Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

Chadwick, Grayson L.; Skennerton, Connor T.; Laso-Pérez, Rafael; Leu, Andy O.; Speth, Daan R.; Yu, Hang; Morgan-Lang, Connor; Hatzenpichler, Roland; Goudeau, Danielle; Malmstrom, Rex; Brazelton, William J.; Woyke, Tanja; Hallam, Steven J.; Tyson, Gene W.; Wegener, Gunter; Boetius, Antje; Orphan, Victoria J.; Wang, ed., Fengping

doi:10.1371/journal.pbio.3001508

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

Journal Article · Wed Jan 05 00:00:00 EST 2022 · PLoS Biology (Online)

DOI:https://doi.org/10.1371/journal.pbio.3001508· OSTI ID:1863468

; ; Laso-Pérez, Rafael; Leu, Andy O.; ; Yu, Hang; Morgan-Lang, Connor; ; Goudeau, Danielle; ; Brazelton, William J.; ; ; ; ; ; ; Wang, ed., Fengping

The anaerobic oxidation of methane coupled to sulfate reduction is a microbially mediated process requiring a syntrophic partnership between anaerobic methanotrophic (ANME) archaea and sulfate-reducing bacteria (SRB). Based on genome taxonomy, ANME lineages are polyphyletic within the phylum Halobacterota , none of which have been isolated in pure culture. Here, we reconstruct 28 ANME genomes from environmental metagenomes and flow sorted syntrophic consortia. Together with a reanalysis of previously published datasets, these genomes enable a comparative analysis of all marine ANME clades. We review the genomic features that separate ANME from their methanogenic relatives and identify what differentiates ANME clades. Large multiheme cytochromes and bioenergetic complexes predicted to be involved in novel electron bifurcation reactions are well distributed and conserved in the ANME archaea, while significant variations in the anabolic C1 pathways exists between clades. Our analysis raises the possibility that methylotrophic methanogenesis may have evolved from a methanotrophic ancestor.

View Journal Article

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Science Foundation (NSF); USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1863468

Alternate ID(s):: OSTI ID: 1838397
OSTI ID: 1865081

Journal Information:: PLoS Biology (Online), Journal Name: PLoS Biology (Online) Journal Issue: 1 Vol. 20; ISSN 1545-7885

Publisher:: Public Library of Science (PLoS)Copyright Statement

Country of Publication:: United States

Language:: English

References (225)

Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules Haimovitz, Rachel; Barak, Yoav; Morag, Ely PROTEOMICS, Vol. 8, Issue 5 https://doi.org/10.1002/pmic.200700486	journal	March 2008
Structure of Coenzyme F420 Dependent Methylenetetrahydromethanopterin Reductase from Two Methanogenic Archaea Shima, S.; Warkentin, E.; Grabarse, W. Journal of Molecular Biology, Vol. 300, Issue 4 https://doi.org/10.1006/jmbi.2000.3909	journal	July 2000
Syntrophism among Prokaryotes Schink, Bernhard; Stams, Alfons J. M. The Prokaryotes https://doi.org/10.1007/0-387-30742-7_11	book	January 2006
ggplot2 Wickham, Hadley Springer New York, NY https://doi.org/10.1007/978-0-387-98141-3	book	January 2009
Gram-Negative Mesophilic Sulfate-Reducing Bacteria Widdel, Friedrich; Bak, Friedhelm The Prokaryotes https://doi.org/10.1007/978-1-4757-2191-1_21	book	January 1992
One carbon metabolism in methanogenic bacteria: Cellular characterization and growth of Methanosarcina barkeri Weimer, P. J.; Zeikus, J. G. Archives of Microbiology, Vol. 119, Issue 1 https://doi.org/10.1007/BF00407927	journal	January 1978
Tetrahydromethanopterin-dependent serine transhydroxymethylase from Methanobacterium thermoautotrophicum Hoyt, J. C.; Oren, A.; Escalante-Semerena, J. C. Archives of Microbiology, Vol. 145, Issue 2 https://doi.org/10.1007/BF00446773	journal	July 1986
Biochemistry, evolution and physiological function of the Rnf complex, a novel ion-motive electron transport complex in prokaryotes Biegel, Eva; Schmidt, Silke; González, José M. Cellular and Molecular Life Sciences, Vol. 68, Issue 4 https://doi.org/10.1007/s00018-010-0555-8	journal	November 2010
Physiological role of the F 420 -non-reducing hydrogenase (Mvh) from Methanothermobacter marburgensis Stojanowic, Alexander; Mander, Gerd J.; Duin, Evert C. Archives of Microbiology, Vol. 180, Issue 3 https://doi.org/10.1007/s00203-003-0577-9	journal	September 2003
Tetrahydrofolate-specific enzymes in Methanosarcina barkeri and growth dependence of this methanogenic archaeon on folic acid or p-aminobenzoic acid Buchenau, B�rbel; Thauer, Rudolf K. Archives of Microbiology, Vol. 182, Issue 4 https://doi.org/10.1007/s00203-004-0714-0	journal	September 2004
Function of coenzyme F 420 -dependent NADP reductase in methanogenic archaea containing an NADP-dependent alcohol dehydrogenase Berk, Holger; Thauer, R. K. Archives of Microbiology, Vol. 168, Issue 5 https://doi.org/10.1007/s002030050514	journal	October 1997
The Evolution of Histidine Biosynthesis in Archaea: Insights into the his Genes Structure and Organization in LUCA Fondi, Marco; Emiliani, Giovanni; Liò, Pietro Journal of Molecular Evolution, Vol. 69, Issue 5 https://doi.org/10.1007/s00239-009-9286-6	journal	November 2009
Thermodynamic and kinetic requirements in anaerobic methane oxidizing consortia exclude hydrogen, acetate, and methanol as possible electron shuttles Sørensen, K. B.; Finster, K.; Ramsing, N. B. Microbial Ecology, Vol. 42, Issue 1 https://doi.org/10.1007/s002480000083	journal	June 2001
Effect of methanogenic substrates on anaerobic oxidation of methane and sulfate reduction by an anaerobic methanotrophic enrichment Meulepas, Roel J. W.; Jagersma, Christian G.; Khadem, Ahmad F. Applied Microbiology and Biotechnology, Vol. 87, Issue 4 https://doi.org/10.1007/s00253-010-2597-0	journal	May 2010
Shuttling happens: soluble flavin mediators of extracellular electron transfer in Shewanella Brutinel, Evan D.; Gralnick, Jeffrey A. Applied Microbiology and Biotechnology, Vol. 93, Issue 1 https://doi.org/10.1007/s00253-011-3653-0	journal	November 2011
Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process Latka, Agnieszka; Maciejewska, Barbara; Majkowska-Skrobek, Grazyna Applied Microbiology and Biotechnology, Vol. 101, Issue 8 https://doi.org/10.1007/s00253-017-8224-6	journal	March 2017
High-resolution mapping of large gas emitting mud volcanoes on the Egyptian continental margin (Nile Deep Sea Fan) by AUV surveys Dupré, S.; Buffet, G.; Mascle, J. Marine Geophysical Researches, Vol. 29, Issue 4 https://doi.org/10.1007/s11001-009-9063-3	journal	December 2008
F ₄₂₀ H ₂ :NADP oxidoreductase from Methanobacterium thermoautotrophicum : identification of the encoding gene via functional overexpression in Escherichia coli Berk, Holger; Thauer, Rudolf K. FEBS Letters, Vol. 438, Issue 1-2 https://doi.org/10.1016/S0014-5793(98)01288-5	journal	October 1998
Cellulosome-like sequences in Archaeoglobus fulgidus : an enigmatic vestige of cohesin and dockerin domains Bayer, Edward A.; Coutinho, Pedro M.; Henrissat, Bernard FEBS Letters, Vol. 463, Issue 3 https://doi.org/10.1016/S0014-5793(99)01634-8	journal	December 1999
Three-dimensional Reconstruction of the Surface Protein of the Extremely Thermophilic Archaebacterium Archaeoglobus fulgidus Kessel, Martin; Volker, Susanne; Santarius, Ute Systematic and Applied Microbiology, Vol. 13, Issue 3 https://doi.org/10.1016/S0723-2020(11)80187-6	journal	August 1990
The organisation of proton motive and non-proton motive redox loops in prokaryotic respiratory systems Simon, Jörg; van Spanning, Rob J. M.; Richardson, David J. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1777, Issue 12 https://doi.org/10.1016/j.bbabio.2008.09.008	journal	December 2008
Energy conservation via electron bifurcating ferredoxin reduction and proton/Na+ translocating ferredoxin oxidation Buckel, Wolfgang; Thauer, Rudolf K. Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 2 https://doi.org/10.1016/j.bbabio.2012.07.002	journal	February 2013
The prokaryotic Mo/W-bisPGD enzymes family: A catalytic workhorse in bioenergetic Grimaldi, Stéphane; Schoepp-Cothenet, Barbara; Ceccaldi, Pierre Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1827, Issue 8-9 https://doi.org/10.1016/j.bbabio.2013.01.011	journal	August 2013
Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens Welte, Cornelia; Deppenmeier, Uwe Biochimica et Biophysica Acta (BBA) - Bioenergetics, Vol. 1837, Issue 7 https://doi.org/10.1016/j.bbabio.2013.12.002	journal	July 2014
Evolutionary origins of members of a superfamily of integral membrane cytochrome c biogenesis proteins Lee, Jong-Hoon; Harvat, Edgar M.; Stevens, Julie M. Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1768, Issue 9 https://doi.org/10.1016/j.bbamem.2007.04.022	journal	September 2007
Reduction of low potential electron acceptors requires the CbcL inner membrane cytochrome of Geobacter sulfurreducens Zacharoff, Lori; Chan, Chi Ho; Bond, Daniel R. Bioelectrochemistry, Vol. 107 https://doi.org/10.1016/j.bioelechem.2015.08.003	journal	February 2016
Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers Wang, Fengbin; Gu, Yangqi; O’Brien, J. Patrick Cell, Vol. 177, Issue 2 https://doi.org/10.1016/j.cell.2019.03.029	journal	April 2019
Geological, geochemical, and microbial processes at the hydrate-bearing Håkon Mosby mud volcano: a review Milkov, Alexei V.; Vogt, Peter R.; Crane, Kathy Chemical Geology, Vol. 205, Issue 3-4 https://doi.org/10.1016/j.chemgeo.2003.12.030	journal	May 2004
A variant System I for cytochrome c biogenesis in archaea and some bacteria has a novel CcmE and no CcmH Allen, James W. A.; Harvat, Edgar M.; Stevens, Julie M. FEBS Letters, Vol. 580, Issue 20 https://doi.org/10.1016/j.febslet.2006.07.073	journal	August 2006
Anaerobic oxidation of methane with sulfate: on the reversibility of the reactions that are catalyzed by enzymes also involved in methanogenesis from CO2 Thauer, Rudolf K. Current Opinion in Microbiology, Vol. 14, Issue 3 https://doi.org/10.1016/j.mib.2011.03.003	journal	June 2011
Cytochrome c biogenesis: the Ccm system Sanders, Carsten; Turkarslan, Serdar; Lee, Dong-Woo Trends in Microbiology, Vol. 18, Issue 6 https://doi.org/10.1016/j.tim.2010.03.006	journal	June 2010
Homocysteine Is Biosynthesized from Aspartate Semialdehyde and Hydrogen Sulfide in Methanogenic Archaea Allen, Kylie D.; Miller, Danielle V.; Rauch, Benjamin J. Biochemistry, Vol. 54, Issue 20 https://doi.org/10.1021/acs.biochem.5b00118	journal	May 2015
Methanococcus maripaludis Employs Three Functional Heterodisulfide Reductase Complexes for Flavin-Based Electron Bifurcation Using Hydrogen and Formate Milton, Ross D.; Ruth, John C.; Deutzmann, Jörg S. Biochemistry, Vol. 57, Issue 32 https://doi.org/10.1021/acs.biochem.8b00662	journal	July 2018
Flavin-Based Electron Bifurcation, A New Mechanism of Biological Energy Coupling Buckel, Wolfgang; Thauer, Rudolf K. Chemical Reviews, Vol. 118, Issue 7 https://doi.org/10.1021/acs.chemrev.7b00707	journal	February 2018
The Tetraheme Cytochrome CymA Is Required for Anaerobic Respiration with Dimethyl Sulfoxide and Nitrite in Shewanella oneidensis ^† Schwalb, Carsten; Chapman, Stephen K.; Reid, Graeme A. Biochemistry, Vol. 42, Issue 31 https://doi.org/10.1021/bi034456f	journal	August 2003
l -Aspartate Semialdehyde and a 6-Deoxy-5-ketohexose 1-Phosphate Are the Precursors to the Aromatic Amino Acids in Methanocaldococcus jannaschii White, Robert H. Biochemistry, Vol. 43, Issue 23 https://doi.org/10.1021/bi0495127	journal	May 2004
Methylglyoxal Is an Intermediate in the Biosynthesis of 6-Deoxy-5-ketofructose-1-phosphate: A Precursor for Aromatic Amino Acid Biosynthesis in Methanocaldococcus jannaschii ^† White, Robert H.; Xu, Huimin Biochemistry, Vol. 45, Issue 40 https://doi.org/10.1021/bi061018a	journal	October 2006
The Mononuclear Molybdenum Enzymes Hille, Russ; Hall, James; Basu, Partha Chemical Reviews, Vol. 114, Issue 7 https://doi.org/10.1021/cr400443z	journal	January 2014
Field and laboratory studies of methane oxidation in an anoxic marine sediment: Evidence for a methanogen-sulfate reducer consortium Hoehler, Tori M.; Alperin, Marc J.; Albert, Daniel B. Global Biogeochemical Cycles, Vol. 8, Issue 4 https://doi.org/10.1029/94GB01800	journal	December 1994
Methane-consuming archaebacteria in marine sediments Hinrichs, Kai-Uwe; Hayes, John M.; Sylva, Sean P. Nature, Vol. 398, Issue 6730 https://doi.org/10.1038/19751	journal	April 1999
A role for excreted quinones in extracellular electron transfer Newman, Dianne K.; Kolter, Roberto Nature, Vol. 405, Issue 6782 https://doi.org/10.1038/35011098	journal	May 2000
A marine microbial consortium apparently mediating anaerobic oxidation of methane Boetius, Antje; Ravenschlag, Katrin; Schubert, Carsten J. Nature, Vol. 407, Issue 6804 https://doi.org/10.1038/35036572	journal	October 2000
The structural basis for peptide selection by the transport receptor OppA Berntsson, Ronnie P-A; Doeven, Mark K.; Fusetti, Fabrizia The EMBO Journal, Vol. 28, Issue 9 https://doi.org/10.1038/emboj.2009.65	journal	March 2009
High rates of denitrification and nitrate removal in cold seep sediments Bowles, Marshall; Joye, Samantha The ISME Journal, Vol. 5, Issue 3 https://doi.org/10.1038/ismej.2010.134	journal	October 2010
Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways Wang, Feng-Ping; Zhang, Yu; Chen, Ying The ISME Journal, Vol. 8, Issue 5 https://doi.org/10.1038/ismej.2013.212	journal	December 2013
Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses Dekas, Anne E.; Connon, Stephanie A.; Chadwick, Grayson L. The ISME Journal, Vol. 10, Issue 3 https://doi.org/10.1038/ismej.2015.145	journal	September 2015
The growing tree of Archaea: new perspectives on their diversity, evolution and ecology Adam, Panagiotis S.; Borrel, Guillaume; Brochier-Armanet, Céline The ISME Journal, Vol. 11, Issue 11 https://doi.org/10.1038/ismej.2017.122	journal	August 2017
A conspicuous nickel protein in microbial mats that oxidize methane anaerobically Krüger, Martin; Meyerdierks, Anke; Glöckner, Frank Oliver Nature, Vol. 426, Issue 6968 https://doi.org/10.1038/nature02207	journal	December 2003
Novel microbial communities of the Haakon Mosby mud volcano and their role as a methane sink Niemann, Helge; Lösekann, Tina; de Beer, Dirk Nature, Vol. 443, Issue 7113 https://doi.org/10.1038/nature05227	journal	October 2006
Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel Wang, Yi; Huang, Yongjian; Wang, Jiawei Nature, Vol. 462, Issue 7272 https://doi.org/10.1038/nature08610	journal	November 2009
The key nickel enzyme of methanogenesis catalyses the anaerobic oxidation of methane Scheller, Silvan; Goenrich, Meike; Boecher, Reinhard Nature, Vol. 465, Issue 7298 https://doi.org/10.1038/nature09015	journal	June 2010
Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically Shima, Seigo; Krueger, Martin; Weinert, Tobias Nature, Vol. 481, Issue 7379 https://doi.org/10.1038/nature10663	journal	November 2011
Zero-valent sulphur is a key intermediate in marine methane oxidation Milucka, Jana; Ferdelman, Timothy G.; Polerecky, Lubos Nature, Vol. 491, Issue 7425 https://doi.org/10.1038/nature11656	journal	November 2012
Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage Haroon, Mohamed F.; Hu, Shihu; Shi, Ying Nature, Vol. 500, Issue 7464 https://doi.org/10.1038/nature12375	journal	July 2013
PAAR-repeat proteins sharpen and diversify the type VI secretion system spike Shneider, Mikhail M.; Buth, Sergey A.; Ho, Brian T. Nature, Vol. 500, Issue 7462 https://doi.org/10.1038/nature12453	journal	August 2013
Single cell activity reveals direct electron transfer in methanotrophic consortia McGlynn, Shawn E.; Chadwick, Grayson L.; Kempes, Christopher P. Nature, Vol. 526, Issue 7574 https://doi.org/10.1038/nature15512	journal	September 2015
Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria Wegener, Gunter; Krukenberg, Viola; Riedel, Dietmar Nature, Vol. 526, Issue 7574 https://doi.org/10.1038/nature15733	journal	October 2015
Thermophilic archaea activate butane via alkyl-coenzyme M formation Laso-Pérez, Rafael; Wegener, Gunter; Knittel, Katrin Nature, Vol. 539, Issue 7629 https://doi.org/10.1038/nature20152	journal	October 2016
Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes Albertsen, Mads; Hugenholtz, Philip; Skarshewski, Adam Nature Biotechnology, Vol. 31, Issue 6 https://doi.org/10.1038/nbt.2579	journal	May 2013
KBase: The United States Department of Energy Systems Biology Knowledgebase Arkin, Adam P.; Cottingham, Robert W.; Henry, Christopher S. Nature Biotechnology, Vol. 36, Issue 7 https://doi.org/10.1038/nbt.4163	journal	July 2018
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life Parks, Donovan H.; Chuvochina, Maria; Waite, David W. Nature Biotechnology, Vol. 36, Issue 10 https://doi.org/10.1038/nbt.4229	journal	August 2018
Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system Speth, Daan R.; in ’t Zandt, Michiel H.; Guerrero-Cruz, Simon Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11172	journal	March 2016
Fast and sensitive protein alignment using DIAMOND Buchfink, Benjamin; Xie, Chao; Huson, Daniel H. Nature Methods, Vol. 12, Issue 1 https://doi.org/10.1038/nmeth.3176	journal	November 2014
Extracellular electron transfer mechanisms between microorganisms and minerals Shi, Liang; Dong, Hailiang; Reguera, Gemma Nature Reviews Microbiology, Vol. 14, Issue 10 https://doi.org/10.1038/nrmicro.2016.93	journal	August 2016
Autotrophic carbon fixation in archaea Berg, Ivan A.; Kockelkorn, Daniel; Ramos-Vera, W. Hugo Nature Reviews Microbiology, Vol. 8, Issue 6, p. 447-460 https://doi.org/10.1038/nrmicro2365	journal	May 2010
The archaeal cell envelope Albers, Sonja-Verena; Meyer, Benjamin H. Nature Reviews Microbiology, Vol. 9, Issue 6 https://doi.org/10.1038/nrmicro2576	journal	May 2011
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction Cai, Chen; Leu, Andy O.; Xie, Guo-Jun The ISME Journal, Vol. 12, Issue 8 https://doi.org/10.1038/s41396-018-0109-x	journal	April 2018
Cryptic CH4 cycling in the sulfate–methane transition of marine sediments apparently mediated by ANME-1 archaea Beulig, F.; Røy, H.; McGlynn, S. E. The ISME Journal, Vol. 13, Issue 2 https://doi.org/10.1038/s41396-018-0273-z	journal	September 2018
Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi Boyd, Joel A.; Jungbluth, Sean P.; Leu, Andy O. The ISME Journal, Vol. 13, Issue 5 https://doi.org/10.1038/s41396-018-0343-2	journal	January 2019
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria Nature Microbiology, Vol. 2, Issue 11 https://doi.org/10.1038/s41564-017-0012-7	journal	September 2017
Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea Borrel, Guillaume; Adam, Panagiotis S.; McKay, Luke J. Nature Microbiology, Vol. 4, Issue 4 https://doi.org/10.1038/s41564-019-0363-3	journal	March 2019
Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep Chen, Song-Can; Musat, Niculina; Lechtenfeld, Oliver J. Nature, Vol. 568, Issue 7750 https://doi.org/10.1038/s41586-019-1063-0	journal	March 2019
Electric field stimulates production of highly conductive microbial OmcZ nanowires Yalcin, Sibel Ebru; O’Brien, J. Patrick; Gu, Yangqi Nature Chemical Biology, Vol. 16, Issue 10 https://doi.org/10.1038/s41589-020-0623-9	journal	August 2020
Cryo-EM reveals the structural basis of long-range electron transport in a cytochrome-based bacterial nanowire Filman, David J.; Marino, Stephen F.; Ward, Joy E. Communications Biology, Vol. 2, Issue 1 https://doi.org/10.1038/s42003-019-0448-9	journal	June 2019
Nitrate and periplasmic nitrate reductases Sparacino-Watkins, Courtney; Stolz, John F.; Basu, Partha Chem. Soc. Rev., Vol. 43, Issue 2 https://doi.org/10.1039/C3CS60249D	journal	January 2014
Methylcobalamin:homocysteine methyltransferase from Methanobacterium thermoautotrophicum . Identification as the metE gene product Schroder, Ilka; Thauer, Rudolf K. European Journal of Biochemistry, Vol. 263, Issue 3 https://doi.org/10.1046/j.1432-1327.1999.00559.x	journal	August 1999
Structure of the F ₄₂₀ H ₂ :quinone oxidoreductase of Archaeoglobus fulgidus: Identification and overproduction of the F ₄₂₀ H ₂ -oxidizing subunit Brüggemann, Holger; Falinski, Frank; Deppenmeier, Uwe European Journal of Biochemistry, Vol. 267, Issue 18 https://doi.org/10.1046/j.1432-1327.2000.01657.x	journal	September 2000
New perspectives on anaerobic methane oxidation Valentine, David L.; Reeburgh, William S. Environmental Microbiology, Vol. 2, Issue 5 https://doi.org/10.1046/j.1462-2920.2000.00135.x	journal	October 2000
In vitro demonstration of anaerobic oxidation of methane coupled to sulphate reduction in sediment from a marine gas hydrate area Nauhaus, Katja; Boetius, Antje; Kruger, Martin Environmental Microbiology, Vol. 4, Issue 5 https://doi.org/10.1046/j.1462-2920.2002.00299.x	journal	May 2002
Diverse syntrophic partnerships from deep-sea methane vents revealed by direct cell capture and metagenomics Pernthaler, A.; Dekas, A. E.; Brown, C. T. Proceedings of the National Academy of Sciences, Vol. 105, Issue 19 https://doi.org/10.1073/pnas.0711303105	journal	May 2008
Multiple archaeal groups mediate methane oxidation in anoxic cold seep sediments Orphan, V. J.; House, C. H.; Hinrichs, K.-U. Proceedings of the National Academy of Sciences, Vol. 99, Issue 11, p. 7663-7668 https://doi.org/10.1073/pnas.072210299	journal	May 2002
Structure of the 2 2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarbonylase/synthase complex Gong, W.; Hao, B.; Wei, Z. Proceedings of the National Academy of Sciences, Vol. 105, Issue 28 https://doi.org/10.1073/pnas.0800415105	journal	July 2008
Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys Brazelton, W. J.; Ludwig, K. A.; Sogin, M. L. Proceedings of the National Academy of Sciences, Vol. 107, Issue 4 https://doi.org/10.1073/pnas.0905369107	journal	January 2010
Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase Costa, K. C.; Wong, P. M.; Wang, T. Proceedings of the National Academy of Sciences, Vol. 107, Issue 24 https://doi.org/10.1073/pnas.1003653107	journal	June 2010
Carbon and sulfur back flux during anaerobic microbial oxidation of methane and coupled sulfate reduction Holler, T.; Wegener, G.; Niemann, H. Proceedings of the National Academy of Sciences, Vol. 108, Issue 52 https://doi.org/10.1073/pnas.1106032108	journal	December 2011
Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria Carlson, H. K.; Iavarone, A. T.; Gorur, A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 5 https://doi.org/10.1073/pnas.1112905109	journal	January 2012
Structure of the surface layer of the methanogenic archaean Methanosarcina acetivorans Arbing, M. A.; Chan, S.; Shin, A. Proceedings of the National Academy of Sciences, Vol. 109, Issue 29 https://doi.org/10.1073/pnas.1120595109	journal	July 2012
Autotrophy as a predominant mode of carbon fixation in anaerobic methane-oxidizing microbial communities Kellermann, M. Y.; Wegener, G.; Elvert, M. Proceedings of the National Academy of Sciences, Vol. 109, Issue 47 https://doi.org/10.1073/pnas.1208795109	journal	November 2012
Networks of energetic and metabolic interactions define dynamics in microbial communities Embree, Mallory; Liu, Joanne K.; Al-Bassam, Mahmoud M. Proceedings of the National Academy of Sciences, Vol. 112, Issue 50 https://doi.org/10.1073/pnas.1506034112	journal	November 2015
Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia Hatzenpichler, Roland; Connon, Stephanie A.; Goudeau, Danielle Proceedings of the National Academy of Sciences, Vol. 113, Issue 28 https://doi.org/10.1073/pnas.1603757113	journal	June 2016
Archaea catalyze iron-dependent anaerobic oxidation of methane Ettwig, Katharina F.; Zhu, Baoli; Speth, Daan Proceedings of the National Academy of Sciences, Vol. 113, Issue 45 https://doi.org/10.1073/pnas.1609534113	journal	October 2016
Bacterial symbionts use a type VI secretion system to eliminate competitors in their natural host Speare, Lauren; Cecere, Andrew G.; Guckes, Kirsten R. Proceedings of the National Academy of Sciences, Vol. 115, Issue 36 https://doi.org/10.1073/pnas.1808302115	journal	August 2018
The F ₄₂₀ H ₂ Dehydrogenase from Methanosarcina mazei Is a Redox-driven Proton Pump Closely Related to NADH Dehydrogenases Bäumer, Sebastian; Ide, Tina; Jacobi, Carsten Journal of Biological Chemistry, Vol. 275, Issue 24 https://doi.org/10.1074/jbc.M000650200	journal	April 2000
Insights into Flavin-based Electron Bifurcation via the NADH-dependent Reduced Ferredoxin:NADP Oxidoreductase Structure Demmer, Julius K.; Huang, Haiyan; Wang, Shuning Journal of Biological Chemistry, Vol. 290, Issue 36 https://doi.org/10.1074/jbc.M115.656520	journal	July 2015
Catalytic and Thermodynamic Properties of Tetrahydromethanopterin-dependent Serine Hydroxymethyltransferase from Methanococcus jannaschii Buchenau, Bärbel; Bossa, Francesco; Angelaccio, Sebastiana Journal of Biological Chemistry, Vol. 278, Issue 43 https://doi.org/10.1074/jbc.M306747200	journal	October 2003
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry Journal of Computational Biology, Vol. 19, Issue 5 https://doi.org/10.1089/cmb.2012.0021	journal	May 2012
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Li, W.; Godzik, A. Bioinformatics, Vol. 22, Issue 13 https://doi.org/10.1093/bioinformatics/btl158	journal	May 2006
Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data Kearse, M.; Moir, R.; Wilson, A. Bioinformatics, Vol. 28, Issue 12 https://doi.org/10.1093/bioinformatics/bts199	journal	April 2012
SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver Bioinformatics, Vol. 28, Issue 14 https://doi.org/10.1093/bioinformatics/bts252	journal	May 2012
InterProScan 5: genome-scale protein function classification Jones, P.; Binns, D.; Chang, H. -Y. Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu031	journal	January 2014
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Stamatakis, Alexandros Bioinformatics, Vol. 30, Issue 9 https://doi.org/10.1093/bioinformatics/btu033	journal	January 2014
Trimmomatic: a flexible trimmer for Illumina sequence data Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern Bioinformatics, Vol. 30, Issue 15 https://doi.org/10.1093/bioinformatics/btu170	journal	April 2014
MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph Li, Dinghua; Liu, Chi-Man; Luo, Ruibang Bioinformatics, Vol. 31, Issue 10 https://doi.org/10.1093/bioinformatics/btv033	journal	January 2015
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Chaumeil, Pierre-Alain; Mussig, Aaron J.; Hugenholtz, Philip Bioinformatics https://doi.org/10.1093/bioinformatics/btz848	journal	November 2019
A Phage Tail-Derived Element with Wide Distribution among Both Prokaryotic Domains: A Comparative Genomic and Phylogenetic Study Sarris, P. F.; Ladoukakis, E. D.; Panopoulos, N. J. Genome Biology and Evolution, Vol. 6, Issue 7 https://doi.org/10.1093/gbe/evu136	journal	July 2014
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data Huerta-Cepas, Jaime; Serra, François; Bork, Peer Molecular Biology and Evolution, Vol. 33, Issue 6 https://doi.org/10.1093/molbev/msw046	journal	February 2016
SMS: Smart Model Selection in PhyML Lefort, Vincent; Longueville, Jean-Emmanuel; Gascuel, Olivier Molecular Biology and Evolution, Vol. 34, Issue 9 https://doi.org/10.1093/molbev/msx149	journal	May 2017
ARB: a software environment for sequence data Ludwig, W. Nucleic Acids Research, Vol. 32, Issue 4 https://doi.org/10.1093/nar/gkh293	journal	February 2004
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin Nucleic Acids Research, Vol. 41, Issue D1 https://doi.org/10.1093/nar/gks1219	journal	November 2012
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks Yilmaz, Pelin; Parfrey, Laura Wegener; Yarza, Pablo Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1209	journal	November 2013
InterPro in 2017—beyond protein family and domain annotations Finn, Robert D.; Attwood, Teresa K.; Babbitt, Patricia C. Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1107	journal	November 2016
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes Chen, I-Min A.; Chu, Ken; Palaniappan, Krishna Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky901	journal	October 2018
Interactive Tree Of Life (iTOL) v4: recent updates and new developments Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 47, Issue W1 https://doi.org/10.1093/nar/gkz239	journal	April 2019
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent Systematic Biology, Vol. 59, Issue 3 https://doi.org/10.1093/sysbio/syq010	journal	March 2010
Mechanistic and structural basis for inhibition of thymidylate synthase ThyX Basta, Tamara; Boum, Yap; Briffotaux, Julien Open Biology, Vol. 2, Issue 10 https://doi.org/10.1098/rsob.120120	journal	October 2012
Geoglobus acetivorans sp. nov., an iron(III)-reducing archaeon from a deep-sea hydrothermal vent Slobodkina, G. B.; Kolganova, T. V.; Querellou, J. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 59, Issue 11 https://doi.org/10.1099/ijs.0.011080-0	journal	July 2009
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T. Genome Research, Vol. 25, Issue 7 https://doi.org/10.1101/gr.186072.114	journal	May 2015
metaSPAdes: a new versatile metagenomic assembler Nurk, Sergey; Meleshko, Dmitry; Korobeynikov, Anton Genome Research, Vol. 27, Issue 5 https://doi.org/10.1101/gr.213959.116	journal	March 2017
Crystal structures and enzymatic properties of three formyltransferases from archaea: Environmental adaptation and evolutionary relationship Mamat, Björn; Roth, Annette; Grimm, Clemens Protein Science, Vol. 11, Issue 9 https://doi.org/10.1110/ps.0211002	journal	September 2002
Methanogenic capabilities of ANME-archaea deduced from ¹³ C-labelling approaches : Methanogenesis of ANME Bertram, Sebastian; Blumenberg, Martin; Michaelis, Walter Environmental Microbiology, Vol. 15, Issue 8 https://doi.org/10.1111/1462-2920.12112	journal	March 2013
Geochemical, metagenomic and metaproteomic insights into trace metal utilization by methane-oxidizing microbial consortia in sulphidic marine sediments: Metal micronutrients for anaerobic oxidation of methane Glass, Jennifer B.; Yu, Hang; Steele, Joshua A. Environmental Microbiology, Vol. 16, Issue 6 https://doi.org/10.1111/1462-2920.12314	journal	November 2013
A reversed genetic approach reveals the coenzyme specificity and other catalytic properties of three enzymes putatively involved in anaerobic oxidation of methane with sulfate: Enzymes involved in anaerobic oxidation of methane Kojima, Hisaya; Moll, Johanna; Kahnt, Jörg Environmental Microbiology, Vol. 16, Issue 11 https://doi.org/10.1111/1462-2920.12475	journal	April 2014
E ndomicrobium proavitum , the first isolate of E ndomicrobia class. nov. (phylum E lusimicrobia ) - an ultramicrobacterium with an unusual cell cycle that fixes nitrogen with a Group IV nitrogenase Zheng, Hao; Dietrich, Carsten; Radek, Renate Environmental Microbiology, Vol. 18, Issue 1 https://doi.org/10.1111/1462-2920.12960	journal	July 2015
Candidatus Desulfofervidus auxilii, a hydrogenotrophic sulfate-reducing bacterium involved in the thermophilic anaerobic oxidation of methane : The partner bacterium in thermophilic methanotrophy Krukenberg, Viola; Harding, Katie; Richter, Michael Environmental Microbiology, Vol. 18, Issue 9 https://doi.org/10.1111/1462-2920.13283	journal	April 2016
Gene expression and ultrastructure of meso- and thermophilic methanotrophic consortia: Interspecies interaction within AOM consortia Krukenberg, Viola; Riedel, Dietmar; Gruber-Vodicka, Harald R. Environmental Microbiology, Vol. 20, Issue 5 https://doi.org/10.1111/1462-2920.14077	journal	April 2018
Electron transport during aceticlastic methanogenesis by Methanosarcina acetivorans involves a sodium-translocating Rnf complex Schlegel, Katharina; Welte, Cornelia; Deppenmeier, Uwe FEBS Journal, Vol. 279, Issue 24 https://doi.org/10.1111/febs.12031	journal	November 2012
Biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of aromatic amino acids and p-aminobenzoic acid in the archaeon Methanococcus maripaludis Porat, Iris; Sieprawska-Lupa, Magdalena; Teng, Quincy Molecular Microbiology, Vol. 62, Issue 4 https://doi.org/10.1111/j.1365-2958.2006.05426.x	journal	November 2006
Methanogenesis by Methanosarcina acetivorans involves two structurally and functionally distinct classes of heterodisulfide reductase Buan, Nicole R.; Metcalf, William W. Molecular Microbiology, Vol. 75, Issue 4 https://doi.org/10.1111/j.1365-2958.2009.06990.x	journal	February 2010
The ‘porin-cytochrome’ model for microbe-to-mineral electron transfer: Microbe-to-mineral electron transfer Richardson, David J.; Butt, Julea N.; Fredrickson, Jim K. Molecular Microbiology, Vol. 85, Issue 2 https://doi.org/10.1111/j.1365-2958.2012.08088.x	journal	May 2012
Characterization of two pterin derivatives isolated from Methanoculleus thermophilicum Raemakers-Franken, Petronella C.; Bongaerts, Roy; Fokkens, Roel European Journal of Biochemistry, Vol. 200, Issue 3 https://doi.org/10.1111/j.1432-1033.1991.tb16245.x	journal	September 1991
Catalytic Properties, Molecular Composition and Sequence Alignments of Pyruvate: Ferredoxin Oxidoreductase from the Methanogenic Archaeon Methanosarcina Barkeri (Strain Fusaro) Bock, Anne-Katrin; Kunow, Jasper; Glasemacher, Jurgen European Journal of Biochemistry, Vol. 237, Issue 1 https://doi.org/10.1111/j.1432-1033.1996.0035n.x	journal	April 1996
Methanol: Coenzyme M Methyltransferase from Methanosarcina Barkeri. Purification, Properties and Encoding Genes of the Corrinoid Protein MT1 Sauer, Karin; Harms, Ulrike; Thauer, Rudolf K. European Journal of Biochemistry, Vol. 243, Issue 3 https://doi.org/10.1111/j.1432-1033.1997.t01-1-00670.x	journal	February 1997
Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities Nauhaus, Katja; Treude, Tina; Boetius, Antje Environmental Microbiology, Vol. 7, Issue 1 https://doi.org/10.1111/j.1462-2920.2004.00669.x	journal	January 2005
Insights into the genomes of archaea mediating the anaerobic oxidation of methane: Genomes of methanotrophic archaea Meyerdierks, Anke; Kube, Michael; Lombardot, Thierry Environmental Microbiology, Vol. 7, Issue 12 https://doi.org/10.1111/j.1462-2920.2005.00844.x	journal	July 2005
In vitro cell growth of marine archaeal-bacterial consortia during anaerobic oxidation of methane with sulfate Nauhaus, Katja; Albrecht, Melanie; Elvert, Marcus Environmental Microbiology, Vol. 9, Issue 1 https://doi.org/10.1111/j.1462-2920.2006.01127.x	journal	January 2007
Methyl sulfides as intermediates in the anaerobic oxidation of methane Moran, James J.; Beal, Emily J.; Vrentas, Jennifer M. Environmental Microbiology, Vol. 0, Issue 0 https://doi.org/10.1111/j.1462-2920.2007.01441.x	journal	September 2007
Assimilation of methane and inorganic carbon by microbial communities mediating the anaerobic oxidation of methane Wegener, Gunter; Niemann, Helge; Elvert, Marcus Environmental Microbiology, Vol. 10, Issue 9 https://doi.org/10.1111/j.1462-2920.2008.01653.x	journal	September 2008
Extensive carbon isotopic heterogeneity among methane seep microbiota House, Christopher H.; Orphan, Victoria J.; Turk, Kendra A. Environmental Microbiology, Vol. 11, Issue 9 https://doi.org/10.1111/j.1462-2920.2009.01934.x	journal	September 2009
Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group Meyerdierks, Anke; Kube, Michael; Kostadinov, Ivaylo Environmental Microbiology, Vol. 12, Issue 2 https://doi.org/10.1111/j.1462-2920.2009.02083.x	journal	February 2010
A distinct freshwater-adapted subgroup of ANME-1 dominates active archaeal communities in terrestrial subsurfaces in Japan: ANME-1 archaea in terrestrial freshwater subsurfaces Takeuchi, Mio; Yoshioka, Hideyoshi; Seo, Yuna Environmental Microbiology, Vol. 13, Issue 12 https://doi.org/10.1111/j.1462-2920.2011.02517.x	journal	June 2011
Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea: Methanogenesis and methanotrophy in ANME-1 archaea Lloyd, Karen G.; Alperin, Marc J.; Teske, Andreas Environmental Microbiology, Vol. 13, Issue 9 https://doi.org/10.1111/j.1462-2920.2011.02526.x	journal	August 2011
Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments: Proteogenomics of ANME-1 in cold seep sediments Stokke, Runar; Roalkvam, Irene; Lanzen, Anders Environmental Microbiology, Vol. 14, Issue 5 https://doi.org/10.1111/j.1462-2920.2012.02716.x	journal	March 2012
Noncellulosomal cohesin- and dockerin-like modules in the three domains of life Peer, Ayelet; Smith, Steven P.; Bayer, Edward A. FEMS Microbiology Letters, Vol. 291, Issue 1 https://doi.org/10.1111/j.1574-6968.2008.01420.x	journal	February 2009
Re-evaluation of the function of the F420 dehydrogenase in electron transport of Methanosarcina mazei: Role of F420 dehydrogenase in Ms. mazei Welte, Cornelia; Deppenmeier, Uwe FEBS Journal, Vol. 278, Issue 8 https://doi.org/10.1111/j.1742-4658.2011.08048.x	journal	March 2011
Contractile injection systems of bacteriophages and related systems: Conserved features of a contractile sheath-rigid tube mechanism Taylor, Nicholas M. I.; van Raaij, Mark J.; Leiman, Petr G. Molecular Microbiology, Vol. 108, Issue 1 https://doi.org/10.1111/mmi.13921	journal	February 2018
Life on the thermodynamic edge: Respiratory growth of an acetotrophic methanogen Prakash, Divya; Chauhan, Shikha S.; Ferry, James G. Science Advances, Vol. 5, Issue 8 https://doi.org/10.1126/sciadv.aaw9059	journal	August 2019
Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis Orphan, V. J. Science, Vol. 293, Issue 5529 https://doi.org/10.1126/science.1061338	journal	July 2001
An Alternative Flavin-Dependent Mechanism for Thymidylate Synthesis Myllykallio, Hannu; Lipowski, Gerard; Leduc, Damien Science, Vol. 297, Issue 5578 https://doi.org/10.1126/science.1072113	journal	July 2002
Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics Hallam, S. J. Science, Vol. 305, Issue 5689 https://doi.org/10.1126/science.1100025	journal	September 2004
A Serpentinite-Hosted Ecosystem: The Lost City Hydrothermal Field Kelley, D. S. Science, Vol. 307, Issue 5714 https://doi.org/10.1126/science.1102556	journal	March 2005
Manganese- and Iron-Dependent Marine Methane Oxidation Beal, E. J.; House, C. H.; Orphan, V. J. Science, Vol. 325, Issue 5937 https://doi.org/10.1126/science.1169984	journal	July 2009
Deep-Sea Archaea Fix and Share Nitrogen in Methane-Consuming Microbial Consortia Dekas, A. E.; Poretsky, R. S.; Orphan, V. J. Science, Vol. 326, Issue 5951 https://doi.org/10.1126/science.1178223	journal	October 2009
Marine Tubeworm Metamorphosis Induced by Arrays of Bacterial Phage Tail–Like Structures Shikuma, Nicholas J.; Pilhofer, Martin; Weiss, Gregor L. Science, Vol. 343, Issue 6170 https://doi.org/10.1126/science.1246794	journal	January 2014
C1 Transfer Enzymes and Coenzymes Linking Methylotrophic Bacteria and Methanogenic Archaea Chistoserdova, L. Science, Vol. 281, Issue 5373 https://doi.org/10.1126/science.281.5373.99	journal	July 1998
Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction Scheller, S.; Yu, H.; Chadwick, G. L. Science, Vol. 351, Issue 6274 https://doi.org/10.1126/science.aad7154	journal	February 2016
Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life Spang, Anja; Caceres, Eva F.; Ettema, Thijs J. G. Science, Vol. 357, Issue 6351 https://doi.org/10.1126/science.aaf3883	journal	August 2017
Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction Wagner, Tristan; Koch, Jürgen; Ermler, Ulrich Science, Vol. 357, Issue 6352 https://doi.org/10.1126/science.aan0425	journal	August 2017
Diversity and Abundance of Aerobic and Anaerobic Methane Oxidizers at the Haakon Mosby Mud Volcano, Barents Sea Losekann, T.; Knittel, K.; Nadalig, T. Applied and Environmental Microbiology, Vol. 73, Issue 10 https://doi.org/10.1128/AEM.00016-07	journal	March 2007
Purification and Characterization of OmcZ, an Outer-Surface, Octaheme c-Type Cytochrome Essential for Optimal Current Production by Geobacter sulfurreducens Inoue, K.; Qian, X.; Morgado, L. Applied and Environmental Microbiology, Vol. 76, Issue 12 https://doi.org/10.1128/AEM.00027-10	journal	April 2010
Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy McGlynn, Shawn E.; Chadwick, Grayson L.; O'Neill, Ariel Applied and Environmental Microbiology, Vol. 84, Issue 11 https://doi.org/10.1128/AEM.00399-18	journal	April 2018
Methane- and Sulfur-Metabolizing Microbial Communities Dominate the Lost City Hydrothermal Field Ecosystem Brazelton, William J.; Schrenk, Matthew O.; Kelley, Deborah S. Applied and Environmental Microbiology, Vol. 72, Issue 9 https://doi.org/10.1128/AEM.00574-06	journal	September 2006
Molecular Characterization of Potential Nitrogen Fixation by Anaerobic Methane-Oxidizing Archaea in the Methane Seep Sediments at the Number 8 Kumano Knoll in the Kumano Basin, Offshore of Japan Miyazaki, J.; Higa, R.; Toki, T. Applied and Environmental Microbiology, Vol. 75, Issue 22 https://doi.org/10.1128/AEM.01184-09	journal	September 2009
Divergent Nrf Family Proteins and MtrCAB Homologs Facilitate Extracellular Electron Transfer in Aeromonas hydrophila Conley, Bridget E.; Intile, Peter J.; Bond, Daniel R. Applied and Environmental Microbiology, Vol. 84, Issue 23 https://doi.org/10.1128/AEM.02134-18	journal	September 2018
Consumption of Methane and CO2 by Methanotrophic Microbial Mats from Gas Seeps of the Anoxic Black Sea Treude, T.; Orphan, V.; Knittel, K. Applied and Environmental Microbiology, Vol. 73, Issue 7 https://doi.org/10.1128/AEM.02685-06	journal	February 2007
Mechanisms Involved in Fe(III) Respiration by the Hyperthermophilic Archaeon Ferroglobus placidus Smith, Jessica A.; Aklujkar, Muktak; Risso, Carla Applied and Environmental Microbiology, Vol. 81, Issue 8 https://doi.org/10.1128/AEM.04038-14	journal	February 2015
Autotrophic Carbon Dioxide Fixation via the Calvin-Benson-Bassham Cycle by the Denitrifying Methanotroph “Candidatus Methylomirabilis oxyfera” Rasigraf, Olivia; Kool, Dorien M.; Jetten, Mike S. M. Applied and Environmental Microbiology, Vol. 80, Issue 8 https://doi.org/10.1128/AEM.04199-13	journal	February 2014
Phylogenetic Analysis of an Anaerobic, Trichlorobenzene-Transforming Microbial Consortium von Wintzingerode, Friedrich; Selent, Burkhard; Hegemann, Werner Applied and Environmental Microbiology, Vol. 65, Issue 1 https://doi.org/10.1128/AEM.65.1.283-286.1999	journal	January 1999
Biomarker Evidence for Widespread Anaerobic Methane Oxidation in Mediterranean Sediments by a Consortium of Methanogenic Archaea and Bacteria Pancost, Richard D.; Sinninghe Damsté, Jaap S.; de Lint, Saskia Applied and Environmental Microbiology, Vol. 66, Issue 3 https://doi.org/10.1128/AEM.66.3.1126-1132.2000	journal	March 2000
Comparative Analysis of Methane-Oxidizing Archaea and Sulfate-Reducing Bacteria in Anoxic Marine Sediments Orphan, V. J.; Hinrichs, K. -U.; Ussler, W. Applied and Environmental Microbiology, Vol. 67, Issue 4 https://doi.org/10.1128/AEM.67.4.1922-1934.2001	journal	April 2001
Membrane-Bound Electron Transport in Methanosaeta thermophila Welte, C.; Deppenmeier, U. Journal of Bacteriology, Vol. 193, Issue 11 https://doi.org/10.1128/JB.00162-11	journal	April 2011
Identification of Different Putative Outer Membrane Electron Conduits Necessary for Fe(III) Citrate, Fe(III) Oxide, Mn(IV) Oxide, or Electrode Reduction by Geobacter sulfurreducens Jiménez Otero, Fernanda; Chan, Chi Ho; Bond, Daniel R. Journal of Bacteriology, Vol. 200, Issue 19 https://doi.org/10.1128/JB.00347-18	journal	July 2018
Autotrophic Methanotrophy in Verrucomicrobia: Methylacidiphilum fumariolicumSolV Uses the Calvin-Benson-Bassham Cycle for Carbon Dioxide Fixation Khadem, A. F.; Pol, A.; Wieczorek, A. Journal of Bacteriology, Vol. 193, Issue 17 https://doi.org/10.1128/JB.00407-11	journal	July 2011
Expression and Association of Group IV Nitrogenase NifD and NifH Homologs in the Non-Nitrogen-Fixing Archaeon Methanocaldococcus jannaschii Staples, C. R.; Lahiri, S.; Raymond, J. Journal of Bacteriology, Vol. 189, Issue 20 https://doi.org/10.1128/JB.00876-07	journal	July 2007
VhuD Facilitates Electron Flow from H2 or Formate to Heterodisulfide Reductase in Methanococcus maripaludis Costa, K. C.; Lie, T. J.; Xia, Q. Journal of Bacteriology, Vol. 195, Issue 22 https://doi.org/10.1128/JB.00895-13	journal	September 2013
Biosynthesis of Phosphoserine in the Methanococcales Helgadóttir, Sunna; Rosas-Sandoval, Guillermina; Söll, Dieter Journal of Bacteriology, Vol. 189, Issue 2 https://doi.org/10.1128/JB.01269-06	journal	October 2006
Partial Functional Replacement of CymA by SirCD in Shewanella oneidensis MR-1 Cordova, C. D.; Schicklberger, M. F. R.; Yu, Y. Journal of Bacteriology, Vol. 193, Issue 9 https://doi.org/10.1128/JB.01355-10	journal	March 2011
Coupled Ferredoxin and Crotonyl Coenzyme A (CoA) Reduction with NADH Catalyzed by the Butyryl-CoA Dehydrogenase/Etf Complex from Clostridium kluyveri Li, F.; Hinderberger, J.; Seedorf, H. Journal of Bacteriology, Vol. 190, Issue 3 https://doi.org/10.1128/JB.01417-07	journal	November 2007
Evidence for a Hexaheteromeric Methylenetetrahydrofolate Reductase in Moorella thermoacetica Mock, J.; Wang, S.; Huang, H. Journal of Bacteriology, Vol. 196, Issue 18 https://doi.org/10.1128/JB.01839-14	journal	July 2014
Genetic Basis for Metabolism of Methylated Sulfur Compounds in Methanosarcina Species Fu, He; Metcalf, William W. Journal of Bacteriology, Vol. 197, Issue 8 https://doi.org/10.1128/JB.02605-14	journal	February 2015
The NADP-Dependent Methylene Tetrahydromethanopterin Dehydrogenase in Methylobacterium extorquens AM1 Vorholt, Julia A.; Chistoserdova, Ludmila; Lidstrom, Mary E. Journal of Bacteriology, Vol. 180, Issue 20 https://doi.org/10.1128/JB.180.20.5351-5356.1998	journal	October 1998
The Trimethylamine Methyltransferase Gene and Multiple Dimethylamine Methyltransferase Genes of Methanosarcina barkeri Contain In-Frame and Read-Through Amber Codons Paul, L.; Ferguson, D. J.; Krzycki, J. A. Journal of Bacteriology, Vol. 182, Issue 9 https://doi.org/10.1128/JB.182.9.2520-2529.2000	journal	May 2000
Function and Regulation of the Formate Dehydrogenase Genes of the Methanogenic Archaeon Methanococcus maripaludis Wood, G. E.; Haydock, A. K.; Leigh, J. A. Journal of Bacteriology, Vol. 185, Issue 8 https://doi.org/10.1128/JB.185.8.2548-2554.2003	journal	April 2003
Electron Transport in the Pathway of Acetate Conversion to Methane in the Marine Archaeon Methanosarcina acetivorans Li, Q.; Li, L.; Rejtar, T. Journal of Bacteriology, Vol. 188, Issue 2 https://doi.org/10.1128/JB.188.2.702-710.2006	journal	December 2005
Anaerobic Methane Oxidation: Occurrence and Ecology Zehnder, Alexander J. B.; Brock, Thomas D. Applied and Environmental Microbiology, Vol. 39, Issue 1 https://doi.org/10.1128/aem.39.1.194-204.1980	journal	January 1980
DNA recovery from soils of diverse composition. Zhou, J.; Bruns, M. A.; Tiedje, J. M. Applied and environmental microbiology, Vol. 62, Issue 2 https://doi.org/10.1128/aem.62.2.316-322.1996	journal	January 1996
Oxidoreductases Involved in Cell Carbon Synthesis of Methanobacterium thermoautotrophicum Zeikus, J. G.; Fuchs, G.; Kenealy, W. Journal of Bacteriology, Vol. 132, Issue 2 https://doi.org/10.1128/jb.132.2.604-613.1977	journal	November 1977
Ultrastructure, inferred porosity, and gram-staining character of Methanospirillum hungatei filament termini describe a unique cell permeability for this archaeobacterium Beveridge, T. J.; Sprott, G. D.; Whippey, P. Journal of Bacteriology, Vol. 173, Issue 1 https://doi.org/10.1128/jb.173.1.130-140.1991	journal	January 1991
The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss Morris, J. Jeffrey; Lenski, Richard E.; Zinser, Erik R. mBio, Vol. 3, Issue 2 https://doi.org/10.1128/mBio.00036-12	journal	March 2012
A Membrane-Bound Cytochrome Enables Methanosarcina acetivorans To Conserve Energy from Extracellular Electron Transfer Holmes, Dawn E.; Ueki, Toshiyuki; Tang, Hai-Yan mBio, Vol. 10, Issue 4 https://doi.org/10.1128/mBio.00789-19	journal	August 2019
Energy Conservation via Hydrogen Cycling in the Methanogenic Archaeon Methanosarcina barkeri Kulkarni, Gargi; Mand, Thomas D.; Metcalf, William W. mBio, Vol. 9, Issue 4 https://doi.org/10.1128/mBio.01256-18	journal	July 2018
Physiological Heterogeneity Triggers Sibling Conflict Mediated by the Type VI Secretion System in an Aggregative Multicellular Bacterium Troselj, Vera; Treuner-Lange, Anke; Søgaard-Andersen, Lotte mBio, Vol. 9, Issue 1 https://doi.org/10.1128/mBio.01645-17	journal	March 2018
Anaerobic Degradation of Non-Methane Alkanes by “ Candidatus Methanoliparia” in Hydrocarbon Seeps of the Gulf of Mexico Laso-Pérez, Rafael; Hahn, Cedric; van Vliet, Daan M. mBio, Vol. 10, Issue 4 https://doi.org/10.1128/mBio.01814-19	journal	August 2019
An Inner Membrane Cytochrome Required Only for Reduction of High Redox Potential Extracellular Electron Acceptors Levar, Caleb E.; Chan, Chi Ho; Mehta-Kolte, Misha G. mBio, Vol. 5, Issue 6 https://doi.org/10.1128/mBio.02034-14	journal	November 2014
Methanotrophic bacteria. Hanson, R. S.; Hanson, T. E. Microbiological reviews, Vol. 60, Issue 2 https://doi.org/10.1128/mr.60.2.439-471.1996	journal	January 1996
Investigation of serine hydroxymethyltransferase in methanogens Lin, Zhaosheng; Sparling, Richard Canadian Journal of Microbiology, Vol. 44, Issue 7 https://doi.org/10.1139/w98-050	journal	July 1998
Biosynthesis of the Metalloclusters of Nitrogenases Hu, Yilin; Ribbe, Markus W. Annual Review of Biochemistry, Vol. 85, Issue 1 https://doi.org/10.1146/annurev-biochem-060614-034108	journal	June 2016
Hydrogenases from Methanogenic Archaea, Nickel, a Novel Cofactor, and H ₂ Storage Thauer, Rudolf K.; Kaster, Anne-Kristin; Goenrich, Meike Annual Review of Biochemistry, Vol. 79, Issue 1 https://doi.org/10.1146/annurev.biochem.030508.152103	journal	June 2010
The Expanding World of Methylotrophic Metabolism Chistoserdova, Ludmila; Kalyuzhnaya, Marina G.; Lidstrom, Mary E. Annual Review of Microbiology, Vol. 63, Issue 1 https://doi.org/10.1146/annurev.micro.091208.073600	journal	October 2009
The Cellulosomes: Multienzyme Machines for Degradation of Plant Cell Wall Polysaccharides Bayer, Edward A.; Belaich, Jean-Pierre; Shoham, Yuval Annual Review of Microbiology, Vol. 58, Issue 1 https://doi.org/10.1146/annurev.micro.57.030502.091022	journal	October 2004
Anaerobic Oxidation of Methane: Progress with an Unknown Process Knittel, Katrin; Boetius, Antje Annual Review of Microbiology, Vol. 63, Issue 1 https://doi.org/10.1146/annurev.micro.61.080706.093130	journal	October 2009
BLAST+: architecture and applications Camacho, Christiam; Coulouris, George; Avagyan, Vahram BMC Bioinformatics, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2105-10-421	journal	January 2009
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Proteinortho: Detection of (Co-)orthologs in large-scale analysis Lechner, Marcus; Findeiß, Sven; Steiner, Lydia BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-124	journal	April 2011
Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes Dos Santos, Patricia C.; Fang, Zhong; Mason, Steven W. BMC Genomics, Vol. 13, Issue 1 https://doi.org/10.1186/1471-2164-13-162	journal	January 2012
Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A Rohlin, Lars; Gunsalus, Robert P. BMC Microbiology, Vol. 10, Issue 1 https://doi.org/10.1186/1471-2180-10-62	journal	January 2010
Electron transport in acetate-grown Methanosarcina acetivorans Wang, Mingyu; Tomb, Jean-Francois; Ferry, James G. BMC Microbiology, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2180-11-165	journal	January 2011
Purine biosynthesis in archaea: variations on a theme Brown, Anne M.; Hoopes, Samantha L.; White, Robert H. Biology Direct, Vol. 6, Issue 1 https://doi.org/10.1186/1745-6150-6-63	journal	January 2011
VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data Laczny, Cedric C.; Sternal, Tomasz; Plugaru, Valentin Microbiome, Vol. 3, Issue 1 https://doi.org/10.1186/s40168-014-0066-1	journal	January 2015
Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments Dombrowski, Nina; Seitz, Kiley W.; Teske, Andreas P. Microbiome, Vol. 5, Issue 1 https://doi.org/10.1186/s40168-017-0322-2	journal	August 2017
Energy Metabolism during Anaerobic Methane Oxidation in ANME Archaea McGlynn, Shawn E. Microbes and environments, Vol. 32, Issue 1 https://doi.org/10.1264/jsme2.ME16166	journal	January 2017
Insight into the Interaction of Metal Ions with TroA from Streptococcus suis Zheng, Beiwen; Zhang, Qiangmin; Gao, Jia PLoS ONE, Vol. 6, Issue 5 https://doi.org/10.1371/journal.pone.0019510	journal	May 2011
An Intertwined Evolutionary History of Methanogenic Archaea and Sulfate Reduction Susanti, Dwi; Mukhopadhyay, Biswarup PLoS ONE, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pone.0045313	journal	September 2012
The Binning of Metagenomic Contigs for Microbial Physiology of Mixed Cultures Strous, Marc; Kraft, Beate; Bisdorf, Regina Frontiers in Microbiology, Vol. 3 https://doi.org/10.3389/fmicb.2012.00410	journal	January 2012
Cytochromes c in Archaea: distribution, maturation, cell architecture, and the special case of Ignicoccus hospitalis Kletzin, Arnulf; Heimerl, Thomas; Flechsler, Jennifer Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00439	journal	May 2015
A Metagenomics-Based Metabolic Model of Nitrate-Dependent Anaerobic Oxidation of Methane by Methanoperedens-Like Archaea Arshad, Arslan; Speth, Daan R.; de Graaf, Rob M. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01423	journal	December 2015
Metabolic Capabilities of Microorganisms Involved in and Associated with the Anaerobic Oxidation of Methane Wegener, Gunter; Krukenberg, Viola; Ruff, S. Emil Frontiers in Microbiology, Vol. 7 https://doi.org/10.3389/fmicb.2016.00046	journal	February 2016
Electron Bifurcation and Confurcation in Methanogenesis and Reverse Methanogenesis Yan, Zhen; Ferry, James G. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.01322	journal	June 2018
Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea Yu, Hang; Susanti, Dwi; McGlynn, Shawn E. Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.02917	journal	December 2018
De novo modeling of the F420-reducing [NiFe]-hydrogenase from a methanogenic archaeon by cryo-electron microscopy Mills, Deryck J.; Vitt, Stella; Strauss, Mike eLife, Vol. 2 https://doi.org/10.7554/eLife.00218	journal	March 2013
An elusive electron shuttle from a facultative anaerobe Mevers, Emily; Su, Lin; Pishchany, Gleb eLife, Vol. 8 https://doi.org/10.7554/eLife.48054	journal	June 2019
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities Kang, Dongwan D.; Froula, Jeff; Egan, Rob PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1165	journal	January 2015
Anvi’o: an advanced analysis and visualization platform for ‘omics data Eren, A. Murat; Esen, Özcan C.; Quince, Christopher PeerJ, Vol. 3 https://doi.org/10.7717/peerj.1319	journal	January 2015
Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments Trembath-Reichert, Elizabeth; Case, David H.; Orphan, Victoria J. PeerJ, Vol. 4 https://doi.org/10.7717/peerj.1913	journal	January 2016
GroopM: an automated tool for the recovery of population genomes from related metagenomes Imelfort, Michael; Parks, Donovan; Woodcroft, Ben J. PeerJ, Vol. 2 https://doi.org/10.7717/peerj.603	journal	January 2014

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea

Citation Formats

References (225)

Similar Records

Related Subjects