All known methanogens belong exclusively to the domain Archaea, although some bacteria, plants, and animal cells are also known to produce methane.
[4] Methanogens are common in various anoxic environments, such as marine and freshwater sediments, wetlands, the digestive tracts of animals, wastewater treatment plants, rice paddy soil, and landfills.
They are exclusively anaerobic organisms that cannot function under aerobic conditions due to the extreme oxygen sensitivity of methanogenesis enzymes and FeS clusters involved in ATP production.
However, Methanosarcina barkeri from a sister family Methanosarcinaceae is exceptional in possessing a superoxide dismutase (SOD) enzyme, and may survive longer than the others in the presence of O2.
[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.
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.
[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.
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.
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.
[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.
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.
However, they play a crucial role in maintaining gut balance by utilizing end products of bacterial fermentation, such as H2, acetate, methanol, and methylamines.
Hence, the unique shared presence of large numbers of proteins by all methanogens could be due to lateral gene transfers.
As sequencing techniques progress and databases become populated with an abundance of genomic data, a greater number of strains and traits can be identified, but many genera have remained understudied.
For example, halophilic methanogens are potentially important microbes for carbon cycling in coastal wetland ecosystems but seem to be greatly understudied.
[36] Genomic signatures not only allow one to mark unique methanogens and genes relevant to environmental conditions; it has also led to a better understanding of the evolution of these archaea.
Functional genes involved with the production of antioxidants have been found in methanogens, and some specific groups tend to have an enrichment of this genomic feature.
H2 donates electrons to the mixed disulfide of HS-CoM and regenerates coenzyme M.[49] 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.
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.
An example is the members of Methanosaeta genus dominate the digestion of palm oil mill effluent (POME) and brewery waste.
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.
The development of genome sequencing directly from environmental samples (metagenomics) allowed the discovery of the first methanogens outside the Euryarchaeota superphylum.
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.
Currently, most of the isolated methanogens belong to one of three archaeal phyla (classification GTDB release 220): Halobacteriota, Methanobacteriota, and Thermoplasmatota.