Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultivated representative of the order Methanocellales

• Published in: PloS one 2011-07, Vol.6 (7), p.e22898-e22898
• Main Authors: Sakai, Sanae, Takaki, Yoshihiro, Shimamura, Shigeru, Sekine, Mitsuo, Tajima, Takahisa, Kosugi, Hiroki, Ichikawa, Natsuko, Tasumi, Eiji, Hiraki, Aiko T, Shimizu, Ai, Kato, Yumiko, Nishiko, Rika, Mori, Koji, Fujita, Nobuyuki, Imachi, Hiroyuki, Takai, Ken
• Format: Article
• Language: English
• Subjects: Acetates - metabolism; Acids; Amino acids; Antioxidants; Archaea; Bicarbonates - metabolism; Bioinformatics; Biological evolution; Biology; Carbon Radioisotopes; Chromosome Mapping; Crop fields; Deferribacter; DNA, Archaeal - analysis; Earth science; Enzymes; Gene sequencing; Genes; Genes, Archaeal; Genome, Archaeal; Genomes; Genomics; Glutamic Acid - metabolism; Megalagrion paludicola; Metabolism; Methane; Methane - metabolism; Methane emissions; Methane production; Methanogenesis; Methanogenic archaea; Methanogenic bacteria; Methanomicrobiales - genetics; Morphology; Nitrogen fixation; Nucleotide sequence; Phylogenetics; Phylogeny; Physiology; Polymerase Chain Reaction; Proteins; Rice fields; Sequence Analysis, DNA; Sulfate reduction; Taxonomy; Tricarboxylic acid cycle
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0022898

We report complete genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella paludicola, the first cultured representative of the order Methanocellales once recognized as an uncultured key archaeal group for methane emission in rice fields. The genome sequence of M. paludicola consists of a single circular chromosome of 2,957,635 bp containing 3004 protein-coding sequences (CDS). Genes for most of the functions known in the methanogenic archaea were identified, e.g. a full complement of hydrogenases and methanogenesis enzymes. The mixotrophic growth of M. paludicola was clarified by the genomic characterization and re-examined by the subsequent growth experiments. Comparative genome analysis with the previously reported genome sequence of RC-I(MRE50), which was metagenomically reconstructed, demonstrated that about 70% of M. paludicola CDSs were genetically related with RC-I(MRE50) CDSs. These CDSs included the genes involved in hydrogenotrophic methane production, incomplete TCA cycle, assimilatory sulfate reduction and so on. However, the genetic components for the carbon and nitrogen fixation and antioxidant system were different between the two Methanocellales genomes. The difference is likely associated with the physiological variability between M. paludicola and RC-I(MRE50), further suggesting the genomic and physiological diversity of the Methanocellales methanogens. Comparative genome analysis among the previously determined methanogen genomes points to the genome-wide relatedness of the Methanocellales methanogens to the orders Methanosarcinales and Methanomicrobiales methanogens in terms of the genetic repertoire. Meanwhile, the unique evolutionary history of the Methanocellales methanogens is also traced in an aspect by the comparative genome analysis among the methanogens.