Methanogens are microorganisms that produce methane as a metabolic byproduct in hypoxic conditions. They are prokaryotic and belong to the domains Archaea and Bacteria. They are common in wetlands, where they are responsible for marsh gas, and in the digestive tracts of animals such as ruminants and many 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.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.

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 archae bacteria 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.

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