Biological Resource Center, NITE (NBRC)

Methanocella paludicola SANAET (= NBRC 101707T)


Rice paddy fields (RPF) are one of the major sources of the greenhouse gas methane, contributing about 10-25% of global methane emission[1]. Methane emission from RPF is caused by the microbial production of methane as the end product of the anaerobic degradation of organic compounds. The actual production of methane is brought about by methanogenic Archaea. Cultivation-independent molecular studies suggested that a specific group of methanogenic Archaea (named Rice Cluster I (RC-I)) are mainly responsible for methane production from RPF[2]. Such a focus of ecological attention resulted in a construction of genome sequence of an RC-I methanogen RC-IMRE50 from an enrichment culture by metagenomic approach[3]. However, a pure culture of RC-I group Archaea had been necessary for understanding of life style such as identification of methane source. Sakai et al. for the first time succeed to isolate archaea belonging to RC-I, by developing a co-culture method with syntrophic bacteria which continuously provide H2[4]. Methanocella paludicola SANAE is a mesophilic, hydrogenotrophic methanogen which utilize H2/CO2 and formate for growth and methane production [5].

Sequencing and annotation of the genome of M. paludicola SANAET (= NBRC 101707T) revealed a single circular chromosome (2,957,635 bp; G+C content of 54.9%) containing 3,004 predicted protein-coding genes. The genome had a full set of genes involved in methanogenesis from H2/CO2 and formate, being in consistent with phenotypic analyses. About two-thirds of the predicted genes were shared with RC-IMRE50 genome, while 40-45% of genes were shared with other methanogenic lineages such as Methanomicrobiales and Methanosarcinales. Further studies cross-linking and comparing both RC-IMRE50 metagenomic information and M. paludicola genome would provide better understanding how RC-I methanogens contribute global methane emission from RPF environments.

Methanocella paludicola SANAET photo by Dr. Sakai in JAMSTEC.


[1] Clime change 2001, the scientific basis.
Dentener F, Derwent R, Dlugokencky E, Holland E, Isaksen I, Katima J, Kirchhoff V, Matson P, Midgley P and Wang M. (2001)
Third Assessment Report of the Intergovernmental Panel on Climate Change. Cambridge: Cambridge University Press.
[2] Rice Cluster I methanogens, an important group of Archaea producing greenhouse gas in soil.
Conrad R, Erkel C, Liesack W. (2006)
Curr. Opin. Biotechnol. 17:262-267. [PMID:16621512]
[3] Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere.
Erkel C, Kube M, Reinhardt R, Liesack W. (2006)
Science 313:370-372. [PMID:168579473]
[4] Isolation of key methanogens for global methane emission from rice paddy fields: a novel isolate affiliated with the clone cluster rice cluster I.
Sakai S, Imachi H, Sekiguchi Y, Ohashi A, Harada H, Kamagata Y. (2007)
Appl. Environ. Microbiol. 73:4326-4331. [PMID:17483259]
[5] Methanocella paludicola gen. nov., sp. nov., a methane-producing archaeon, the first isolate of the lineage 'Rice Cluster I', and proposal of the new archaeal order Methanocellales ord. nov.
Sakai S, Imachi H, Hanada S, Ohashi A, Harada H, Kamagata Y. (2008)
Int. J. Syst. Evol. Microbiol. 58:929-936. [PMID:18398197]
[6] Genome Sequence of a Mesophilic Hydrogenotrophic Methanogen Methanocella paludicola, the First Cultivated Representative of the Order Methanocellales.
Sakai S, Takaki Y, Shimamura S, Sekine M, Tajima T, Kosugi H, Ichikawa N, Tasumi E, Hiraki AT, Shimizu A, Kato Y, Nishiko R, Mori K, Fujita N, Imachi H, Takai K. (2011)
PLoS One. 6(7) [PMID:21829548]
Genomic size: 2,957,635 bp
The number of ORFs: 3,004
GC content: 54.9%
Genome Database: DOGAN
NBRC No. : 101707
Distribution of Our Microbial Genomic DNAs
At the Biological Resource Center of the National Institute of Technology and Evaluation (NITE Biological Resource Center, an Incorporated Administrative Agency), we have been distributing the microbial genomic DNA.

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