In anaerobic environments, methanogens play a vital ecological role, removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration.[17] Methanogens typically thrive in environments in which all electron acceptors other than CO2 (such as oxygen, nitrate, ferric iron (Fe(III)), and sulfate) have been depleted. Such environments include wetlands and rice paddy soil, the digestive tracts of various animals (ruminants, arthropods, humans),[18][19][20] wastewater treatment plants and landfills, deep-water oceanic sediments, and hydrothermal vents.[21] Most of those environments are not categorized as extreme and thus methanogens that inhabit them. However, many well studied methanogens are thermophiles such as Methanopyrus kandlerii, Methanthermobacter marburgensis, Methanocaldococcus jannaschii. On the other hand, gut methanogens such as Methanobrevibacter smithii common in humans or Methanobrevibacter ruminantium omnipresent in ruminants are mesophiles.
Methanogens in extreme environments
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In deep basaltic rocks near the mid-ocean ridges, methanogens can obtain their hydrogen from the serpentinization reaction of olivine as observed in the hydrothermal field of Lost City. The thermal breakdown of water and water radiolysis are other possible sources of hydrogen. Methanogens are key agents of remineralization of organic carbon in continental margin sediments and other aquatic sediments with high rates of sedimentation and high sediment organic matter. Under the correct conditions of pressure and temperature, biogenic methane can accumulate in massive deposits of methane clathrates[22] that account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.[23]
Methanogens have been found in several extreme environments on Earth – buried under kilometres of ice in Greenland and living in hot, dry desert soil. They are known to be the most common archaea in deep subterranean habitats. Live microbes making methane were found in a glacial ice core sample retrieved from about three kilometres under Greenland by researchers from the University of California, Berkeley. They also found a constant metabolism able to repair macromolecular damage, at temperatures of 145 to –40 °C.[6]
Another study[7] has also discovered methanogens in a harsh environment on Earth. Researchers studied dozens of soil and vapour samples from five different desert environments in Utah, Idaho and California in the United States, and in Canada and Chile. Of these, five soil samples and three vapour samples from the vicinity of the Mars Desert Research Station in Utah were found to have signs of viable methanogens.[8]
Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet.[24] In June 2019, NASA's Curiosity rover detected methane, commonly generated by underground microbes such as methanogens, which signals possibility of life on Mars.[25]
Closely related to the methanogens are the anaerobic methane oxidizers, which utilize methane as a substrate in conjunction with the reduction of sulfate and nitrate.[26] Most methanogens are autotrophic producers, but those that oxidize CH3COO− are classed as chemotroph instead.
Methanogens in the digestive tract of animals
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The digestive tract of animals is characterized by a nutrient-rich and predominantly anaerobic environment, making it an ideal habitat for many microbes, including methanogens. Despite this, methanogens and archaea, in general, were largely overlooked as part of the gut microbiota until recently. However, they play a crucial role in maintaining gut balance by utilizing end products of bacterial fermentation, such as H2, acetate, methanol, and methylamines.
Recent extensive surveys of archaea presence in the animal gut, based on 16S rRNA analysis, have provided a comprehensive view of archaea diversity and abundance.[27][28][29] These studies revealed that only a few archaeal lineages are present, with the majority being methanogens, while non-methanogenic archaea are rare and not abundant. Taxonomic classification of archaeal diversity identified that representatives of only three phyla are present in the digestive tracts of animals: Methanobacteriota (order Methanobacteriales), Thermoplasmatota (order Methanomassiliicoccales), and Halobacteriota (orders Methanomicrobiales and Methanosarcinales). However, not all families and genera within these orders were detected in animal guts, but only a few genera, suggesting their specific adaptations to the gut environment.
Initially, methanogens were considered to be bacteria, as it was not possible to distinguish archaea and bacteria before the introduction of molecular techniques such as DNA sequencing and PCR. Since the introduction of the domain Archaea by Carl Woese in 1977,[57] methanogens were for a prolonged period considered a monophyletic group, later named Euryarchaeota (super)phylum. However, intensive studies of various environments have proved that there are more and more non-methanogenic lineages among methanogenic ones.
The development of genome sequencing directly from environmental samples (metagenomics) allowed the discovery of the first methanogens outside the Euryarchaeota superphylum. The first such putative methanogenic lineage was Bathyarchaeia,[58] a class within the Thermoproteota phylum. Later, it was shown that this lineage is not methanogenic but alkane-oxidizing utilizing highly divergent enzyme Acr similar to the hallmark gene of methanogenesis, methyl-CoM reductase (McrABG).[59] The first isolate of Bathyarchaeum tardum from sediment of coastal lake in Russia showed that it metabolizes aromatic compounds and proteins[60] as it was previously predicted based on metagenomic studies.[61][62][63] However, more new putative methanogens outside of Euryarchaeota were discovered based on the presence McrABG.
For instance, methanogens were found in the phyla Thermoproteota (orders Methanomethyliales, Korarchaeales, Methanohydrogenales, Nezhaarchaeales) and Methanobacteriota_B (order Methanofastidiosales). Additionally, some new lineages of methanogens were isolated in pure culture, which allowed the discovery of a new type of methanogenesis: H2-dependent methyl-reducing methanogenesis, which is independent of the Wood-Ljungdahl pathway. For example, in 2012, the order Methanoplasmatales from the phylum Thermoplasmatota was described as a seventh order of methanogens.[64] Later, the order was renamed Methanomassiliicoccales based on the isolated from human gut Methanomassiliicoccus luminyensis.[65][66]
Another new lineage in the Halobacteriota phylum, order Methanonatronarchaeales, was discovered in alkaline saline lakes in Siberia in 2017.[67][68] It also employs H2-dependent methyl-reducing methanogenesis but intriguingly harbors almost the full Wood-Ljungdahl pathway. However, it is disconnected from McrABG as no MtrA-H complex was detected.[69][70]
The taxonomy of methanogens reflects the evolution of these archaea, with some studies suggesting that the Last Archaeal Common Ancestor was methanogenic.[71] If correct, this suggests that many archaeal lineages lost the ability to produce methane and switched to other types of metabolism. Currently, most of the isolated methanogens belong to one of three archaeal phyla (classification GTDB release 220): Halobacteriota, Methanobacteriota, and Thermoplasmatota. Under the International Code of Nomenclature for Prokaryotes,[72] all three phyla belong to the same kingdom, Methanobacteriati.[73][74] In total, more than 150 methanogen species are known in culture, with some represented by more than one strain.[75]
Phylum Halobacteriota
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Order Methanocellales
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Family Methanocellaceae
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Genus Methanocella Sakai et al. 2008
Methanocella paludicola Sakai et al. 2008 (type species)
Methanocella arvoryzae Sakai et al. 2010
Methanocella conradii Lü and Lu 2012
Class Methanomicrobia
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Order Methanomicrobiales
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Family Methanocalculaceae Zhilina et al. 2014
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Family Methanocorpusculaceae Zellner et al. 1989
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Methanocorpusculum Zellner et al. 1988
Methanocorpusculum parvum Zellner et al. 1988 (type species)
Methanocorpusculum bavaricum Zellner et al. 1989
Methanocorpusculum labreanum
Methanocorpusculum sinense Zellner et al. 1989
Family Methanomicrobiaceae Balch and Wolfe 1981
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Genus Methanomicrobium Balch and Wolfe 1981
Methanomicrobium mobile (Paynter and Hungate 1968) Balch and Wolfe 1981 (type species)
Methanomicrobium antiquum Mochimaru et al. 2016
Genus Methanoculleus Maestrojuán et al. 1990
Methanoculleus bourgensis corrig. (Ollivier et al. 1986) Maestrojuán et al. 1990 (type species)
Methanoculleus chikugoensis Dianou et al. 2001
Methanoculleus horonobensis Shimizu et al. 2013
Methanoculleus hydrogenitrophicus Tian et al. 2010
Methanoculleus marisnigri
Methanoculleus palmolei Zellner et al. 1998
Methanoculleus receptaculi Cheng et al. 2008
Methanoculleus sediminis Chen et al. 2015
Methanoculleus submarinus Mikucki et al. 2003
Methanoculleus taiwanensis Weng et al. 2015
Methanoculleus thermophilus corrig. (Rivard and Smith 1982) Maestrojuán et al. 1990
Genus Methanogenium Romesser et al. 1981
Methanogenium cariaci Romesser et al. 1981 (type species)
Methanogenium frigidum
Methanogenium marinum Chong et al. 2003
Methanogenium organophilum
Genus Methanofollis Zellner et al. 1999
Methanofollis tationis (Zabel et al. 1986) Zellner et al. 1999 (type strains)
Methanofollis aquaemaris Lai and Chen 2001
Methanofollis ethanolicus Imachi et al. 2009
Methanofollis fontis Chen et al. 2020
Methanofollis formosanus Wu et al. 2005
Methanofollis liminatans (Zellner et al. 1990) Zellner et al. 1999
Family Methanoregulaceae Sakai et al. 2012
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Genus Methanoregula Bräuer et al. 2011
Methanoregula boonei Bräuer et al. 2011 (type species)
Methanoregula formicica Yashiro et al. 2011
Family Methanospirillaceae Boone et al. 2002
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Methanospirillum Ferry et al. 1974
Methanospirillum hungatei corrig. Ferry et al. 1974 (type species)
Methanospirillum lacunae Iino et al. 2010
Methanospirillum psychrodurum Zhou et al. 2014
Methanospirillum stamsii Parshina et al. 2014
Class Methanonatronarchaeia
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Order Methanonatronarchaeales
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Family Methanonatronarchaeaceae Sorokin et al. 2018
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Genus Methanonatronarchaeum Sorokin et al. 2018
Methanonatronarchaeum thermophilum Sorokin et al. 2018 (type species)
Class Methanosarcinia
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Order Methanosarcinales
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Family Methanosarcinaceae
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Genus Methanosarcina Kluyver and van Niel 1936
Methanosarcina barkeri Schnellen 1947 (type species)
Methanosarcina acetivorans
Methanosarcina baltica von Klein et al. 2002
Methanosarcina flavescens Kern et al. 2016
Methanosarcina horonobensis Shimizu et al. 2011
Methanosarcina lacustris Simankova et al. 2002
Methanosarcina mazei (Barker 1936) Mah and Kuhn 1984
Methanosarcina semesiae Lyimo et al. 2000
Methanosarcina siciliae (Stetter and König 1989) Ni et al. 1994
Methanosarcina soligelidi Wagner et al. 2013
Methanosarcina spelaei Ganzert et al. 2014
Methanosarcina subterranea Shimizu et al. 2015
Methanosarcina thermophila Zinder et al. 1985
Methanosarcina vacuolata Zhilina and Zavarzin 1987
Genus Methanimicrococcus corrig. Sprenger et al. 2000
Methanimicrococcus blatticola corrig. Sprenger et al. 2000
Genus Methanococcoides Sowers and Ferry 1985
Methanococcoides methylutens Sowers and Ferry 1985 (type species)
Methanococcoides alaskense Singh et al. 2005
Methanococcoides burtonii Franzmann et al. 1993
Methanococcoides orientis Liang et al. 2022
Methanococcoides vulcani L'Haridon et al. 2014
Genus Methanohalobium Zhilina and Zavarzin 1988
Methanohalobium evestigatum corrig. Zhilina and Zavarzin 1988 (type species)
Genus Methanohalophilus Paterek and Smith 1988
Methanohalophilus mahii Paterek and Smith 1988 (type species)
Methanohalophilus halophilus (Zhilina 1984) Wilharm et al. 1991
Methanohalophilus levihalophilus Katayama et al. 2014
Methanohalophilus portucalensis Boone et al. 1993
Methanohalophilus profundi L'Haridon et al. 2021
Genus Methanolobus König and Stetter 1983
Methanolobus tindarius König and Stetter 1983 (type species)
Methanolobus bombayensis Kadam et al. 1994
Methanolobus chelungpuianus Wu and Lai 2015
Methanolobus halotolerans Shen et al. 2020
Methanolobus mangrovi Zhou et al. 2023
Methanolobus oregonensis (Liu et al. 1990) Boone 2002
Methanolobus profundi Mochimaru et al. 2009
Methanolobus psychrotolerans Chen et al. 2018
Methanolobus sediminis Zhou et al. 2023
Methanolobus taylorii Oremland and Boone 1994
Methanolobus vulcani Stetter et al. 1989
Methanolobus zinderi Doerfert et al. 2009
Genus Methanomethylovorans Lomans et al. 2004
Methanomethylovorans hollandica Lomans et al. 2004 (type species)
Methanomethylovorans thermophila Jiang et al. 2005
Methanomethylovorans uponensis Cha et al. 2014
Genus Methanosalsum Boone and Baker 2002
Methanosalsum zhilinae (Mathrani et al. 1988) Boone and Baker 2002 (type species)
Methanosalsum natronophilum Sorokin et al. 2015
Family Methanotrichaceae
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Genus Methanothrix Huser et al. 1983
Methanothrix soehngenii Huser et al. 1983 (type species)
Methanothrix harundinacea (Ma et al. 2006) Akinyemi et al. 2021
Methanothrix thermoacetophila corrig. Nozhevnikova and Chudina 1988
"Candidatus Methanothrix paradoxa" corrig. Angle et al. 2017
Family Methermicoccaceae
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Genus Methermicoccus Cheng et al. 2007
Methermicoccus shengliensis Cheng et al. 2007 (type species)
Phylum Methanobacteriota
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Class Methanobacteria
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Order Methanobacteriales
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Family Methanobacteriaceae
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Genus Methanobacterium Kluyver and van Niel 1936
Methanobacterium formicicum Schnellen 1947 (type species)
Methanobacterium bryantii
Genus Methanobrevibacter Balch and Wolfe 1981
Methanobrevibacter ruminantium (Smith and Hungate 1958) Balch and Wolfe 1981 (type species)
Methanobrevibacter arboriphilicus
Methanobrevibacter gottschalkii
Methanobrevibacter smithii
Genus Methanosphaera Miller and Wolin 1985
Methanosphaera stadtmanae corrig. Miller and Wolin 1985 (type species)
Genus Methanothermobacter Wasserfallen et al. 2000
Methanothermobacter thermautotrophicus corrig. (Zeikus and Wolfe 1972) Wasserfallen et al. 2000 (type species)
Methanothermobacter crinale Cheng et al. 2012
Methanothermobacter defluvii (Kotelnikova et al. 1994) Boone 2002
Methanothermobacter marburgensis Wasserfallen et al. 2000
Methanothermobacter tenebrarum Nakamura et al. 2013
Methanothermobacter thermoflexus (Kotelnikova et al. 1994) Boone 2002
Methanothermobacter thermophilus (Laurinavichus et al. 1990) Boone 2002
Methanothermobacter wolfei corrig. (Winter et al. 1985) Wasserfallen et al. 2000
Family Methanothermaceae
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Genus Methanothermus Stetter 1982
Methanothermus fervidus Stetter 1982 (type species)
Order Methanopyrales
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Family Methanopyraceae
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Genus Methanopyrus Kurr et al. 1992
Methanopyrus kandleri Kurr et al. 1992 (type species)
Order Methanococcales
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Family Methanococcaceae Balch and Wolfe 1981
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Genus Methanococcus Kluyver and van Niel 1936
Methanococcus vannielii Stadtman and Barker 1951 (type species)
Methanococcus aeolicus
Methanococcus burtonii
Methanococcus chunghsingensis
Methanococcus deltae
Methanococcus jannaschii
Methanococcus maripaludis
Genus Methanofervidicoccus
Methanofervidicoccus abyssi Sakai et al. 2019 (type species)
Genus Methanothermococcus
Methanothermococcus thermolithotrophicus (Huber et al. 1984) Whitman 2002 (type species)
Family Methanocaldococcaceae
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Genus Methanocaldococcus
Methanocaldococcus jannaschii (Jones et al. 1984) Whitman 2002 (type species)
Genus Methanotorris
Methanotorris igneus (Burggraf et al. 1990) Whitman 2002 (type species)
Phylum Thermoplasmatota
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Class Thermoplasmata
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Order Methanomassiliicoccales
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Family Methanomassiliicoccaceae
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Genus Methanomassiliicoccus Dridi et al. 2012
Methanomassiliicoccus luminyensis Dridi et al. 2012 (type species)
Family Methanomethylophilaceae
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Genus Methanomethylophilus Borrel et al. 2024
Methanomethylophilus alvi Borrel et al. 2024 (type species)