Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domain of archaea. They are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and humans, where they are responsible for the methane content of belching in ruminants and flatulence in humans. In marine sediments the biological production of methane, also termed methanogenesis, is generally confined to where sulfates are depleted, below the top layers. Moreover, methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments. Others are extremophiles, found in environments such as hot springs and submarine hydrothermal vents as well as in the "solid" rock of Earth's crust, kilometers below the surface.
Methanogens are coccoid (spherical shaped) or bacilli (rod shaped). There are over 50 described species of methanogens, which do not form a monophyletic group, although all known methanogens belong to Archaea. They are mostly anaerobic organisms that cannot function under aerobic conditions, but recently a species (Candidatus Methanothrix paradoxum) has been identified that can function in anoxic microsites within aerobic environments. They are very sensitive to the presence of oxygen even at trace level. Usually, they cannot sustain oxygen stress for a prolonged time. However, Methanosarcina barkeri is exceptional in possessing a superoxide dismutase (SOD) enzyme, and may survive longer than the others in the presence of O2. Some methanogens, called hydrogenotrophic, use carbon dioxide (CO2) as a source of carbon, and hydrogen as a reducing agent.
- CO2 + 4 H2 → CH4 + 2H2O
Some of the CO2 reacts with the hydrogen to produce methane, which creates an electrochemical gradient across the cell membrane, used to generate ATP through chemiosmosis. In contrast, plants and algae use water as their reducing agent.
Methanogens lack peptidoglycan, a polymer that is found in the cell walls of Bacteria but not in those of Archaea. Some methanogens have a cell wall that is composed of pseudopeptidoglycan. Other methanogens do not, but have at least one paracrystalline array (S-layer) made up of proteins that fit together like a jigsaw puzzle.
Extreme living areas
Methanogens play a vital ecological role in anaerobic environments of removing excess hydrogen and fermentation products that have been produced by other forms of anaerobic respiration. 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. In deep basaltic rocks near the mid ocean ridges, they can obtain their hydrogen from the serpentinisation 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, which account for a significant fraction of organic carbon in continental margin sediments and represent a key reservoir of a potent greenhouse gas.
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 archaebacteria 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.
Another study 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.
Some scientists have proposed that the presence of methane in the Martian atmosphere may be indicative of native methanogens on that planet. In June 2019, NASA’s Curiosity rover detected methane, commonly generated by underground microbes such as methanogens, which signals possibility of life on Mars.
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. Most methanogens are autotrophic producers, but those that oxidize CH3COO− are classed as chemotroph instead.
Comparative genomics and molecular signatures
Comparative genomic analysis has led to the identification of 31 signature proteins which are specific for methanogens (also known as Methanoarchaeota). Most of these proteins are related to methanogenesis, and they could serve as potential molecular markers for methanogens. Additionally, 10 proteins found in all methanogens which are shared by Archaeoglobus, suggest that these two groups are related. In phylogenetic trees, methanogens are not monophyletic and they are generally split into three clades. Hence, the unique shared presence of large numbers of proteins by all methanogens could be due to lateral gene transfers.
Methanogens are known to produce methane from substrates such as H2/CO2, acetate, formate, methanol and methylamines in a process called methanogenesis. Different methanogenic reactions are catalyzed by unique sets of enzymes and coenzymes. While reaction mechanism and energetics vary between one reaction and another, all of these reactions contribute to net positive energy production by creating ion concentration gradients that are used to drive ATP synthesis. The overall reaction for H2/CO2 methanogenesis is:
- (∆G˚’ = -134 kJ/mol CH4)
Well-studied organisms that produce methane via H2/CO2 methanogenesis include Methanosarcina barkeri, Methanobacterium thermoautotrophicum, and Methanobacterium wolfei. These organism are typically found in anaerobic environments.
In the earliest stage of H2/CO2 methanogenesis, CO2 binds to methanofuran (MF) and is reduced to formyl-MF. This endergonic reductive process (∆G˚’= +16 kJ/mol) is dependent on the availability of H2 and is catalyzed by the enzyme formyl-MF dehydrogenase.
The formyl constituent of formyl-MF is then transferred to the coenzyme tetrahydromethanopterin (H4MPT) and is catalyzed by a soluble enzyme known as formyl transferase. This results in the formation of formyl-H4MPT.
Formyl-H4MPT is subsequently reduced to methenyl-H4MPT. Methenyl-H4MPT then undergoes a one-step hydrolysis followed by a two-step reduction to methyl-H4MPT. The two-step reversible reduction is assisted by coenzyme F420 whose hydride acceptor spontaneously oxidizes. Once oxidized, F420’s electron supply is replenished by accepting electrons from H2. This step is catalyzed by methylene H4MPT dehydrogenase.
- (Formyl-H4MPT reduction)
- (Methenyl-H4MPT hydrolysis)
- (H4MPT reduction)
The final step of H2/CO2 methanogenic involves methyl-coenzyme M reductase and two coenzymes: N-7 mercaptoheptanoylthreonine phosphate (HS-HTP) and coenzyme F430. HS-HTP donates electrons to methyl-coenzyme M allowing the formation of methane and mixed disulfide of HS-CoM. F430, on the other hand, serves as a prosthetic group to the reductase. H2 donates electrons to the mixed disulfide of HS-CoM and regenerates coenzyme M.
- (Formation of methane)
- (Regeneration of coenzyme M)
Methanogens are widely used in anaerobic digestors to treat wastewater as well as aqueous organic pollutants. Industries have selected methanogens for their ability to perform biomethanation during wastewater decomposition thereby rendering the process sustainable and cost-effective.
Bio-decomposition in the anaerobic digester involves a four-staged cooperative action performed by different microorganisms. The first stage is the hydrolysis of insoluble polymerized organic matter by anaerobes such as Streptococcus and Enterobacterium. In the second stage, acidogens break down dissolved organic pollutants in wastewater to fatty acids. In the third stage, acetogens convert fatty acids to acetates. In the final stage, methanogens metabolize acetates to gaseous methane. The byproduct methane leaves the aqueous layer and serves as an energy source to power wastewater-processing within the digestor, thus generating a self-sustaining mechanism.
Methanogens also effectively decrease the concentration of organic matter in wastewater run-off. For instance, agricultural wastewater, highly rich in organic material, has been a major cause of aquatic ecosystem degradation. The chemical imbalances can lead to severe ramifications such as eutrophication. Through anaerobic digestion, the purification of wastewater can prevent unexpected blooms in water systems as well as trap methanogenesis within digesters. This allocates biomethane for energy production and prevents a potent greenhouse gas, methane, from being released into the atmosphere.
The organic components of wastewater vary vastly. Chemical structures of the organic matter select for specific methanogens to perform anaerobic digestion. An example is the members of Methanosaeta genus dominate the digestion of palm oil mill effluent (POME) and brewery waste. Modernizing wastewater treatment systems to incorporate higher diversity of microorganisms to decrease organic content in treatment is under active research in the field of microbiological and chemical engineering. Current new generations of Staged Multi-Phase Anaerobic reactors and Upflow Sludge Bed reactor systems are designed to have innovated features to counter high loading wastewater input, extreme temperature conditions, and possible inhibitory compounds.
- Methanobacterium bryantii
- Methanobacterium formicum
- Methanobrevibacter arboriphilicus
- Methanobrevibacter gottschalkii
- Methanobrevibacter ruminantium
- Methanobrevibacter smithii
- Methanococcus chunghsingensis
- Methanococcus burtonii
- Methanococcus aeolicus
- Methanococcus deltae
- Methanococcus jannaschii
- Methanococcus maripaludis
- Methanococcus vannielii
- Methanocorpusculum labreanum
- Methanoculleus bourgensis (Methanogenium olentangyi & Methanogenium bourgense)
- Methanoculleus marisnigri
- Methanoflorens stordalenmirensis
- Methanofollis liminatans
- Methanogenium cariaci
- Methanogenium frigidum
- Methanogenium organophilum
- Methanogenium wolfei
- Methanomicrobium mobile
- Methanopyrus kandleri
- Methanoregula boonei
- Methanosaeta concilii
- Methanosaeta thermophila
- Methanosarcina acetivorans
- Methanosarcina barkeri
- Methanosarcina mazei
- Methanosphaera stadtmanae
- Methanospirillium hungatei
- Methanothermobacter defluvii (Methanobacterium defluvii)
- Methanothermobacter thermautotrophicus (Methanobacterium thermoautotrophicum)
- Methanothermobacter thermoflexus (Methanobacterium thermoflexum)
- Methanothermobacter wolfei (Methanobacterium wolfei)
- Methanothrix sochngenii
- Joseph W. Lengeler (1999). Biology of the Prokaryotes. Stuttgart: Thieme. p. 796. ISBN 978-0-632-05357-5.
- J.K. Kristjansson; et al. (1982). "Different Ks values for hydrogen of methanogenic bacteria and sulfate-reducing bacteria: an explanation for the apparent inhibition of methanogenesis by sulfate". Arch. Microbiol. 131 (3): 278–282. doi:10.1007/BF00405893.
- Tabatabaei, Meisam; Rahim, Raha Abdul; Abdullah, Norhani; Wright, André-Denis G.; Shirai, Yoshihito; Sakai, Kenji; Sulaiman, Alawi; Hassan, Mohd Ali (2010). "Importance of the methanogenic archaea populations in anaerobic wastewater treatments" (PDF). Process Biochemistry. 45 (8): 1214–1225. doi:10.1016/j.procbio.2010.05.017.
- Peters V; Conrad R (1995). "Methanogenic and other strictly anaerobic bacteria in desert soil and other oxic sois". Applied and Environmental Microbiology. 61 (4): 1673–1676. PMC 1388429. PMID 16535011.
- "Archived copy". Archived from the original on 2009-03-27. Retrieved 2009-09-20.CS1 maint: archived copy as title (link)
- Boone, David R. (2015). "Methanobacterium". Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley & Sons, Ltd. pp. 1–8. doi:10.1002/9781118960608.gbm00495. ISBN 9781118960608.
- Kvenvolden, K. (1995). "A review of the geochemistry of methane in natural gas hydrate". Organic Geochemistry. 23 (11–12): 997–1008. doi:10.1016/0146-6380(96)00002-2.
- Milkov, Alexei V (2004). "Global estimates of hydrate-bound gas in marine sediments: how much is really out there?". Earth-Science Reviews. 66 (3–4): 183–197. Bibcode:2004ESRv...66..183M. doi:10.1016/j.earscirev.2003.11.002.
- Tung, H. C.; Bramall, N. E.; Price, P. B. (2005). "Microbial origin of excess methane in glacial ice and implications for life on Mars". Proceedings of the National Academy of Sciences. 102 (51): 18292–6. Bibcode:2005PNAS..10218292T. doi:10.1073/pnas.0507601102. PMC 1308353. PMID 16339015.
- Icarus (vol. 178, p. 277)cs:Methanogen
- Extreme bugs back idea of life on Mars
- "Crater Critters: Where Mars Microbes Might Lurk". Space.com. Retrieved 16 December 2014.
- "NASA Rover on Mars Detects Puff of Gas That Hints at Possibility of Life". The New York Times. 22 June 2019.
- Thauer, R. K. & Shima, S. (2006). "Biogeochemistry: Methane and microbes". Nature. 440 (7086): 878–879. Bibcode:2006Natur.440..878T. doi:10.1038/440878a. PMID 16612369.
- Gao B; Gupta RS (2007). "Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis". BMC Genomics. 8: 86. doi:10.1186/1471-2164-8-86. PMC 1852104. PMID 17394648.
- Gribaldo S; Brochier-Armanet C (2006). "The origin and evolution of Archaea: a state of the art". Philos Trans R Soc Lond B Biol Sci. 361 (1470): 1007–1022. doi:10.1098/rstb.2006.1841. PMC 1578729. PMID 16754611.
- Blaut, M. (1994). "Metabolism of methanogens". Antonie van Leeuwenhoek. 66 (1–3): 187–208. doi:10.1007/bf00871639. ISSN 0003-6072. PMID 7747931.
- Dybas, M; Konisky, J (1992). "Energy transduction in the methanogen Methanococcus voltae is based on a sodium current". J Bacteriol. 174 (17): 5575–5583. doi:10.1128/jb.174.17.5575-5583.1992. PMC 206501. PMID 1324904.
- Karrasch, M.; Börner, G.; Enssle, M.; Thauer, R. K. (1990-12-12). "The molybdoenzyme formylmethanofuran dehydrogenase from Methanosarcina barkeri contains a pterin cofactor". European Journal of Biochemistry. 194 (2): 367–372. doi:10.1111/j.1432-1033.1990.tb15627.x. ISSN 0014-2956. PMID 2125267.
- Börner, G.; Karrasch, M.; Thauer, R. K. (1991-09-23). "Molybdopterin adenine dinucleotide and molybdopterin hypoxanthine dinucleotide in formylmethanofuran dehydrogenase from Methanobacterium thermoautotrophicum (Marburg)". FEBS Letters. 290 (1–2): 31–34. doi:10.1016/0014-5793(91)81218-w. ISSN 0014-5793. PMID 1915887.
- Schmitz, Ruth A.; Albracht, Simon P. J.; Thauer, Rudolf K. (1992-11-01). "A molybdenum and a tungsten isoenzyme of formylmethanofuran dehydrogenase in the thermophilic archaeon Methanobacterium wolfei". European Journal of Biochemistry. 209 (3): 1013–1018. doi:10.1111/j.1432-1033.1992.tb17376.x. ISSN 1432-1033. PMID 1330558.
- Zirngibl, C (February 1990). "N5,N10-Methylenetetrahydromethanopterin dehydrogenase from Methanobacterium thermoautotrophicum has hydrogenase activity". Laboratorium Fir Mikrobiologie. 261 (1): 112–116. doi:10.1016/0014-5793(90)80649-4.
- te Brömmelstroet, B. W.; Geerts, W. J.; Keltjens, J. T.; van der Drift, C.; Vogels, G. D. (1991-09-20). "Purification and properties of 5,10-methylenetetrahydromethanopterin dehydrogenase and 5,10-methylenetetrahydromethanopterin reductase, two coenzyme F420-dependent enzymes, from Methanosarcina barkeri". Biochimica et Biophysica Acta. 1079 (3): 293–302. doi:10.1016/0167-4838(91)90072-8. ISSN 0006-3002. PMID 1911853.
- Kengen, Servé W. M.; Mosterd, Judith J.; Nelissen, Rob L. H.; Keltjens, Jan T.; Drift, Chris van der; Vogels, Godfried D. (1988-08-01). "Reductive activation of the methyl-tetrahydromethanopterin: coenzyme M methyltransferase from Methanobacterium thermoautotrophicum strain ΔH". Archives of Microbiology. 150 (4): 405–412. doi:10.1007/BF00408315. ISSN 0302-8933.
- Bobik, T. A.; Olson, K. D.; Noll, K. M.; Wolfe, R. S. (1987-12-16). "Evidence that the heterodisulfide of coenzyme M and 7-mercaptoheptanoylthreonine phosphate is a product of the methylreductase reaction in Methanobacterium". Biochemical and Biophysical Research Communications. 149 (2): 455–460. doi:10.1016/0006-291x(87)90389-5. ISSN 0006-291X. PMID 3122735.
- Ellermann, J.; Hedderich, R.; Böcher, R.; Thauer, R. K. (1988-03-15). "The final step in methane formation. Investigations with highly purified methyl-CoM reductase (component C) from Methanobacterium thermoautotrophicum (strain Marburg)". European Journal of Biochemistry. 172 (3): 669–677. doi:10.1111/j.1432-1033.1988.tb13941.x. ISSN 0014-2956. PMID 3350018.
- Appels, Lise; et.al. (2008). "Principles and potential of the anaerobic digestion of waste-activated sludge" Progress in Energy and Combustion Science. 34 (6): 755 -781. doi: 10.1016/j.pecs.2008.06.002
- Christensen, Thomas H; et.al. (2010). "Anaerobic Digestion: Process" Solid Waste Technology & Management, Volume 1 & 2. doi: 10.1002/9780470666883.ch372
- Shah, Fayyaz Ali, et. al. (2014). “Microbial Ecology of Anaerobic Digesters: The Key Players of Anaerobiosis” ScientificWorldJournal. 3852369 (1). doi:10.1155/2014/183752
- Lettinga, G (1995). "Anaerobic Digestion and Wastewater Treatment Systems". Antonie van Leeuwenhoek. 67 (1): 3–28. doi:10.1007/bf00872193. PMID 7741528.
- Tabatabaei, Meisa; et al. (2010). "Importance of the methanogenic archaea populations in anaerobic wastewater treatments" (PDF). Process Biochemistry. 45 (8): 1214–1225. doi:10.1016/j.procbio.2010.05.017.
- Marihiro, Takashi., Sekiguchi, Yuji. (2007). "Microbial communities in anaerobic digestion processes for waste and wastewater treatment: a microbiological update" Current Opinion in Biotechnology. 18 (3): 273-278. doi: 10.1016/j.copbio.2007.04.003
- "Advanced anaerobic wastewater treatment in the near future". Water Science and Technology. 35 (10). 1997. doi:10.1016/S0273-1223(97)00222-9.
- Mondav, Rhiannon; Woodcroft, Ben J.; Kim, Eun-Hae; McCalley, Carmody K.; Hodgkins, Suzanne B.; Crill, Patrick M.; Chanton, Jeffrey; Hurst, Gregory B.; Verberkmoes, Nathan C.; Saleska, Scott R.; Hugenholtz, Philip; Rich, Virginia I.; Tyson, Gene W. (2014). "Discovery of a novel methanogen prevalent in thawing permafrost" (PDF). Nature Communications. 5: 3212. Bibcode:2014NatCo...5.3212M. doi:10.1038/ncomms4212. PMID 24526077.