Methanogenesis is an anaerobic respiration that generates methane as the final product of metabolism. In aerobic respiration, organic matter such as glucose is oxidized to CO, and O is reduced to HO. In contrast, during hydrogenotrophic methanogenesis, H is oxidized to H, and CO is reduced to CH. Although similar in principle to other types of respiration, methanogenesis has some distinctive features: the energy yield is very low, ≤1 ATP per methane generated, and only methanogens - organisms capable of this specialized metabolism - carry out biological methane production. Methanogens, like the process they catalyze, are similarly distinctive. Methanogens are comprised exclusively of archaea. They are obligate methane producers, that is, they do not grow using fermentation or alternative electron acceptors for respiration. Finally, methanogens are strict anaerobes and do not grow in the presence of O. Historically, methanogenesis has been viewed as a highly specialized metabolism restricted to a narrow group of prokaryotes. However, recent developments have revealed enormous diversity within the methanogens and suggest that this metabolism is one of the most ancient on earth.

Methanococcus maripaludis is a rapidly growing, hydrogenotrophic, and genetically tractable methanogen with unique capabilities to convert formate and CO 2 to CH 4 . The existence of genome-scale metabolic models and an established, robust system for both large-scale and continuous cultivation make it amenable for industrial applications. However, the lack of molecular tools for differential gene expression has hindered its application as a microbial cell factory to produce biocatalysts and biochemicals. In this study, a library of differentially regulated promoters was designed and characterized based on the pst promoter, which responds to the inorganic phosphate concentration in the growth medium. Gene expression increases by 4-to 6-fold when the medium phosphate drops to growthlimiting concentrations. Hence, this regulated system decouples growth from heterologous gene expression without the need for adding an inducer. The minimal pst promoter is identified and contains a conserved AT-rich region, a factor B recognition element, and a TATA box for phosphate-dependent regulation. Rational changes to the factor B recognition element and start codon had no significant impact on expression; however, changes to the transcription start site and the 5′ untranslated region resulted in the differential protein production with regulation remaining intact. Compared to a previous expression system based upon the histone promoter, this regulated expression system resulted in significant improvements in the expression of a key methanogenic enzyme complex, methyl-coenzyme M reductase, and the potentially toxic arginine methyltransferase MmpX.

Me.tha'no.thrix. N.L. neut. n. methanum methane; Gr. fem. n. thrix , hair; N.L. fem. n. Methanothrix , methane (‐producing) hair. Halobacterota / Methanosarcinia / Methanotrichales / Methanotrichaceae / Methanothrix Straight, rod‐shaped cells with flat ends, usually 0.8–1.3 μm wide by 2.0–6.0 μm long enclosed in a tubular sheath. Forms short (∼5–25 μm) to long (>150 μm) flexible chains of cells within the sheath. Nonmotile. Gram‐stain‐negative. Lipids contain myo ‐inositol, ethanolamine, and galactose as the polar head groups. Oxygen‐tolerant anaerobe. Organotrophic, splitting acetate into methane and CO 2 for energy generation. Some strains split formate into H 2 and CO 2 without producing methane. CO 2 can be reduced to methane in coculture with Geobacter spp. via direct interspecies electron transfer (DIET). Growth factors such as vitamins are stimulatory. Yeast extract is required, stimulatory or inhibitory, depending on the strain. NaCl is not required for growth. Optimal temperatures range from 34 to 37°C for mesophilic strains and 55 to 60°C for thermophilic strains; optimal pH range is 7.0–7.8. Gas vacuoles are generally found in thermophilic strains. Occur in both mesophilic and thermophilic anaerobic sludge digesters as well as anaerobic sediments. Synonymous with the genus Methanosaeta . DNA G + C content (mol%) : 51–61 (genome). Type species : Methanothrix soehngenii Huser et al. 1982, VL10.

Me.tha.no.cor.pus'cu.lum. N.L. neut. n. methanum methane; L. neut. n. corpusculum a particle; N.L. neut. n. Methanocorpusculum a methane‐producing particle. Halobacteriota / Methanomicrobia / Methanomicrobiales / Methanocorpusculaceae / Methanocorpusculum Small, irregular cocci, <2 μm in diameter. Endospores not formed. Stain Gram‐negative. Lysed by detergent or hypotonic shock. Nonmotile or very weakly motile. Strictly anaerobic. Fastest growth at 30–37°C, pH near 7.0. No requirement of NaCl for growth but moderately NaCl tolerant, depending on the species. Energy production by reduction of CO 2 to CH 4 with H 2 , formate, and sometimes secondary alcohols as electron donors; acetate, methylamines, or methanol are not catabolized. Acetate and either yeast extract, peptones, or rumen fluid are required as carbon and nitrogen sources. Sulfide serves as a sulfur source. Occurs in sewage sludge digesters, anaerobic wastewater treatment plants, and anaerobic reactors. Methanocorpusculum is the only genus in the family Methanocorpusculaceae and currently comprises four species with validly published names. DNA G  +  C content (mol%) : 49.8–52.4 (Genome). Type species : Methanocorpusculum parvum Zellner et al. 1987, VL24.

The nucleotide binding protein 35 (Nbp35)/cytosolic Fe‐S cluster deficient 1 (Cfd1)/alternative pyrimidine biosynthetic protein C (ApbC) protein homologs have been identified in all three domains of life. In eukaryotes, the Nbp35/Cfd1 heterocomplex is an essential Fe‐S cluster assembly scaffold required for the maturation of Fe‐S proteins in the cytosol and nucleus, whereas the bacterial ApbC is an Fe‐S cluster transfer protein only involved in the maturation of a specific target protein. Here, we show that the Nbp35/ApbC homolog MMP0704 purified from its native archaeal host Methanococcus maripaludis contains a [4Fe‐4S] cluster that can be transferred to a [4Fe‐4S] apoprotein. Deletion of mmp0704 from M. maripaludis does not cause growth deficiency under our tested conditions. Our data indicate that Nbp35/ApbC is a nonessential [4Fe‐4S] cluster transfer protein in methanogenic archaea.

Me.tha.no.ge'ni.um. N.L. neut. n. methanum, methane; N.L. suff. ‐genes (from L. v. gigno ) producing; N.L. neut. n. Methanogenium , a methane producer. Euryarchaeota / Methanomicrobiales / Methanomicrobiales / Methanomicrobiaceae / Methanogenium Irregular cocci occurring singly or in pairs, usually 0.5–2.6 µm in diameter. Gram‐stain‐negative. Does not form spores. No motility observed, although some strains are flagellated. Strictly anaerobic. Chemolithotrophic, utilizing H 2 or sometimes formate and primary or secondary alcohols as electron donors, reducing carbon dioxide to methane. Growth factors required. NaCl generally required or stimulatory for growth. Optimal temperature range 15–35 ° C; optimal pH 6.0–7.9. Draft‐genome sequences have been determined for both M. cariaci JCM 10550 and M. frigidum Ace‐2 T . Occur in cold anaerobic marine or freshwater sulfate‐depleted sediments. DNA G + C content (mol%) : 47–52. Type species : Methanogenium cariaci Romesser, Wolfe, Mayer, Spiess and Walther‐Mauruschat 1981, 216 VP (Effective publication: Romesser, Wolfe, Mayer, Spiess and Walther‐Mauruschat 1979, 152).

Me.tha.no.pla'nus. N.L. neut. n. methanum methane; N.L. pref. methano‐ pertaining to methane; N.L. masc. adj. planus flat; N.L. masc. n. Methanoplanus the methane (−producing) plate. Euryarchaeota / Methanomicrobiales / Methanomicrobiales / Methanomicrobiaceae / Methanoplanus Cells are angular, crystal‐like plates, or disc shaped. They are 1–3.5‐µm long, 1–2‐µm wide, and only 0.07–0.3‐µm thick. They occur singly or in pairs and are sometimes branched, without septa. Stain Gram‐negative. Flagella or pilus‐like structures are found. Strictly anaerobic. Chemolithotrophic growth on H 2 and CO 2 or formate. These substrates serve as an energy source for growth and methane formation. No growth on methanol or methylamines. During growth on molecular hydrogen in the presence of S 0 , H 2 S is formed in addition to methane. The organisms are mesophilic, with optimum growth temperatures between 32 and 40°C at neutral pH. On the basis of the 16S rRNA sequence data, Methanoplanus belongs to the family Methanomicrobiaceae . DNA G + C content (mol%) : 39–47.5. Type species : Methanoplanus limicola Wildgruber, Thomm and Stetter 1984, 270 VP (Effective publication: Wildgruber, Thomm, König, Ober, Richiuto and Stetter 1982, 36).

Me.tha.no.py.ra'les. N.L. masc. n. Methanopyrus type genus of the order; ‐ ales the ending to denote an order; N.L. fem. pl. n. Methanopyrales the order of Methanopyrus . Euryarchaeota / Methanopyria / Methanopyrales The order currently consists of one family Methanopyraceae and one genus Methanopyrus with one species Methanopyrus kandleri . Cells are rods and nonsporulating. Cell division by septum formation. Cell wall consists of an inner pseudomurein and an outer proteinaceous S‐layer. Gram‐stain‐positive. Strictly anaerobic. Growth is chemolithoautotrophic with H 2 /CO 2 converted to CH 4 as energy‐forming reaction. 2,3‐Di‐ O ‐phytanyl‐ sn ‐glycerol and 2,3‐di‐ O ‐geranylgeranyl‐ sn ‐glycerol present in the lipids. Cyclic 2,3‐diphosphoglycerate present intracellularly at high concentrations. Growth optimum near pH 6.5. Hyperthermophilic. No growth occurs below 84°C. Optimum growth temperature, 98–100°C; maximum, up to 116°C. Occur in deep‐sea hydrothermal fields. Genome sequences have been determined for the type strain of the type species, Methanopyrus kandleri AV19 T , and two other unclassified strains, Methanopyrus sp. SNP6 and KOL6. DNA G + C content (mol%) : 57.7–61.2 (Genome). Type genus : Methanopyrus Kurr et al. 1991, VL41.