1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Microbiology
  4. Volume 76, 2022
  5. Article

Annual Review of Microbiology

Volume 76, 2022

Diversity and Evolution of Methane-Related Pathways in Archaea

Abstract

Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl–coenzyme M reductase complex (Mcr). Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.

Keyword(s): alkanotrophy, archaea, evolution, methanogenesis, methanotrophy
Loading

Article metrics loading...

/content/journals/10.1146/annurev-micro-041020-024935
2022-09-08
2024-04-27
Loading full text...

Full text loading...

/deliver/fulltext/micro/76/1/annurev-micro-041020-024935.html?itemId=/content/journals/10.1146/annurev-micro-041020-024935&mimeType=html&fmt=ahah

Literature Cited

  1. 1.
    Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC. 2014. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLOS ONE 9:10e110726
     [Google Scholar]
  2. 2.
    Adam PS, Borrel G, Brochier-Armanet C, Gribaldo S. 2017. The growing tree of Archaea: new perspectives on their diversity, evolution and ecology. ISME J 11:112407–25
     [Google Scholar]
  3. 3.
    Adam PS, Borrel G, Gribaldo S. 2018. Evolutionary history of carbon monoxide dehydrogenase/acetyl-CoA synthase, one of the oldest enzymatic complexes. PNAS 115:25E5837
     [Google Scholar]
  4. 4.
    Adam PS, Borrel G, Gribaldo S. 2019. An archaeal origin of the Wood-Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy. Nat. Microbiol. 4:122155–63
     [Google Scholar]
  5. 5.
    Adam PS, Kolyfetis GE, Bornemann TLV, Vorgias CE, Probst AJ. 2021. Genomic remnants of ancestral hydrogen and methane metabolism in Archaea drive anaerobic carbon cycling. bioRxiv 2021.08.02.454722, Aug. 2
  6. 6.
    Arshad A, Speth DR, De Graaf RM, Op den Camp HJM, Jetten MSM, Welte CU. 2015. A metagenomics-based metabolic model of nitrate-dependent anaerobic oxidation of methane by Methanoperedens-like archaea. Front. Microbiol. 6:1423
     [Google Scholar]
  7. 7.
    Bapteste E, Brochier C, Boucher Y. 2005. Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1:5353–63
     [Google Scholar]
  8. 8.
    Baron SF, Ferry JG. 1989. Reconstitution and properties of a coenzyme F420-mediated formate hydrogenlyase system in Methanobacterium formicicum. J. Bacteriol. 171:73854–59
     [Google Scholar]
  9. 9.
    Bastviken D, Cole JJ, Pace ML, Van de Bogert MC. 2008. Fates of methane from different lake habitats: connecting whole-lake budgets and CH4 emissions. J. Geophys. Res. Biogeosci. 113:G02024
     [Google Scholar]
  10. 10.
    Berger S, Welte C, Deppenmeier U. 2012. Acetate activation in Methanosaeta thermophila: characterization of the key enzymes pyrophosphatase and acetyl-CoA synthetase. Archaea 2012:315153
     [Google Scholar]
  11. 11.
    Berghuis BA, Yu FB, Schulz F, Blainey PC, Woyke T, Quake SR. 2019. Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. PNAS 116:115037–44
     [Google Scholar]
  12. 12.
    Bertram PA, Thauer RK. 1994. Thermodynamics of the formylmethanofuran dehydrogenase reaction in Methanobacterium thermoautotrophicum. Eur. J. Biochem. 226:3811–18
     [Google Scholar]
  13. 13.
    Boetius A, Ravenschlag K, Schubert CJ, Rickert D, Widdel F et al. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:6804623–26
     [Google Scholar]
  14. 14.
    Borrel G, Adam PS, Gribaldo S. 2016. Methanogenesis and the Wood-Ljungdahl pathway: an ancient, versatile, and fragile association. Genome Biol. Evol. 8:61706–11
     [Google Scholar]
  15. 15.
    Borrel G, Adam PS, McKay LJ, Chen L-X, Sierra-García IN et al. 2019. Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat. Microbiol. 4:603–13
     [Google Scholar]
  16. 16.
    Borrel G, O'Toole PW, Harris HMB, Peyret P, Brugère JF, Gribaldo S. 2013. Phylogenomic data support a seventh order of methylotrophic methanogens and provide insights into the evolution of methanogenesis. Genome Biol. Evol. 5:101769–80
     [Google Scholar]
  17. 17.
    Borrel G, Parisot N, Harris HM, Peyretaillade E, Gaci N et al. 2014. Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genom 15:1679
     [Google Scholar]
  18. 18.
    Boyd J, Jungbluth SP, Leu A, Evans PN, Woodcroft BJ et al. 2019. Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. ISME J 13:51269–79
     [Google Scholar]
  19. 19.
    Castelle CJ, Brown CT, Anantharaman K, Probst AJ, Huang RH, Banfield JF. 2018. Biosynthetic capacity, metabolic variety and unusual biology in the CPR and DPANN radiations. Nat. Rev. Microbiol. 16:10629–45
     [Google Scholar]
  20. 20.
    Catling DC, Claire MW, Zahnle KJ. 2007. Anaerobic methanotrophy and the rise of atmospheric oxygen. Philos. Trans. R. Soc. A 365:1867–88
     [Google Scholar]
  21. 21.
    Chadwick GL, Skennerton CT, Laso-Pérez R, Leu AO, Speth DR 2022. Comparative genomics reveals electron transfer and syntrophic mechanisms differentiating methanotrophic and methanogenic archaea. PLOS Biol 20:1e3001508
     [Google Scholar]
  22. 22.
    Chen S-C, Musat N, Lechtenfeld OJ, Paschke H, Schmidt M et al. 2019. Anaerobic oxidation of ethane by archaea from a marine hydrocarbon seep. Nature 568:7750108–11
     [Google Scholar]
  23. 23.
    Clark JE, Ljungdahl LG. 1984. Purification and properties of 5, 10-methylenetetrahydrofolate reductase, an iron-sulfur flavoprotein from Clostridium formicoaceticum. J. Biol. Chem. 259:1710845–49
     [Google Scholar]
  24. 24.
    Colman DR, Lindsay MR, Boyd ES. 2019. Mixing of meteoric and geothermal fluids supports hyperdiverse chemosynthetic hydrothermal communities. Nat. Commun. 10:681
     [Google Scholar]
  25. 25.
    Conrad R. 2009. The global methane cycle: recent advances in understanding the microbial processes involved. Environ. Microbiol. Rep. 1:5285
     [Google Scholar]
  26. 26.
    Conrad R. 2020. Importance of hydrogenotrophic, aceticlastic and methylotrophic methanogenesis for methane production in terrestrial, aquatic and other anoxic environments: a mini review. Pedosphere 30:125–39
     [Google Scholar]
  27. 27.
    Costa KC, Wong PM, Wang T, Lie TJ, Dodsworth JA et al. 2010. Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase. PNAS 107:2411050–55
     [Google Scholar]
  28. 28.
    Cozannet M, Borrel G, Roussel E, Moalic Y, Allioux M et al. 2021. New insights into the ecology and physiology of Methanomassiliicoccales from terrestrial and aquatic environments. Microorganisms 9:130
     [Google Scholar]
  29. 29.
    Deobald D, Adrian L, Schöne C, Rother M, Layer G 2018. Identification of a unique radical SAM methyltransferase required for the sp3-C-methylation of an arginine residue of methyl-coenzyme M reductase. Sci. Rep. 8:17404
     [Google Scholar]
  30. 30.
    Dridi B, Fardeau ML, Ollivier B, Raoult D, Drancourt M. 2012. Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int. J. Syst. Evol. Microbiol. 62:81902–7
     [Google Scholar]
  31. 31.
    Ermler U, Grabarse W, Shima S, Goubeaud M, Thauer RK. 1997. Crystal structure of methyl-coenzyme M reductase: the key enzyme of biological methane formation. Science 278:1457–62
     [Google Scholar]
  32. 32.
    Ettwig KF, Zhu B, Speth D, Keltjens JT, Jetten MSM, Kartal B. 2016. Archaea catalyze iron-dependent anaerobic oxidation of methane. PNAS 113:4512792–96
     [Google Scholar]
  33. 33.
    Evans PN, Boyd JA, Leu AO, Woodcroft BJ, Parks DH et al. 2019. An evolving view of methane metabolism in the Archaea. Nat. Rev. Microbiol. 17:4219–32
     [Google Scholar]
  34. 34.
    Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ et al. 2015. Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350:6259434–38
     [Google Scholar]
  35. 35.
    Fournier GP, Gogarten JP. 2008. Evolution of acetoclastic methanogenesis in Methanosarcina via horizontal gene transfer from cellulolytic Clostridia. J. Bacteriol. 190:31124–27
     [Google Scholar]
  36. 36.
    Fricke WF, Seedorf H, Henne A, Krüer M, Liesegang H et al. 2006. The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J. Bacteriol. 188:2642–58
     [Google Scholar]
  37. 37.
    Gao B, Gupta RS. 2007. Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genom 8:186
     [Google Scholar]
  38. 38.
    Gottschalk G, Thauer RK. 2001. The Na+-translocating methyltransferase complex from methanogenic archaea. Biochem. Biophs. Acta Bioenerg. 1505:28–36
     [Google Scholar]
  39. 39.
    Gray ND, Sherry A, Hubert C, Dolfing J, Head IM. 2010. Methanogenic degradation of petroleum hydrocarbons in subsurface environments: remediation, heavy oil formation, and energy recovery. Adv. Appl. Microbiol. 72:137–61
     [Google Scholar]
  40. 40.
    Hahn CJ, Laso-Pérez R, Vulcano F, Vaziourakis K-M, Stokke R et al. 2020. “Candidatus Ethanoperedens,” a thermophilic genus of archaea mediating the anaerobic oxidation of ethane. mBio 11:2e00600–20
     [Google Scholar]
  41. 41.
    Hahn CJ, Lemaire ON, Kahnt J, Engilberge S, Wegener G, Wagner T. 2021. Crystal structure of a key enzyme for anaerobic ethane activation. Science 373:6550118–21
     [Google Scholar]
  42. 42.
    Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D et al. 2004. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305:56891457–62
     [Google Scholar]
  43. 43.
    Haroon MF, Hu S, Shi Y, Imelfort M, Keller J et al. 2013. Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500:7464567–70
     [Google Scholar]
  44. 44.
    He Y, Li M, Perumal V, Feng X, Fang J et al. 2016. Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments. Nat. Microbiol. 1:616035
     [Google Scholar]
  45. 45.
    Hoedt EC, Parks DH, Volmer JG, Rosewarne CP, Denman SE et al. 2018. Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. ISME J 12:122942–53
     [Google Scholar]
  46. 46.
    Hoehler TM, Alperin MJ, Albert DB, Martens CS. 1994. Field and laboratory studies of methane oxidation in an anoxic marine sediment: evidence for a methanogen-sulfate reducer consortium. Global Biogeochem. Cycles 8:4451–63
     [Google Scholar]
  47. 47.
    Hua Z-S, Wang Y-L, Evans PN, Qu Y-N, Goh KM et al. 2019. Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea. Nat. Commun. 10:4574
     [Google Scholar]
  48. 48.
    Kaster A-K, Moll J, Parey K, Thauer RK. 2011. Coupling of ferredoxin and heterodisulfide reduction via electron bifurcation in hydrogenotrophic methanogenic archaea. PNAS 108:72981–86
     [Google Scholar]
  49. 49.
    Kasting JF, Siefert JL. 2002. Life and the evolution of Earth's atmosphere. Science 296:55701066–68
     [Google Scholar]
  50. 50.
    Keltjens JT, Vogels GD. 1993. Conversion of methanol and methylamines to methane and carbon dioxide. Methanogenesis: Ecology, Physiology, Biochemistry & Genetics JG Ferry 253–303 New York: Springer Sci. Bus. Media
     [Google Scholar]
  51. 51.
    Klein M, Friedrich M, Roger AJ, Hugenholtz P, Fishbain S et al. 2001. Multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. J. Bacteriol. 183:206028–35
     [Google Scholar]
  52. 52.
    Klenk H-P, Clayton RA, Tomb J-F, White O, Nelson KE et al. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:6658364–70
     [Google Scholar]
  53. 53.
    Knittel K, Boetius A. 2009. Anaerobic oxidation of methane: progress with an unknown process. Annu. Rev. Microbiol. 63:311–34
     [Google Scholar]
  54. 54.
    Kröninger L, Steiniger F, Berger S, Kraus S, Welte CU, Deppenmeier U. 2019. Energy conservation in the gut microbe Methanomassiliicoccus luminyensis is based on membrane-bound ferredoxin oxidation coupled to heterodisulfide reduction. FEBS J 286:193831–43
     [Google Scholar]
  55. 55.
    Kurth JM, den Camp HJMO, Welte CU. 2020. Several ways one goal—methanogenesis from unconventional substrates. Appl. Microbiol. Biotechnol. 104:166839–54
     [Google Scholar]
  56. 56.
    Kurth JM, Nobu MK, Tamaki H, de Jonge N, Berger S et al. 2021. Methanogenic archaea use a bacteria-like methyltransferase system to demethoxylate aromatic compounds. ISME J. 15:123549–65
     [Google Scholar]
  57. 57.
    Laso-Pérez R, Hahn C, van Vliet DM, Tegetmeyer HE, Schubotz F et al. 2019. Anaerobic degradation of non-methane alkanes by “Candidatus Methanoliparia” in hydrocarbon seeps of the Gulf of Mexico. mBio 10:4e01814–19
     [Google Scholar]
  58. 58.
    Laso-Pérez R, Wegener G, Knittel K, Widdel F, Harding KJ et al. 2016. Thermophilic archaea activate butane via alkyl-coenzyme M formation. Nature 539:7629396–401
     [Google Scholar]
  59. 59.
    Latimer MT, Ferry JG. 1993. Cloning, sequence analysis, and hyperexpression of the genes encoding phosphotransacetylase and acetate kinase from Methanosarcina thermophila. J. Bacteriol. 175:216822–29
     [Google Scholar]
  60. 60.
    Leu AO, Cai C, McIlroy SJ, Southam G, Orphan VJ et al. 2020. Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. ISME J 14:41030–41
     [Google Scholar]
  61. 61.
    Leu AO, McIlroy SJ, Ye J, Parks DH, Orphan VJ, Tyson GW. 2020. Lateral gene transfer drives metabolic flexibility in the anaerobic methane-oxidizing archaeal family Methanoperedenaceae. mBio 11:3e01325–20
     [Google Scholar]
  62. 62.
    Lie TJ, Costa KC, Lupa B, Korpole S, Whitman WB, Leigh JA. 2012. Essential anaplerotic role for the energy-converting hydrogenase Eha in hydrogenotrophic methanogenesis. PNAS 109:3815473–78
     [Google Scholar]
  63. 63.
    Liu Y-F, Chen J, Zaramela LS, Wang L-Y, Mbadinga SM et al. 2020. Genomic and transcriptomic evidence supports methane metabolism in Archaeoglobi. mSystems 5:2e00651–19
     [Google Scholar]
  64. 64.
    Liu Y, Whitman WB. 2008. Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann. N. Y. Acad. Sci. 1125:171–89
     [Google Scholar]
  65. 65.
    Lu Y-Z, Fu L, Ding J, Ding Z-W, Li N, Zeng RJ 2016. Cr(VI) reduction coupled with anaerobic oxidation of methane in a laboratory reactor. Water Res 102:445–52
     [Google Scholar]
  66. 66.
    Luo J-H, Chen H, Hu S, Cai C, Yuan Z, Guo J. 2018. Microbial selenate reduction driven by a denitrifying anaerobic methane oxidation biofilm. Environ. Sci. Technol. 52:74006–12
     [Google Scholar]
  67. 67.
    Lyu Z, Shao N, Chou C-W, Shi H, Patel R et al. 2020. Posttranslational methylation of arginine in methyl coenzyme M reductase has a profound impact on both methanogenesis and growth of Methanococcus maripaludis. J. Bacteriol. 202:3e00654–19
     [Google Scholar]
  68. 68.
    Mand TD, Metcalf WW. 2019. Energy conservation and hydrogenase function in methanogenic archaea, in particular the genus Methanosarcina. Microbiol. Mol. Biol. Rev. 83:4e00020–19
     [Google Scholar]
  69. 69.
    Mayumi D, Mochimaru H, Tamaki H, Yamamoto K, Yoshioka H et al. 2016. Methane production from coal by a single methanogen. Science 354:6309222–25
     [Google Scholar]
  70. 70.
    McGlynn SE. 2017. Energy metabolism during anaerobic methane oxidation in ANME archaea. Microbes Environ 32:15–13
     [Google Scholar]
  71. 71.
    McGlynn SE, Chadwick GL, Kempes CP, Orphan VJ. 2015. Single cell activity reveals direct electron transfer in methanotrophic consortia. Nature 526:7574531–35
     [Google Scholar]
  72. 72.
    McKay LJ, Dlakić M, Fields MW, Delmont TO, Eren AM et al. 2019. Co-occurring genomic capacity for anaerobic methane and dissimilatory sulfur metabolisms discovered in the Korarchaeota. Nat. Microbiol. 4:4614–22
     [Google Scholar]
  73. 73.
    Meyerdierks A, Kube M, Kostadinov I, Teeling H, Glöckner FO et al. 2010. Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group. Environ. Microbiol. 12:2422–39
     [Google Scholar]
  74. 74.
    Miller TL, Wolin MJ. 1985. Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch. Microbiol. 141:2116–22
     [Google Scholar]
  75. 75.
    Milucka J, Ferdelman TG, Polerecky L, Franzke D, Wegener G et al. 2012. Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature 491:7425541–46
     [Google Scholar]
  76. 76.
    Moore SJ, Sowa ST, Schuchardt C, Deery E, Lawrence AD et al. 2017. Elucidation of the biosynthesis of the methane catalyst coenzyme F430. Nature 544:764378–82
     [Google Scholar]
  77. 77.
    Moran JJ, Beal EJ, Vrentas JM, Orphan VJ, Freeman KH, House CH. 2008. Methyl sulfides as intermediates in the anaerobic oxidation of methane. Environ. Microbiol. 10:1162–73
     [Google Scholar]
  78. 78.
    Nauhaus K, Treude T, Boetius A, Krüger M. 2005. Environmental regulation of the anaerobic oxidation of methane: a comparison of ANME-I and ANME-II communities. Environ. Microbiol. 7:198–106
     [Google Scholar]
  79. 79.
    Nayak DD, Liu A, Agrawal N, Rodriguez-Carerro R, Dong S-H et al. 2020. Functional interactions between posttranslationally modified amino acids of methyl-coenzyme M reductase in Methanosarcina acetivorans. PLOS Biol. 18:2e3000507
     [Google Scholar]
  80. 80.
    Nayak DD, Mahanta N, Mitchell DA, Metcalf WW 2017. Post-translational thioamidation of methyl-coenzyme M reductase, a key enzyme in methanogenic and methanotrophic archaea. eLife 6:e29218
     [Google Scholar]
  81. 81.
    Nobu MK, Narihiro T, Kuroda K, Mei R, Liu W-T. 2016. Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME J 10:2478–87
     [Google Scholar]
  82. 82.
    Oremland RS, Polcin S. 1982. Methanogenesis and sulfate reduction: competitive and noncompetitive substrates in estuarine sediments. Appl. Environ. Microbiol. 44:61270–76
     [Google Scholar]
  83. 82a.
    Oren A, Garrity GM 2021. Candidatus list no. 2: lists of names of prokaryotic Candidatus taxa. Int. J. Syst. Evol. Microbiol. 71:004671
     [Google Scholar]
  84. 83.
    Orphan VJ, House CH, Hinrichs KU, McKeegan KD, DeLong EF. 2001. Methane-consuming archaea revealed by directly coupled isotopic and phylogenetic analysis. Science 293:5529484–87
     [Google Scholar]
  85. 84.
    Petitjean C, Deschamps P, López-García P, Moreira D. 2015. Rooting the domain Archaea by phylogenomic analysis supports the foundation of the new kingdom Proteoarchaeota. Genome Biol. Evol. 7:1191–204
     [Google Scholar]
  86. 85.
    Prakash D, Wu Y, Suh SJ, Duin EC. 2014. Elucidating the process of activation of methyl-coenzyme M reductase. J. Bacteriol. 196:132491–98
     [Google Scholar]
  87. 86.
    Radle MI, Miller DV, Laremore TN, Booker SJ. 2019. Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. J. Biol. Chem. 294:3111712–25
     [Google Scholar]
  88. 87.
    Raymann K, Brochier-Armanet C, Gribaldo S. 2015. The two-domain tree of life is linked to a new root for the Archaea. PNAS 112:216670–75
     [Google Scholar]
  89. 88.
    Reeburgh WS. 2007. Oceanic methane biogeochemistry. Chem. Rev. 107:2486–513
     [Google Scholar]
  90. 89.
    Rothman DH, Fournier GP, French KL, Alm EJ, Boyle EA et al. 2014. Methanogenic burst in the end-Permian carbon cycle. PNAS 111:155462–67
     [Google Scholar]
  91. 90.
    Saunois M, Jackson RB, Bousquet P, Poulter B, Canadell JG. 2016. The growing role of methane in anthropogenic climate change. Environ. Res. Lett. 11:120207
     [Google Scholar]
  92. 91.
    Seitz KW, Dombrowski N, Eme L, Spang A, Lombard J et al. 2019. Asgard archaea capable of anaerobic hydrocarbon cycling. Nat. Commun. 10:11822
     [Google Scholar]
  93. 92.
    Shima S, Huang G, Wagner T, Ermler U. 2020. Structural basis of hydrogenotrophic methanogenesis. Annu. Rev. Microbiol. 74:713–33
     [Google Scholar]
  94. 93.
    Sieber JR, McInerney MJ, Gunsalus RP. 2012. Genomic insights into syntrophy: the paradigm for anaerobic metabolic cooperation. Annu. Rev. Microbiol. 66:429–52
     [Google Scholar]
  95. 94.
    Söhngen NL. 1910. Sur le rôle du méthane dans la vie organique. Recl. Trav. Chim. Pays-Bas Belgique 29:7238–74
     [Google Scholar]
  96. 95.
    Söllinger A, Urich T. 2019. Methylotrophic methanogens everywhere—physiology and ecology of novel players in global methane cycling. Biochem. Soc. Trans. 47:61895–907
     [Google Scholar]
  97. 96.
    Sorokin DY, Makarova KS, Abbas B, Ferrer M, Golyshin PN et al. 2017. Discovery of extremely halophilic, methyl-reducing euryarchaea provides insights into the evolutionary origin of methanogenesis. Nat. Microbiol. 2:17081
     [Google Scholar]
  98. 97.
    Sprenger WW, Van Belzen MC, Rosenberg J, Hackstein JHP, Keltjens JT. 2000. Methanomicrococcus blatticola gen. nov., sp. nov., a methanol- and methylamine-reducing methanogen from the hindgut of the cockroach Periplaneta americana. Int. J. Syst. Evol. Microbiol. 50:61989–99
     [Google Scholar]
  99. 98.
    Spring S, Scheuner C, Lapidus A, Lucas S, Glavina Del Rio T et al. 2010. The genome sequence of Methanohalophilus mahii SLPT reveals differences in the energy metabolism among members of the Methanosarcinaceae inhabiting freshwater and saline environments. Archaea 2010:690737
     [Google Scholar]
  100. 99.
    Stokke R, Roalkvam I, Lanzen A, Haflidason H, Steen IH. 2012. Integrated metagenomic and metaproteomic analyses of an ANME-1-dominated community in marine cold seep sediments. Environ. Microbiol. 14:51333–46
     [Google Scholar]
  101. 100.
    Thauer RK. 1998. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology 144:Part 92377–406
     [Google Scholar]
  102. 101.
    Thauer RK. 2019. Methyl (alkyl)-coenzyme M reductases: nickel F-430-containing enzymes involved in anaerobic methane formation and in anaerobic oxidation of methane or of short chain alkanes. Biochemistry 58:525198–220
     [Google Scholar]
  103. 102.
    Thauer RK, Kaster A-K, Goenrich M, Schick M, Hiromoto T, Shima S. 2010. Hydrogenases from methanogenic archaea, nickel, a novel cofactor, and H2 storage. Annu. Rev. Biochem. 79:507–36
     [Google Scholar]
  104. 103.
    Thauer RK, Kaster A-K, Seedorf H, Buckel W, Hedderich R. 2008. Methanogenic archaea: ecologically relevant differences in energy conservation. Nat. Rev. Microbiol. 6:8579–91
     [Google Scholar]
  105. 104.
    Thomas C, Desmond-Le Quemener E, Gribaldo S, Borrel G 2021. Factors shaping the abundance and diversity of archaea in the animal gut. Research Square rs-789824, ver. 1. https://doi.org/10.21203/rs.3.rs-789824/v1
    [Crossref]
  106. 105.
    Thomas CM, Taib N, Gribaldo S, Borrel G. 2021. Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host-adaptation in archaea and the evolution of methanogenesis. ISME Commun 1:47
     [Google Scholar]
  107. 106.
    Timmers PHA, Welte CU, Koehorst JJ, Plugge CM, Jetten MSM, Stams AJM 2017. Reverse methanogenesis and respiration in methanotrophic archaea. Archaea 2017:16542
     [Google Scholar]
  108. 107.
    Ueno Y, Yamada K, Yoshida N, Maruyama S, Isozaki Y. 2006. Evidence from fluid inclusions for microbial methanogenesis in the early Archaean era. Nature 440:7083516–19
     [Google Scholar]
  109. 108.
    Vanwonterghem I, Evans PN, Parks DH, Jensen PD, Woodcroft BJ et al. 2016. Methylotrophic methanogenesis discovered in the novel archaeal phylum Verstraetearchaeota. Nat. Microbiol. 1:16170
     [Google Scholar]
  110. 109.
    Wagner T, Ermler U, Shima S. 2016. The methanogenic CO2 reducing-and-fixing enzyme is bifunctional and contains 46 [4Fe-4S] clusters. Science 354:6308114–17
     [Google Scholar]
  111. 110.
    Wagner T, Ermler U, Shima S. 2016. MtrA of the sodium ion pumping methyltransferase binds cobalamin in a unique mode. Sci. Rep. 6:128226
     [Google Scholar]
  112. 111.
    Wagner T, Koch J, Ermler U, Shima S. 2017. Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction. Science 357:6352699–703
     [Google Scholar]
  113. 112.
    Wang Y, Wegener G, Hou J, Wang F-P, Xiao X 2019. Expanding anaerobic alkane metabolism in the domain of Archaea. Nat. Microbiol. 4:595–602
     [Google Scholar]
  114. 113.
    Wang Y, Wegener G, Ruff SE, Wang F. 2021. Methyl/alkyl-coenzyme M reductase-based anaerobic alkane oxidation in archaea. Environ. Microbiol. 23:2530–41
     [Google Scholar]
  115. 114.
    Wang Y, Wegener G, Williams TA, Xie R, Hou J et al. 2021. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. Sci. Adv. 7:27eabj1453
     [Google Scholar]
  116. 115.
    Warke MR, Di Rocco T, Zerkle AL, Lepland A, Prave AR et al. 2020. The great oxidation event preceded a paleoproterozoic “snowball Earth.”. PNAS 117:2413314–20
     [Google Scholar]
  117. 116.
    Wegener G, Krukenberg V, Riedel D, Tegetmeyer HE, Boetius A. 2015. Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria. Nature 526:7574587–90
     [Google Scholar]
  118. 117.
    Welte C, Deppenmeier U. 2014. Bioenergetics and anaerobic respiratory chains of aceticlastic methanogens. Biochem. Biophys. Acta Bioenerg. 1837:71130–47
     [Google Scholar]
  119. 118.
    Williams TA, Szöllősi GJ, Spang A, Foster PG, Heaps SE et al. 2017. Integrative modeling of gene and genome evolution roots the archaeal tree of life. PNAS 114:23E4602–11
     [Google Scholar]
  120. 119.
    Wolfe JM, Fournier GP. 2018. Horizontal gene transfer constrains the timing of methanogen evolution. Nat. Ecol. Evol. 2:5897–903
     [Google Scholar]
  121. 120.
    Wongnate T, Sliwa D, Ginovska B, Smith D, Wolf MW et al. 2016. The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase. Science 352:6288953–58
     [Google Scholar]
  122. 121.
    Zengler K, Richnow HH, Rosselló-Mora R, Michaelis W, Widdel F. 1999. Methane formation from long-chain alkanes by anaerobic microorganisms. Nature 401:266–69
     [Google Scholar]
  123. 122.
    Zhao R, Biddle JF. 2021. Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica margin. ISME Commun 1:25
     [Google Scholar]
  124. 123.
    Zheng K, Ngo PD, Owens VL, Yang X, Mansoorabadi SO 2016. The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea. Science 354:6310339–42
     [Google Scholar]
  125. 124.
    Zhou Z, Zhang C, Liu P, Fu L, Laso-Pérez R et al. 2022. Non-syntrophic methanogenic hydrocarbon degradation by an archaeal species. Nature 601:257–62
     [Google Scholar]
/content/journals/10.1146/annurev-micro-041020-024935
Loading
Diversity and Evolution of Methane-Related Pathways in Archaea
Annual Review of Microbiology 76, 727 (2022); https://doi.org/10.1146/annurev-micro-041020-024935
/content/journals/10.1146/annurev-micro-041020-024935
/content/journals/10.1146/annurev-micro-041020-024935
Loading

Data & Media loading...

Supplemental Material

Supplementary Data

  • Download the Supplemental Material (PDF). Includes Supplemental Figures 1-2 and Supplemental Tables 1-3.

  • Article Type: Review Article

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error