity of oil to sea ice and skimmer material was quantified experimentally for three different types of oils at various degrees of weathering. Contact angle measurements of crude oil droplets were performed on the top of and under sea ice and polyethylene-based skimmer material, being submerged in seawater (?2?°C). In addition, “dip- and refloat” tests were performed to quantify the adhesion and study the re-floating process of oil from sea ice at ?2?°C (moist ice) and ?20?°C (cold dry ice), and from a skimmer material prior to and subsequently to its submersion in seawater (?2?°C). The results indicated limited interaction of oils with sea ice submerged in seawater, but a strong affinity of oils towards polyethylene-based skimmer material.Okwananke, A., Hassanpouryouzband, A., Vasheghani Farahani, M., Yang, J., Tohidi, B., Chuvilin, E., Istomin, V., Bukhanov, B., 2019. Methane recovery from gas hydrate-bearing sediments: An experimental study on the gas permeation characteristics under varying pressure. Journal of Petroleum Science and Engineering 180, 435-444. this paper, characteristics of gas permeation through gas hydrate-bearing sediments were explored under varying differential pressure for three types of sedimentary core samples, including 100?wt % silica sand, 95?wt % silica sand +5?wt % montmorillonite clay, and consolidated sandstone using a standard core-holder. Results of the experiments indicate that capillary breakthrough, hydrate-forced heave or agglomeration and also Klinkenberg effect play important roles in controlling the gas permeation through different porous sediments, depending on the sediment type and properties such as grain/pore size distribution and degree of consolidation. It was observed that due to the presence of large pores in unconsolidated silica sand core samples, the gas flow is dominated at both hydrate-free and hydrate-bearing cases by the capillary breakthrough mechanism rather than the gas slippage which resulted in direct relationship between the gas permeability and the differential pressure. This mechanism was also observed to be dominant while measuring the gas permeability for the hydrate-free sandstone core sample. For the unconsolidated sand-clay core samples, higher saturation of methane hydrate led to relatively higher gas permeability due to hydrate-forced heave phenomenon which pushed the sediment grains apart from each other or hydrate agglomeration that formed inter-grain pores. Klinkenberg effect became significant for the hydrate-free sand-clay and hydrate-bearing sandstone core samples; however, it was not observed to be dominant in the hydrate-bearing sand-clay core samples due to the hydrate-forced heave and agglomeration until the inlet pressure was sufficiently high.Olds, P., 2019. Hypervelocity impacts and exposed lithospheric mantle: A way to recognize large terrestrial impact basins? Journal of Earth Science 30, 451-459. the Moon and Mars olivine of probable mantle origin is detected at rims of large Late Heavy Bombardment (LHB) age impact basins for which excavation depth estimates exceed crustal thickness estimates. But lunar Crisium size impact basins are not recognized on Earth nor expected in the Phanerozoic from conventional interpretations of crater size frequency distributions. In this study several large circular to elliptical basin structures on Earth, for which hypothesized impact excavation depth would greatly exceed crustal thickness, are examined for the presence of exposed lithospheric mantle, expressed as ophiolite, at the rims. Three Phanerozoic impact basins, modified by plate tectonics and tentatively correlated with “ophiolite obduction” plus global extinction events, are proposed here. These tentatively suggested Phanerozoic impact basins are: (1) Yucatan Basin/Puerto Rico Trench with a Greater Antilles ophiolite rim. Cretaceous-Paleogene Boundary global extinction may correlate with Maastrichtian ophiolite obduction in Southeast Cuba. (2) Loyalty Basin with a New Caledonia ophiolite plus d’Entrecasteaux Ridge rim. Late Eocene global extinction may correlate with obduction of the New Caledonia Peridotite Nappe. (3) Sulu Sea Basin with a Palawan, Sabah etc. ophiolite rim. The Middle Miocene Disruption Event may correlate with ophiolite obduction plus ophiolitic mélange emplacement in Sabah and in Palawan. These originally circular to elliptical belts of exposed lithospheric mantle may serve as strain markers for relative plate motions in the vicinity of plate boundaries during post-impact geologic times. It is further speculated that plate boundaries may be initiated and/or modified by such impacts.Olita, A., Fazioli, L., Tedesco, C., Simeone, S., Cucco, A., Quattrocchi, G., Ribotti, A., Perilli, A., Pessini, F., Sorgente, R., 2019. Marine and coastal hazard assessment for three coastal oil rigs. Frontiers in Marine Science 6, 274. doi: 10.3389/fmars.2019.00274. forecasting and hazard assessment system for oil dispersion from Italian oil rigs was set up within the framework of a national research project. The system is based on 3D hydrodynamic, mesoscale resolving models providing forcing fields for a Lagrangian module of oil dispersion and slick evolution (oil transport and transformation). The tool provides,daily, the outputs of numerical simulations of possible oil spills from extraction platform sites. In this work we present the results for the 3 platforms closest to the Italian coast. Aside the operational usage, the numerical outputs are also stored and adopted to compute statistics of the slick distributions in the coastal and marine areas of interest. The hazard was assessed by means of two different indices (Hazard Index and Occurrence Index) based on the operational system outputs, for the estimation of the hazard at sea (marine hazard or aerial hazard). As short forecasts (2 days long) often do not allow the oil to reach the coast, an extra set of long-period simulations has been performed in order to compute a third Hazard Index (Coastal Hazard Index) suitable to estimate the hazard along the shorelines.\\ The adopted methodology allowed, as a whole, to assess both coastal and marine oil spill hazard due to oil spill extraction activities. The indices constitute a basic informative layer on which the environmental risk could be also evaluated, once opportunely combined with coastal vulnerability and sensitivity layers.Ordo?ez, L., Vogel, H., Sebag, D., Ariztegui, D., Adatte, T., Russell, J.M., Kallmeyer, J., Vuillemin, A., Friese, A., Crowe, S.A., Bauer, K.W., Simister, R., Henny, C., Nomosatryo, S., Bijaksana, S., 2019. Empowering conventional Rock-Eval pyrolysis for organic matter characterization of the siderite-rich sediments of Lake Towuti (Indonesia) using End-Member Analysis. Organic Geochemistry 134, 32-44. and quantitative changes of organic and carbonate carbon in sedimentary records are frequently used to reconstruct past environments, paleoproductivity and sediment provenance. Amongst the most commonly used proxies are Total Organic Carbon (TOC), Mineral Carbon (MinC), as well as Hydrogen (HI) and Oxygen Indices (OI) of organic matter (OM). Rock Eval pyrolysis enables the assessment of these quantitative and qualitative parameters with a single analysis. This is achieved through transient pyrolysis of the samples up to 650?°C followed by combustion up to 850?°C, with hydrocarbons, CO and CO2 measured during the thermal decomposition of both OM and carbonate minerals.Carbonate minerals with low thermal cracking temperatures, such as siderite (<400?°C), can induce significant matrix effects which bias the TOC, MinC and OI Rock-Eval parameters. Here we assess the applicability of End-Member Analysis (EMA) as a means of correcting Rock-Eval thermograms for siderite matrix effects. For this, we performed Rock-Eval pyrolysis on sideritic sediments of Lake Towuti (Indonesia). New thermal boundaries were constrained in Rock-Eval thermograms using EMA to limit siderite matrix effects and improve TOC, MinC and OI calculations. Our approach allowed us to: (1) evaluate the influence of siderite matrix effects on Rock-Eval thermograms; (2) properly exploit a Rock-Eval dataset to characterize the type and sources of OM in siderite-rich sediments and (3) identify the OM behind degradation and mineralization processes. The Rock-Eval dataset revealed sediments with a substantial amount of refractory OM, especially in those where TOC is high and HI characteristic of autochthonous biomass. These results, associated to alternative indices used to assess OM preservation, suggest that refractory OM is residually enriched following strong degradation of labile compounds. Finally, relatively labile and refractory organic fractions may be consumed in the formation of siderite during this sequential process of OM mineralization.Ortega, M.F., García-Martínez, M.-J., Bolonio, D., Canoira, L., Llamas, J.F., 2019. Weighted linear models for simulation and prediction of biodegradation in diesel polluted soils. Science of The Total Environment 686, 580-589. purpose of this research is to find a mathematical model based on a statistical analysis to predict the evolution of the total petroleum hydrocarbons (TPH) concentrations with time in the bioremediation process of diesel contaminated soils. The analysis is useful to compare and ascertain the efficiency of different remediation treatments and the influence of both soil characteristics and initial concentration levels of hydrocarbons on the biodegradation process. An experimental design, considering two types of soil, two concentration levels of hydrocarbons and six different amendments was carried out. A total of 336 laboratory tests were conducted during a year in 48 land plots of 4?×?4?m, spreading over eight field campaigns. The results show, for the first time to the best of our knowledge, that the bioremediation process can be adjusted quantitatively to an exponential model, following a first-order kinetic equation. The model explains correctly the higher efficiency of some treatments. In the case of hydrocarbon concentrations <16,000?mg/kg, it is advisable to use slow-release fertilizer without the use of surfactant; whereas, for concentrations above 30,000?mg/kg, the addition of surfactants improves the results considerably.Oskay, R.G., Bechtel, A., Karayi?it, A.?., 2019. Mineralogy, petrography and organic geochemistry of Miocene coal seams in the K?n?k coalfield (Soma Basin-Western Turkey): Insights into depositional environment and palaeovegetation. International Journal of Coal Geology 210, Article 103205. K?n?k coalfield is located in the south-westernmost part of the Soma Basin in western Turkey and hosts all three Miocene coal seams (from bottom to top: kM2, kM3 and kP1). This study presents the coal-petrographical, mineralogical and organic geochemical features of samples collected from two deep cores. Samples from seam kM2 generally display low ash yields and high TOC content, whereas the kM3 and kP1 seams are characterized by relatively high ash yields and low TOC values. Furthermore, total S content of the kP1 is very high (up to 7.0%, on dry basis). The maceral composition, the coal facies diagrams, and the distributions of n-alkanes and diterpenoids indicate changes of depositional conditions and vegetation in the palaeomires of the kM2 seam during Early Miocene. The precursor peat of kM2 seam started accumulating under limnotelmatic conditions followed by pure telmatic ones. Consequently, initial mixed vegetation was replaced by a conifer-dominant assemblage in the palaeomires, in the upper parts of the kM2 seam.The coal facies indices and high concentrations of n-alkanes, along with the relatively low di-/ (di+tri-)terpenoid ratios, are indicators of the higher contribution of herbaceous species and minor abundance of conifers in the palaeomires of kM3 and kP1 seams. Nevertheless, the mineralogical composition of the kM3 and kP1 seams indicate increased clastic input and alkalinity in the palaeomires that could reduce preservation of organic matter. Thus, high ash yields and low TOC were obtained from these seams. In addition, sulphate-rich water supply along with synchronous pyroclastic air-borne input into the palaeomires caused elevated total S content of the kP1 seam.Ouyang, B., Renock, D., Akob, D.M., 2019. Effects of organic ligands and background electrolytes on barite dissolution. Geochimica et Cosmochimica Acta 256, 6-19. dissolution rates and features were investigated under conditions that combine a variety of organic ligands with different background electrolyte solutions. The organic ligands included low molecular weight organic compounds (LMWO) that can be produced by halophilic bacteria and are common in natural environments, as well as synthetic chelators that were previously studied in barite dissolution. Background electrolyte solutions included deionized water, 0.72?M NaCl and 2?M NaCl solutions designed to simulate freshwater, seawater, and brine fluids, respectively. Barite dissolution rates and corresponding rate constants normalized for saturation states were calculated for most experiments. Equal or lower rates and rate constants for pure LMWO relative to controls at all background electrolyte concentrations and pH values indicated that LMWO do not promote barite dissolution. Synthetic chelators showed higher rates and rate constants at pH 10 at static conditions than controls, indicating enhanced barite dissolution. Distinctive etch pit morphologies on the barite (001) face were observed in the presence of synthetic chelators, suggesting a direct contact dissolution mechanism by synthetic chelators. The effect of synthetic chelators on barite dissolution was significantly reduced in the presence of 2?M NaCl and/or at pH 6.5 due to salting out effects. Under hypersaline conditions, barite dissolution rates and rate constants by bacterial activities were up to four times higher than those of synthetic chelators. The wide range of conditions studied in this work provides insights into prediction of barite dissolution behavior in various natural environments as well as in industrial treatment procedures.Palos, R., Kek?l?inen, T., Duodu, F., Gutiérrez, A., Arandes, J.M., J?nis, J., Casta?o, P., 2019. Screening hydrotreating catalysts for the valorization of a light cycle oil/scrap tires oil blend based on a detailed product analysis. Applied Catalysis B: Environmental 256, Article 117863. the hydrotreating performance of industrial catalysts used for upgrading heavy oils is hampered by the unknown chemistry behind it. In this work, we have used a set of chromatographic and mass spectrometric techniques (APPI/ESI FTICR MS, FID-MS GC?×?GC and PFPD GC) for acquiring a more precise composition of the feed and products of the hydrotreatment of a blend of light cycle oil and scrap tire oil (20?vol%) using three benchmark catalysts: CoMo/Al2O3, NiMo/SiO2-Al2O3 and NiW/USY zeolite. Despite the different nature of the catalysts, the composition of the products was relatively similar, indicating the slower and controlled transformation of the heaviest molecules of the feed, particularly in tire oil. A faithful analysis of these molecules by combining the results of the analysis clarifies the multiple mechanics affecting hydrotreating simultaneously: hydrodearomatization, hydrocracking, hydrodesulfurization, hydrode-oxygenation and hydrodenitrification. An effort has been made to use these results in a quantitative manner for catalyst screening.Palumbo, A.M., Head, J.W., 2019. Oceans on Mars: The possibility of a Noachian groundwater-fed ocean in a sub-freezing martian climate. Icarus 331, 209-225. Noachian climate of Mars is thought by many to have been “warm and wet”, characterized by a global mean annual temperature (MAT) >273?K and abundant rainfall infiltrating into the groundwater system. In this “warm and wet” scenario, when the groundwater system was in contact with the surface in the northern lowlands, a groundwater-fed ocean could form. In contrast, 1-dimensional climate models and 3-dimensional general circulation models (GCMs) are unable to reproduce long-lived, continuous “warm and wet” conditions due to the influence of the faint young Sun when considering a pure CO2-H2O atmosphere; these models instead predict “cold and icy” conditions, characterized by MAT ~225?K and water trapped as snow and ice in the southern highlands. Furthermore, a kilometers-thick globally continuous cryosphere is predicted in this “cold and icy” scenario, precluding direct connection of the groundwater system and the surface, and disfavoring a Noachian northern lowlands ocean. However, global MAT values lack information about regional and seasonal temperature variations, which may vary significantly from global MAT. In this work, we explore whether regional or seasonal temperature variations could permit the formation of a Noachian ocean in a climate with global MAT <273?K. We use a combination of a 3D climate model and a 1D thermal model to determine the climatic conditions in which the required criteria for groundwater release could be met: (1) temperatures above 273?K, required for there to be no cryosphere preventing the groundwater from being released onto the surface, and (2) a sufficiently large groundwater reservoir, required for the groundwater table to intersect the surface. Our results suggest that the formation of a groundwater-fed ocean does not require a continuous and long-lived “warm and wet” climate with global MAT >273?K. If the long-lived Noachian global MAT was >255?K (~30?K above the nominal ambient “cold and icy” climate) and the subsurface contained >63?m global equivalent layer (GEL) of groundwater, then groundwater could be released onto the surface and pond on the floor of the Hellas basin; global MAT >258?K and a subsurface water inventory of >170?m GEL are required for release of groundwater into the topographically lowest regions of Utopia Planitia. If a subsurface water reservoir of ≥770?m GEL existed and local MAT was ≥273?K at Utopia, groundwater release could occur at Utopia and lead to flooding of the northern lowlands and formation of an ocean up to the level of Contact 1. Further, in a “cold and icy” MAT 225?K climate, short-term punctuated heating that raised global MAT to >255?K for at least a few thousand years could lead to groundwater release and flooding of the lowest points on Mars. Under the influence of these very cold climates (global MAT ~255–260?K), these bodies of water would remain ice-free for a geologically short period of time, possibly only a few hundred days, and would completely freeze and sublime in only a few thousand years.Pan, Y., Li, M., Sun, Y., Li, Z., Liu, P., Jiang, B., Liao, Y., 2019. Characterization of free and bound bitumen fractions in a thermal maturation shale sequence. Part 1: Acidic and neutral compounds by negative-ion ESI FT-ICR MS. Organic Geochemistry 134, 1-15. evaluate petroleum generation and expulsion processes, pyrolysis experiments that simulate increased overburden pressures were conducted on an immature organic-rich shale with type-Ⅱ kerogen. Expelled oils and residual rocks with different maturities covering the oil window were recovered from the experiments. The residual rocks were then subjected to stepwise extraction in conjunction with stepwise dissolution of the carbonate and silicate minerals to obtain free and bound bitumen fractions. The compositions of acidic and neutral compounds in both expelled oils and bitumen fractions were investigated by negative-ion electrospray (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Neutral nitrogen compounds were found to only exist in expelled oil and free bitumen, while acidic compounds (typically contain carboxylic functional group(s)) were prevalent in bound bitumen. Oxygen-containing functional groups with high polarity in oxygen-containing compounds and oxygenated nitrogen/sulfur compounds are proposed to be the dominant bonding forces that facilitate the interaction between bitumen and mineral matrix or kerogen. Semiquantitative results of acidic compounds reveal that the distributions of acidic compounds in both free and bound bitumens vary throughout the oil window stage, especially for those in the bound phase after an intense oil expulsion from the shale at Easy%Ro > 0.9. During maturation, acidic compounds in free and bound bitumens gradually decreased in their abundances. However, oil expulsion from the shale brought about a significant redistribution of acidic compounds among expelled oil, free and bound bitumens. These results indicate that polar components in shales are closely related to thermal maturation of organic matter and oil expulsion from the shales in a petroleum system.Pan, Y., Yang, X., Sun, G., Xu, M., 2019. Functional response of sediment bacterial community to iron-reducing bioaugmentation with Shewanella decolorationis S12. Applied Microbiology and Biotechnology 103, 4997-5005. with exogenously functional microbes is a widely used technology in bioengineering and environmental remediation. Generally, the colonization of inoculated bacteria is considered to be the determining factor in technical success. However, increasing reports have shown that bioaugmentation was still effective when the colonization of inoculated bacteria was unsuccessful. Here, an augmentation study with iron-reducing bacteria (IRB, Shewanella decolorationis S12) was conducted in Fe(II)-poor sediments to elucidate the role of exogenously inoculated bacteria for bioaugmentation performance. The results showed that a sufficient amount of IRB inputs enhanced the iron reduction in bioaugmented sediments, even though the exogenous IRB did not colonize after the beginning of the experiment (less than 1% at day 3). The iron reduction function responded to stimulation of the indigenous IRB community such as Clostridium, Cupriavidus, Fervidicella, and Acinetobacter, which comprised less than 1% in the initial sediments. Moreover, compared with microbial community in control sediment, more positive correlations between OTUs were observed for that in S12-added sediments upon network analysis. The pH and oxidation-reduction potential of sediment were found to be the predominant factors shaping the iron-reducing microbial communities. It meant that exogenous IRB successfully trigged functional community via altering microenvironment by the inoculated bacteria. Overall, this study provides a new insight into the understanding of the role of single strain addition in iron-reducing bioaugmentation.Pandey, M.K., Dasgupta, C.N., Mishra, S., Srivastava, M., Gupta, V.K., Suseela, M.R., Ramteke, P.W., 2019. Bioprospecting microalgae from natural algal bloom for sustainable biomass and biodiesel production. Applied Microbiology and Biotechnology 103, 5447-5458. algal bloom consists of promising algal species which could be a feasible option for the source of bulk biomass and biodiesel production. It has been found in five natural fresh water algal blooms (Uttar Pradesh, India), containing high nitrogen (N) (4.6?±?0.32?mg/L) and phosphorus (P) (4.12?±?0.29?mg/L) concentration during spring (23.9–25.9?°C) and summer season (32.0–35.0?°C). Among the isolated algae from naturally occurring bloom, Chlorella sorokiniana MKP01 exhibited highest biomass (1.02?±?0.02?g/L) and lipid content (174.1?±?9.6?mg/L) in untreated tap water and urea/single super phosphate (SSP) in the ratio (2:1). The biodiesel quality was assessed and found to be with the Indian and international standards. Algal bloom was artificially developed in the open pond containing 10,000?l tap water supplemented with Urea/SSP (2:1) for a consistent supply of bulk biomass, yielded 8?kg of total biomass and lipid 1.3?kg.Pang, Y., Chen, S., Soliman, M.Y., Morse, S.M., Hu, X., 2019. Evaluation of matrix swelling behavior in shale induced by methane sorption under triaxial stress and strain conditions. Energy & Fuels 33, 4986-5000. sorption can lead to the volumetric swelling of the shale matrix and reduction of the effective pore volume, which further impacts the gas transportation in micro- and nanopores in shale. At present, it is very challenging to directly measure the pore volume shrinkage (i.e., pore volumetric strain) in the laboratory. In this study, an innovative method is proposed to quantify the pore volumetric strain resulting from the sorption-induced matrix swelling in shale. More specifically, Gibbs methane sorption capacities of the Barnett and Eagle Ford shale core samples were determined via volumetric and gravimetric methods, respectively. Meanwhile, the bulk volume swelling of the shale core sample was also measured during the gas sorption process. Correlations between the sorption-induced bulk and pore volumetric strains were developed to calculate the pore volume shrinkage ascribed to the gas sorption, which was further validated with the measured gas sorption capacities. It is found that the pore volume shrinkage is 3.7–4.8 times greater than the bulk volume swelling during the gas sorption process for the Barnett shale, while such a ratio reaches as high as 59.8–67.1 times for the Eagle Ford shale. In addition, the sorption-induced bulk and pore volumetric strains follow a power law relationship for both Barnett and Eagle Ford shales, which yields a nearly identical absolute gas sorption isotherm with the ones determined using volumetric and gravimetric methods. The results of this study give insight into the feasibility of characterizing the sorption-induced pore volume shrinkage in shales and illustrate the benefits of applying both gravimetric and volumetric methods to evaluate the gas sorption behaviors.Pankratova, G., Hederstedt, L., Gorton, L., 2019. Extracellular electron transfer features of Gram-positive bacteria. Analytica Chimica Acta 1076, 32-47. microorganisms possess the unique ability to transfer electrons to or from solid phase electron conductors, e.g., electrodes or minerals, through various physiological mechanisms. The processes are commonly known as extracellular electron transfer and broadly harnessed in microbial electrochemical systems, such as microbial biosensors, microbial electrosynthesis, or microbial fuel cells. Apart from a few model microorganisms, the nature of the microbe-electrode conductive interaction is poorly understood for most of the electroactive species. The interaction determines the efficiency and a potential scaling up of bioelectrochemical systems.Gram-positive bacteria generally have a thick electron non-conductive cell wall and are believed to exhibit weak extracellular electron shuttling activity. This review highlights reported research accomplishments on electroactive Gram-positive bacteria. The use of electron-conducting polymers as mediators is considered as one promising strategy to enhance the electron transfer efficiency up to application scale. In view of the recent progress in understanding the molecular aspects of the extracellular electron transfer mechanisms of Enterococcus faecalis, the electron transfer properties of this bacterium are especially focused on.Fundamental knowledge on the nature of microbial extracellular electron transfer and its possibilities can provide insight in interspecies electron transfer and biogeochemical cycling of elements in nature. Additionally, a comprehensive understanding of cell-electrode interactions may help in overcoming insufficient electron transfer and restricted operational performance of various bioelectrochemical systems and facilitate their practical applications.Park, E., Hefter, J., Fischer, G., Iversen, M.H., Ramondenc, S., N?thig, E.-M., Mollenhauer, G., 2019. Seasonality of archaeal lipid flux and GDGT-based thermometry in sinking particles of high-latitude oceans: Fram Strait (79°N) and Antarctic Polar Front (50°S). Biogeosciences 16, 2247-2268. relative abundance of individual archaeal membrane lipids, namely of glycerol dialkyl glycerol tetraethers (GDGTs) with different numbers of cyclopentane rings, varies with temperature, which enables their use as a paleotemperature proxy index. The first GDGT-based index in marine sediments called TEX86 is believed to reflect mean annual sea surface temperature (maSST). The TEXL86 is an alternative temperature proxy for “low-temperature” regions (<15?°C), where the original TEX86 proxy calibration shows a larger scatter. However, TEXL86-derived temperatures still display anomalous estimates in polar regions. In order to elucidate the potential cause of the disagreement between the TEXL86 estimate and SST, we analyzed GDGT fluxes and TEXL86-derived temperatures in sinking particles collected with time-series sediment traps in high-northern- and high-southern-latitude regions. At 1296?m depth in the eastern Fram Strait (79°?N), a combination of various transporting mechanisms for GDGTs might result in seasonally different sinking velocities for particles carrying these lipids, resulting in strong variability in the TEXL86 signal. The similarity of flux-weighted TEXL86 temperatures from sinking particles and surface sediments implies an export of GDGTs without alteration in the Fram Strait. The estimated temperatures correspond to temperatures in water depths of 30–80?m, where nitrification might occur, indicating the favorable depth habitat of Thaumarchaeota. In the Antarctic Polar Front of the Atlantic sector (50°?S), TEXL86-derived temperatures displayed warm and cold biases compared to satellite-derived SSTs at 614?m depth, and its flux-weighted mean signal differs from the deep signal at 3196?m. TEXL86-derived temperatures at 3196?m depth and the surface sediment showed up to 7?°C warmer temperatures relative to satellite-derived SST. Such a warm anomaly might be caused by GDGT contributions from Euryarchaeota, which are known to dominate archaeal communities in the circumpolar deep water of the Antarctic Polar Front. The other reason might be that a linear calibration is not appropriate for this frontal region. Of the newly suggested SST proxies based on hydroxylated GDGTs (OH-GDGTs), only those with OH-GDGT–0 and crenarchaeol or the ring index (RI) of OH-GDGTs yield realistic temperature estimates in our study regions, suggesting that OH-GDGTs could be applied as a potential temperature proxy in high-latitude oceans.Park, T., Jeon, M.-K., Yoon, S., Lee, K.S., Kwon, T.-H., 2019. Modification of interfacial tension and wettability in oil–brine–quartz system by in situ bacterial biosurfactant production at reservoir conditions: Implications for microbial enhanced oil recovery. Energy & Fuels 33, 4909-4920. of oil–brine–minerals interfacial properties with biosurfactant-producing microorganisms and their extracellular metabolites has been considered as one of the viable strategies for microbial enhanced oil recovery (MEOR). In this study, the effect of lipopeptide biosurfactant produced by Bacillus subtilis on the interfacial tension (IFT) and wettability in oil–brine–mineral systems was quantitatively examined by monitoring dodecane–brine IFT and the contact angle of a dodecane–brine–quartz system during cultivation of B. subtilis. The effect of high temperature (35–45 °C) and pressure (～10 MPa), emulating conditions of in situ reservoir environments, on the effectiveness of the biosurfactant producers was also assessed using a custom-designed high-pressure bioreactor. Within the examined temperature range, it was confirmed that B. subtilis produced the lipopeptide biosurfactant (surfactin) with and without oxygen using nitrate (NO3–) as the alternative electron acceptor. Thereby, the IFT was reduced from ～50 to ～10 mN/m and the wettability was modified from the values indicating an intermediate water-wet condition (θ = ～45–50°) to a strong water-wet condition (θ = ～20–25°). With the significantly improved capillary factor (γ cos θ) by a factor of 4.4, the two-phase flow simulations using the pore network model estimated significant increases in oil recovery rates in microbially treated reservoirs. The lowest rate and amount of surfactin production were observed at 45 °C, suggesting that higher temperatures may not be favorable for surfactin production by Bacillus spp. These results provide unique quantitative experimental evidence corroborating the feasibility of utilizing biosurfactant-producing microorganisms for MEOR practices targeting reservoirs with high pressure and moderately high temperature.Patterson, B.D., Mo, F., Borgschulte, A., Hillestad, M., Joos, F., Kristiansen, T., Sunde, S., van Bokhoven, J.A., 2019. Renewable CO2 recycling and synthetic fuel production in a marine environment. Proceedings of the National Academy of Sciences 116, 12212-12219.: Humankind must cease CO2 emissions from fossil fuel burning if dangerous climate change is to be avoided. However, liquid carbon-based energy carriers are often without practical alternatives for vital mobility applications. The recycling of atmospheric CO2 into synthetic fuels, using renewable energy, offers an energy concept with no net CO2 emission. We propose to implement, on a large scale, marine-based artificial islands, on which solar or wind energy powers the production of hydrogen and the extraction of CO2 from seawater and where these gases are catalytically reacted to yield liquid methanol fuel. The present work proposes specifications for such facilities and highlights essential challenges in physics, chemistry, and engineering which must be met to realize this ambitious proposal.Abstract: A massive reduction in CO2 emissions from fossil fuel burning is required to limit the extent of global warming. However, carbon-based liquid fuels will in the foreseeable future continue to be important energy storage media. We propose a combination of largely existing technologies to use solar energy to recycle atmospheric CO2 into a liquid fuel. Our concept is clusters of marine-based floating islands, on which photovoltaic cells convert sunlight into electrical energy to produce H2 and to extract CO2 from seawater, where it is in equilibrium with the atmosphere. These gases are then reacted to form the energy carrier methanol, which is conveniently shipped to the end consumer. The present work initiates the development of this concept and highlights relevant questions in physics, chemistry, and mechanics.Paudel, L., Nagana Gowda, G.A., Raftery, D., 2019. Extractive ratio analysis NMR spectroscopy for metabolite identification in complex biological mixtures. Analytical Chemistry 91, 7373-7378. complexity of biological mixtures continues to challenge efforts aimed at unknown metabolite identification in the metabolomics field. To address this challenge, we provide a new method to identify related peaks from individual metabolites in complex NMR spectra. Extractive ratio analysis NMR spectroscopy (E-RANSY) builds on our previously described ratio analysis method [Wei et al. Anal. Chem. 2011, 83, 7616?7623] and exploits the simplified NMR spectra provided by the extraction of metabolites under varied pH conditions. Under such conditions, metabolites from the same biological specimen are extracted differentially, and the resulting NMR spectra exhibit characteristics favorable for unraveling unknown metabolite peaks using ratio analysis. We demonstrate the utility of the E-RANSY method by extracting carboxylic acid containing metabolites from human urine, one of the highly complex biological mixtures encountered in the metabolomics field. E-RANSY performs better than STOCSY and the original RANSY method and offers new avenues to identify unknown metabolites in complex biological mixtures.Paun, V.I., Icaza, G., Lavin, P., Marin, C., Tudorache, A., Per?oiu, A., Dorador, C., Purcarea, C., 2019. Total and potentially active bacterial communities entrapped in a late glacial through Holocene ice core from Scarisoara Ice Cave, Romania. Frontiers in Microbiology 10, 1193. doi: 10.3389/fmicb.2019.01193. understanding of the icy-habitat microbiome is likely limited by a lack of reliable data on microorganisms inhabiting underground ice that has accumulated inside caves. To characterize how environmental variation impacts cave ice microbial community structure, we determined the composition of total and potentially active bacterial communities along a 13,000-year-old ice core from Scarisoara cave (Romania) through 16S rRNA gene Illumina sequencing. An average of 2,546 prokaryotic gDNA operational taxonomic units (OTUs) and 585 cDNA OTUs were identified across the perennial cave ice block and analyzed in relation to the geochemical composition of ice layers. The total microbial community and the putative active fraction displayed dissimilar taxa profiles. The ice-contained microbiome was dominated by Actinobacteria with a variable representation of Proteobacteria, while the putative active microbial community was equally shared between Proteobacteria and Firmicutes. Accordingly, a major presence of Cryobacterium, Lysinomonas, Pedobacter, and Aeromicrobium phylotypes homologous to psychrotrophic and psychrophilic bacteria from various cold environments were noted in the total community, while the prevalent putative active bacteria belonged to Clostridium, Pseudomonas, Janthinobacterium, Stenotrophomonas, and Massilia genera. Variation in the microbial cell density of ice strata with the dissolved organic carbon (DOC) content and the strong correlation of DOC and silicon concentrations revealed a major impact of depositional processes on microbial abundance throughout the ice block. Post-depositional processes appeared to occur mostly during the 4,000–7,000 years BP interval. A major bacterial composition shift was observed in 4,500–5,000-year-old ice, leading to a high representation of Beta- and Deltaproteobacteria in the potentially active community in response to the increased concentrations of DOC and major chemical elements. Estimated metabolic rates suggested the presence of a viable microbial community within the cave ice block, characterized by a maintenance metabolism in most strata and growth capacity in those ice deposits with high microbial abundance and DOC content. This first survey of microbial distribution in perennial cave ice formed since the Last Glacial period revealed a complex potentially active community, highlighting major shifts in community composition associated with geochemical changes that took place during climatic events that occurred about 5,000 years ago, with putative formation of photosynthetic biofilms.Pavlova, O.N., Lomakina, A.V., Novikova, A.S., Chernitsyna, S.M., Khanaeva, T.A., Pogodaeva, T.V., Khabuev, A.V., Zemskaya, T.I., 2019. Thermophilic bacteria in Lake Baikal bottom sediments associated with hydrocarbon discharge. Microbiology 88, 335-342. research was aimed at detection of thermophilic microorganisms in Lake Baikal low-temperature sediments associated with discharge of gas-saturated fluids. Members of the order Clostridiales were revealed in enrichment cultures obtained from the bottom sediments at three sites (methane seep, oil-methane seep, and mud volcano). No thermophilic prokaryotes were found in the enrichment culture with sediment samples from a background area. The presence of thermophilic microorganisms at the sites of hydrocarbon discharge may result from their migration to the bottom surface with the gas-bearing mineralized fluid moving along the fracture zones. Unlike marine cold sediments, where the endospores of thermophilic bacteria belong to strict anaerobes existing due to fermentation of organic substrates or sulfate reduction, Lake Baikal sediments associated with discharge of gas-saturated fluids were found to contain facultatively anaerobic thermophilic prokaryotes.Pei, H., Wang, C., Wang, Y., Yang, H., Xie, S., 2019. Distribution of microbial lipids at an acid mine drainage site in China: Insights into microbial adaptation to extremely low pH conditions. Organic Geochemistry 134, 77-91. of acid mine drainage (AMD), a typically extremely acidic environment, can provide opportunities to determine how microorganisms adapt to low pH environments by regulating membrane lipid compositions. In this study, to gain an understanding of microbial pH adaptation mechanisms, we investigated the distribution of lipid biomarkers, primarily of microbial origin, in an AMD site at Dexing copper mine, Jiangxi, China. Microbial lipid biomarkers, including glycerol dialkyl glycerol tetraethers (GDGTs), monoalkyl glycerol ethers, fatty acids (FAs), 3-hydroxy fatty acids (3-OH-FAs), sterols, and hopanoids, were detected in surface and 10-cm-deep core sediments. Branched FAs and 3-OH-FAs were found to occur at low levels in the extremely low pH conditions. Similarly, there were fewer methyl moieties in branched GDGTs detected in the AMD, as reflected by the lower methylation degree of branched tetraethers, indicating that a reduction in membrane lipid methyl moieties may be a common strategy whereby bacteria adapt to low pH environments. The presence of only small amounts of crenarchaeol in the AMD suggests that the extremely acidic conditions are inimical to the growth of Thaumarchaeota. In contrast, abundant Euryarchaeota inhabit the AMD and produce an isoprenoid GDGT (isoGDGT) profile dominated by GDGT-2, along with GDGT-5 and GDGT-6, which are rarely detected in non-extreme environments. Furthermore, the GDGT-2/(GDGT-1?+?GDGT-3) ratio in the AMD was found to be significantly higher than that in soils and was negatively correlated with pH. These findings indicate that increases in the cyclopentyl rings of isoGDGTs may be favorable for maintaining an osmotic balance across archaeal cell membranes. All the modifications adopted by bacteria and archaea result in more condensed cell membranes.Peng, W., Guo, F., Hu, G., Lyu, Y., Gong, D., Liu, J., Feng, Z., Guo, J., Guo, Y., Han, W., 2019. Geochemistry and accumulation process of natural gas in the Shenmu Gas Field, Ordos Basin, central China. Journal of Petroleum Science and Engineering 180, 1022-1033. chemical and stable isotopic compositions of 24 gas samples were investigated to determine the geochemistry and accumulation process of the Shenmu Gas Field (SGF), Ordos Basin, central China. Natural gas of the SGF includes both wet and dry gas with dryness coefficients (C1/C1?5) between 0.907 and 0.958. δ13C1 and δD1 values range from ?39.4‰ to ?35.6‰ and ?191‰ to ?201‰, respectively, displaying a positive isotopic series. Geochemical characteristics indicate that gases of the upper Paleozoic reservoirs of the SGF are typical coal-type gas, whereas gases of the lower Paleozoic reservoirs are primarily oil-type gas (occasionally containing a small proportion of coal-type gas). Gas-source correlation demonstrates that gases of the upper Paleozoic reservoirs of the SGF display near-source accumulation, primarily derived from the underlying Carboniferous–Permian humic source rocks, while gases of the lower Paleozoic reservoirs in the SGF are mainly sourced from the carbonate Majiagou Formation (O1m). SGF reservoirs were generally tight prior to gas accumulation. Integrated with the maturation process of source rocks, the accumulation process of gas in the SGF could be separated into four stages: prenatal (before early Jurassic), development (early–late Jurassic), prime (early Cretaceous), and formative (late Cretaceous–present).Pérez-del-Olmo, A., Nachev, M., Zimmermann, S., Fernández, M., Sures, B., 2019. Medium-term dynamics of element concentrations in a sparid fish and its isopod parasite after the Prestige oil-spill: Shifting baselines? Science of The Total Environment 686, 648-656., the European Atlantic is probably the most important oil-spill hotspot worldwide. One of the most recent accidents occurred in 2002 when the oil-tanker Prestige sank over the Galician Bank causing two major oil-spills followed by several small leaks until March 2003. This resulted in contamination of virtually all types of marine habitat. Considering that parasites have proved to be good effect and accumulation bioindicators, the present study addresses the medium-term changes in trace element content after the Prestige oil-spill in a model host-parasite system, the bogue, Boops boops (Sparidae) and the isopod Ceratothoa oestroides. To our knowledge, this study is the first to address trace element concentrations in natural fish and parasite populations associated with the effects of an oil-spill. We observed that both test organisms examined, the host and the parasite, indicate a detectable change in the relative composition of trace element concentrations before and after the Prestige oil-spill. Multivariate analyses also indicated a differential response of the different tissues to the temporal sampling sequence. However, analyses of both host and parasite tissues supported the pattern of a gradual temporal transition to a state of relative trace element content distinctly departing from the pre-spill situation. Moreover, the parasite-host element accumulation ratios better depicted this temporal pattern. Additionally, changes in V concentrations in fish liver tissues and Ni concentrations in the parasite tissues suggest that this host-parasite system may be a useful tool to assess these two element contaminations linked to heavy fuel oil-spill.Perez, A., Rossano, S., Trcera, N., Verney-Carron, A., Rommevaux, C., Fourdrin, C., Agnello, A.C., Huguenot, D., Guyot, F., 2019. Direct and indirect impact of the bacterial strain Pseudomonas aeruginosa on the dissolution of synthetic Fe(III)- and Fe(II)-bearing basaltic glasses. Chemical Geology 523, 9-18. study investigates the direct and indirect bacterial contributions that influence the dissolution of basaltic glass. In this regard, three different types of glasses – with or without Fe, in the reduced Fe(II) or oxidized Fe(III) states – were prepared on the basis of a simplified basaltic glass composition. In order to prevent the direct contact between the glasses and the model siderophore-producing strain Pseudomonas aeruginosa, the glass samples were isolated in dialysis bags and immersed at 25?°C and pH?6.5 in bacterial cultures. Throughout the dissolution experiments, the following parameters were monitored: determination of bacterial growth, quantification of siderophore (i.e. pyoverdine) production, microscopic observation of the glass surface and determination of dissolution kinetics.Isolating the glass from the bacterial suspension only triggered the biosynthesis of siderophores in the Fe(III)-bearing glass dissolution experiments. Siderophores were produced in the presence of Fe(II)-bearing and Fe-free glass, independently on the experimental setup. The siderophore production appeared to be either continuous in the absence of Fe (glass-free control, Fe-free glass dissolution experiments) or stopped as soon as the bacteria entered their stationary phase when an Fe source was present (Fe(II) and Fe(III)-bearing glass dissolution experiments). The increase in the dissolution rates of each glass was correlated to the complex stability constants of the siderophore with the metallic cations in presence (KFe2+?<?KAl3+???KFe3+). Among the three glasses, only the Fe(III)-bearing one seemed to be significantly impacted by the dialysis process: its dissolution rate was doubled by isolating the glass grains from the cells. These results particularly allow to separate the impact of such bacterial exudates from physical contact effects: they showed the efficiency of pyoverdine in increasing the dissolution of an Fe(III)-bearing glass and evidenced that a direct bacterial cell attachment to the surface of such a glass results in a more moderate enhancement of its dissolution process. This work is a new contribution regarding the high affinity of microorganisms for basaltic glasses as an Fe-source. It highlights the role of Fe(III) accessibility upon the bacterial cells as a key parameter regulating their activity and their efficiency in accelerating the dissolution.Perez Calderon, L.J., Gontikaki, E., Potts, L.D., Shaw, S., Gallego, A., Anderson, J.A., Witte, U., 2019. Pressure and temperature effects on deep-sea hydrocarbon-degrading microbial communities in subarctic sediments. MicrobiologyOpen 8, Article e00768. Hatton-Rockall Basin (North-East Atlantic) is an area with potential for deep-sea (2,900?m) hydrocarbon exploration. Following the Deepwater Horizon oil spill, many investigations into the responses of sediment microbial communities to oil pollution have been undertaken. However, hydrostatic pressure is a parameter that is often omitted due to the technical difficulties associated with conducting experiments at high pressure (>10?MPa). In this study, sediments from 2,900?m in the Hatton-Rockall Basin, following a one-week decompression period in a temperature-controlled room at 5°C, were incubated in factorial combinations of 0.1 and 30?MPa, 5 and 20°C, and contamination with a hydrocarbon mixture or uncontaminated controls to evaluate the effect of these environmental variables on the bacterial community composition. Our results revealed varying effects of pressure, temperature, and oil contamination on the composition of the bacterial community within the sediment. Temperature was the strongest determinant of differences in the bacterial community structure between samples followed by pressure. Oil contamination did not exert a strong change in the sediment bacterial community structure when pressure and temperature conditions were held at in situ levels (30?MPa and 5°C). The γ-proteobacteria Pseudomonas and Colwellia, and several Bacteroidetes dominated communities at 30?MPa. In contrast, hydrocarbon degraders such as Halomonas, Alcanivorax, and Marinobacter decreased in relative abundance at the same pressure. This study highlights the importance of considering hydrostatic pressure in ex situ investigations into hydrocarbon-degrading deepwater microbial communities.Pescini, V., 2019. Which origin for charcoal in soils? Case-studies of Environmental Resources Archaeology (ERA) from the Ligurian Apennines, seventh to the twentieth century. Frontiers in Environmental Science 7, 77. doi: 10.3389/fenvs.2019.00077., soils types such as Amerindian “Terra Preta” or “charcoal earth” are considered as archaeological/anthropogenic soils, where explicit human impacts have transformed the patterns, chemistry and shape of the soil. There are several woodmanship practices, poorly visible in archaeological features, that have modified the characteristics of these soils and sediments. Today, these activities are difficult to identify, especially those relating to the multiple management of environmental resources (e.g. agro-sylvo-pastoral systems) due to their abandonment and disappearance in southern Europe during the 19th and 20th centuries. Describing a selection of researches conducted by the Laboratory of Archaeology and Environmental History (LASA) team in the Ligurian Apennines, this article explores the potential role of Environmental Resources Archaeology (ERA) and site(s)-level historical ecology approaches to past land use and woodmanship practices characterisation. In particular, focus is given to the practices derived from analysis of microcharcoal in the soils and sediments. Such an approach involves and combines the use of multiple sources (documentary, oral, observational and bio-stratigraphic sources), a regressive analysis method and a strong spatial and social contextualization.Pfeiffer-Herbert, A.S., Prahl, F.G., Peterson, T.D., Wolhowe, M., 2019. Methane dynamics associated with tidal processes in the lower Columbia River. Estuaries and Coasts 42, 1249-1264. varying methane (CH4) concentrations in estuaries may arise from physical advection and by chemical effects tied to varying exposure to salinity. An investigation of spatial and temporal variability in water-column CH4 was conducted in the lower Columbia River using shipboard surveys and time series data from fixed stations. Peaks in CH4 coincided with ebb tides at multiple sites located along the flank of the estuary adjacent to tidal flats and wetlands. High-resolution measurements taken at the outflow of a shallow lateral bay revealed that these CH4 peaks were positively related to tidal amplitude when the lateral bay was exposed exclusively to freshwater over the tide cycle; in contrast, this relationship was inversed when brackish waters were involved. A positive relationship between tidal amplitude and CH4 is consistent with a mechanism of tidal pumping from bottom sediments in the bay. In the presence of saltwater, however, a higher-than-expected flux of CH4 could occur via suppression of removal processes such as biological oxidation. We present a conceptual model of tidal pumping modified by diurnal inequality in tidal amplitude and effects of salinity on sediment CH4 oxidation to explain CH4 variability on tidal to seasonal time-scales. The combined influences of tides and salinity likely affect CH4 emissions in estuaries worldwide, making sea level rise and estuarine geomorphological change relevant factors for consideration when accounting for estuarine contributions to global methane budgets.Phillips, S.C., Flemings, P.B., You, K., Meyer, D.W., Dong, T., 2019. Investigation of in situ salinity and methane hydrate dissociation in coarse-grained sediments by slow, stepwise depressurization. Marine and Petroleum Geology 109, 128-144. (8–15 day), stepwise, degassing of synthesized methane hydrate-bearing sand packs was used to determine in situ salinity to within 0.5?wt%. Rebounds in pressure during shut-in intervals between degassing steps record gradual hydrate dissociation. During successive dissociation steps and pressure rebounds, the pressure decreases more than predicted for a sample with homogenous salinity and temperature at thermodynamic equilibrium. We interpret that hydrate dissociation is limited by local pore water freshening and endothermic cooling around the dissociating hydrate. These results suggest that during production, hydrate dissociation in a reservoir will occur along the freshwater phase boundary even though the bulk salinity of the system may be higher. Pore pressure rebound during shut-in is more rapid in freshwater experiments than in brine experiments, which indicates that salt diffusion plays a role in limiting recovery to homogenous bulk equilibrium during hydrate dissociation. We demonstrate that it is possible to interpret the in-situ salinity from the temperature and pressure at the onset of dissociation. This approach can be applied to actual hydrate-bearing pressure core samples and the results will assist our understanding of how these hydrates form. Depressurization experiments with controlled shut-in periods provide insight into the role of salt and heat diffusion on dissociation in coarse-grained sediments, particularly relevant to pauses in production and in regions of a hydrate reservoir near the hydrate phase boundary.Ping, H., Chen, H., Zhai, P., Zhu, J., George, S.C., 2019. Petroleum charge history in the Baiyun depression and Panyu lower uplift in the Pearl River Mouth Basin, northern South China Sea: Constraints from integration of organic geochemical and fluid inclusion data. American Association of Petroleum Geologists Bulletin 103, 1401-1442. source, thermal maturity, and charge history of oil and gas condensate in the Baiyun depression and the Panyu lower uplift were determined using organic geochemical and fluid inclusion data. Nearly all the gas condensates and oil in the study area originated from Eocene Enping Formation source rocks, whereas the condensate fluids in the eastern area originated from the Enping and Zhuhai Formations. The condensate fluids have a relatively low thermal maturity with a calculated vitrinite reflectance equivalent that typically ranges from 0.8% to 1.0% based on the C29 sterane isomerization ratios and aromatic hydrocarbon maturity parameters. Four types of oil inclusions with various fluorescence colors (yellow–blue) and API gravities (25°–44°) were recognized in the Oligocene and lower Miocene reservoir units, which suggest multiple oil charging events. The homogenization temperatures of the fluid inclusions recorded the oil charge events accompanying large-scale hot fluid movement, which was most likely caused by the charging of high-temperature natural gas from the deeper Wenchang Formation. The trapping pressures of the oil inclusions and the reconstructed burial histories were used to determine the timing of oil charge. The main oil charge occurred from 16–7 Ma throughout the Baiyun depression and Panyu lower uplift, whereas the Panyu lower uplift experienced an additional oil charge from 5–0 Ma. The natural gas charge occurred during the main oil charging period and may continue to the present day. Multiple physical processes, such as gas injection (without gas exsolution), gas washing (with gas exsolution), and migration fractionation, have played important roles in gas condensate formation and controlling the petroleum distribution in the Baiyun depression and Panyu lower uplift.Pinkston, F.W.M., Flemings, P.B., 2019. Overpressure at the Macondo Well and its impact on the Deepwater Horizon blowout. Scientific Reports 9, Article 7047. the Macondo well, the overpressure (fluid pressure greater than hydrostatic) in the main reservoir is nearly identical to that within a stratigraphically equivalent sandstone at the Galapagos development 21 miles (34?km) to the south; we interpret that the reservoirs share a permeable, laterally extensive, and hydraulically connected aquifer. At Macondo, pore pressure approximately parallels the overburden stress to a depth of 17,640?ft (5,377?m) subsea and thereafter decreases abruptly by 1,200?psi (8.3?MPa) over 370?ft (113?m) as the main sandstone reservoir is approached. In contrast, at Galapagos, pore pressure increases with the overburden stress for the entire well depth. The pore pressure regression at Macondo was responsible for a reduction in the least principal stress. This, in combination with the extreme pore pressures within overlying strata, drastically narrowed the range of safe operational borehole pressures. These geologic phenomena produced challenging conditions for drilling, prevented successful temporary abandonment of the well, and contributed to the well’s failure.Piramoon, H., Moraveji, M.K., Parvareh, A., Azimi, A., 2019. Experimental study of the formation of natural gas hydrates in the presence of NaCl and KCl. Petroleum Science and Technology 37, 1924-1930. this work, the conditions for the formation of natural gas hydrate in pure water as well as in the presence of two electrolytic inhibitors of NaCl and KCl were investigated at different concentrations using the isochoric method. This study has been conducted on natural gas source field (Pazanan2 region) and due to the uniqueness of this gas, it may be considered significant. In order to estimate the conditions for the formation of natural gas hydrate in the presence of pure water, hydrate equations have been used. Experiments were carried out at the different temperatures and pressures.Pires, A.P.P., Arauzo, J., Amador, I.F., Domine, M.E., Fernández Arroyo, A., Garcia-Perez, M.E., Montoya, J., Chejne, F., Pfromm, P., Garcia-Perez, M., 2019. Challenges and opportunities for bio-oil refining: A review. Energy & Fuels 33, 4683-4720. derived from fast pyrolysis of lignocellulosic materials is among the most complex and inexpensive raw oils that can be produced today. Although commercial or demonstration scale fast pyrolysis units can readily produce this oil, the pyrolysis industry has not grown to significant commercial impact due to the lack of bio-oil market pull. This paper is a review of the challenges and opportunities for bio-oil upgrading and refining. Pyrolysis oil consists of six major fractions (water 15–30 wt %, light oxygenates 8–26 wt %, monophenols 2–7 wt %, water insoluble oligomers derived from lignin 15–25 wt %, and water-soluble molecules 10–30 wt %). The composition of water-soluble oligomers is relatively poorly studied. In the 1880s, bio-oil refining (formally known as wood distillation) targeted the separation and commercialization of C1–C4 light oxygenated compounds to produce methanol, acetic acid, and acetone with the commercialization of the lignin derived water insoluble fraction for preserving wooden sailing vessels against rot. More recently, the company Ensyn extracted and commercialized condensed natural smoke as a food additive. Most research efforts in the last 20 years have focused on the two-step hydrotreatment concept for the production of transportation fuels. In spite of major progress, this concept remains at the demonstration scale. In this review, the opportunities and progress to separate bio-oil fractions and chemicals, mainly acetic acid (HAc), hydroxyacetaldehyde (HHA), acetol, and levoglucosan, and convert them into value added coproducts are thoroughly discussed. In spite of the large number of separation schemes and products tested, very few of them have been tested as part of fully integrated bio-oil refinery concepts. The synthesis and techno-economic and environmental evaluation of novel integrated bio-oil refinery concepts is likely to become a subject of intense research activity in the coming years.Polyakov, D.M., Maryash, A.A., Khodorenko, N.D., 2019. Dynamics of the organic matter content of bottom sediments along the Razdolnaya River–Amur Bay boundary (Sea of Japan). Oceanology 59, 208-213. contents of Corg, humiс acids (HA), and fulvic acids (FA) in soil and riverine and marine bottom sediments have been investigated along a transect between the Razdolnaya River and Amur Bay. The revealed higher Corg content of soil compared to that of riverine and marine sediments is associated with peatlands. The increased HA content of sediments compared to the FA content, corresponding to the initial period of water mixing, is explained by flocculation. The identified riverine sediments with increased FA, Fe, and Mn contents indicate active processes of flocculation and the formation of Fe and Mn oxyhydroxides. Soil shows significantly larger amounts of humified organic matter than marine sediments. Marine sediments contain mostly biochemically unrecycled organic matter.Porter, A.S., Evans-Fitz.Gerald, C., Yiotis, C., Monta?ez, I.P., McElwain, J.C., 2019. Testing the accuracy of new paleoatmospheric CO2 proxies based on plant stable carbon isotopic composition and stomatal traits in a range of simulated paleoatmospheric O2:CO2 ratios. Geochimica et Cosmochimica Acta 259, 69-90. drive to improve long-term estimates of atmospheric CO2 change through Earths history has led to the development of novel paleoproxy CO2 methods applicable to fossil plants. This paper compares two of these paleoproxy CO2 methods (1) the empirical model of Schubert and Jahren (2012, 2015) termed the C3 plant proxy, which was developed using the hyperbolic relationship observed between plant carbon isotope discrimination (Δ13C) and pCO2 and (2) the mechanistic model of Franks et al. (2014), which utilizes stomatal anatomy measurements and plant carbon isotopic composition and is based on established equations for leaf gas exchange and photosynthesis. To date both models lack detailed experimental testing of the robustness and accuracy of their pCO2 predictions in relation to phylogenetic differences in Δ13C between C3 plant groups and/or species and atmospheric O2 concentration, which has co-fluctuated with CO2 in the geological past. Here, we investigate if these novel paleoproxy CO2 approaches can produce phylogenetically independent estimates of pCO2 that are not influenced by variations in atmospheric oxygen. To address this, model estimates of pCO2 were compared with measured CO2 values for ten plant species representing four major vascular plant groups (lycophytes, monilophytes, gymnosperms and angiosperms) grown for 6?months in walk-in plant growth chambers under varying O2:CO2 ratios. Results from the mechanistic model reveal that species-specific plant responses to atmospheric CO2 accounted for the large variability in CO2 predictions between species and overestimations of pCO2 by ～+232?ppm to 940?ppm. Adjustments to the model that involved: (1) corrections to the photorespiratory compensation point (to account for fluctuating oxygen) and (2) removal of the phylogenetic effect on Δ13C, reduced between-species variability (by 50%) and led to better pCO2 estimates within 58–229?ppm of measured values. The C3 plant proxy (empirical approach) produced accurate CO2 estimates within +37 to +71?ppm of measured values, however it was affected by species-specific differences in Δ13C and for some species resulted in negative estimates of pCO2. Sub-ambient O2 (16%) resulted in erroneously high CO2 estimates (～100?ppm higher than the control) for a number of species, as plant responses to decreasing O2 mimicked those of increasing CO2. We conclude that both models (with phylogenetic corrections to Franks et al. (2014)) can produce accurate estimates of paleo-CO2 when a mix of three to four species, preferably containing representatives from both pteridophytes and spermatophytes, is used to obtain a consensus pCO2 estimate. We advocate a fossil assemblage rather than a single-species approach to paleo-CO2 estimation in future application of either method.Pothier Bouchard, G., Mentzer, S.M., Riel-Salvatore, J., Hodgkins, J., Miller, C.E., Negrino, F., Wogelius, R., Buckley, M., 2019. Portable FTIR for on-site screening of archaeological bone intended for ZooMS collagen fingerprint analysis. Journal of Archaeological Science: Reports 26, 101862. remains play an important role in helping reconstruct Palaeolithic hunter-gatherer subsistence and mobility strategies. However, differential bone preservation is an issue in southern European prehistoric sites, which often makes morphological identification impossible. Zooarchaeology by Mass Spectrometry (ZooMS) is a new, low-cost method that can improve NISP statistical significance in a replicable way by using diagnostic peptides of the dominant collagen protein as a fingerprint of animal (including hominin) species. It is also a powerful tool to assess collagen preservation for radiocarbon dating. This paper presents the proof of concept of a method for evaluating collagen preservation in a quick and minimally destructive way in the field prior to ZooMS analysis by using a portable Fourier Transform Infrared Spectrometer (FTIR) equipped with an attenuated total reflectance accessory (ATR). The method was tested on faunal assemblages from two north-western Italian sites: Riparo Bombrini and Arma Veirana. Both are important sites for understanding the Middle and Upper Palaeolithic of Liguria but are located in two distinct environmental contexts (coast vs. mountainous hinterland) that impacted collagen preservation. The relative abundance of collagen in powdered bone samples was evaluated by calculating the Amide I to phosphate ratio (CO/P) from spectra collected with two portable and three laboratory-based FTIR instruments. The bones were then analysed by ZooMS and the results were compared to evaluate the effectiveness of using FTIR as a screening technique. Results indicate that FTIR instruments are excellent tools to predict collagen preservation in fragmented archaeological bones, but a screening method should be first calibrated on the analysed faunal assemblage by conducting a test of the CO/P screening procedure with various measurement systems on a single FTIR instrument.Prasad, R.K., Chatterjee, S., Mazumder, P.B., Gupta, S.K., Sharma, S., Vairale, M.G., Datta, S., Dwivedi, S.K., Gupta, D.K., 2019. Bioethanol production from waste lignocelluloses: A review on microbial degradation potential. Chemosphere 231, 588-606. explosion of population has led to about 200% increment of total energy consumptions in last twenty-five years. Apart from conventional fossil fuel as limited energy source, alternative non-conventional sources are being explored worldwide to cater the energy requirement. Lignocellulosic biomass conversion for biofuel production is an important alternative energy source due to its abundance in nature and creating less harmful impacts on the environment in comparison to the coal or petroleum-based sources. However, lignocellulose biopolymer, the building block of plants, is a recalcitrant substance and difficult to break into desirable products. Commonly used chemical and physical methods for pretreating the substrate are having several limitations. Whereas, utilizing microbial potential to hydrolyse the biomass is an interesting area of research. Because of the complexity of substrate, several enzymes are required that can act synergistically to hydrolyse the biopolymer producing components like bioethanol or other energy substances. Exploring a range of microorganisms, like bacteria, fungi, yeast etc. that utilizes lignocelluloses for their energy through enzymatic breaking down the biomass, is one of the options. Scientists are working upon designing organisms through genetic engineering tools to integrate desired enzymes into a single organism (like bacterial cell). Studies on designer cellulosomes and bacteria consortia development relating consolidated bioprocessing are exciting to overcome the issue of appropriate lignocellulose digestions. This review encompasses up to date information on recent developments for effective microbial degradation processes of lignocelluloses for improved utilization to produce biofuel (bioethanol in particular) from the most plentiful substances of our planet.Prata, J.C., da Costa, J.P., Gir?o, A.V., Lopes, I., Duarte, A.C., Rocha-Santos, T., 2019. Identifying a quick and efficient method of removing organic matter without damaging microplastic samples. Science of The Total Environment 686, 131-139. organic matter may confound the detection of microplastics, requiring a removal step. However, most available protocols are long and lack information on removal efficiency and polymer degradation. Thus, we have determined the digestion efficiency (%) for a pool of organic matter (algae, driftwood, feathers, fish muscle, paraffin, palm oil) for five digestion solutions, hydrogen peroxide (H2O2), hydrogen peroxide with iron catalyst (H2O2?+?Fe), potassium hydroxide (KOH), nitric acid (HNO3), and sodium dodecyl sulphate (SDS), under two temperatures (room temperature at 25?°C, 50?°C) and two periods (1, 6?h). H2O2?+?Fe and KOH at 50?°C for 1?h had the highest digestion efficiencies, of 65.9% and 58.3% respectively (mostly limited by driftwood and paraffin). Further testing revealed that H2O2?+?Fe is more appropriate for plant material and KOH for animal tissue. Weight loss (%), Fourier transform infrared spectrometry and carbonyl index of 9 virgin and 6 weathered polymers (polyethylene, polypropylene, polystyrene, polyethylene terephthalate, polyvinyl chloride, cellulose acetate, nylon) revealed that only identification of cellulose acetate was hindered. Filters were also tested revealing that quartz and glass fibre filters are resistant to these protocols. Thus, a digestion protocol based on H2O2?+?Fe or KOH at 50?°C for 1?h may be used on microplastic samples.Procópio, L., 2019. The role of biofilms in the corrosion of steel in marine environments. World Journal of Microbiology and Biotechnology 35, 73. corrosion is a major global concern in many economic sectors. The degradation of metal surfaces is responsible for losses in values that account for about 3% of gross domestic product (GDP) only in the US. Parts of all corrosion processes described in different environments are present mainly in marine environments. The marine environment is characterized as favoring the corrosion processes of several metallic alloys, damaging structures used in the construction of ships, ports, oil pipelines, and others. Despite chemical corrosion being the most frequently described in these environments, studies show the participation of microorganisms in direct corrosion processes or in the acceleration/influence of the corrosive action, through the formation of complex biofilms. These structures create favorable conditions for microorganisms to degrade metal surfaces, causing damage known as pitting and crevices. Currently, diverse technicians are employed in biocorrosion research, e.g. electronic microscopy, and DNA sequencing. These techniques have clarified the dynamic process of the formation of biofilm structures, allowing understanding of the succession of different species during the evolution of the structure. Improving the understanding of how this interaction between biofilm and metallic surface occurs will enable better evaluation of strategies to avoid or decelerate the degradation of metallic structures in marine environments.Pu, J., Nguyen, T.-S., Leclerc, E., Lorentz, C., Laurenti, D., Pitault, I., Tayakout-Fayolle, M., Geantet, C., 2019. Lignin catalytic hydroconversion in a semi-continuous reactor: an experimental study. Applied Catalysis B: Environmental 256, 117769. valorization of lignin coming from pulp industry or bio-ethanol refineries into renewable chemicals is one of the great challenges of the biorefinery concept. Among the several processes proposed to depolymerize lignin, catalytic hydroconversion appeared efficient to get high liquid yield and can provide targeted aromatic monomers. A new semi-continuous set-up consisting in a batch reactor opened on the gas-phase was implemented to carry out the catalytic lignin liquefaction into phenolic and deoxygenated aromatic compounds with continuous H2 feeding. The interest of this equipment is the continuous removing of light products and water from the reacting mixture whereas the hydrogen donor solvent is reintroduced in the reactor via a reflux/condensing system. A Co-promoted Mo sulfide catalyst was used and thanks to efficient separation and extensive analysis, the components of the different gaseous, liquid and solid fractions obtained were identified and quantified. The evolution of the various fractions in function of the time and the deep investigation of the composition, allowed to propose a reaction scheme for the lignin depolymerization in those operating conditions.Qasim, D., Fedoseev, G., Lamberts, T., Chuang, K.-J., He, J., Ioppolo, S., K?stner, J., Linnartz, H., 2019. Alcohols on the rocks: Solid-state formation in a H3CC≡CH + OH cocktail under dark cloud conditions. ACS Earth and Space Chemistry 3, 986-999. number of recent experimental studies have shown that solid-state complex organic molecules (COMs) can form under conditions that are relevant to the CO freeze-out stage in dense clouds. In this work, we show that alcohols can be formed well before the CO freeze-out stage (i.e., during the very early stage of the H2O-rich ice phase). This joint experimental and computational investigation shows that isomers n-propanol and isopropanol (H3CCH2CH2OH and H3CCHOHCH3) and n-propenol and isopropenol (H3CCH═CHOH and H3CCOH═CH2) can be formed in radical-addition reactions starting from propyne (H3CC≡CH) + OH at the low temperature of 10 K, where H3CC≡CH is one of the simplest representatives of stable carbon chains already identified in the interstellar medium (ISM). The resulting average abundance ratio of 1:1 for n-propanol:isopropanol is aligned with the conclusions from the computational work that the geometric orientation of strongly interacting species is influential to the extent of which “mechanism” is participating and that an assortment of geometries leads to an averaged-out effect. Three isomers of propanediol are also tentatively identified in the experiments. It is also shown that propene and propane (H3CCH═CH2 and H3CCH2CH3) are formed from the hydrogenation of H3CC≡CH. This experimental finding falls in line with the lower activation barrier of hydrogenation of a C═C bond in comparison to a C≡C bond. Reactants and products are probed by temperature-programmed desorption–quadrupole mass spectrometry (TPD-QMS) and reflection absorption infrared spectroscopy (RAIRS). Product relative abundances are determined from TPD-QMS data. Computationally derived activation barriers give additional insight into what types of reactions and mechanisms are more likely to occur in the laboratory and in the ISM. Our findings not only suggest that the alcohols studied here share common chemical pathways and therefore can show up simultaneously in astronomical surveys but also that their extended counterparts that derive from polyynes containing H3C–(C≡C)n–H structures may exist in the ISM. Such larger species, such as fatty alcohols, are the possible constituents of simple lipids that primitive cell membranes on the early Earth are thought to be partially composed of.Qiao, F., Wang, G., Yin, L., Zeng, K., Zhang, Y., Zhang, M., Xiao, B., Jiang, S., Chen, H., Chen, G., 2019. Modelling oil trajectories and potentially contaminated areas from the Sanchi oil spill. Science of The Total Environment 685, 856-866. spills are major threats to marine ecosystems. Here, we establish a three-dimensional oil spill model to simulate and project the short- and long-term trajectories of oil slicks and oil-contaminated water that leaked from the Sanchi wreckage. The pollution probability in surrounding areas for the period up to 180?days after the Sanchi sank is statistically analysed. The short-term simulations are consistent with synchronous SAR images and observational reports. The potentially polluted areas depend on the properties of the released oil. The coastal areas most likely to be affected by the bunker oil are located in the Ryukyu Island Chain, Tsushima Strait, on the south and east coasts of Japan. Approximately 50% to 70% of oil particles remain in the ocean and mainly expand along the Ryukyu Island Chain and the region southeast of the Sanchi wreck. Subsurface oil-contaminated water is likely to enter the Sea of Japan along the Tsushima Strait. Due to the rapid evaporation rate of condensate oil, the potentially polluted area is confined to regions within a 100?×?100?km area around the location of the shipwreck, and the contaminated region is closely associated with the surface wind.Qin, S., Huang, C., Zhang, B., Yang, Y., Yuan, M., 2019. Relationships of the iC4/nC4 and iC5/nC5 ratios with maturity of coal-derived gases of Triassic Xujiahe Formation in central Sichuan Basin, SW China. Petroleum Exploration and Development 46, 496-503. original gas reservoirs in different areas and different layers of the Triassic Xujiahe Formation in the central Sichuan Basin are studied to reveal the relationships of iC4/nC4 and iC5/nC5 ratios in coal-derived gas components with maturity using conventional natural gas geochemical research methods. The testing results of 73 gas samples from 8 gas fields show that the iC4/nC4 and iC5/nC5 ratios in coal-derived gas have a good positive correlation, and the correlation coefficient is above 0.8. Both the iC4/nC4 and iC5/nC5 ratios become higher with the increase of natural gas dryness coefficient (C1/C1+) and the methane carbon isotope becoming less negative. These parameters are highly correlated. This study not only reveals characteristics of heavy hydrocarbon isomers generated by coal formation, but also puts forward new identification indicators reflecting the maturity of coal-derived gas, the regression between iC4/nC4, iC5/nC5 and Ro, which can provide an important reference for maturity, migration and accumulation of coal-derived gas, and late stage reformation of coal-derived gas reservoirs.Rajan Babu, N., Vargas, F.M., 2019. Modeling of asphaltene deposition in a packed bed column. Energy & Fuels 33, 5011-5023. deposit buildup in production pipelines and subsea flowlines greatly affects the production rate of oil and, hence, is a major concern for the upstream oil and gas industry. To better understand the behavior of asphaltenes under different production scenarios and operating conditions, the physics of asphaltene deposition and effectively develop mitigation strategies to overcome this problem, experimental techniques, and modeling methods are extremely important. Recently, deposition tests using a packed bed column have been performed to measure and quantify asphaltene deposition in the laboratory. This work focuses on the development of a modeling technique to simulate the process of asphaltene deposition occurring in the packed bed column. A computational fluid dynamics model has been developed to analyze the multi-step process of asphaltene phase separation, aggregation, diffusion, and deposition. Three-dimensional transient flow simulations have been performed using an indigenous in-house finite element solver developed on MATLAB platform. A surface deposition mechanism has been employed to capture asphaltenes deposited on the packed bed spheres. The effects of precipitant, precipitant concentration, and experimental run time on the extent of deposition have been studied in detail. It has been found that the magnitude of asphaltene deposition, the deposition rate, and consequently, the deposition risk increase with an increase in the concentration of phase-separated asphaltene primary particles and the driving force for precipitation and deposition. The model has also been modified to comprehend the effect of chemical dosage on asphaltene deposition. The developed methodology can be applied to analyze the effectiveness of industrially available asphaltene deposition dispersants and solvents and, hence, help us in developing strategies for asphaltene deposition problem mitigation and remediation. This study provides a computationally efficient modeling technique that helps in simulating asphaltene deposition studied in an experimental setup, recognizing the competing phenomena of asphaltene aggregation and deposition that are simultaneously taking place in the system and, hence, providing a better understanding of the asphaltene deposition process.Ramos-Barbero, M.D., Martínez, J.M., Almansa, C., Rodríguez, N., Villamor, J., Gomariz, M., Escudero, C., Rubin, S.d.C., Antón, J., Martínez-García, M., Amils, R., 2019. Prokaryotic and viral community structure in the singular chaotropic salt lake Salar de Uyuni. Environmental Microbiology 21, 2029-2042. de Uyuni (SdU) is the largest hypersaline salt flat and the highest lithium reservoir on Earth. In addition to extreme temperatures and high UV irradiance, SdU has high concentrations of chaotropic salts which can be important factors in controlling microbial diversity. Here, for the first time we characterize the viral diversity of this hypersaline environment during the two seasons, as well as the physicochemical characteristics and the prokaryotic communities of the analysed samples. Most of the selected samples showed a peculiar physicochemical composition and prokaryotic diversity, mostly different from each other even for samples from locations in close proximity or the same season. In contrast to most hypersaline systems Bacteria frequently outnumbered Archaea. Furthermore, an outstanding percentage of members of Salinibacter sp., likely a species different from the cosmopolitan Salinibacter ruber, was obtained in most of the samples. Viral communities displayed the morphologies normally found in hypersaline environments. Two seasonal samples were chosen for a detailed metagenomic analysis of the viral assemblage. Both viral communities shared common sequences but were dominated by sample‐specific viruses, mirroring the differences also observed in physicochemical and prokaryotic community composition. These metaviromes were distinct from those detected in other hypersaline systems analysed to date.Ramos-Madrigal, J., Runge, A.K.W., Bouby, L., Lacombe, T., Samaniego Castruita, J.A., Adam-Blondon, A.-F., Figueiral, I., Hallavant, C., Martínez-Zapater, J.M., Schaal, C., T?pfer, R., Petersen, B., Sicheritz-Pontén, T., This, P., Bacilieri, R., Gilbert, M.T.P., Wales, N., 2019. Palaeogenomic insights into the origins of French grapevine diversity. Nature Plants 5, 595-603. Eurasian grapevine (Vitis vinifera) has long been important for wine production as well as being a food source. Despite being clonally propagated, modern cultivars exhibit great morphological and genetic diversity, with thousands of varieties described in historic and contemporaneous records. Through historical accounts, some varieties can be traced to the Middle Ages, but the genetic relationships between ancient and modern vines remain unknown. We present target-enriched genome-wide sequencing data from 28 archaeological grape seeds dating to the Iron Age, Roman era and medieval period. When compared with domesticated and wild accessions, we found that the archaeological samples were closely related to western European cultivars used for winemaking today. We identified seeds with identical genetic signatures present at different Roman sites, as well as seeds sharing parent–offspring relationships with varieties grown today. Furthermore, we discovered that one seed dated to ~1100 ce was a genetic match to ‘Savagnin Blanc’, providing evidence for 900?years of uninterrupted vegetative propagation.Rasmussen, B., Muhling, J.R., Tosca, N.J., Tsikos, H., 2019. Evidence for anoxic shallow oceans at 2.45 Ga: Implications for the rise of oxygenic photosynthesis. Geology 47, 622-626. proxies indicate that atmospheric oxygen levels were <10–5 times present atmospheric levels (10–5 × PAL) until the start of the Great Oxidation Event (GOE; 2.33 Ga). However, trace metal and isotopic data from sedimentary rocks have been interpreted to reflect the presence of oxygenated surface oceans ≥2.5 b.y. ago, implying decoupling of the atmosphere and shallow marine systems. Evidence for oxygen in shallow oceans has fueled the idea that oxygenic photosynthesis evolved long before the GOE and that oxygen did not accumulate in the atmosphere because it was scavenged by reductants such as dissolved Fe2+, a process thought by some to have formed banded iron formations (BIFs). Here we present high-resolution microscopy showing that 2.45 Ga shallow-water BIFs were deposited as ferrous iron-rich muds dominantly composed of greenalite; these muds were rapidly cemented by silica on the seafloor, and subsequently eroded and redeposited as intraformational chert clasts. Our experimental results and kinetic models show that the accumulation of greenalite required seawater oxygen concentrations <10–6 × PAL on the shallow shelf. We infer that oxygen levels of the surface oceans and atmosphere were not decoupled 2.45 b.y. ago, but that both were exceedingly low (<10–5 × PAL). Our findings support the hypothesis that oxygenic photosynthesis evolved shortly before atmospheric oxygenation and was a direct cause of the GOE.Reinecke, T., Naylor, C.N., Clowers, B.H., 2019. Ion multiplexing: Maximizing throughput and signal to noise ratio for ion mobility spectrometry. TrAC Trends in Analytical Chemistry 116, 340-345. balancing signal to noise ratio and spectral resolving power, drift tube ion mobility spectrometry (IMS) experiments are often conducted with instrumental duty cycles below 1%. Multiplexing techniques, specifically Fourier and Hadamard approaches, represent a considerably different approach to conduct drift tube IMS experiments and realize ion utilization efficiencies approaching 50% without sacrificing separating power. In addition to providing a succinct account of the history of Hadamard and Fourier techniques in IMS, this review outlines, in tractable language, the origins of the signal to noise ratio (SNR) gains observed in multiplexing experiments. A cursory evaluation of the technological maturing of multiplexing approaches applied to IMS suggest that future efforts will enable seamless integration of ion multiplexing technologies especially for hybrid instrumentation. Moreover, as developments associated with state-of-the-art signal processing techniques gain traction within the community, further gains in SNR and resolution are anticipated.Reinhardt, M., Goetz, W., Duda, J.-P., Heim, C., Reitner, J., Thiel, V., 2019. Organic signatures in Pleistocene cherts from Lake Magadi (Kenya) – implications for early Earth hydrothermal deposits. Biogeosciences 16, 2443-2465. matter in Archean hydrothermal cherts may provide an important archive for molecular traces of the earliest life on Earth. The geobiological interpretation of this archive, however, requires a sound understanding of organic matter preservation and alteration in hydrothermal systems. Here we report on organic matter (including molecular biosignatures) enclosed in hydrothermally influenced cherts of the Pleistocene Lake Magadi (Kenya; High Magadi Beds and Green Beds). The Magadi cherts contain low organic carbon (<?0.4?wt?%) that occurs in the form of finely dispersed clots, layers, or encapsulated within microscopic carbonate rhombs. Both extractable (bitumen) and non-extractable organic matter (kerogen) were analyzed. The bitumens contain immature “biolipids” like glycerol mono- and diethers (e.g., archaeol and extended archaeol), fatty acids, and alcohols indicative for, inter alia, thermophilic cyanobacteria, sulfate reducers, and haloarchaea. However, co-occurring “geolipids” such as n-alkanes, hopanes, and polycyclic aromatic hydrocarbons (PAHs) indicate that a fraction of the bitumen has been thermally altered to early or peak oil window maturity. This more mature fraction likely originated from defunctionalization of dissolved organic matter and/or hydrothermal petroleum formation at places of higher thermal flux. Like the bitumens, the kerogens also show variations in thermal maturities, which can partly be explained by admixture of thermally pre-altered macromolecules. However, findings of archaea-derived isoprenoid moieties (C20 and C25 chains) in kerogen pyrolysates indicate rapid sequestration of some archaeal lipids into kerogen while hydrothermal alteration was active. We posit that such early sequestration may enhance the resistance of molecular biosignatures against in situ hydrothermal and post-depositional alteration. Furthermore, the co-occurrence of organic matter with different thermal maturities in the Lake Magadi cherts suggests that similar findings in Archean hydrothermal deposits could partly reflect original environmental conditions and not exclusively post-depositional overprint or contamination. Our results support the view that kerogen in Archean hydrothermal cherts may contain important information on early life. Our study also highlights the suitability of Lake Magadi as an analog system for hydrothermal chert environments on the Archean Earth.Ren, M., Tang, Z., Wu, X., Spengler, R., Jiang, H., Yang, Y., Boivin, N., 2019. The origins of cannabis smoking: Chemical residue evidence from the first millennium BCE in the Pamirs. Science Advances 5, Article eaaw1391. is one of the oldest cultivated plants in East Asia, grown for grain and fiber as well as for recreational, medical, and ritual purposes. It is one of the most widely used psychoactive drugs in the world today, but little is known about its early psychoactive use or when plants under cultivation evolved the phenotypical trait of increased specialized compound production. The archaeological evidence for ritualized consumption of cannabis is limited and contentious. Here, we present some of the earliest directly dated and scientifically verified evidence for ritual cannabis smoking. This phytochemical analysis indicates that cannabis plants were burned in wooden braziers during mortuary ceremonies at the Jirzankal Cemetery (ca. 500 BCE) in the eastern Pamirs region. This suggests cannabis was smoked as part of ritual and/or religious activities in western China by at least 2500 years ago and that the cannabis plants produced high levels of psychoactive compounds.Ren, X., Geng, N., Zhang, H., Wang, F., Gong, Y., Song, X., Luo, Y., Zhang, B., Chen, J., 2019. Comparing the disrupting effects of short-, medium- and long-chain chlorinated paraffins on cell viability and metabolism. Science of The Total Environment 685, 297-307. the phasing out of short-chain chlorinated paraffins (SCCPs), the production and emissions of medium- and long-chain chlorinated paraffins (MCCPs and LCCPs) are expected to increase. In this study, cell viability assay and pseudotargeted metabolomics approach were adopted to define and compare the toxic effects induced by SCCPs, MCCPs and LCCPs. The dose response curves indicated that three CP mixtures with comparable chlorine contents produced similar inhibitory effects on cell viability. At exposure concentration of 100?μg/L, three CP mixtures all induced significant increases in levels of reactive oxygen species (ROS) and malondialdehyde (MDA) and a significant reduction in level of adenosine triphosphate production (ATP), and produced similar impact intensities on overall metabolism. A stronger perturbation in phospholipid and fatty acid metabolism was observed in all CP exposure groups. In comparison with SCCPs and MCCPs, LCCPs produced a stronger suppressive effect on amino acid transport across cell membrane and induced an opposite effect on purine metabolism. Furthermore, the toxicity mechanism and possible health risks of the three types of CPs were discussed. MCCPs shared the most similar cytotoxicity and metabolic perturbation with SCCPs, suggesting that there should be concern about using MCCPs as alternatives to SCCPs.Reolid, M., Abad, I., Benito, M.I., 2019. Upper Pliensbachian-Lower Toarcian methane cold seeps interpreted from geochemical and mineralogical characteristics of celestine concretions (South Iberian palaeo-margin). Palaeogeography, Palaeoclimatology, Palaeoecology 530, 15-31. sulfate mineralizations are recorded in the Upper Pliensbachian-Lower Toarcian marly-limestones and marls of La Cerradura section (Betic Cordillera, South Spain). These mineralizations are celestine concretions (6–41?cm in diameter), sulfated wood coal remains and yellow-powder patches composed mainly of natrojarosite, native sulfur and gypsum. These deposits are mostly recorded in the base of Serpentinum Zone (Lower Toarcian) in the interval with the highest TOC values (0.4?wt%) and a negative carbon isotopic excursion, correlative with the Toarcian Oceanic Anoxic Event. The 87Sr/86Sr and δ18O values of celestine are within the values of the Early Toarcian seawater but δ34S values are anomalously high. The isotopic composition of these sulfates is congruent with their precipitation from fluids that have been submitted to variable degrees of microbial sulfate-reduction combined with anaerobic oxidation of methane, as reported from recent examples. The record of thin laminated crusts composed of celestine with calcite as the nucleus of concretions containing fossil filaments (observed under scanning electron microscopy) is compatible with the activity of sulfate-reducing bacteria. Therefore, celestine concretions have been related to methane cold seeps or high methane concentrations in the sediment. The source of the methane, which moved within the pore-space of marine sediment via diffusion or as bubbles, was the microbial methanogenesis of the organic-rich marls. The very high δ34S values indicate that celestine crystals formed in a semi-closed system below the sediment-water interface, which favored the efficient microbial sulfate-reduction that preferentially removed the light 32S isotope from pore-water. The celestine crystals grew from mixing of this 34S-enriched sulfate pool with reducing and Sr-rich seep fluids advecting with the methane hydrates. The precipitation of celestine in the dark marls of the Serpentinum Zone occurred in some cases over wood coal remains. Fossil chimneys related to the cold seeps have not been recorded in the studied outcrop indicating that the amount of methane hydrates reaching the sea-bottom was not enough for building this kind of structures. The growth of each celestine concretions ended when the source of methane, the organic matter, was spent and the activity of methanogenic microbes and sulfate-reducing bacteria decreased. New celestine concretions developed when new methane bubbles were channeled upwards in different layers.Richardson, E., Dacks, J.B., 2019. Microbial eukaryotes in oil sands environments: Heterotrophs in the spotlight. Microorganisms 7, Article 178. extraction and exploitation is a global, trillion-dollar industry. However, for decades it has also been known that fossil fuel usage is environmentally detrimental; the burning of hydrocarbons results in climate change, and environmental damage during extraction and transport can also occur. Substantial global efforts into mitigating this environmental disruption are underway. The global petroleum industry is moving more and more into exploiting unconventional oil reserves, such as oil sands and shale oil. The Albertan oil sands are one example of unconventional oil reserves; this mixture of sand and heavy bitumen lying under the boreal forest of Northern Alberta represent one of the world’s largest hydrocarbon reserves, but extraction also requires the disturbance of a delicate northern ecosystem. Considerable effort is being made by various stakeholders to mitigate environmental impact and reclaim anthropogenically disturbed environments associated with oil sand extraction. In this review, we discuss the eukaryotic microbial communities associated with the boreal ecosystem and how this is affected by hydrocarbon extraction, with a particular emphasis on the reclamation of tailings ponds, where oil sands extraction waste is stored. Microbial eukaryotes, or protists, are an essential part of every global ecosystem, but our understanding of how they affect reclamation is limited due to our fledgling understanding of these organisms in anthropogenically hydrocarbon-associated environments and the difficulties of studying them. We advocate for an environmental DNA sequencing-based approach to determine the microbial communities of oil sands associated environments, and the importance of studying the heterotrophic components of these environments to gain a full understanding of how these environments operate and thus how they can be integrated with the natural watersheds of the region. Rico, K.I., Sheldon, N.D., Gallagher, T.M., Chappaz, A., 2019. Redox chemistry and molybdenum burial in a Mesoproterozoic lake. Geophysical Research Letters 46, 5871-5878. ;While marine sediments have been used to constrain a history of redox chemistry throughout the Precambrian, far fewer data have been generated from lakes. With major biological innovations thought to have occurred in Proterozoic lakes, understanding their chemistry is critical for understanding the evolution of eukaryotic life. We use sediment geochemistry to characterize the redox conditions of the Nonesuch Formation (~1.1 Ga) and a modern analogue for the Proterozoic: the Middle Island Sinkhole in Lake Huron (USA). Iron speciation, Mo contents, and Mo‐U covariation demonstrate oxic and anoxic—not euxinic—environments, with no clear indicators of enhanced biological productivity in the Nonesuch Formation. Moderate Mo enrichments observed in the Nonesuch Formation are not attributed to euxinia, but instead to an authigenic particulate shuttle. We suggest that the Fe and Mo sediment geochemistry of these lacustrine systems reflect only local water column and sediment burial conditions and not atmospheric oxygenation.Plain Language Summary: Lakes are proposed to have been critical environments for the evolution of life during the Proterozoic (~2.5 to 0.5 billion years ago). However, relatively little is known about the chemistry of ancient lakes, including the availability of oxygen for biological productivity, and how local oxygen availability can be extrapolated to understand global oxygen availability. In addition, with no lakes remaining from the Proterozoic, the only way to study ancient lakes is to use the chemistry of the sediments left behind. This study uses the sediment chemistry of elements that are sensitive to oxygen to understand oxygen availability in a Proterozoic lake environment. These data were then compared to modern lake environments with known chemistry and oxygen levels in order to interpret the results better. We found that oxygen availability in the Proterozoic lake was variable, with no clear indicators of abundant biological productivity. We conclude that ancient lake sediments only constrain the chemistry of the local environment, with no major implications for global or even regional atmospheric oxygenation.Ridgeway, M.E., Bleiholder, C., Mann, M., Park, M.A., 2019. Trends in trapped ion mobility – Mass spectrometry instrumentation. TrAC Trends in Analytical Chemistry 116, 324-331. Ion Mobility Spectrometry (TIMS) is a recently developed form of ion mobility spectrometry (IMS) which is flexible in its operation and readily hybridized with mass spectrometry (MS). Prototype TIMS-MS instruments are applicable to a wide range of analytical problems including separation of isobars and isomers, the study of analyte conformation and unfolding, general separation of complex mixtures, and omics. Hybridization of TIMS with high performance mass analyzers such as ion cyclotron resonance (ICR) allows for the more effective analysis of highly complex samples. Adding trapping ahead of TIMS has enabled technologies such as Parallel Accumulation Serial Fragmentation (PASEF) for improved shotgun proteomics. Finally, tandem TIMS (tTIMS) adds flexibility, especially in top down proteomics. Here we highlight recent advances in TIMS-MS and their analytical applications.Rigano, F., Tranchida, P.Q., Dugo, P., Mondello, L., 2019. High-performance liquid chromatography combined with electron ionization mass spectrometry: A review. TrAC Trends in Analytical Chemistry 118, 112-122. present review illustrates the state of the art in the field of liquid chromatography (LC) hyphenated to electron ionization mass spectrometry (EI MS). An overview of applications over the last decades is given, in order to demonstrate the benefits arisen from the use of EI for the characterization of typically LC-amenable samples. Key advantages are related to the extensive fragmentation pattern useful for structure elucidation and the absence of matrix effects, differently from the most commonly employed LC-MS interfaces (e.g., electrospray). Different interfaces which made the LC-EI MS coupling feasible are described, along with several approaches proposed to overcome well-known incompatibility issues.Rillig, M.C., Antonovics, J., 2019. Microbial biospherics: The experimental study of ecosystem function and evolution. Proceedings of the National Academy of Sciences 116, 11093-11098. that our planet is a self-supporting biosphere with sunlight as its major source of energy for life has resulted in a long-term historical fascination with the workings of self-supporting ecological systems. However, the studies of such systems have never entered the canon of ecological or evolutionary tools and instead, have led a fringe existence connected to life support system engineering and space travel. We here introduce a framework for a renaissance in biospherics based on the study of matter-closed, energy-open ecosystems at a microbial level (microbial biospherics). Recent progress in genomics, robotics, and sensor technology makes the study of closed systems now much more tractable than in the past, and we argue that the time has come to emancipate the study of closed systems from this fringe context and bring them into a mainstream approach for studying ecosystem processes. By permitting highly replicated long-term studies, especially on predetermined and simplified systems, microbial biospheres offer the opportunity to test and develop strong hypotheses about ecosystem function and the ecological and evolutionary determinants of long-term system failure or persistence. Unlike many sciences, ecosystem ecology has never fully embraced a reductionist approach and has remained focused on the natural world in all its complexity. We argue that a reductionist approach to ecosystem ecology, using microbial biospheres, based on a combination of theory and the replicated study of much simpler self-enclosed microsystems could pay huge dividends.Ripmeester, M.J., Duford, D.A., 2019. Method for routine “naphthenic acids fraction compounds” determination in oil sands process-affected water by liquid-liquid extraction in dichloromethane and Fourier-Transform Infrared Spectroscopy. Chemosphere 233, 687-696. classified as naphthenic acids, “naphthenic acids fraction compounds” (NAFC) have become the subject of increasing research, in particular in view of their ubiquitous presence in the Canadian oil sands of Northern Alberta and oil sands process-affected waters (OSPW). NAFC, defined herein as the polar acid-extractable organics fraction of OSPW extractable in dichloromethane, are released into OSPW during the aqueous extraction of oil sands. A method for determining total NAFC concentration based on acidification, liquid-liquid extraction, and Fourier-Transform Infrared Spectroscopy (FT-IR) was developed by Jivraj et?al. in 1995. It has become widely used in the oil sands industry for routine monitoring of NAFC. Since then, multiple variations of the method are practiced by different laboratories using different calibration materials and different extraction solvents, differences which were found to affect the results by as much as 38 and 64 percent respectively. The goal of this study was to establish a robust method for routinely quantifying NAFC that does not require complex and expensive laboratory equipment such as mass spectrometers. Described improvements include a semi-automated rolling extraction and the use of a vacuum evaporator unit to reduce the method's environmental impact. The improved FT-IR method avoids emulsions, is precise, provides good agreement with gravimetric determinations of NAFC, increases sample throughput, is inexpensive compared to MS methods, and offers a typical reporting limit of 0.1?mg?kg?1. The residue recovered by this method with minimal losses can be further analyzed by MS techniques to characterize and identify individual NAFC components if desired.Roberts, J.J., Bell, A.F., Wood, R.A., Haszeldine, R.S., 2019. Geospatial statistics elucidate competing geological controls on natural CO2 seeps in Italy. Geofluids 2019, Article 8147345. selection for the geological storage of CO2 for long timespans requires an understanding of the controls on containment, migration, and surface seepage of subsurface CO2 fluids. Evidence of natural CO2 migration from depth to the surface is documented at 270 sites from Italy, a prolific CO2 province. Previous studies indicate that CO2 delivery to and from buried structures that host CO2 accumulations is fault controlled but competing controls on the CO2 flow pathways affect the location and style of CO2 release. Here, we conduct a meta-analysis using a novel geospatial approach to statistically determine the relationship between the geological setting and structures and the CO2 seep spatial distribution and characteristics (morphological type, flux, and temperature) in Central Italy. We find that seep distribution differs on two spatial scales corresponding to the geological setting. On large scales (>5?km), seeps are isotropically distributed and align with regional structures such as anticlines, decollements, and extensional faults. On local scales (<5?km), seeps cluster and align with subsidiary geologic structures, including faults and lithological boundaries. The detailed location and flux of seeps within clusters are influenced by the regional structural domain: in the Tyrrhenian, seeps tend to be located along fault traces, whereas seeps are located as springs in the tip and ramp regions of fault scarps in the Apennines. Thus, our geospatial approach evidences, at a regional scale, how macrocrustal fluid flow is governed by deep extensional and compressional features but once CO2 reaches shallower structures, it evidences how smaller scale features and hydrogeological factors distribute the CO2 fluids in the near surface, dependent on the geological setting. This work not only demonstrates useful application of a novel geospatial approach to characterize competing crustal controls on CO2 flow at different scales but also informs the design of appropriate site characterization and surface monitoring programs at engineered carbon stores.Rodriguez, L.E., House, C.H., Smith, K.E., Roberts, M.R., Callahan, M.P., 2019. Nitrogen heterocycles form peptide nucleic acid precursors in complex prebiotic mixtures. Scientific Reports 9, Article 9281. ability to store information is believed to have been crucial for the origin and evolution of life; however, little is known about the genetic polymers relevant to abiogenesis. Nitrogen heterocycles (N-heterocycles) are plausible components of such polymers as they may have been readily available on early Earth and are the means by which the extant genetic macromolecules RNA and DNA store information. Here, we report the reactivity of numerous N-heterocycles in highly complex mixtures, which were generated using a Miller-Urey spark discharge apparatus with either a reducing or neutral atmosphere, to investigate how N-heterocycles are modified under plausible prebiotic conditions. High throughput mass spectrometry was used to identify N-heterocycle adducts. Additionally, tandem mass spectrometry and nuclear magnetic resonance spectroscopy were used to elucidate reaction pathways for select reactions. Remarkably, we found that the majority of N-heterocycles, including the canonical nucleobases, gain short carbonyl side chains in our complex mixtures via a Strecker-like synthesis or Michael addition. These types of N-heterocycle adducts are subunits of the proposed RNA precursor, peptide nucleic acids (PNAs). The ease with which these carbonylated heterocycles form under both reducing and neutral atmospheres is suggestive that PNAs could be prebiotically feasible on early Earth.Rollion-Bard, C., Milner Garcia, S., Burckel, P., Angiolini, L., Jurikova, H., Toma?ov?ch, A., Henkel, D., 2019. Assessing the biomineralization processes in the shell layers of modern brachiopods from oxygen isotopic composition and elemental ratios: Implications for their use as paleoenvironmental proxies. Chemical Geology 524, 49-66. brachiopod shells are often used as valuable archives to reconstruct paleoenvironmental conditions in deep time. However, biomineralization processes can impact their fidelity as geochemical proxies. Brachiopod shells comprise an outer primary layer, a secondary fibrous layer and sometimes, a tertiary columnar layer. Therefore, it is essential to assess the potential effects of the biomineralization processes in each of the different shell microstructures of modern brachiopods. This study analyses the oxygen isotopic composition together with Li/Ca, Na/Ca Mg/Ca and Sr/Ca data at high spatial (20-50?μm) resolution in seven modern brachiopod species, focusing on differences between the primary, secondary and tertiary layers. In all studied species, δ18O values of the outer primary layer are consistently out of equilibrium with seawater. Also, this shell layer is enriched in Li, Na, Mg and Sr. Contrary to the primary layer, the innermost secondary layer is near or at oxygen isotopic and elemental equilibrium with ambient seawater. The columnar tertiary shell layer, if present, has the least variable and the heaviest oxygen isotopic composition, within the range of equilibrium values with seawater. This tertiary layer, however, is depleted in minor and trace elements relative to the other shell layers. Thus, the tertiary layer is more suitable for oxygen isotopic studies, whereas the innermost secondary layer of the most mature parts of the shell is the best target in two-layered shells. While we do not observe any clear interspecific relationships between Mg/Ca and Sr/Ca ratios, on one hand, and environmental parameters such as temperature, salinity and pH, on the other hand, there is a positive interspecific relationship between Na/Ca and salinity and a negative interspecific relationship between Li/Ca and temperature, suggesting their potential use as proxies of physicochemical parameters of seawater.Roslin, A., Pokrajac, D., Zhou, Y., 2019. Cleat structure analysis and permeability simulation of coal samples based on micro-computed tomography (micro-CT) and scan electron microscopy (SEM) technology. Fuel 254, Article 115579. has been playing an important role as a valuable source of energy for many years. In turn, gas production from coal reservoirs is a modern development and coal bed methane (CBM), also known as coal seam gas (CSG), is attracting global attention due to its wide occurrence and benefits for the environment as opposed to the conventional energy sources. Developing coal bed methane reservoirs requires better understanding of the flow behaviours of gas and liquids in cleats and analysis of possible contribution of pores to the flow. This paper describes the implementation of micro computed tomography (micro-CT) and scan electron microscopy (SEM) techniques for analysis of coal samples. Intermediate rank coal samples used in this study were collected from Southern Qinshui Basin (China). In the course of the described research, coal samples were scanned, processed and segmented to study the cleat spacing and permeability. Due to the partial volume effect, the resolution of cleats needed improvement which was achieved by subvoxel processing using a novel algorithm as explained in detail in the paper. Permeability was obtained through simulation of one phase flow using Lattice Boltzmann method (LBM). The results show that the simulated permeability is comparable to the analytical approximation. The subvoxel processing has proved an effective method of overcoming the partial volume effect for the low resolution micro-CT images.Rosvold, J., Hansen, G., R?ed, K.H., 2019. From mountains to towns: DNA from ancient reindeer antlers as proxy for domestic procurement networks in medieval Norway. Journal of Archaeological Science: Reports 26, 101860. medieval archaeology there are long traditions for studying foreign, exotic material culture as proxy for procurement networks of international reach. A paradox is that domestic networks, which brought products to consumers at home, has attracted little attention. During the Middle Ages (1030–1537), antler from reindeer was a north Scandinavian outland resource that found its way from remote mountains to settlements at home and abroad for use in hair combs. In the current pilot study, molecular genetic methods were employed to test whether antler debris from comb production workshops in the four medieval Norwegian towns Bergen, Trondheim, Skien and Oslo can be assigned to its original reindeer population. The study shows that ancient DNA (aDNA) can be used to provenance antler material to its origin with varying degrees of certainty: When samples from the four towns are considered as collective units, there is a high level of certainty in the discovered provenance pattern, whereas there is more uncertainty attached to provenancing individual antler fragments. Some immediate culture historical insights from the project's results are that urban comb makers used antler from the closest mountain areas, while analysis of individual-reindeer-based relationships on resource procurement adds some possible nuances to this picture. Furthermore, assigning dated antler debris to its population of origin adds new dates for commercial exploitation of reindeer resources in the specific mountain areas and adds new and high-definition empirical substance to the picture of long traditions for far-reaching procurement networks for Norwegian outland resources.Ru, Z., An, K., Hu, J., 2019. The impact of sulfur precipitation in developing a sour gas reservoir with pressure-sensitive effects. Advances in Geo-Energy Research 3, 268-276. the development of high sulfur gas fields, gaseous sulfur is likely to precipitate and deposit in the reservoirs due to the changes of temperature, pressure, and gas compositions. Therefore, how to establish an accurate prediction model of elemental sulfur solubility in gas mixtures is a key issue. At present, most scholars use Roberts elemental sulfur solubility model (SPE Reserv. Eng. 1997, 12(2): 118-123) to describe the damage caused by sulfur deposition in high-sulfur gas reservoirs. However, some scholars believe that the Roberts model needs to be improved and relevant works have been done. In this study, a one-dimensional radial production model is established using the HU model (J. Nat. Gas. Sci. Eng. 2014, 18: 31-38) and the Roberts elemental sulfur solubility model. These models can be used to describe the permeability and pressure changes caused by sulfur deposition more accurately. The results show that the permeability and pressure changes in the Roberts model are larger than that of which in the HU model and the pressure-sensitive effects may increase the reservoir damage. The comparison of the calculated results with the true values shows that the HU model is more accurate. This paper may change a number of views about sulfur deposition in high-sulfur gas reservoirs. Rüger, C.P., Maillard, J., Le Ma?tre, J., Ridgeway, M., Thompson, C.J., Schmitz-Afonso, I., Gautier, T., Carrasco, N., Park, M.A., Giusti, P., Afonso, C., 2019. Structural study of analogues of Titan’s haze by trapped ion mobility coupled with a Fourier transform ion cyclotron mass spectrometer. Journal of The American Society for Mass Spectrometry 30, 1169-1173. aerosols present in the atmosphere of the Saturn’s moon Titan are of particular planetary science interest and several spacecraft missions are already allowed to gather spectroscopic data. Titan haze’s analogs, so-called tholins, were produced on earth to push forward the comprehension of their formation and properties. In this study, this highly complex mixture was analyzed here for the first time by trapped ion mobility spectrometry coupled to ultra-high resolution mass spectrometry (FTICR MS). Electrospray ionization revealed the characteristic CHNx-class components, with CHN5–6 and DBE 6–7 most abundant. Deploying specialized visualization, enabled by accurate mass measurements and elemental composition assignments, the adapted Kendrick mass defect analysis highlights the C2H3N homolog series, whereas the nitrogen-modified van Krevelen diagram exhibits a clear trend towards H/C 1.5 and N/C 0.5. More interestingly, the representation of m/z versus collision cross section (CCS) allowed hypothesizing a ramified N-PAH structural motif. State-of-the-art IMS is currently not able to resolve the isomeric continuum of ultra-complex mixtures; thus, peak parameters other than the CCS value are explored. As such, analyzing the mobility peak width versus m/z shows a linear increase in isomeric diversity between m/z 170 and 350 and a near plateau in diversity at higher m/z for the N-PAH-like structure. Due to the high complexity of the sample, these structural insights are only to be revealed by TIMS-FTICR MS.Rui, J., Zhang, H., Zhang, D., Han, F., Guo, Q., 2019. Total organic carbon content prediction based on support-vector-regression machine with particle swarm optimization. Journal of Petroleum Science and Engineering 180, 699-706. organic carbon (TOC) is a significant factor to evaluate the hydrocarbon potential of the unconventional reservoir, while it is difficult to obtain the continuous and accurate prediction result of TOC by traditional methods due to the non-linear relationship between TOC content and wireline log data. However, support vector regress machine is an efficient supervised learning artificial intelligence algorithm, and performs well to deal with non-linear relationship dataset. Therefore, in order to explore a more efficient way for TOC content prediction, the support vector regress machine was tried to predict TOC content through wireline log data. To further verify this, some data tests have been conducted on an offshore exploration prior well data in the northern of Beibu Gulf Basin. After analyzing various kernel functions and optimization methods by cross-validation and error analysis, it can be indicated that the Gaussian kernel function and the particle swarm optimization (PSO) algorithm which used the linear decreasing inertia coefficient and mutated particles are suitable for SVR model and model parameter selection, respectively. Finally, the prediction result of SVR with the best model and model parameters is compared with the results of an improved ΔlogR method and multilayer perceptron method. The comparison results show that SVR has a higher correlation coefficient than other methods. In conclusion, the prediction result of SVR can be thought of as an efficient and reliable method for TOC content prediction. Through the continuous prediction of organic carbon content, the qualitative and quantitative evaluation of high-quality source rocks in this area can be realized, which is of great practical significance for determining the exploration field and the search for favorable target reservoirs.Runge, J., Bathiany, S., Bollt, E., Camps-Valls, G., Coumou, D., Deyle, E., Glymour, C., Kretschmer, M., Mahecha, M.D., Mu?oz-Marí, J., van Nes, E.H., Peters, J., Quax, R., Reichstein, M., Scheffer, M., Sch?lkopf, B., Spirtes, P., Sugihara, G., Sun, J., Zhang, K., Zscheischler, J., 2019. Inferring causation from time series in Earth system sciences. Nature Communications 10, Article 2553. heart of the scientific enterprise is a rational effort to understand the causes behind the phenomena we observe. In large-scale complex dynamical systems such as the Earth system, real experiments are rarely feasible. However, a rapidly increasing amount of observational and simulated data opens up the use of novel data-driven causal methods beyond the commonly adopted correlation techniques. Here, we give an overview of causal inference frameworks and identify promising generic application cases common in Earth system sciences and beyond. We discuss challenges and initiate the benchmark platform to close the gap between method users and developers.Rush, D., Talbot, H.M., van der Meer, M.T.J., Hopmans, E.C., Douglas, B., Sinninghe Damsté, J.S., 2019. Biomarker evidence for the occurrence of anaerobic ammonium oxidation in the eastern Mediterranean Sea during Quaternary and Pliocene sapropel formation. Biogeosciences 16, 2467-2479. eastern Mediterranean Sea sedimentary record is characterised by intervals of organic-rich sapropel sediments, indicating periods of severe anoxia triggered by astronomical forcing. It has been hypothesised that nitrogen fixation was crucial in injecting the Mediterranean Sea with bioavailable nitrogen (N) during sapropel events. However, the evolution of the N biogeochemical cycle of sapropels is poorly understood. For example, the role of the complementary removal reactions like anaerobic ammonium oxidation (anammox) has not been investigated because the traditional lipid biomarkers for anammox, ladderane fatty acids, are not stable over long periods in the sedimentary record. Using an alternative lipid biomarker for anammox, bacteriohopanetetrol stereoisomer (BHT isomer), we present here for the first time N removal throughout the progression, e.g. formation, propagation, and termination, of basin-wide anoxic events. BHT isomer and ladderanes were analysed in sapropel records taken from three eastern Mediterranean sediment cores, spanning S1 to Pliocene sapropels. Ladderanes were rapidly degraded in sediments, as recently as the S5 sapropel. BHT isomer, however, was present in all sapropel sediments, as far back as the Pliocene, and clearly showed the response of anammox bacteria to marine water column redox shifts in high-resolution records. Two different N removal scenarios were observed in Mediterranean sapropels. During S5, anammox experienced Black Sea-type water column conditions, with the peak of BHT isomer coinciding with the core of the sapropel. Under the alternative scenario observed in the Pliocene sapropel, the anammox biomarker peaked at onset and termination of said sapropel, which may indicate sulfide inhibition of anammox during the core of sapropel deposition. This study shows the use of BHT isomer as a biomarker for anammox in the marine sediment record and highlights its potential in reconstructing anammox during past anoxic events that are too old for ladderanes to be applied, e.g. the history of oxygen minimum zone expansion and oceanic anoxic events.Safi, E., Telling, J., Parnell, J., Chojnacki, M., Patel, M.R., Realff, J., Blamey, N.J.F., Payler, S., Cockell, C.S., Davies, L., Boothroyd, I.M., Worrall, F., Wadham, J.L., 2019. Aeolian abrasion of rocks as a mechanism to produce methane in the Martian atmosphere. Scientific Reports 9, Article 8229. changes in methane background levels and methane spikes have been detected in situ a metre above the Martian surface, and larger methane plumes detected via ground-based remote sensing, however their origin have not yet been adequately explained. Proposed methane sources include the UV irradiation of meteoritic-derived organic matter, hydrothermal reactions with olivine, organic breakdown via meteoroid impact, release from gas hydrates, biological production, or the release of methane from fluid inclusions in basalt during aeolian erosion. Here we quantify for the first time the potential importance of aeolian abrasion as a mechanism for releasing trapped methane from within rocks, by coupling estimates of present day surface wind abrasion with the methane contents of a variety of Martian meteorites, analogue terrestrial basalts and analogue terrestrial sedimentary rocks. We demonstrate that the abrasion of basalt under present day Martian rates of aeolian erosion is highly unlikely to produce detectable changes in methane concentrations in the atmosphere. We further show that, although there is a greater potential for methane production from the aeolian abrasion of certain sedimentary rocks, to produce the magnitude of methane concentrations analysed by the Curiosity rover they would have to contain methane in similar concentrations as economic reserved of biogenic/thermogenic deposits on Earth. Therefore we suggest that aeolian abrasion is an unlikely origin of the methane detected in the Martian atmosphere, and that other methane sources are required.Saintilan, N.J., Spangenberg, J.E., Chiaradia, M., Chelle-Michou, C., Stephens, M.B., Fontboté, L., 2019. Petroleum as source and carrier of metals in epigenetic sediment-hosted mineralization. Scientific Reports 9, Article 8283. ore deposits contribute a significant amount (up to 65%) of the global resources of lead and zinc. Among them, the Mississippi-Valley type deposits and related oil fields often comprise large-scale hydrothermal systems where regional host rocks are stained with disseminated liquid petroleum (crude oil) and other organic compounds. Current models for the formation of those epigenetic Pb-Zn sulphide deposits consider that metals are mostly leached from basement rocks and their detrital erosional products, and transported by oxidized basinal hydrothermal fluids as chloride complexes. Sulphide precipitation mainly occurs when these basinal brines interact with fluids rich in reduced sulphur species produced mostly by thermochemical sulphate reduction (TSR) mediated by hydrocarbons. Here, using organic geochemistry and Pb isotopes, we provide evidence that petroleum and associated water were key for the formation of sulphide mineralization in the world-class sandstone-hosted ore deposit at Laisvall, not only by supplying reduced sulphur but also by contributing metals in significant amounts. The lead originally found in bitumen of the Alum Shale Formation was transported —during an arc-continent collisional event— by liquid petroleum and associated water to the site of sulphide mineralization. The alteration of petroleum by TSR made lead available for precipitation as sulphide. The petroleum-associated lead represents 40 to 60% of the metal budget in the deposit, the remainder being sourced by leaching of basement rocks.Salama, E.-S., Govindwar, S.P., Khandare, R.V., Roh, H.-S., Jeon, B.-H., Li, X., 2019. Can omics approaches improve microalgal biofuels under abiotic stress? Trends in Plant Science 24, 611-624. hold the promise of an inexpensive and sustainable source of biofuels. The existing microalgal cultivation technologies need significant improvement to outcompete other biofuel sources such as terrestrial plants. Application of ‘algomics’ approaches under different abiotic stress conditions could be an effective strategy for optimization of microalgal growth and production of high-quality biofuels. In this review, we discuss the roles of omics in understanding genome structure and biocomponents metabolism in various microalgal species to optimize sustainable biofuel production. Application of individual and integrated omics revealed that genes and metabolic pathways of microalgae have been altered under multiple stress conditions, resulting in an increase in biocomponents, providing a research platform for expansion of genetic engineering studies in microalgal strains.Saleh, T.A., Fadillah, G., Saputra, O.A., 2019. Nanoparticles as components of electrochemical sensing platforms for the detection of petroleum pollutants: A review. TrAC Trends in Analytical Chemistry 118, 194-206. monitoring of environmental pollutants has become a primary concern due to rapid progress in the oil industry during recent years. Nanoparticles (NPs) for electrochemical sensing are emerging as crucial tools for pollutant monitoring such as aromatics hydrocarbon, polyphenols, and toxic gases produced by the oil industry. NPs provided increasing the sensitivity and selectivity of the sensor through increasing the surface area, owing to the high surface-to-volume ratios, and a highly active site area so that the molecules could be easily adsorbed on the surface electrode to undergo a redox reaction. This paper presents a comprehensive overview of the latest nanoparticles used for electrochemical sensing. Moreover, some parameters such as sensitivity, selectivity, the limit of detection, including a specific mechanism detection of analyte targets, and response time have been discussed to determine optimum condition for polyphenols, aromatic compounds, and toxic gases detection. Some recent results have been presented and discussed.Samuels, T., Pybus, D., Wilkinson, M., Cockell, C.S., 2019. Evidence for in vitro and in situ pyrite weathering by microbial communities inhabiting weathered shale. Geomicrobiology Journal 36, 600-611. pyrite oxidation is an important driver of biological weathering within shale, making a significant contribution toward biogeochemical cycling, bedrock expansion, and soil formation. These processes are of global importance, both within natural systems and in anthropogenic environments. Despite its significance, there is a lack of research that directly investigates microbe– pyrite interactions within shale. In this study, we use both field and laboratory approaches to inspect microbial pyrite oxidation in weathered shale environments within North Yorkshire, UK. Incubation of polished pyrite samples within iron-oxidizing enrichment cultures in vitro resulted in extensive colonization and surface pitting, demonstrating the weathering potential of shale microbial communities. Mineral samples were buried for 1 year within the floor of a shale rock mine, to explore pyrite bioweathering in situ. Image analysis revealed the formation of dissolution channels by microbial filaments, a novel mechanism of pyrite oxidation that broadens the taxonomic range of known microbe-pyrite interactions in weathered shale.Santos Silva, H., Alfarra, A., Vallverdu, G., Bégué, D., Bouyssiere, B., Baraille, I., 2019. Asphaltene aggregation studied by molecular dynamics simulations: role of the molecular architecture and solvents on the supramolecular or colloidal behavior. Petroleum Science 16, 669-684. aggregation is a subject under vivid discussion: There are several parameters one needs to determine before its behavior can be mastered and better target solutions can be tailored. The nature of asphaltene aggregation (colloidal or supramolecular) and the role of solvents and their mixtures are among the least understood parameters in asphaltene science. This paper addresses molecular dynamic simulations to correlate the aggregation properties of asphaltenes, their molecular structure and the concentration of these solvents. We show that the formation of the nanoaggregate depends, primarily, on the size of the conjugated core and on the eventual presence of polar groups capable of forming H-bonds. Heteroatoms on the conjugated core do not change their shape or type of aggregation but may induce stronger π-π interactions. The macroaggregation formation depends upon the length of the lateral chains of asphaltenes and also on the presence of polar groups at its end. Moreover, n-heptane and water may interact selectively with asphaltenes in function of their molecular architecture. Given this fact and the aggregation behavior observed, we advocate toward the assumption that a colloidal behavior of asphaltenes might be a particular case of a more general model, based on a supramolecular description.Saowapon, M.T., Thurbide, K.B., 2019. Dehydration of a water stationary phase as a novel separation gradient in capillary supercritical fluid chromatography. Chromatographia 82, 991-1001. novel alternative to gradient elution in capillary supercritical fluid chromatography (SFC) based upon the systematic removal of a water stationary phase from the column, using a pure CO2 mobile phase, is introduced. By adjusting the flow of water used to humidify the system, the stationary phase can be removed at different rates and this results in proportionately faster analyte elution. As well, the phase can be readily restored within a few minutes. The method demonstrates good reproducibility with analyte retention times yielding an RSD of 1.2% in consecutive trials. Further, it provides results that compare well to a conventional pressure program in capillary SFC, but without the problematic convolution of system pressure and flow rate. The technique also demonstrated the ability to refocus analytes into sharper peaks, resulting in a 30-fold increase in their peak height. This effect can improve detection limits and also allow ionizable analytes like amines and dicarboxylic acids to be eluted with improved peak shape. Results indicate that systematic removal of a water stationary phase from the column is an interesting and potentially effective alternate means of controlling and improving analyte elution in capillary SFC.Savenko, A.V., Savenko, V.S., 2019. Effect of natural organic acids on mobilization of macro- and microelements from rocks. Doklady Earth Sciences 485, 331-335. study of leaching of the main cations (Na, K, Mg, and Ca), alkaline and alkali-earth microelements (Li, Rb, Cs, Be, Sr, and Ba), heavy metals (Mn, Fe, Co, Ni, Cu, Zn, Cd, Tl, and Pb), hydrolyzate elements (Y, RZ, Ti, Th, and U), and anionic elements (F, Si, P, and V) from rocks of different acidity with distilled water and a multicomponent solution of organic acids, having the distribution of dissociation constants corresponding to natural dissolved organic matter was carried out. It has been shown that carboxylic acids, which are part of the dissolved organic matter contained in surface waters, cause a sharp increase in the mobilization of both the main cations and trace elements from silicate rocks. The chemical properties of the elements are of secondary importance, as was shown by the general correlation between the parameter related to the mobility of the elements at the initial stage of the leaching and their content in the rocks.Savvichev, A.S., Kadnikov, V.V., Kallistova, A.Y., Rusanov, I.I., Voronov, D.A., Krasnova, E.D., Ravin, N.V., Pimenov, N.V., 2019. Light-dependent methane oxidation is the major process of the methane cycle in the water column of the Bol’shie Khruslomeny polar lake. Microbiology 88, 370-374. abstract. Our understanding of the microorganisms and microbial communities responsible for methane oxidation in marine and freshwater basins has recently changed significantly. Aerobic methanotrophic proteobacteria of types I and II, possessing methane monooxygenase (MMO), the enzyme complex catalyzing the key reaction of methane oxidation to methanol with oxygen, were previously considered the major methane oxidizers in freshwater basins. Direct evidence of anaerobic methane oxidation (AOM) coupled to sulfate reduction was initially obtained almost 20 years ago (Boetius et al, 2000; Knittel and Boetius, 2009). This process involves a consortium of methanotrophic archaea and sulfate-reducing bacteria. It was subsequently found that in the absence of sulfate, nitrite, nitrate, and Fe or Mn oxidized forms could act as electron acceptors for AOM (Beal et al, 2009; Haron et al, 2013; Ettwig et al, 2016). The works of the last decade brought new insights on the metabolic capabilities of methanotrophic bacteria. Thus, it was found that in the absence of oxygen bacteria “Ca. Methylomirabilis oxyfera” (group NC10) carried out nitrite-dependent AOM via an “intracellular aerobic” pathway, in which molecular oxygen was released inside the cell due to NO disproportionation and was then used for respiration and MMO-dependent methane oxidation (Ettwig et al., 2010). Methanotrophic gammaproteobacteria (type I), which were previously considered strict aerobes, were recently reported to retain activity in hypoxic and even anoxic conditions (Chistoserdova, 2015). Trophic interaction between aerobic methanotrophs and oxygenic phototrophs is among the possible explanations of activity of methanotrophic gammaproteobacteria under hypoxic conditions. Oxygen produced by the phototrophs is immediately consumed by methanotrophs for methane oxidation (Milucka et al., 2015; Oswald et al., 2015). Light-dependent methane oxidation was experimentally confirmed in the stratified freshwater lakes Kadano, Rotsee (Switzerland), and La Cruz (Milucka et al., 2015; Oswald et al., 2015, 2016), as well as by our research on a freshwater meromictic Lake Svetloe (Arkhangelsk oblast, Russia) (Кallistova et al., 2019). Light-induced stimulation of methane oxidation was revealed by radiotracer experiments at the lower border of the redox zone, where oxygen was not revealed analytically. In the same zone, aerobic methanotrophs of the genus Methylobacter, methylotrophs of the genus Methylotenera, and cyanobacteria of the genera Synechococcus and Prochlorococcus were revealed. Thus, investigation of stratified/meromictic basins, where complex microbial communities develop in the water column at the border between oxic and anoxic water layers and where they often form mutilevel trophic relationships, will lead to significant progress in investigation of the mechanisms of methane oxidation under hypoxic and anoxic conditions.The subject of the study was Lake Bol’shie Khruslomeny, a polar meromictic lake at the Kandalaksha Bay coast, White sea (Krasnova et al., 2018). The lake is characterized by constant inflow of seawater through permeable rocks, which results in elevated salinity below the chemocline (up to 22 ‰ in the near-bottom horizons). The water samples were collected in early September 2017 from a boat (sampling site coordinates: 66° 42' 59" N, 32° 51' 29" E) using a submerged pump, which made it possible to collect the water column horizons with high resolution (up to 5?10 cm) (Fig. 1). Water salinity and temperature were measured with a submerged prob. Dissolved oxygen in the water column was determined by the Winkler method; sulfide was determined colorimetrically; and methane was measured by gas chromatography as described previously (Savvichev et al., 2018). The lake (~18 m deep) exhibited pronounced stratification, with the chemocline and halocline at 2?4 m (Fig 2a). Water temperature during sampling varied from 7.3 to 13.5°C, with the temperature maximum located in the chemocline, at the depth of 3.5?3.75 m (Fig. 2a). Oxygen concentrations in this depth interval decreased from 0.35 mmol L?1 at 2 m to 2.5 ?mol L?1 at 4 m. Sulfide was detected at 4 m, and its concentration in the near-bottom horizons was 17.8 mmol L?1 (Fig. 2a). Apart from the high sulfide level, extremely high methane concentrations were also found in the hypolimnion (up to 1.8 mmol L?1 at 18-m depth). Methane concentrations decreased sharply in the 3.75?5.5-m horizon, reaching 0.04?1.13 ?mol L?1 in the oxic zone (0?3.5 m). The rates of light and dark CO2 assimilation required for the photosynthesis profile, as well as the effect of light on the rate of methane oxidation were measured using radiotracer techniques with NaH14CO3 (specific activity 2.04 GBq mmol?1, 5 ?Ci/sample) and 14CH4 (2 ?Ci/sample, specific activity 1.16 GBq mmol?1) as was described previously (Кallistova et al., 2019)....Permeation of sulfate-enriched seawater to Lake B. Khruslomeny, which resulted in extremely high sulfide concentrations, suggested occurrence of sulfate-dependent methane oxidation in the anoxic monimolimnion. However, no 16S rRNA gene sequences of ANME archaea were retrieved. Bacteria of the NC10, responsible for methane oxidation with nitrite, were also not detected.Thus, our results indicate that light-dependent methane oxidation is not limited to freshwater stratified lakes, but may contribute significantly to the oxidation of this important greenhouse gas in brackish continental lakes and in shallow stratified marine basins.Sazanova, K.V., Senik, S.V., Kirtsideli, I.Y., Shavarda, A.L., 2019. Metabolomic profiling and lipid composition of Arctic and Antarctic strains of micromycetes Geomyces pannorum and Thelebolus microsporus grown at different temperatures. Microbiology 88, 282-291. reactions of Arctic and Antarctic strains of psychrophilic micromycetes Geomyces pannorum and Thelebolus microsporus to growth within a broad temperature range were studied. Adaptation of these species to different temperatures was found to result from both morphological and biochemical changes, including changes in the concentration of small molecules and lipid membrane components. These biochemical, morphological, and physiological mechanisms exhibited the patterns common to all strains, as well as species and strain differences. The general patterns included temperature-dependent changes in amounts of monosaccharides, some disaccharides, and free linoleic and linolenic acids. The differences between the Arctic and Antarctic strains were mainly associated with the differences in lipid composition, while interspecies differences resulted from metabolomic modifications. Antarctic strains showed lower ability to survive elevated temperatures, which correlated with weaker manifestation of the lipid-dependent adaptive mechanisms compared to the Arctic strains. Among the interstrain differences, higher growth parameters and mannitol accumulation were found in the Arctic isolates. Adaptation of T. microsporus was characterized by more diverse changes in the concentrations of small organic molecules in the metabolome profile and by pronounced changes in mycelial morphology. The results of metabolomic analysis and their subsequent treatment by the methods of multivariant statistics supported the suggestion of higher dispersion of metabolomic characteristics under unfavorable conditions and of lower dispersion of metabolomic data under optimal conditions.Scheidweiler, D., Peter, H., Pramateftaki, P., de Anna, P., Battin, T.J., 2019. Unraveling the biophysical underpinnings to the success of multispecies biofilms in porous environments. The ISME Journal 13, 1700-1710. regulate critical processes in porous ecosystems. However, the biophysical underpinnings of the ecological success of these biofilms are poorly understood. Combining experiments with fluidic devices, sequencing and modeling, we reveal that architectural plasticity enhances space exploitation by multispecies biofilms in porous environments. Biofilms consistently differentiated into an annular base biofilm coating the grains and into streamers protruding from the grains into the pore space. Although different flow-related processes governed the differentiation of these architectures, both BB and streamers were composed of similar bacterial assemblages. This is evidence for architectural plasticity. Architectural plasticity allowed for complementary use of the space provided by the grain–pore complexes, which increased biofilm carrying capacity at the larger scale of the porous system. This increase comes potentially at the cost of a tradeoff. Contrasting time scales of oxygen replenishment and consumption, we show that streamers locally inhibit the growth of the BB downstream from the grains. Our study provides first insights into the biophysical underpinnings to the success of multispecies biofilms in porous environments.Schiffries, C.M., Mangum, A.J., Mays, J.L., Hoon-Starr, M., Hazen, R.M., 2019. The Deep Carbon Observatory: A ten-year quest to study carbon in Earth. Engineering 5, 372-378. Deep Carbon Observatory (DCO) is a ten-year research program to investigate the quantities, movements, forms, and origins of carbon in Earth. More than 90% of Earth’s carbon may reside in the planet’s deep interior, and DCO’s overarching mission is to understand Earth’s entire carbon cycle—beyond the atmosphere, oceans, and shallow crustal environments, which have drawn most previous research attention—to include the deep carbon cycle [1], [2]. A decade of focused research has led to major discoveries by DCO scientists on the physical, chemical, and biological roles of carbon in Earth.To pursue its multidisciplinary mission, DCO connects more than 1200 scientists worldwide, broadly grouping them into four Science Communities: Extreme Physics and Chemistry, Reservoirs and Fluxes, Deep Energy, and Deep Life (Table 1). The program also emphasizes four crosscutting activities that bridge community boundaries—namely, data science, instrumentation, field studies, and modeling and visualization—and several cross-community groups that provide essential services to the entire DCO community (Fig. 1).In addition to its scientific advances, DCO has created an enduring legacy of interdisciplinary and international community building, successfully establishing a diverse, dynamic, and collaborative community of geologists, physicists, chemists, and biologists in more than 50 countries. In particular, DCO has focused on cultivating the next generation of deep carbon researchers by supporting early career scientists who will carry on the tradition of exploration and discovery for decades to come.The vision, guiding questions, and scientific goals of DCO were initially framed at an international Deep Carbon Cycle Symposium at the Carnegie Institution for Science in 2008. This symposium led to a successful proposal to the Alfred P. Sloan Foundation to establish a decadal research program on deep carbon science from 2009 to 2019. The Alfred P. Sloan Foundation pledged seed funding of 50 million USD over ten years to foster DCO. DCO has leveraged the support from the Alfred P. Sloan Foundation with more than 500 million USD in support from other sources, including international organizations, national science agencies, foundations, and the private sector.Scholtz, G., Staude, A., Dunlop, J.A., 2019. Trilobite compound eyes with crystalline cones and rhabdoms show mandibulate affinities. Nature Communications 10, Article 2503. knowledge about the structure, function, and evolution of early compound eyes is based on investigations in trilobites. However, these studies dealt mainly with the cuticular lenses and little was known about internal anatomy. Only recently some data on crystalline cones and retinula cells were reported for a Cambrian trilobite species. Here, we describe internal eye structures of two other trilobite genera. The Ordovician Asaphus sp. reveals preserved crystalline cones situated underneath the cuticular lenses. The same is true for the Devonian species Archegonus (Waribole) warsteinensis, which in addition shows the fine structure of the rhabdom in the retinula cells. These results suggest that an apposition eye with a crystalline cone is ancestral for Trilobita. The overall similarity of trilobite eyes to those of myriapods, crustaceans, and hexapods corroborates views of a phylogenetic position of trilobites in the stem lineage of Mandibulata.Schuerger, A.C., Moores, J.E., Smith, D.J., Reitz, G., 2019. A lunar microbial survival model for predicting the forward contamination of the Moon. Astrobiology 19, 730-756. surface conditions on the Moon are extremely harsh with high doses of ultraviolet (UV) irradiation (26.8 W?·?m?2 UVC/UVB), wide temperature extremes (?171°C to 140°C), low pressure (10?10 Pa), and high levels of ionizing radiation. External spacecraft surfaces on the Moon are generally >100°C during daylight hours and can reach as high as 140°C at local noon. A Lunar Microbial Survival (LMS) model was developed that estimated (1) the total viable bioburden of all spacecraft landed on the Moon as ～4.57?×?1010 microbial cells/spores at contact, (2) the inactivation kinetics of Bacillus subtilis spores to vacuum as approaching ?2?logs per 2107 days, (3) the inactivation of spores on external surfaces due to concomitant low-pressure and high-temperature conditions as ?6?logs per 8?h for local noon conditions, and (4) the ionizing radiation by solar wind particles as approaching ?3?logs per lunation on external surfaces only. When the biocidal factors of solar UV, vacuum, high-temperature, and ionizing radiation were combined into an integrated LMS model, a ?231?log reduction in viable bioburden was predicted for external spacecraft surfaces per lunation at the equator. Results indicate that external surfaces of landed or crashed spacecraft are unlikely to harbor viable spores after only one lunation, that shallow internal surfaces will be sterilized due to the interactive effects of vacuum and thermal cycling from solar irradiation, and that deep internal surfaces would be affected only by vacuum with a degradation rate of ?0.02?logs per lunation.Schuerger, A.C., Moores, J.E., Smith, D.J., Reitz, G., 2019. A lunar microbial survival model for predicting the forward contamination of the Moon. Astrobiology 19, 730-756. surface conditions on the Moon are extremely harsh with high doses of ultraviolet (UV) irradiation (26.8 W?·?m?2 UVC/UVB), wide temperature extremes (?171°C to 140°C), low pressure (10?10 Pa), and high levels of ionizing radiation. External spacecraft surfaces on the Moon are generally >100°C during daylight hours and can reach as high as 140°C at local noon. A Lunar Microbial Survival (LMS) model was developed that estimated (1) the total viable bioburden of all spacecraft landed on the Moon as ～4.57?×?1010 microbial cells/spores at contact, (2) the inactivation kinetics of Bacillus subtilis spores to vacuum as approaching ?2?logs per 2107 days, (3) the inactivation of spores on external surfaces due to concomitant low-pressure and high-temperature conditions as ?6?logs per 8?h for local noon conditions, and (4) the ionizing radiation by solar wind particles as approaching ?3?logs per lunation on external surfaces only. When the biocidal factors of solar UV, vacuum, high-temperature, and ionizing radiation were combined into an integrated LMS model, a ?231?log reduction in viable bioburden was predicted for external spacecraft surfaces per lunation at the equator. Results indicate that external surfaces of landed or crashed spacecraft are unlikely to harbor viable spores after only one lunation, that shallow internal surfaces will be sterilized due to the interactive effects of vacuum and thermal cycling from solar irradiation, and that deep internal surfaces would be affected only by vacuum with a degradation rate of ?0.02?logs per lunation.Schwanz, T.G., Bokowski, L.V.V., Marcelo, M.C.A., Jandrey, A.C., Dias, J.C., Maximiano, D.H., Canova, L.S., Pontes, O.F.S., Sabin, G.P., Kaiser, S., 2019. Analysis of chemosensory markers in cigarette smoke from different tobacco varieties by GC×GC-TOFMS and chemometrics. Talanta 202, 74-89. cigarettes are made from a blend of different tobacco varieties, which in turn are the results of different agronomic practices and post-harvest curing processes. The highly complex mixture of smoke compounds reflects each tobacco variety and the levels of sensory-relevant markers. Therefore, the aim of this work was to identify potential relevant chemosensory markers in the mainstream smoke of four main types of commercial tobaccos and establish any possible relationship between them and the tobacco growing/curing practices. The tobacco samples were segregated into four segments: (1) three curing stages of flue-cured Virginia, (2) three curing stages of air-cured Burley, (3) three geo-regions of sun-cured Oriental and (4) three different process applied to tobacco. One hundred and twenty cigarettes (10 batches per flavour category) were produced and smoked under standard machine-smoking protocols. The mainstream smoke samples collected were extracted and analysed by GC?×?GC TOFMS. The processed data was analysed by partial least square discriminant analysis (PLS-DA) and the selectivity ratio was used to identify key chemosensory markers responsible for the four segments. All models had sensitivity and specificity equal to unity. Flue-cured Virginia (193 markers) and air-cured Burley (184 markers) showed a similar trend for O-heterocycles markers in the lighter leaf colours and N-heterocycles in the darker leaf colours post-processing, but they had compounds of different flavour descriptions, e. g. sweet and nutty. The three geo-regions of sun-cured Oriental (290 markers) also presented O-heterocycles markers in correlation with leaf sugar contents in addition of sucrose esters markers. The three unusually processed tobacco generated many chemical markers (436 markers), some derived from the so-called Cavendish fermentation process with sweet, spicy and peppery notes, whereas the dark fermented air-cured tobacco presented similar descriptors as air-cured Burley. In addition, some polycyclic aromatic hydrocarbons (PAH) were detected as markers from the fire-curing process. The PLS-DA with selectivity ratio evidenced total of 1098 chemosensory markers in cigarette smoke, in which 173 were tentatively identified.Sébastien, R., Youri, H., Rémy, D., Valérie, B., Marta, G., Daniel, P., Maria-Fernanda, R.-S., 2019. Patterns of organic carbon enrichment in a lacustrine system across the K-T boundary: Insight from a multi-proxy analysis of the Yacoraite Formation, Salta rift basin, Argentina. International Journal of Coal Geology 210, Article 103208. this study, an integrated approach was applied using available sedimentary, geochronology, geochemical and isotopic datasets to better understand the complex interactions between production, destruction, and dilution processes that characterize the organic-rich sediments dynamic across the K-T boundary in a lacustrine system. This approach was tested here on the Late Cretaceous to Early Cenozoic Yacoraite Formation, a typical lacustrine source rock from the Salta rift Basin (NW Argentina). The Yacoraite Formation corresponds to a mixed carbonate-siliciclastic lacustrine sedimentary system, deposited during the sag phase (post-rift). We demonstrated here that new ashes U-Pb dating tie the K-T boundary during the deposition of the Yacoraite Formation.The Yacoraite Formation recorded major climate changes that can be documented in terms of catchment dynamic, erosion processes, carbonate accumulation trends, lacustrine dynamic and source rock quality. The pattern of organic carbon enrichment in the Yacoraite Formation illustrates how a biological pump came across a major climatic change. The background organic matter correspond to Type I dominated by algal growth (mean HI 600–800?mgHC/gTOC, TOC0 1–2?wt%). The K-T boundary was the climax of a climate change initiated ca. 0.3?Myr before and induced a major change in the catchment weathering processes, which temporally corresponds to the accumulation of poor quality source rock intervals (TOC0?≤?0.2?wt% and HI?<?50?mgHC/gTOC) in these series. The K-T boundary is highlighted by the main negative anomaly in δ13C of the carbonate deposits of the Yacoraite Formation. It was followed by a major pulse in paleoproductivity, itself followed by a major pulse in TOC0 (10–15?wt%) under anoxia conditions. In ca. 0.2?Myr the lacustrine dynamic and its related organic?carbon enrichment resumed to their initial setting, just prior to the preluding K-T boundary climate change. Results suggest that the Yacoraite Formation can be considered as a world-class example to illustrate how the K-T boundary is recorded in lacustrine sediments.Sêco, S.L.R., Silva, R.L., Watson, N., Duarte, L.V., Pereira, A.J.S.C., Wach, G., 2019. Application of petrophysical methods to estimate total organic carbon in Lower Jurassic source rocks from the offshore Lusitanian Basin (Portugal). Journal of Petroleum Science and Engineering 180, 1058-1068. Jurassic outcrops in the westernmost part of the Lusitanian Basin (S?o Pedro de Moel area, Portugal) reveal three stratigraphic units with source rock potential: i) Unit F from the Coimbra Formation, ii) the Polvoeira Member of the ?gua de Madeiros Formation, and iii) the Marly Limestones with Organic-rich Facies Member of the Vale das Fontes Formation. Despite decades of research, these source rocks have not yet been characterised in the offshore areas of the Lusitanian Basin.As a consequence of the discrepancy between organic matter contents in correlative surface-subsurface intervals, this paper investigates the applicability of petrophysical methods to semi-quantitatively estimate total organic carbon (TOC) and delineate source rock intervals in Lower Jurassic (Sinemurian–Pliensbachian) units in the offshore Lusitanian Basin. This study is based on the i) high-resolution stratigraphic correlation between well 14A-1 and the S?o Pedro de Moel section and ii) calibration of the TOC curve calculated for well 14A-1 using the high-resolution TOC datasets from S?o Pedro de Moel.Sonic transit time vs resistivity cross-plot shows that several intervals of the aforementioned lithostratigraphic units deviate from the (organic) lean sediment baseline, interpreted to indicate the presence of hydrocarbons and low-density organic matter. Thermal maturity from cuttings samples were used to estimate vitrinite reflectance for each well point measurement. These values vary between 0.51 and 0.87, indicating that the studied interval has reached the oil generation window. The level of organic metamorphism is in accordance with the hydrocarbon generation window interval, varying between 9.49 and 9.76. Neutron/resistivity, density/resistivity, and sonic/resistivity cross-plots and the petrophysical-based method for TOC calculation outlined in Passey et al. (1990) demonstrate the close similarity between TOC curves calculated for well 14A-1 and TOC measurements from the S?o Pedro de Moel outcrops. This comparison highlights the organic-rich nature of Unit F, the Polvoeira Member and the Marly Limestones with Organic-rich Facies Member in the offshore areas of the Lusitanian Basin and their potential as hydrocarbons source intervals.This work demonstrates a feasible solution to semi-quantitatively estimate TOC in subsurface source rocks when there is large uncertainty regarding sample quality. Delineation of source rock intervals in the offshore wells of the Lusitanian Basin reduces uncertainty, minimises risk, and may aid in new exploration concepts for hydrocarbons offshore Portugal. On a broader scale, this work reinforces the importance of outcrop control to correlate and improve the current knowledge of Portugal's offshore areas.Sevastyanov, V.S., Fedulov, V.S., Fedulova, V.Y., Kuznetsova, O.V., Dushenko, N.V., Naimushin, S.G., Stennikov, A.V., Krivenko, A.P., 2019. Isotopic and geochemical study of organic matter in marine sediments from the Indigirka Delta to the ice shelf border of the East-Siberian Sea. Geochemistry International 57, 489-498. hydrocarbon gases (СН4, С2Н4, С2Н6, С3Н6, С3Н8, С4Н8, n-С4Н10) and CO2 have been extracted in low concentrations from different layers of marine sediments up to 2 m thick on the continental shelf of the East Siberian Sea along the profile from the mouth of the Indigirka River to the ice shelf border. A freshwater complex supplied by the Indigirka and other rivers has the dominant influence on the composition of organic matter (OM) in the almost entire studied area of the East Siberian Sea. Concentrations of most common gases CH4 and CO2 increase with increasing sampling depth in sediment core collected at station 5602-2, while the carbon isotopic composition of CO2 decreases, reaching a value of –24‰. A sulfate reduction area was found at sediment depth of 48–70 cm. It was shown for the first time that the diagenesis of OM results in a systematic change in isotope fractional characteristics (IFC). IFC was obtained for the low-maturation OM, for OM from the sulfate reduction area, and for the high-maturation OM. OM in the low horizons of the sediment (below 77 cm from the surface) is much more evolved compared with the immature sediments of the upper horizons.Shakirov, R.B., Yatsuk, A.V., Mishukova, G.I., Obzhirov, A.I., Yugai, I.G., Cuong, D.H., Lan, N.H., Legkodimov, A.A., Shakirova, M.V., 2019. Methane flux into the atmosphere in the South China Sea. Doklady Earth Sciences 486, 533-536. regional gas geochemical profile was first performed in the South China Sea in the north–south direction in January 2017 (42nd cruise of the R/V Akademik Boris Petrov). Five zones with methane emission into the atmosphere with a maximum of 30 mole km–2 day–1, were revealed above the oil- and gas-bearing structures in the southern part of the sea, in the Nam Con Son Basin. Methane emission into the atmosphere is generally related to ascending migration of methane from hydrocarbon deposits along fault zones. The expedition was set up by the Council for the Earth’s Hydrosphere of the Federal Agency for Scientific Organization as part of the international project “The 2nd International Indian Ocean Expedition (IIOE-2).”Shi, W., Wang, X., Zhang, C., Feng, A., Huang, Z., 2019. Experimental study on gas content of adsorption and desorption in Fuling shale gas field. Journal of Petroleum Science and Engineering 180, 1069-1076. gas mainly exists in organic-rich shale in the form of free gas and adsorbed gas. Shale gas content has a direct impact on the productivity and life of the gas well, and is also an important indicator for areal selection and reservoir evaluation. Through the study of gas content experiments of shale gas, we can better guide the exploration and development of shale gas. According to the isothermal adsorption and desorption experiments of Wufeng-Longmaxi Formations in Jiaoshiba block of the Fuling shale gas field in Sichuan basin, China, 7 core samples from isothermal adsorption experiment and 30 core samples from desorption experiment were analyzed. The experimental results show that the isothermal adsorption experiment is an effective way to obtain Langmuir Volume (VL) and Langmuir Pressure (PL). The total gas content obtained from shale desorption experiment in the drilling site is mainly adsorption gas content, and the free gas content is relatively small. The desorption rate is different in different desorption stages, and the samples with higher total organic carbon (TOC) content have faster desorption rate and higher total desorption gas content. The carbon isotope value of methane gradually increases with the increase of desorption time. The results of methane isotope analysis in the desorption experiment are compared with the results of carbon isotope monitoring in the producing process. The findings reveal that after years of development in Jiaoshiba block of the Fuling shale gas field, the methane isotope in gas wells has basically remained unchanged, and the current gas production should be dominated by free gas.Shields, M.R., Bianchi, T.S., Kolker, A.S., Kenney, W.F., Mohrig, D., Osborne, T.Z., Curtis, J.H., 2019. Factors controlling storage, sources, and diagenetic state of organic carbon in a prograding subaerial delta: Wax Lake Delta, Louisiana. Journal of Geophysical Research: Biogeosciences 124, 1115-1131. Wax Lake Delta, southern Louisiana, is a coastal delta that formed following the dredging of a river channel in 1941 and is a field model for investigating the geomorphology, ecology, carbon dynamics, and carbon storage capacity in young prograding deltas. However, it is unknown how the transition from subaqueous to subaerial sediments affects the sources and quality of the sequestered carbon. We investigated these variations within the sediments of Wax Lake Delta using amino acid, lignin, and stable carbon isotope compositions of the organic matter (OM). A principal component analysis of these proxies highlighted variability in organic carbon (OC) composition with changes in elevation. The transition from subaqueous to subaerial sediments at 0-cm mean lower low water is an important component of the OM composition. In addition to the changes observed for OM source and quality, the OC loadings (OC/SA; mg C/m2) also increase as the delta aggrades and accumulates sediments with loadings typical of delta topsets and mobile mud banks (OC/SA?<?0.4) to riverine sediments (0.5?<?OC/SA?<?1) and eventually to highly productive regions (OC/SA?>?1). Linking this multiproxy approach with environmental variables such as elevation provides a path for incorporating OM dynamics into geomorphic models.Shields, M.R., Bianchi, T.S., Osburn, C.L., Kinsey, J.D., Ziervogel, K., Schnetzer, A., Corradino, G., 2019. Linking chromophoric organic matter transformation with biomarker indices in a marine phytoplankton growth and degradation experiment. Marine Chemistry 214, 103665. production and transformation of marine chromophoric dissolved organic matter (CDOM) provides a window into the marine biological pump as it is present at all depths and can be measured both in the field and via satellite. However, outside of lignin for terrestrial DOM, few studies have linked marine CDOM characteristics with biomarker indices. In this study, we quantified five fluorescent components of marine CDOM and base-extractable particulate organic matter (BEPOM) in a growth and degradation experiment using a natural plankton assemblage, and compared those results to bacterial abundances, hydrolytic enzyme activities, and amino acid concentrations and associated diagenetic indices. Rotating glass bottles containing plankton were sampled initially (day 0), during the mid-exponential (day 13) and stationary (day 20) growth phases, and again following a dark degradation period that lasted 42?days. Protein-like fluorescence (tryptophan-like and tyrosine-like) was correlated with the total amino acid concentrations for both the DOM and BEPOM through all phases of the incubation. However, tryptophan-like fluorescence showed a stronger correlation for aromatic amino acids. The concentration of particulate organic carbon changed significantly during each phase of the experiment and this substrate correlated with hydrolytic enzyme activities and bacterial abundance. This heterotrophy diagenetically altered the POM during the stationary phase and ultimately resulted in the increased production of more humic-like CDOM after degradation in the dark. Results from this study indicate that CDOM formation and cycling may play a prominent role in the ocean's nitrogen cycle.Shimizu, K., Ushikubo, T., Murai, T., Matsu’ura, F., Ueno, Y., 2019. In situ analyses of hydrogen and sulfur isotope ratios in basaltic glass using SIMS. GEOCHEMICAL JOURNAL 53, 195-207. developed in situ analyses of hydrogen and sulfur isotope ratios of basaltic glass using high-resolution, multi-collection secondary ion mass spectrometry (CAMECA IMS-1280HR). Hydrogen and sulfur isotopes of standard basaltic glasses were determined by a high-temperature conversion elemental analyzer/isotope ratio mass spectrometer (IRMS) and IRMS, respectively. For the in situ analysis of sulfur isotopes, a defocused Cs beam (~0.5 nA; ~10 μm diameter) was used, but for hydrogen isotopes, we used a larger defocused beam (~5 nA; ~15 μm diameter) to decrease the hydrogen background. For analyses of D/H (34S/32S) ratios, 16OH (32S) and 16OD (34S) were measured in multi-detection mode with a Faraday cup and an axial electron multiplier, respectively. Each measurement time was 6–7 minutes. Precisions (2 standard errors) for D/H and 34S/32S ratios were ~6‰ (H2O > 1 wt%) and ~0.6‰ (S > 1000 ppm), respectively. Our developed method for rapid and high spatial resolution analysis can determine multiple elements and isotopes of volatiles in a single small melt inclusion of ~30 μm diameter. Using this method, we analyzed hydrogen and sulfur isotope ratios of submarine basaltic glasses from mid-oceanic ridges and oceanic islands of Hawaii and confirmed that their D/H and S isotope ratios were consistent with reported values.Shiraishi, F., Matsumura, Y., Chihara, R., Okumura, T., Itai, T., Kashiwabara, T., Kano, A., Takahashi, Y., 2019. Depositional processes of microbially colonized manganese crusts, Sambe hot spring, Japan. Geochimica et Cosmochimica Acta 258, 1-18. contribution of microbially mediated and purely abiotic processes during Mn(II) oxidation is evaluated by investigating microbially colonized manganese deposits at the Sambe hot spring in Japan. Microscopic observations and DNA analyses suggest that manganese-oxidizing bacteria are present in the deposits at all of the sites investigated, while thick microbial mats, which consist mainly of phototrophic microorganisms, are developed at only one site. Microelectrode measurements (pH, O2 concentration, and Mn(II) concentration) near the deposit surface indicate that microbially mediated processes are dominant at all sites. These microbially mediated processes exceed the purely abiotic process by more than 2–24 times. At sites without abundant phototrophs, the major microbially mediated process that is occurring is light-independent oxidation (e.g., direct/indirect oxidation via manganese-oxidizing bacteria/fungi). In contrast, the site with abundant phototrophs is characterized by the occurrence of light-independent oxidation (mostly indirect oxidation by oxygenic phototrophs), and the contribution of light-independent oxidation is subordinate. Chemical gradients, which are established within a diffusive boundary layer and microbial mat, drive indirect oxidation by oxygenic phototrophs, and the O2 concentration gradient is particularly important when the concentration of dissolved inorganic carbon is higher than ca. 3?mM. X-ray diffraction and X-ray absorption fine-structure spectrometry analyses indicate that microbially mediated processes yield poorly-crystalline birnessite (i.e., vernadite) regardless of their relative contribution. The observations of this study imply that (1) photosynthetic increases in the O2 concentration drive indirect oxidation by oxygenic phototrophs at high concentrations of dissolved inorganic carbon like the Precambrian ocean, and that (2) the contribution of indirect oxidation by oxygenic phototrophs to ancient manganese oxides can be evaluated via geochemical redox proxies.Shu, Y., Lin, Y., Liu, Y., Yu, Z., 2019. Control of magmatism on gas accumulation in Linxing area, Ordos Basin, NW China: Evidence from fluid inclusions. Journal of Petroleum Science and Engineering 180, 1077-1087. paper takes the Linxing area of the eastern margin of Ordos Basin as an example. Based on the data of reservoir fluid inclusions (FI) and combined with the history of buried thermal history in Linxing area, the main effects of magmatism on the gas accumulation time, accumulation period, gas accumulation dynamics and accumulation pattern are studied. The vitrinite reflectance (Ro) in source rocks of Zijinshan tectonic area is higher than that in gentle tectonic area. The closer to Zijinshan pluton, the more it tends to single period natural gas charging, the earlier time of gas charging. The characteristics of natural gas accumulation are evidently regional and zonal. Gas accumulation in gentle tectonic area conforms to the law of “gas accumulation in near source reservoir is earlier than remote source reservoir”. The gas generated from the source rocks in the lower formation of the Zijinshan tectonic area reached the upper formation rapidly through the faults and fractures caused by the uplift of the Zijinshan pluton, and the accumulation interval time between the near source and remote source formation is relatively short. The Zijinshan tectonic area is the long-term high-pressure area and high-fluid potential area. The fluid potential in gentle tectonic area is low, and the fluid potential difference between the north and south is the motive force to promote the long distance lateral migration of gas. Zijinshan tectonic area is the hydrocarbon generation center and driving force source area, and gas accumulated rapidly from bottom to top. The features of gas accumulation in gentle tectonic area are dominated by vertical accumulation, supplemented by lateral supplementation. Since the Late Cretaceous, a large number of deep faults have been caused by the strong uplift of Zijinshan pluton, and a large number of natural gas are scattered through the faults and the reservoirs are destroyed. The faults in gentle tectonic area are not developed, and the natural gas preservation conditions are good, with good exploration prospects.Sikora, M., Pitulko, V.V., Sousa, V.C., Allentoft, M.E., Vinner, L., Rasmussen, S., Margaryan, A., de Barros Damgaard, P., de la Fuente, C., Renaud, G., Yang, M.A., Fu, Q., Dupanloup, I., Giampoudakis, K., Nogués-Bravo, D., Rahbek, C., Kroonen, G., Peyrot, M., McColl, H., Vasilyev, S.V., Veselovskaya, E., Gerasimova, M., Pavlova, E.Y., Chasnyk, V.G., Nikolskiy, P.A., Gromov, A.V., Khartanovich, V.I., Moiseyev, V., Grebenyuk, P.S., Fedorchenko, A.Y., Lebedintsev, A.I., Slobodin, S.B., Malyarchuk, B.A., Martiniano, R., Meldgaard, M., Arppe, L., Palo, J.U., Sundell, T., Mannermaa, K., Putkonen, M., Alexandersen, V., Primeau, C., Baimukhanov, N., Malhi, R.S., Sj?gren, K.-G., Kristiansen, K., Wessman, A., Sajantila, A., Lahr, M.M., Durbin, R., Nielsen, R., Meltzer, D.J., Excoffier, L., Willerslev, E., 2019. The population history of northeastern Siberia since the Pleistocene. Nature 570, 182-188. Siberia has been inhabited by humans for more than 40,000?years but its deep population history remains poorly understood. Here we investigate the late Pleistocene population history of northeastern Siberia through analyses of 34 newly recovered ancient genomes that date to between 31,000 and 600?years ago. We document complex population dynamics during this period, including at least three major migration events: an initial peopling by a previously unknown Palaeolithic population of ‘Ancient North Siberians’ who are distantly related to early West Eurasian hunter-gatherers; the arrival of East Asian-related peoples, which gave rise to ‘Ancient Palaeo-Siberians’ who are closely related to contemporary communities from far-northeastern Siberia (such as the Koryaks), as well as Native Americans; and a Holocene migration of other East Asian-related peoples, who we name ‘Neo-Siberians’, and from whom many contemporary Siberians are descended. Each of these population expansions largely replaced the earlier inhabitants, and ultimately generated the mosaic genetic make-up of contemporary peoples who inhabit a vast area across northern Eurasia and the Americas.Silva, A.C., Barbosa, M.S., Barral, U.M., Silva, B.P.C., Fernandes, J.S.C., Viana, A.J.S., Filho, C.V.M., Bispo, D.F.A., Christófaro, C., Ragonezi, C., Guilherme, L.R.G., 2019. Organic matter composition and paleoclimatic changes in tropical mountain peatlands currently under grasslands and forest clusters. CATENA 180, 69-82. peatlands are important ecosystems for Planet Earth, as they store large amounts of carbon and water. A better understanding of the impact of vegetation type and altitude in content, composition, and rate of accumulation of organic matter is key for assessing the current role of such environments. This study evaluated fibric and soluble fractions as well as the lignocellulosic and the isotopic compositions of the peat organic matter from four tropical mountain peatlands located at different altitudes of the Serra do Espinha?o Meridional, state of Minas Gerais, Brazil. The peatlands are currently under grasslands and forest clusters. Samples of peat under both vegetation types were collected and analyzed for organic matter fractions, cellulose, and lignin (van Soest method), as well as carbon and nitrogen isotopes. Different depths were chosen for radiocarbon dating of selected samples. The organic matter of peatlands currently under grasslands and forest clusters presented differences in soluble fractions, lignocellulosic composition, and δ13C values. Multivariate analyses allowed grouping the peatlands by altitude and vegetation type. The chronological succession of grassland and forest clusters in tropical mountain peatlands was influenced by altitude and was related to paleoclimatic changes.Simkus, D.N., Aponte, J.C., Elsila, J.E., Hilts, R.W., McLain, H.L., Herd, C.D.K., 2019. New insights into the heterogeneity of the Tagish Lake meteorite: Soluble organic compositions of variously altered specimens. Meteoritics & Planetary Science 54, 1283-1302. Tagish Lake carbonaceous chondrite exhibits a unique compositional heterogeneity that may be attributed to varying degrees of aqueous alteration within the parent body asteroid. Previous analyses of soluble organic compounds from four Tagish Lake meteorite specimens (TL5b, TL11h, TL11i, TL11v) identified distinct distributions and isotopic compositions that appeared to be linked to their degree of parent body processing (Herd et?al. 2011; Glavin et?al. 2012; Hilts et?al. 2014). In the present study, we build upon these initial observations and evaluate the molecular distribution of amino acids, aldehydes and ketones, monocarboxylic acids, and aliphatic and aromatic hydrocarbons, including compound-specific δ13C compositions, for three additional Tagish Lake specimens: TL1, TL4, and TL10a. TL1 contains relatively high abundances of soluble organics and appears to be a moderately altered specimen, similar to the previously analyzed TL5b and TL11h lithologies. In contrast, specimens TL4 and TL10a both contain relatively low abundances of all of the soluble organic compound classes measured, similar to TL11i and TL11v. The organic-depleted composition of TL4 appears to have resulted from a relatively low degree of parent body aqueous alteration. In the case of TL10a, some unusual properties (e.g., the lack of detection of intrinsic monocarboxylic acids and aliphatic and aromatic hydrocarbons) suggest that it has experienced extensive alteration and/or a distinct organic-depleted alteration history. Collectively, these varying compositions provide valuable new insights into the relationships between asteroidal aqueous alteration and the synthesis and preservation of soluble organic compounds.Simonov, V.A., Terleev, A.A., Kotlyarov, A.V., Tokarev, D.A., Kanygin, A.V., 2019. Physicochemical conditions of the existence of Early Cambrian chemotrophic microbiota in the zone of influence of sulfide ore-forming hydrothermal solutions. Doklady Earth Sciences 486, 512-516. studies of the Early Cambrian Kyzyl-Tashtyg pyrite deposit (East Tuva) allowed us to reconstruct the paleohydrothermal systems, to understand the physicochemical conditions of hydrothermal processes, and to study the patterns of existence of ancient hydrothermal biota in the zone of activity of solutions participating at all stages of the formation of ore-bearing structures starting from the influence of postmagmatic fluids and up to low-temperature hydrotherms. The data on the biota reported were obtained during study of the objects occurring in the zone of influence of relatively low-temperature hydrothermal systems. In some cases, microorganisms were found in basaltic complexes hosting ore bodies; in other cases, fauna was related to the ferrous–siliceous deposits. It was found that microorganisms in basaltic amygdules were formed at temperatures of ~110–140°C under the influence of hydrothermal solutions of the Kyzyl-Tashtyg deposit. Much lower temperatures (up to 100°C) existed during the evolution of microfossils in the quartz–hematite hydrothermal structures of the Kyzyl-Tashtyg deposit.Singhroha, S., Chand, S., Bünz, S., 2019. Constraints on gas hydrate distribution and morphology in Vestnesa Ridge, western Svalbard margin, using multicomponent ocean-bottom seismic data. Journal of Geophysical Research: Solid Earth 124, 4343-4364. hydrates occur within sediments on the western Svalbard continental margin and the Vestnesa Ridge, a large sediment drift that extends in a west-northwest direction from the margin toward the mid-ocean ridge. We acquired multicomponent ocean-bottom seismic (OBS) data at 10 locations on the crest area of the eastern segment of the Vestnesa Ridge, an area with active gas seepage. P and S wave velocities are estimated using traveltime inversion, and self-consistent approximation/differential effective medium rock physics modeling is used to estimate gas hydrate and free gas saturation at OBS stations. We apply 1-D full waveform inversion at a selected OBS station to study detailed variations of P wave velocity near the bottom simulating reflection (BSR). High interval P wave velocity (c≈ 1.73-1.82 km/s) and S wave velocity (>0.35 km/s) are observed in a layer above the BSR and low interval P wave velocity (Vp ≈ 1.28-1.53 km/s) in a layer below the BSR. We estimate 10-18% gas hydrate and 1.5-4.1% free gas saturation at different OBS stations in a layer above and below the BSR, respectively. We find significant variation in gas hydrate and free gas saturation across faults suggesting a structural control on the distribution of gas hydrate and free gas in the Vestnesa Ridge. Differences in gas hydrate saturation derived from P wave velocities and earlier estimates obtained from electromagnetic surveys indicate the presence of gas hydrates in faults and fractures. Moreover, beneath some OBS sites, the combined study of P and S waves, resistivity and seismic quality factor (Q), suggests the coexistence of free gas and gas hydrates.Sirén, K., Fischer, U., Vestner, J., 2019. Automated supervised learning pipeline for non-targeted GC-MS data analysis. Analytica Chimica Acta: X 1, Article 100005. analysis is nowadays applied in many different domains of analytical chemistry such as metabolomics, environmental and food analysis. Conventional processing strategies for GC-MS data include baseline correction, feature detection, and retention time alignment before multivariate modeling. These techniques can be prone to errors and therefore time-consuming manual corrections are generally necessary. We introduce here a novel fully automated approach to non-targeted GC-MS data processing. This new approach avoids feature extraction and retention time alignment. Supervised machine learning on decomposed tensors of segmented chromatographic raw data signal is used to rank regions in the chromatograms contributing to differentiation between sample classes. The performance of this novel data analysis approach is demonstrated on three published datasets.Sirhan, S.T., Katsman, R., Lazar, M., 2019. Methane bubble ascent within fine-grained cohesive aquatic sediments: Dynamics and controlling factors. Environmental Science & Technology 53, 6320-6329. (CH4) is a potent greenhouse gas. Its release from aquatic sediments to the water column and potentially to the atmosphere, is a subject of great concern. A coupled macroscopic single-bubble mechanical/reaction-transport numerical model was used to explore the ascent of a mature CH4 bubble toward the seafloor in muddy aquatic sediment. Two bubble ascent scenarios were demonstrated: stable and dynamic. For small effective overburden loads (≤11 kPa), stable ascent is followed by dynamic ascent (which has not been previously demonstrated to the best of the our knowledge). This ultimately leads to the bubble being released to the water column. Higher effective overburden loads induce only stable bubble ascent, which stops at the gas horizon frequently observed below the seafloor. The depth of the gas horizon increases, while bubble rise velocity decreases with an increase in the overburden load. It is shown that the bubble migration scenario is managed predominantly by inner bubble pressure, which defines a bubble solute exchange with ambient porewaters. Predicting a bubble ascent scenario in muddy sediment will further allow estimation of CH4 emission to the atmosphere and evaluation of changes in the effective mechanical properties of aquatic sediment due to the ascending bubbles.Smirnov, M.B., Poludetkina, E.N., Fadeeva, N.P., 2019. Anoxia in the photic layer of the sedimentation basin: Markers in the oils of Tatarstan. Geochemistry International 57, 635-644. source rocks of the oils in Tatarstan were determined to be formed under similar conditions, at anoxia in the photic layer of the sedimentation basin, with anoxia continuing throughout the whole time when the initial organic matter was accumulated, at a significant thickness of the H2S-infected layer. For some of the oils, disturbances in the anoxia may have occurred, or the thickness of the H2S-infected layer may have been reduced, and this resulted in a decrease in the content of anoxia markers in these oils. Biocenoses of microflora in the sedimentation layer contaminated with H2S show evidence of high stability. Transformation conditions of the buried organic matter in the course of diagenesis and catagenesis were uniform, as follows from the merely insignificantly varying relations between the depth of the complete hydrogenation and cyclization of the initial polyene aromatic carotenoids, the similarity in the molecular mass distributions of the destruction products of the C–C bond in C40 components, and the relatively small differences in ratios of the total concentration of monoaromatic compounds to the totals of hydrogenated analogues of the initial aromatic carotenoids. The source rocks of oils in Tatarstan can be identified based on analysis for concentrations of components that are anoxia markers in all of the Devonian rocks.Smith, A.R., Kieft, B., Mueller, R., Fisk, M.R., Mason, O.U., Popa, R., Colwell, F.S., 2019. Carbon fixation and energy metabolisms of a subseafloor olivine biofilm. The ISME Journal 13, 1737-1749.’s largest aquifer ecosystem resides in igneous oceanic crust, where chemosynthesis and water-rock reactions provide the carbon and energy that support an active deep biosphere. The Calvin Cycle is the predominant carbon fixation pathway in cool, oxic, crust; however, the energy and carbon metabolisms in the deep thermal basaltic aquifer are poorly understood. Anaerobic carbon fixation pathways such as the Wood-Ljungdahl pathway, which uses hydrogen (H2) and CO2, may be common in thermal aquifers since water-rock reactions can produce H2 in hydrothermal environments and bicarbonate is abundant in seawater. To test this, we reconstructed the metabolisms of eleven bacterial and archaeal metagenome-assembled genomes from an olivine biofilm obtained from a Juan de Fuca Ridge basaltic aquifer. We found that the dominant carbon fixation pathway was the Wood-Ljungdahl pathway, which was present in seven of the eight bacterial genomes. Anaerobic respiration appears to be driven by sulfate reduction, and one bacterial genome contained a complete nitrogen fixation pathway. This study reveals the potential pathways for carbon and energy flux in the deep anoxic thermal aquifer ecosystem, and suggests that ancient H2-based chemolithoautotrophy, which once dominated Earth’s early biosphere, may thus remain one of the dominant metabolisms in the suboceanic aquifer today.Smith, K.E., House, C.H., Arevalo, R.D., Dworkin, J.P., Callahan, M.P., 2019. Organometallic compounds as carriers of extraterrestrial cyanide in primitive meteorites. Nature Communications 10, Article 2777. delivery of cyanide may have been crucial for the origin of life on Earth since cyanide is involved in the abiotic synthesis of numerous organic compounds found in extant life; however, little is known about the abundance and species of cyanide present in meteorites. Here, we report cyanide abundance in a set of CM chondrites ranging from 50?±?1 to 2472?±?38 nmol·g?1, which relates to the degree of aqueous alteration of the meteorite and indicates that parent body processing influenced cyanide abundance. Analysis of the Lewis Cliff 85311 meteorite shows that its releasable cyanide is primarily in the form of [FeII(CN)5(CO)]3? and [FeII(CN)4(CO)2]2?. Meteoritic delivery of iron cyanocarbonyl complexes to early Earth likely provided an important point source of free cyanide. Iron cyanocarbonyl complexes may have served as precursors to the unusual FeII(CN)(CO) moieties that form the catalytic centers of hydrogenases, which are thought to be among the earliest enzymes.Sobecki, N., Nieto-Draghi, C., Di Lella, A., Ding, D.Y., 2019. Phase behavior of hydrocarbons in nano-pores. Fluid Phase Equilibria 497, 104-121. nanopores, solid-fluid interactions are of the same order of magnitude as intermolecular interactions of fluid molecules. This fact strongly modifies the thermodynamic properties of confined fluids with respect to bulk phases. Tight oil and shale gas reservoirs, where the proportion of micro (below 2?nm) and mesopores (between 2 and 50?nm) can reach more than 20% of the volume distribution, represent an environment with such problems and industrial challenges to hydrocarbon fluid pressure/volume/temperature (PVT) modeling. This study provides a detailed understanding of the thermodynamic behavior of confined fluid and reference data of the thermodynamic properties of pure components (methane, ethane, n-pentane, n-decane) and mixtures (methane/ethane, ethane/n-pentane) confined in graphite slit pores. Furthermore, a detailed explanation of the different pressures considered in a porous medium with nano-pores is given. The Gibbs Ensemble Monte Carlo (GEMC) NVT simulation is used for pure components instead of the more traditional Grand Canonical Monte Carlo ensemble (GCMC) simulation to get more precise results of liquid and vapor confined pressure avoiding the phase change location determination problem. The evolution of critical temperature and pressure versus pore radius is compared to literature correlations and confined vapor and liquid densities are calculated. A new and robust method in the GEMC ensemble called GEMC NPT Bubble point Monte Carlo (BPMC) completed with GEMC NVT simulations has been developed to get thermodynamic properties including pressures at equilibrium of confined mixtures. Pressure versus density diagrams, pressure versus molar fraction isotherms and examples of pressure versus temperature diagram for a specific composition are built. The phase envelope of the confined fluid is shifted and closes with respect to phase envelope of bulk fluid. The critical temperature and pressure are shifted from the bulk value to a lower value and the bubble point pressure is decreased as the dew point pressure is increased. With regards to the selectivity of the confined system compared to the bulk fluid, for the methane/ethane and ethane/n-pentane mixtures, the heavier component is preferentially adsorbed in the vapor phase and the lighter component is preferentially adsorbed in the liquid phase. All these results for pure components and mixtures provide relevant information concerning the understanding of the phase behavior in confined systems such as shale gas and tight oil reservoirs, emphasizing the difference from the bulk fluid. Furthermore all these data may be used as references for pore radius dependent equation of state (EOS) calibration.Sobolev, N.V., Tomilenko, A.A., Bul'bak, T.A., Logvinova, A.M., 2019. Composition of hydrocarbons in diamonds, garnet, and olivine from diamondiferous peridotites from the Udachnaya pipe in Yakutia, Russia. Engineering 5, 471-478. components in diamonds, associated garnet (pyrope), and olivine from two extremely rare xenoliths of diamondiferous peridotites recovered from the Udachnaya kimberlite pipe in Yakutia, Russia, were analyzed by gas chromatography-mass spectrometry (GC-MS) using a Focus GS-DSQ II Series Single Quadrupole MS (Thermo Scientific, USA). These xenoliths are pyrope lherzolite and pyrope dunite based upon compositions of coexisting minerals. Unlike the pyrope lherzolite, which contained pyrope with moderate calcium (Ca)-component content (about 15 mol %), the dunite contained subcalcic chromium (Cr)-pyrope with low Ca-component content (less than 10 mol %). All investigated minerals contained dominating hydrocarbons and their derivatives represented by aliphatic (paraffins, olefins), cyclic (naphthenes, arenes), oxygenated (alcohols, ethers), and heterocyclic (dioxanes, furans) hydrocarbons; nitrogenated, chlorinated, and sulfonated compounds; carbon dioxide (CO2); and water (H2O). Total hydrocarbon content was (in rel %) 79.7 for diamonds, 69.1 for garnet, and 92.6 for olivine, with a general amount of components ranging from 161 to 206. New data on volatiles in diamonds, associated garnet, and olivine suggest the presence of a wide spectrum of hydrocarbons along with (nitrogen) N2, CO2, and H2O in some upper mantle areas.Sobolev, S.V., Brown, M., 2019. Surface erosion events controlled the evolution of plate tectonics on Earth. Nature 570, 52-57. tectonics is among the most important geological processes on Earth, but its emergence and?evolution remain unclear. Here we extrapolate models of present-day plate tectonics to the past and propose that since about three billion years ago?the rise of continents and the accumulation of sediments at continental edges and in trenches has?provided lubrication for the stabilization of subduction and has been crucial in the development?of plate tectonics on Earth. We conclude that the two largest surface erosion and subduction lubrication events occurred after the Palaeoproterozoic Huronian global glaciations (2.45 to 2.2 billion years ago), leading to the formation of the Columbia supercontinent, and after the Neoproterozoic ‘snowball’ Earth glaciations (0.75 to 0.63 billion years ago). The snowball Earth event followed the ‘boring billion’—a period of reduced plate tectonic activity about 1.75 to 0.75 billion years ago?that was probably caused by a shortfall?of sediments in trenches—and it kick-started the modern episode of active plate tectonics.Sogabe, S., Hatleberg, W.L., Kocot, K.M., Say, T.E., Stoupin, D., Roper, K.E., Fernandez-Valverde, S.L., Degnan, S.M., Degnan, B.M., 2019. Pluripotency and the origin of animal multicellularity. Nature 570, 519-522. widely held—but rarely tested—hypothesis for the origin of animals is that they evolved from a unicellular ancestor, with an apical cilium surrounded by a microvillar collar, that structurally resembled modern sponge choanocytes and choanoflagellates. Here we test this view of animal origins by comparing the transcriptomes, fates and behaviours of the three primary sponge cell types—choanocytes, pluripotent mesenchymal archaeocytes and epithelial pinacocytes—with choanoflagellates and other unicellular holozoans. Unexpectedly, we find that the transcriptome of sponge choanocytes is the least similar to the transcriptomes of choanoflagellates and is significantly enriched in genes unique to either animals or sponges alone. By contrast, pluripotent archaeocytes upregulate genes?that control cell proliferation and gene expression, as in other metazoan stem cells and in the proliferating stages of two unicellular holozoans, including a colonial choanoflagellate. Choanocytes in the sponge Amphimedon queenslandica exist in a transient metastable state and readily transdifferentiate into archaeocytes, which can differentiate into a range of other cell types. These sponge cell-type conversions are similar to the temporal cell-state changes that occur in unicellular holozoans. Together, these analyses argue against homology of sponge choanocytes and choanoflagellates, and the view that the first multicellular animals were simple balls of cells with limited capacity to differentiate. Instead, our results are consistent with the first animal cell being able to transition between multiple states in a manner similar to modern transdifferentiating and stem cells.Soloveva, O.V., Tikhonova, E.A., Klimenko, T.L., Skrupnik, G.V., Votinova, T.V., 2019. Organic compounds in bottom sediments under conditions of coastal urbanization (a case study of Kazach’ya Bay of the Black Sea). Oceanology 59, 214-222. on the hydrocarbon composition of bottom sediments from a water area adjacent to an area with massive cottage construction (Kazach’ya Bay, coast of Sevastopol, the Black Sea) are presented. Analysis of bottom sediments performed in the summer 2015 provided values for the pH, Eh, natural humidity, and content of chloroform-extractable compounds, petroleum hydrocarbons, petrochemicals, polyaromatic hydrocarbons, and n-paraffins. Sites with unfavorable and moderately unsatisfactory ecological state were identified. The effect of urban development on the coast on the deterioration of bottom sediments was demonstrated.Song, L., Warner, T., Carr, T., 2019. An efficient, consistent, and trackable method to quantify organic matter–hosted porosity from ion-milled scanning electron microscope images of mudrock gas reservoirs. American Association of Petroleum Geologists Bulletin 103, 1473-1492. precisely quantify pore space and organic matter (OM) from two-dimensional scanning electron microscope (SEM) images, an efficient and consistent workflow using adaptive local thresholding, Otsu thresholding and Image Calculator are presented. It can offer an automated segmentation of pore space and OM, then differentiates the porosity hosted by OM and minerals. The workflow is demonstrated on a widely distributed set of core samples from Mahantango and Marcellus shale units of the Appalachian basin. The vitrinite reflectance of these samples ranges from 1.36% to 2.89%, covering a spectrum of thermal maturity. Organic matter abundance and mineralogy also vary significantly. The results are compared with routine rock property tests, such as helium porosimeter (Gas Research Institute method), and total OM. The proposed workflow improves quantitative determination of porosity above a certain pore size and OM in shale samples. Advantages of this workflow include improved consistency and speed of analysis of SEM images of shale samples at the nanoscale.Song, Y., Ma, X., Liu, S., Jiang, L., Hong, F., Qin, Y., 2019. Gas accumulation conditions and key exploration & development technologies in Qinshui coalbed methane field. Acta Petrolei Sinica 40, 621-634. Qinshui Basin has been explored for more than 60 years through two stages of oil and gas reconnaissance survey and exploration & development of coalbed methane (CBM), it has become the largest CBM industrialization base in China and also is a model which successfully realize commercialization of CBM of high rank coal-bearing basin in the world. Although the high-rank coal field is characterized by low pressure, low permeability, low saturation and strong heterogeneity, the exploration practice and research show that the accumulation conditions of CBM reservoir in Qinshui Basin are superior. As main productive intervals, No.15 coal seam of Taiyuan Formation and No.3 coal seam of Shanxi Formation respectively belong to the epicontinental-sea carbonate platform sedimentary system and the epicontinental-sea shallow-water delta sedimentary system. The coal seam has large thickness, and is mostly composed of humic coal and mainly contains vitrinite. Affected by tectonic thermal events in Yanshanian period, the coal rank is high, the adsorption capacity is strong, and the gas content is large. Formation of the CBM reservoir goes through three stages including two stages of hydrocarbon generation, gas phase transformation and sealing of hydrodynamics and roof and floor. In view of the characteristics of Qinshui Basin topography and the high rank coal, a series of key technologies for exploration and development are developed, including mountainous region seismic acquisition, processing and interpretation technology, drilling and completion technology of multiple wells, drilling and completion technology of multiple horizontal wells dominated by compound V type, deplugging secondary fracturing stimulation technology, control technology of high rank CBM drainage, and CBM gathering and transportation technology, which effectively supports the scale and industrialization development of high rank CBM in Qinshui Basin.Soreghan, G.S., Soreghan, M.J., Heavens, N.G., 2019. Explosive volcanism as a key driver of the late Paleozoic ice age. Geology 47, 600-604. CO2 exerts a robust and well-documented control on Earth’s climate, but the timing of glaciation during the late Paleozoic Ice Age (LPIA; ca. 360–260 Ma) is inconsistent with pCO2 reconstructions, hinting at another factor. Stratospheric volcanic aerosols produce a large but temporary negative radiative forcing under modern conditions. Here we examine explosive volcanism over 200 m.y. of Earth history to show that the LPIA corresponded with a sustained increase in volcanism in both tropical and extratropical latitudes. A major peak in explosive volcanism at ca. 300 Ma likely corresponded to stratospheric sulfur-injecting eruptions at least three to eight times more frequent than at present. This level of volcanism created a steady, negative radiative forcing potentially sufficient to initiate and, most critically, sustain icehouse conditions, even under increasing levels of pCO2, and helps resolve discrepancies between glacial timing and CO2 records. Accounting for the radiative forcing effects of CO2 and sulfate indicates that both are required to explain the LPIA, with sulfate producing an especially strong effect at peak icehouse ca. 298–295 Ma. Frequent explosive volcanism would have increased atmospheric acidity, enhancing the reactivity of iron in abundant volcanic ash and glacially generated mineral dust, thus strengthening the climate impact of volcanism through a marine biological pump further primed by feedback with glaciation.Souza, F.F.C., Rissi, D.V., Pedrosa, F.O., Souza, E.M., Baura, V.A., Monteiro, R.A., Balsanelli, E., Cruz, L.M., Souza, R.A.F., Andreae, M.O., Reis, R.A., Godoi, R.H.M., Huergo, L.F., 2019. Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest. Science of The Total Environment 688, 83-86. aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2?m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250?bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.Sowani, H., Deshpande, A., Gupta, V., Kulkarni, M., Zinjarde, S., 2019. Biodegradation of squalene and n-hexadecane by Gordonia amicalis HS-11 with concomitant formation of biosurfactant and carotenoids. International Biodeterioration & Biodegradation 142, 172-181. amicalis HS-11 has been enriched from a hydrocarbon contaminated tropical soil sample. The ability of this organism to utilize a triterpenic polyunsaturated hydrocarbon, squalene (2,6,10,15,19,23-hexamethyl-6,6,10,14,18,20-tetracosahexane) and the model saturated hydrocarbon n-hexadecane is described here. The isolate degraded squalene and n-hexadecane (79?±?3.02 and 96?±?4.11%, respectively) after eight days of incubation. The isolate produced an extracellular biosurfactant that reduced surface tension from 69?±?2.83 to 40?±?1.63 and 35?±?2.34?mN?m?1 with squalene and n-hexadecane as carbon sources, respectively, after 6 days. The Actinomycete cleaved squalene to geranylacetone and farnesyl acetaldehyde that were further utilized for supporting growth. n-Hexadecane was degraded via monoterminal oxidation and activities of important enzymes (alkane hydroxylase and alcohol dehydrogenase) were highest (215?±?8.76 and 169?±?6.02 units mg?1 protein, respectively) after four days. Cells grown on squalene were short and with n-hexadecane there were clumps of longer cells. Squalene and n-hexadecane-grown cell surfaces were smooth possibly due to extracellular surface active compounds. While growing on hydrophobic substrates, some cells were seen adhering to droplets and others were in the free form. The culture was able to simultaneously degrade hydrocarbons and produce two commercially relevant value-added products. The yield of the extracellular biosurfactant on n-hexadecane was 480?mg?l?1 and cells grown on squalene and n-hexadecane also yielded carotenoids (2.3?±?0.14 and 2.9?±?0.10?mg?g?1 dry cell weight, respectively). This is the first report on the utilization of squalene by Gordonia.Spalletti, L.A., Remírez, M.N., Sagasti, G., 2019. Geochemistry of aggradational - progradational sequence sets of the Upper Jurassic – Lower Cretaceous Vaca Muerta shales (A?elo area, Neuquén Basin, Argentina): Relation to changes in accommodation and marine anoxia. Journal of South American Earth Sciences 93, 495-509. shale plays have received marked attention over the last years because of their economic potential for hydrocarbon generation. The size and geology of the Neuquén Basin of western Argentina lends to large volumes of unconventional shale gas, particularly within the marine shales of the Upper Tithonian -- Valanginian Vaca Muerta Formation. This unit is characterized by a well-developed lithological transition from Tithonian monotonous organic-rich marly shales of several hundred metres thickness, to Lower Cretaceous increasingly carbonate-rich marls and marly limestones. Samples from four wells located in the central sector of the Neuquén Basin (A?elo area) were selected for petrographic, X-ray fluorescence and TOC analysis. Based on seismic interpretation of the strata geometry, these data were grouped according to their location in aggradational (AAS) and progradational accommodation sets (PAS). The AAS is composed of basinal black shale facies showing a planar stacking pattern, whereas the PAS is characterized by low-angle sigmoidal strata in which bottomset, foreset and topset deposits (and coeval basinal deposits) are recognized. Petrographic studies allowed to distinguish lithological variations between basinal (organic-rich, laminated unbioturbated shales and marly shales), bottomset (dark gray, diffuse laminated, slightly bioturbated shaly marls and marls), and foreset and topset deposits (gray, massive, bioturbated marls and calcareous marls with a wacky texture). Basinal deposits show a clear tendency towards compositions rich in silica. These distal deposits, together with the distalmost bottomset facies of the clinoforms, are relatively enriched in Al2O3. In turn, the content of CaO, MgO and P2O5 supplied by carbonate biogenic activity are higher in the shallower topset and foreset deposits. Distal (basinal and bottomset) deposits are significantly enriched in redox-sensitive elements (Mo, V, Co, S, Cr) and in organic productivity indicators (Zn, Ba, Cu and TOC).Basinal deposits accumulated under conditions of maximum sediment starvation, restricted circulation and low dissolved oxygen levels. These conditions partially persisted for the more distal progradational (bottomset) deposits, together with a progressive increase in carbonate intrabasinal productivity. Conversely, the foreset and topset deposits of the PAS formed under normal seawater oxygenation. These conditions favoured the increase of carbonate productivity associated with an ostensible decline of organic matter productivity and preservation. This approach to geochemical analysis in the sequence stratigraphic framework of the Vaca Muerta Formation suggests that redox conditions, biogenic carbonate productivity, detrital siliciclastic fluxes and carbon accumulation rates, were closely related to basin isolation, space available for sediment accumulation, and changes in water depth and marine water circulation.Spilker, L., 2019. Cassini-Huygens’ exploration of the Saturn system: 13 years of discovery. Science 364, 1046-1051.: The Cassini-Huygens mission to Saturn provided a close-up study of the gas giant planet, as well as its rings, moons, and magnetosphere. The Cassini spacecraft arrived at Saturn in 2004, dropped the Huygens probe to study the atmosphere and surface of Saturn’s planet-sized moon Titan, and orbited Saturn for the next 13 years. In 2017, when it was running low on fuel, Cassini was intentionally vaporized in Saturn’s atmosphere to protect the ocean moons, Enceladus and Titan, where it had discovered habitats potentially suitable for life. Mission findings include Enceladus’ south polar geysers, the source of Saturn’s E ring; Titan’s methane cycle, including rain that creates hydrocarbon lakes; dynamic rings containing ice, silicates, and organics; and Saturn’s differential rotation. This Review discusses highlights of Cassini’s investigations, including the mission’s final year.Editor's summary: Cassini's last look at Saturn's rings. During the final stages of the Cassini mission, the spacecraft flew between the planet and its rings, providing a new view on this spectacular system (see the Perspective by Ida). Setting the scene, Spilker reviews the numerous discoveries made using Cassini during the 13 years it spent orbiting Saturn. Iess et al. measured the gravitational pull on Cassini, separating the contributions from the planet and the rings. This allowed them to determine the interior structure of Saturn and the mass of its rings. Buratti et al. present observations of five small moons located in and around the rings. The moons each have distinctive shapes and compositions, owing to accretion of ring material. Tiscareno et al. observed the rings directly at close range, finding complex features sculpted by the gravitational interactions between moons and ring particles. Together, these results show that Saturn's rings are substantially younger than the planet itself and constrain models of their origin.Sreenivas, B., Dey, S., Bhaskar Rao, Y.J., Vijaya Kumar, T., Babu, E.V.S.S.K., Williams, I.S., 2019. A new cache of Eoarchaean detrital zircons from the Singhbhum craton, eastern India and constraints on early Earth geodynamics. Geoscience Frontiers 10, 1359-1370. dominant geodynamic processes that underpin the formation and evolution of Earth's early crust remain enigmatic calling for new information from less studied ancient cratonic nuclei. Here, we present U–Pb ages and Hf isotopic compositions of detrital zircon grains from ～2.9?Ga old quartzites and magmatic zircon from a 3.505?Ga old dacite from the Iron Ore Group of the Singhbhum craton, eastern India. The detrital zircon grains range in age between 3.95?Ga and 2.91?Ga. Together with the recently reported Hadean, Eoarchean xenocrystic (up to 4.24?Ga) and modern detritus zircon grains from the Singhbhum craton, our results suggest that the Eoarchean detrital zircons represent crust generated by recycling of Hadean felsic crust formed at ～4.3–4.2?Ga and ～3.95?Ga. We observe a prominent shift in Hf isotope compositions at ～3.6–3.5?Ga towards super-chondritic values, which signify an increased role for depleted mantle and the relevance of plate tectonics. The Paleo-, Mesoarchean zircon Hf isotopic record in the craton indicates crust generation involving the role of both depleted and enriched mantle sources. We infer a short-lived suprasubduction setting around ～3.6–3.5?Ga followed by mantle plume activity during the Paleo-, Mesoarchean crust formation in the Singhbhum craton. The Singhbhum craton provides an additional repository for Earth's oldest materials.St Clair, B., Pottenger, J., Debes, R., Hanselmann, K., Shock, E., 2019. Distinguishing biotic and abiotic iron oxidation at low temperatures. ACS Earth and Space Chemistry 3, 905-921. rates of microbial and abiotic iron oxidation were determined in a variety of cold (T = 9–12 °C), circumneutral (pH = 5.5–9.0) environments in the Swiss Alps. These habitats include iron–bicarbonate springs, iron–arsenic–bicarbonate springs, and alpine lakes. Rates of microbial iron oxidation were measured up to a pH of 7.4, with only abiotic processes detected at higher pH values. Iron oxidizing bacteria (FeOB) were responsible for 39–89% of the net oxidation rate at locations where biological iron oxidation was detected. Members of putative iron oxidizing genera, especially Gallionella, are abundant in systems where biological iron oxidation was measured. Geochemical sampling suites accompanying each experiment include field data (temperature, pH, conductivity, dissolved oxygen, and redox sensitive solutes), solute concentrations, and sediment composition. Dissolved inorganic carbon concentrations indicate that bicarbonate and carbonate are typically the most abundant anions in these systems. Speciation calculations reveal that ferrous iron typically exists as FeCO3(aq), FeHCO3+, FeSO4(aq), or Fe2+ in these systems. The abundance of ferrous carbonate and bicarbonate species appears to lead to a dramatic increase in the abiotic rate of reaction compared to the rate expected from chemical oxidation in dilute solution. This approach, integrating geochemistry, rates, and community composition, reveals locations and geochemical conditions that permit microbial iron oxidation and locations where the abiotic rate is too fast for the biotic process to compete.Staninska-Pi?ta, J., Piotrowska-Cyplik, A., Juzwa, W., Zgo?a-Grze?kowiak, A., Wolko, ?., Sydow, Z., Kaczorowski, ?., Powierska-Czarny, J., Cyplik, P., 2019. The impact of natural and synthetic surfactants on bacterial community during hydrocarbon biodegradation. International Biodeterioration & Biodegradation 142, 191-199. aim of this study was to analyse the basic mechanisms of the interaction of surfactants anionic rhamnolipids and non-ionic polysorbate-80 on a microbial consortium during the biodegradation of diesel oil under model conditions. The analysed surfactants significantly influenced the metapopulation changes of microorganisms and caused a decrease in metabolic activity; however, they did not decrease the biodiversity of the studied system. Polysorbate-80 was relatively resistant to biological decomposition, whereas rhamnolipids were subjected to biodegradation as well as microbial transformation, as confirmed by the activity of the RhlC gene. Determination of biodegradation kinetics confirmed the positive influence of polysorbate-80 on the degradation efficiency of diesel oil hydrocarbons. The addition of this surfactant in 2-fold and 4-fold critical micelle concentration revealed a positive influence on the total petroleum hydrocarbons biodegradation by 18% and 15% respectively. Rhamnolipids exhibited an inhibiting effect in all fractions, with the exception of n-alkanes. The biodegradation efficiency of total petroleum hydrocarbons was 47% and 40% lower in samples containing biosurfactants in 2-fold and 4-fold critical micelle concentration, compare to that of the control sample. The surfactant-enhanced bioremediation method is a promising alternative to traditional methods; however, the method's efficiency is associated with the proper selection of a surfactant and its concentration and consideration of the occurrence of toxic effects as well as changes in the local soil metapopulation.Staudigel, P.T., Swart, P.K., 2019. A diagenetic origin for isotopic variability of sediments deposited on the margin of Great Bahama Bank, insights from clumped isotopes. Geochimica et Cosmochimica Acta 258, 97-119. clumped isotope temperature proxy has been used to investigate the diagenetic history of carbonate sediments in two cores recovered during ODP Leg 166 on the margin of Great Bahama Bank. While periplatform sediments constitute a tempting archive of paleo ocean chemistry as they are unlikely to be subducted, their primary limitation is a well-documented susceptibility to post-depositional diagenetic reworking. The crystallization temperatures reconstructed using the clumped isotope proxy, as well as the mineralogy and δ13C and δ18O values have been used to determine the relative effects of sediment mixing and sediment recrystallization. Results show that as sediments undergo diagenetic alteration at the seafloor, their initially “warm” clumped isotope composition is overprinted at cooler benthic temperatures. This process appears to occur in an environment with sufficient fluid exchange to overprint carbon isotopes; an observation confirmed in a separate study by analyses of calcium, a similarly rock-buffered element. This early reactive exchange between carbonates and fluids is likely driven by the conversion of metastable aragonite to calcite. This partially occurs within the “flushed zone”, where porewater compositions remain compositionally similar to seawater throughout the upper ～40 meters of the sediment column. Sediments dominated by open system isotopic compositions correspond to a period of minimal sediment accumulation between 2 and 3?Ma. More deeply buried Miocene sediments of the more platform-proximal Site 1003 show evidence of subsequent recrystallization, incorporating the warmer geothermal TΔ47 values, and more as well as modified water δ18O values, likely driven by co-evolving porewater and carbonate oxygen isotopes. Reconstructed water δ18O values of these deeper sediments at Site 1003 are considerably more positive than the measured modern values, suggesting that porewater δ18O values were more positive during the Miocene. Sediments deposited at the platform distal Site 1006 between the early and middle Miocene did not show evidence for this deeper recrystallization. Differences in diagenetic behavior between the two sites cannot be solely accounted for by differences in sediment accumulation rate. To illustrate this, time-integrated models were constructed which simulated the burial of identically reactive material through the depositional history of each site, the sediments deposited at Site 1006 appear to “stabilize” after an initial phase of neomorphism, whereas the more platform proximal Site 1003 continues to recrystallize during deeper burial, apparently in the presence of a parent fluid with a more positive δ18O value than observed today. We conclude that despite consisting of the same end-member sediment sources, and being spatially separated by less than 30?km, the difference in clumped and oxygen isotopic composition between Sites 1003 and 1006 can be predominantly attributed to differences in the rate and duration of recrystallization during burial.Stewart, L.C., Algar, C.K., Fortunato, C.S., Larson, B.I., Vallino, J.J., Huber, J.A., Butterfield, D.A., Holden, J.F., 2019. Fluid geochemistry, local hydrology, and metabolic activity define methanogen community size and composition in deep-sea hydrothermal vents. The ISME Journal 13, 1711-1721. size and biogeochemical impact of the subseafloor biosphere in oceanic crust remain largely unknown due to sampling limitations. We used reactive transport modeling to estimate the size of the subseafloor methanogen population, volume of crust occupied, fluid residence time, and nature of the subsurface mixing zone for two low-temperature hydrothermal vents at Axial Seamount. Monod CH4 production kinetics based on chemostat H2 availability and batch-culture Arrhenius growth kinetics for the hyperthermophile Methanocaldococcus jannaschii and thermophile Methanothermococcus thermolithotrophicus were used to develop and parameterize a reactive transport model, which was constrained by field measurements of H2, CH4, and metagenome methanogen concentration estimates in 20–40?°C hydrothermal fluids. Model results showed that hyperthermophilic methanogens dominate in systems where a narrow flow path geometry is maintained, while thermophilic methanogens dominate in systems where the flow geometry expands. At Axial Seamount, the residence time of fluid below the surface was 29–33?h. Only 1011 methanogenic cells occupying 1.8–18?m3 of ocean crust per?m2 of vent seafloor area were needed to produce the observed CH4 anomalies. We show that variations in local geology at diffuse vents can create fluid flow paths that are stable over space and time, harboring persistent and distinct microbial communities.Stigall, A.L., Edwards, C.T., Freeman, R.L., Rasmussen, C.M.?., 2019. Coordinated biotic and abiotic change during the Great Ordovician Biodiversification Event: Darriwilian assembly of early Paleozoic building blocks. Palaeogeography, Palaeoclimatology, Palaeoecology 530, 249-270. Ordovician Period records an extraordinary biodiversity increase known as the Great Ordovician Biodiversification Event (GOBE), which coincided with a series of environmental changes to the Earth System, notably a cooling global ocean, increased oxygenation, and increased nutrient supply from volcanism and continental weathering. The co-evolution of Earth and its biota during this interval has been studied in various contexts on multiple paleocontinents. Emerging patterns depend on the lens of investigation. Here we summarize the current state of understanding by reviewing and synthesizing the fossil and sedimentary records.Recent paleontological studies, mainly focused on rhynchonelliform (articulated) brachiopods, bryozoa, cephalopods, trilobites, graptolites, echinoderms, and reef organisms, have documented details of diversification, body size increase, development of ecosystem complexity, and intensification of inter-continental dispersal from the late Cambrian through Late Ordovician. Biomass increased markedly between the Early and Middle Ordovician. Furthermore, diversification rates increase statistically during the mid-Darriwilian Age both globally and regionally.Coincident with these biotic changes, geochemical proxies record significant changes to Earth's physical system. Oceanic temperatures decreased, and atmospheric oxygen levels increased to near modern levels in concert with the Middle Ordovician diversification of shelly fauna. Anoxic pulses ceased and evidence for deep ocean ventilation prevails in Middle Ordovician strata. Furthermore, a major Middle–Late Ordovician change in oceanic strontium isotopic composition indicates increased weathering of juvenile volcanic rocks and delivery of nutrients to marine settings. This multi-proxy dataset records near-simultaneous changes in fossil-rich shallow marine environments during exactly the interval of greatest diversification.By integrating biotic and geochemical datasets, a clear picture of the co-evolution of Earth and its biota emerges indicating that the Darriwilian was the critical interval facilitating increased capacity of ecosystems. We, therefore, recommend restricting the term “GOBE” to indicate this short interval of rapid diversification and ecosystem change, and using “Ordovician Radiation” when referencing the sum of diversifications that occurred throughout the Ordovician Period.Stone, A.C., 2019. The lineages of the first humans to reach northeastern Siberia and the Americas. Nature 570, 170-172. reached the Americas from northeastern Siberia during the last ice age. Genomic analyses of ancient and modern individuals reveal the history of the peoples who have populated these regions. The far northeast of Siberia was the gateway to the Americas for ancient humans, and today is home to diverse cultures whose members speak many languages. During the Late Pleistocene period (the ice age that lasted from about 126,000 to 11,700 years ago), this area of Siberia was connected to North America; the land bridge and adjacent areas formed a region known as Beringia. Hunter-gatherer populations seem to have ranged widely1–3 across Siberia and into Beringia, sustained by megafauna such as woolly mammoths, and other animals. Writing in Nature, Sikora et al.4 and Flegontov et al.5 examine the genetic footprints of past peoples in northeastern Siberia and northern North America, to work out their relationships to modern communities. Sikora and colleagues also examine how these peoples were affected by climate change over the past 40,000 years.Sikora et al. analysed genomic data from 34 people from ancient northeastern Siberia. Two individuals were buried at Yana RHS in Russia — a 31,600-year-old archaeological site that contains the earliest human remains found in the far northeast of Siberia — and the others date from 9,800 to 600 years ago. The Yana individuals provide the only genomic data gathered so far from northeastern Siberia before the Last Glacial Maximum (LGM, about 26,500 to 19,000 years ago), although there is evidence of human occupation in central Siberia as early as 45,000 years ago6. The limited availability of genomic data from pre-LGM Eurasians has made it challenging for researchers to understand the landscape of human variation at the time. Sikora and colleagues’ analyses support the idea that these populations were wide-ranging, yet structured (there were genetic differences between groups). The authors also suggest that the Yana represent a group that the team calls Ancient North Siberians (ANS), who diverged from Western Eurasians about 38,000 years ago, soon after the latter group split from East Asians. The land bridge between Eurasia and North America existed from about 34,000 to 11,000 years ago3,7, and it is thought that people migrated onto this bridge sometime between 30,000 and 15,000 years ago. Using palaeoclimate simulations and genetic data, Sikora et al. suggest that at least some ANS moved to southern Beringia during the LGM (Fig. 1), and that these individuals are ancestral both to the first people who inhabited the Americas (sometimes referred to as the First Peoples) and to another group that emerged at about the same time, whom the authors call Ancient Palaeo-Siberians. East Asians contributed 75% of their DNA to the Ancient Palaeo-Siberians, and 63% to the First Peoples, which suggests that there was some geographical separation between the latter two groups. The authors argue that these groups diverged about 24,000 years ago.After the LGM, major environmental and cultural changes occurred on both sides of the land bridge (as they did elsewhere). In Siberia, archaeological evidence shows that a change in tool technologies occurred, coinciding with a scarcity of mammoth ivory8. This evidence, together with Sikora and colleagues’ genetic data, indicates that population and cultural changes occurred as a result of the expansion of the Ancient Palaeo-Siberian population. The Ancient Palaeo-Siberians were then replaced by, or admixed (produced offspring) with, a group called the Neo-Siberians, between 11,000 and 4,000 years ago.Also just after the LGM, the First Peoples began their movement southwards9,10. Other groups remained in the north, and it is their subsequent history that is the focus of Flegontov and co-workers’ study. More specifically, the authors examine the relationships between people from several archaeologically defined cultures, including the Palaeo-Eskimos, who spread across the American Arctic from about 5,000 years ago, and the Neo-Eskimos, whose population expanded and might have replaced the Palaeo-Eskimos from about 800 years ago (Fig. 2). The researchers also study how these ancient peoples are related to modern populations who speak Eskimo-Aleut, Na-Dene and other languages.Flegontov et al. examined about 1.24 million variable nucleotide sites across the genome from 48 ancient individuals and from modern I?upiat, who live in northern Alaska. Previous research11 has led to debate about whether the Palaeo-Eskimo admixed with other groups. Flegontov and colleagues’ data demonstrate that the Palaeo-Eskimo lineage did indeed contribute to the Neo-Eskimo group, and thus its members are among the ancestors of modern Eskimo-Aleut speakers, as well as of Na-Dene-speaking peoples.Both of the new papers present analyses and discussions of the Palaeo-Eskimo peoples: Sikora et al. focus on their Siberian ancestors, whereas Flegontov et al. examine their relationship to subsequent populations in North America. Sikora et al. identify Palaeo-Eskimo individuals (including a Saqqaq individual, who lived in Greenland) as being admixtures of the Ancient Palaeo-Siberian and East Asian lineages; Flegontov et al. call this Siberian ancestry the Proto-Palaeo-Eskimo lineage. Both papers also describe evidence of ancient people interacting across the Bering Strait, and of migration back to Siberia. Sikora et al. suggest that Ancient Palaeo-Siberians contributed DNA to modern Na-Dene speakers, but (unlike Flegontov et al.) propose that this came from Siberian ancestors, rather than from Palaeo-Eskimos.One limitation of the two papers is that, although some of the DNA samples analysed by the two research groups came from the same archaeological sites, it is difficult to tell whether the same individuals were sampled — a problem that can arise in studies of archaeological material. A general code of practice would be useful for this field, to encourage scientists to provide the identifiers used by the original excavators, thus enabling cross-study comparisons and validations. This would help to ensure that the destructive sampling of archaeological remains, which are non-renewable resources, is properly coordinated and minimized. The code of practice could also ensure that descendants of ancient individuals are engaged in discussions about sampling (as exemplified by Flegontov et al., who note that they consulted Alaskan communities in their study).Both studies reveal not only the complexity of the interactions that occurred within and between Siberian and northern North American populations over time, but also the impact of climate change — specifically, how the ice-age climate drove people to ‘refugia’ (locations where humans could survive) during the LGM, and subsequent population expansions into other regions when the ice receded or the climate improved. However, we have no human genetic data from the roughly 20,000-year period after the initial occupation of the Yana site. This is a huge gap, in archaeological terms. Further studies of Siberian and Beringian populations during this period are now needed to learn more about the genetic and cultural diversity of these groups.More work is also needed to understand where the refugia were in northeastern Siberia, and what environmental conditions were like in these regions. In particular, what was the population structure in the Beringian refugium, and does this support the Beringian standstill hypothesis — which posits that the First Peoples became isolated during the LGM, before the southward expansion of the ice sheets12? In the ongoing debate about how many ‘waves’ of migration led to the establishment of human populations in the Americas, the new papers could be interpreted as suggesting that there were just two: the First Peoples and the Palaeo-Eskimo peoples. If so, then how does this tally with the idea that some Amazonian populations seem to share DNA13,14 with people who speak Austronesian languages (who live today in southeast Asia, Oceania and Madagascar)? Did the populations in the Beringian refugium also have this ancestry? Lastly, how did environmental changes, human migrations and cultural and genetic adaptations interplay in northeastern Siberia and the far northern Americas? The two latest studies will help us to get our bearings as we work to understand the ancient humans who lived around the Bering Strait.References1. Nogués–Bravo, D., Rodríguez, J., Hortal, J., Batra, P. & Araújo, M. B. PLoS Biol. 6, e79 (2008).2. Pitulko, V., Pavlova, E. & Nikolskiy, P. Quat. Sci. Rev. 165, 127–148 (2017).3. Hoffecker, J. F., Elias, S. A., O’Rourke, D. H., Scott, G. R. & Bigelow, N. H. Evol. Anthropol. 25, 64–78 (2016).4. Sikora, M. et al. Nature 570, 182–188 (2019)5. Flegontov, P. et al. Nature 570, 236–240 (2019).6. Pitulko, V. V. et al. Science 351, 260–263 (2016).7. Hu, A. et al. Nature Geosci. 3, 118–121 (2010).8. Pitulko, V. V. & Nikolskiy, P. A. World Archaeol. 44, 21–42 (2012).9. Fagundes, N. J. R. et al. Am. J. Hum. Genet. 82, 583–592 (2008).10. Goebel, T., Waters, M. R. & O’Rourke, D. H. Science 319, 1497–1502 (2008).11. Raghavan, M. et al. Science 345, 1255832 (2014).12. Tamm, E. et al. PloS ONE 2, e829 (2007).13. Raghavan, M. et al. Science 349, aab3884 (2015).14. Skoglund, P. et al. Nature 525, 104–108 (2015).Strack, M., Hayne, S., Lovitt, J., McDermid, G.J., Rahman, M.M., Saraswati, S., Xu, B., 2019. Petroleum exploration increases methane emissions from northern peatlands. Nature Communications 10, Article 2804. are globally significant sources of atmospheric methane (CH4). In the northern hemisphere, extensive geologic exploration activities have occurred to map petroleum deposits. In peatlands, these activities result in soil compaction and wetter conditions, changes that are likely to enhance CH4 emissions. To date, this effect has not been quantified. Here we map petroleum exploration disturbances on peatlands in Alberta, Canada, where peatlands and oil deposits are widespread. We then estimate induced CH4 emissions. By our calculations, at least 1900?km2 of peatland have been affected, increasing CH4 emissions by 4.4–5.1?kt?CH4?yr?1 above undisturbed conditions. Not currently estimated in Canada’s national reporting of greenhouse gas (GHG) emissions, inclusion would increase current emissions from land use, land use change and forestry by 7–8%. However, uncertainty remains large. Research further investigating effects of petroleum exploration on peatland GHG fluxes will allow appropriate consideration of these emissions in future peatland management.Su, G., Zhang, H., Geng, T., Yuan, S., 2019. Effect of SDS on reducing the viscosity of heavy oil: A molecular dynamics study. Energy & Fuels 33, 4921-4930. stabilization of heavy oil plays an important role in the aggregation of asphaltene and resin molecules. Many experiments have been carried out to study the complex aggregation structures of asphaltene and resin molecules in heavy crude oils, but at the molecular level, these microstructures and properties are still unclear. As an auxiliary tool, molecular dynamics simulation can be used to simulate the behavior of asphaltene and resin molecules in heavy oil droplets or emulsified oil droplets. The simulation results show that (i) whether carboxylic acid asphaltene molecules or ordinary asphaltene molecules and resin molecules can form the netlike structure in heavy oil through face-to-face or side-to-side stacking interaction. (ii) When a surfactant molecules is added into heavy oil phase, ordinary asphaltene molecules move from the oil/water interface to the center of the emulsified oil droplet, but carboxylic acid asphaltene molecules are still at the oil/water interface. (iii) Molecular dynamics simulation shows that the emulsified oil drops at the hydrophilic interface, the hydrogen bond between the water molecules, and the relaxation time have a significant increase. Moreover, through the tensile simulation of the simulated system, the maximum force of the oil droplets formed by pulling apart the carboxylic acid asphaltene molecules is significantly smaller than that of the ordinary asphaltenes. When the sodium dodecyl sulfate molecule is added to the system, the maximum force of the oil droplets formed by pulling apart the ordinary asphaltene molecules is significantly reduced.Su, X., Zhou, M., Hu, P., Xiao, Y., Wang, Z., Mei, R., Hashmi, M.Z., Lin, H., Chen, J., Sun, F., 2019. Whole-genome sequencing of an acidophilic Rhodotorula sp. ZM1 and its phenol-degrading capability under acidic conditions. Chemosphere 232, 76-86. goal of this work was to investigate the genetics of an acidophilic phenol-degrading yeast strain using whole-genome sequencing (WGS), characterize the growth of the strain and phenol degradation capability as well as degradation pathway under extremely acidic conditions. The result showed that the strain ZM1 isolated from an acid mine drainage (AMD) belongs to basidiomycetous yeast Rhodotorula sp., which possesses some unique genes compared to other four closely related Rhodotorula species. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis suggested that ZM1 possessed the degradation potentials for aromatic compounds. ZM1 was acidophilic with the optimum growth at the initial pH of 3.0. It could adjust pH to desired levels probably by acid production during the cultivation. Notably, at pH 3.0, the strain ZM1 showed a high phenol-degrading capability that almost completely degraded 1100?mg/L of phenol in 120?h with the highest degradation rate of 0.074?g/(g cell dry weight h). Under the same pH, the strain could completely degrade 500?mg/L phenol within 48?h?at NaCl concentration up to 10?g/L. The identification of the gene catA by the KEGG analysis, together with the presence of metabolic intermediate of cis, cis-muconic acid detected by gas chromatography-mass spectrometry, confirmed that the strain ZM1 degraded phenol via ortho-cleavage pathway. These findings suggest that the indigenous yeasts strain ZM1 could be exploited as an important member for in-situ biodegradation of aromatic compounds in the extremely acidic environments.Suchéras-Marx, B., Mattioli, E., Allemand, P., Giraud, F., Pittet, B., Plancq, J., Escarguel, G., 2019. The colonization of the oceans by calcifying pelagic algae. Biogeosciences 16, 2501-2510. rise of calcareous nannoplankton in Mesozoic oceans has deeply impacted ocean chemistry and contributed to shaping modern oceans. Nevertheless, the calcareous nannoplankton colonization of past marine environments remains poorly understood. Based on an extensive compilation of published and unpublished data, we show that their accumulation rates in sediments increased from the Early Jurassic (～200?Ma) to the Early Cretaceous (～120?Ma), although these algae diversified up to the end of the Mesozoic (66?Ma). After the middle Eocene (～45?Ma), a decoupling occurred between accumulation rates, diversity and coccolith size. The time series analyzed points toward a three-phase evolutionary dynamic. An invasion phase of the open-ocean realms was followed by a specialization phase occurring along with taxonomic diversification, ended by an establishment phase where a few small-sized species dominated. The current hegemony of calcareous nannoplankton in the world ocean results from a long-term and complex evolutionary history shaped by ecological interactions and abiotic forcing.Sukhanova, E.V., Shtykova, Y.R., Suslova, M.Y., Pestunova, O.S., Kostornova, T.Y., Khanaev, I.V., Zimens, E.A., Podlesnaya, G.V., Parfenova, V.V., 2019. Diversity and physiological and biochemical properties of heterotrophic bacteria isolated from Lake Baikal epilithic biofilms. Microbiology 88, 324-334. total of 170 heterotrophic bacterial strains were isolated from Lake Baikal epilithic biofilms. Identification of the isolates was carried out using the 16S rRNA gene sequencing and physiological and biochemical characteristics. Phylogenetic analysis revealed 59 phylotypes, with three strains probably belonging to new prokaryotic taxa. Members of the cultured biofilm community belonged to 4 phyla and 32 bacterial genera: Proteobacteria (51%), Firmicutes (30%), Actinobacteria (15%), and Bacteroidetes (4%). The genera Aeromonas, Pseudomonas, and Bacillus were predominant. Diversity of the cultured microbial community was higher in the epilithic biofilms than in the water column, neuston, and sponges. Among the isolates, members of ten genera have not been previously found in the Lake Baikal ecosystem: Actinobacteria (Microcella, Pseudoclavibacter, Glaciihabitans, Plantibacter, and Sanguibacter), Proteobacteria (Devosia, Roseomonas, Hydrogenophaga, Iodobacter, and Rhizobium); Glaciihabitans spp. ВА-51-09, ВА-73-09 and Rhizobium sp. ВА-57-09 were new prokaryotic taxa. Statistically significant differences were revealed in the frequency of occurrence of the strains isolated from biofoulings on a steel plate and on natural substrates, as well as on nutrient media with different composition of organic compounds. Most isolates of the genera Aeromonas, Pseudomonas, and Bacillus were capable of degradation of six different polymer substrates, which may indicate their active involvement in organic matter decomposition in biofilms and in Lake Baikal ecosystem in general.Sun, M., Zhang, L., Hu, Q., Pan, Z., Yu, B., Sun, L., Bai, L., Connell, L.D., Zhang, Y., Cheng, G., 2019. Pore connectivity and water accessibility in Upper Permian transitional shales, southern China. Marine and Petroleum Geology 107, 407-422. connectivity of shale controls shale gas migration and production behavior. The pore connectivity and water accessibility in clay-rich Upper Permian transitional shales remain unclear. Contrast matching small-angle neutron scattering (CM-SANS) tests were used to determine the accessibility of water to pores in the transitional shales. Complementary analyses with SANS, gas (CO2 and N2) physisorption isotherm, mercury intrusion capillary pressure (MICP), helium ion microscopy (HIM), as well as field emission-scanning electron microscopy (FE-SEM) were conducted to study the pore connectivity and distribution characteristics of closed pores. The results show that closed pores (inaccessible to nitrogen molecules and mercury) are mainly distributed in pore diameters ＜10?nm and associated with organic pores and interlayer spaces of illite-smectite mixed-layer mineral. The pore volume values obtained from MICP and N2 adsorption underestimate the large pores (pore diameters ＞100?nm) in shales. Based on deuterated water CM-SANS tests, 87–98% of the pores (2–200?nm diameters) are water-connected in transitional samples. The low accessibility to water is at pore-sizes of 5–10?nm and 20–30?nm. Results from in-situ gas contents show that closed pores have a certain gas bearing capacity, but micropores (pore diameters ＜2?nm) control the gas occurrence in transitional samples. The connectivity of the organic pore network and between organic pores and surrounding interparticle pores is directly supported by FE-SEM and HIM imaging. Overall, improving pore-fracture connectivity through effective fracturing techniques is a means of mitigating the rapid decline in shale gas production.Sun, P., Young, B., Elgowainy, A., Lu, Z., Wang, M., Morelli, B., Hawkins, T., 2019. Criteria air pollutants and greenhouse gas emissions from hydrogen production in U.S. steam methane reforming facilities. Environmental Science & Technology 53, 7103-7113. global and U.S. domestic effort to develop a clean energy economy and curb environmental pollution incentivizes the use of hydrogen as a transportation fuel, owing to its zero tailpipe pollutant emissions and high fuel efficiency in fuel cell electric vehicles (FCEVs). However, the hydrogen production process is not emissions free. Conventional hydrogen production via steam methane reforming (SMR) is energy intensive, coproduces carbon dioxide, and emits air pollutants. Thus, it is necessary to quantify the environmental impacts of SMR hydrogen production alongside the use-phase of FCEVs. This study fills the information gap, analyzing the greenhouse gas (GHG) and criteria air pollutant (CAP) emissions associated with hydrogen production in U.S. SMR facilities by compiling and matching the facility-reported GHG and CAP emissions data with facilities’ hydrogen production data. The actual amounts of hydrogen produced at U.S. SMR facilities are often confidential. Thus, we have developed four approaches to estimate the hydrogen production amounts. The resultant GHG and CAP emissions per MJ of hydrogen produced in individual facilities were aggregated to develop emission values for both a national median and a California state median. This study also investigates the breakdown of facility emissions into combustion emissions and noncombustion emissions.Sun, X., Zhao, H., Zhang, Y., Liu, Y., Chen, G., Wang, W., 2019. An experimental study on the oil-soluble surfactant-assisted cyclic mixed solvent injection process for heavy oil recovery after primary production. Fuel 254, Article 115656. solvent injection (CSI) has shown a significant potential to enhance heavy oil recovery after primary production. However, the principal limitation of this process is quick solvent liberation due to the high gas mobility and oil viscosity regainment during the production period. In this study, a novel variation of CSI, called oil-soluble surfactant-assisted cyclic mixed solvent injection (OSFA-CMSI), is proposed to overcome these limitations. During this process, an oil-soluble surfactant and a specially designed solvent mixture (produced gas and propone) are cyclically injected into reservoirs in two separate slugs. The designed solvent mixture renders the process technically sound and effectively viable, and the surfactant induces the formation of an effective foamy oil flow by dispersing the released or undissolved gaseous solvent during the production period. A series of experiments were performed by using a patented core holder to prove the viability of the OSFA-CMSI process and to study the effects of the solvent composition, pressure depletion rate, wormhole presence, and confining pressure on the OSFA-CMSI performance. The experimental results show that the selected oil-soluble surfactant FlourN? 20158M can create an effective foamy oil phenomenon in heavy oil, which contributes to the enhanced oil swelling effect and gas dispersion that delays the formation of free gas. The OSFA-CMSI process is a potentially feasible method for heavy oil recovery after primary production, especially for post-cold heavy oil production with sand reservoirs. The most efficient test improves oil recovery by 41.64% of the original oil in place (OOIP) compared to that of the traditional CSI process. There is an optimal C3H8 content in the solvent mixture (46?mol% in this study), beyond which the performance of the OSFA-CMSI process worsens. The solvent mixture should be injected at or near its dew point without any liquefaction to achieve maximum solubility and generate an effective foamy oil flow. Increases in the pressure depletion rate and confining pressure are beneficial when using OSFA-CMSI to enhance the oil recovery factor over a short production time but result in lower final oil recovery factors.Suri, N., Gassara, F., Stanislav, P., Voordouw, G., 2019. Microbially enhanced oil recovery by alkylbenzene-oxidizing nitrate-reducing bacteria. Frontiers in Microbiology 10, 1243. doi: 10.3389/fmicb.2019.01243. enhanced oil recovery (MEOR) of heavy oil and bitumen is challenging because light hydrocarbons, which can feed resident microbial communities are present in low concentrations, if at all. We have recently shown that increasing the toluene concentration of heavy oil by aqueous injection followed by injection of nitrate boosts the activity of toluene-oxidizing nitrate-reducing bacteria in heavy oil-containing sand pack columns, giving production of residual oil in place (ROIP). In the current work we found that ethylbenzene is as effective as toluene. Microbial community analyses indicated Thauera and Pseudomonas to be main components of nitrate-containing batch and continuous cultures, regardless whether ethylbenzene or toluene was used as the electron donor. Biomass from batch cultures grown with heavy oil amended with ethylbenzene or toluene and nitrate or biomass from continuous cultures grown on ethylbenzene or toluene and nitrate had similar MEOR activity. Increasing the concentration of injected biomass from continuous cultures increased the fraction of ROIP recovered both in the absence and in the presence of nitrate. Nitrate increased the fraction of ROIP recovered by about 2-fold by increasing the concentration of biomass in the columns. Emulsification of oil by surface-adhering biomass and blocking of aqueous flow channels by oil emulsion droplets are proposed as a possible mechanism of hydrocarbon- and nitrate-mediated MEOR. Pure isolates Thauera sp. NS1 and Pseudomonas sp. NS2, which used both ethylbenzene and toluene, were obtained but did not offer improved MEOR compared to the use of batch and continuous cultures.Swart, P.K., Bl?ttler, C.L., Nakakuni, M., Mackenzie, G.J., Betzler, C., Eberli, G.P., Reolid, J., Alonso-García, M., Slagle, A.L., Wright, J.D., Kroon, D., Reijmer, J.J.G., Hui Mee, A.L., Young, J.R., Alvarez-Zarikian, C.A., Bialik, O.M., Guo, J.A., Haffen, S., Horozal, S., Inoue, M., Jovane, L., Lanci, L., Laya, J.C., Lüdmann, T., Nagender Nath, B., Niino, K., Petruny, L.M., Pratiwi, S.D., Su, X., Sloss, C.R., Yao, Z., 2019. Cyclic anoxia and organic rich carbonate sediments within a drowned carbonate platform linked to Antarctic ice volume changes: Late Oligocene-early Miocene Maldives. Earth and Planetary Science Letters 521, 1-13. paper reports on the newly discovered occurrence of thick sequences (～100 m) of Late Oligocene and Early Miocene (～24.9 to ～20 Ma) interbedded organic-rich sediments (sapropels) and pelagic (organic poor) carbonates at Sites U1466 and U1468 drilled in the Maldives archipelago during the International Ocean Discovery Program (IODP) Expedition 359. This occurrence is unusual in that this sequence is located > 1000 m above the surrounding ocean floor within an inter-atoll basin and not linked to any known global oceanic events. Total organic content reaches as high as 35% in the darker layers, while the interbedded carbonates have concentrations of less than 0.1%. Trace elements characteristic of anoxic waters, such as Mo, V, Cr, U, and Pb, correlate positively with concentrations of organic carbon. Nitrogen isotopic data show no evidence that the intervals of high total organic carbon are related to enhanced productivity driven by upwelling. Instead, high organic carbon is associated with intervals of anoxia. We propose that sea-level fluctuations linked to changes in Antarctic ice volume restricted exchange with the open ocean causing bottom waters of the inter-atoll basin to become anoxic periodically. The architecture of the platform at the end of the Oligocene, combined with the global sea-level highstand, set the stage for orbitally-driven sea-level changes producing cyclic deposition of sapropels. The proposed mechanism may serve as an analogue for other occurrences of organic carbon-rich sediments within carbonate platform settings.Swinley, J., de Coning, P., 2019. A Practical Guide to Gas Analysis by Gas Chromatography. Elsevier. pp. Practical Gas Analysis by Gas Chromatography provides a detailed overview of the most important aspects of gas analysis by gas chromatography (GC) for both the novice and expert. Authors John Swinley and Piet de Coning provide the necessary information on the selection of columns and components, thus allowing the reader to assemble custom gas analysis systems for specific needs. The book brings together a wide range of disparate literature on this technique that will fill a crucial gap for those who perform different types of research, including lab operators, separation scientists, graduate students and academic researchers. This highly practical, up-to-date reference can be consulted in the lab to guide key decisions about proper setup, hardware and software selection, calibration, analysis, and more, allowing researchers to avoid the common pitfalls caused by incorrect infrastructure.Key FeaturesShows, in detail, how valve configurations work, allowing readers to understand the building blocks of extremely complex systemsPresents the complete infrastructure for setting up a gas analysis laboratory in a single sourceIncludes a full chapter on practical analytical systems for analyzing various gas mixturesReadershipResearchers performing gas analysis who are new to gas chromatography, including graduate tutors and students, lab operators, and separation scientists. All persons who need to understand the interpretation of gas results e.g. chemical engineers; in-house metrology staff at suppliers and users of specialized gases; those involved in teaching and training of staff for gas analysis; any person interested in starting a gas analysis laboratory; chromatographers in environmental, petrochemical, electronic and other industriesTable of ContentsOverview and theory2. Gas analysis laboratory3. The gas chromatograph4. Standards, calibration and samples5. Valves6. Sampling and sample introduction7. GC columns for gas analysis8. GC detectors9. Data system and data handling10. Multidimensional gas analysis11. Practical Guidelines for selected gas analysis applications12. TroubleshootingTabor, C.R., Feng, R., Otto-Bliesner, B.L., 2019. Climate responses to the splitting of a supercontinent: Implications for the breakup of Pangea. Geophysical Research Letters 46, 6059-6068.; Reconstructing deep time climate often relies on a limited number of data points, which can hinder inference of the large‐scale climate state. Here we use an Earth system model with idealized boundary conditions to simulate climate responses to paleogeographic changes associated with the breakup of a supercontinent. After the supercontinent splits, weaker tropical easterlies occur in the larger ocean basin, which dampens the Walker circulation and warms the equatorial ocean through reduced upwelling. Additionally, cloud formation increases across the midlatitude ocean, causing locally cooler sea surface temperatures. Over land, there is dramatic tropical cooling post breakup due to enhanced moisture and cloud formation. Consequently, the latitudinal temperature gradient responses over land and ocean oppose each other, which makes inferring large scale climate changes from spatially spare proxy records particularly challenging in this scenario. Our findings emphasize the tight coupling between geography and planetary scale climate dynamics in the tropics and subtropics.Plain Language Summary: The gradual opening of the Atlantic Ocean by seafloor spreading led to one of the most dramatic changes in land/sea distribution of the past few hundred million years. We show that this opening of an ocean basin causes tropical humidification and large‐scale reorganization of tropical circulation as well as global and regional temperature change, especially on land. These responses have implications for interpretation of past temperature reconstructions.Takir, D., Stockstill-Cahill, K.R., Hibbitts, C.A., Nakauchi, Y., 2019. 3-μm reflectance spectroscopy of carbonaceous chondrites under asteroid-like conditions. Icarus 333, 243-251. measured 3-μm reflectance spectra of 21 meteorites that represent all carbonaceous chondrite types available in terrestrial meteorite collections. The measurements were conducted at the Laboratory for Spectroscopy under Planetary Environmental Conditions (LabSPEC) at the Johns Hopkins University Applied Physics Laboratory (JHU APL) under vacuum and thermally-desiccated conditions (asteroid-like conditions). This is the most comprehensive 3-μm dataset of carbonaceous chondrites ever acquired in environments similar to the ones experienced by asteroids. The 3-μm reflectance spectra are extremely important for direct comparisons with and appropriate interpretations of reflectance data from ground-based telescopic and spacecraft observations of asteroids. We found good agreement between 3-μm spectral characteristics of carbonaceous chondrites and carbonaceous chondrite classifications. The 3-μm band is diverse, indicative of varying composition, thus suggesting that these carbonaceous chondrites experienced distinct parent body aqueous alteration and metamorphism environments. The spectra of CI chondrites, from which significant amount of water adsorbed under ambient conditions was removed, are consistent with Mg-serpentine and clay minerals. The high abundances of organics in CI chondrites is also associated with the mineralogy of these chondrites, oxyhydroxides- and complex clay minerals-rich. CM chondrites, which are cronstedtite-rich, have shallower 3-μm band than CI chondrites, suggesting they experienced less aqueous alteration. CR chondrites showed moderate aqueous alteration relative to CI and CM chondrites. CV chondrites, except for Efremovka, have a very shallow 3-μm band, consistent with their lower phyllosilicate proportions. CO chondrites, like most CVs, have a very shallow 3-μm band that suggest they experienced minor aqueous alteration. The 3-μm band in CH/CBb is deep and broad centered ~3.11?μm, possibly due to the high abundance of FeNi metal and presence of heavily hydrated clasts in these chondrites. The 3-μm spectra of Essebi (C2-ung) and EET 83226 are more consistent with CM chondrites' spectra. The 3-μm spectra of Tagish lake (C2-ung), on the other hand, are consistent with CI chondrites. None of these spectral details could have been resolved without removing the adsorbed water before acquiring spectra.Tan, S.P., Barsotti, E., Piri, M., 2019. Application of material balance for the phase transition of fluid mixtures confined in nanopores. Fluid Phase Equilibria 496, 31-41. has been customary to describe the phase equilibria of confined fluids using an equation of state (EOS) coupled with the Young-Laplace equation to account for the effect of surface curvature due to confinement. The equilibrium phases in this approach are the vapor (V) in the bulk phase and the confined liquid-like phase (?) in the pores, which are separated by a surface that introduces a pressure difference between the phases. Consequently, we refer to this approach as the V? method. The condition of phase transitions for confined fluids has been assumed to be the same as that for bulk fluids, so that calculations for dew-point and bubble-point curves do not need a material balance because the mole fraction of the condensed phase is zero for the former and unity for the latter. However, the situation of confined fluids is different from that in the bulk because the equilibrium phases reside in separate regions that have different pressures. In the V? method, the vapor phase resides in the bulk and drives the chemical potential of the whole system, while the liquid-like phase condenses inside the pores subject to strong interaction with the pore wall. As discussed in the paper, this situation needs a material balance to comprehensively describe the phase transitions. Supporting evidence is also presented from a static experiment using a gravimetric apparatus. New insights derived from generalization of the V? method in this work enable further investigations that could disclose more unknowns in the phase behavior of confined mixtures.Tang, L., Song, Y., Jiang, Z., Jiang, S., Li, Q., 2019. Pore structure and fractal characteristics of distinct thermally mature shales. Energy & Fuels 33, 5116-5128. investigate the shale pore structure and fractal characteristics during thermal evolution, 30 shale samples from two wells with contrasting maturities (the Ro values of Yanchang samples are 0.71–1.06% and the Ro values of Longmaxi samples are 2.79–3.41%) were subjected to field emission-scanning electron microscopy observation, low-pressure N2 adsorption experiment, and other analytical measurements. The Frenkel–Halsey–Hill model was used to obtain the double-fractal dimensions (D1 and D2) of shale pores for different suits of samples. Analysis shows that the shale pores undergo a complicated evolution process with the increase of thermal maturity. Hence, the evolution trends of pore structure parameters with distinct thermal maturity are not in the same trend. The pore volume and porosity have a trend of increasing first and then decreasing with increase of Ro, which is mainly related to hydrocarbon generation of organic matter (OM). With the increase of Ro, the average pore size and specific surface area show overall monotonic evolution trends. Because of the higher thermal maturity, the fractal dimensions of the Longmaxi samples are generally larger than those of the Yanchang samples, which correlates with the changes of pore structure features. Further analyses suggest that thermal maturity together with OM and mineral compositions jointly contribute to the direct evolution of the pore structure and fractal characteristics of shales. Comprehensive evolution models with thermal maturity also indicate that the pore structure characteristics are the combined results of sedimentary, tectonism, diagenesis, and hydrocarbon generation.Tangirala, S., Sheng, J.J., 2019. Investigation of oil production and flowback in hydraulically-fractured water-wet formations using the Lab-on-a-Chip method. Fuel 254, Article 115543. is generally believed that a higher efficiency of flowback of the invaded fluid will result in a reduced formation damage and a higher oil rate. However, in water-wet formations having flow characteristics close to those seen in low permeability formations, high flowback does not always result in high oil production rates. In such reservoirs, the strength of capillary gradient across the matrix-fracture interface controls the amount of invaded-fluid flowback. This paper discusses two factors which impact the strength of capillary gradient: depth of fracture fluid invasion and presence of moderate interfacial tension (IFT) surfactant in the fracture fluid. Microfluidic-chip or otherwise called Lab-on-a-Chip based experiments are conducted in this work to highlight the discussed factors.For a water wetting chip, it is observed that as the depth of fracture fluid invasion into the matrix increases, flowback efficiency is improved while the late-time oil production rate decreases. Additionally, it is found that the presence of a moderate IFT-reducing surfactant in the fracture fluid aids in reducing the invasion-induced formation damage compared to a fracture fluid without surfactant. The work presented strongly impacts the oil industry in contemporary times when hydraulic fracturing is significantly prevalent. The results obtained provide a better understanding of the flow behavior of in-situ and invaded fracture fluids during production phase of the operation.Thilakanayaka, V., Chuanxiu, L., Xiang, R., Devendra, D., Dasanayaka, S.A.H.K., Jiang, W., Rahman, A., Kumar, S., Ariful, G.M., 2019. Sediment provenance of the Nansha Trough since 40 ka B.P. in the South China Sea: Evidence from δ13Corg, TOC and pollen composition. Frontiers in Earth Science 7. proxies in organic matter (OM) are considered to be reliable proxies for deciphering types of paleo-vegetation (C3 plants and C4 plants) and their abundance. The contributions of total organic carbon (TOC), stable carbon isotopes (δ13Corg), total nitrogen (TN) and organic carbon to total nitrogen ratios (C/N) were obtained from a gravity core NS07-25 (6°39.945′ N, 113°32.936′ E, water depth 2006 m), extracted from the southern South China Sea (SCS). These data were used to reconstruct the climate changes of the Nansha Trough since 40 ka B.P. by comparing them with pollen data from the same core, and this comparison provides better sediment provenance details in the study area. During the periods between 37 and 27 ka, and from 12.5 ka to modern day, the majority of terrestrial sediment received from Borneo, and some climatic events have been governed by aeolian fluxes from mid-latitude areas (mainland China). These periods were relatively humid, compared to 27–12.5 ka, where the majority of terrestrial sediment came from the Sunda Shelf through riverine pathways. This study serves as the first study to correlate deep oceanic pollen and geochemical proxies in order to identify the weaken terrestrial OM signals in the deep ocean.Thomas, F., Corre, E., Cébron, A., 2019. Stable isotope probing and metagenomics highlight the effect of plants on uncultured phenanthrene-degrading bacterial consortium in polluted soil. The ISME Journal 13, 1814-1830. aromatic hydrocarbons (PAHs) are ubiquitous soil pollutants. The discovery that plants can stimulate microbial degradation of PAHs has promoted research on rhizoremediation strategies. We combined DNA-SIP with metagenomics to assess the influence of plants on the identity and metabolic functions of active PAH-degrading bacteria in contaminated soil, using phenanthrene (PHE) as a model hydrocarbon. 13C-PHE dissipation was 2.5-fold lower in ryegrass-planted conditions than in bare soil. Metabarcoding of 16S rDNA revealed significantly enriched OTUs in 13C-SIP incubations compared to 12C-controls, namely 130 OTUs from bare soil and 73 OTUs from planted soil. Active PHE-degraders were taxonomically diverse (Proteobacteria, Actinobacteria and Firmicutes), with Sphingomonas and Sphingobium dominating in bare and planted soil, respectively. Plant root exudates favored the development of PHE-degraders having specific functional traits at the genome level. Indeed, metagenomes of 13C-enriched DNA fractions contained more genes involved in aromatic compound metabolism in bare soil, whereas carbohydrate catabolism genes were more abundant in planted soil. Functional gene annotation allowed reconstruction of complete pathways with several routes for PHE catabolism. Sphingomonadales were the major taxa performing the first steps of PHE degradation in both conditions, suggesting their critical role to initiate in situ PAH remediation. Active PHE-degraders act in a consortium, whereby complete PHE mineralization is achieved through the combined activity of taxonomically diverse co-occurring bacteria performing successive metabolic steps. Our study reveals hitherto underestimated functional interactions for full microbial detoxification in contaminated soils.Thombre, R.S., Sivaraman, E.S., Bhalamurugan, Vaishampayan, P.A., Seuylemezian, A., Meka, J.K., Vijayan, S., Kulkarni, P.P., Pataskar, T., Patil, B.S., 2019. Survival of extremotolerant bacteria from the Mukundpura meteorite impact crater. Astrobiology 19, 785–796. meteorites provide clues with regard to prebiotic chemistry and the origin of life. Geological Survey of India recorded a carbonaceous chondrite meteorite fall in Mukundpura, India, on June 6, 2017. We conducted a study to investigate the microbial community that survived the meteorite impact. 16S rRNA metagenomic sequencing indicates the presence of Actinobacteria, Proteobacteria, and Acidobacteria in meteorite impact soil. Comparative phylogenetic analysis revealed an intriguing abundance of class Bacilli in the impact soil. Bacillus thermocopriae IR-1, a moderately thermotolerant organism, was isolated from a rock, impacted by the Mukundpura meteorite. We investigated the resilience of B. thermocopriae IR-1 to environmental stresses and impact shock in a Reddy shock tube. Bacillus thermocopriae IR-1 survived (28.82% survival) the effect of shock waves at a peak shock pressure of 300?kPa, temperature 400?K, and Mach number of 1.47. This investigation presents the first report on the effect of impact shock on B. thermocopriae IR-1. The study is also the first report on studying the microbial diversity and isolation of bacteria from impact crater soil immediately after meteorite impact event. Thompson, L.R., Haroon, M.F., Shibl, A.A., Cahill, M.J., Ngugi, D.K., Williams, G.J., Morton, J.T., Knight, R., Goodwin, K.D., Stingl, U., 2019. Red Sea SAR11 and Prochlorococcus single-cell genomes reflect globally distributed pangenomes. Applied and Environmental Microbiology 85, Article e00369-19.: Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations under conducive growth conditions. However, studies supporting this “microbial seed bank” hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, and II) and 5 Prochlorococcus (ecotype HLII) samples from the Red Sea and combined them with globally sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically cryptic Prochlorococcus ecotypes LLII and LLIII. Compared with reference genomes, 1% of Prochlorococcus and 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they are functional. Searching Tara Oceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence/absence of OGs.Importance: Studies have shown that as we sequence seawater from a selected environment deeper and deeper, we approach finding every bacterial taxon known for the ocean as a whole. However, such studies have focused on taxonomic marker genes rather than on whole genomes, raising the possibility that the lack of endemism results from the method of investigation. We took a geographically isolated water body, the Red Sea, and sequenced single cells from it. We compared those single-cell genomes to available genomes from around the ocean and to ocean-spanning metagenomes. We showed that gene ortholog groups found in Red Sea genomes but not in other genomes are nevertheless common across global ocean metagenomes. These results suggest that Baas Becking’s hypothesis “everything is everywhere, but the environment selects” also applies to gene ortholog groups. This widely dispersed functional diversity may give oceanic microbial communities the functional capacity to respond rapidly to changing conditions.Tonai, S., Kubo, Y., Tsang, M.-Y., Bowden, S., Ide, K., Hirose, T., Kamiya, N., Yamamoto, Y., Yang, K., Yamada, Y., Morono, Y., Heuer, V.B., Inagaki, F., Expedition 370 Scientists, 2019. A new method for quality control of geological cores by X-ray computed tomography: application in IODP Expedition 370. Frontiers in Earth Science 7, 117. doi: 10.3389/feart.2019.00117. computed tomography (XCT) can be used to identify lithologies and deformation structures within geological core, with the potential for the identification processes to be applied automatically. However, because of drilling disturbance and other artefacts, the use of large XCT-datasets in automated processes requires methods of quality control that can be applied systematically. We propose a new systematic method for quality control of XCT data that applies numerical measures to CT slices, and from this obtains data reflective of core quality. Because the measures are numerical they can be applied quickly and consistently between different sections and cores. This quality control processing protocol produces downhole radiodensity profiles from mean CT-values that can be used for geological interpretation. The application of this quality control protocols was applied to XCT data from International Ocean Discovery Program (IODP) Expedition 370 Site C0023 located at the toe of the Nankai accretionary complex. The evaluation of core quality based on this protocol was found to be a good fit to standard-evaluations based on the visual description of core, and could be used to select samples free from drilling disturbance or contamination. The quality-controlled downhole mean CT-value profile has features that can be used to identify lithologies within a formation, the presence and type of deformation structures and to distinguish formations.Torres, M.A., Dong, S., Nealson, K.H., West, A.J., 2019. The kinetics of siderophore-mediated olivine dissolution. Geobiology 17, 401-416. minerals represent an important reservoir of nutrients at Earth's surface and a source of alkalinity that modulates long‐term geochemical cycles. Due to the slow kinetics of primary silicate mineral dissolution and the potential for nutrient immobilization by secondary mineral precipitation, the bioavailability of many silicate‐bound nutrients may be limited by the ability of micro‐organisms to actively scavenge these nutrients via redox alteration and/or organic ligand production. In this study, we use targeted laboratory experiments with olivine and the siderophore deferoxamine B to explore how microbial ligands affect nutrient (Fe) release and the overall rate of mineral dissolution. Our results show that olivine dissolution rates are accelerated in the presence of micromolar concentrations of deferoxamine B. Based on the non‐linear decrease in rates with time and formation of a Fe3+‐ligand complex, we attribute this acceleration in dissolution rates to the removal of an oxidized surface coating that forms during the dissolution of olivine at circum‐neutral pH in the presence of O2 and the absence of organic ligands. While increases in dissolution rates are observed with micromolar concentrations of siderophores, it remains unclear whether such conditions could be realized in natural environments due to the strong physiological control on microbial siderophore production. So, to contextualize our experimental results, we also developed a feedback model, which considers how microbial physiology and ligand‐promoted mineral dissolution kinetics interact to control the extent of biotic enhancement of dissolution rates expected for different environments. The model predicts that physiological feedbacks severely limit the extent to which dissolution rates may be enhanced by microbial activity, though the rate of physical transport modulates this limitation.Tromer, E.C., van Hooff, J.J.E., Kops, G.J.P.L., Snel, B., 2019. Mosaic origin of the eukaryotic kinetochore. Proceedings of the National Academy of Sciences 116, 12873-12882.: Eukaryotes, which include diverse species like animals, fungi, and plants, have cells that are fundamentally more complex than prokaryotic cells, such as bacteria. However, eukaryotes did evolve from prokaryotes, so they must have acquired this cellular complexity after they diverged from prokaryotes. A key cellular feature unique to eukaryotes is the kinetochore, a large, multiprotein structure that plays an essential role in cell division. Here we shed light on the origination of the kinetochore by studying the evolution of its proteins. We find that the kinetochore has diverse evolutionary roots and that it expanded via gene duplications. We present a mode by which eukaryotic systems originated and illuminate the prokaryote-to-eukaryote transition.Abstract: The emergence of eukaryotes from ancient prokaryotic lineages embodied a remarkable increase in cellular complexity. While prokaryotes operate simple systems to connect DNA to the segregation machinery during cell division, eukaryotes use a highly complex protein assembly known as the kinetochore. Although conceptually similar, prokaryotic segregation systems and the eukaryotic kinetochore are not homologous. Here we investigate the origins of the kinetochore before the last eukaryotic common ancestor (LECA) using phylogenetic trees, sensitive profile-versus-profile homology detection, and structural comparisons of its protein components. We show that LECA’s kinetochore proteins share deep evolutionary histories with proteins involved in a few prokaryotic systems and a multitude of eukaryotic processes, including ubiquitination, transcription, and flagellar and vesicular transport systems. We find that gene duplications played a major role in shaping the kinetochore; more than half of LECA’s kinetochore proteins have other kinetochore proteins as closest homologs. Some of these have no detectable homology to any other eukaryotic protein, suggesting that they arose as kinetochore-specific folds before LECA. We propose that the primordial kinetochore evolved from proteins involved in various (pre)eukaryotic systems as well as evolutionarily novel folds, after which a subset duplicated to give rise to the complex kinetochore of LECA.Trumbo, S.K., Brown, M.E., Hand, K.P., 2019. Sodium chloride on the surface of Europa. Science Advances 5, Article eaaw7123. potential habitability of Europa’s subsurface ocean depends on its chemical composition, which may be reflected in that of Europa’s geologically young surface. Investigations using Galileo Near-Infrared Mapping Spectrometer data led to the prevailing view that Europa’s endogenous units are rich in sulfate salts. However, recent ground-based infrared observations have suggested that, while regions experiencing sulfur radiolysis may contain sulfate salts, Europa’s more pristine endogenous material may reflect a chloride-dominated composition. Chlorides have no identifying spectral features at infrared wavelengths, but develop distinct visible-wavelength absorptions under irradiation, like that experienced on the surface of Europa. Using spectra obtained with the Hubble Space Telescope, we present the detection of a 450-nm absorption indicative of irradiated sodium chloride on the surface. The feature correlates with geologically disrupted chaos terrain, suggesting an interior source. The presence of endogenous sodium chloride on the surface of Europa has important implications for our understanding of its subsurface chemistry.Tu, J., Zhou, Z., Li, T., Zhu, Z.-J., 2019. The emerging role of ion mobility-mass spectrometry in lipidomics to facilitate lipid separation and identification. TrAC Trends in Analytical Chemistry 116, 332-339. represent an important class of biomolecules, and play numerous roles in physiological and pathological processes and activates. The enormous chemical and compositional diversity of lipids presents a significant challenge for lipidomics. The emerging technology of ion mobility-mass spectrometry (IM-MS) has provided an orthogonal separation to effectively improve resolving power and selectivity in lipid analysis. Meanwhile, IM-MS has also provided a valuable physiochemical property, namely, collision cross section (CCS), to facilitate lipid identification. In this review, we introduced the use of IM-MS technology to separate different lipid species and isomers. Then, we highlighted the applications of IM-MS for lipid structural identification in lipidomics. Finally, we discussed the potentials of IM-MS for the measurement and annotation of novel lipid species in biological samples.Tudisco, E., Etxegarai, M., Hall, S.A., Charalampidou, E.M., Couples, G.D., Lewis, H., Tengattini, A., Kardjilov, N., 2019. Fast 4-D imaging of fluid flow in rock by high-speed neutron tomography. Journal of Geophysical Research: Solid Earth 124, 3557-3569. High-speed neutron tomographies (1-min acquisition) have been acquired during water invasion into air-filled samples of both intact and deformed (ex situ) Vosges sandstone. Three-dimensional volume images have been processed to detect and track the evolution of the waterfront and to calculate full-field measurement of its speed of advance. The flow process correlates well with known rock properties and is especially sensitive to the distribution of the altered properties associated with observed localized deformation, which is independently characterized by Digital Volume Correlation of X-ray tomographies acquired before and after the mechanical test. The successful results presented herein open the possibility of in situ analysis of the local evolution of hydraulic properties of rocks due to mechanical deformation.Turchyn, A.V., DePaolo, D.J., 2019. Seawater chemistry through Phanerozoic time. Annual Review of Earth and Planetary Sciences 47, 197-224. major ion balance of the ocean, particularly the concentrations of magnesium (Mg), calcium (Ca), and sulfate (SO4), has evolved over the Phanerozoic (last 550 million years) in concert with changes in sea level and the partial pressure of carbon dioxide (pCO2). We review these changes, along with changes in Mg/Ca and strontium/calcium (Sr/Ca) of the ocean; how the changes were reconstructed; and the implication of the suggested changes for the overall charge balance of the ocean. We conclude that marine Mg, Ca, and SO4 concentrations are responding to different aspects of coupled tectonic changes over the Phanerozoic and the resulting effect on sea level. We suggest a broad conceptual model for the Phanerozoic changes in Mg, Ca, and SO4 concentrations along with the seawater 87Sr/86Sr and sulfur isotope composition. Turner-Walker, G., 2019. Light at the end of the tunnels? The origins of microbial bioerosion in mineralised collagen. Palaeogeography, Palaeoclimatology, Palaeoecology 529, 24-38. bioerosion, in all its manifestations, is one of the major factors determining the long-term survival of archaeologically and environmentally important artefacts and ecofacts made from mineralised collagen – bones, antler, teeth and ivory. The bone diagenesis literature contains extensive descriptions of different morphologies and classifications of microbial bioerosion – microscopical focal destruction, Wedl tunnels, linear longitudinal, budded and lamellate tunnelling, etc. but the causative agents remain to be discovered. Palaeontologists are in a similar situation when describing ichnofossils where bioerosion is classified by its characteristic morphology and only tentatively assigned to specific causes. In archaeological bones, Wedl tunnels have traditionally been ascribed to fungi but a re-examination of Wedl's original paper and subsequent literature has shown that all the early specimens examined came from aquatic environments and that euendolithic microflora (cyanobacteria or chlorophytes) might have been responsible. These microorganisms are known to tunnel into marine shells. Linear longitudinal, budded and lamellate tunnelling have all been ascribed to bacteria. However, analyses using a combination of backscatter SEM (BSEM) and mercury intrusion porosimetry (HgIP) of bones excavated from terrestrial soils suggest that the various tunnelling morphologies described by earlier researchers are actually all manifestations of a single architecture, the differences arising from the inherent variability of bone microstructure and the hydrology of the burial environment. An examination of the BSEM and HgIP data also indicates that the bacteria responsible may spread through dead bone tissues by expanding the canalicular network (or dentinal tubules in teeth) rather than creating new tunnels.Long-term field burial experiments using de-fleshed cow bone specimens have now demonstrated that bacterial tunnelling develops over decades rather than months as was previously thought, even in warm tropical soils. This has obvious implications for the origin of the bacteria responsible (soil bacteria versus endogenous gut bacteria) since the bone specimens were quickly isolated from gut contents. Although no attempt is made here to identify a specific organism or organisms responsible for tunnelling in terrestrial archaeological bones a tentative model is proposed for how cycles of wetting and drying, or changes in local dissolved oxygen levels, could lead a common gram positive soil bacterium to produce the pattern of bacterial bioerosion seen in exhumed bones. This soil organism may act in a similar way to Staphylococcus aureus which proliferates in living bone (causing osteomyelitis) by infiltrating and enlarging the canalicular network.Tusch, J., Sprung, P., van de L?cht, J., Hoffmann, J.E., Boyd, A.J., Rosing, M.T., Münker, C., 2019. Uniform 182W isotope compositions in Eoarchean rocks from the Isua region, SW Greenland: The role of early silicate differentiation and missing late veneer. Geochimica et Cosmochimica Acta 257, 284-310. rocks from the Isua region in southern West Greenland are known to exhibit isotope anomalies of 182W and 142Nd. The excess 182W in many rocks from the Isua region have been explained by two endmember models: (1) missing late veneer or (2) silicate differentiation shortly after Earth’s formation. Furthermore, it has been proposed that pristine W isotope systematics in rocks from the Isua region (herein the Isua supracrustal belt and adjacent area) have been obscured by metamorphic disturbance. To address these issues, we present a comprehensive dataset, combining high precision 182W isotope data with trace element data, including high precision elemental W-Th-U-Ta abundance data. We present an improved analytical protocol that allows processing gram-sized samples with W abundances in the lower ng/g range. This protocol also results in markedly improved ion exchange column yields and cleaner W fractions, thereby minimizing nuclear volume effects on 183W. To compare with previous studies, our dataset includes some samples from previously investigated units in the Isua region (Isua Supracrustal Belt (ISB) mafic–ultramafic assemblages and Ameralik dikes). In addition, several Eoarchean key units in the Isukasia terrane (Isua region) and the F?ringehavn terrane (Nuuk region) have been examined for their W isotope composition in this study for the first time. These newly investigated units include recently recognized mantle-like peridotites from both terranes that display PGE abundances and patterns similar to modern depleted mantle peridotites, felsic lithologies from the ISB, as well as key amphibolite and TTG localities from low-strain domains south of the ISB. Virtually all rocks from the Isua region show significant W enrichment with W/Th of up to 160 in mafic to ultramafic samples. None of the samples from SW Greenland that were object of 182W isotope analysis in this study and virtually all previous studies appear to have preserved near canonical W/Th ratios (i.e., between 0.09 and 0.24). Independent of W enrichment, however, it can now be shown that there is a uniform 182W isotope excess in the different rock types from the Itsaq Gneiss Complex (IGC) (average 12.8?ppm?±?1?ppm, 95% confidence interval). Importantly, none of the rock suites investigated exhibit modern mantle-like 182W isotope signatures of ?182W?=?0. By combining 182W signatures in the different lithologies with elemental W systematics, we therefore can infer that the 182W excess in Eoarchean rocks from the Isua region is widespread, and independent of W enrichment. Hence, we regard the 182W excess as an intrinsic feature of the Eoarchean assemblages in the Isua region. Notably, mantle-like peridotites from both the Isukasia and F?ringehavn terranes display the same 182W excess, as all other units, although they have been shown to display the full inventory of Highly Siderophile Elements (HSE) found in Phanerozoic mantle peridotites. Evidently, the W isotope budget in these rocks is clearly decoupled from HSE systematics, which hampers a straightforward explanation for 182W isotope excesses in terms of the missing late veneer model. As Platinum Group Element (PGE) patterns in mantle-like Eoarchean peridotites from the Isua region are similar to those in Phanerozoic rocks, we rather propose that to a large extent the 182W excesses are a vestige of early silicate differentiation processes, in line with positive 142Nd anomalies found in rocks from the Isua region, suggesting initial silicate differentiation prior to 4.50?Ga.Van Audenhaege, L., Fari?as-Bermejo, A., Schultz, T., Lee Van Dover, C., 2019. An environmental baseline for food webs at deep-sea hydrothermal vents in Manus Basin (Papua New Guinea). Deep Sea Research Part I: Oceanographic Research Papers 148, 88-99. webs and trophic interactions provide a measure of ecosystem function and have been highlighted as an important element for environmental baselines and environmental impact assessments. Stable isotopes have long been used in the deep sea as a means to explore and summarize food webs, especially in chemosynthetic ecosystems, where there may be multiple sources of primary production with distinctive isotopic compositions. Hydrothermal vents in Manus Basin have been targeted for mining and, if mining proceeds, vent food webs will be altered. Here we describe a pre-mining baseline for the food-web state for 3 active vent fields. Manus vents support at least 9 feeding guilds, and both reverse TriCarboxylic Acid (rTCA) and Calvin-Benson-Bassham (CBB) carbon fixation pathways are inferred for symbionts of holobiont taxa. There are site differences in the C-N-S isotopic trait spaces (convex hulls) of Manus Basin vent food webs that likely reflect environmental variability. Isotopic diversity metrics (divergence, dispersion, evenness) are similar in Solwara 1, South Su, and PACMANUS vent food webs, but South Su has a higher degree of isolation in isotopic space (uniqueness). Because convex hull and isotopic diversity metrics are easy to calculate from multidimensional isotopic data, they may be useful food-web indicators for environmental management.van de Velde, S., Jorissen, E.L., Neubauer, T.A., Radan, S., Pavel, A.B., Stoica, M., Van Baak, C.G.C., Martínez Gándara, A., Popa, L., de Stigter, H., Abels, H.A., Krijgsman, W., Wesselingh, F.P., 2019. A conservation palaeobiological approach to assess faunal response of threatened biota under natural and anthropogenic environmental change. Biogeosciences 16, 2423-2442. records are required to test ecological hypotheses necessary for conservation strategies as short-term observations can insufficiently capture natural variability and identify drivers of biotic change. Here, we demonstrate the importance of an integrated conservation palaeobiology approach when making validated decisions for conservation and mitigating action. Our model system is the Razim–Sinoie lake complex (RSL) in the Danube Delta (Black Sea coast, Romania), a dynamic coastal lake system hosting unique Pontocaspian mollusc species that are now severely under threat. The Pontocaspians refer to an endemic species group that evolved in the Black Sea and Caspian Sea basins under reduced salinity settings over the past few million years. The natural, pre-industrial RSL contained a salinity gradient from fresh to mesohaline (18?ppm) until human intervention reduced the inflow of mesohaline Black Sea water into the lake system. We reconstruct the evolution of the RSL over the past 2000 years from integrated sedimentary facies and faunal analyses based on 11 age-dated sediment cores and investigate the response of mollusc species and communities to those past environmental changes. Three species associations (“marine”, “Pontocaspian” and “freshwater”) exist and their spatio-temporal shifts through the system are documented. Variable salinity gradients developed, with marine settings (and faunas) dominating in the southern part of the system and freshwater conditions (and faunas) in the northern and western parts. Pontocaspian species have mostly occurred in the centre of the RSL within the marine–freshwater salinity gradient. Today, freshwater species dominate the entire system, and only a single Pontocaspian species (Monodacna colorata) is found alive. We show that the human-induced reduced marine influence in the system has been a major driver of the decline of the endemic Pontocaspian biota. It urges improved conservation action by re-establishing a salinity gradient in the lake system to preserve these unique species.Van Geem, K., 2019. Chapter 6 - Kinetic modeling of the pyrolysis chemistry of fossil and alternative feedstocks, in: Faravelli, T., Manenti, F., Ranzi, E. (Eds.), Computer Aided Chemical Engineering. Elsevier, pp. 295-362. is one of the most important processes in the chemical industry not only for producing many of today's chemical building blocks via steam cracking. Pyrolysis also plays a key role in biomass conversion processes, chemical recycling of plastic waste, refinery processes, such as visbreaking and even in combustion. Essential to further improving, this process is understanding the reaction kinetics of these complex feeds, representative model compounds, and certain building blocks (e.g., lignin, cellulose, and hemicellulose). For solid feeds numerous TGA studies have provided valuable information on the overall kinetics. The presence of heat and mass transfer limitations implies that it is not obvious to scale the results. Nevertheless, mass loss-based apparent kinetic approaches are still being used to compare pyrolysis of different feedstocks due to its simplicity and ease in calculations. More multiplexed experimental studies on model compounds are needed to improve our current understanding. When aiming to construct an intrinsic chemical kinetic model, able to describe a system under diverse conditions, researchers have been relying on the automatic generation of these models for several reasons. One of the main challenges that still needs to be overcome is how to deal with data scarcity. The calculation power of supercomputers is certainly a strong driver for automatic kinetic model generation, but calculating all the rate coefficients using high level computational chemistry methods is still too time consuming at present. Several model assumptions for constructing the kinetic models can be used for reducing the stiffness of the whole set of reactor model equations or just simplify the complexity of the kinetic model. This has made that detailed kinetic models are widely applied both in industry and in the academic World.van Hardenbroek, M., Heiri, O., Leng, M.J., 2019. Stable isotopes in biological and chemical fossils from lake sediments: Developing and calibrating palaeoenvironmental proxies. Quaternary Science Reviews 218, 157-159. isotope records of H, C, N, O, and Si derived from lake sediments provide valuable information about changing environmental conditions, with diverse applications in Quaternary research. A key issue with the interpretation of stable isotope data is understanding the hydrological, ecological, metabolic, and taphonomic processes that affect stable isotope values measured on individual taxa and specific compounds. In order to provide a better overview of these processes, we brought together specialists in stable isotope biogeochemistry working on lake sediment records during a workshop in Southampton in July 2016. Articles in this special issue provide an overview of the data presented during the workshop as well as the outcome of group discussions. The aim of this special issue is to improve the accuracy, robustness and reliability of interpretations of palaeolimnological stable isotope records, hence there is a focus on modern monitoring, calibration, and experimental studies to understand spatial and temporal variability and taphonomic processes. Studies that provide detailed comparisons with other proxies to constrain the interpretations of stable isotope data are also included.The special issue starts with a review of approaches based on stable isotopes of H, C, N, O, Si, measured on remains of specific organism groups, such as diatoms frustules, calcareous and chitinous invertebrate remains, fish fossils, and plant macrofossils (van Hardenbroek et al., 2018a). Stable isotope analyses of these remains give insights into ecological processes affecting parent organisms (e.g. habitat-specific biogeochemistry, food sources), but also on environmental conditions in and around lakes (e.g. climate, hydrology). An important advantage of these remains compared with the use of bulk sedimentary organic matter or carbonate is that they can provide more specific and detailed information on past ecosystem, food web and environmental changes affecting different compartments of lake ecosystems. The paper reviews factors (including growth, diet, migration, and taphonomy), which affect the stable isotope composition of remains. It gives an overview of calibration, culturing and modelling studies used to quantify the extent to which these factors influence stable isotope composition.A parallel review by Holtvoeth et al. (2019) focuses on compound-specific stable isotopes. It covers alkyl lipids, amino acids, GDGTs, pigment derivatives, hopanoids, steroids and cellulose and the analysis of H, C, O, and in some cases N and S isotope values of these compounds. For each compound class, its sources/synthesis are discussed together with several examples of applications in palaeolimnology. The paper reviews the mechanisms leading to fractionation in these compounds. These mechanisms include differences in sources/substrates and the chemical reactions and environmental conditions during the synthesis and derivatisation of different compounds, as well as taphonomic processes in lakes that cause degradation of these compounds.Next follow a set of papers that provide (contemporary) calibration datasets to improve the interpretation of stable isotopes in the remains of different groups of invertebrates and methodological studies that aim to reduce errors from contamination and sample bias. Roberts et al. (2018) investigate the impact of cleaning methods on the Mg/Ca and δ18O values of ostracod valves. The authors use the carapaces of Cyprideis torosa, treating one valve as control and the other valve with a cleaning treatment. In this way, the impacts of different pretreatment methods on δ18O analyses are assessed, including the effects of soaking in hydrogen peroxide, soaking in sodium hypochlorite, soaking in hydrogen peroxide, soaking in hydrous hydrazine/ammonium citrate, sonication, low-temperature ashing in oxygen plasma, and vacuum roasting. Certain cleaning methods have the potential to cause alteration to the geochemical signal, particularly for measurements of Mg/Ca and δ18O. For trace element determinations the authors recommend cleaning by sonication and for stable isotopes, oxidation by hydrogen peroxide. These methods remove contamination, yet do not significantly alter the geochemical signal.Another methodological paper (Schilder et al., 2018) investigates, for the first time, the variability in δ13C values of individual ephippia, the resting stages of Cladocera. The authors successfully use laser ablation, nano combustion gas chromatography and isotope ratio mass spectrometry (LA/nC/GC/IRMS) to perform multiple isotope analyses on individual ephippia, and show a high degree of reproducibility (standard deviations 0.1–0.5‰). The authors also note that δ13C values of ephippia from a well-oxygenated lake closely reflect δ13C values of algae. In contrast, ephippia from two seasonally anoxic lakes with higher methane concentrations have a much larger range of δ13C values (10.7 and 20.0‰). These larger ranges are attributed to seasonal variation in the incorporation of methane-derived carbon. The authors highlight that this potentially large (seasonal) variability between individual ephippia should be taken into consideration when interpreting stable isotope records of samples consisting of few ephippia.Next, Lacey et al. (2018) investigate the potential to use stable isotopes measured on fragments of bivalve shells (Dreissena) for palaeohydrology studies. The authors analyse stable carbon and oxygen isotope values of a modern, whole Dreissena shell from Lake Dojran, Macedonia, and compare these with the isotope composition of lake water DIC, suggesting the shell carbonate most likely precipitated in isotopic equilibrium with lake water and shell δ13C and δ18O are primarily a function of temperature and water balance. The authors then present δ13C and δ18O data of endogenic carbonates, shell fragments, and two whole shells from a Holocene record of the same lake. The range of stable isotope data on whole shells overlaps that of the broken shell fragments, suggesting the fragments broadly record lake water conditions across the time of deposition. Shell fragment isotope data also broadly reflect the signal of environmental change recorded in other proxy data from the same core and could be used (like endogenic carbonate) to provide information on past changes in lake level, in particular in the absence of other endogenic carbonates.The study by Van Hardenbroek et al. (2018b) analyses δ13C and δ15N values of chitinous resting stages of Cladocera and freshwater Bryozoa (moss animals) in modern flotsam of 33 lakes across Europe. These resting stages are often abundant in lake sediment records, but little is known about what influences their stable isotopic composition. The authors compare the stable isotope values of resting stages with lake water chemistry and with the isotopic composition of surface sediment organic matter (SOM). The δ13C values of cladoceran ephippia were correlated to SOM and negatively correlated to deep water methane concentrations, indicating that methane-derived carbon can enter food webs in stratifying lakes. Mean δ15N values of bryozoan statoblasts and SOM were correlated, probably reflecting δ15N values of phytoplankton. With this modern dataset, the authors provide insight in how environmental variables in lakes influence the δ13C and δ15N values in cladoceran and bryozoan resting stages, which is an important step towards improving interpretations of palaeoenvironmental stable isotope records based on the remains of these organisms.The following two papers focus on enhancing the understanding of the distribution of lipid biomarkers in time and space as well as their stable isotope values. Firstly, Van Bree et al. (2018), investigate the seasonal variation of different lipid biomarkers at different depths in the water column of Lake Chala. The authors find seasonal variation of (i) total phytoplankton biovolume reflected in phytadiene concentrations, (ii) chlorophyte blooms reflected by specific n-alkanes, (iii) diatom peaks related to loliolide and isololiolide, (iv) the eustigmatophyte peak reflected in C30 and C32 1,15 diols, and (v) cyanobacteria tentatively related to C19:1 n-alkene abundance. In addition, the authors indicate that the concentration, seasonal variability, and low δ13C values of the C28 fatty acid in suspended particles suggest that this biomarker is produced in the water column, instead of having the typically assumed vascular plant origin. All aquatic biomarkers become increasingly more negative (by up to 16‰) during periods of high productivity, when more positive values would be expected. The authors suggest this can be best explained by chemically enhanced diffusion under high pH conditions in periods of high productivity, generating strongly 13C-depleted HCO3. As this process causes seasonality in δ13C values of lipid biomarkers, it is vital to consider it when interpreting long-term trends in palaeorecords of biomarker δ13C in high-alkalinity lakes.St?tter et al. (2018) investigate the relationship between fatty acid (FA) biomarkers methane oxidizing bacteria (MOB) and methane concentrations in 29 lakes across Europe. The authors analyse concentrations and δ13C values of FAs, including FAs produced by MOB (C16:1ω7c, C16:1ω5c/t, and C18:1ω7c), and methane concentrations. The FAs also produced by MOB had significantly lower δ13C values compared with other analysed FAs. Furthermore, samples with higher MOB-derived FA abundance are associated with (i) higher MOB concentrations based on quantitative Polymerase Change Reaction (qPCR) analysis and (ii) higher methane concentrations. The strongest correlations are found between the relative abundance of MOB-derived FAs and methane concentrations in anoxic deep-water environments. The results confirm robust relationships between in-lake CH4 concentrations and 13C-depleted groups of FAs produced by MOB, but also indicate that different relationships exist for oxic and anoxic lake sediments.The final three papers in this issue present case studies providing examples of stable isotope records used in multi-proxy palaeoenvironmental studies. Street-Perrott et al. (2018) measure the δ13Ccellulose and δ18Ocellulose values of bulk cellulose and moss fragments from an ～11.4ka-long core from Lake ?ntu Sinij?rv, Estonia. The authors show how modern lake water isotope data are essential to understand the hydrological system under study and to support geochemical interpretations. C/N ratios and aquatic algal biomarker indices are used together with data on pollen and plant macrofossils to reconstruct the origin of cellulose in down core samples. This indicates that sedimentary organic matter was predominantly aquatic with significant cellulose inputs from microalgae (～11.4–10.4 ka), charophytes (～10.4–3.5 ka), bryophytes (～3.5 to at least 0.23 ka) and again microalgae (the last few decades). The δ13Ccellulose record is linked closely to changes in terrestrial carbon cycling during the Holocene, whereas the δ18Ocellulose record records major cold events (the Preboreal Oscillation, the 8.2 ka event and an unnamed event at ～3.25 ka).Swann et al. (2018) undertake a reconstruction of Central Asian precipitation using δ18O values of diatom silica in sediment records from Lake Baikal. The authors first perform a calibration in time using δ18Odiatom from short cores and measured changes in the amount of inflow during the years 1900–2010 (which is strongly related to local precipitation in the same period). A strong relationship is found between δ18Odiatom and decadal smoothed annual precipitation (span?=?10 years), using linear regression. Next, this relationship is used to predict precipitation from δ18Odiatom measured on a Holocene sediment record from Lake Baikal. Significant variability in mean precipitation (558?±?41?mm/yr) is estimated for the mid-Holocene warm interval (9–5 ka). The record suggests markedly higher precipitation for most of the Holocene compared with the last century, with values only comparable to mean modern day conditions (450?mm/yr) at 3.3 ka, 5.7 ka and 10.2 ka. This finding contrasts with local pollen-based precipitation reconstructions and climate model simulations, which suggest drier conditions in the region since 7 ka and at 6 ka, respectively.Finally, Panizzo et al. (2018) present the first application of δ30Si as a proxy for nutrient uptake by diatoms over the Last Interglacial (MIS 5e) in Lake Baikal. The authors show that both diatom productivity and the utilisation of dissolved silicon (DSi) as a nutrient by diatoms were significantly higher during MIS 5e than the current interglacial. This is supported by high diatom biovolume accumulation rates during MIS 5e and agrees with vegetation reconstructions suggesting temperatures warmer for this interval than during the Holocene. The data suggest an early interglacial stage (128–124 ka) with high DSi demand by diatoms in response to regional climate warming, but a low DSi supply based on catchment vegetation and weathering regime indices. Between 124–120 ka data suggest a high nutrient supply, likely caused by an increase in spring convective mixing as there is little evidence for catchment weathering. After 120 ka, a lower diatom productivity is proposed, with lower DSi supply despite increased catchment weathering. The authors suggest that diatom nutrient uptake is linked to mechanisms such as lake ice duration and turbulent convective mixing and not only related to supply of DSi from the catchment.We would like to thank all our colleagues who gave their time reviewing the papers and provided thorough and constructive feedback. All participants of the workshop are also thanked for their inputs during discussions that helped shape the two review papers. We would also like to thank the University of Southampton (Department of Geography and Environment and the School of Ocean and Earth Science, National Oceanography Centre Southampton) for hosting the workshop, especially Jessica Whiteside and Sargent Bray. Financial support from AOC Labs, Beta Analytic, and Elementar are gratefully acknowledged for their financial support to the workshop, which allowed more early career researchers to attend.ReferencesJ. Holtvoeth, J.H. Whiteside, S. Engels, F.S. Freitas, K. Grice, P. Greenwood, S. Johnson, I. Kendall, S.K. Lengger, A. Lücke, C. Mayr, B.D.A. Naafs, M. Rohrssen, J. Sepúlveda. The paleolimnologist's guide to compound-specific stable isotope analysis – an introduction to principles and applications of CSIA for Quaternary lake sediments. Quat. Sci. Rev., 207 (2019), pp. 101-133J.H. Lacey, M.J. Leng, E.N. Peckover, J.R. Dean, T. Wilke, A. Francke, X. Zhang, A. Masi, B. Wagner. Investigating the environmental interpretation of oxygen and carbon isotope data from whole and fragmented bivalve shells. Quat. Sci. Rev., 194 (2018), pp. 55-61V.N. Panizzo, G.E.A. Swann, A.W. Mackay, V. Pashley, M.S.A. Horstwood. Modelling silicon supply during the Last Interglacial (MIS 5e) at Lake Baikal. Quat. Sci. Rev., 190 (2018), pp. 114-122L.R. Roberts, J.A. Holmes, M.J. Leng, H.J. Sloane, D.J. Horne. Effects of cleaning methods upon preservation of stable isotopes and trace elements in shells of Cyprideis torosa (Crustacea, Ostracoda): implications for palaeoenvironmental reconstruction. Quat. Sci. Rev., 189 (2018), pp. 197-209J. Schilder, L. van Roij, G.-J. Reichart, A. Sluijs, O. Heiri. Variability in δ13C values between individual Daphnia ephippia: implications for palaeo-studies. Quat. Sci. Rev., 189 (2018), pp. 127-133St?tter et al., 2018. T. St?tter, D. Bastviken, P.L.E. Bodelier, M. van Hardenbroek, P. Rinta, J. Schilder, C.J. Schubert, O. Heiri. Abundance and δ13C values of fatty acids in lacustrine surface sediments: relationships with in-lake methane concentrations. Quat. Sci. Rev., 191 (2018), pp. 337-347F.A. Street-Perrott, J.A. Holmes, I. Robertson, K.J. Ficken, T. Koff, N.J. Loader, J.D. Marshall, T. Martma. The Holocene isotopic record of aquatic cellulose from Lake ?ntu Sinij?rv, Estonia: influence of changing climate and organic-matter sources. Quat. Sci. Rev., 193 (2018), pp. 68-83G.E.A. Swann, A.W. Mackay, E. Vologina, M.D. Jones, V.N. Panizzo, M.J. Leng, H.J. Sloane, A.M. Snelling, M. Sturm. Lake baikal isotope records of Holocene central Asian precipitation. Quat. Sci. Rev., 189 (2018), pp. 210-222L.G.J. van Bree, F. Peterse, M.T.J. van der Meer, J.J. Middelburg, A.M.D. Negash, W. De Crop, C. Cocquyt, J.J. Wieringa, D. Verschuren, J.S. Sinninghe Damsté. Seasonal variability in the abundance and stable carbon-isotopic composition of lipid biomarkers in suspended particulate matter from a stratified equatorial lake (Lake Chala, Kenya/Tanzania): implications for the sedimentary record. Quat. Sci. Rev., 192 (2018), pp. 208-224M. van Hardenbroek, A. Chakraborty, K.L. Davies, P. Harding, O. Heiri, A.C.G. Henderson, J.A. Holmes, G.E. Lasher, M.J. Leng, V.N. Panizzo, L. Roberts, J. Schilder, C.N. Trueman, M.J. Wooller. The stable isotope composition of organic and inorganic fossils in lake sediment records: current understanding, challenges, and future directions. Quat. Sci. Rev., 196 (2018), pp. 154-176M. van Hardenbroek, P. Rinta, M.J. Wooller, J. Schilder, T. St?tter, O. Heiri. Flotsam samples can help explain the δ13C and δ15N values of invertebrate resting stages in lake sediment. Quat. Sci. Rev., 189 (2018), pp. 187-196van Outersterp, R.E., Houthuijs, K.J., Berden, G., Engelke, U.F., Kluijtmans, L.A.J., Wevers, R.A., Coene, K.L.M., Oomens, J., Martens, J., 2019. Reference-standard free metabolite identification using infrared ion spectroscopy. International Journal of Mass Spectrometry 443, 77-85. chromatography-mass spectrometry (LC-MS) is, due to its high sensitivity and selectivity, currently the method of choice in (bio)analytical studies involving the (comprehensive) profiling of metabolites in body fluids. However, as closely related isomers are often hard to distinguish on the basis of LC-MS(MS) and identification is often dependent on the availability of reference standards, the identification of the chemical structures of detected mass spectral features remains the primary limitation. Infrared ion spectroscopy (IRIS) aids identification of MS-detected ions by providing an infrared (IR) spectrum containing structural information for a detected MS-feature. Moreover, IR spectra can be routinely and reliably predicted for many types of molecular structures using quantum-chemical calculations, potentially avoiding the need for reference standards. In this work, we demonstrate a workflow for reference-free metabolite identification that combines experiments based on high-pressure liquid chromatography (HPLC), MS and IRIS with quantum-chemical calculations that efficiently generate IR spectra and give the potential to enable reference-standard free metabolite identification. Additionally, a scoring procedure is employed which shows the potential for automated structure assignment of unknowns. Via a simple, illustrative example where we identify lysine in the plasma of a hyperlysinemia patient, we show that this approach allows the efficient assignment of a database-derived molecular structure to an unknown.Vasiliev, A.A., Melnikov, V.P., Semenov, P.B., Oblogov, G.E., Streletskaya, I.D., 2019. Methane concentration and emission in dominant landscapes of typical tundra of western Yamal. Doklady Earth Sciences 485, 284-287. concentration in dominant landscapes of typical tundra of Western Yamal has been measured. The highest methane content in the active layer was measured in tundra bogs, wet gully bottoms, and polygonal tundra. Within these landscapes, methane concentration reaches 5000 ppm, while in other landscapes it does not exceed 300 ppm. Thus, only bogs, polygonal tundra, and gully bottoms, which occupy approximately 30–40% of the area, are the main sources of methane emission in the typical tundra zone. Measurements of methane emission to the atmosphere have been performed. During the summer maximum of emission, daily methane flux in bogs reaches 14.4 mg/m2 (20.3 ml/m2).Vasudev, V., Ku, X., Lin, J., 2019. Kinetic study and pyrolysis characteristics of algal and lignocellulosic biomasses. Bioresource Technology 288, Article 121496. comparative kinetic study on the pyrolysis of six algal and lignocellulosic biomasses was performed and six heating rates were employed to obtain the kinetic equations and analyze the compensation effect. Due to complexity, the whole pyrolysis process of algal biomass was divided into two reaction zones in which the analysis was carried out individually. The activation energies were first evaluated within the conversion range of 0.05 to 0.95, which were 125–147?kJ/mol and 113–138?kJ/mol for lignocellulosic biomass and zone-1 of algal biomass, respectively. Regression analysis was also conducted to determine the appropriate kinetic model. Moreover, Z(α) master plots suggested that the nucleation model was dominant at lower and higher temperatures for lignocellulosic biomass. Besides, the pre-exponential factor was calculated and a compensation effect between activation energies and pre-exponential factors was completely observed in zone-2 of algal biomass and partially seen in zone-1 of algal biomass and lignocellulosic biomass.Veselkin, D.V., Chashchina, O.E., Kuyantseva, N.B., Mumber, A.G., 2019. Stable carbon and nitrogen isotopes in woody plants and herbs near the large copper smelting plant. Geochemistry International 57, 575-582. of stable carbon (13С and 12С) and nitrogen (15N and 14N) isotopic composition are analyzed in forest plants subjected to the emissions of large copper smelting plant. The studies were carried out in pine forests at ten test plots near the Karabash copper smelting plant and in the Ilmen State Reserve at South Urals. The 13С/12С and 15N/14N isotopic ratios were analyzed in leaves of plants of different functional groups (with ecto-, ericoid, or arbuscular mycorrhiza; with nitrogen-fixing symbiosis, and non-mycorrhizal). The 13С/12С ratio did not change under technogenic pollution. The low isotopic 15N/14N ratio was established in ectomycorrhizal trees, while the high ratio was found in herbs with arbuscular mycorrhiza, nitrogen-fixing symbiosis, and non-mycorrhizal groups. As compared to nonpolluted habitats, the 15N content in leaves near the copper smelting plant increases by 2.7‰ in the ectomycorrhizal trees and by 3.4‰ in undershrubs with ericoid mycorrhiza, and by 2.2‰ in herbs with arbuscular mycorrhiza. This indicates a significant change in conditions of mineral feeding of plants under heavy metal pollution of natural ecosystems.Veselova, M.A., Plyuta, V.A., Khmel, I.A., 2019. Volatile compounds of bacterial origin: Structure, biosynthesis, and biological activity. Microbiology 88, 261-274. produce various volatile compounds, including volatile organic compounds and complex combinations of volatile compounds. The ecological and functional role of these compounds is presently the subject of intense study. Volatile organic compounds of microbial origin may possess antimicrobial properties, suppress or stimulate plant growth, and act as signals for long-distance communication between organisms (infochemicals), which propagate in the air and in aquatic solutions. Chemical diversity of volatile organic compounds of microbial origin provides a source of new compounds which may find application in medicine, biotechnology, and agriculture. Presently known bacterial volatile compounds, their structure, biosynthesis, and biological activity are discussed, with special emphasis on organic volatile compounds and their effect on bacteria.Vezinet, A., Thomassot, E., Pearson, D.G., Stern, R.A., Luo, Y., Sarkar, C., 2019. Extreme δ18O signatures in zircon from the Saglek Block (North Atlantic Craton) document reworking of mature supracrustal rocks as early as 3.5 Ga. Geology 47, 605-608. most ancient rocks in the geological record provide insights into the processes that shaped the evolution and composition of the first continental masses. To better constrain these processes, we made a detailed study of a ca. 3.86 Ga felsic meta-igneous rock from the Eoarchean Saglek Block (North Atlantic Craton) that experienced high-grade metamorphism at ca. 3.5 Ga. Our robust zircon-isotope plus trace-element analyses reveal metamorphic zircon domains with δ18O values up to +9‰ at ca. 3.5 Ga, which are the highest values so far measured in any pre–3.0 Ga zircons, metamorphic or igneous, extracted from unambiguous (meta)igneous host rocks. Such elevated zircon δ18O signatures clearly document the involvement of mature supracrustal precursors (mafic volcanics ± clastic/chemical sediments) during the reworking of 3.86 Ga crust at ca. 3.5 Ga. This study provides unequivocal evidence for hydrosphere–crust interactions and reworking processes resulting in metamorphic zircon growth at ca. 3.5 Ga, namely 1 Ga before the Archean-Proterozoic transition.Vijay, D., Akhtar, M.K., Hess, W.R., 2019. Genetic and metabolic advances in the engineering of cyanobacteria. Current Opinion in Biotechnology 59, 150-156. are a group of photosynthetic microorganisms with high commercial potential. They can utilize sunlight directly to convert carbon dioxide or even nitrogen into a variety of industrially relevant chemicals. However, commercial platforms for the renewable and sustainable production of chemicals have yet to be demonstrated for cyanobacteria. Diverse strategies have therefore been employed in recent years to improve the production yields and efficiency of target chemicals. These include the use of CRISPR/Cas systems for mutant selection, synthetic RNA elements for controlling transcription, metabolic network modelling for understanding pathway fluxes, enzyme engineering, improving growth rates, alleviating product toxicity and microbial consortia. More elaborate strategies for engineering cyanobacteria, however, are still very much required if we are to meet the grand challenge of employing cyanobacteria as photosynthetic workhorses for large-scale industrial applications.Viktor, Z., Farcet, C., Moire, C., Brothier, F., Pfukwa, H., Pasch, H., 2019. Comprehensive two-dimensional liquid chromatography for the characterization of acrylate-modified hyaluronic acid. Analytical and Bioanalytical Chemistry 411, 3321-3330. acid and its acrylate derivatives are important intermediates for various pharmaceutical, biomedical, and cosmetic applications due to their biocompatibility and viscoelasticity properties. However, these polymers are inherently difficult to characterize due to their significant heterogeneity regarding molar mass and chemical composition (degree of substitution, DS). The present study describes the development of a comprehensive online two-dimensional liquid chromatography (2D-LC) approach to characterize hyaluronic acid and its acrylate derivatives (DS ranging from 0.4 to 3.1) in terms of molar mass and degree of substitution. In the first dimension of the 2D-LC method, separation according to chemical composition/DS was achieved by using a stepwise solvent gradient and a reversed phase C8 column. Fractions from the first dimension were automatically transferred to the second dimension comprising size exclusion chromatographic separation of the fractions according to molar mass. It was found that the hyaluronic acid derivatives were broadly distributed with regard to both chemical composition and molar mass. Fractions with different degrees of substitution were identified, and their molar mass distributions were determined. The study proved that comprehensive 2D-LC is a powerful approach to reveal the complex nature of hyaluronic acid and its derivatives.Vishal, V., Chandra, D., Bahadur, J., Sen, D., Hazra, B., Mahanta, B., Mani, D., 2019. Interpreting pore dimensions in gas shales using a combination of SEM imaging, small-angle neutron scattering, and low-pressure gas adsorption. Energy & Fuels 33, 4835-4848. shales of Barakar formation in India were investigated to study their pore structure to understand their potential for natural gas production and possible CO2 sequestration. The studied shale samples with variable clay content were of early mature stage and contained low (<2%) total organic carbon. Initially, a combination of small-angle neutron scattering (SANS) and low-pressure gas adsorption (LPGA) was used to identify the pore sizes and fractal dimensions of Indian shales. It was found that the quenched surface density functional theory model in the LPGA method gave better pore size distribution (PSD) estimates over the nonlocal density functional theory model. The micropores and smaller mesopores contribute the most to the total pore volume and the surface area of the studied shale samples. The average pore size decreased with an increase in pore volume. The fractal studies using SANS reveal that all studied shales possess similar fractal dimension despite being different in mineralogy, maturity, and total pore volume. The PSD and its possible relation with the mineral composition and the accessibility of the pores in terms of gas storage have been elucidated. Pore morphology was analyzed using image analysis of field emission scanning electron microscopy and low-pressure adsorption, corroborated by SANS results. The effects of dissolution and deposition probability on the fractal dimension of the shale were interpreted using the Monte Carlo-based computer modeling. The fractal dimension was higher in the case of shales that underwent simultaneous dissolution and deposition processes.Vorkamp, K., Balmer, J., Hung, H., Letcher, R.J., Rigét, F.F., 2019. A review of chlorinated paraffin contamination in Arctic ecosystems. Emerging Contaminants 5, 219-231. paraffins (CPs) present a complex mixture of congeners which are often analysed and assessed as short-, medium- and long-chain CPs, i.e. ΣSCCP (C10–C13), ΣMCCP (C14–C17) and ΣLCCP (≥C18). Their complexity makes the chemical analysis challenging, in particular in terms of accurate quantification, but promising developments involving ultra-high resolution mass spectrometry have been presented lately. Most Arctic data exist for SCCPs, while LCCPs have not yet been studied in the Arctic. ΣSCCP concentrations in Arctic air often exceeded those of ΣMCCP, usually with a predominance of the most volatile C10 congeners, and of banned persistent organic pollutants (POPs), such as polychlorinated biphenyls (PCBs). The presence of SCCPs and MCCPs in Arctic air, as well as in the Antarctic and in the remote regions of the Tibetan plateau, provides evidence of their long-range transport including sufficient environmental persistence to reach the Arctic. Arctic vegetation accumulated SCCPs partly from air and partly through root uptake from soil, with consequences for the SCCP profile found in Arctic plants. No results have yet been reported for CPs in terrestrial Arctic animals. Results for freshwater sediment and fish confirmed the long-range transport of SCCPs and MCCPs and documented their bioaccumulation. Where additional PCB data were available, ΣPCB was usually higher than ΣSCCP in freshwater fish. Both SCCPs and MCCPs were widely present in marine Arctic biota (e.g. mussels, fish, seabirds, seals, whales, polar bears). In mussels and Atlantic cod, ΣMCCP concentrations exceeded those of ΣSCCP, while this was less clear for other marine species. Marine mammals and the long-lived Greenland shark roughly had ΣSCCP concentrations of 100–500?ng/g lipid weight, often dominated by C11 congeners. Biomagnification appeared to be more pronounced for ΣSCCP than for ΣMCCP, but more studies will be needed. Increasing ΣSCCP concentrations were observed in Arctic air and sediment over time, but not in beluga monitored since the 1980s. For both SCCPs and MCCPs, increasing concentrations over time have been shown in blue mussels and Atlantic cod at some, but not all stations. Indications exist of local sources of SCCPs in the Arctic, including Arctic settlements and research stations. In studies involving multiple locations, a general decrease of SCCP concentrations with increasing latitude or distance from point sources was observed as well as relatively more MCCPs at locations closer to potential CP sources. Monitoring of SCCPs and MCCPs has been initiated in some Arctic regions and will be important to assess the effect of recent regulations of SCCPs and the use of potential replacement chemicals.Vysotskii, S.V., Khanchuk, A.I., Kuleshevich, L.V., Ignatiev, A.V., Slabunov, A.I., Velivetskaya, T.A., 2019. The multi-isotope composition of sulfur in sulfides and microfossils of the Mesoarchean Leksa pyrite ore occurrence of the Karelian Craton: New data on abiogenic and biogenic effects on the formation of ancient ores. Doklady Earth Sciences 485, 409-412. ores have been formed on the Earth from the Archean to the present. The most important component, sulfur, can be provided by the following three sources: igneous, sedimentary, and sulfates of seawater. Studies of contemporary hydrothermal systems of the seabed, which are considered to be the ore-generating mechanism responsible for the oldest pyrite deposits, have shown that magmatic sulfur and seawater sulfate make the major contribution to the total sulfur budget in ore formation. The question of the influence of the simplest forms of life on the processes of ore formation, which is especially important and debatable for the Archaean deposits, is also widely discussed. However, our understanding of the processes occurring at the early stage of the Earth’s development is limited to a few available well-preserved geological samples, while the overwhelming majority of Archean rocks have experienced some degree of metamorphic changes.Wacey, D., Sirantoine, E., Saunders, M., Strother, P., 2019. 1 billion-year-old cell contents preserved in monazite and xenotime. Scientific Reports 9, Article 9068. microfossil preservation, whereby sub-cellular details of an organism are conserved, remains extremely rare in the Precambrian rock record. We here report the first occurrence of exceptional cellular preservation by the rare earth element (REE) phosphates monazite and xenotime. This occurs in ~1 billion-year-old lake sediments where REEs were likely concentrated by local erosion and drainage into a closed lacustrine basin. Monazite and xenotime preferentially occur inside planktonic cells where they preserve spheroidal masses of plasmolyzed cell contents, and occasionally also membranous fragments. They have not been observed associated with cell walls or sheaths, which are instead preserved by clay minerals or francolite. REE phosphates are interpreted to be the earliest minerals precipitated in these cells after death, with their loci controlled by the micro-scale availability of inorganic phosphate (Pi) and REEs, probably sourced from polyphosphate granules within the cells. The strong affinity of REEs for phosphate and the insolubility of these minerals once formed means that REE phosphates have the potential for rapid preservation of cellular morphology after death and durability in the rock record. Hence, authigenic REE phosphates provide a promising new target in the search for the preservation of intra-cellular components of fossilised microorganisms.Waliczek, M., Machowski, G., Wi?c?aw, D., Konon, A., Wandycz, P., 2019. Properties of solid bitumen and other organic matter from Oligocene shales of the Fore-Magura Unit in Polish Outer Carpathians: Microscopic and geochemical approach. International Journal of Coal Geology 210, Article 103206. this study, we apply microscopic and geochemical (Rock-Eval) methods to evaluation of both the origin and maturity of solid bitumen and other organic matter dispersed in Oligocene shales from the Skrzydlna Tectonic Bay and the Mszana Dolna Tectonic Window of the Fore Magura Unit, Outer Carpathians, Poland. Homogenous solid bitumen occurs in early mature and mature samples of rocks from the Skrzydlna Tectonic Bay (vitrinite reflectance VR from 0.60 to 0.80%). It reaches reflectance values (BR) from 0.31 to 0.61% and is interpreted as the intermediate product between kerogen and oil originated during the oil generation process. In the late mature and post-mature samples from the Mszana Dolna Tectonic Window (VR from 1.10 to 1.49%), homogenous solid bitumen reflectance varies from 1.45 to 1.76%. This is an indigenous, thermally altered solid bitumen or residue after hydrocarbon generation, hence, it should be called the pyrobitumen. In samples from both locations, granular solid bitumen was found, as well, of reflectance values (GBR) from 0.25 to 0.92%.A very strong correlation of homogenous solid bitumen, pyrobitumen and granular solid bitumen reflectances with vitrinite reflectance was found in studied samples. When measured in the same sample, the solid bitumen from the Skrzydlna Tectonic Bay always showed lower reflectance values than the coexisting vitrinite. In samples from the Mszana Dolna Tectonic Window, in which measured vitrinite reflectance VR was always above 1,0%, the, observed pyrobitumen invariably showed the higher reflectance values whereas the granular solid bitumen consistently revealed lower reflectance than vitrinite, homogenous solid bitumen or pyrobitumen coexisting in the same sample. The Rock-Eval analyses confirmed that bitumen is indigenous in all studied samples. The degree of thermal maturation of organic matter based on vitrinite reflectance measurements was equivalent to organic matter maturity determined by the Rock-Eval Tmax values, which could be confirmation that our microscopic observations and selection of vitrinite fragments were correct.We were able to perform more individual measurements of homogenous solid bitumen particles and we obtained lower average standard deviation for BR values than for VR values. Due to the dark vitrinite abundant in samples taken in the Skrzydlna Tectonic Bay and the small-size vitrinite particles seen in samples from the Mszana Dolna Tectonic Window we found it difficult to select proper vitrinite particles for microscopic examinations. By contrast, both the solid bitumen and the pyrobitumen particles were often easier to recognize due to their characteristic shape and larger size than those of vitrinite fragments. For these set of samples we conclude that reflectance measurements run on homogenous solid bitumen are more reliable in comparison with those performed on vitrinite.Wang, B., Liu, F., Zheng, S., Hao, Q., 2019. Trophic strategy of diverse methanogens across a river-to-sea gradient. Journal of Microbiology 57, 470-478. are an important biogenic source of methane, especially in estuarine waters across a river-to-sea gradient. However, the diversity and trophic strategy of methanogens in this gradient are not clear. In this study, the diversity and trophic strategy of methanogens in sediments across the Yellow River (YR) to the Bohai Sea (BS) gradient were investigated by high-throughput sequencing based on the 16S rRNA gene. The results showed that the diversity of methanogens in sediments varied from multitrophic communities in YR samples to specific methylotrophic communities in BS samples. The methanogenic community in YR samples was dominated by Methanosarcina, while that of BS samples was dominated by methylotrophic Methanococcoides. The distinct methanogens suggested that the methanogenic community of BS sediments did not originate from YR sediment input. High-throughput sequencing of the mcrA gene revealed that active Methanococcoides dominated in the BS enrichment cultures with trimethylamine as the substrate, and methylotrophic Methanolobus dominated in the YR enrichment cultures, as detected to a limited amount in in situ sediment samples. Methanosarcina were also detected in this gradient sample. Furthermore, the same species of Methanosarcina mazei, which was widely distributed, was isolated from the area across a river-to-sea gradient by the culture-dependent method. In summary, our results showed that a distribution of diverse methanogens across a river-to-sea gradient may shed light on adaption strategies and survival mechanisms in methanogens.Wang, B., Yang, J., Jiang, H., Zhang, G., Dong, H., 2019. Chemical composition of n-alkanes and microbially mediated n-alkane degradation potential differ in the sediments of Qinghai-Tibetan lakes with different salinity. Chemical Geology 524, 37-48. proxies are widely employed to reconstruct paleoclimate and paleoenvironment in lacustrine environments. However, little is known about the influence of microbially mediated alkane-degradation on n-alkane-derived proxies. In this study, the chemical composition of n-alkanes and microbially mediated n-alkane degradation potential were investigated in the surface sediment samples collected from seven lakes with a range of salinity from freshwater to salt saturation on the northern Qinghai-Tibetan Plateau (QTP). The results showed that the chemical composition of n-alkanes differed among the studied QTP lakes. Significant correlations were observed between salinity and some n-alkane-based paleoclimate and paleoenvironment proxies, such as ratio of C21?/C22+, average chain length (ACL) and carbon preference index (CPI). This suggested that salinity may affect the validity of some n-alkane-based paleoclimate and paleoenvironment proxies. Alkane-degrading bacteria were abundant and widespread in the studied freshwater and saline/hypersaline lakes but were minor or absent in salt-saturation lakes. The obtained alkane-degrading bacterial strains showed active ability to degrade n-hexadecane. This suggested that the salinity influence on the n-alkane distribution may be partially related to microbial degradation, which awaits further in-situ investigation. So salinity variation should be taken into account when using n-alkane-based proxies for reconstructing paleoclimate and paleoenvironment in lakes.Wang, D.-D., Li, Z.-X., Liu, H.-Y., Lyu, D.-W., Dong, G.-Q., 2019. The genetic environmental transformation mechanism of coal and oil shale deposits in eastern China’s continental fault basins and the developmental characteristics of the area’s symbiotic assemblages—taking Huangxian Basin as an example. Petroleum Science 16, 469-491. and oil shale are two common sedimentary energy sources which are often symbiotically developed in Mesozoic–Cenozoic continental fault basins. However, the mechanisms and characteristics of the symbiotic development are not yet clearly known. In this research study, the typical continental fault basins of eastern China were chosen as examples for the purpose of conducting an examination of the coal and oil shale symbiotic assemblage types, genetic environmental differences, and transformation mechanisms, as well as the development and occurrence characteristics of different assemblage types. Through a large number of investigations, systematic experimental testing, and sequence stratigraphy studies, the following conclusions were obtained: (1) There were five types of coal and oil shale symbiotic assemblages observed in the continental fault basins, (2) The development of coal and oil shale deposits requires a warm and humid climate, stable structure, abundant organic matter supply, a certain water depth, and a lower terrestrial source debris supply. The observed differences were that the water depth conditions were diversified in the study area, as well as the sources, types, and content of the organic matter. (3) The rapid transformations of the coal and oil shale genetic environments were mainly controlled by the tectonic settings and climatic conditions, which were determined to control the changes in the water depths, salinity, redox conditions, and lake productivity of the genetic environments. Also, in the symbiotic assemblages, genetic environment changes had induced the development of oil shale deposits, which gradually evolved into coal genetic environments. (4) In the isochronous sequence stratigraphic framework of the coal and oil shale symbiotic assemblages, the lake expansion system tracts (EST) were determined to be the most beneficial to the growth of all the types of assemblages and were characterized by more assemblage development phases and smaller bed thicknesses. From the early to the late stages of the EST, and from the lakesides to lake centers, the thicknesses of the coal seams in the symbiotic assemblages showed trends of thinning, while the thicknesses of the oil shale deposits exhibited increasing trends. The early stages of high stand system tracts were found to be beneficial to the development of the symbiotic assemblages of coal seams overlying the oil shale. This tract type generally presented large bed thicknesses and distribution ranges. The low stand system tract and the late high stand system tract were determined to be unconducive to the development of the symbiotic assemblages.Wang, H., He, Y., Liu, W., Zhou, A., Kolpakova, M., Krivonogov, S., Liu, Z., 2019. Lake water depth controlling archaeal tetraether distributions in midlatitude Asia: Implications for paleo lake-level reconstruction. Geophysical Research Letters 46, 5274-5283.: Lake‐level reconstructions, related to terrestrial hydrological changes, are important for our understanding of past and future climates. Currently, however, reliable lake‐level proxies are still limited. Here we report distributions of archaeal tetraether lipids in 70 surface sediment samples collected from 55 lakes in midlatitude Asia. We have found that among various lake physico‐chemical characteristics, the relative abundances of crenarchaeol and Hydroxylated isoprenoid glycerol dialkyl glycerol tetraethers (%cren and %OH‐GDGTs) are best correlated with lake water depth, due to a preference of Thaumarchaeota, the producer of these biomarkers, for a niche in subsurface lake water. This supports the recent hypothesis based on single‐lake investigations that %cren and %OH‐GDGTs are potentially novel lake‐level proxies. Our results also suggest that %OH‐GDGTs is less affected by soil input than %cren. Nevertheless, other confounding factors should be well constrained and local/site‐specific calibrations are needed before the two molecular proxies are used quantitatively in down‐core applications.Plain Language Summary: Lake‐level reconstructions can provide useful information about past changes in hydroclimate, which impact both ecosystems and socio‐economic sustainable development in fundamental ways, but reliable lake‐level proxies are still limited to date. Here we show that the %cren and %OH‐GDGTs indices, calculated based on the distributions of archaeal membrane lipids, are controlled by lake water depth in lake surface sediments across a variety of lake conditions. This suggests that past lake level changes can be inferred by analyzing the ubiquitous archaeal lipids preserved in downcore lake sediments.Wang, J., Guo, G.-J., Han, Y., Hou, Q., Geng, M., Zhang, Z., 2019. Mechanolysis mechanisms of the fused aromatic rings of anthracite coal under shear stress. Fuel 253, 1247-1255. fused aromatic rings (FARs) of coal are considered to be relatively stable during coalification. However, it is speculated that defects may form in FARs during the deformation of coals under tectonic stress. In order to investigate the possibly existed mechanolysis reactions of FARs, we performed molecular dynamics simulations with the reactive force field to study an anthracite coal model under shear stress. The results show that the FAR rupture reactions occur much more efficiently than expected. There are two important ways to initiate FAR rupture: attacked rupture and direct rupture. Among the mechanisms, two types of rearrangement reactions play crucial roles. The first type is intra-ring rearrangement where the FAR forms a three-membered ring and a five-membered ring before rupture. The second type is extra-ring rearrangement where the location of substituent group changes. Both rearrangement reactions determine which bond in the FAR preferentially breaks but in different manners, and then promote the subsequent reactions. Comparing to pyrolysis mechanism, mechanolysis mechanism follows completely different reaction pathways and result in different products. This research will aid in understanding the reaction mechanisms of coal mechanochemistry, and it opposes the traditional standpoint that the FARs of coal are relatively stable and very hard to be destroyed during coalification.Wang, J., Wu, D., Chen, X., 2019. Geochemical characteristics of Site-4B sediments from the Shenhu area of the South China Sea: Implications for methane seepage. Acta Sedimentologica Sinica 37, 648-660. studies on Site 4B suggested the presence of methane seepage in this area. In this study, we systematically analyzed the particle size distribution, minerals, and chemical compositions of the sediments at an interval of 15 cm.The particle size distribution varied significantly at a depth of 98 cm, which is ascribed to the changed hydrodynamic conditions. Significantly increased particle size was discovered at depths of 161 cm, 186 cm, and 213 cm. According to the sedimentation rate, these abnormally increased particle sizes occurred 24.15 ka, 27.47 ka, and 31.05 ka, which may be related to methane seeping events.The chemical compositions of the sediments changed with the particle size variation. At depths lower than 98 cm, the concentrations of CaO, Na2O, and Sr increased with depth, while that of SiO2, Al2O3, Fe2O3, Px dramatically decreased. At depths larger than 98 cm, on the contrary, these elements did not change significantly with depth. The positive correlations between CaO, Na2O, and Sr, as well as the negative correlations between these elements and SiO2 indicated that the carbonates (containing Ca and Sr) were affected by secondary processes, e.g., the production of authigenic carbonate from methane seepage.The variation of the Mg/Ca and Sr/Ca ratios as a function of depth suggests that the sediment might be affected by mud volcanic activity before 15.78 ka. The mud volcanic activity arrived at a maximum at 35.96 ka, where the highest Mg/Ca and Sr/Ca ratios were measured. Furthermore, we calculated the relative contents of aragonite, high-Mg calcite, biogenic calcite, and detrital materials by using Bayon's model. The results indicate that the detrital materials likely originated from a stable source, while the calcite and aragonite were authigenic carbonates produced by microbial activities related to methane seepage. Combined with previous studies on pyrite and the particle characteristics of the sediments, we postulated that the methane seepage was related to the mud volcano activity before 15.78 ka. These periodic mud volcanic activities brought the deep-sourced methane to a shallow depth. Then the anaerobic oxidation of methane produced authigenic carbonates (including high-Mg calcite and aragonite). Strong methane seepage was observed at 24.15 ka, 27.47 ka, and 31.05 ka, where the maximum seepage occurred at 31.05 ka. At <98 cm (after 15.78 ka), however, the sediments were affected by both terrigenous inputs and methane seepage.This study investigated the timing and intensity of methane seepagw in Site-4B using Mg/Ca and Sr/Ca ratios for the first time. It is important for unveiling the methane seeping history in the Northern SCS.Wang, K., Wang, G., Jiang, Y., Wang, S., Han, W., Chen, X., 2019. How transport properties of a shale gas reservoir change during extraction: A strain-dependent triple-porosity model. Journal of Petroleum Science and Engineering 180, 1088-1100. this study, we consider a shale gas reservoir as a triple-porosity media consisting of organic matrix, inorganic matrix, and fractures. A strain-dependent triple-porosity model is established by accurately expressing the deformation of each medium to reveal the change in the transport properties of a shale gas reservoir during production and to predict the reservoir recovery. The deformation of each medium is based on a combination of mechanical deformation and desorption-induced shrinkage behavior, and fracture aperture as well as the difference of effective stress in each medium were considered. We find that the transport properties of shale gas reservoirs are related to the porosity and diffusion coefficient of the organic matrix, and the porosity and permeability of the fracture system and inorganic matrix. The triple-porosity model is then incorporated into the governing equations for gas flow. The finite element method is used to solve the governing equations. By comparing the simulation result with field data, analytical solution, and previous simulation result, we are able to verify the accuracy of our model. Then, we analyze and reveal in detail how the transport properties of shale gas reservoirs change during extraction through the combined evolution of gas pressure, volumetric strain, and strain induced by the adsorption/desorption of gas in the organic matrix. Finally, we conduct sensitive analysis focusing on how the initial transport properties affect their evolutions. We find that the relationship between mechanical deformation and strain induced by adsorption/desorption is not always competitive during gas extraction.Wang, K., Zhang, Y., Huang, R.-J., Wang, M., Ni, H., Kampf, C.J., Cheng, Y., Bilde, M., Glasius, M., Hoffmann, T., 2019. Molecular characterization and source identification of atmospheric particulate organosulfates using ultrahigh resolution mass spectrometry. Environmental Science & Technology 53, 6192-6202. (OSs) have been observed as substantial constituents of atmospheric organic aerosol (OA) in a wide range of environments; however, the chemical composition, sources, and formation mechanism of OSs are still not well understood. In this study, we first created an “OS precursor map” based on the elemental composition of previous OS chamber experiments. Then, according to this “OS precursor map”, we estimated the possible sources and molecular structures of OSs in atmospheric PM2.5 (particles with aerodynamic diameter ≤ 2.5 μm) samples, which were collected in urban areas of Beijing (China) and Mainz (Germany) and analyzed by ultrahigh-performance liquid chromatography (UHPLC) coupled with an Orbitrap mass spectrometer. On the basis of the “OS precursor map”, together with the polarity information provided by UHPLC, OSs in Mainz samples are suggested to be mainly derived from isoprene/glyoxal or other unknown small polar organic compounds, while OSs in Beijing samples were generated from both isoprene/glyoxal and anthropogenic sources (e.g., long-chain alkanes and aromatics). The nitrooxy-OSs in the clean aerosol samples were mainly derived from monoterpenes, while much fewer monoterpene-derived nitrooxy-OSs were obtained in the polluted aerosol samples, showing that nitrooxy-OS formation is affected by different precursors in clean and polluted air conditions.Wang, L., Zhao, Y., Yang, D., Kang, Z., Zhao, J., 2019. Effect of pyrolysis on oil shale using superheated steam: A case study on the Fushun oil shale, China. Fuel 253, 1490-1498. the in situ pyrolysis of oil shale (OS) with superheated steam (SS), the internal pores and fractures of the OS act as channels for the migration of steam and locations for heat exchange. After a laboratory test of the in situ pyrolysis of OS with SS, 30 OS samples located in different zones between the injection and production wells were collected. The main parameters of pore and fracture structures inside OS samples were investigated. The results first showed that in each position along the bedding planes, the effective porosity was greater than 19.41%. The internal OS fractures were mainly dominated by microfractures, with lengths between 100??m and 500??m. The average pore diameter of the orebody was between 52.77?nm and 69.01?nm, and the aperture of the microfractures was between 59.31??m and 68.85??m. Then, in the position near the roof bedrock perpendicular to the bedding directions (BD), the effective porosity and pore diameter of the orebody were small. Only a few cracks were observed in the rock mass, and the distribution of the pore groups in the 3D space was fragmented and had poor connectivity. Finally, in the whole studied OS orebody, the proportion of ore layers with permeabilities ranging from 1.8?×?10?17 m2 to 3.0?×?10?17 m2 was 63.51%, which proved that the connectivity of the pores and fractures in the large area was superior to other areas.Wang, Q., Wei, Z., Yi, X., Tang, J., Feng, C., Dang, Z., 2019. Biogenic iron mineralization of polyferric sulfate by dissimilatory iron reducing bacteria: Effects of medium composition and electric field stimulation. Science of The Total Environment 684, 466-475. sulfate (PFS) is a coagulant widely used for removing contaminants from the aqueous phase; however, PFS destabilizes and recrystallizes in the solid phase in the presence of dissimilatory iron reducing bacteria (DIRB), which has a profound influence on the cycle of Fe and the fate of the associated pollutants. Our objective is to investigate the combined effects of medium composition and electric field stimulation on the biomineralization of PFS. Batch experiments were conducted with PFS and the DIRB Shewanella oneidensis MR-1 under anoxic conditions to examine the microbial reduction of PFS to Fe(II) and its subsequent biotransformation. The high concentration of phosphorous in phosphate buffer solution (PBS) is responsible for slower and less extensive Fe(II) generation compared to the lower concentration of phosphorous in a medium of 1,4-piperazinediethanesulfonic acid (PIPES). The PBS system induces the formation of green rust (SO42?) and vivianite as the major minerals; in contrast, magnetite is the predominant end product in the PIPES system. The application of an anodic potential of 0.2?V significantly stimulates Fe(II) release from PFS, leading to precipitation and transformation of more crystalline minerals in increased quantities. The results demonstrate that Fe(II) catalyzes biomineralization of PFS to a variety of secondary products; this electron transfer process is highly dependent on the rate and magnitude of PFS reduction and the surface reaction with the host compound and adsorbed ions.Wang, S., Sun, S., Shan, C., Pan, B., 2019. Analysis of trace phosphonates in authentic water samples by pre-methylation and LC-Orbitrap MS/MS. Water Research 161, 78-88. is an important phosphorous species in the effluent of wastewater treatment plant (WWTP), contributing to eutrophication and interfering with phosphate removal in WWTP. It is particularly difficult to determine phosphonates in samples of complex solution chemistry, resulting in very limited information on their presence in environmental matrices. Herein, we proposed a sensitive method based on liquid chromatography tandem mass spectrometry (LC-MS/MS) to determine six quantitatively most important phosphonates even at the ng/L level, i.e., 2-phosphonobutane-1,2,4-tricarboxylic acid, 1-hydroxyethane 1,1-diphosphonic acid, nitrilotris(methylene phosphonic acid), ethylenediamine tetra(methylene phosphonic acid), hexamethylenediamine tetra(methylene phosphonic acid) and diethylenetriamine penta(methylene phosphonic acid). Trimethylsilyldiazomethane (TMSCHN2) derivatization of the target phosphonates is pre-requisite since it could greatly increase the sensitivity up to 2-3 orders of magnitude over direct analysis of the virgin ones. The sample pretreatment methods (including ion exchange and solid phase extraction(SPE)), the derivatization procedures, and the LC-MS/MS conditions were systematically optimized. The limits of quantitation for the six phosphonates in the background of tap water ranged from 1.4?μg/L to 57?μg/L for direct analysis, and from 5.0?ng/L to 200?ng/L for SPE enabled pre-concentration analysis, respectively. The reliability of the proposed method was successfully validated by analysis of authentic water samples collected from one river and three WWTPs (0.088–7200?μg/L phosphonates) with satisfactory recoveries (72–126%). To the best of knowledge, this is the first report on quantification of phosphonates in environmental samples in China.Wang, X., Foster, W.J., Yan, J., Li, A., Mutti, M., 2019. Delayed recovery of metazoan reefs on the Laibin-Heshan platform margin following the Middle Permian (Capitanian) mass extinction. Global and Planetary Change 180, 1-15. the Middle Permian (Capitanian) mass extinction there was a global ‘reef eclipse’, and this event had an important role in the Paleozoic-Mesozoic transition of reef ecosystems. Furthermore, the recovery pattern of reef ecosystems in the Wuchiapingian of South China, before the radiation of Changhsingian reefs, is poorly understood. Here, we present a detailed sedimentological account of the Tieqiao section, South China, which records the only known Wuchiapingian reef setting from South China. Six reef growing phases were identified within six transgressive-regressive cycles. The cycles represent changes of deposition in a shallow basin to a subtidal outer platform setting, and the reefal build-ups are recorded in the shallowest part of the cycles above wave base in the euphotic zone. Our results show that the initial reef recovery started from the shallowing up part of the 1st cycle, within the Clarkina leveni conodont zone, which is two conodont zones earlier than previously recognized. In addition, even though metazoans, such as sponges, do become important in the development of the reef bodies, they are not a major component until later in the Wuchiapingian in the 5th and 6th transgressive-regressive cycles. This suggests a delayed recovery of metazoan reef ecosystems following the Middle Permian extinction. Furthermore, even though sponges do become abundant within the reefs, it is the presence and growth of the encrusters Archaeolithoporella and Tubiphytes and abundance of microbial micrites that play an important role in stabilizing the reef structures that form topographic highs.Wang, X., Zou, C., Li, J., Wei, G., Chen, J., Xie, Z., Li, Z., Guo, J., Lin, S., Pan, S., Hao, A., Yang, C., Qi, X., 2019. Comparison on rare gas geochemical characteristics and gas originations of Kuche and Southwestern Depressions in Tarim Basin, China. Geofluids 2019, Article 1985216. Kuche Depression is considered as the most important gas resource potential and gas exploring area with great gas resource potential and prospect in the Tarim Basin. Based on geochemical experimental analyses and comprehensive geological studies, the general geochemical characteristics of molecular and isotope compositions of rare gases as well as hydrocarbon gases and nonhydrocarbon gases are comparatively studied in the Kuche and Southwestern Depressions. Then, their genetic types are separately identified and gas originations are comprehensively discussed. The main results are as follows. (1) Gas fields in the Kuche Depression have a higher methane abundance, accompanied with low N2 and CO2 abundances, but the Akemomu gas field in the Southwestern Depression has a relatively lower average methane abundance, accompanied with high average N2 and CO2 abundances. The helium abundance of natural gases in gas fields from the Kuche Depression general has 1 order of magnitude higher than the air value. Comparatively, it has more than 2 orders of magnitude higher than the atmospheric value in the Akemomu gas field from the Southwestern Depression. The neon, argon, krypton, and xenon abundances in both Kuche and Southwestern Depressions are lower than the corresponding air values. (2) Natural gases from gas fields in the Kuche Depression and the Southwestern Depressions are generally typical coal-formed gases. The rare gases in the Kuche Depression have typical crustal genesis, mainly deriving from the radioactive decay of elements in the crust, while in the Akemomu gas field from the Southwestern Depression, the rare gases have main crustal genesis with a proportion of 92.5%, probably accompanied with a little mantled genetic contribution. (3) Natural gases in the Kuche Depression are generally derived from coal measure source rocks of Jurassic and Triassic, which principally originated from Jurassic in strata period and coals in source rock types. The Jurassic source rocks account for 55%-75% and the Triassic source rocks account for 25%-45% approximately, while coals occupy 68% and mudstones occupy 32% separately. Natural gases from the Akemomu gas field in the Southwestern Depression mainly originated from humic mudstones of marine and continental transitional source rocks of Carboniferous to Permian.Wang, Y., Chen, J.-H., Althaus, S.M., Yu, M., Chen, J., 2019. Electrical properties of unconventional source rocks from Micro-CT using numerical mixing law. Fuel 254, Article 115576. rock characterization is critical in using resistivity and dielectric methods for source rocks. However, conventional mixing theories cannot address scenarios where the high volume inclusion exists for rocks with anisotropic electrical parameters. In this paper, an electromagnetic numerical technique using finite difference method was developed to investigate the electrical and anisotropic properties of source rocks based on 3D rock Micro-CT images. Numerical experiments were applied to study the effects of pyrites and fluids on the effective resistivity and electronic anisotropy in source rocks. It was found that less than 1% pyrite or brine significantly changed the electric property and enhanced their anisotropy.Ward, L.M., Stamenkovi?, V., Hand, K., Fischer, W.W., 2019. Follow the oxygen: Comparative histories of planetary oxygenation and opportunities for aerobic life. Astrobiology 19, 811–824. respiration—the reduction of molecular oxygen (O2) coupled to the oxidation of reduced compounds such as organic carbon, ferrous iron, reduced sulfur compounds, or molecular hydrogen while conserving energy to drive cellular processes—is the most widespread and bioenergetically favorable metabolism on Earth today. Aerobic respiration is essential for the development of complex multicellular life; thus the presence of abundant O2 is an important metric for planetary habitability. O2 on Earth is supplied by oxygenic photosynthesis, but it is becoming more widely understood that abiotic processes may supply meaningful amounts of O2 on other worlds. The modern atmosphere and rock record of Mars suggest a history of relatively high O2 as a result of photochemical processes, potentially overlapping with the range of O2 concentrations used by biology. Europa may have accumulated high O2 concentrations in its subsurface ocean due to the radiolysis of water ice at its surface. Recent modeling efforts suggest that coexisting water and O2 may be common on exoplanets, with confirmation from measurements of exoplanet atmospheres potentially coming soon. In all these cases, O2 accumulates through abiotic processes—independent of water-oxidizing photosynthesis. We hypothesize that abiogenic O2 may enhance the habitability of some planetary environments, allowing highly energetic aerobic respiration and potentially even the development of complex multicellular life which depends on it, without the need to first evolve oxygenic photosynthesis. This hypothesis is testable with further exploration and life-detection efforts on O2-rich worlds such as Mars and Europa, and comparison to O2-poor worlds such as Enceladus. This hypothesis further suggests a new dimension to planetary habitability: “Follow the Oxygen,” in which environments with opportunities for energy-rich metabolisms such as aerobic respiration are preferentially targeted for investigation and life detection. Washburn, A.M., Hudson, S.M., Selby, D., Abdullayev, N., Shiyanova, N., 2019. Constraining the timing and depositional conditions of the Maikop Formation within the Kura Basin, eastern Azerbaijan, through the application of Re-Os geochronology and chemostratigraphy. Journal of Petroleum Geology 42, 281-299. Oligocene – Miocene Maikop Formation is the key source rock in the South Caspian and Kura Basins. The Maikop is composed of a thick (up to 3 km) succession of clay‐rich mudstones containing up to 15% total organic carbon (TOC). Despite decades of study, the mudstones often lack precise age control – Maikop strata rarely contain diagnostic microfaunal assemblages which can be used for dating, stratigraphic correlation, or constraining the depositional setting. Using rhenium‐osmium geochronology, this study adds important numerical age data for the Maikop Formation. Of five sample suites analysed from the Kura Basin, eastern Azerbaijan, one Re‐Os data‐set produced a significant range in 187Re/188Os versus 187Os/188Os space to yield an isochron of 17.2 ± 3.2 Ma (Early Miocene). Other sample suites yielded imprecise Re‐Os age constraints as a result of variable initial 187Os/188Os values and a limited range in 187Re/188Os versus 187Os/188Os space. The initial 187Os/188Os values of these data‐sets were compared with the known 187Os/188Os values of seawater for the past 70 Ma to provide more qualitative age constraints. Pre‐Maikopian strata from the Perikeshkul locality were found to coincide in 187Os/188Os values with an isotope excursion at the Eocene – Oligocene Transition (EOT), therefore indicating that deposition of Maikopian strata began around the EOT. While values such as this match well with global values, there are several 187Os/188Os values that are not easily explained by global ratios. Intervals with initial 187Os/188Os values that deviate significantly from global 187Os/188Os values suggest periodic basin restriction and the development of anoxia at discrete times as the basin transitioned towards a closed system. High Os abundances outside of expected global values are often coupled with enrichment in detrital elements (Al, Ti, Ga, Sc and La) and changes in basin circulation, suggesting changing basinal conditions and sediment routing dynamics related to the initial uplift of the Greater Caucasus Mountains, changes in sediment provenance, or changing proximity to the sediment source. Through generation of isochron age dates and imprecise Re‐Os age constraints from the Maikop Formation, we gain a better understanding of the timing and nature of the evolution of the South Caspian Basin during this critical time period. Better age constrains will also help to better constrain the wealth of geochemical information already gathered within this petroleum‐rich basin.Wei, S., He, S., Pan, Z., Guo, X., Yang, R., Dong, T., Yang, W., Gao, J., 2019. Models of shale gas storage capacity during burial and uplift: Application to Wufeng-Longmaxi shales in the Fuling shale gas field. Marine and Petroleum Geology 109, 233-244. shales in South China, such as the Upper Ordovician Wufeng (O3w) and Lower Silurian Longmaxi (S1l) shales, have generally experienced a long-term burial and rapid uplift process. The variations of temperature and pressure caused by the complex tectonic movements have significant effects on the shale gas storage capacities. Based on the supercritical Dubinin-Radushkevich (SDR) equation and high-pressure methane (CH4) adsorption experiments, equations to calculate the shale gas storage capacities under geological conditions were established in this work. Using the derived equations, the gas storage capacities in two basic geological processes were modeled, namely, the burial process, which has an increased gas content, and the uplift process, which has a constant gas content. The two basic models were applied to investigate the evolution of the shale gas content of the O3w-S1l shales in the JY 1 Well in the Fuling shale gas field, Sichuan Basin, South China. Geological models of the gas storage capacities of the shales during burial show that the storage capacity of adsorbed gas (SCadsorbed gas) initially rapidly increases and then slowly decreases with the increasing burial depth. The storage capacities of free gas (SCfree gas) and total gas (SCtotal gas) increase with the increasing burial depth. Compared with SCadsorbed gas, SCfree gas significantly increases as the pore pressure increases. Such an obvious difference implies that free gas is the predominant gas form in the initial stage of shale gas production. During uplift, the gas content remains unchanged, resulting in a linear decrease in SCfree gas and a linear increase in SCtotal gas. Nonetheless, SCfree gas during uplift is still higher than SCfree gas during burial at the same burial depth. The modeling of the shale gas content evolution of the O3w-S1l shales in the JY 1 shows that from the maximum burial depth of 6200?m to the present-day burial depth of 2415?m, the free gas content declines by 0.89?m3/t, from 2.30?m3/t to 1.41?m3/t, while the adsorbed gas content only increases by 0.58?m3/t, from 0.47?m3/t to 1.05?m3/t. This difference indicates that only a small amount (0.31?m3/t) of shale gas was lost during the uplift and that most (0.58?m3/t) of the reduced free gas was converted into adsorbed gas. A unique aspect of this study is that we illustrate how adsorbed and free gas are converted when the total gas content remains constant. Moreover, the two basic geological models established in this study can also be applied to other shale gas systems with complex tectonic movements.Weiss, G.M., Roepert, A., Middelburg, J.J., Schouten, S., Sinninghe Damsté, J.S., van der Meer, M.T.J., 2019. Hydrogen isotope fractionation response to salinity and alkalinity in a calcifying strain of Emiliania huxleyi. Organic Geochemistry 134, 62-65. isotope ratios of long-chain alkenones (δ2HC37) correlate with water isotope ratios and salinity, albeit with varying degrees of biological fractionation between alkenones and water. These differences in fractionation are the result of environmental and species related effects, which in some cases have consequences for the magnitude of the δ2HC37 response per unit increase in salinity. Earlier culture experiments have focused on constraining hydrogen isotope fractionation factor α in non-calcifying strains of Emiliania huxleyi. Here we studied isotopic fractionation in a calcifying strain of E. huxleyi and show that although absolute fractionation is different, the response to changes in salinity and alkalinity is similar to those of non-calcifying species. This suggests that calcification does not alter the δ2HC37 response to salinity significantly.Wen, M., Jiang, Z., Zhang, K., Song, Y., Jiang, S., Jia, C., Liu, W., Huang, Y., Liu, T., Xie, X., Sun, Y., Fan, S., Cao, X., Zhu, L., Zhou, C., 2019. Difference analysis of organic matter enrichment mechanisms in Upper Ordovician-Lower Silurian shale from the Yangtze region of southern China and its geological significance in shale gas exploration. Geofluids 2019, Article 9524507. upper Ordovician-lower Silurian shale has always been the main target of marine shale gas exploration in southern China. However, the shale gas content varies greatly across different regions. The organic matter content is one of the most important factors in determining gas content; therefore, determining the enrichment mechanisms of organic matter is an important problem that needs to be solved urgently. In this paper, upper Ordovician-lower Silurian shale samples from the X-1 and Y-1 wells that are located in the southern Sichuan area of the upper Yangtze region and the northwestern Jiangxi area of the lower Yangtze region, respectively, are selected for analysis. Based on the core sample description, well logging data analysis, mineral and elemental composition analysis, silicon isotope analysis, and TOC (total organic carbon) content analysis, the upper Ordovician-lower Silurian shale is studied to quantitatively calculate its content of excess silicon. Subsequently, the results of elemental analysis and silicon isotope analysis are used to determine the origin of excess silicon. Finally, we used U/Th to determine the characteristics of the redox environment and the relationship between excess barium and TOC content to judge paleoproductivity and further studied the mechanism underlying sedimentary organic matter enrichment in the study area. The results show that the excess silicon from the upper Ordovician-lower Silurian shale in the upper Yangtze area is derived from biogenesis. The sedimentary water body is divided into an oxygen-rich upper water layer that has higher paleoproductivity and a strongly reducing lower water that is conducive to the preservation of sedimentary organic matter. Thus, for the upper Ordovician-lower Silurian shale in the upper Yangtze region, exploration should be conducted in the center of the blocks with high TOC contents and strongly reducing water body. However, the excess silicon in the upper Ordovician-lower Silurian shale of the lower Yangtze area originates from hydrothermal activity that can enhance the reducibility of the bottom water and carry nutrients from the crust to improve paleoproductivity and enrich sedimentary organic matter. Therefore, for the upper Ordovician-lower Silurian shale in the lower Yangtze region, exploration should be conducted in the blocks near the junction of the two plates where hydrothermal activity was active.Westbrook, C.K., Curran, H.J., 2019. Chapter 7 - Detailed kinetics of fossil and renewable fuel combustion, in: Faravelli, T., Manenti, F., Ranzi, E. (Eds.), Computer Aided Chemical Engineering. Elsevier, pp. 363-443. kinetic reaction mechanisms for modern combustion systems are described, including historical highlights and key developments from the past 50 years and evolution of kinetic modeling capabilities up to the present. Fundamental chemical principles, including fuel molecular structure, thermochemical limitations, and kinetic reaction pathways are all included in the discussions. Combustion kinetics of fuel classes ranging from alkanes, olefins, alcohols, aromatics, cyclic paraffins, furans and alkyl esters are each described in detail, showing how those classes influence their combustion properties. Models to describe fuels derived from petroleum and from biomass are included, and the similarities and differences in their combustion chemistries are outlined. Basic concepts of chain branching and propagation are illustrated and methods of including chain reaction features in reaction mechanisms are employed and differences in chain reaction characteristics of models for different fuels are discussed. Computational features of these kinetic models are outlined.Wijker, R.S., Sessions, A.L., Fuhrer, T., Phan, M., 2019. 2H/1H variation in microbial lipids is controlled by NADPH metabolism. Proceedings of the National Academy of Sciences 116, 12173-12182.: The deuterium/protium (2H/1H) ratio of microbial lipids varies substantially and appears to be correlated with the mode of metabolism in the host organism, with lipids from chemoautotrophs and photoautotrophs 2H-depleted and heterotrophs in many cases 2H-enriched. Such patterns suggest that the H-isotope ratios of lipids could be used to infer the metabolism of environmental organisms, with applications ranging from Earth history to global carbon cycling and ecology. Here, we learn to understand this information by using metabolic flux analysis. We show that the full range of lipid 2H/1H ratios from a diverse set of aerobic heterotrophs can be quantitatively explained by fluxes through various NADP+-reducing reactions due to differences in their kinetic isotope effects.Abstract: The hydrogen-isotopic compositions (2H/1H ratios) of lipids in microbial heterotrophs are known to vary enormously, by at least 40% (400‰) relative. This is particularly surprising, given that most C-bound H in their lipids appear to derive from the growth medium water, rather than from organic substrates, implying that the isotopic fractionation between lipids and water is itself highly variable. Changes in the lipid/water fractionation are also strongly correlated with the type of energy metabolism operating in the host. Because lipids are well preserved in the geologic record, there is thus significant potential for using lipid 2H/1H ratios to decipher the metabolism of uncultured microorganisms in both modern and ancient ecosystems. But despite over a decade of research, the precise mechanisms underlying this isotopic variability remain unclear. Differences in the kinetic isotope effects (KIEs) accompanying NADP+ reduction by dehydrogenases and transhydrogenases have been hypothesized as a plausible mechanism. However, this relationship has been difficult to prove because multiple oxidoreductases affect the NADPH pool simultaneously. Here, we cultured five diverse aerobic heterotrophs, plus five Escherichia coli mutants, and used metabolic flux analysis to show that 2H/1H fractionations are highly correlated with fluxes through NADP+-reducing and NADPH-balancing reactions. Mass-balance calculations indicate that the full range of 2H/1H variability in the investigated organisms can be quantitatively explained by varying fluxes, i.e., with constant KIEs for each involved oxidoreductase across all species. This proves that lipid 2H/1H ratios of heterotrophic microbes are quantitatively related to central metabolism and provides a foundation for interpreting 2H/1H ratios of environmental lipids and sedimentary hydrocarbons.Wilf, P., Nixon, K.C., Gandolfo, M.A., Cúneo, N.R., 2019. Eocene Fagaceae from Patagonia and Gondwanan legacy in Asian rainforests. Science 364, Article eaaw5139. Fagaceae from Patagonia. The oak family Fagaceae is thought to have its evolutionary origins in northern temperate forests and Southeast Asia. Wilf et al. now report 52-million-year-old fossils from the Southern Hemisphere belonging to the still-living genus Castanopsis. Hypotheses of Fagaceae origins have focused only on the Northern Hemisphere. Ancestral Castanopsis may represent one of numerous paleo-Antarctic plant genera that are found with Castanopsis today in Southeast Asian rainforests.Structured AbstractIntroduction: The flowering plant family Fagaceae includes all oaks, beeches, chestnuts, stone oaks, and allies across 10 genera and >900 species. The family stands out for its very high biomass and its domination of forests from the northern temperate zone to the tropics, especially the Southeast (SE) Asian tropics. Numerous Fagaceae are keystone species that define forest structure, supply substantial food reserves through their famously nutritious fruits, and hold considerable economic and cultural importance. Until now, no living or fossil member of Fagaceae had been found south of the Malay Archipelago, and, accordingly, the Southern Hemisphere has not been seriously considered in the family’s history (the southern beech, Nothofagus, belongs to a separate family).Rationale: We discovered two fossil infructescences of Fagaceae, one mature and one immature with >110 fruits preserved, along with abundant fagaceous leaves in the early Eocene (52-million-year-old) Laguna del Hunco flora of Chubut, southern Argentina. The highly diverse fossil assemblage represents rainforest vegetation from the terminal phase of Gondwana; South America, Antarctica, and Australia had not yet separated, and global warmth allowed floral and faunal interchange among those landmasses. Subsequently, Australia moved northward and eventually collided with SE Asia, initiating new biotic exchanges. The Laguna del Hunco flora reflects these Earth processes in preserving numerous taxa that survive in Australasia and SE Asia, among which several characteristically associate with tropical Fagaceae today and provide rich biogeographic context for the discovery. Examples include Eucalyptus (gum), Gymnostoma (rhu), engelhardioid Juglandaceae (walnut family), Ceratopetalum (coachwood), Lauraceae (laurels), Ripogonum (supplejack), Agathis (kauri), diverse podocarps (yellowwoods), Papuacedrus (a New Guinean cypress), and Todea (king fern).Results: We place the new fossil infructescences in Fagaceae and the living Asian genus Castanopsis, a close relative of the chestnuts, because of their preservation of cupule-fruit complexes with lateral, solitary placement on their spikelike infructescence axes; complete enclosure of the (single) nut; (two) asymmetrical valves; scaly ornamentation; lobed perianth; and three linear styles with unexpanded stigmas. The fossil leaves are also consistent with Castanopsis and in all likelihood represent the same source plant as the infructescences; both occur in the same strata with the just-listed taxa that are local associates of living Castanopsis, especially in New Guinea’s montane rainforests. The new fossils represent a major southern extension of the historical range of Fagaceae, as well as the oldest record, by ~8 million years, of the genus Castanopsis, which has ~120 living species and is dominant at lower montane elevations from New Guinea to the Himalaya and Japan.Conclusion: The fossils’ diagnostic characters, early Eocene age, and occurrence in floral associations markedly similar to today’s all suggest that Castanopsis evolved in the Southern Hemisphere, most likely from an ancestor that had dispersed earlier from North America, and followed the southern route to Asia along with the associated survivor taxa. This discovery substantially increases the known Gondwanan legacy in Asia and Malesia and shows the persistence of the survivor lineages, which tracked their preferred cool-wet rainforest environments through time and space from Gondwana to Asia. The modern analog forests, often located in biodiverse watershed areas, are now threatened by anthropogenic change that is occurring orders of magnitude more rapidly than in the geologic past. The abundant fossil leaves with feeding marks from diverse insects, the large nuts, and the associated flora all indicate that the ancient trees were keystone species in early Eocene “oak-laurel” forests of Patagonia, much like Castanopsis is today in Asia. Subsequently, Castanopsis and many other rainforest taxa appear to have gone extinct in Patagonia with the earliest phases of Antarctic separation and drying regional climates.Williams, J.J., Mills, B.J.W., Lenton, T.M., 2019. A tectonically driven Ediacaran oxygenation event. Nature Communications 10, Article 2690. diversification of complex animal life during the Cambrian Period (541–485.4?Ma) is thought to have been contingent on an oxygenation event sometime during ~850 to 541?Ma in the Neoproterozoic Era. Whilst abundant geochemical evidence indicates repeated intervals of ocean oxygenation during this time, the timing and magnitude of any changes in atmospheric pO2 remain uncertain. Recent work indicates a large increase in the tectonic CO2 degassing rate between the Neoproterozoic and Paleozoic Eras. We use a biogeochemical model to show that this increase in the total carbon and sulphur throughput of the Earth system increased the rate of organic carbon and pyrite sulphur burial and hence atmospheric pO2. Modelled atmospheric pO2 increases by ~50% during the Ediacaran Period (635–541?Ma), reaching ~0.25 of the present atmospheric level (PAL), broadly consistent with the estimated pO2?>?0.1–0.25?PAL requirement of large, mobile and predatory animals during the Cambrian explosion.Worsham, E.A., Burkhardt, C., Budde, G., Fischer-G?dde, M., Kruijer, T.S., Kleine, T., 2019. Distinct evolution of the carbonaceous and non-carbonaceous reservoirs: Insights from Ru, Mo, and W isotopes. Earth and Planetary Science Letters 521, 103-112. work has identified a nucleosynthetic isotope dichotomy between “carbonaceous” (CC) and “non-carbonaceous” (NC) meteorites. Here, we report new Ru isotope data for rare iron meteorite groups belonging to the NC and CC suites. We show that by studying the relative isotopic characteristics of Ru, Mo, and W in iron meteorites, it is possible to constrain the processes leading to the distinct isotope heterogeneities in both reservoirs. In NC meteorites, internally normalized, mass-independent isotope ratios of Mo and Ru are correlated, but those of Mo and W are not. In CC meteorites, Mo and W isotope ratios are correlated, but those of Mo and Ru are not; specifically, Mo isotopic compositions are variable and those of Ru are more restricted. The contrasting behaviors of Ru and W relative to Mo in the two reservoirs likely require processing of the presolar carriers under distinct redox conditions. This provides further evidence that NC and CC meteorites originated from spatially separated reservoirs that evolved under different prevailing conditions.Wu, C., De Visscher, A., Gates, I.D., 2019. On naphthenic acids removal from crude oil and oil sands process-affected water. Fuel 253, 1229-1246. acids (NAs) are widely present in crude oil and oil sands process-affected water (OSPW). NAs in crude oil lead to corrosion problems, promote emulsion formation, decrease oil quality, and deactivate catalysts, making it critical to isolate NAs. Owing to their toxicity and recalcitrance, the existence of NAs induces serious environmental problems and is the primary target for treating OSPW. The current review provides a summary on the properties and adverse effects of NAs and compares existing techniques to separate NAs from crude oil and OSPW. The mechanisms of these approaches as well as limitations are described. Given the environmental impacts of NAs, new, more effective technologies for extracting and treating these materials must be found.Wu, H., Yao, Y., Zhou, Y., Qiu, F., 2019. Analyses of representative elementary volume for coal using X-ray μ-CT and FIB-SEM and its application in permeability predication model. Fuel 254, Article 115563. representative elemental volume (REV) study provides a bridge between macro and micro properties’ research, which is critical for understanding and predicting the heterogeneous properties of a porous media. Permeability, one of the essential properties, dominates the capability of fluid flow in porous media, which is scale dependent and thus one of the most rationale way to predict macro scale permeability is to calculate the permeability at REV. Porosity is the most common parameter to determine REV, however, the porosity based REV works less satisfactory for complex pore system. In this work, we determined the REV based on fractal dimension, which is a fundamental parameter to characterize the complex pore network, and then the relation between fractal dimension and sample size was investigated extensively. We then determined and compared the REV from the porosity and fractal dimension that calculated from various sample sizes. Our results reveal that the relationship between fractal dimension-based REV and porosity-based REV can be classified as four cases, and the most common case is porosity declines if the domain is larger than fractal dimension-based REV size. The relation discussed above can be applied to existing fractal permeability models to predict the permeability at different scales.Wu, J., Zhang, W., Ma, C., Wang, F., Zhou, X., Chung, K.H., Hou, D., Zhang, Y., Shi, Q., 2019. Isolation and characterization of sulfur compounds in a lacustrine crude oil. Fuel 253, 1482-1489. high-sulfur (4.69?wt%) crude oil was discovered in the China Bohai Bay Basin which is known to contain low sulfur crude oil. The composition of this high sulfur crude oil and its geological origin are unknown. In this study, thiophenic and sulfidic sulfur compounds were isolated from the crude oil by methylation/demethylation and characterized using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and gas chromatography-mass spectrometry (GC–MS). Relatively high abundance of sulfur compounds with 30 carbon atoms and 5–7 double bond equivalence (DBE), which were assigned to sulfurated steranes with thiophene or tetrahydrothiophene moieties. Some of these compounds have not been reported in fossil fuels. In addition to commonly found sulfur compounds in petroleum feedstock, such as benzothiophenes and dibenzothiophenes, other structural sulfur compound types were detected: long-chain 2,5-di-n-alkylthiolanes, 2,5-di-n-alkylthianes, bicyclic terpenoid sulfides, isoprenoid thiophenes, and isoprenoid benzothiophenes. The presence of abundant biomarker sulfur compounds suggests that the sulfuration of the high sulfur crude oil was occurred in the early diagenesis stage instead of a thermochemical sulphate reduction (TSR) process.Wu, P., Hou, D., Gan, J., Ding, W., Liang, G., Li, X., Feng, X., Wang, H., 2019. Developmental model of Oligocene source rock in the eastern deep-water area of Qiongdongnan Basin. Acta Sedimentologica Sinica 37, 633-647. eastern deep-water area in Qiongdongnan Basin (QDNB) is in the early stages of exploration stage, and some drilling samples collected from this area are severely contaminated by the oil-based mud. Little research regarding the organic geochemistry of the Oligocene source rock deposited in the marine or transitional environments in this area has been performed so far. In this paper, effective oil-cleaning experiments and organic geochemical analysis were carried out for Oligocene mudstone cuttings contaminated by oil-based mud in the eastern deep-water area, coupled with organic geochemical and petrological data of mudstone cuttings in the shallow-water area, and the geochemical characteristics, paleoenvironment, controlling factors, and developmental model of Oligocene source rocks from different sedimentary facies in the eastern QDNB were analyzed. Two distinct models of delta front source rock and neritic source rock were developed according to their organic matter sources and geochemical characteristics. Transitional delta front source rock has fair to good quality and gas-prone type organic matter, and its biomarkers are characterized by pristane/phytane bigger than 3, (nC21+nC22/nC28+nC29) smaller than 1.2, high ratios of oleanane/C30 hopane, T-bicadinane/C30 hopane, low ratios of C23 tricyclic terpane/C30 hopane, C27 sterane/C29 sterane, gammacerane/C30 hopane, and C35 homohopane/C34 homohopane. There exists a strong correlation between total organic carbon (TOC) and total sulfur, which means water in the delta front subface was of oxidation fresh or brackish condition. Organic matter abundance in the delta front source rock is heavily controlled by terrigenous organic matter input. Neritic source rock has fair quality and an organic matter type prone to generating both oil and gas, and the biomarkers are characterized by pristane/phytane smaller than 3, (nC21+nC22/nC28+nC29) bigger than 1.5, low ratios of oleanane/C30 hopane, T-bicadinane/C30 hopane, high ratios of C23 tricyclic terpane/C30 hopane, C27sterane/C29 sterane, gammacerane/C30 hopane, and C35 homohopane/C34 homohopane. However, there exists no correlation between TOC and total sulfur, which means water in the neritic face was of the weak oxidation brackish or saline condition. Organic matter abundance in the neritic source rock is controlled by aquatic organic matter input and influenced by the water environment. Littoral source rock is generally of poor to medium quality and is seldom influenced by organic matter sources and water condition, and the source rock depositional model is considered to be a destructive model.Wu, S., Zhai, X., Yang, Z., Bale, H., Hong, Y., Cui, J., Pan, S., Lin, S., 2019. Characterization of fracture formation in organic-rich shales - An experimental and real time study of the Permian Lucaogou Formation, Junggar Basin, northwestern China. Marine and Petroleum Geology 107, 397-406. fracturing in horizontal wells represents a principal technology in the effective economic development of unconventional shale oil and gas reservoirs. However, the number of intervals that were effectively fractured by this technology only account for 20%–50% of the total designed sections. Fracture development characteristics and the factors controlling artificial fracture growth in organic-rich shale require detailed evaluation; this cannot be accomplished using microseismic monitoring technology or well-log interpretation. In this paper, formation processes of micro- and nano-scale fractures in the organic-rich shales of the Lucaogou Formation, Jimusaer Sag, Junggar Basin, northwestern China, were presented. The study focused on the application of in situ, nano-scale CT imaging technology, in combination with rock mechanics analysis. Results allowed the visualization of fracture growth in the shale reservoirs, and revealed the influence of organic matter, mineral composition, and pore structure on the formation and distribution of artificial fractures. A three-dimensional dynamic growth model of micro- and nano-scale fractures in organic-rich shale was established. Data revealed that the Lucaogou Formation shale contained dolomite and illite intragranular pores, with a low abundance of organic pores; pore size ranged between 200?nm and 2?μm. Micro- and nano-size fractures were observed. The development of artificial fractures was positively correlated with the loading stress. The initiation stress of new generated fractures was 475?mN, which could break up dolomite, albite, K-feldspar, and the original pore system as well. The original pore system was generally conducive to fracture extension and expansion. As loading stress increased from 50 mN to 515?mN, the sample extension increased from 2 μm to 14?μm, and artificial fracture width increased from 0.3 μm to 10?μm. The total porosity increased from 5.45% to 8.35%, and volume growth rate reached 53.2%. These findings provide valuable insights into the study of fracture growth in organic-rich shales, and have implications for the design of hydro-fracturing in organic-rich shales.Wu, Y., Tahmasebi, P., Lin, C., Ren, L., Dong, C., 2019. Multiscale modeling of shale samples based on low- and high-resolution images. Marine and Petroleum Geology 109, 9-21. modeling of shale samples is very crucial for evaluating and predicting the physical properties. However, obtaining large-scale and high-resolution images of shales using a single imaging tool such as X-ray computed tomography or scanning electron microscopy machine might not be plausible as there is always a trade-off between the resolution and field-of-view. On the other hand, relying on small-scale images may jeopardize the accuracy of porous media modeling. One solution scheme for addressing these issues is to fuse the spatial information from the multiscale and multiresolution images into a multiscale high-resolution image. As such, a novel multiscale modeling algorithm based on template matching for complex rocks is proposed in this study. This algorithm can fuse multiscale and multiresolution structural patterns from the images with different scales, resolution, and phases into one single image. The accuracy of the presented algorithm is tested using two heterogeneous shale samples and the results are compared with the actual large and high-resolution images. We found that the algorithm can generate an accurate image after comparing the geometrical properties of pore systems, correlation functions, and image similarity indicators of the generated image and reference image.Wu, Y., Ya, M., Chen, H., Li, Y., Guo, W., Wang, X., 2019. Distribution and isotopic composition of sedimentary black carbon in a subtropical estuarine-coastal region of the western Taiwan Strait: Implications for tracing anthropogenic inputs. Science of The Total Environment 684, 509-518. and coastal margins are strongly influenced by anthropogenic inputs. To trace anthropogenic inputs to the subtropical Jiulong River Estuary (JRE) and the adjacent western Taiwan Strait (WTS), black carbon (BC) and its stable carbon isotope composition (δ13СBC) in surface sediments were investigated as an indicator of human activities. The concentrations of sedimentary BC were measured by an emerging method of thermal/optical reflectance with wet-chemical treatment (BCTOR, including char and soot), and the conventional method of chemothermal oxidation (BCCTO, related to the soot fraction) was also used to determine BCCTO concentrations and δ13СBC compositions. In the JRE and adjacent WTS, the concentrations of BCTOR (0.77 to 3.79?mg?g?1) were higher than those of BCCTO (0.55 to 2.46?mg?g?1), and both were similar to the moderate ranges obtained in other coastal sediments around the world. The small offsets between δ13СTOC and δ13СBC and the relatively low char/soot ratios revealed that fossil fuel combustion-derived contributions were likely more significant compared with inputs from biomass burning. The decreasing BC concentrations and increasing δ13СBC values with increasing distance from the JRE towards the adjacent WTS, indicates the decline of land-based anthropogenic inputs through fluvial transport. Furthermore, the differences in BC/TOC and char/soot values between the southern and northern WTS, indicated an effective preferential dispersal of the fluvial BC to the southern coast. The estimation for mass inventories of sedimentary BC in the coastal WTS showed that direct riverine discharge from the JRE was nearly equivalent to atmospheric deposition, and both of them contributed half of the sedimentary BC sink. To balance the sedimentary BC budget in the coastal WTS, long-range alongshore sediment transport driven by the Fujian-Zhejiang coastal current containing Yangtze River derived materials (indirect riverine discharge) could be another significant input pathway to contribute sedimentary BC.Xiao, F., Huang, D., Zhang, B., Tang, D., Ran, Q., Tang, Q., Yin, H., 2019. Geochemical characteristics and geological significance of natural gas in Jurassic Shaximiao Formation, Sichuan Basin. Acta Petrolei Sinica 40, 568-576. natural gas in Jurassic Shaximao Formation of Sichuan Basin has the advantages of shallow burial, excellent quality, low development cost, short period and quick response. As an important practical field of efficient development under low oil prices, it has attracted much attention from exploration developers for a long term. Through analyzing the natural gas geochemical experimental data such as natural gas components and natural gas carbon isotopes of the Jurassic Shaximiao Formation, it is revealed that natural gas from the Jurassic Shaximiao Formation in the western Sichuan Basin originates from coal source rocks of the underlying Xujiahe Formation. The natural gas of Shaximiao Formation in the northern part of central Sichuan Basin is sourced from the underlying Jurassic source rocks, and the natural gas of the Jurassic Shaximiao Formation in the northeast of Sichuan Basin is from coal source rocks of the underlying Xujiahe Formation and the Jurassic lake source rocks. In combination with gas source analysis results, structural background as well as the current exploration and development degree of tight gas in the basin, the general policy of "deepening and abandoning exploration and development" is clarified for the Jurassic shallow tight gas from Shaximiao Formation towards the northwestern, north-central and northeastern regions of Sichuan Basin. Of these, in the northern section of the front edge of Longmen Mountain in the western Sichuan Basin, Jinhua, Qiulin, Gongshanmiao and Yingshan in the northern part of central Sichuan Basin as well as the Wubaochang and Duduhe areas on the front edge of Dabashan in the northeastern Sichuan Basin have good accumulation conditions, which is a key exploration area of shallow tight gas.Xie, Q.-F., Cai, Y.-F., Dong, Y.-P., Zhai, M.-G., Li, D.-P., 2019. Geochemical characteristics of the Permian marine mudstone and constraints on its provenance and paleoenvironment in the Fenghai area, Fujian Province, southeastern China. Petroleum Science 16, 527-540. marine strata have gradually become a research focus in the world. The marine strata of the Late Permian Dalong Formation (P3d) in the Fenghai area, Fujian Province, have become more and more important as their geochemical characteristics record important geological information and are a good indicator for recovering and reconstructing the paleo-sedimentary environments and tectonic attributes. The major elements, trace elements and rare earth elements were analyzed by XRF and ICP-MS, respectively. Based on the results of detailed field geological surveys, profile measurements as well as typical sample collection, the tectonic setting and provenance of Permian marine mudstone were comprehensively discussed. The results showed that the Dalong Formation (P3d) was deposited in an active continental margin tectonic environment as revealed by the relation between Fe2O3?+?MgO and TiO2 and Al2O3/SiO2. The fingerprint characteristics of Mn, Fe, Co, Ni and REE and the ratio of U/Th, V/Cr, Sr/Ba, (La/Yb)N and V/(V?+?Ni) indicated that the sedimentary provenance was mainly derived from potassium feldspar, followed by muscovite. Sedimentary water bodies showed a gradually decreasing depositional rate trend, water depth gradually shallowing and paleo-salinity and productivity gradually increasing. Moreover, since transient delamination occurred during sedimentary processes, sedimentary water bodies showed obvious neritic characteristics. It was consistent with the results revealed by lithological and geochemical characteristics. Calcareous mudstone and siltstone transitioned into fine sandstone from bottom to top, indicating paleo-water bodies became shallow. The research results provided good reference and guidance for understanding Permian paleo-sedimentary environments and tectonic attributes of the Yong’an area, Fujian Province, southeastern China.Xu, C., Chin, W.-C., Lin, P., Chen, H., Chiu, M.-H., Waggoner, D.C., Xing, W., Sun, L., Schwehr, K.A., Hatcher, P.G., Quigg, A., Santschi, P.H., 2019. Comparison of microgels, extracellular polymeric substances (EPS) and transparent exopolymeric particles (TEP) determined in seawater with and without oil. Marine Chemistry 215, 103667. polymeric substances (EPS), produced by microorganisms, are implicated for greatly influencing the fate of environmental contaminants, including oil. Transparent exopolymeric particles (TEP) are gel-like acidic polysaccharide particles that can be stained with Alcian blue, whereas Coomassie stainable particles (CSP) contain proteins and are stained with Coomassie brilliant blue. Marine microgels are reversibly formed from EPS. These terms are often used interchangeably, but they have rarely been measured simultaneously. Mesocosm and bottle experiments provided an opportunity to compare EPS, TEP, CSP and microgels in a water-accommodated fraction (WAF) of oil and seawater (control). Our results reveal that the biopolymers making up EPS, TEP and CSP consisted primarily of polysaccharides and proteins, mostly likely as proteoglycans and glycoproteins. Significant correlations were found between concentrations of TEP-C vs particulate organic carbon (POC), TEP-C vs particulate organic nitrogen (PON), TEP vs EPS, TEP vs CSP, TEP vs carbohydrates, proteins, CSP and carbohydrates, CSP vs proteins, and carbohydrates vs proteins. Chemical analysis of whole particles and colloids yielded both protein and polysaccharides concentrations higher than those in EDTA extraction, thus providing an upper limit of actual EPS contents in the particulate phase. The EPS that was electrostatically held onto particle surfaces (extractable by 1% EDTA) accounted for a minor (~4%) yet relatively constant proportion of TEP. Overall, the concentrations of the three terms ranked in the order of [gels]?>?[TEP]?>?[particulate EPS] in the water. Lastly, spectrophotometric methods have limitations in identifying complex or refractory polysaccharides, as evidenced by the comparison between NMR-quantified EPS and the total EPS determined by spectrophotometric methods. This study is the first time these terms were compared in the same sample. They provide useful information when reviewing historical TEP, CSP, EPS data collected field- and laboratory-studies, and provide linkages between them. In addition, they also demonstrate that they could provide complementary information relevant to ecosystem and flux studies.Xu, H., Zhou, W., Hu, Q., Xia, X., Zhang, C., Zhang, H., 2019. Fluid distribution and gas adsorption behaviors in over-mature shales in southern China. Marine and Petroleum Geology 109, 223-232. better understand the mechanism of hydrocarbon accumulation and fluid migration in Chinese shales, several samples from two leading marine shales (Longmaxi and Niutitang) were collected for geochemical and mineral analysis, the characterization of pore structure, preliminary studies on fluid flow, and the distribution and investigation of different methane adsorption behaviors. Firstly, the Longmaxi and Niutitang marine shales were found to be in an over-matured stage and dry gas window. Pore structures and connectivity were characterized by field emission - scanning electron microscopy (FE-SEM). The SEM images showed that the micro-fracture, interparticle pores, and organic pores had better connectivity than intraparticle pores. Results from contact angles indicated that the Longmaxi and Niutitang shales tended to have higher affinities for oil rather than for water. The connectivity of pores, distribution of fluids (water and gas) and fluid flow behaviors in the over-matured shale were analyzed using spontaneous imbibition (SI) and tracer diffusion tests. It was found the tracer fluids flow in the way of network flow inside of shale matrix. The connected pore network may be the main path for fluid migration in shale. Additionally, a gravimetric isothermal adsorption experiment was applied to assess methane adsorption capacity in shale. Shale samples with higher total organic carbon (TOC) contents had higher methane adsorption capacities. Organic matter (including kerogen and bitumen), had much greater adsorption capabilities than inorganic minerals (quartz, clay, and others). Finally, the fluid distribution patterns in over-matured marine shale were studied. Shale gas was originally generated in organic matter and then migrated out through connected pores, under differential pressure, between internal and external organic matter hydrocarbon generation areas. These hydrocarbons replaced the water in the pores. Therefore, shale gas may adsorb in organic pores and is freely stored in connected inorganic pores, with bound water, whereas isolated pores are saturated with water. Two different adsorption patterns on mineral surfaces (organic matters and inorganic minerals) were established to explain the different shale gas adsorption behaviors in organic pores and connected pores, with bound water.Xu, X., Zhang, X., Carrillo, G., Zhong, Y., Kan, H., Zhang, B., 2019. A systematic assessment of carcinogenicity of chemicals in hydraulic-fracturing fluids and flowback water. Environmental Pollution 251, 128-136.: Thousands of chemicals exist in hydraulic-fracturing (HF) fluids and wastewater from unconventional oil gas development. The carcinogenicity of these chemicals in HF fluids and wastewater has never been systematically evaluated.Objectives: In this study, we assessed the carcinogenicity of 1,173 HF-related chemicals in the HF chemical data from the US Environmental Protection Agency (EPA).Methods: We linked the HF chemical data with the agent classification data from the International Agency for Research on Cancer (IARC) at the World Health Organization (WHO) (N?=?998 chemicals) to evaluate human carcinogenic risk of the chemicals and with the Carcinogenic Potency Database (CPDB) from Toxnet (N?=?1,534 chemicals) to evaluate potential carcinogenicity of the chemicals.Results: The Chemical Abstract Service Registry Numbers (CASRNs) for chemicals were used for data linkage. Among 1,173 chemicals, 1,039 were identified only in HF fluids, 97 only in wastewater, and 37 in both. Compared with IARC, we found information of 104 chemicals, and 48 of them may have potentially carcinogenic risk to human, among which 14 are definitely carcinogenic, 7 probably carcinogenic, and 27 possibly carcinogenic. Using the CPDB data, it suggests that 66 chemicals are potentially carcinogenic based on rats and mouse models.Conclusions: Conclusions Our evaluation suggests that exposure to some chemicals in HF fluids and wastewater may increase cancer risk, and the identified chemicals could be selected as the priority list for drinking water exposure assessment or cancer-related health studies.Xue, J., Li, C., He, Q., 2019. Modeling of wax and asphaltene precipitation in crude oils using four-phase equilibrium. Fluid Phase Equilibria 497, 122-132. thermodynamic model is developed for predicting wax and asphaltene precipitation in crude oil mixtures with up to four phases, i.e. vapor, liquid, wax-rich and asphaltene-rich. The model adopts the experimentally supported hypothesis that asphaltenes precipitate before waxes with decreasing temperature and aggregate as the nucleus of wax crystals. The simplified perturbed chain statistical associating fluid theory (sPC-SAFT) equation of states (EOS) is applied in order to describe phase behavior in crude oils. In this research, a characterization method is proposed for mixtures containing asphaltenes and waxes using the sPC-SAFT EOS. And a correlation is modified for prediction of binary interaction parameter for the sPC-SAFT based on measured binary solid solubilities of twelve n-alkane mixtures. The universal quasi chemical activity coefficient (UNIQUAC) model is used to account for the non-ideality of the wax-rich phase. It is shown that the cloud point and the amount of wax and asphaltene precipitates obtained in the proposed model have an excellent agreement with the experimental data.Yamaguchi, T., Sato, M., Hashihama, F., Ehama, M., Shiozaki, T., Takahashi, K., Furuya, K., 2019. Basin-scale variations in labile dissolved phosphoric monoesters and diesters in the central north Pacific Ocean. Journal of Geophysical Research: Oceans 124, 3058-3072.: Labile dissolved phosphoric esters act as important phosphorus sources for microorganisms in the low‐phosphate oligotrophic ocean. Despite the significant role of labile dissolved phosphoric esters, previous studies have only focused on phosphoric monoesters, and the spatial distribution and dynamics of phosphoric ester species, including diesters, remain unclear. Thus, we aimed to elucidate basin‐scale variations in both monoesters and diesters and their role on microorganisms particularly in terms of diazotrophs. This is the first study to report the concentrations of these phosphoric esters in low‐ to middle‐latitudinal areas of the central North Pacific Ocean, concurrent with their hydrolysis rates. Hydrolysable monoester and diester concentrations ranged from undetectable levels to 40 nM, and their sum accounted for <11% of dissolved organic phosphorus on average. While monoester concentrations were significantly low in the low phosphate (<100 nM) region, there was no obvious trend between diester and phosphate concentrations. Monoesterase and diesterase activities showed significantly high values under low phosphate conditions when normalized by chlorophyll a concentrations. This indicated that both esters served as alternative phosphorus sources for microbial communities including phytoplankton. Diester concentrations and diesterase activities were positively correlated with nitrogen fixation activities, whereas such relationships were not observed for monoester concentrations and monoesterase activities. Thus, our results suggest that diesters have high affinity to diazotrophs compared with monoesters, which are utilized by a broad spectrum of microorganisms.Plain Language Summary: Phosphate, the most commonly utilized form of phosphorus, is scarce in some oceanic regions, such as subtropical regions. In such regions, microbes are known to utilize phosphoric esters instead, because some esters are easily hydrolyzed. However, limited quantitative data on these hydrolysable esters are available to date, and basic information is still lacking. Thus, we examined the concentrations and hydrolysis rates of representative hydrolysable esters (monoesters and diesters) in the central North Pacific Ocean. The results showed that both ester concentrations varied among a narrow and low range (under detection limit to 40 nM), although the distribution patterns were different between monoesters and diesters. This new information will contribute to a better understanding of why and how they are distributed in such a manner. We also found an interesting link between diesters and nitrogen fixation, a globally important process in marine ecosystems, suggesting that diesters play a significant role on nitrogen fixing organisms. Therefore, our study indicates that diesters may have a greater significance in the ocean than previously thought.Yan, G., Xu, Y.-H., Liu, Y., Tang, P.-H., Liu, W.-B., 2019. Evolution and organic geochemical significance of bicyclic sesquiterpanes in pyrolysis simulation experiments on immature organic-rich mudstone. Petroleum Science 16, 502-512.? are ubiquitous components of crude oils and ancient sediments. Liquid saturated hydrocarbons from simulated pyrolysis experiments on immature organic-rich mudstone collected from the Lower Cretaceous Hesigewula Sag were analyzed by gas chromatography–mass spectrometry (GC–MS). C14 bicyclic sesquiterpanes, namely, 8β(H)-drimane, 8β(H)-homodrimane, and 8α(H)-homodrimane were detected and identified on basis of their diagnostic fragment ions (m/z 123, 179, 193, and 207), and previously published mass spectra data, and these bicyclic sesquiterpanes presented relatively regular characteristics in their thermal evolution. The ratios 8β(H)-drimane/8β(H)-homodrimane, 8β(H)-homodrimane/8α(H)-homodrimane, and 8β(H)-drimane/8α(H)-homodrimane all show a clear upward trend with increasing temperature below the temperature turning point. Thus, all these ratios can be used as evolution indexes of source rocks in the immature–low-maturity stage. However, the last two ratios may be more suitable than the first ratio as valid parameters for measuring the extent of thermal evolution of organic matter in the immature–low-maturity stage because their change amplitude with increasing temperature is more obvious.Yang, H., Wang, D., Gao, Y., Wang, J., Li, Z., Qian, G., 2019. Neogene natural gas genesis and hydrocarbon differential enrichment mechanism in the basin marginal sag of Bohai Bay Basin: a case study of the eastern subsag of Huanghekou sag. Acta Petrolei Sinica 40, 509-518. was previously considered that the basin marginal sag had shallow buried depth, small area and limited hydrocarbon generation capacity, thus attracting little attention. Now the basin marginal sag has become the key hotspot of oil and gas exploration in the Bohai Bay Basin, and the hydrocarbon accumulation mechanisms and enrichment laws needs to be further explored. Based on the geochemical data, the Neogene hydrocarbon accumulation mechanism and distribution laws of the eastern subsag in Huanghekou sag were systematically studied. The results show that the Neogene crude oil and natural gas of the eastern subsag in Huanghekou sag have different sources and geneses; the crude oil originated from source rocks in the Paleogene Members 3 and 4 of Shahejie Formation, while the natural gas was the secondary biogas resulting from crude oil degradation in Neogene reservoirs. The formation of crude oil was earlier than that of natural gas, while gas reservoir is shallower than that of oil reservoir. However, the specific distribution of gas and oil reservoirs was controlled by the sealing capacities of three sets of regional caps in the mid-upper Neogene Guantao Formation, the mid-lower Minghuazhen Formation and the upper bottom of Minghuazhen Formation, showing an overall distribution law of "rich oil in the south, rich gas in the north; rich oil in the west, rich gas in the east; rich oil in the lower part, rich gas in the upper part".Yang, J., Huang, B., 2019. Origin and migration model of natural gas in L gas field, eastern slope of Yinggehai Sag, China. Petroleum Exploration and Development 46, 471-481. on the chemical and stable carbon isotopic composition of natural gas and light hydrocarbons, along with regional geological data, the genetic type, origin and migration of natural gases in the L lithologic gas field, the eastern slope of Yinggehai Sag were investigated. The results show that these gases have a considerable variation in chemical composition, with 33.6%–91.5% hydrocarbon, 0.5%–62.2% CO2, and dryness coefficients ranging from 0.94 to 0.99. The alkane gases are characterized by δ13C1 values of –40.71‰––27.40‰, δ13C2 values of –27.27‰––20.26‰, and the isoparaffin contents accounting for 55%–73% of the total C5–C7 light hydrocarbons. These data indicate that the natural gases belong to the coal-type gas and are mainly derived from the Miocene terrigenous organic-rich source rocks. When the CO2 contents are greater than 10%, the δ13CCO2 values are –9.04‰ to – 0.95‰ and the associated helium has a 3He/4He value of 7.78×10–8, suggesting that the CO2 here is crustal origin and inorganic and mainly sourced from the thermal decomposition of calcareous mudstone and carbonate in deep strata. The gas migrated in three ways, i.e., migration of gas from the Miocene source rock to the reservoirs nearby; vertical migration of highly mature gas from deeper Meishan and Sanya Formations source rock through concealed faults; and lateral migration along permeable sandbodies. The relatively large pressure difference between the “source” and “reservoir” is the key driving force for the vertical and lateral migration of gas. Short-distance migration and effective “source – reservoir” match control the gas distribution.Yang, R., Hu, Q., Yi, J., Zhang, B., He, S., Guo, X., Hou, Y., Dong, T., 2019. The effects of mineral composition, TOC content and pore structure on spontaneous imbibition in Lower Jurassic Dongyuemiao shale reservoirs. Marine and Petroleum Geology 109, 268-278. imbibition (SI) is a capillary-force controlled process, which has been identified as one of the most important mechanisms to affect hydrocarbon recovery from unconventional shale reservoirs. In this work, we focus on the mineral composition, total organic carbon (TOC) content, pore geometry characteristics and fluid imbibition behaviors of the terrestrial Lower Jurassic Dongyuemiao shale reservoirs. The pore morphology is directly imaged and observed via field emission-scanning electronic microscope (FE-SEM). Nitrogen (N2) physisorption and mercury intrusion porosimetry (MIP) are applied to investigate the pore geometry characteristics. The slopes of deionized (DI) water/n-decane imbibition from fluid imbibition experiments are used to evaluate the pore connectivity characteristics of hydrophilic and hydrophobic pore spaces, respectively. Finally, the relationships between shale dominant mineral composition, TOC content and pore structure parameters on fluid imbibition behavior are discussed. Experimental results show that clay and quartz are the two dominant minerals in the Dongyuemiao shales. In this study, four typical lithofacies are identified in the Dongyuemiao shales, including laminated or massive mudstone, silty mudstone, shell limestone and argillaceous siltstone. Organic matter (OM) pores and interP pores are the dominant pore types in the Dongyuemiao shales, and most of the pores with sizes smaller than 50?nm. The imbibition slopes of n-decane are generally higher than that of DI water, indicating better pore connectivity of hydrophobic pores. Due to protection by quartz grains, samples with higher abundances of quartz are beneficial for forming a connected pathway for DI water migration, resulting in a better-connected water-wet pathway. The hydrophobic and hydrophilic pore networks in samples with higher TOC content are better connected, which are speculated to be related to the high volume of connected organic matter in shale matrix. Positive correlations occur between porosity/pore volume and fluid (including DI water and n-decane) imbibition slopes, suggesting that the connectivity of pore networks become better as porosity and pore volume increase, regardless of whether the pores are hydrophobic or hydrophilic.Yang, W., Zuo, R., Chen, D., Jiang, Z., Guo, L., Liu, Z., Chen, R., Zhang, Y., Zhang, Z., Song, Y., Luo, Q., Wang, Q., Wang, J., Chen, L., Li, Y., Zhang, C., 2019. Climate and tectonic-driven deposition of sandwiched continental shale units: New insights from petrology, geochemistry, and integrated provenance analyses (the western Sichuan subsiding Basin, Southwest China). International Journal of Coal Geology 211, 103227. the depositional setting efficiently governs the characteristic sandwiched continental shale units remains uncertain, which restricts an integrated assessment of organic-rich fluvio-lacustrine shale reservoirs, and accurate estimation of potential natural gas resources. Here, we present new results from petrological observations, element geochemical fingerprinting, and integrated analyses of heavy mineral, basinal subsidence history, and sandstone / stratum ratio on typical and terrigenous sandwiched-like depositional systems of the targeted Upper Triassic Xujiahe Formation in the western Sichuan subsiding Bain, Southwest China. In view of the representative and environment-sensitive indices, we suggest that passive continental margin and continental island arc dominated by granite to granodiorite source are the major tectonic settings of the provenance, and both a more warm-humid climate characterized by intensified chemical weathering conditions and a calm tectonically quiescent setting are identified as two major drivers forcing the accumulation and preservation of organic matter in organic-rich continental shale units. Finally, a comprehensive depositional model is established for providing new insights into the linkage between palaeoclimatic conditions, tectonic pulses and terrigenous clastic sedimentation. Both the cyclic palaeoclimate fluctuations and episodic tectonic activities are believed to have exerted a very considerable force on development of the unique sandwiched-like stratigraphic framework, and the coupling interactions between the tectono-climatic evolution and fine-grained sedimentation are thus also stressed.Yang, Y., Huang, D., 2019. Geological characteristics and new understandings of exploration and development of Jurassic lacustrine shale oil and gas in the Sichuan Basin. Natural Gas Industry 39, 22-33. and gas exploration has been successively developed in the lacustrine shale of the Da'anzhai Member of the Jurassic Ziliujin Fm in the Sichuan Basin by many companies at home and abroad such as PetroChina, Sinopec, Shell, etc. However, there are still doubts about why the proved reserves is out of proportion to the rich hydrocarbon resources and the oil and gas yield rates unmatched with the tight petrophysical properties of the reservoirs in this study area. In view of this, in combination with cores, outcrops, drilling, logging, oil test, geochemical analysis data, we made research on geological characteristics and exploration targets of shale oil & gas in this study area. The following findings were obtained. (1) Three sets of quality shale layers including the Dongyuemiao, Da'anzhai members in the Ziliujing Fm, and the upper member of Lianggaoshan Fm, are featured by source–reservoir integration and tight connection, among which the Da'anzhai member is typical of well-developed shale reservoirs. (2) The Da'anzhai shale reservoir has such characteristics as high content of organic matters and brittle minerals, moderate thermal evolution degree, strong hydrocarbon generation capacity, good petrophysical behaviors, favorable storage property, good source–reservoir relationship, great thickness, good hydrocarbon-bearing property, and so on. (3) Many test data in detail from a successful well in the Da'anzhai member such as organic matter content, pyrolytic parameter, petrophysical properties, etc., demonstrated that oil and gas supply is quite enough for both shale and crustal limestone reservoirs there, and the former ones are so much stronger that the Da'anzhai is the main target of effective utilization of lacustrine shale oil and gas reserves in the Jurassic strata. (4) Based upon the current new understandings, technical measures for unconventional hydrocarbon resources like horizontal wells and volumetric fracturing, should be adopted to explore shale oil and gas resources in this study area, which will be hopefully succeeded. In conclusion, this paper provides a theoretic and technical support for new discoveries and effective utilization of reserves in this study area.Yang, Z., Li, X., Li, D., Yin, T., Zhang, P., Dong, Z., Lin, M., Zhang, J., 2019. New method based on CO2-switchable wormlike micelles for controlling CO2 breakthrough in a tight fractured oil reservoir. Energy & Fuels 33, 4806-4815. widely used for enhanced oil recovery (EOR) as a result of its high ability of washing oil and favorable injectivity, especially for a tight oil reservoir. During the EOR process, the oil recovery is significantly affected by gas channeling and the sweep efficiency of CO2 is limited. Herein, we report CO-switchable smart wormlike micelles (WLMs) based on sodium dodecyl sulfate (SDS) and diethylenetriamine (DETA) to prevent gas channeling of CO2 in a tight fractured oil reservoir. The proof to the microstructure, formation mechanism, and plugging performance of CO2-switchable WLMs was studied by cryo-transmission electron microscopy, dynamic light scattering, nuclear magnetic resonance, rheology, and plugging property measurement. The results indicated that the system can be reversibly circulated between spherical micelles and wormlike micelles by repeatedly bubbling and removing CO2. When CO2 is introduced to the solution, part of DETA molecules is protonated and two SDS molecules are “bridged” to form a pseudo-gemini surfactant by non-covalent electrostatic attraction, behaving as a high-viscosity fluid. Upon removal of CO2, the protonated DETA molecules return to the original state, causing the pseudo-gemini structure to be destroyed and the viscosity of the fluid to be recovered. Moreover, on the basis of the results of the plugging property measurement, the solution presents conspicuous injection and plugging performance. This WLM viscoelastic fluid might have potential application in the enhancement of CO2 flooding in a tight fracture reservoir.Yang, Z., Shao, D., Mei, Y., Yang, W., Wang, Y., Sun, L., Xie, Z., 2019. The controlling mechanism of mid- to late Holocene carbon isotopic variations of Tridacnidae in the South China Sea. Marine Geology 415, 105958. carbon isotopic fractionation process in biogenic carbonate is very complex, and the mechanism for seasonal and long-term variations in biogenic carbonate δ13C remains a matter of debate. In this study, 5 Tridacnidae samples were collected from the South China Sea and analyzed in detail to study seasonal variations. The high-resolution δ13C records exhibited cyclic variations, likely related to seasonality in environmental parameters (e.g., Chl-a concentration, salinity, SST, rainfall). 57 Tridacnidae were collected and analyzed to study the millennium-scale changes of Tridacnidae δ13C during the mid- to late Holocene and the controlling mechanism. The Tridacnidae δ13C over the period 500–5500 BP is statistically significantly correlated with solar activity (TSI and sunspot number), likely attributed to the presence of symbiotic zooxanthellae within Tridacnidae's mantle lobes. Solar activity could significantly affect the metabolic activity of zooxanthellae, Tridacnidae's microenvironment, and thus Tridacnidae's δ13C composition. The decoupling between the Tridacnidae δ13C and solar activity over the past 200?years is most likely due to increased amount of anthropogenic CO2 and the oceanic δ13C Suess effect. This study improves our understanding about the seasonal and long-term variations of δ13C in Tridacnidae.Yang, Z., Zou, C., Hou, L., Wu, S., Lin, S., Luo, X., Zhang, L., Zhao, Z., Cui, J., Pan, S., 2019. Division of fine-grained rocks and selection of “sweet sections” in the oldest continental shale in China: Taking the coexisting combination of tight and shale oil in the Permian Junggar Basin. Marine and Petroleum Geology 109, 339-348. Permian formation in the Junggar Basin contains the oldest continental shale in China and has abundant petroleum resources. The lithofacies and lithology of the shale strata in the Lucaogou Formation, which are characterized by two sets of coexisting combinations of tight oil and shale oil in the Jimsar Sag, eastern Junggar Basin, are studied via experiments to explore their petrophysics, geochemistry, reservoir pores, and oil-bearing properties. The results show that (1) the Lucaogou Formation in the Jimsar Sag consists of shallow-deep lacustrine sediments and can be divided into six stratigraphic units vertically; 2) fine-grained sediments in the sag composed of shale, dolomite, and siltstone can be specifically divided into carbonate mudstone (CM), siliceous mudstone (SM), carbonate rock (CC), carbonate sandstone (CS), and siliceous sandstone (SS); (3) CM and SM are good source rocks for shale oil, and P2l2 and P2l5 are the “sweet sections” for shale oil; CC, CS, and SS are reservoirs of tight oil, and P2l1 and P2l4 are the “sweet sections” for tight oil. Finally, definitions are discussed and proposed for tight oil and shale oil.Yao, H., Hong, W.-L., Panieri, G., Sauer, S., Torres, M.E., Lehmann, M.F., Gründger, F., Niemann, H., 2019. Fracture-controlled fluid transport supports microbial methane-oxidizing communities at Vestnesa Ridge. Biogeosciences 16, 2221-2232. report a rare observation of a mini-fracture in near-surface sediments (30?cm below the seafloor) visualized using a rotational scanning X-ray of a core recovered from the Lomvi pockmark, Vestnesa Ridge, west of Svalbard (1200?m water depth). Porewater geochemistry and lipid biomarker signatures revealed clear differences in the geochemical and biogeochemical regimes of this core compared with two additional unfractured cores recovered from pockmark sites at Vestnesa Ridge, which we attribute to differential methane transport mechanisms. In the sediment core featuring the shallow mini-fracture at pockmark Lomvi, we observed high concentrations of both methane and sulfate throughout the core in tandem with moderately elevated values for total alkalinity, 13C-depleted dissolved inorganic carbon (DIC), and 13C-depleted lipid biomarkers (diagnostic for the slow-growing microbial communities mediating the anaerobic oxidation of methane with sulfate – AOM). In a separate unfractured core, recovered from the same pockmark about 80?m away from the fractured core, we observed complete sulfate depletion in the top centimeters of the sediment and much more pronounced signatures of AOM than in the fractured core. Our data indicate a gas advection-dominated transport mode in both cores, facilitating methane migration into sulfate-rich surface sediments. However, the moderate expression of AOM signals suggest a rather recent onset of gas migration at the site of the fractured core, while the geochemical evidence for a well-established AOM community at the second coring site suggest that gas migration has been going on for a longer period of time. A third core recovered from another pockmark along the Vestnesa Ridge Lunde pockmark was dominated by diffusive transport with only weak geochemical and biogeochemical evidence for AOM. Our study highlights that advective fluid and gas transport supported by mini-fractures can be important in modulating methane dynamics in surface sediments.Yao, J., Wang, H., Chen, M., Yang, M., 2019. Recent advances in graphene-based nanomaterials: properties, toxicity and applications in chemistry, biology and medicine. Microchimica Acta 186, 395. review (with 239 refs.) summarizes the progress that has been made in applications of graphene-based nanomaterials (such as plain?graphene, graphene oxides, doped graphene oxides, graphene quantums dots) in biosensing, imaging, drug delivery and diagnosis. Following an introduction into the field, a first large section covers the toxicity of graphene and its derivatives (with subsections on bacterial toxicity and tissue toxicity). The use of graphene-based nanomaterials in sensors is reviewed next, with subsections on electrochemical, FET-based, fluorescent, chemiluminescent and colorimetric sensors and probes. The large field of imaging is treated next, with subchapters on optical, PET-based, and magnetic resonance based methods. A concluding section summarizes the current status, addresses current challenges, and gives an outlook on potential future trends.Yao, S., Li, Y., Wang, W., Song, G., Shi, Z., Wang, X., Liu, S., 2019. Experimental investigation on the microscopic decomposition process of natural gas hydrate particles. Energy & Fuels 33, 5208-5215. decomposition is an essential part of hydrate mining and has important research significance. In this paper, hydrate thermal decomposition experiments were carried out in a self-designed high-pressure stirring hydrate reaction system, and the microscopic behaviors of the decomposition were captured by a high-speed camera. The main content of the study is the microscopic morphology of hydrate decomposition. According to the experimental data, three kinds of hydrate particles, including granular, flake, and block hydrate particles, were defined, and their decomposition behaviors were analyzed. Finally, based on the independent physical models of the three hydrate particles, physical model of the hydrate particle flow decomposition was established.Yao, W., Xu, J., Xia, W., Wang, Q., Rao, D., Chen, Q., 2019. A characteristic analysis between acidolysis gas and absorbed gas and its application to gas–source correlation in Mao 1 Member, Fuling area, Sichuan Basin. Natural Gas Industry 39, 45-50. acidolysis gas in source rocks is the desorbed hydrocarbon gas in non-connected pores and carbonate crystal lattice, while the absorbed gas lies in the connected pores and is absorbed by surface. It is controversial about whether to use absorbed gas or acidolysis gas in gassource correlation. Using the absorbed gas and acidolysis gas in the first member of the Middle Permian Maokou Fm (hereinafter referred to as Mao 1 member) of Fuling area in the Sichuan Basin, the differences of components and carbon isotopes between absorbed gas and acidolysis gas and their applicable conditions in gas–source correlation were discussed. The results show that: (1) there are larger differences of components and isotopes between absorbed gas and acidolysis gas. The absorbed gas has more heavy hydrocarbons and heavier carbon isotope. This difference can be attributed to the easier diffusion of methane and light hydrocarbons in absorbed gas, leading to relatively enriched heavy hydrocarbons and heavier carbon isotope in absorbed gas; (2) acidolysis gas is a mixture of hydrocarbon gas formed during different stages, while absorbed gas is the result of equilibrium between diffusion and supply of hydrocarbon gas, which can result in the differences on carbon isotope sequences between them; (3) the characteristics of natural gas produced after acid fracturing in the Mao 1 member in Fuling area resembles those of acidolysis gas in source rocks, while the characteristics of natural gas produced without acid fracturing are more similar to those of adsorbed gas; (4) the natural gas pool of the Mao 1 member is a carbonate gas pool with self-generation and self-storage. It is concluded that for the gas pool formed after migration, its producing pays have not been processed by acid fracturing, the produced gas should be correlated with the adsorbed gas in source rocks; for the carbonate gas pool with self-generation and self-storage, acid fracturing is usually needed, and the produced gas should be correlated with the acidolysis gas in source rocks.Yao, X., Sipler, R.E., Stanley, B.C., Roberts, Q.N., Sanderson, M.P., Bott, C.B., Bronk, D.A., 2019. Quantifying effluent dissolved organic nitrogen (EDON) uptake by microbial communities along a salinity gradient in the York River. Estuaries and Coasts 42, 1265-1280. discharged from water reclamation facilities (WRFs) contains dissolved organic nitrogen, termed effluent dissolved organic nitrogen (EDON), that subsequently enters coastal waterways. It is still unclear at what rate EDON can be taken up by microbial communities relative to other nitrogen (N) substrates. Bench-scale sequencing batch reactors (SBRs), used to mimic WRFs, were supplied with 15N-labeled ammonium (15NH4+) to produce 15N-labeled EDON (EDO15N) that was subsequently used to measure uptake rates along a salinity gradient of the York River, Virginia, USA, in the spring and summer. Although NH4+ dominated influent N pools, only a small fraction (4.1%) of EDON was produced from NH4+ microbial assimilation in biological treatment processes. When added as a short-term (4-h) tracer, the EDO15N was taken up by estuarine microbes at rates 0.01–0.434 μmol N L?1 h?1, which are similar to rates of NH4+ and nitrate uptake. When added to 48-h bioassays, EDON stimulated phytoplankton growth more at the lower salinity (0–8‰) sites (8.5–13.8 μg Chl a L?1) than at the higher salinity (20‰) site (up to 0.4 μmol Chl a L?1). The microbes in the 0.7–5 μm size fraction had significantly higher EDO15N uptake rates than the larger size fraction (e.g., >?5 μm, p?<?0.05). Taken together with urea and amino acids, DON plays a more important role in N nutrition for microbes during the summer months. This study provides the first EDO15N uptake rates using EDO15N produced from 15NH4+ in SBRs, and the results provide conclusive evidence that organic N in effluent is biologically available to estuarine microbes.You, Y., Zheng, S., Zang, H., Liu, F., Liu, F., Liu, J., 2019. Stimulatory effect of magnetite on the syntrophic metabolism of Geobacter co-cultures: Influences of surface coating. Geochimica et Cosmochimica Acta 256, 82-96. direct interspecies electron transfer (DIET) can facilitate syntrophic metabolism in natural microbial communities and also promote the performance of the engineered systems based on syntrophic interactions. In this study, the stimulatory effect of bare synthetic magnetite (Mt), humic acid coated magnetite, and SiO2 coated magnetite (Mt-SiO2) on DIET in defined co-cultures of Geobacter metallireducens/Geobacter sulfurreducens were studied. Magnetite coated with Aldrich humic acid (HA) and Elliott Soil humic acid (HAES), respectively, were prepared, and the two kinds of humic acid influenced the ability of Mt to promote syntrophic metabolism of the co-cultures in a similar way. When weight concentration was the same, pure humic acid presented the stimulatory effect on DIET similar to bare magnetite. However, the presence of HA coating on magnetite surface caused 50% and 61%, respectively, decrease in the rates of ethanol consumption (Re) and succinate production (Rs) in DIET processes. Pure HA in the same weight concentration as the HA coating in Mt-HA induced the similar metabolism rates as Mt-HA. In the Mt-HA mediated DIET, most electrons from ethanol metabolism were transferred to G. sulfurreducens selectively through the HA coating, and magnetite core hardly contributed to DIET processes. The SiO2 coating on magnetite resulted in 81% and 89%, respectively, decreases in Re and Rs, mainly because the non-conductive SiO2 layer hindered electron transfer between magnetite core and bacteria. After eight-day incubation with the co-cultures, bare magnetite nanoparticles formed relatively larger and more compact aggregates with cells than Mt-HA and Mt-SiO2, due to the different surface charge between bare and coated Mt. The generation of dissolved Fe(II) and HCl-extractable Fe(II) due to microbial reduction of magnetite by G. metallireducens and vivianite formation were observed along with DIET processes in all DIET experiments. Based on these results, different pathways of electron transfer in defined co-cultures of Geobacters with bare and coated magnetite nanoparticles were proposed. The findings in this study demonstrate the significant effects of surface properties on the ability of magnetite to stimulate DIET, which needs to be considered in order to comprehensively understand the role and mechanisms of mineral-mediated DIET in natural and engineered systems.Yu, Q.-Y., Bagas, L., Yang, P.-H., Zhang, D., 2019. GeoPyTool: A cross-platform software solution for common geological calculations and plots. Geoscience Frontiers 10, 1437-1447. is an open source application developed for geological calculations and plots, such as geochemical classification, parameter calculation, basic statistical analysis and diagrams for structural geology. More than acting as a link from raw data stored in Microsoft Excel? (MS Excel) files to vector graphic files, GeoPyTool includes recently developed routines that have not been included in previous software, such as the calculation of the Ce(IV)/Ce(III) ratio for zircons as a method to examine the temporal evolution of oxygen fugacity in the magmatic source for igneous rocks, and the temperature calculator with titanium in zircon and zirconium in rutile. Besides these routines, GeoPyTool also allows users to load any figure from articles or books as a base map. As a Python-based cross-platform program, GeoPyTool works on Windows?, MacOS X? and GNU/Linux. GeoPyTool can do the whole process from data to results without the dependence of Microsoft Excel?, CorelDraw? and other similar software. It takes Excel? XLSX and CSV (Comma Separated Value) as the formats of both the input data source files and the output calculation results files. The figures generated by GeoPyTool can be saved as portable network graphics (PNG), scalable vector graphics (SVG) or portable document format (PDF). Another highlight of GeoPyTool is the multilingual support, the official version of GeoPyTool supports both Chinese and English, and additional languages can be loaded through interface files. GeoPyTool is still in the development stage and will be expanded with further geochemical and structural geology routines. As an open source project, all source code of GeoPyTool are accessible on Github (). Users with Python experience can join in the development team and build more complex functions expanding the capabilities of GeoPyTool.Yu, T., Kelly, R., Mu, L., Ross, A., Kennedy, J., Broly, P., Xia, F., Zhang, H., Wang, B., Dilcher, D., 2019. An ammonite trapped in Burmese amber. Proceedings of the National Academy of Sciences 116, 11345-11350.: Aquatic organisms are rarely found in amber, but when they occur they provide invaluable evidence for the better understanding of amber taphonomy and past ecosystems. We report an ammonite and several marine gastropods alongside a mixed assemblage of intertidal and terrestrial forest floor organisms in mid-Cretaceous Burmese amber. Our discovery indicates that the Burmese amber forest was living near a dynamic and shifting coastal environment. The ammonite also provides supporting evidence for the age of the amber, which is still debated, and represents a rare example of dating using fossils present inside the amber.Abstract: Amber is fossilized tree resin, and inclusions usually comprise terrestrial and, rarely, aquatic organisms. Marine fossils are extremely rare in Cretaceous and Cenozoic ambers. Here, we report a record of an ammonite with marine gastropods, intertidal isopods, and diverse terrestrial arthropods as syninclusions in mid-Cretaceous Burmese amber. We used X-ray–microcomputed tomography (CT) to obtain high-resolution 3D images of the ammonite, including its sutures, which are diagnostically important for ammonites. The ammonite is a juvenile Puzosia (Bhimaites) and provides supporting evidence for a Late Albian–Early Cenomanian age of the amber. There is a diverse assemblage (at least 40 individuals) of arthropods in this amber sample from both terrestrial and marine habitats, including Isopoda, Acari (mites), Araneae (spiders), Diplopoda (millipedes), and representatives of the insect orders Blattodea (cockroaches), Coleoptera (beetles), Diptera (true flies), and Hymenoptera (wasps). The incomplete preservation and lack of soft body of the ammonite and marine gastropods suggest that they were dead and underwent abrasion on the seashore before entombment. It is most likely that the resin fell to the beach from coastal trees, picking up terrestrial arthropods and beach shells and, exceptionally, surviving the high-energy beach environment to be preserved as amber. Our findings not only represent a record of an ammonite in amber but also provide insights into the taphonomy of amber and the paleoecology of Cretaceous amber forests.Yu, Y., Luo, X., Wang, Z., Cheng, M., Lei, Y., Zhang, L., Yin, J., 2019. A new correction method for mercury injection capillary pressure (MICP) to characterize the pore structure of shale. Journal of Natural Gas Science and Engineering 68, 102896. economic and accurate measurement of micron or submicron size pores in shale is still a challenge. The mercury injection capillary pressure (MICP) measurement of shale particles is an effective method to evaluate the macropore structure, but it is questionable without proper data interpretation. In this study, the fractal theory was applied to identify the four stages of MICP measurement: Stage A is controlled by the interparticle voids in the particle assemblage; Stage B can reflect mercury intrusion into the pores of the shale; and Stage C and D indicate the shale matrix compression and pore structure change induced by high pressure, respectively. Based on the consistent fractal dimension derived from Stage A, the conformance volume induced by interparticle voids at each pressure step in Stage B was quantitatively simulated using the linear fitting method. The correction results show that simultaneous mercury filling of interparticle voids has an important impact on the pore volume in the pore size range larger than 1?μm. To cover the complete pore size range, the MICP data in Stage C and D were substituted by gas adsorption data. The new correction method for MICP data was verified by the good match between the MICP-gas adsorption combined porosity and the helium porosity of the same sample and by the good agreement between the pore size distribution (PSD) curves from the MICP and N2 adsorption measurements in their overlapped pore size range. Therefore, the MICP and gas adsorption methods can be used in conjunction to characterize the pore structure of shale in the complete pore size range. The application of this method is particularly good for the silty samples of lacustrine shale in the study area compared with the clayey samples. To further improve the convergence of different fluid injection methods, more efforts are needed to determine the optimum particle size class and optimum data interpretation model for different shale lithofacies.Yuan, B., Muir, D., MacLeod, M., 2019. Methods for trace analysis of short-, medium-, and long-chain chlorinated paraffins: Critical review and recommendations. Analytica Chimica Acta 1074, 16-32. methods for quantifying chlorinated paraffins (CPs) yield only a total concentration of the mixture as a single value. With appropriate analytical instrumentation and quantification methods, more reliable and detailed analysis can be performed by quantifying total concentrations of short-, medium-, and long-chain CPs (SCCPs, MCCPs, and LCCPs), and in the current optimal situation by quantifying individual carbon-chlorine congener groups (CnClm). Sample extraction and clean-up methods for other persistent organochlorines that have been adapted for recovery of CPs must be applied prior to quantification with appropriate quality assurance and quality control to ensure applicability of the methods for SCCPs, MCCPs, and LCCPs. Part critical review, part tutorial, and part perspective, this paper provides practical guidance to analytical chemists who are interested in establishing a method for analysis of CPs in their lab facilities using commercial reference standards, or for expanding existing analysis of total CPs or SCCPs to analysis of SCCPs, MCCPs, and LCCPs, or to analysis of CnClm congener groups.Yuan, C., Sleighter, R.L., Weavers, L.K., Hatcher, P.G., Chin, Y.-P., 2019. Fast photomineralization of dissolved organic matter in acid mine drainage impacted waters. Environmental Science & Technology 53, 6273-6281. mine drainage (AMD) formed from pyrite (iron disulfide) weathering contributes to ecosystem degradation in impacted waters. Solar irradiation has been shown to be an important factor in the biogeochemical cycling of iron in AMD-impacted waters, but its impact on dissolved organic matter (DOM) is unknown. With a typical AMD-impacted water (pH 2.7–3) collected from the Perry State Forest watershed in Ohio, we observed highly efficient (>80%) photochemical mineralization of DOM within hours in a solar simulator resembling twice summer sunlight at 40°N. We confirmed that the mineralization was initially induced by ?OH formed from FeOH2+ photodissociation and was inhibited 2-fold by dissolved oxygen removal, suggesting the importance of both the photochemical reaction and oxygen involvement. Size exclusion chromatography and Fourier transform ion cyclotron resonance mass spectrometry elucidated that any remaining organic matter was comprised of smaller and highly aliphatic compounds. The quantitative and qualitative changes in DOM are likely to constitute an important component in regional carbon cycling and nutrient release and to influence downstream aquatic ecosystems in AMD-affected watersheds.Yuan, J., Zhong, L., Vakili, M., Segun, G.A., 2019. New modeling method to simulate asphaltenes at oil sands process in water management. Journal of Molecular Graphics and Modelling 91, 1-9. study of various structures, physicochemical structures and dynamic characteristics of oil-water interface asphaltenes is an important basis for the large-scale development and efficient clean utilization of oil sands. The molecular dynamics simulations method provides a possibility for revealing the physicochemical structure and dynamic characteristics of oil sands. The emphasis of this paper is to study the physic-chemical structure of tar sands asphaltenes and the changes of their kinetic properties by using molecular dynamics simulations. Molecular dynamics was used to simulate the physicochemical and dynamic characteristics of asphaltenes in water treatment of the oil sands. In this research, the structural and dynamic properties of asphaltenes, such as density distribution, correlation (radial distribution function), root-mean-square deviation (RMSD), and mean azimuth shift (MSD), diffusion coefficient, the radius of gyration, volume viscosity and free energy in water treatment were systematically discussed. The simulation results of asphaltene at the oil-water interface revealed that, in the oil-water interface, oil and water will affect the solubility of asphaltene. The asphaltene molecules have different mobility and the ability to break molecular association, indicating that the structure and dynamic properties of asphaltene in the oil-water interface and the water-water interface are different.Zahl, P., Zhang, Y., 2019. Guide for atomic force microscopy image analysis to discriminate heteroatoms in aromatic molecules. Energy & Fuels 33, 4775-4780. are essential for functional groups in organic structures and are complementary to hydrocarbon molecules in reactivities and properties. However, it is still a challenge to quickly identify heteroatoms with only non-contact atomic force microscopy (nc-AFM) to resolve chemical structures in complex unknown mixtures. This study aimed to understand the effect of elemental types on the contrast of atomic force microscopy (AFM) images using a few selected model heterocycles, including dibenzothiophene (DBT), acridine (ACR), and carbazole (CBZ). We identified several features that can be used to find common heteroatoms (S and N) and discriminated them from carbon atoms (C) using nc-AFM images alone. The mechanism of the atom and bond contrast was studied with image simulations and was found to be mostly correlated to van der Waals radii, but other factors, such as bonding geometry, electron density, and substrate interaction, need to be considered. This work will allow for rapid identification of these common heteroatoms in petroleum with AFM.Zanardi-Lamardo, E., Mitra, S., Vieira-Campos, A.A., Cabral, C.B., Yogui, G.T., Sarkar, S.K., Biswas, J.K., Godhantaraman, N., 2019. Distribution and sources of organic contaminants in surface sediments of Hooghly river estuary and Sundarban mangrove, eastern coast of India. Marine Pollution Bulletin 146, 39-49. study investigated polycyclic aromatic hydrocarbons (PAHs) and organochlorine compounds such as polychlorinated biphenyls (PCBs) and DDT-related pesticides in surface sediments of Hooghly estuary and the Sundarban mangrove wetlands. Concentrations of ∑17PAH, ∑182PCB and ∑6DDT ranged from 15.4 to 1731, not detected (nd) to 13.5 and nd to 8.97?ng?g?1 dry weight, respectively. Low levels of PCBs and low to moderate concentrations of DDTs and PAHs reflected recent development in West Bengal, which was dominated by agriculture and multifarious industries in the past. Diagnostic ratios suggested that major sources of PAHs are combustion processes, DDTs are input by agriculture, antifouling paints and public health campaigns, and organochlorines are predominantly from industrial origin. Heavier PCB congeners suggest local sources and short-range transport of such chemicals. Decision makers may use these findings for managing the Hooghly River watershed in order to promote a sustainable development on the eastern coast of India.Zang, X., Monge, M.E., Fernández, F.M., 2019. Mass spectrometry-based non-targeted metabolic profiling for disease detection: Recent developments. TrAC Trends in Analytical Chemistry 118, 158-169. spectrometry (MS) plays an important role in seeking biomarkers for disease detection. High-quality quantitative data is needed for accurate analysis of metabolic perturbations in patients. This article describes recent developments in MS-based non-targeted metabolomics research with applications to the detection of several major common human diseases, focusing on study cohorts, MS platforms utilized, statistical analyses and discriminant metabolite identification. Potential disease biomarkers recently discovered for type 2 diabetes, cardiovascular disease, hepatocellular carcinoma, breast cancer and prostate cancer through metabolomics are summarized, and limitations are discussed.Zavyalova, A.P., Chupakhina, V.V., Stoupakova, A.V., Gatovsky, J.A., Kalmykov, G.A., Korobova, N.I., Suslova, A.A., Bolshakova, M.A., Sannikova, I.A., Kalmykov, A.G., 2019. Comparison of the Domanic outcrops in the Volga-Ural and Timan-Pechora basins. Moscow University Geology Bulletin 74, 56-72. (and domanicoid) deposits are of great interest to researchers and oil producing companies, since they possess authigenic oil and gas contents. This work presents the results of studying the domanic outcrops in the Volga-Ural and Timan-Pechora basins. The stratigraphic interval included sediments from the Middle Frasnian stage of the Upper Devonian to the Tournaisian stage of the Lower Carboniferous. The main types of rocks are characterized by microscopic examinations of thin sections and geochemical parameters of organic matter are determined. It is shown that the domanic deposits of the Timan-Pechora basin are similar in structure and lithological composition to the domanic deposits of the Volga-Ural Basin. The upper part of the domanicoid section is distinguished by the domination of carbonate-siliceous types of rocks over kerogen mixed varieties. According to the geochemical parameters, the organic matter in the rocks from the domanic deposits of the Volga-Ural and Timan-Pechora basins belongs to type II; however, the organic matter of the high-carbon sequence is more mature in the outcrops of the Volga-Ural region than in the Timan-Pechora outcrops. Russian Text published in Vestnik Moskovskogo Universiteta, Seriya 4: Geologiya, 2018, No. 6, pp. 57–73.Zeaiter, Z., Marasco, R., Booth, J.M., Prosdocimi, E.M., Mapelli, F., Callegari, M., Fusi, M., Michoud, G., Molinari, F., Daffonchio, D., Borin, S., Crotti, E., 2019. Phenomics and genomics reveal adaptation of Virgibacillus dokdonensis strain 21d to its origin of isolation, the seawater-brine interface of the Mediterranean Sea deep hypersaline anoxic basin discovery. Frontiers in Microbiology 10, 1304. doi: 10.3389/fmicb.2019.01304. adaptation of sporeformers to extreme environmental conditions is frequently questioned due to their capacity to produce highly resistant endospores that are considered as resting contaminants, not representing populations adapted to the system. In this work, in order to gain a better understanding of bacterial adaptation to extreme habitats, we investigated the phenotypic and genomic characteristics of the halophile Virgibacillus sp. 21D isolated from the seawater-brine interface (SBI) of the MgCl2-saturated deep hypersaline anoxic basin Discovery located in the Eastern Mediterranean Sea. Vegetative cells of strain 21D showed the ability to grow in the presence of high concentrations of MgCl2, such as 14.28% corresponding to 1.5M. Biolog phenotype MicroArray (PM) was adopted to investigate the strain phenotype, with reference to carbon energy utilization and osmotic tolerance. The strain was able to metabolize only 8.4% of 190 carbon sources provided in the PM1 and PM2 plates, mainly carbohydrates, in accordance with the low availability of nutrients in its habitat of origin. By using in silico DNA-DNA hybridization the analysis of strain 21D genome, assembled in one circular contig, revealed that the strain belongs to the species Virgibacillus dokdonensis. The genome presented compatible solute-based osmoadaptation traits, including genes encoding for osmotically activated glycine-betaine/carnitine/choline ABC transporters, as well as ectoine synthase enzymes. Osmoadaptation of the strain was then confirmed with phenotypic assays by using the osmolyte PM9 Biolog plate and growth experiments. Furthermore, the neutral isoelectric point of the reconstructed proteome suggested that the strain osmoadaptation was mainly mediated by compatible solutes. The presence of genes involved in iron acquisition and metabolism indicated that osmoadaptation was tailored to the iron-depleted saline waters of the Discovery SBI. Overall, both phenomics and genomics highlighted the potential capability of V. dokdonensis 21D vegetative cells to adapt to the environmental conditions in Discovery SBI.Zeebe, R.E., Tyrrell, T., 2019. History of carbonate ion concentration over the last 100 million years II: Revised calculations and new data. Geochimica et Cosmochimica Acta 257, 373-392. an earlier contribution to this journal, we provided a reconstruction of seawater carbonate ion concentration over the last 100 million years (Tyrrell and Zeebe, 2004; TZ04 hereafter). Since then, multiple new and more robust data sets on past ocean carbonate chemistry, atmospheric CO2, and major ion seawater composition have emerged, which prompt new CO2 system reconstructions. In addition, we have gained new insight into the effects of past major ion seawater composition on equilibrium constants affecting CO2 system calculations — most notably due to sulfate. Here we present new reconstructions of past ocean carbonate chemistry and atmospheric CO2 based on new data and revised calculations, including error analysis. We also provide simple corrections for past equilibrium constants, supported by experimental data and well-suited for numerical models and observational studies on multi-million year time scales. Our updated result for just the seawater carbonate ion concentration (～2.3 to 4-fold lower 100 Myr ago) is similar to TZ04, indicating that our core approach is robust. However, all revised reconstructions using new alkenone and boron data now suggest that long-term ocean inventories of total dissolved inorganic carbon (DIC) and total alkalinity (TA) were similar to modern over the Cenozoic. This result contrasts strongly with one of TZ04’s scenarios, which featured high Paleocene-Eocene DIC/TA inventories and was based on boron-derived pH values that have recently been revised. Because the carbonate system has two degrees of freedom, consistency checks can be made when three or more parameters are determined. Overall, our estimated long-term trends in CO2 system parameters across the Cenozoic appear consistent, regardless of whether we combine our carbonate ion concentration with alkenone-derived pCO2 or boron-derived pH. Our results suggest convergence towards a consistent picture of Cenozoic atmospheric CO2 and seawater chemistry. Finally, we identify changes in past seawater sulfate as a conceptual and practical problem for seawater pH reconstructions.Zeng, J., Liu, S., Cai, W., Jiang, H., Lu, X., Li, G., Li, J., Liu, J., 2019. Emerging lipidome patterns associated with marine Emiliania huxleyi-virus model system. Science of The Total Environment 688, 521-528. huxleyi (Coccolithophore) plays a prominent role in the global carbon cycle and in climate processes. The annual collapse of massive E. huxleyi blooms in the marine environment has been shown to be frequently linked to viral control. These host-virus interactions shape the evolution and dynamics of oceanic microscale ecosystems, yet we still understand little of the molecular mechanism of these virus-mediated processes. Here, we present a detailed characterization of the lipidome of E. huxleyi BOF92 strain, both of uninfected cells and those infected with its specific lytic virus EhV-99B1. Non-targeted lipidomics analysis was performed in order to evaluate the dynamic alterations underlying virus-induced metabolic remodeling. The host lipidome (both lipid content and composition) significantly changed in response to the viral infection. The most statistically significant differential lipids were screened as potential biomarkers for assessing E. huxleyi population sensitivity to EhV infection. Our results reveal that the remodeling of lipid metabolism that underlies the pathogenesis of this infection primarily involved sphingolipid, glycerolipid and fatty acid metabolic pathways. Our study provides insights into how viruses shape their hosts metabolism to support their unique life cycle and a lipid-based chemical arms race during host-virus dynamic interactions in a marine environment.Zhai, Y., Xu, Q., Tang, Y., Liu, S., Li, D., Xu, W., 2019. Boosting the sensitivity and selectivity of a miniature mass spectrometer using a hybrid ion funnel. Analytical Chemistry 91, 7911-7919. high portability, high analytical performances are also crucial concerns for a miniature mass spectrometer to meet the demands in in situ analysis. As a continuous effort in improving analytical performances of the miniature mass spectrometer with continuous atmospheric pressure interface, a hybrid ion funnel was developed and coupled into the system in this study. The hybrid ion funnel consisted of a rectangular ion funnel region and a planar quadrupole field region, which were fabricated by the printed circuit board technology. After systematic optimization, a limit of detection of 1 ng/mL was obtained, which was improved by 10 folds relative to that of 10 ng/mL previously reported for the miniature mass spectrometer. Besides improved ion transmission efficiency, this hybrid ion funnel was also capable of filtering ions according to their mobilities, thus improving the system selectivity. This capability was demonstrated by separation and selective transmission of protein ions at different charge states, reserpine in PEG background and isobaric peptide ions. Resolution of this system was also tested by analyzing isotopic peaks of reserpine. The ppb-level detection sensitivity and isotope resolving capability achieved in this work would greatly expand the application range of miniature mass spectrometers.Zhang, D., Huang, Q., Zheng, H., Wang, W., Cheng, X., Li, R., Li, W., 2019. Effect of wax crystals on nucleation during gas hydrate formation. Energy & Fuels 33, 5081-5090. formation and wax deposition pose great flow assurance challenges to subsea oil pipes, especially when the two phenomena co-occur. Wax crystals can have a significant impact on hydrate nucleation and growth kinetics, but this phenomenon has not been studied in great detail. Here, the effect of wax crystals on hydrate nucleation was investigated using both molecular dynamics simulation methods and experiments conducted using a custom-designed high-pressure autoclave equipped with an on-line viscometer. Both the simulation and the experimental results demonstrated that the presence of wax crystals inhibits hydrate nucleation. The simulations showed that water droplets tend to approach and adsorb on wax crystals prior to nucleation, thus inhibiting the formation of hydrate cages. The experiments demonstrated that water cut and stirring rate play a significant role in determining the hydrate nucleation rate. In addition, adding more wax increased the viscosity of the emulsion, which limits mass transfer of gas to the oil–water interface.Zhang, D., Yang, Y., Hu, J., Ran, Y., Mao, J., 2019. Occurrence of aliphatic biopolymer in chlorophyceae algae and cyanobacteria-rich phytoplankton. Organic Geochemistry 135, 1-10. cultured chlorophyceae algae and two cyanobacteria-rich phytoplankton were separated into five fractions and characterized by 13C cross polarization/total sideband suppression (CP/TOSS) nuclear magnetic resonance spectroscopy (NMR), X-ray photoelectron spectroscopy (XPS), Rock-Eval and closed pyrolysis analyses. The structures of the acid nonhydrolyzable organic matter (NHOM) fractions were similar to those of poly(methylene)-rich aliphatic algaenan. We found that the cyanobacteria-rich phytoplankton contained aliphatic nonhydrolyzable biopolymers. The NMR and Rock-Eval analyses showed that the isolated NHOM exhibited high oil-prone potentials. Pyrolysis analysis of the field-collected NHOM from Liuhuahu Park in Guangzhou (GP_NHOM) indicated that it exhibited high oil-prone potential and comprised a long, saturated and unbranched hydrocarbon chain (up to C33) structural unit. The maximum oil and gaseous hydrocarbon generation potentials reached 55.9% and 7.2%, respectively and were very close to those derived from 13C CP/TOSS NMR, suggesting that 13C NMR is an effective approach for evaluation of oil and gas production potentials. This investigation is helpful for improving understanding of kerogen formation mechanisms through selective preservation and the generation mechanisms of biocrude oil.Zhang, N., Su, L., Man, S., Lei, X., Huang, T., Zhu, C., Zhang, L., Wu, X., 2019. Task-specific solid-phase microextraction based on ionic liquid/polyhedral oligomeric silsesquioxane hybrid coating for sensitive analysis of polycyclic aromatic hydrocarbons by gas chromatography–mass spectrometry. Journal of Chromatography A 1598, 49-57. direct immersion solid-phase microextraction (DI-SPME) approach for gas chromatography-mass spectrometry (GC–MS) based on hybrid fiber coating of ionic liquid and polyhedral oligomeric silsesquioxane (POSS) is presented. To fabricate the task-specific coating for the enrichment of polycyclic aromatic hydrocarbons (PAHs), 1-butyl-3-vinylimidazolium bis[(trifluoromethyl)sulfonyl]imide (IL) and POSS were rapidly photoinitiated copolymerized within 5?min on a stainless steel fiber. The high efficient extraction of target analytes can be attributed to a combined result of multiple interactions including the strong CF?HC pseudohydrogen bonding, π-π stacking, hydrophobic force, and molecular sieve effect. A wide linear range (0.04–400?ng L?1) with low detection limits in the range of 0.004 and 0.5?ng L?1 were obtained for PAHs by GC–MS. The applicability of this coupling method was successfully demonstrated by the analysis of trace PAHs in real river water and soil samples, with satisfied recoveries (84.2–108.6%) and relative standard deviations (<8.1%). Compared to the other commercial fiber-based SPME methods, the IL/POSS hybrid coating-based SPME is much cheaper, thermally stable and capable of eliminating possible deleterious effects as well.Zhang, S., Liu, H., Wang, M., Liu, X., Liu, H., Bao, Y., Wang, W., Li, R., Luo, X., Fang, Z., 2019. Shale pore characteristics of Shahejie Formation: Implication for pore evolution of shale oil reservoirs in Dongying sag, north China. Petroleum Research 4, 113-124. pore characteristics of shale reservoirs in the lower submember of Member 3 to upper submember of Member 4 of Shahejie Formation in Dongying sag are analyzed, influences of mineral content and organic matter content on porosity and pore size are also investigated, and through the diagenetic thermal simulation experiment, the main pore evolution is further discussed. The results show that the pore structure of shale reservoirs is complex, the micron-nanometer pores can storage liquid hydrocarbons, and the free-phase crude oil is mainly distributed in intergranular dissolution pores of calcite, recrystallized intergranular pores, intergranular shrinkage fractures of clay mineral which have large pore size. Framework minerals and organic matter content directly influence porosity and pore size of shale reservoirs, relationship between porosity and content of felsic mineral as well as content of organic matter content is linear and positive, while relationship between content of carbonated mineral is negative. At the buried depth from 2500 to 3500?m, concentration of organic acid from hydrocarbon generation and expulsion of organic matter, increasing range of pressure coefficient, are well corresponding to high-porosity intervals; pore formation in shale oil reservoirs are almost controlled by diagenetic evolution of clay minerals; framework storage spaces formed by carbonate grain crystals as well as intergranular and intergranular dissolution pores of carbonate increases porosity of shale oil reservoirs; local increase of porosity at the depth of 3500–3800?m is mainly caused by coupling of hydrocarbon-generating overpressure and dissolution, and size, distribution and connectivity of pores are enhanced obviously.Zhang, S., Pu, H., Zhao, J.X., 2019. Experimental and numerical studies of spontaneous imbibition with different boundary conditions: Case studies of Middle Bakken and Berea cores. Energy & Fuels 33, 5135-5146. oil and gas are becoming increasingly important energy sources in North America. Spontaneous imbibition is an important mechanism in oil and gas recovery from tight reservoirs. In this study, countercurrent spontaneous imbibition experiments and nuclear magnetic resonance (NMR) were combined to study the imbibition and the fluid distribution in eight core samples. NMR is able to detect fluid distribution in different sizes of pores ranging from micropores to fractures. Before the experiments, Middle Bakken and Berea cores were saturated with air. Then imbibition experiments with one end open (OEO) and two ends closed (TEC) boundary conditions were carried out. The numerical solutions of spontaneous imbibition models were matched with experimental results by choosing reasonable parameters. The capillary pressure and relative permeability were obtained from the matching. Moreover, the gravity effect on the spontaneous imbibition was analyzed. It was found that the gravity can be neglected for tight rocks. However, it has significant impacts on high-permeability rocks. The recovery factor of OEO imbibition exhibits a linear relationship with √i. However, the TEC imbibition shows a poor linear relationship with at the late stage. This research provides new methods to obtain capillary pressure and relative permeability from spontaneous imbibition experiments with OEO and TEC boundary conditions and advances crucial mechanisms for the development of tight reservoirs.Zhang, Z., Zhang, Y., Zhu, G., Han, J., Chi, L., 2019. Geochemical and isotopic evidence of the genesis of a condensate in the eastern Tarim Basin, China: Implications for petroleum exploration. Energy & Fuels 33, 4849-4856. exploration activities in the eastern Tarim Basin have been thwarted over the last decade after the discovery of several Jurassic gas condensate fields. In this study, the two-dimensional gas chromatography/time-of-flight mass spectrometry (GC × GC-TOFMS) and compound-specific carbon isotope analysis were performed on a Jurassic condensate (Yingnan2) and the associated gas to determine its genesis and the accumulation process in this area. The geochemical and isotopic features suggested that the condensate analyzed was a mixture of the Ordovician cracked paleo-oil with the Jurassic intact oil as evidenced by the concentrated diamondoids and ethanoadamantanes, the high gas generation temperature (～195 °C), the heavy whole oil δ13C (?28.6‰), and the significant variation in the isotopic profile of n-alkanes. As the gas amount was constantly elevated due to both oil cracking and the mixing of the kerogen-cracking gas from the Cambrian source rock, phase transition occurred and thus formed the Yingnan2 secondary condensate. The constant mixing of nitrogen-rich kerogen-cracking gas complementarily caused an increase in the nitrogen gas content. The accumulation model of the condensate in the eastern Tarim Basin was proposed with consideration of the post-accumulation alterations including thermal cracking and mixing, which complicated the quality and distribution of subsurface petroleums. It was further speculated that abundant gas and condensate resources may be preserved in favorable reservoir-seal assemblages in this field.Zhao, J., Jin, Z., Hu, Q., Liu, K., Liu, G., Gao, B., Liu, Z., Zhang, Y., Wang, R., 2019. Geological controls on the accumulation of shale gas: A case study of the early Cambrian shale in the Upper Yangtze area. Marine and Petroleum Geology 107, 423-437. results of sedimentological, mineralogical, geochemical and petrophysical studies on the early Cambrian shale in the Upper Yangtze area are summarized to provide insights on the paleoenvironmental conditions, diagenetic evolution and preservation conditions that give rise to shale gas accumulation. The lower Cambrian organic-rich Qiongzhusi shale is mainly developed in the outer shelf facies of an intracratonic sag [average total organic carbon (TOC): 1.3–2.5%] and in the southeast margin (average TOC: 3.5–5.5%) of the Upper Yangtze area. The thermal maturity values (Reqv) of the Qiongzhusi shale range from 2.19 to 4.23%, while first increasing and then decreasing from the center of the Sichuan Basin outward. The average porosities of the Qiongzhusi shale from the outer shelf facies association (FA5) in the intracratonic rift range from 1.5 to 3.41%, and those from the outer shelf facies association (FA4) in the southeast Sichuan and Guizhou areas range from 1.32 to 2.56%. The organic matter (OM) content and the development degree of OM pores are the main factors that control the porosity and pore structure of the Qiongzhusi shale. For the outer shelf deposits in the intracratonic rift, a quartz (detrital origin) content ranging between 25 and 35% is most favorable for providing an effective support framework for OM pore development due to the mixture of brittle and clay minerals. For the outer shelf deposits in the southeastern margin of the Upper Yangtze area, the high OM content and poor compaction resistance cause a poor development of OM pores, with a smaller average pore diameter than that in the outer shelf shale of the intracratonic rift. In addition, the carbonization of OM in the overmature Qiongzhusi shale change the microstructure and decrease the OM pore volume. Due to poor preservation conditions, the gas content is generally low in the organic-rich shale in the eastern and southeastern parts of the Upper Yangtze region. The Qiongzhusi shale in the interior of the Sichuan Basin, with good preservation conditions, high pressure coefficients, and high gas contents, is a favorable area for shale gas accumulation and potential exploitation.Zhao, P., Guo, Y., Dewald, H.D., Chen, H., 2019. Improvements for absolute quantitation using electrochemical mass spectrometry. International Journal of Mass Spectrometry 443, 41-45. recently reported a new quantitation method using mass spectrometry (MS) in combination with electrochemistry (EC, J.?Am. Soc. Mass Spectrom., 2019, 30, 685). The strength of this method is that no reference standard or isotope-labeled compound is required for absolute quantitation. The method relies on electrochemical oxidation of an electrochemically active target compound to determine the amount of the oxidized compound using Faraday's Law. On the other hand, the oxidation reaction yield can be determined based on the MS signal change following electrolysis. Therefore, the absolute amount of the analyte can be calculated. Our experiment is carried out using a coupled liquid chromatography/electrochemistry/mass spectrometry (LC/EC/MS) apparatus. In this study, the method is further optimized. First, quantifying the compounds in a mixture is possible after the chromatographic separation. Gradient elution is used for separation and each compound can be quantified using the electrochemical mass spectrometry method. Second, for compounds that are already purified, LC column is not necessary and can be removed (i.e., flow-through analysis), thus shortening the analysis time for each injected sample from 10?min to 2?min. With using an LC auto-sampler, multiple samples can be injected sequentially. All the quantitation errors shown in this study are within 5%, indicating a good accuracy of our method.Zhao, W., Zhang, S., He, K., Zeng, H., Hu, G., Zhang, B., Wang, Z., Li, Y., 2019. Origin of conventional and shale gas in Sinian–lower Paleozoic strata in the Sichuan Basin: Relayed gas generation from liquid hydrocarbon cracking. American Association of Petroleum Geologists Bulletin 103, 1265-1296. amounts of natural gas have been discovered recently, both in carbonate reservoirs and in shales in the Sinian–Silurian strata of the Sichuan Basin, southern China. Although numerous studies have been conducted to learn about the accumulation of conventional and shale gas, the gas generation history, the origins of the two types of gas, and gas resources in the basin remain unclear. In this study, the hydrocarbon generation histories of Cambrian and Silurian source rocks were reconstructed on the basis of thermal history and hydrocarbon generation kinetic parameters. Intensive cracking of crude oil to generate considerable amounts of secondary cracking gas in Silurian and Cambrian formations occurred during deep burial. The high abundance of overmature pyrobitumen in carbonate reservoirs and shale demonstrates the occurrence of large-scale in situ cracking of liquid hydrocarbons. A mixing model was proposed to quantitatively determine the contribution of kerogen and oil-cracking gas in shale gas accumulations. The mixing of two thermogenic gases with different maturities resulted in a reversal and a rollover of the carbon isotope compositions of shale gas. Moreover, gas resources from the cracking of three occurrence states of liquid hydrocarbons—including dispersed residual bitumen in source rocks, dispersed oil outside the source, and accumulated oil in reservoirs—were evaluated in Sinian–Cambrian and Silurian petroleum systems in the Sichuan Basin, providing a guide for future deep gas exploration of similar formations in China and elsewhere.Zhao, X., Pu, X., Jin, F., Han, W., Shi, Z., Cai, A., Wang, A., Guan, Q., Jiang, W., Zhang, W., 2019. Geological characteristics and key exploration technologies of continental shale oil sweet spots: A case study of Member 2 of Kongdian Formation in the Cangdong sag in the Huanghua depression, Bohai Bay Basin. Petroleum Research 4, 97-112. the general trend of stepping-up oil and gas exploration and development in China, the unconventional oil and gas resources such as shale oil and gas have become an important alternative. Abundant continental shale oil resources are developed in Member 2 of Kongdian Formation (Ek2) of the Cangdong sag in the Huanghua depression of the Bohai Bay Basin which has complex structure, strong heterogeneity, and large buried depth, thus, the geological characteristic of shale oil accumulation and key exploration technologies are investigated on base of the system coring of 635.8?m, centimeter-level fine description and analysis of over ten thousand samples, therefore, the “four accurate” technologies have been developed, including the accurate selection of sweet spot areas, accurate drilling of sweet spot layers, accurate fracturing of sweet spot layers and accurate measure of fracture-rich sections. The results show that the continental shale strata in Member 2 of Kongdian Formation can be divided into three types: felsic shale, limy dolomitic shale and mixed shale. The Member 2 of Kongdian Formation is characterized by diverse mineral components, abundant laminae, good source rocks and medium thermal evolution degree, tight reservoir with rich micropore and microfractures, high oil saturation and brittle mineral content, indicating good prospect of shale oil exploration. Through sedimentological study, TOC and Ro evaluation, brittle mineral calculation, and seismic fusion inversion, a total of 126?km2 of Class I sweet spots in Member 2 of Kongdian Formation was delineated comprehensively, which guides horizontal well deployment (Well GD1701H and Well GD1702H). The drilling rate of sweet spot of these two horizontal wells is up to 96% by tracing thin layer through fine calibration, locating compartment through fine inversion, ensuring window entry through precise positioning, and tracking sweet spot through adjustment. The "one-excellent and five-highs” criterion is used to select perforation points to realize differential designs of fracturing intervals and clusters. Micro-seismic and potentiometry monitoring show that the artificial fractures formed by volumetric fracturing are 300–400?m long and 120?m high, and control a volume of about 0.07?km3. The maximum daily oil production of two horizontal wells is 48?t and 66?t respectively to realize the economic exploitation of shale oil reserves controlled by fractures. The shale oil exploration in Member 2 of Kongdian Formation shows that the continental shale oil has great potential of exploration and development, and the above technologies are critical and effective for shale oil efficient recovery.Zhao, X., Yu, Y., Zhang, X., Huang, B., Bai, P., Xu, C., Li, D., Zhang, B., Liu, C., 2019. Decreased biofilm formation ability of Acinetobacter baumannii after spaceflight on China's Shenzhou 11 spacecraft. MicrobiologyOpen 8, Article e00763. China has prepared for construction of a space station by the early 2020s. The mission will require astronauts to stay on the space station for at least 180?days. Microbes isolated from the International Space Station (ISS) have shown profound resistance to clinical antibiotics and environmental stresses. Previous studies have demonstrated that the space environment could affect microbial survival, growth, virulence, biofilms, metabolism, as well as their antibiotic-resistant phenotypes. Furthermore, several studies have reported that astronauts experience a decline in their immunity during long-duration spaceflights. Monitoring microbiomes in the ISS or the spacecraft will be beneficial for the prevention of infection among the astronauts during spaceflight. The development of a manned space program worldwide not only provides an opportunity to investigate the impact of this extreme environment on opportunistic pathogenic microbes, but also offers a unique platform to detect mutations in pathogenic bacteria. Various microorganisms have been carried on a spacecraft for academic purposes. Acinetobacter baumannii is a common multidrug-resistant bacterium often prevalent in hospitals. Variations in the ability to cope with environmental hazards increase the chances of microbial survival. Our study aimed to compare phenotypic variations and analyze genomic and transcriptomic variations in A.?baumannii among three different groups: SS1 (33?days on the Shenzhou 11 spacecraft), GS1 (ground control), and Aba (reference strain). Consequently, the biofilm formation ability of the SS1 strain decreased after 33?days of spaceflight. Furthermore, high-throughput sequencing revealed that some differentially expressed genes were downregulated in the SS1 strain compared with those in the GS1 strain. In conclusion, this present study provides insights into the environmental adaptation of A.?baumannii and might be useful for understanding changes in the opportunistic pathogenic microbes on our spacecraft and on China's future ISS.Zheng, D., Pang, X., Ma, X., Li, C., Zheng, T., Zhou, L., 2019. Hydrocarbon generation and expulsion characteristics of the source rocks in the third member of the Upper Triassic Xujiahe Formation and its effect on conventional and unconventional hydrocarbon resource potential in the Sichuan Basin. Marine and Petroleum Geology 109, 175-192. third member of the Upper Triassic Xujiahe Formation (T3x3) is a typical source-reservoir-cap unit for natural gas exploration in the Sichuan Basin. However, most previous studies mainly focused on the T3x3 as a source rock, ignoring its role as a reservoir. As a result, the evaluation of hydrocarbon resource potential was not accurate. This study established a hydrocarbon generation and expulsion model through analyzing the geological and geochemical characteristics of the T3x3 source rocks, and calculated the resource potential of conventional gas, tight gas and shale gas systematically with combining the lower boundary of buoyancy-dominated accumulation (LBBA). The results indicated that the thickness of the source rocks dominated by mudstone was distributed widely, with an average value of more than 45?m. The sedimentary environment was salty lacustrine deposits. They have a high content of total organic carbon (TOC) with an average value of 4.80?wt%, the kerogen is mainly type III with minor type II, and the thermal evolution has entered the high to over mature stage. The hydrocarbon generation threshold was determined to be 0.5%Ro, while the hydrocarbon expulsion threshold and the LBBA were determined to be 0.83%Ro and 1.12%Ro, respectively. The efficiency of hydrocarbon expulsion was relatively high, with an average of about 56%. Also, the maximum hydrocarbon generation and expulsion intensity reached to 110?×?108?m3/km2 and 53?×?108?m3/km2. The amounts of hydrocarbon generation, expulsion and residual associated with the T3x3 source rocks were 125.68?×?1012m3, 70.38?×?1012m3, and 55.30?×?1012m3, respectively. Under the criterion condition of the LBBA, the conventional gas resource was 7.21?×?1010m3, the tight gas resource was 294.34?×?1010m3, and the shale gas resource was 2488.50?×?1010m3. It indicated good prospects for exploration.Zhong, C., Li, J., Flynn, S.L., Nesb?, C.L., Sun, C., von Gunten, K., Lanoil, B.D., Goss, G.G., Martin, J.W., Alessi, D.S., 2019. Temporal changes in microbial community composition and geochemistry in flowback and produced water from the Duvernay Formation. ACS Earth and Space Chemistry 3, 1047-1057. activity in flowback and produced water (FPW) may negatively influence shale oil and gas extraction. However, the impacts of using recycled produced water (RPW) for subsequent fracturing jobs are not well-understood. In this study, we compared time series of FPW samples from two horizontally fractured wells drilled into the Duvernay Formation in Alberta, Canada; well 1 used RPW in the makeup of the hydraulic fracturing fluid (HFF) whereas well 2 did not. 16S rRNA gene sequencing and live/dead cell enumeration were used to track microbial communities. Within 20 days of flowback, total dissolved solids in well 1 and well 2 increased from 5310 mg/L and 288 mg/L to over 150,000 mg/L, and FPW temperatures increased from 20 and 9 °C to 77 and 71 °C, respectively. Alkyl dimethyl benzyl ammonium chloride (biocide) in well 2 decreased from 25 μg/L to below the detection limit of 0.5 μg/L. Cellular biomass decreased from ～105 cells mL–1 to less than the detection limit of 105 cells mL–1 in both wells, and the community in the samples was initially diverse but rapidly shifted to become dominated by the sulfidogenic lineage Halanaerobium. Methanogens were detected at low relative abundance within archaea, with DNA concentrations in FPW after 20 days inadequate for sequencing. Comparing the two wells, the start time of Halanaerobium enrichment was considerably shortened in well 1 relative to well 2. Our results suggest that subsurface environmental parameters primarily drive the rapid enrichment of sulfidogenic and halotolerant bacteria and current recycling strategies can facilitate the growth of these bacteria, whereas biocide seems to be a less important factor in this shift.Zhou, J., Mao, Q., Luo, K.H., 2019. Effects of moisture and salinity on methane adsorption in kerogen: A molecular simulation study. Energy & Fuels 33, 5368-5376. adsorption characteristics of methane in shales play a critical role in the assessment of shale gas resources. The microscopic adsorption mechanism of methane considering the effect of moisture and especially salinity remains to be explored. In this work, combined molecular dynamics and grand canonical Monte Carlo simulations are conducted to investigate the adsorption behaviors of methane in the realistic kerogen matrixes containing different moisture contents (0–6 wt %) and various salinities (0–6 mol/L NaCl). Adsorption processes are simulated under realistic reservoir conditions at four temperatures in the range from 298.15 to 358.15 K and pressures up to 40 MPa. Effects of the moisture content on methane adsorption capacities are analyzed in detail. Simulation results show that the methane adsorption capacity declines as the moisture content increases. In comparison to the dry kerogen matrix, the reduction in the maximum CH4 adsorption capacity is as high as 42.5% in moist kerogen, with a moisture content of 6.0 wt % at 338.15 K. The overlap observed in the density distributions of water molecules and decrease in adsorbed methane indicates that the water molecules occupy the adsorption sites and, thus, lead to the reduction in methane adsorption capacity. Besides, the effects of salinity on CH4 adsorption isotherms are discussed. The salinity is found to have a negative influence on the methane adsorption capacity. The maximum CH4 adsorption capacity reduces around 6.0% under the salinity of 6 mol/L at 338.15 K. Adsorption of methane in kerogens of constant salinity but different moisture contents are further discussed. Results from the present study show that the moisture content has a greater impact on the adsorption of methane compared to that of salinity. The findings of this study have important implications for more accurate estimation of shale gas in place.Zhou, L., Wang, Z., Gao, W., Zhang, K., Li, H., Zhang, L., 2019. Provenance and tectonic setting of the Lower Cambrian Niutitang formation shales in the Yangtze platform, South China: Implications for depositional setting of shales. Geochemistry 79, 384-398. compositions of the Lower Cambrian Niutitang Formation shales in the southeastern Yangtze Platform margin were investigated for provenance, tectonic setting, and depositional environment. The shale samples are characterized by higher abundances of large ion lithophile elements (Cs, Ba, and Pb), lower abundances of high field strength elements (Cr, Sc, and Co) and transition elements (Th, Zr, Hf, Nb, and Ta) relative to average shale. North American shale composition (NASC) -normalized rare earth element (REE) patterns are observed, with negative Ce anomalies, negative Eu anomalies, and positive Y anomalies. The chemical index of alteration (CIA) varies from 68.67–74.93. Alkali and alkaline element contents and CIA values suggest that the source rocks have undergone moderate weathering. The index of compositional variability (ICV), Zr/Sc and Th/Sc ratios vary from 0.53 to 1.07, 5.31 to 8.18 and 0.52–1.02, respectively. ICV values and relationships between Zr/Sc and Th/Sc ratios indicate negligible sedimentary recycling. The Al2O3/TiO2 (14–26) and TiO2/Zr (56–77) ratios imply that the source rocks of the investigated shales had intermediate igneous compositions. However, Cr/V ratios and a La/Th–Hf discrimination diagram suggest that the intermediate compositional signal of the source rocks was derived from a mixture of 75% mafic and 25% felsic igneous rocks rather than intermediate igneous rocks. The major source was the Jiangnan continental island arc with bimodal igneous rocks, lying to the south of the study area, together with a contribution from granites and gneisses uplifted and eroded in the Yangtze Block. Discrimination of tectonic setting using major and trace elements indicates that the source rocks originated in a transitional setting from active continental to passive margin, consistent with the failed intracontinental rift model for the evolution of the South China plate. The Niutitang Formation shales were deposited in a rift basin setting under conditions of anoxic bottom water in a redox-stratified water column, with organic-rich shales prospective for shale-gas production being found in deep-water downslope and basin environments rather than the shallow-water shelf.Zhou, S., Hwang, B.C.H., Lakey, P.S.J., Zuend, A., Abbatt, J.P.D., Shiraiwa, M., 2019. Multiphase reactivity of polycyclic aromatic hydrocarbons is driven by phase separation and diffusion limitations. Proceedings of the National Academy of Sciences 116, 11658-11663.: Polycyclic aromatic hydrocarbons (PAHs) are among the most prominent toxic compounds in the air. Heterogeneous reactions involving O3 can change the toxicity of PAHs, but the reaction mechanism and kinetics remain to be elucidated. Based on new experiments combined with state-of-the-art kinetic and thermodynamic models, we show that phase separation plays a critical role in the ozonolysis of PAHs mixed with secondary organic aerosols and organic oils. Ozonolysis products of PAHs phase separate to form viscous surface crusts, which protect underlying PAHs from ozonolysis to prolong their chemical lifetime. These results have significant implications for outdoor and indoor air quality by affecting PAH long-range transport and fate in indoor environments.Abstract: Benzo[a]pyrene (BaP), a key polycyclic aromatic hydrocarbon (PAH) often associated with soot particles coated by organic compounds, is a known carcinogen and mutagen. When mixed with organics, the kinetics and mechanisms of chemical transformations of BaP by ozone in indoor and outdoor environments are still not fully elucidated. Using direct analysis in real-time mass spectrometry (DART-MS), kinetics studies of the ozonolysis of BaP in thin films exhibited fast initial loss of BaP followed by a slower decay at long exposure times. Kinetic multilayer modeling demonstrates that the slow decay of BaP over long times can be simulated if there is slow diffusion of BaP from the film interior to the surface, resolving long-standing unresolved observations of incomplete PAH decay upon prolonged ozone exposure. Phase separation drives the slow diffusion time scales in multicomponent systems. Specifically, thermodynamic modeling predicts that BaP phase separates from secondary organic aerosol material so that the BaP-rich layer at the surface shields the inner BaP from ozone. Also, BaP is miscible with organic oils such as squalane, linoleic acid, and cooking oil, but its oxidation products are virtually immiscible, resulting in the formation of a viscous surface crust that hinders diffusion of BaP from the film interior to the surface. These findings imply that phase separation and slow diffusion significantly prolong the chemical lifetime of PAHs, affecting long-range transport of PAHs in the atmosphere and their fates in indoor environments.Zhou, X., Zhao, S., Xu, C., Chung, K.H., Shi, Q., 2019. Molecular structure of heavy petroleum: Revealed by molecular composition of ruthenium-ion-catalyzed oxidation products. Energy & Fuels 33, 4781-4791. oxidation (RICO) is an approach for investigating the structure of heavy oils by selectively removing aromatic carbon from petroleum fractions, while leaving the structural integrity of aliphatic units intact. Six petroleum vacuum residue (VR) samples originating from various sources were separated into saturate, aromatic, resin, and asphaltene (SARA) fractions. The aromatics, resins, and asphaltenes were subjected to the RICO reaction, and the products were characterized by gas chromatography (GC) and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). The alkyl side chains on aromatic cores of various VRs were significantly different in terms of their contents and carbon number distribution ranges. Normal alkyl side chains were dominant in all VRs; isoparaffin side chains were ubiquitous but in low concentrations, even in severely biodegraded oils. The content of the methyl group was much more than those of other alkyl groups and the content of the side chain decreased with an increased carbon number. For a given VR, the aromatics, resins, and asphaltenes had similar alkyl side chains, especially for aromatics and resins. The archipelago structures were rare, if they existed; nevertheless, asphaltenes appeared to have relatively more archipelago structures than aromatics and resins. FT-ICR MS analysis indicated that many structural moieties, except alkyl side chains, were connected to aromatic cores, which were abundant. The upper limits of the carbon number of alkyl chains determined by FT-ICR MS analysis were much higher than those obtained by GC analysis. For a given VR, the upper limits of the side chain carbon number in aromatics, resins, and asphaltenes were comparable. The relative abundances of short chains and naphthenic structures in asphaltenes were higher than those in resins and aromatics.Zhou, Y., Gao, Y., Xie, Q., Wang, J., Yue, Z., Wei, L., Yang, Y., Li, L., Chen, T., 2019. Reduction and transformation of nanomagnetite and nanomaghemite by a sulfate-reducing bacterium. Geochimica et Cosmochimica Acta 256, 66-81. and maghemite are important components of iron oxides that determine the magnetic properties of rocks, soils, and sediments, and are also materials with broad industrial applications. We investigated the reduction and transformation of both phases with a strain of sulfate-reducing bacteria (SRB). SRB growth resulted in 28.1% and 7.1% sulfate to acid volatile sulfur conversion in magnetite and maghemite, respectively. Transmission electron microscopy and X-ray photoelectron spectroscopy (XPS) analyses indicate that monosulfides (mackinawite and greigite) and polysulfides are the main secondary sulfides in the magnetite experiment, while the maghemite experiment also contained a high proportion of pyrite. XPS analyses indicate the reduction of Fe(III) to Fe(II) on the surface of magnetite and maghemite both by dissolved sulfides and SRB. M?ssbauer spectroscopy measurements reveal the formation of superparamagnetic phases in microbial experiments, which indicates the dissolution and particle size decrease of the two minerals both by dissolved sulfides and SRB. X-ray diffraction and M?ssbauer spectroscopy analyses suggest a complete transformation of nanomaghemite to nanomagnetite under the mediation of SRB through solid phase Fe(III) reduction. This transformation controls the changing and different patterns of both magnetic susceptibility and magnetic hysteresis for the two minerals. It is suggested that the structural similarity between magnetite and maghemite, and the conductivity of magnetite, constrain the unique solid phase transformation. Our findings indicate that the maghemite–magnetite solid solution is a potential natural battery for the growth of anaerobic microbes in sulfidic environments.Zhu, C.-j., Ren, J., Wan, J., Lin, B.-q., Yang, K., Li, Y., 2019. Methane adsorption on coals with different coal rank under elevated temperature and pressure. Fuel 254, 115686. methane recovery rates from coal mines reduces greenhouse gas emissions and benefits mining safety. In recent years, raising the temperature of coal seams has been recognized as a potential method of improving methane recovery. However, the effect of elevated temperature (especially higher than 80?°C) on methane adsorption on coals is rarely studied. In this study, we investigated the effects of elevated temperature and pressure on methane adsorption on different types (ranking) of coal, and their thermal stability. We found that for all six coal samples measured, maximum methane adsorption capacities sharply decrease with increasing temperature, showing a linear relationship (r2?=?0.705–0.975), and that coals began to pyrolyze at 267–500?°C depending on the coal type. We defined the temperature-dependent decrease in methane adsorption of coal as its thermal desorption capacity, and found that coal types with higher fixed carbon content have a larger magnitude thermal desorption capacity. These results indicate that raising the coal seam temperature while capturing methane is a promising method for obtaining higher coalbed methane recovery rates, reducing greenhouse gas emissions, and improving mining safety.Zhu, C., Qin, X., Li, Y., Gong, H., Li, Z., Xu, L., Dong, M., 2019. Adsorption and dissolution behaviors of CO2 and n-alkane mixtures in shale: Effects of the alkane type, shale properties and temperature. Fuel 253, 1361-1370. adsorbed and dissolved oil in the shale reservoirs can be produced during CO2 injection. However, the effects of different factors on the adsorption and dissolution behaviors of CO2 and oil mixtures in the shale were unclear, such as the oil composition, shale properties and temperature. In this study, a series of adsorption and dissolution tests of CO2 and different n-alkane mixtures in organic-rich shales were performed under different condition. The effects of the alkane type, shale properties and temperature on the adsorption and dissolution amount of mixtures and the replace ability of CO2 to n-alkane were discussed, respectively. The results indicate that the dissolution amount was decreased with the chain length of alkane and increased with TOC and temperature. The adsorption amount of the mixtures in shale was low and only account for 3–16% of total adsorption and dissolution amount, which mainly depended on the specific surface area of the shale samples. Additionally, the replace ability of CO2 to dissolved n-alkane was decreased with the chain length of alkane and temperature. However, there are no obvious rules between the replace ability with TOC of shale. This study can provide useful information for EOR of shale oil reservoirs by CO2 injection and the geological storage of CO2 in shale oil reservoir.Zhu, G., Chi, L., Zhang, Z., Li, T., Yang, H., Chen, W., Zhao, K., Yan, H., 2019. Composition and origin of molecular compounds in the condensate oils of the Dabei gas field, Tarim Basin, NW China. Petroleum Exploration and Development 46, 504-517. Dabei gas field in the Kuqa Depression of the Tarim Basin is the most complex and deep continental condensate gas field in China. Comprehensive two-dimensional gas chromatography-time of flight mass spectrometer (GC×GC-TOFMS) analysis was conducted on five condensate oil samples from this field. The results show that the samples have n-alkane series in complete preservation and rich adamantanes. According to the methyladamantane index, the condensate oil is the product of the source rock with vitrinite reflectance (Ro) of 1.3%–1.6%. According to the gas maturity calculated through carbon isotope and vitrinite reflectance, the natural gas is corresponding to Ro of 1.3%–1.7%, reflecting that the natural gas and condensate oil are basically formed during the same period at the high maturity stage of source rock. The Dabei gas field has favorable geological conditions for hydrocarbon accumulation: thick salt rock in the Paleogene acts as a regional high-quality caprock directly overlying the high-quality sandstone reservoir of the Cretaceous, the coal source rocks have high hydrocarbon generation intensity and provide continuous oil and gas, and the subsalt thrust structures develop in rows with rich faults, providing migration pathways for oil and gas migration. These factors together controlled the formation of the Dabei gas field.Zhu, G., Liu, F., Li, P., He, S., Zhu, S., Gao, Q., Feng, Y., 2019. Profiling free fatty acids in edible oils via magnetic dispersive extraction and comprehensive two-dimensional gas chromatography-mass spectrometry. Food Chemistry 297, Article 124998. analysis of free fatty acids (FFAs) in edible oils can provide important information for quality control and oil authentication. Herein, we report the comprehensive profiling of FFAs in edible oils via magnetic dispersive extraction combined with comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC-MS). A magnetic extractant was designed for dispersive extraction of FFAs. The extraction conditions were carefully optimized. To assess the extraction method, we first use the method for analysis of 7 targeted FFAs. The limits of detection range from 5.6 to 25.8 ng g-1, and the recoveries in oil samples are 81% to 107%. We then performed comprehensive profiling of untargeted FFAs in oil by combining the extraction method with GC×GC-MS. A total of 64 FFAs were identified positively or putatively. The proposed method can provide FFA fingerprint data to guide the processing, storage and authentication of edible oils.Zhu, G., Milkov, A.V., Zhang, Z., Sun, C., Zhou, X., Chen, F., Han, J., Zhu, Y., 2019. Formation and preservation of a giant petroleum accumulation in superdeep carbonate reservoirs in the southern Halahatang oil field area, Tarim Basin, China. American Association of Petroleum Geologists Bulletin 103, 1703-1743. petroleum accumulations worldwide with burial depths more than 7000 m (>23,000 ft) occur mostly in Mesozoic and Cenozoic reservoirs and yield predominantly natural gas. Recently, however, a giant oil accumulation with reservoir depths between 7000 m (23,000 ft) and 8000 m (26,000 ft) was discovered in the lower Paleozoic section in the southern part of the Halahatang region in the Tarim Basin, China. Petroleum sourced from lower Paleozoic rocks is contained in Ordovician karst fracture-cave reservoirs and sealed by Middle–Upper Ordovician limestones and mudstones. The newly discovered superdeep accumulation is among the deepest black single-phase oil accumulations worldwide and opens up new avenues for petroleum exploration in deep-marine carbonate reservoirs. Reservoir pressures are between 75 MPa (10,878 psi) and 85 MPa (12,328 psi), with pressure coefficients between 1.2 and 1.7 and temperatures ranging between 140°C (284°F) and 172°C (342°F). Charging and accumulation of petroleum occurred during the late Hercynian orogeny, followed by subsequent gradual deep burial, which took place before rapid subsidence beginning circa 5 Ma. Following subsidence, the thickness of overlying strata increased by more than 2000 m (>6600 ft) before finally attaining current depth. Therefore, this oil accumulation represents a well-preserved ancient petroleum system. Based on the geochemical features of oils and gases, the crude oils can be classified as mature, sourced from mixed marine organofacies of shale, marl, and carbonate, whereas the gases were cogenerated with oils. Despite very high present-day reservoir temperatures, no oil cracking has occurred because of the relatively short exposure of oils to high temperatures in a low geothermal gradient regime. Thus, there is significant exploration potential under similar conditions for liquid petroleum in superdeep strata. Faults and reservoirs are major factors controlling petroleum accumulation. Interlayer karsts with excellent fracture-cavity connectivity developed adjacent to faults, generally resulting in the enrichment of oil and gas along fault zones. High-quality reservoirs in this area are easy to identify because they exhibit strong bead-like amplitude features in seismic sections. Wells located near faults produce relatively large amounts of oil and gas. Effective karst fracture-cave reservoirs with noncracked oil may exist below 8000 m (26,000 ft) in the Tarim Basin and represent a significant exploration target in China.Zhu, M., Jiang, B., Li, S., Yu, Q., Yu, X., Zhang, Y., Bi, X., Yu, J., George, C., Yu, Z., Wang, X., 2019. Organosulfur compounds formed from heterogeneous reaction between SO2 and particulate-bound unsaturated fatty acids in ambient air. Environmental Science & Technology Letters 6, 318-322. studies have demonstrated that uptake of SO2 on oleic acid (OLA) could directly produce organosulfates (OS); yet, it is unknown whether this pathway is significant in secondary organosulfur production in ambient air. Here, we collected filter-based samples of ambient fine particles (PM2.5) in the Pearl River Delta region in southern China and determined organosulfur compounds with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). The results are in agreement with the occurrence of organosulfurs formed from the reactive uptake of SO2 by OLA and a wider range of C14–C24 unsaturated fatty acids in ambient air as reported by laboratory studies, as well as additional species that are likely oxidation products of the primary products previously identified. OS formed from the heterogeneous reaction between SO2 and unsaturated fatty acids accounted for 7%–13% sulfur of the CHOS species and 5%–7% sulfur of all the CHOS and CHONS species. They contributed about 0.3‰–0.9‰ of the total organic mass of the fine particle samples collected.Zhu, X.-K., Sun, J., Li, Z.-H., 2019. Iron isotopic variations of the Cryogenian banded iron formations: A new model. Precambrian Research 331, Article 105359. Fe isotope composition of banded iron formation (BIF) is regarded as a powerful tracer in paleoceanography, and the Cryogenian banded iron formation associated with “Snowball Earth Events” provides a precious record of environmental change in the Neoproterozoic. However, Fe isotope studies on Cryogenian BIFs are rare and previous interpretations of Cryogenian Fe isotope data are problematic. Here we present a systematic investigation of the Fe isotope composition of the Cryogenian Xinyu BIF sections from four localities in the Yangtze region, South China. These BIF sections comprise banded magnetite quartzite, banded chlorite-magnetite quartzite, and magnetite-bearing chlorite phyllite, in stratigraphically ascending order. The δ56FeIRMM-014 values of the Xinyu BIF vary significantly and show an overall increase upsection, from ca. 0‰ to ca. 1.5‰. This stratigraphic trend in Fe isotope compositions is similar to those reported previously for Cryogenian BIFs in North America and Australia, and thus seems to be a common phenomenon. We interpret Fe isotope variation in Cryogenian BIF to be essentially controlled by varying degrees of Fe precipitation in seawater, rather than resulted from “a water column Fe isotope gradient” as proposed previously. The variation in the degree of Fe precipitation can be controlled by changes of Eh and/or pH conditions in seawater resulting from transgression or ocean acidification.Zhuo, X., Huang, H., Lan, F., He, C., Pan, Q., Zhang, Y., Shi, Q., 2019. Molecular transformation of dissolved organic matter in high-temperature hydrogen peroxide oxidation of a refinery wastewater. Environmental Chemistry Letters 17, 1117-1123. oxidation processes have been extensively used in industrial wastewater treatment. However, the molecular transformation of dissolved organic matter (DOM) during oxidation process is poorly known. In this study, a refinery wastewater was oxidized at high temperature using H2O2. Negative-ion electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry was applied to analyze the molecular changes of DOM. 68 heteroatom class species including Ox, OxS1, OxS2, N1Ox, N2Ox, N3Ox, and N1OxS1 were assigned from a single spectrum of the raw water, in which Ox and OxS1 class species were dominant. The molecular composition changed during oxidation. Sulfur- and nitrogen-containing compounds were almost completely removed. The removal of oxygen compounds by oxidation and the new production of oxygen compounds were simultaneous. Chain scission and oxidation of Ox compounds were the major reactions. Abundant chlorinated compounds were detected in the oxidation product. These compounds are considered as reaction products of DOM molecules with chloride ions in the water.Zou, C., Guo, Q., Yang, Z., Wu, S., Chen, N., Lin, S., Pan, S., 2019. Resource potential and core area prediction of lacustrine tight oil: The Triassic Yanchang Formation in Ordos Basin, China. American Association of Petroleum Geologists Bulletin 103, 1493-1523. liquid-rich hydrocarbons in marine shale systems in North America, the Triassic Yanchang oil is preserved in tight sandstone reservoirs deposited in a lacustrine setting. The tight reservoir covers an area of 30,000 km2 (11,600 mi2) and is characterized by ultralow permeability (～0.001–1.00 md [～0.001 × 10?3–1.00 × 10?3 μm2]), a low subsurface pressure coefficient (0.6–0.8), and low single-well yield (several tons [10–40 bbl] to >10 tons [>70 bbl] per day). The reservoir also features a high content of quartz, feldspar, and carbonate (averaging 70%–80%) and low crude oil density of 0.84 g/cm3 (36.5° API) with an oil saturation of approximately 60%–80%. For the first time, this study employs the assessment of petroleum in-place resources based on the genesis and statistics predicting method (GSPM) and estimated ultimate recovery method for the tight oil in the Ordos Basin. The advantage of GSPM over previously reported methodologies is the suitable combination of genetic and statistical methods to estimate proximally sourced tight oil. The results show that the total in-place resource potential of the investigated tight oil is approximately 42.26 × 108 t (～295.82 × 108 bbl), with an average abundance of 15 × 104 t/km2 (99 × 104 bbl/mi2). The recoverable resources for the 50% probability of the Chang 7 tight oil accumulation is 3.11 × 108 t (21.77 × 108 bbl) in the Ordos Basin. The top two grades of the Chang 7 tight oil core area cover the total area of three layers comprising 12,745 km2 (4921 mi2), with 22.51 × 108 t (157.57 × 108 bbl) of in situ resources. Furthermore, the four most promising zones have been identified.Zou, C., Yang, Z., Huang, S., Ma, F., Sun, Q., Li, F., Pan, S., Tian, W., 2019. Resource types, formation, distribution and prospects of coal-measure gas. Petroleum Exploration and Development 46, 451-462. gas is the natural gas generated by coal, carbonaceous shale, and dark shale in coal-measure strata. It includes resources of continuous-type coalbed methane (CBM), shale gas and tight gas reservoirs, and trap-type coal-bearing gas reservoirs. Huge in resources, it is an important gas source in the natural gas industry. The formation and distribution characteristics of coal-measure gas in San Juan, Surat, West Siberia and Ordos basins are introduced in this paper. By reviewing the progress of exploration and development of coal-measure gas around the world, the coal-measure gas is confirmed as an important strategic option for gas supply. This understanding is mainly manifested in three aspects. First, globally, the Eurasian east-west coal-accumulation belt and North American north-south coal-accumulation belt are two major coal-accumulation areas in the world, and the Late Carboniferous–Permian, Jurassic and end of Late Cretaceous–Neogene are 3 main coal-accumulation periods. Second, continuous-type and trap-type are two main accumulation modes of coal-measure gas; it is proposed that the area with gas generation intensity of greater than 10×108 m3/km2 is essential for the formation of large coal-measure gas field, and the CBM generated by medium- to high-rank coal is usually enriched in syncline, while CBM generated by low-rank coal is likely to accumulate when the source rock and caprock are in good configuration. Third, it is predicted that coal-measure gas around the world has huge remaining resources, coal-measure gas outside source is concentrated in Central Asia-Russia, the United States, Canada and other countries/regions, while CBM inside source is largely concentrated in 12 countries. The production of coal-measure gas in China is expected to exceed 1000×108 m3 by 2030, including (500–550)×108 m3 conventional coal-measure gas, (400–450)×108 m3 coal-measure tight gas, and (150–200)×108 m3 CBM.Zou, H., Cui, W., Wang, Z.-L., Wang, Z., 2019. The hitchhiker's guide to core samples: Key issues and lessons learned. Science of The Total Environment 685, 867-885. samples may be used as valuable geochronometers for storing historical pollution footprints of organic pollutants. A number of studies have used core samples to evaluate temporal depositions, loading inventories, and effectiveness of environmental mitigation measures. However, in order to get a reliable estimation, certain prerequisites must be satisfied to rule out various confounding factors such as biomixing and melting. This review aims to understand when core samples can or cannot be used as natural archives for organic pollutants. First, we systematically review existing studies of organic pollutants in soil, sediment and ice cores and possible factors that may influence post-depositional fate of chemicals. Then, building on field evidence, model simulation and laboratory leaching tests findings, we discuss issues of post-depositional downward movement in detail. To assist future core sample studies, we summarize lessons learned on study design in the context of sampling design, data analysis, and data reporting. In particular, the combination of a careful study design and appropriate numerical model(s) will help to elevate core samples as a more reliable tool for retrospective understanding of chemical pollution. This review is an initial step toward a better and more accurate use of core samples, and further interdisciplinary cooperation is needed to develop standardized protocols, guidelines and tools.Zou, J., Chen, W., Yang, D., Yuan, J., Jiao, Y.-Y., 2019. Fractal characteristics of the anisotropic microstructure and pore distribution of low-rank coal. American Association of Petroleum Geologists Bulletin 103, 1297-1319. coal reserves account for nearly 55% of the national coal reserves in China, and it is extremely important to understand their anisotropic microstructure and coalbed methane storage and sorption characteristics. In this study, microstructures that develop parallel to and perpendicular to bedding of low-rank coals are studied through scanning electron microscopy. The micromorphology and microfracture and mineral distributions are examined. Based on fractal theory and digital image processing technology, the fractal box-counting dimensions of microfracture distributions that form parallel as well as perpendicular to the coal bedding planes are calculated, and the anisotropic fractal characteristics of these microfracture distributions are characterized. The pore-size distribution and the fractal characteristics of the microscopic pore structure are systematically examined by means of nitrogen adsorption and mercury intrusion tests. The results of the fractal box-counting dimension calculations indicate that microfractures distributed perpendicular to coal bedding are rougher and more irregular than those distributed along a bedding plane, with the former exhibiting higher space filling and methane adsorption capacity. The fractal dimension of the microscopic pore structure reveals two inflection points measuring approximately 5 and 80 nm, thereby indicating that the low-rank coal exhibits a microscopic pore structure with a three-level fractal characteristic. ................
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