Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

Gilmore, Sean P.; Henske, John K.; Sexton, Jessica A.; Solomon, Kevin V.; Seppälä, Susanna; Yoo, Justin I.; Huyett, Lauren M.; Pressman, Abe; Cogan, James Z.; Kivenson, Veronika; Peng, Xuefeng; Tan, YerPeng; Valentine, David L.; O’Malley, Michelle A.

doi:10.1186/s12864-017-4036-4

Title: Genomic analysis of methanogenic archaea reveals a shift towards energy conservation

Journal Article · Mon Aug 21 00:00:00 EDT 2017 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-017-4036-4· OSTI ID:1618559

Gilmore, Sean P.; Henske, John K.; Sexton, Jessica A.; Solomon, Kevin V.; Seppälä, Susanna; Yoo, Justin I.; Huyett, Lauren M.; Pressman, Abe; Cogan, James Z.; Kivenson, Veronika; Peng, Xuefeng; Tan, YerPeng; Valentine, David L.;

The metabolism of archaeal methanogens drives methane release into the environment and is critical to understanding global carbon cycling. Methanogenesis operates at a very low reducing potential compared to other forms of respiration and is therefore critical to many anaerobic environments. Harnessing or altering methanogen metabolism has the potential to mitigate global warming and even be utilized for energy applications. Here, we report draft genome sequences for the isolated methanogens Methanobacterium bryantii, Methanosarcina spelaei, Methanosphaera cuniculi, and Methanocorpusculum parvum. These anaerobic, methane-producing archaea represent a diverse set of isolates, capable of methylotrophic, acetoclastic, and hydrogenotrophic methanogenesis. Assembly and analysis of the genomes allowed for simple and rapid reconstruction of metabolism in the four methanogens. Comparison of the distribution of Clusters of Orthologous Groups (COG) proteins to a sample of genomes from the RefSeq database revealed a trend towards energy conservation in genome composition of all methanogens sequenced. Further analysis of the predicted membrane proteins and transporters distinguished differing energy conservation methods utilized during methanogenesis, such as chemiosmotic coupling in Msar. spelaei and electron bifurcation linked to chemiosmotic coupling in Mbac. bryantii and Msph. cuniculi. Methanogens occupy a unique ecological niche, acting as the terminal electron acceptors in anaerobic environments, and their genomes display a significant shift towards energy conservation. The genome-enabled reconstructed metabolisms reported here have significance to diverse anaerobic communities and have led to proposed substrate utilization not previously reported in isolation, such as formate and methanol metabolism in Mbac. bryantii and CO₂ metabolism in Msph. cuniculi. The newly proposed substrates establish an important foundation with which to decipher how methanogens behave in native communities, as CO₂ and formate are common electron carriers in microbial communities.

View Journal Article

Cite

Export

Save

Research Organization:: Univ. of California, Santa Barbara, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); Univ. of California (United States); US Army Research Office (ARO); National Science Foundation (NSF); VILLUM Foundation (Denmark)

Grant/Contract Number:: SC0010352; W911NF-09-0001; OCE-1046144; DGE 1144085; VKR023128

OSTI ID:: 1618559

Alternate ID(s):: OSTI ID: 1424613

Journal Information:: BMC Genomics, Journal Name: BMC Genomics Vol. 18 Journal Issue: 1; ISSN 1471-2164

Publisher:: Springer Science + Business MediaCopyright Statement

Country of Publication:: United Kingdom

Language:: English

Citation Metrics:

Cited by: 26 works

Citation information provided by
Web of Science

References (76)

Rerouting Cellular Electron Flux To Increase the Rate of Biological Methane Production Catlett, Jennie L.; Ortiz, Alicia M.; Buan, Nicole R. Applied and Environmental Microbiology, Vol. 81, Issue 19 https://doi.org/10.1128/AEM.01162-15	journal	July 2015
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
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
BayesHammer: Bayesian clustering for error correction in single-cell sequencing Nikolenko, Sergey I.; Korobeynikov, Anton I.; Alekseyev, Max A. BMC Genomics, Vol. 14, Issue Suppl 1 https://doi.org/10.1186/1471-2164-14-S1-S7	journal	January 2013
Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands Cadillo-Quiroz, H.; Brauer, S. L.; Goodson, N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 5 https://doi.org/10.1099/ijs.0.059964-0	journal	January 2014
Methanobacillus omelianskii, a symbiotic association of two species of bacteria Bryant, M. P.; Wolin, E. A.; Wolin, M. J. Archiv f�r Mikrobiologie, Vol. 59, Issue 1-3 https://doi.org/10.1007/BF00406313	journal	January 1967
Metabolism of methanogens Blaut, Michael Antonie van Leeuwenhoek, Vol. 66, Issue 1-3 https://doi.org/10.1007/BF00871639	journal	January 1994
Enzymology of the fermentation of acetate to methane by Methanosarcina thermophila Ferry, James G. BioFactors, Vol. 6, Issue 1 https://doi.org/10.1002/biof.5520060104	journal	January 1997
Higher-level classification of the Archaea: evolution of methanogenesis and methanogens Bapteste, Éric; Brochier, Céline; Boucher, Yan Archaea, Vol. 1, Issue 5 https://doi.org/10.1155/2005/859728	journal	January 2005
Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis Sorokin, Dimitry Y.; Makarova, Kira S.; Abbas, Ben Nature Microbiology, Vol. 2, Issue 8 https://doi.org/10.1038/nmicrobiol.2017.81	journal	May 2017
Influence of temperature on energetics of hydrogen metabolism in homoacetogenic, methanogenic, and other anaerobic bacteria Conrad, Ralf; Wetter, Bettina Archives of Microbiology, Vol. 155, Issue 1 https://doi.org/10.1007/BF00291281	journal	December 1990
Metabolic versatility in methanogens Costa, Kyle C.; Leigh, John A. Current Opinion in Biotechnology, Vol. 29 https://doi.org/10.1016/j.copbio.2014.02.012	journal	October 2014
Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum, Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov. Zellner, G.; Stackebrandt, E.; Messner, P. Archives of Microbiology, Vol. 151, Issue 5 https://doi.org/10.1007/BF00416595	journal	April 1989
Circular genome visualization and exploration using CGView Stothard, P.; Wishart, D. S. Bioinformatics, Vol. 21, Issue 4 https://doi.org/10.1093/bioinformatics/bti054	journal	October 2004
The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review Demirel, Burak; Scherer, Paul Reviews in Environmental Science and Bio/Technology, Vol. 7, Issue 2 https://doi.org/10.1007/s11157-008-9131-1	journal	January 2008
RefSeq microbial genomes database: new representation and annotation strategy Tatusova, Tatiana; Ciufo, Stacy; Fedorov, Boris Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1274	journal	December 2013
Comparison of growth characteristics of anaerobic fungi isolated from ruminant and non-ruminant herbivores during cultivation in a defined medium Teunissen, M. J.; Op den Camp, H. J. M.; Orpin, C. G. Journal of General Microbiology, Vol. 137, Issue 6 https://doi.org/10.1099/00221287-137-6-1401	journal	June 1991
Archaea associated with human surfaces: not to be underestimated Bang, Corinna; Schmitz, Ruth A. FEMS Microbiology Reviews, Vol. 39, Issue 5 https://doi.org/10.1093/femsre/fuv010	journal	April 2015
Adaptations to energy stress dictate the ecology and evolution of the Archaea Valentine, David L. Nature Reviews Microbiology, Vol. 5, Issue 4 https://doi.org/10.1038/nrmicro1619	journal	March 2007
Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens Anderson, Iain; Ulrich, Luke E.; Lupa, Boguslaw PLoS ONE, Vol. 4, Issue 6 https://doi.org/10.1371/journal.pone.0005797	journal	June 2009
Methane Production from Formate by Syntrophic Association of Methanobacterium bryantii and Desulfovibrio vulgaris JJ Guyot, Jean-Pierre; Brauman, Alain Applied and Environmental Microbiology, Vol. 52, Issue 6 https://doi.org/10.1128/AEM.52.6.1436-1437.1986	journal	January 1986
BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons Alikhan, Nabil-Fareed; Petty, Nicola K.; Ben Zakour, Nouri L. BMC Genomics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2164-12-402	journal	August 2011
The complete biosynthesis of the genetically encoded amino acid pyrrolysine from lysine Gaston, Marsha A.; Zhang, Liwen; Green-Church, Kari B. Nature, Vol. 471, Issue 7340 https://doi.org/10.1038/nature09918	journal	March 2011
A Ferredoxin- and F ₄₂₀ H ₂ -Dependent, Electron-Bifurcating, Heterodisulfide Reductase with Homologs in the Domains Bacteria and Archaea Yan, Zhen; Wang, Mingyu; Ferry, James G. mBio, Vol. 8, Issue 1 https://doi.org/10.1128/mBio.02285-16	journal	February 2017
Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake Ganzert, L.; Schirmack, J.; Alawi, M. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 10 https://doi.org/10.1099/ijs.0.064956-0	journal	July 2014
Complete genome sequence of Methanocorpusculum labreanum type strain Z Anderson, Iain J.; Sieprawska-Lupa, Magdalena; Goltsman, Eugene Standards in Genomic Sciences, Vol. 1, Issue 2 https://doi.org/10.4056/sigs.35575	journal	September 2009
KEGG for integration and interpretation of large-scale molecular data sets Kanehisa, M.; Goto, S.; Sato, Y. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr988	journal	November 2011
Genome-Scale Metabolic Reconstruction and Hypothesis Testing in the Methanogenic Archaeon Methanosarcina acetivorans C2A Benedict, M. N.; Gonnerman, M. C.; Metcalf, W. W. Journal of Bacteriology, Vol. 194, Issue 4 https://doi.org/10.1128/JB.06040-11	journal	December 2011
More Than 200 Genes Required for Methane Formation from H ₂ and CO ₂ and Energy Conservation Are Present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus Kaster, Anne-Kristin; Goenrich, Meike; Seedorf, Henning Archaea, Vol. 2011 https://doi.org/10.1155/2011/973848	journal	January 2011
Involvement of Ech hydrogenase in energy conservation of Methanosarcina mazei: Function of Ech in energy conservation Welte, Cornelia; Krätzer, Christian; Deppenmeier, Uwe FEBS Journal, Vol. 277, Issue 16 https://doi.org/10.1111/j.1742-4658.2010.07744.x	journal	July 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
Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis Lie, T. J.; Costa, K. C.; Lupa, B. Proceedings of the National Academy of Sciences, Vol. 109, Issue 38 https://doi.org/10.1073/pnas.1208779109	journal	August 2012
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs Zerbino, D. R.; Birney, E. Genome Research, Vol. 18, Issue 5 https://doi.org/10.1101/gr.074492.107	journal	February 2008
Isolation and characterization of "Methanosphaera cuniculi" sp. nov. Biavati, B.; Vasta, M.; Ferry, J. G. Applied and Environmental Microbiology, Vol. 54, Issue 3 https://doi.org/10.1128/AEM.54.3.768-771.1988	journal	January 1988
Functionally distinct genes regulated by hydrogen limitation and growth rate in methanogenic Archaea Hendrickson, E. L.; Haydock, A. K.; Moore, B. C. Proceedings of the National Academy of Sciences, Vol. 104, Issue 21 https://doi.org/10.1073/pnas.0701157104	journal	May 2007
CDD: NCBI's conserved domain database Marchler-Bauer, Aron; Derbyshire, Myra K.; Gonzales, Noreen R. Nucleic Acids Research, Vol. 43, Issue D1 https://doi.org/10.1093/nar/gku1221	journal	November 2014
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees Letunic, Ivica; Bork, Peer Nucleic Acids Research, Vol. 44, Issue W1 https://doi.org/10.1093/nar/gkw290	journal	April 2016
H2: heterodisulfide oxidoreductase complex from Methanobacterium thermoautotrophicum. Composition and properties Setzke, Edgar; Hedderich, Reiner; Heiden, Stefanie European Journal of Biochemistry, Vol. 220, Issue 1 https://doi.org/10.1111/j.1432-1033.1994.tb18608.x	journal	February 1994
Humic substances as fully regenerable electron acceptors in recurrently anoxic environments Klüpfel, Laura; Piepenbrock, Annette; Kappler, Andreas Nature Geoscience, Vol. 7, Issue 3 https://doi.org/10.1038/ngeo2084	journal	February 2014
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
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
The ENZYME database in 2000 Bairoch, A. Nucleic Acids Research, Vol. 28, Issue 1 https://doi.org/10.1093/nar/28.1.304	journal	January 2000
A new model for electron flow during anaerobic digestion: direct interspecies electron transfer to Methanosaeta for the reduction of carbon dioxide to methane Rotaru, Amelia-Elena; Shrestha, Pravin Malla; Liu, Fanghua Energy Environ. Sci., Vol. 7, Issue 1 https://doi.org/10.1039/C3EE42189A	journal	January 2014
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, R.; Altman, T.; Dreher, K. Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr1014	journal	November 2011
Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes Solomon, Kevin V.; Haitjema, Charles H.; Henske, John K. Science, Vol. 351, Issue 6278 https://doi.org/10.1126/science.aad1431	journal	February 2016
Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea Liu, Yuchen; Whitman, William B. Annals of the New York Academy of Sciences, Vol. 1125, Issue 1 https://doi.org/10.1196/annals.1419.019	journal	March 2008
Confidence Limits on Phylogenies: an Approach Using the Bootstrap Felsenstein, Joseph Evolution, Vol. 39, Issue 4 https://doi.org/10.1111/j.1558-5646.1985.tb00420.x	journal	July 1985
The Genome Sequence of the Rumen Methanogen Methanobrevibacter ruminantium Reveals New Possibilities for Controlling Ruminant Methane Emissions Leahy, Sinead C.; Kelly, William J.; Altermann, Eric PLoS ONE, Vol. 5, Issue 1 https://doi.org/10.1371/journal.pone.0008926	journal	January 2010
Characterization of a Methanosarcina acetivorans mutant unable to translate UAG as pyrrolysine Mahapatra, Anirban; Patel, Asmita; Soares, Jitesh A. Molecular Microbiology, Vol. 59, Issue 1 https://doi.org/10.1111/j.1365-2958.2005.04927.x	journal	January 2006
A New Type of Sulfite Reductase, a Novel Coenzyme F ₄₂₀ -dependent Enzyme, from the Methanarchaeon Methanocaldococcus jannaschii Johnson, Eric F.; Mukhopadhyay, Biswarup Journal of Biological Chemistry, Vol. 280, Issue 46 https://doi.org/10.1074/jbc.M503492200	journal	July 2005
Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut Samuel, B. S.; Hansen, E. E.; Manchester, J. K. Proceedings of the National Academy of Sciences, Vol. 104, Issue 25 https://doi.org/10.1073/pnas.0704189104	journal	June 2007
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen Krogh, Anders; Larsson, Björn; von Heijne, Gunnar Journal of Molecular Biology, Vol. 305, Issue 3 https://doi.org/10.1006/jmbi.2000.4315	journal	January 2001
Isolation and characterization of Methanocorpusculum parvum, gen. nov., spec. nov., a new tungsten requiring, coccoid methanogen Zellner, G.; Alten, C.; Stackebrandt, E. Archives of Microbiology, Vol. 147, Issue 1 https://doi.org/10.1007/BF00492898	journal	January 1987
RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes Brettin, Thomas; Davis, James J.; Disz, Terry Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep08365	journal	February 2015
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets Kumar, Sudhir; Stecher, Glen; Tamura, Koichiro Molecular Biology and Evolution, Vol. 33, Issue 7 https://doi.org/10.1093/molbev/msw054	journal	March 2016
Stop codons in bacteria are not selectively equivalent Povolotskaya, Inna S.; Kondrashov, Fyodor A.; Ledda, Alice Biology Direct, Vol. 7, Issue 1 https://doi.org/10.1186/1745-6150-7-30	journal	January 2012
Disruption of the Operon Encoding Ehb Hydrogenase Limits Anabolic CO2 Assimilation in the Archaeon Methanococcus maripaludis Porat, I.; Kim, W.; Hendrickson, E. L. Journal of Bacteriology, Vol. 188, Issue 4 https://doi.org/10.1128/JB.188.4.1373-1380.2006	journal	February 2006
Methanogenic archaea: ecologically relevant differences in energy conservation Thauer, Rudolf K.; Kaster, Anne-Kristin; Seedorf, Henning Nature Reviews Microbiology, Vol. 6, Issue 8 https://doi.org/10.1038/nrmicro1931	journal	June 2008
Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine Borrel, Guillaume; Parisot, Nicolas; Harris, Hugh MB BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-679	journal	January 2014
A novel pH2 control on the expression of flagella in the hyperthermophilic strictly hydrogenotrophic methanarchaeaon Methanococcus jannaschii Mukhopadhyay, B.; Johnson, E. F.; Wolfe, R. S. Proceedings of the National Academy of Sciences, Vol. 97, Issue 21 https://doi.org/10.1073/pnas.97.21.11522	journal	October 2000
Energy Conservation by the H2:Heterodisulfide Oxidoreductase from Methanosarcina mazei Gö1: Identification of Two Proton-Translocating Segments Ide, Tina; Bäumer, Sebastian; Deppenmeier, Uwe Journal of Bacteriology, Vol. 181, Issue 13 https://doi.org/10.1128/JB.181.13.4076-4080.1999	journal	July 1999
Scaffolding pre-assembled contigs using SSPACE Boetzer, Marten; Henkel, Christiaan V.; Jansen, Hans J. Bioinformatics, Vol. 27, Issue 4 https://doi.org/10.1093/bioinformatics/btq683	journal	December 2010
Purification and properties of F420-and NADP+-dependent alcohol dehydrogenases of Methanogenium liminatans and Methanobacterium palustre, specific for secondary alcohols Bleicher, Karl; Winter, Josef European Journal of Biochemistry, Vol. 200, Issue 1 https://doi.org/10.1111/j.1432-1033.1991.tb21046.x	journal	August 1991
Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea Kaster, A. -K.; Moll, J.; Parey, K. Proceedings of the National Academy of Sciences, Vol. 108, Issue 7 https://doi.org/10.1073/pnas.1016761108	journal	January 2011
The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis Fricke, W. F.; Seedorf, H.; Henne, A. Journal of Bacteriology, Vol. 188, Issue 2 https://doi.org/10.1128/JB.188.2.642-658.2006	journal	December 2005
Reversing methanogenesis to capture methane for liquid biofuel precursors Soo, Valerie W. C.; McAnulty, Michael J.; Tripathi, Arti Microbial Cell Factories, Vol. 15, Issue 1 https://doi.org/10.1186/s12934-015-0397-z	journal	January 2016
TCDB: the Transporter Classification Database for membrane transport protein analyses and information Saier, M. H. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj001	journal	January 2006
Inhibitory effects of nitrate, nitrite, NO and N2O on methanogenesis by Methanosarcina barkeri and Methanobacterium bryantii Klüber, H. FEMS Microbiology Ecology, Vol. 25, Issue 4 https://doi.org/10.1016/S0168-6496(97)00102-5	journal	April 1998
Prospects for inferring very large phylogenies by using the neighbor-joining method Tamura, K.; Nei, M.; Kumar, S. Proceedings of the National Academy of Sciences, Vol. 101, Issue 30 https://doi.org/10.1073/pnas.0404206101	journal	July 2004
A parts list for fungal cellulosomes revealed by comparative genomics Haitjema, Charles H.; Gilmore, Sean P.; Henske, John K. Nature Microbiology, Vol. 2, Issue 8 https://doi.org/10.1038/nmicrobiol.2017.87	journal	May 2017
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
Comparative genomics of three M ethanocellales strains reveal novel taxonomic and metabolic features : Comparative genomics of three Lyu, Zhe; Lu, Yahai Environmental Microbiology Reports, Vol. 7, Issue 3 https://doi.org/10.1111/1758-2229.12283	journal	April 2015
Engineering the Autotroph Methanococcus maripaludis for Geraniol Production Lyu, Zhe; Jain, Rachit; Smith, Peyton ACS Synthetic Biology, Vol. 5, Issue 7 https://doi.org/10.1021/acssynbio.5b00267	journal	February 2016
Microbial communities for bioprocessing: lessons learned from nature Peng, Xuefeng “Nick”; Gilmore, Sean P.; O’Malley, Michelle A. Current Opinion in Chemical Engineering, Vol. 14 https://doi.org/10.1016/j.coche.2016.09.003	journal	November 2016
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases Caspi, Ron; Altman, Tomer; Dale, Joseph M. Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp875	journal	October 2009
RefSeq microbial genomes database: new representation and annotation strategy Tatusova, T.; Ciufo, S.; Fedorov, B. Nucleic Acids Research, Vol. 43, Issue 7 https://doi.org/10.1093/nar/gkv278	journal	March 2015

Cited By (6)

Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes Swift, Candice L.; Brown, Jennifer L.; Seppälä, Susanna Journal of Industrial Microbiology & Biotechnology, Vol. 46, Issue 9-10 https://doi.org/10.1007/s10295-019-02188-0	journal	May 2019
Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size Hoedt, Emily C.; Parks, Donovan H.; Volmer, James G. The ISME Journal, Vol. 12, Issue 12 https://doi.org/10.1038/s41396-018-0225-7	journal	August 2018
Toward a mechanistic and physiological understanding of a ferredoxin:disulfide reductase from the domains Archaea and Bacteria Prakash, Divya; Walters, Karim A.; Martinie, Ryan J. Journal of Biological Chemistry, Vol. 293, Issue 24 https://doi.org/10.1074/jbc.ra118.002473	journal	May 2018
Comparative Genomic Analysis of Members of the Genera Methanosphaera and Methanobrevibacter Reveals Distinct Clades with Specific Potential Metabolic Functions Poehlein, Anja; Schneider, Dominik; Soh, Melissa Archaea, Vol. 2018 https://doi.org/10.1155/2018/7609847	journal	August 2018
Heterogeneous development of methanogens and the correlation with bacteria in the rumen and cecum of sika deer (Cervus nippon) during early life suggest different ecology relevance Li, Zhipeng; Wang, Xiaoxu; Zhang, Ting BMC Microbiology, Vol. 19, Issue 1 https://doi.org/10.1186/s12866-019-1504-9	journal	June 2019
Prokaryotic Community Structure and Metabolisms in Shallow Subsurface of Atacama Desert Playas and Alluvial Fans After Heavy Rains: Repairing and Preparing for Next Dry Period Fernández-Martínez, Miguel Ángel; dos Santos Severino, Rita; Moreno-Paz, Mercedes Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01641	journal	July 2019

Linked Research (12)

Similar Records

Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments

Journal Article · Tue Aug 23 00:00:00 EDT 2016 · The ISME Journal · OSTI ID:1618559

Browne, Patrick; Tamaki, Hideyuki; Kyrpides, Nikos; +8 more

Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis

Journal Article · Thu Dec 15 00:00:00 EST 2016 · Journal of Bacteriology · OSTI ID:1618559

Richards, Matthew A.; Lie, Thomas J.; Zhang, Juan; +4 more

Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea

Journal Article · Mon Mar 04 00:00:00 EST 2019 · Nature Microbiology · OSTI ID:1618559

Borrel, Guillaume; Adam, Panagiotis S.; McKay, Luke J.; +13 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATION
Methanogenesis
Archaea
Metabolism
Anaerobes
Energy

Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300 The current record is supplemented by this dataset	dataset	August 2017
Genomic analysis of methanogenic archaea reveals a shift towards energy conservation [Supplementary Data] Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300.v1 The current record is supplemented by this dataset	dataset	August 2017
Additional file 1: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300_d1 The current record is supplemented by this dataset	dataset	August 2017
Additional file 1: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300_d1.v1 The current record is supplemented by this dataset	dataset	August 2017
Additional file 2: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/M9.FIGSHARE.C.3859300_D2 The current record is supplemented by this dataset	dataset	August 2017
Additional file 2: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300_d2.v1 The current record is supplemented by this dataset	dataset	August 2017
Additional file 3: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/M9.FIGSHARE.C.3859300_D3 The current record is supplemented by this dataset	dataset	March 0074
Additional file 3: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300_d3.v1 The current record is supplemented by this dataset	dataset	August 2017
Additional file 4: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/M9.FIGSHARE.C.3859300_D4 The current record is supplemented by this dataset	dataset	August 2017
Additional file 4: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300_d4.v1 The current record is supplemented by this dataset	dataset	August 2017
Additional file 5: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300_d5 The current record is supplemented by this dataset	dataset	August 2017
Additional file 5: of Genomic analysis of methanogenic archaea reveals a shift towards energy conservation Gilmore, Sean; Henske, John; Sexton, Jessica https://doi.org/10.6084/m9.figshare.c.3859300_d5.v1 The current record is supplemented by this dataset	dataset	August 2017