Skip to main content
SpringerLink
Log in

Diversity and Taxonomy of Methanogens

Biogenesis of Hydrocarbons

Part of the book series: Handbook of Hydrocarbon and Lipid Microbiology ((HHLM))

Abstract

Methanogens are strictly anaerobic, methane-producing archaea. All characterized members belong to the phylum Euryarchaeota, but methanogenesis pathway is also predicted to be present in the newly proposed phyla Bathyarchaeota and Verstraetearchaeota. This indicates that the diversity of methanogens may be larger than previously excepted. Although methanogens share a set of physiological characteristics, they are phylogenetically very diverse. The current taxonomy classifies methanogens into seven well established orders: Methanobacteriales, Methanococcales, Methanomicrobiales, Methanosarcinales, Methanopyrales, Methanocellales, and Methanomassiliicoccales. This taxonomy is supported by 16S rRNA gene sequences as well as a number of physiological properties, e.g. substrates for methanogenesis, nutritional requirements, morphologies, and structures of cell envelopes. Methanogens are abundant in a wide variety of anaerobic environments where they catalyze the terminal step in the anaerobic food chain by converting methanogenic substrates to methane. The complexity of methanogenesis pathways suggests an ancient monophyletic origin of methanogens, a hypothesis that is supported by phylogenetic analyses based upon DNA sequences.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution

Institutional subscriptions

References

  • Anderson I et al (2009) Genomic characterization of methanomicrobiales reveals three classes of methanogens. PLoS One 4(6):e5797

    Article  PubMed  PubMed Central  Google Scholar 

  • Angel R et al (2011) Activation of methanogenesis in arid biological soil crusts despite the presence of oxygen. PLoS One 6(5):e20453

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Angel R et al (2012) Methanogenic archaea are globally ubiquitous in aerated soils and become active under wet anoxic conditions. ISME J 6(4):847–862

    Article  CAS  PubMed  Google Scholar 

  • Balch WE et al (1979) Methanogens: reevaluation of a unique biological group. Microbiol Mol Biol Rev 43(2):260–296

    CAS  Google Scholar 

  • Bapteste E et al (2005) Higher-level classification of the Archaea: evolution of methanogenesis and methanogens. Archaea 1(5):353–363

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belay N et al (1988) Methanogenic bacteria from human dental plaque. Appl Environ Microbiol 54(2):600–603

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bellack A et al (2011) Methanocaldococcus villosus sp. nov., a heavily flagellated archaeon that adheres to surfaces and forms cell–cell contacts. Int J Syst Evol Microbiol 61(6):1239–1245

    Article  PubMed  Google Scholar 

  • Belyaev SS et al (1983) Methanogenic bacteria from the Bondyuzhskoe oil field: general characterization and analysis of stable-carbon isotopic fractionation. Appl Environ Microbiol 45(2):691–697

    CAS  PubMed  PubMed Central  Google Scholar 

  • Biavati B et al (1988) Isolation and characterization of “Methanosphaera cuniculi” sp. nov. Appl Environ Microbiol 54(3):768–771

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bleicher K et al (1989) Growth of methanogens on cyclopentanol/CO2 and specificity of alcohol dehydrogenase. FEMS Microbiol Lett 59(3):307–312

    Article  CAS  Google Scholar 

  • Bonin A, Boone D (2006) The order Methanobacteriales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 231–243

    Chapter  Google Scholar 

  • Boone DR (1987) Request for an opinion: replacement of the type strain of Methanobacterium formicicum and reinstatement of Methanobacterium bryantii sp. nov. nom. rev. (ex Balch and Wolfe, 1981) with M.o.H. (DSM 863) as the type strain. Int J Syst Bacteriol 37(2):172–173

    Article  Google Scholar 

  • Boone DR et al (1993a) Isolation and characterization of Methanohalophilus portucalensis sp. nov. and DNA reassociation study of the genus Methanohalophilus. Int J Syst Bacteriol 43(3):430–437

    Article  Google Scholar 

  • Boone DR et al (1993b) Diversity and taxonomy of methanogens. In: Ferry JG (ed) Methanogenesis: ecology, physiology, biochemistry and genetics. Chapman & Hall, New York, pp 35–80

    Chapter  Google Scholar 

  • Boone DR et al (2001a) In: Boone DR, Castenholtz RW, Garrity GM (eds) Methanobacteriales Bergy’s manual of systematic bacteriology, vol 1. Springer, New York, pp 213–235

    Chapter  Google Scholar 

  • Boone DR et al (2001b) In: Boone DR, Castenholtz RW, Garrity GM (eds) Methanomicrobiales Bergy’s manual of systematic bacteriology, vol 1. Springer, New York, pp 246–267

    Google Scholar 

  • Boone DR et al (2001c) In: Boone DR, Castenholtz RW, Garrity GM (eds) Methanosarcinales Bergy’s manual of systematic bacteriology, vol 1. Springer, New York, pp 268–294

    Google Scholar 

  • Borrel G et al (2012a) Genome sequence of “Candidatus Methanomethylophilus alvus” Mx1201, a methanogenic archaeon from the human gut belonging to a seventh order of methanogens. J Bacteriol 194(24):6944–6945

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Borrel G et al (2012b) Methanobacterium lacus sp. nov., isolated from the profundal sediment of a freshwater meromictic lake. Int J Syst Evol Microbiol 62(7):1625–1629

    Article  CAS  PubMed  Google Scholar 

  • Borrel G et al (2013) Genome sequence of “Candidatus Methanomassiliicoccus intestinalis” Issoire-Mx1, a third Thermoplasmatales-related methanogenic archaeon from human feces. Genome Announc 1(4): e00453-13

    Article  Google Scholar 

  • Borrel G et al (2014) Comparative genomics highlights the unique biology of Methanomassiliicoccales, a Thermoplasmatales-related seventh order of methanogenic archaea that encodes pyrrolysine. BMC Genomics 15:679

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Brauer SL et al (2006) Isolation of a novel acidiphilic methanogen from an acidic peat bog. Nature 442(7099):192–194

    Article  PubMed  CAS  Google Scholar 

  • Bräuer SL et al (2011) Methanoregula boonei gen. nov., sp. nov., an acidiphilic methanogen isolated from an acidic peat bog. Int J Syst Evol Microbiol 61(1):45–52

    Article  PubMed  CAS  Google Scholar 

  • Brochier C et al (2004) Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox. Genome Biol 5(3):R17

    Article  PubMed  PubMed Central  Google Scholar 

  • Brugere JF et al (2014) Archaebiotics: proposed therapeutic use of archaea to prevent trimethylaminuria and cardiovascular disease. Gut Microbes 5(1):5–10

    Article  PubMed  Google Scholar 

  • Bruggen JJA et al (1986) Isolation and characterization of Methanoplanus endosymbiosus sp. nov., an endosymbiont of the marine sapropelic ciliate Metopus contortus quennerstedt. Arch Microbiol 144(4):367–374

    Article  Google Scholar 

  • Brusa T et al (1987) The presence of methanobacteria in human subgingival plaque. J Clin Periodontol 14(8):470–471

    Article  CAS  PubMed  Google Scholar 

  • Bryant MP, Boone DR (1987) Emended description of strain MST(DSM 800T), the type strain of Methanosarcina barkeri. Int J Syst Bacteriol 37(2):169–170

    Article  Google Scholar 

  • Burggraf S et al (1990) Methanococcus igneus sp. nov., a novel hyperthermophilic methanogen from a shallow submarine hydrothermal system. Syst Appl Microbiol 13:263–269

    Article  CAS  PubMed  Google Scholar 

  • Burggraf S et al (1991) Methanopyrus kandleri: an archaeal methanogen unrelated to all other known methanogens. Syst Appl Microbiol 14:346–351

    Article  CAS  PubMed  Google Scholar 

  • Cadillo-Quiroz H et al (2008) Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. Appl Environ Microbiol 74(7):2059–2068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cadillo-Quiroz H et al (2009) Methanosphaerula palustris gen. nov., sp. nov., a hydrogenotrophic methanogen isolated from a minerotrophic fen peatland. Int J Syst Evol Microbiol 59(5):928–935

    Article  CAS  PubMed  Google Scholar 

  • Cadillo-Quiroz H et al (2010) Diversity and community structure of archaea inhabiting the rhizoplane of two contrasting plants from an acidic bog. Microb Ecol 59(4):757–767

    Article  CAS  PubMed  Google Scholar 

  • Cadillo-Quiroz H et al (2014) Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium lacus isolated from northern peatlands. Int J Syst Evol Microbiol 64(5):1473–1480

    Article  CAS  PubMed  Google Scholar 

  • Cha I-T et al (2013) Methanomethylovorans uponensis sp. nov., a methylotrophic methanogen isolated from wetland sediment. Antonie Van Leeuwenhoek 104(6):1005–1012

    Article  CAS  PubMed  Google Scholar 

  • Chen S-C et al (2015) Methanoculleus sediminis sp. nov., a methanogen from sediments near a submarine mud volcano. Int J Syst Evol Microbiol 65(7):2141–2147

    Article  CAS  PubMed  Google Scholar 

  • Cheng L et al (2007) Methermicoccus shengliensis gen. nov., sp. nov., a thermophilic, methylotrophic methanogen isolated from oil-production water, and proposal of Methermicoccaceae fam. nov. Int J Syst Evol Microbiol 57:2964–2969.

    Article  CAS  Google Scholar 

  • Cheng L et al (2008) Isolation and characterization of Methanoculleus receptaculi sp. nov. from Shengli oil field, China. FEMS Microbiol Lett 285(1):65–71

    Article  CAS  PubMed  Google Scholar 

  • Cheng L et al (2011) Isolation and characterization of Methanothermobacter crinale sp. nov., a novel hydrogenotrophic methanogen from the Shengli oil field. Appl Environ Microbiol 77(15):5212–5219

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chin KJ et al (2004) Archaeal community structure and pathway of methane formation on rice roots. Microb Ecol 47(1):59–67

    Article  CAS  PubMed  Google Scholar 

  • Chong S et al (2002) Methanogenium marinum sp. nov., a H2-using methanogen from Skan Bay, Alaska, and kinetics of H2 utilization. Antonie Van Leeuwenhoek 81(1):263–270

    Article  CAS  PubMed  Google Scholar 

  • Clementino M et al (2008) Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world. Extremophiles 12(4):595–604

    Article  CAS  PubMed  Google Scholar 

  • Conrad R et al (2006) Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil. Curr Opin Biotechnol 17(3):262–267

    Article  CAS  PubMed  Google Scholar 

  • Conrad R et al (2008) Soil type links microbial colonization of rice roots to methane emission. Glob Chang Biol 14(3):657–669

    Article  Google Scholar 

  • Cuzin N et al (2001) Methanobacterium congolense sp. nov., from a methanogenic fermentation of cassava peel. Int J Syst Evol Microbiol 51(2):489–493

    Article  CAS  PubMed  Google Scholar 

  • Davidova IA et al (1997) Taxonomic description of Methanococcoides euhalobius and its transfer to the Methanohalophilus genus. Antonie Van Leeuwenhoek 71(4):313–318

    Article  CAS  PubMed  Google Scholar 

  • Dianou D et al (2001) Methanoculleus chikugoensis sp. nov., a novel methanogenic archaeon isolated from paddy field soil in Japan, and DNA-DNA hybridization among Methanoculleus species. Int J Syst Evol Microbiol 51(5):1663–1669

    Article  CAS  PubMed  Google Scholar 

  • Diaz E et al (2003) Molecular ecology of anaerobic granular sludge grown at different conditions. Water Sci Technol 48(6):57–64

    Article  CAS  PubMed  Google Scholar 

  • Dighe A et al (2004) Comparison of 16S rRNA gene sequences of genus Methanobrevibacter. BMC Microbiol 4(1):20

    Article  PubMed  PubMed Central  Google Scholar 

  • Doerfert SN et al (2009) Methanolobus zinderi sp. nov., a methylotrophic methanogen isolated from a deep subsurface coal seam. Int J Syst Evol Microbiol 59(5):1064–1069

    Article  CAS  PubMed  Google Scholar 

  • Dridi B et al (2012) Methanomassiliicoccus luminyensis gen. nov., sp. nov., a methanogenic archaeon isolated from human faeces. Int J Syst Evol Microbiol 62(8):1902–1907

    Article  CAS  PubMed  Google Scholar 

  • Earl J et al (2003) Analysis of methanogen diversity in a hypereutrophic lake using PCR-RFLP analysis of mcr sequences. Microb Ecol 46(2):270–278

    Article  CAS  PubMed  Google Scholar 

  • Elberson MA, Sowers KR (1997) Isolation of an aceticlastic strain of Methanosarcina siciliae from marine canyon sediments and emendation of the species description for Methanosarcina siciliae. Int J Syst Bacteriol 47(4):1258–1261

    Article  CAS  PubMed  Google Scholar 

  • Embley TM et al (1992) The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont. J Gen Microbiol 138(7):1479–1487

    Article  CAS  PubMed  Google Scholar 

  • Erkel C et al (2006) Genome of Rice Cluster I archaea – the key methane producers in the rice rhizosphere. Science 313(5785):370–372

    Article  CAS  PubMed  Google Scholar 

  • Evans PN et al (2015) Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics. Science 350(6259):434–438

    Article  CAS  PubMed  Google Scholar 

  • Ferrari A et al (1994) Isolation and characterization of Methanobrevibacter oralis sp. nov. Curr Microbiol 29(1):7–12

    Article  CAS  Google Scholar 

  • Ferry JG et al (1974) Methanospirillum, a new genus of methanogenic bacteria, and characterization of Methanospirillum hungatii sp. nov. Int J Syst Bacteriol 24(4):465–469

    Article  CAS  Google Scholar 

  • Franzmann PD et al (1992) A methanogenic archaeon from Ace Lake, Antarctica: Methanococcoides burtonii sp. nov. Syst Appl Microbiol 15(4):573–581

    Article  Google Scholar 

  • Franzmann PD et al (1997) Methanogenium frigidum sp. nov., a psychrophilic, H2-using methanogen from Ace Lake, Antarctica. Int J Syst Bacteriol 47(4):1068–1072

    Article  CAS  PubMed  Google Scholar 

  • Frimmer U, Widdel F (1989) Oxidation of ethanol by methanogenic bacteria. Arch Microbiol 152(5):479–483

    Article  CAS  Google Scholar 

  • Gagen EJ et al (2013) Novel Cultivation-Based Approach To Understanding the Miscellaneous Crenarchaeotic Group (MCG) Archaea from Sedimentary Ecosystems. Appl Environ Microbiol 79(20):6400–6406

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gan Y et al (2012) Syntrophic oxidation of propionate in rice field soil at 15 and 30°C under methanogenic conditions. Appl Environ Microbiol 78(14):4923–4932

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ganzert L et al (2014) Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake. Int J Syst Evol Microbiol 64(10):3478–3484

    Article  PubMed  CAS  Google Scholar 

  • Gao B, Gupta R (2007) Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis. BMC Genomics 8(1):86

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Garcia JL et al (2006) The order Methanobacteriales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 208–230

    Chapter  Google Scholar 

  • Göker M et al (2014) Genome sequence of the mud-dwelling archaeon Methanoplanus limicola type strain (DSM 2279T), reclassification of Methanoplanus petrolearius as Methanolacinia petrolearia and emended descriptions of the genera Methanoplanus and Methanolacinia. Stand Genomic Sci 9(3):1076–1088

    Article  PubMed  PubMed Central  Google Scholar 

  • Goris J et al (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91

    Article  CAS  PubMed  Google Scholar 

  • Gribaldo S, Brochier-Armanet C (2006) The origin and evolution of Archaea: a state of the art. Philos Trans R Soc B 361(1470):1007–1022

    Article  CAS  Google Scholar 

  • Hafenbradl D et al (1993) A novel unsaturated archaeal ether core lipid from the hyperthermophile Methanopyrus kandleri. Syst Appl Microbiol 16(2):165–169

    Article  CAS  Google Scholar 

  • Hedderich R, Whitman WB (2006) Physiology and biochemistry of the methane-producing Archaea. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, p 2

    Google Scholar 

  • Hendrickson EL et al (2004) Complete genome sequence of the genetically tractable hydrogenotrophic methanogen Methanococcus maripaludis. J Bacteriol 186(20):6956–6969

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hofmann K et al (2016) Abundance and potential metabolic activity of methanogens in well-aerated forest and grassland soils of an alpine region. FEMS Microbiol Ecol 92(2): 1-11

    Article  PubMed  CAS  Google Scholar 

  • Huber H et al (1982) Methanococcus thermolithotrophicus, a novel thermophilic lithotrophic methanogen. Arch Microbiol 132(1):47–50

    Article  Google Scholar 

  • Iino T et al (2010) Methanospirillum lacunae sp. nov., a methane-producing archaeon isolated from a puddly soil, and emended descriptions of the genus Methanospirillum and Methanospirillum hungatei. Int J Syst Evol Microbiol 60(11):2563–2566

    Article  CAS  PubMed  Google Scholar 

  • Iino T et al (2013) Candidatus Methanogranum caenicola: a novel methanogen from the anaerobic digested sludge, and proposal of Methanomassiliicoccaceae fam. nov. and Methanomassiliicoccales ord. nov., for a methanogenic lineage of the class Thermoplasmata. Microbes Environ 28(2):244–250

    Article  PubMed  PubMed Central  Google Scholar 

  • Imachi H et al (2008) Methanolinea tarda gen. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge. Int J Syst Evol Microbiol 58(1):294–301

    Article  CAS  PubMed  Google Scholar 

  • Imachi H et al (2009) Methanofollis ethanolicus sp. nov., an ethanol-utilizing methanogen isolated from a lotus field. Int J Syst Evol Microbiol 59(4):800–805

    Article  CAS  PubMed  Google Scholar 

  • Inagaki F et al (2003) Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk. Appl Environ Microbiol 69(12):7224–7235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jeanthon C et al (1998) Methanococcus infernus sp. nov., a novel hyperthermophilic lithotrophic methanogen isolated from a deep-sea hydrothermal vent. Int J Syst Bacteriol 48(3):913–919

    Article  CAS  PubMed  Google Scholar 

  • Jeanthon C et al (1999) Methanococcus vulcanius sp. nov., a novel hyperthermophilic methanogen isolated from East Pacific Rise, and identification of Methanococcus sp. DSM 4213T as Methanococcus fervens sp. nov. Int J Syst Bacteriol 49(2):583–589

    Article  PubMed  Google Scholar 

  • Jetten MSM et al (1992) Methanogenesis from acetate: a comparison of the acetate metabolism in Methanothrix soehngenii and Methanosarcina spp. FEMS Microbiol Lett 88(3–4):181–197

    Article  CAS  Google Scholar 

  • Jiang B et al (2005) Methanomethylovorans thermophila sp. nov., a thermophilic, methylotrophic methanogen from an anaerobic reactor fed with methanol. Int J Syst Evol Microbiol 55(6):2465–2470

    Article  CAS  PubMed  Google Scholar 

  • Jones WJ et al (1983a) Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch Microbiol 136(4):254–261

    Article  CAS  Google Scholar 

  • Jones WJ et al (1983b) Characterization of Methanococcus maripaludis sp. nov., a new methanogen isolated from salt marsh sediment. Arch Microbiol 135(2):91–97

    Article  Google Scholar 

  • Joulian C et al (2000) Methanobacterium oryzae sp. nov., a novel methanogenic rod isolated from a Philippines ricefield. Int J Syst Evol Microbiol 50(2):525–528

    Article  PubMed  Google Scholar 

  • Kadam PC, Boone DR (1995) Physiological characterization and emended description of Methanolobus vulcani. Int J Syst Bacteriol 45(2):400–402

    Article  Google Scholar 

  • Kadam PC et al (1994) Isolation and characterization of Methanolobus bombayensis sp. nov., a methylotrophic methanogen that requires high concentrations of divalent cations. Int J Syst Bacteriol 44(4):603–607

    Article  CAS  Google Scholar 

  • Kamagata Y, Mikami E (1991) Isolation and characterization of a novel thermophilic Methanosaeta strain. Int J Syst Bacteriol 41(2):191–196

    Article  Google Scholar 

  • Katayama T et al (2014) Methanohalophilus levihalophilus sp. nov., a slightly halophilic, methylotrophic methanogen isolated from natural gas-bearing deep aquifers, and emended description of the genus Methanohalophilus. Int J Syst Evol Microbiol 64(6):2089–2093

    Article  CAS  PubMed  Google Scholar 

  • Kemnitz D et al (2004) Community analysis of methanogenic archaea within a riparian flooding gradient. Environ Microbiol 6(5):449–461

    Article  CAS  PubMed  Google Scholar 

  • Kendall MM, Boone DR (2006) The order Methanosarcinales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 244–256

    Chapter  Google Scholar 

  • Kendall MM et al (2006) Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. Int J Syst Evol Microbiol 56(7):1525–1529

    Article  CAS  PubMed  Google Scholar 

  • Kern T et al (2015) Methanobacterium aggregans sp. nov., a hydrogenotrophic methanogenic archaeon isolated from an anaerobic digester. Int J Syst Evol Microbiol 65(6):1975–1980

    Article  CAS  PubMed  Google Scholar 

  • Keswani J, Whitman W (2001) Relationship of 16S rRNA sequence similarity to DNA hybridization in prokaryotes. Int J Syst Evol Microbiol 51(2):667–678

    Article  CAS  PubMed  Google Scholar 

  • Keswani J et al (1996) Phylogeny and taxonomy of mesophilic Methanococcus spp. and comparison of rRNA, DNA hybridization, and phenotypic methods. Int J Syst Bacteriol 46(3):727–735

    Article  CAS  PubMed  Google Scholar 

  • Kitamura K et al (2011) Methanobacterium kanagiense sp. nov., a hydrogenotrophic methanogen, isolated from rice-field soil. Int J Syst Evol Microbiol 61(6):1246–1252

    Article  PubMed  Google Scholar 

  • Koenig H (1984) Isolation and characterization of Methanobacterium uliginosum sp.nov. from a marshy soil. Can J Microbiol 30(12):1477–1481

    Article  CAS  Google Scholar 

  • Konig K, Stetter KO (1982) Isolation and characterization of Methanolobus tindarius, sp. nov., a coccoid methanogen growing only on methanol and methylamines. Zentralblatt Bakteriol Parasitenkd Infekt Hyg Abt 1 Orig C3:478–490

    Google Scholar 

  • Kotelnikova SV et al (1993) Methanobacterium thermoflexum sp. nov. and Methanobacterium defluvii sp. nov.: thermophilic rod-shaped methanogens isolated from anaerobic digestor sludge. Syst Appl Microbiol 16(3):427–435

    Article  Google Scholar 

  • Kotelnikova S et al (1998) Methanobacterium subterraneum sp. nov., a new alkaliphilic, eurythermic and halotolerant methanogen isolated from deep granitic groundwater. Int J Syst Bacteriol 48(2):357–367

    Article  PubMed  Google Scholar 

  • Krivushin KV et al (2010) Methanobacterium veterum sp. nov., from ancient Siberian permafrost. Int J Syst Evol Microbiol 60(2):455–459

    Article  CAS  PubMed  Google Scholar 

  • Krüger M et al (2005) Activity, structure and dynamics of the methanogenic archaeal community in a flooded Italian rice field. FEMS Microbiol Ecol 51(3):323–331

    Article  PubMed  CAS  Google Scholar 

  • Kudo Y et al (1997) Methanogen flora of paddy soils in Japan. FEMS Microbiol Ecol 22(1):39–48

    Article  CAS  Google Scholar 

  • Kurr M et al (1991) Methanopyrus kandleri, gen. and sp. nov. represents a novel group of hyperthermophilic methanogens, growing at 110°C. Arch Microbiol 156(4):239–247

    Article  CAS  Google Scholar 

  • Kushwaha SC et al (1981) Novel complex polar lipids from the methanogenic archaebacterium Methanospirillum hungatei. Science 211(4487):1163–1164

    Article  CAS  PubMed  Google Scholar 

  • L’Haridon S et al (2003) Methanocaldococcus indicus sp. nov., a novel hyperthermophilic methanogen isolated from the Central Indian Ridge. Int J Syst Evol Microbiol 53(6):1931–1935

    Article  PubMed  CAS  Google Scholar 

  • L’Haridon S et al (2014) Methanococcoides vulcani sp. nov., a marine methylotrophic methanogen that uses betaine, choline and N,N-dimethylethanolamine for methanogenesis, isolated from a mud volcano, and emended description of the genus Methanococcoides. Int J Syst Evol Microbiol 64(6):1978–1983

    Article  PubMed  CAS  Google Scholar 

  • Lai MC, Chen SC (2001) Methanofollis aquaemaris sp. nov., a methanogen isolated from an aquaculture fish pond. Int J Syst Evol Microbiol 51(5):1873–1880

    Article  CAS  PubMed  Google Scholar 

  • Lai MC et al (2002) Methanocalculus taiwanensis sp. nov., isolated from an estuarine environment. Int J Syst Evol Microbiol 52(5):1799–1806

    CAS  PubMed  Google Scholar 

  • Lai M-C et al (2004) Methanocalculus chunghsingensis sp. nov., isolated from an estuary and a marine fishpond in Taiwan. Int J Syst Evol Microbiol 54(1):183–189

    Article  CAS  PubMed  Google Scholar 

  • Lauerer G et al (1986) Methanothermus sociabilis sp. nov., a second species within the Methanothermaceae growing at 97°C. Syst Appl Microbiol 8(1–2):100–105

    Article  Google Scholar 

  • Laurinavichyus KS et al (1988) New species of thermophilic methane-producing bacteria Methanobacterium thermophilum. Mikrobiologiya 57(6):1035–1041

    Google Scholar 

  • Leadbetter JR, Breznak JA (1996) Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes. Appl Environ Microbiol 62(10):3620–3631

    CAS  PubMed  PubMed Central  Google Scholar 

  • Leadbetter JR et al (1998) Methanobrevibacter filiformis sp. nov., a filamentous methanogen from termite hindguts. Arch Microbiol 169(4):287–292

    Article  CAS  PubMed  Google Scholar 

  • Lee J-H et al (2013) Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle. Int J Syst Evol Microbiol 63(11):4196–4201

    Article  CAS  PubMed  Google Scholar 

  • Lin C, Miller TL (1998) Phylogenetic analysis of Methanobrevibacter isolated from feces of humans and other animals. Arch Microbiol 169(5):397–403

    Article  CAS  PubMed  Google Scholar 

  • Liu Y (2010a) Methanobacteriales. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer Berlin Heidelberg, Berlin/Heidelberg, pp 559–571

    Chapter  Google Scholar 

  • Liu Y (2010b) Methanococcales. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer Berlin Heidelberg, Berlin/Heidelberg, pp 573–581

    Chapter  Google Scholar 

  • Liu Y (2010c) Methanomicrobiales. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer Berlin Heidelberg, Berlin/Heidelberg, pp 583–593

    Chapter  Google Scholar 

  • Liu Y (2010d) Methanosarcinales. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer Berlin Heidelberg, Berlin/Heidelberg, pp 595–604

    Chapter  Google Scholar 

  • Liu Y (2010e) Taxonomy of methanogens. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer Berlin Heidelberg, Berlin/Heidelberg, pp 547–558

    Chapter  Google Scholar 

  • Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125(Incredible Anaerobes From Physiology to Genomics to Fuels):171–189

    Article  CAS  PubMed  Google Scholar 

  • Liu Y et al (1990) Methanohalophilus oregonense sp. nov., a methylotrophic methanogen from an alkaline, saline aquifer. Int J Syst Bacteriol 40(2):111–116

    Article  Google Scholar 

  • Liu W-T et al (2002) Characterization of microbial community in granular sludge treating brewery wastewater. Water Res 36(7):1767–1775

    Article  CAS  PubMed  Google Scholar 

  • Liu PF et al (2011) Syntrophomonadaceae-affiliated species as active butyrate-utilizing syntrophs in paddy field soil. Appl Environ Microbiol 77(11):3884–3887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lomans BP et al (1999) Isolation and characterization of Methanomethylovorans hollandica gen. nov., sp. nov., isolated from freshwater sediment, a methylotrophic methanogen able to grow on dimethyl sulfide and methanethiol. Appl Environ Microbiol 65(8):3641–3650

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lu YH, Conrad R (2005) In situ stable isotope probing of methanogenic archaea in the rice rhizosphere. Science 309(5737):1088–1090

    Article  CAS  PubMed  Google Scholar 

  • Lü Z, Lu Y (2012a) Complete genome sequence of a thermophilic methanogen, Methanocella conradii HZ254, isolated from chinese rice field soil. J Bacteriol 194(9):2398–2399

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lü Z, Lu Y (2012b) Methanocella conradii sp. nov., a thermophilic, obligate hydrogenotrophic methanogen, isolated from chinese rice field soil. PLoS One 7(4):e35279

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Lu Y et al (2005) Detecting active methanogenic populations on rice roots using stable isotope probing. Environ Microbiol 7(3):326–336

    Article  CAS  PubMed  Google Scholar 

  • Lueders T et al (2001) Molecular analyses of methyl-coenzyme M reductase alpha-subunit (mcrA) genes in rice field soil and enrichment cultures reveal the methanogenic phenotype of a novel archaeal lineage. Environ Microbiol 3(3):194–204

    Article  CAS  PubMed  Google Scholar 

  • Lueders T et al (2004) Stable-isotope probing of microorganisms thriving at thermodynamic limits: syntrophic propionate oxidation in flooded soil. Appl Environ Microbiol 70(10):5778–5786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luton PE et al (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148(11):3521–3530

    Article  CAS  PubMed  Google Scholar 

  • Lyimo TJ et al (2000) Methanosarcina semesiae sp. nov., a dimethylsulfide-utilizing methanogen from mangrove sediment. Int J Syst Evol Microbiol 50(1):171–178

    Article  CAS  PubMed  Google Scholar 

  • Lyu Z, Lu Y (2015) Comparative genomics of three Methanocellales strains reveal novel taxonomic and metabolic features. Environ Microbiol Rep 7(3):526–537

    Article  CAS  PubMed  Google Scholar 

  • Lyu Z, Lu Y (2017) Metabolic shift at the class level sheds light on adaptation of methanogens to oxidative environments. ISME J 12(2):411–423

    Article  PubMed  CAS  Google Scholar 

  • Ma K et al (2005) Methanobacterium beijingense sp. nov., a novel methanogen isolated from anaerobic digesters. Int J Syst Evol Microbiol 55(1):325–329

    Article  CAS  PubMed  Google Scholar 

  • Ma K et al (2006) Methanosaeta harundinacea sp. nov., a novel acetate-scavenging methanogen isolated from a UASB reactor. Int J Syst Evol Microbiol 56(1):127–131

    Article  CAS  PubMed  Google Scholar 

  • Mah RA, Kuhn DA (1984) Transfer of the type species of the genus Methanococcus to the genus Methanosarcina, naming it Methanosarcina mazei (Barker 1936) comb. nov. et emend. and conservation of the genus Methanococcus (Approved Lists 1980) with Methanococcus vannielii (Approved Lists 1980) as the type species: request for an opinion. Int J Syst Bacteriol 34(2):263–265

    Article  Google Scholar 

  • Markowitz VM et al (2007a) IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 36(Database):D534–D538

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Markowitz VM et al (2007b) The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res 36(Database):D528–D533

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Markowitz VM et al (2009) IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 25(17):2271–2278

    Article  CAS  PubMed  Google Scholar 

  • Martinson GO et al (2010) Methane emissions from tank bromeliads in neotropical forests. Nat Geosci 3(11):766–769

    Article  CAS  Google Scholar 

  • Mathrani IM et al (1988) Methanohalophilus zhilinae sp. nov., an alkaliphilic, halophilic, methylotrophic methanogen. Int J Syst Bacteriol 38(2):139–142

    Article  CAS  PubMed  Google Scholar 

  • Mayumi D et al (2016) Methane production from coal by a single methanogen. Science 354(6309):222–225

    Article  CAS  PubMed  Google Scholar 

  • Mikucki JA et al (2003) Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarinus sp. nov. Appl Environ Microbiol 69(6):3311–3316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller TL, Lin C (2002) Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrevibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov. Int J Syst Evol Microbiol 52(3):819–822

    CAS  PubMed  Google Scholar 

  • Miller TL, Wolin MJ (1985) Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch Microbiol 141(2):116–122

    Article  CAS  PubMed  Google Scholar 

  • Mochimaru H et al (2007) Microbial diversity and methanogenic potential in a high temperature natural gas field in Japan. Extremophiles 11(3):453–461

    Article  CAS  PubMed  Google Scholar 

  • Mori K, Harayama S (2011) Methanobacterium petrolearium sp. nov. and Methanobacterium ferruginis sp. nov., mesophilic methanogens isolated from salty environments. Int J Syst Evol Microbiol 61(1):138–143

    Article  CAS  PubMed  Google Scholar 

  • Mori K et al (2000) Methanocalculus pumilus sp. nov., a heavy-metal-tolerant methanogen isolated from a waste-disposal site. Int J Syst Evol Microbiol 50(5):1723–1729

    Article  CAS  PubMed  Google Scholar 

  • Nakamura K et al (2013) Methanothermobacter tenebrarum sp. nov., a hydrogenotrophic, thermophilic methanogen isolated from gas-associated formation water of a natural gas field. Int J Syst Evol Microbiol 63(2):715–722

    Article  CAS  PubMed  Google Scholar 

  • Nazina T et al (2006) Phylogenetic diversity and activity of anaerobic microorganisms of high-temperature horizons of the Dagang oil field (P. R. China). Microbiology 75(1):55–65

    Article  CAS  Google Scholar 

  • Nicholson M et al (2007) Analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis:identification of uncultured methanogens. Microb Ecol 54(1):141–150

    Article  CAS  PubMed  Google Scholar 

  • Nilsen R, Torsvik T (1996) Methanococcus thermolithotrophicus isolated from North Sea oil field reservoir water. Appl Environ Microbiol 62(2):728–731

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nobu MK et al (2016) Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen. ISME J 10(10):2478–2487

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nolling J et al (1996) Phylogeny of Methanopyrus kandleri based on methyl coenzyme M reductase operons. Int J Syst Bacteriol 46(4):1170–1173

    Article  CAS  PubMed  Google Scholar 

  • Ohkuma M et al (1995) Phylogeny of symbiotic methanogens in the gut of the termite Reticulitermes speratus. FEMS Microbiol Lett 134(1):45–50

    Article  CAS  PubMed  Google Scholar 

  • Ollivier BM, Mah RA, Garcia JL, Boone DR (1986) Isolation and characterization of Methanogenium bourgense sp. nov. Int J Syst Bacteriol 36(2):297–301

    Article  CAS  Google Scholar 

  • Ollivier B et al (1997) Methanoplanus petrolearius sp. nov., a novel methanogenic bacterium from an oil-producing well. FEMS Microbiol Lett 147(1):51–56

    Article  CAS  PubMed  Google Scholar 

  • Ollivier B et al (1998) Methanocalculus halotolerans gen. nov., sp. nov., isolated from an oil-producing well. Int J Syst Bacteriol 48(3):821–828

    Article  PubMed  Google Scholar 

  • Oremland RS, Boone DR (1994) Methanolobus taylorii sp. nov., a new methylotrophic, estuarine methanogen. Int J Syst Bacteriol 44(3):573–575

    Article  Google Scholar 

  • Orphan VJ et al (2000) Culture-dependent and culture-independent characterization of microbial assemblages associated with high-temperature petroleum reservoirs. Appl Environ Microbiol 66(2):700–711

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parshina SN et al (2014) Methanospirillum stamsii sp. nov., a psychrotolerant, hydrogenotrophic, methanogenic archaeon isolated from an anaerobic expanded granular sludge bed bioreactor operated at low temperature. Int J Syst Evol Microbiol 64(1):180–186

    Article  CAS  PubMed  Google Scholar 

  • Patel GB, Sprott GD (1990) Methanosaeta concilii gen. nov., sp. nov. (“Methanothrix concilii”) and Methanosaeta thermoacetophila nom. rev., comb. nov. Int J Syst Bacteriol 40(1):79–82

    Article  Google Scholar 

  • Patel GB et al (1990) Isolation and characterization of Methanobacterium espanolae sp. nov., a mesophilic, moderately acidiphilic methanogen. Int J Syst Bacteriol 40(1):12–18

    Article  Google Scholar 

  • Paterek JR, Smith PH (1988) Methanohalophilus mahii gen. nov., sp. nov., a methylotrophic halophilic methanogen. Int J Syst Bacteriol 38(1):122–123

    Article  Google Scholar 

  • Paynter MJB, Hungate RE (1968) Characterization of Methanobacterium mobilis, sp. n., isolated from the bovine rumen. J Bacteriol 95(5):1943–1951

    CAS  PubMed  PubMed Central  Google Scholar 

  • Peng J et al (2008) Dynamics of the methanogenic archaeal community during plant residue decomposition in an anoxic rice field soil. Appl Environ Microbiol 74(9):2894–2901

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petitjean C et al (2015) Rooting the domain archaea by phylogenomic analysis supports the foundation of the new kingdom proteoarchaeota. Genome Biol Evol 7(1):191–204

    Article  Google Scholar 

  • Poulsen M et al (2013) Methylotrophic methanogenic Thermoplasmata implicated in reduced methane emissions from bovine rumen. Nat Commun 4:1428

    Article  PubMed  CAS  Google Scholar 

  • Price MN (2010) FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments. PLoS ONE 5(3):e9490.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Purdy KJ et al (2002) Comparison of the molecular diversity of the methanogenic community at the brackish and marine ends of a UK estuary. FEMS Microbiol Ecol 39(1):17–21

    Article  CAS  PubMed  Google Scholar 

  • Rea S et al (2007) Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth. Int J Syst Evol Microbiol 57(3):450–456

    Article  CAS  PubMed  Google Scholar 

  • Rivard CJ, Smith PH (1982) Isolation and characterization of a thermophilic marine methanogenic bacterium Methanogenium thermophilicum sp. nov. Int J Syst Bacteriol 32(4):430–436

    Article  Google Scholar 

  • Rivard CJ et al (1983) Isolation and characterization of Methanomicrobium paynteri sp. nov., a mesophilic methanogen isolated from marine sediments. Appl Environ Microbiol 46(2):484–490

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rivera MC, Lake JA (1996) The phylogeny of Methanopyrus kandleri. Int J Syst Bacteriol 46(1):348–351

    Article  CAS  PubMed  Google Scholar 

  • Romesser JA et al (1979) Methanogenium, a new genus of marine methanogenic bacteria, and characterization of Methanogenium cariaci sp. nov. and Methanogenium marisnigri sp. nov. Arch Microbiol 121(2):147–153

    Article  CAS  Google Scholar 

  • Rui J et al (2011) Syntrophic acetate oxidation under thermophilic methanogenic condition in Chinese paddy field soil. FEMS Microbiol Ecol 77(2):264–273

    Article  CAS  PubMed  Google Scholar 

  • Sakai S et al (2008) Methanocella paludicola gen. nov., sp nov., a methane-producing archaeon, the first isolate of the lineage ‘Rice Cluster I’, and proposal of the new archaeal order Methanocellales ord. nov. Int J Syst Evol Microbiol 58:929–936

    Article  PubMed  Google Scholar 

  • Sakai S et al (2009) Cultivation of methanogens under low-hydrogen conditions by using the coculture method. Appl Environ Microbiol 75(14):4892–4896

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakai S et al (2010) Methanocella arvoryzae sp nov., a hydrogenotrophic methanogen isolated from rice field soil. Int J Syst Evol Microbiol 60:2918–2923

    Article  CAS  PubMed  Google Scholar 

  • Sakai S et al (2011) Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales. PLoS One 6(7):e22898

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakai S et al (2012) Methanolinea mesophila sp. nov., a hydrogenotrophic methanogen isolated from rice field soil, and proposal of the archaeal family Methanoregulaceae fam. nov. within the order Methanomicrobiales. Int J Syst Evol Microbiol 62(6):1389–1395

    Article  CAS  PubMed  Google Scholar 

  • Savant DV et al (2002) Methanobrevibacter acididurans sp. nov., a novel methanogen from a sour anaerobic digester. Int J Syst Evol Microbiol 52(4):1081–1087

    CAS  PubMed  Google Scholar 

  • Schirmack J et al (2014) Methanobacterium movilense sp. nov., a hydrogenotrophic, secondary-alcohol-utilizing methanogen from the anoxic sediment of a subsurface lake. Int J Syst Evol Microbiol 64(2):522–527

    Article  CAS  PubMed  Google Scholar 

  • Schönheit P et al (1980) Growth parameters (Ks, μmax, Ys) of Methanobacterium thermoautotrophicum. Arch Microbiol 127(1):59–65

    Article  Google Scholar 

  • Schuchmann K, Muller V (2014) Autotrophy at the thermodynamic limit of life: a model for energy conservation in acetogenic bacteria. Nat Rev Microbiol 12(12):809–821

    Article  CAS  PubMed  Google Scholar 

  • Shcherbakova V et al (2011) Methanobacterium arcticum sp. nov., a methanogenic archaeon from Holocene Arctic permafrost. Int J Syst Evol Microbiol 61(1):144–147

    Article  CAS  PubMed  Google Scholar 

  • Shieh J et al (1988) Pseudoauxotrophy of Methanococcus voltae for acetate, leucine, and isoleucine. J Bacteriol 170(9):4091–4096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shimizu S et al (2011) Methanosarcina horonobensis sp. nov., a methanogenic archaeon isolated from a deep subsurface Miocene formation. Int J Syst Evol Microbiol 61(10):2503–2507

    Article  CAS  PubMed  Google Scholar 

  • Shimizu S et al (2013) Methanoculleus horonobensis sp. nov., a methanogenic archaeon isolated from a deep diatomaceous shale formation. Int J Syst Evol Microbiol 63(11):4320–4323

    Article  CAS  PubMed  Google Scholar 

  • Shimizu S et al (2015) Methanosarcina subterranea sp. nov., a methanogenic archaeon isolated from a deep subsurface diatomaceous shale formation. Int J Syst Evol Microbiol 65(4):1167–1171

    Article  CAS  PubMed  Google Scholar 

  • Shlimon AG et al (2004) Methanobacterium aarhusense sp. nov., a novel methanogen isolated from a marine sediment (Aarhus Bay, Denmark). Int J Syst Evol Microbiol 54(3):759–763

    Article  CAS  PubMed  Google Scholar 

  • Simankova MV et al (2001) Methanosarcina lacustris sp. nov., a new psychrotolerant methanogenic archaeon from anoxic lake sediments. Syst Appl Microbiol 24(3):362–367

    Article  CAS  PubMed  Google Scholar 

  • Singh N et al (2005) Isolation and characterization of methylotrophic methanogens from anoxic marine sediments in Skan Bay, Alaska: description of Methanococcoides alaskense sp. nov., and emended description of Methanosarcina baltica. Int J Syst Evol Microbiol 55(6):2531–2538

    Article  CAS  PubMed  Google Scholar 

  • Sizova MV et al (2003) Isolation and characterization of oligotrophic acido-tolerant methanogenic consortia from a Sphagnum peat bog. FEMS Microbiol Ecol 45(3):301–315

    Article  CAS  PubMed  Google Scholar 

  • Slesarev AI et al (1994) Purification and characterization of DNA topoisomerase V. An enzyme from the hyperthermophilic prokaryote Methanopyrus kandleri that resembles eukaryotic topoisomerase I. J Biol Chem 269(5):3295–3303

    CAS  PubMed  Google Scholar 

  • Slesarev AI et al (2002) The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A 99(7):4644–4649

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smith PH, Hungate RE (1958) Isolation and characterization of Methanobacterium ruminantium N. SP. J Bacteriol 75(6):713–718

    CAS  PubMed  PubMed Central  Google Scholar 

  • Smith KS, Ingram-Smith C (2007) Methanosaeta, the forgotten methanogen? Trends Microbiol 15(4):150–155

    Article  CAS  PubMed  Google Scholar 

  • Sorokin DY et al (2015) Methanosalsum natronophilum sp. nov., and Methanocalculus alkaliphilus sp. nov., haloalkaliphilic methanogens from hypersaline soda lakes. Int J Syst Evol Microbiol 65(10):3739–3745

    Article  CAS  PubMed  Google Scholar 

  • Sowers KR, Ferry JG (1983) Isolation and characterization of a methylotrophic marine methanogen, Methanococcoides methylutens gen. nov., sp. nov. Appl Environ Microbiol 45(2):684–690

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sowers KR et al (1984) Methanosarcina acetivorans sp. nov., an acetotrophic methane-producing bacterium isolated from marine sediments. Appl Environ Microbiol 47(5):971–978

    CAS  PubMed  PubMed Central  Google Scholar 

  • Sprenger WW et al (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(6):1989–1999

    Article  CAS  PubMed  Google Scholar 

  • Springer E et al (1995) Partial gene sequences for the A subunit of methyl-coenzyme M reductase (mcrI) as a phylogenetic tool for the family Methanosarcinaceae. Int J Syst Bacteriol 45(3):554–559

    Article  CAS  PubMed  Google Scholar 

  • Sprott GD, McKellar RC (1980) Composition and properties of the cell wall of Methanospirillum hungatii. Can J Microbiol 26(2):115–120

    Article  CAS  PubMed  Google Scholar 

  • Sprott GD et al (1983) Isolation and chemical composition of the cytoplasmic membrane of the archaebacterium Methanospirillum hungatei. J Biol Chem 258(6):4026–4031

    CAS  PubMed  Google Scholar 

  • Stackebrandt E et al (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52(3):1043–1047

    CAS  PubMed  Google Scholar 

  • Stadtman TC, Barker HA (1951) Studies on the methane fermentation X.: a new formate-decomposing bacterium, Methanococcus vannielii. J Bacteriol 62(3):269–280

    CAS  PubMed  PubMed Central  Google Scholar 

  • Stetter KO et al (1981) Methanothermus fervidus, sp. nov., a novel extremely thermophilic methanogen isolated from an Icelandic hot spring. Mikrobiol HYG, I ABT C 2(2):166–178

    CAS  Google Scholar 

  • Stewart LC et al (2015) Methanocaldococcus bathoardescens sp. nov., a hyperthermophilic methanogen isolated from a volcanically active deep-sea hydrothermal vent. Int J Syst Evol Microbiol 65(4):1280–1283

    Article  CAS  PubMed  Google Scholar 

  • Takai K et al (2002) Methanothermococcus okinawensis sp. nov., a thermophilic, methane-producing archaeon isolated from a Western Pacific deep-sea hydrothermal vent system. Int J Syst Evol Microbiol 52(4):1089–1095

    CAS  PubMed  Google Scholar 

  • Takai K et al (2004) Methanotorris formicicus sp. nov., a novel extremely thermophilic, methane-producing archaeon isolated from a black smoker chimney in the Central Indian Ridge. Int J Syst Evol Microbiol 54(4):1095–1100

    Article  CAS  PubMed  Google Scholar 

  • Tian J et al (2010) Methanoculleus hydrogenitrophicus sp. nov., a methanogenic archaeon isolated from wetland soil. Int J Syst Evol Microbiol 60(9):2165–2169

    Article  CAS  PubMed  Google Scholar 

  • Vanwonterghem I et al (2016) Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota. Nat Microbiol 1:16170

    Article  CAS  PubMed  Google Scholar 

  • Ver Eecke HC et al (2013) Growth kinetics and energetics of a deep-sea hyperthermophilic methanogen under varying environmental conditions. Environ Microbiol Rep 5(5):665–671

    Google Scholar 

  • Vetriani C et al (1999) Population structure and phylogenetic characterization of marine benthic Archaea in deep-sea sediments. Appl Environ Microbiol 65(10):4375–4384

    Google Scholar 

  • von Klein D et al (2002) Methanosarcina baltica, sp. nov., a novel methanogen isolated from the Gotland Deep of the Baltic Sea. Extremophiles 6(2):103–110

    Article  Google Scholar 

  • Wagner D et al (2013) Methanosarcina soligelidi sp. nov., a desiccation- and freeze-thaw-resistant methanogenic archaeon from a Siberian permafrost-affected soil. Int J Syst Evol Microbiol 63(8):2986–2991

    Article  CAS  PubMed  Google Scholar 

  • Wang S et al (2009) A new positive/negative selection scheme for precise BAC recombineering. Mol Biotechnol 42(1):110–116

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wasserfallen A et al (2000) Phylogenetic analysis of 18 thermophilic Methanobacterium isolates supports the proposals to create a new genus, Methanothermobacter gen. nov., and to reclassify several isolates in three species, Methanothermobacter thermautotrophicus comb. nov., Methanothermobacter wolfeii comb. nov., and Methanothermobacter marburgensis sp. nov. Int J Syst Evol Microbiol 50(1):43–53

    Article  CAS  PubMed  Google Scholar 

  • Wayne LG et al (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  • Weiss A et al (2008) Diversity of the resident microbiota in a thermophilic municipal biogas plant. Appl Microbiol Biotechnol 81(1):163–173

    Article  CAS  PubMed  Google Scholar 

  • Weng C-Y et al (2015) Methanoculleus taiwanensis sp. nov., a methanogen isolated from deep marine sediment at the deformation front area near Taiwan. Int J Syst Evol Microbiol 65(3):1044–1049

    Article  CAS  PubMed  Google Scholar 

  • Whitman WB, Jeanthon C (2006) Methanococcales. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 257–273

    Chapter  Google Scholar 

  • Whitman WB et al (1982) Nutrition and carbon metabolism of Methanococcus voltae. J Bacteriol 149(3):852–863

    CAS  PubMed  PubMed Central  Google Scholar 

  • Whitman WB et al (2001a) In: Boone DR, Castenholtz RW, Garrity GM (eds) Methanococcales. Bergy’s manual of systematic bacteriology, vol 1. Springer, New York, pp 236–246

    Google Scholar 

  • Whitman WB et al (2001b) Taxonomy of methanogenic archaea. In: Boone DR, Castenholtz RW, Garrity GM (eds) Bergey’s mannual of systematic bacteriology. Springer, New York, p 1

    Google Scholar 

  • Whitman WB et al (2006) The methanogenic bacteria. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes. Springer, New York, pp 165–207

    Chapter  Google Scholar 

  • Widdel F (1986) Growth of methanogenic bacteria in pure culture with 2-propanol and other alcohols as hydrogen donors. Appl Environ Microbiol 51(5):1056–1062

    CAS  PubMed  PubMed Central  Google Scholar 

  • Widdel F et al (1988) Classification of secondary alcohol-utilizing methanogens including a new thermophilic isolate. Arch Microbiol 150(5):477–481

    Article  CAS  Google Scholar 

  • Wildgruber G et al (1982) Methanoplanus limicola, a plate-shaped methanogen representing a novel family, the Methanoplanaceae. Arch Microbiol 132(1):31–36

    Article  CAS  Google Scholar 

  • Wilharm T et al (1991) DNA-DNA hybridization of methylotrophic halophilic methanogenic bacteria and transfer of Methanococcus halophilusvp to the genus Methanohalophilus as Methanohalophilus halophilus comb. nov. Int J Syst Bacteriol 41(4):558–562

    Article  Google Scholar 

  • Winter J et al (1984) Methanobacterium wolfei, sp.nov., a new tungsten-requiring, thermophilic, autotrophic methanogen. Syst Appl Microbiol 5(4):457–466

    Article  CAS  Google Scholar 

  • Worakit S et al (1986) Methanobacterium alcaliphilum sp. nov., an H2-utilizing methanogen that grows at high pH values. Int J Syst Bacteriol 36(3):380–382

    Article  Google Scholar 

  • Wright A-DG et al (2004) Molecular diversity of rumen methanogens from sheep in western Australia. Appl Environ Microbiol 70(3):1263–1270

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu S-Y, Lai M-C (2011) Methanogenic archaea isolated from Taiwan’s Chelungpu fault. Appl Environ Microbiol 77(3):830–838

    Article  CAS  PubMed  Google Scholar 

  • Wu S-Y et al (2005) Methanofollis formosanus sp. nov., isolated from a fish pond. Int J Syst Evol Microbiol 55(2):837–842

    Article  CAS  PubMed  Google Scholar 

  • Wu XL et al (2006) Diversity and ubiquity of thermophilic methanogenic archaea in temperate anoxic soils. Environ Microbiol 8(3):394–404

    Article  CAS  PubMed  Google Scholar 

  • Zabel HP et al (1984) Isolation and characterization of a new coccoid methanogen, Methanogenium tatii spec. nov. from a solfataric field on Mount Tatio. Arch Microbiol 137(4):308–315

    Article  CAS  Google Scholar 

  • Zeikus JG, Henning DL (1975) Methanobacterium arbophilicum sp.nov. An obligate anaerobe isolated from wetwood of living trees. Antonie Van Leeuwenhoek 41(4):543–552

    Article  CAS  PubMed  Google Scholar 

  • Zeikus JG, Wolee RS (1972) Methanobacterium thermoautotrophicus sp. n., an anaerobic, autotrophic, extreme thermophile. J Bacteriol 109(2):707–713

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zellner G et al (1987) Isolation and characterization of Methanocorpusculum parvum, gen. nov., spec. nov., a new tungsten requiring, coccoid methanogen. Arch Microbiol 147(1):13–20

    Article  CAS  Google Scholar 

  • Zellner G et al (1988) Characterization of a new mesophilic, secondary alcohol-utilizing methanogen, Methanobacterium palustre spec. nov. from a peat bog. Arch Microbiol 151(1):1–9

    Article  Google Scholar 

  • Zellner G et al (1989) Methanocorpusculaceae fam. nov., represented by Methanocorpusculum parvum, Methanocorpusculum sinense spec. nov. and Methanocorpusculum bavaricum spec. nov. Arch Microbiol 151(5):381–390

    Article  CAS  PubMed  Google Scholar 

  • Zellner G et al (1990) Methanogenium liminatans spec. nov., a new coccoid, mesophilic methanogen able to oxidize secondary alcohols. Arch Microbiol 153(3):287–293

    Article  CAS  Google Scholar 

  • Zellner G et al (1998) Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in North-Sumatra, Indonesia. Int J Syst Bacteriol 48(4):1111–1117

    Article  CAS  PubMed  Google Scholar 

  • Zhao H et al (1988) An extremely thermophilic Methanococcus from a deep sea hydrothermal vent and its plasmid. Arch Microbiol 150(2):178–183

    Article  CAS  Google Scholar 

  • Zhao Y et al (1989) Isolation and characterization of Methanocorpusculum labreanum sp. nov. from the LaBrea Tar Pits. Int J Syst Bacteriol 39(1):10–13

    Article  Google Scholar 

  • Zhilina TN, Zavarzin GA (1987a) Methanohalobium evestigatus, n. gen., n. sp., the extremely halophilic methanogenic Archaebacterium. Dokl Akad Nauk SSSR 293:464–468

    CAS  Google Scholar 

  • Zhilina TN, Zavarzin GA (1987b) Methanosarcina vacuolata sp. nov., a vacuolated Methanosarcina. Int J Syst Bacteriol 37(3):281–283

    Article  CAS  Google Scholar 

  • Zhilina TN et al (2013) Methanocalculus natronophilus sp. nov., a new alkaliphilic hydrogenotrophic methanogenic archaeon from a soda lake, and proposal of the new family Methanocalculaceae. Microbiology 82(6):698–706

    Article  CAS  Google Scholar 

  • Zhu J et al (2011) Methanobacterium movens sp. nov. and Methanobacterium flexile sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 61(12):2974–2978

    Article  CAS  PubMed  Google Scholar 

  • Zinder SH et al (1985) Methanosarcina thermophila sp. nov., a thermophilic, acetotrophic, methane-producing bacterium. Int J Syst Bacteriol 35(4):522–523

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Microbiology, University of Georgia, Athens, GA, USA

    Zhe Lyu

  2. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA

    Yuchen Liu

Authors
  1. Zhe Lyu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuchen Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yuchen Liu .

Editor information

Editors and Affiliations

  1. Laboratory of Microbiology, Wageningen University, HB Wageningen, The Netherlands

    Alfons J.M. Stams

  2. Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands

    Diana Sousa

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG

About this entry

Check for updates. Verify currency and authenticity via CrossMark

Cite this entry

Lyu, Z., Liu, Y. (2018). Diversity and Taxonomy of Methanogens. In: Stams, A., Sousa, D. (eds) Biogenesis of Hydrocarbons. Handbook of Hydrocarbon and Lipid Microbiology . Springer, Cham. https://doi.org/10.1007/978-3-319-53114-4_5-1

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-53114-4_5-1

  • Received:

  • Accepted:

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-53114-4

  • Online ISBN: 978-3-319-53114-4

  • eBook Packages: Springer Reference Biomedicine and Life SciencesReference Module Biomedical and Life Sciences

Publish with us

Policies and ethics

Chapter history

  1. Latest

    Diversity and Taxonomy of Methanogens
    Published:
    22 May 2018

    DOI: https://doi.org/10.1007/978-3-319-53114-4_5-2

  2. Original

    Diversity and Taxonomy of Methanogens
    Published:
    27 March 2018

    DOI: https://doi.org/10.1007/978-3-319-53114-4_5-1

Search

Navigation