New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”

Abstract

The recently discovered seventh order of methanogens, the Methanomassiliicoccales (previously referred to as "Methanoplasmatales"), so far consists exclusively of obligately hydrogen-dependent methylotrophs. We sequenced the complete genome of "Candidatus Methanoplasma termitum" from a highly enriched culture obtained from the intestinal tract of termites and compared it with the previously published genomes of three other strains from the human gut, including the first isolate of the order. Like all other strains, "Ca. Methanoplasma termitum" lacks the entire pathway for CO 2 reduction to methyl coenzyme M and produces methane by hydrogen-dependent reduction of methanol or methylamines, which is consistent with additional physiological data. However, the shared absence of cytochromes and an energy-converting hydrogenase for the reoxidation of the ferredoxin produced by the soluble heterodisulfide reductase indicates that Methanomassiliicoccales employ a new mode of energy metabolism, which differs from that proposed for the obligately methylotrophic Methanosphaera stadtmanae. Instead, all strains possess a novel complex that is related to the F 420 :methanophenazine oxidoreductase (Fpo) of Methanosarcinales but lacks an F 420 -oxidizing module, resembling the apparently ferredoxin-dependent Fpo-like homolog in Methanosaeta thermophila. Since all Methanomassiliicoccales also lack the subunit E of the membrane-bound heterodisulfide reductase (HdrDE), we propose that the Fpo-like complex interacts directly with subunit D, forming an energy-converting ferredoxin:heterodisulfide oxidoreductase. The dual function of heterodisulfide in Methanomassiliicoccales, which serves both in electron bifurcation and as terminal acceptor in a membrane-associated redox process, may be a unique characteristic of the novel order. Methanogenesis is catalyzed exclusively by members of the archaeal domain. Methanogenic archaea occur only in the phylum Euryarchaeota and are phylogenetically diverse. The species described to date fall into seven orders that differ both in the biochemistry of their catabolic pathways and in their ecological niches (1, 2).Methanogens from all basal orders (Methanopyrales, Methanococcales, and Methanobacteriales) are hydrogenotrophs. They reduce CO 2 to CH 4 via the C 1 pathway, using H 2 or sometimes formate as an electron donor (1, 2). The hydrogenotrophic pathway is found also in most of the derived lineages of methanogens (Methanomicrobiales and Methanocellales) and was most probably present already in the common ancestor of the Euryarchaeota (3). Hydrogenotrophic methanogens typically lack cytochromes and conserve energy with the methyltetrahydromethanopterin (methyl-H 4 MPT):coenzyme M methyltransferase complex (Mtr), which uses the free energy of methyl transfer to establish a Na ϩ -motive force across the membrane (4). The low-potential reducing equivalents for CO 2 reduction are provided by electron bifurcation at the cytoplasmic heterodisulfide reductase complex (HdrABC) (5, 6).Members of the orde...

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

“…Methanogenic archaea are widespread in nature and have been detected in a diverse range of environments including wetlands, rice agriculture, landfills, hydrothermal vents, ruminants and termites 1,2 . Traditionally, all methanogens belonged to the archaeal phylum Euryarchaeota and until recently were classified into seven orders 1,3,5 (Methanobacteriales, Methanococcales, Methanomicrobiales, Methanosarcinales, Methanocellales, Methanopyrales and Methanomassiliicoccales). Substrates for methane production include H 2 /CO 2 (hydrogenotrophic), acetate (acetoclastic) and methylated compounds (methylotrophic) 5 .…”

“…Traditionally, all methanogens belonged to the archaeal phylum Euryarchaeota and until recently were classified into seven orders 1,3,5 (Methanobacteriales, Methanococcales, Methanomicrobiales, Methanosarcinales, Methanocellales, Methanopyrales and Methanomassiliicoccales). Substrates for methane production include H 2 /CO 2 (hydrogenotrophic), acetate (acetoclastic) and methylated compounds (methylotrophic) 5 . Hydrogenotrophic methanogenesis is the most widespread 1 , being found in all methanogenic orders with the exception of Methanomassiliicoccales, and it has been suggested that this is the ancestral form of methane production 6 .…”

“…Hydrogenotrophic methanogenesis is the most widespread 1 , being found in all methanogenic orders with the exception of Methanomassiliicoccales, and it has been suggested that this is the ancestral form of methane production 6 . Although the prevailing source of atmospheric methane is through direct acetate cleavage 7 , only members of the Methanosarcinales are capable of acetoclastic methanogenesis 5,7 . Methylotrophic methanogens are found in the orders Methanosarcinales, Methanobacteriales and Methanomassiliicoccales, and can be classified in two groups based on the presence or absence of cytochromes.…”

“…Methylotrophic methanogens are found in the orders Methanosarcinales, Methanobacteriales and Methanomassiliicoccales, and can be classified in two groups based on the presence or absence of cytochromes. Methylotrophs without cytochromes are obligately H 2 -dependent, while those that possess cytochromes (that is, members of the Methanosarcinales), can also oxidize methyl groups to CO 2 via a membrane-bound electron transport chain 5 . Our knowledge of methanogenic substrate utilization and energy conservation is still incomplete but is rapidly expanding through the development of new molecular techniques such as genome-centric metagenomics.…”

“…Our knowledge of methanogenic substrate utilization and energy conservation is still incomplete but is rapidly expanding through the development of new molecular techniques such as genome-centric metagenomics. This includes the discovery of hydrogenotrophic methanogenesis genes encoded in Methanosaeta 8 , a genus originally thought to be strictly acetoclastic, the hypothesized mode of energy metabolism in Methanonomassiliiccocales 5,9 , and the recently described sixth class of euryarchaeotal methanogens, Candidatus 'Methanofastidiosa', which is restricted to methanogenesis through methylated thiol reduction 10 . The hypothesis that methane metabolism originated early in the evolution of the Euryarchaeota 11 has recently been challenged following the discovery of putative methane metabolism in the archaeal phylum Bathyarchaeota (formerly Miscellaneous Crenarchaeota Group) 12,13 .…”