Clostridium gelidum sp. nov., a psychrotrophic anaerobic bacterium isolated from rice field soil

  • Sachi Honma
    Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
  • Atsuko Ueki
    Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
  • Akio Tonouchi
    Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho 3, Hirosaki, Aomori 036-8561, Japan
  • Nobuo Kaku
    Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan
  • Katsuji Ueki
    Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka, Yamagata 997-8555, Japan

抄録

<jats:p>A cold-adapted or psychrotrophic anaerobic bacterial strain (C5S11<jats:sup>T</jats:sup>) was isolated from rice field soil in Japan using an enrichment culture incubated at 5 °C. C5S11<jats:sup>T</jats:sup> grew at 0 °C and optimum growth was observed at 10 °C. Cells of C5S11<jats:sup>T</jats:sup> were Gram-stain-positive, motile, spore-forming rods with peritrichous flagella. C5S11<jats:sup>T</jats:sup> was assigned to a large branch consisted of various mesophilic species of the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.3878" xlink:type="simple">Clostridium</jats:ext-link> </jats:named-content> </jats:italic> in the phylogenetic trees reconstructed using the 16S rRNA gene sequences. The most closely related species of the strain was <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.22684" xlink:type="simple">Clostridium chromiireducens</jats:ext-link> </jats:named-content> </jats:italic> DSM 23318<jats:sup>T</jats:sup> (98.5 % sequence similarity). C5S11<jats:sup>T</jats:sup> fermented various carbohydrates, including polysaccharides (starch, inulin, pectin and xylan), and produced acetate, butyrate and H<jats:sub>2</jats:sub> as major products. The major cellular fatty acids were C<jats:sub>16 : 0</jats:sub>, C<jats:sub>16 : 1</jats:sub>ω9<jats:italic>c</jats:italic>, C<jats:sub>14 : 0</jats:sub> and C<jats:sub>16 : 1</jats:sub>ω7<jats:italic>c</jats:italic>. The diagnostic diamino acid of the cell wall peptidoglycan was <jats:italic>meso</jats:italic>-diaminopimelic acid. The genome size of C5S11<jats:sup>T</jats:sup> was 6.04 Mb and the genomic DNA G+C content was 29.0 mol%. Average nucleotide identity by <jats:sc>blast</jats:sc> (ANIb), avaerage amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values between the genomes of C5S11<jats:sup>T</jats:sup> and <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.22684" xlink:type="simple">C. chromiireducens</jats:ext-link> </jats:named-content> </jats:italic> DSM 23318<jats:sup>T</jats:sup> were 80.0, 75.2 and 26.4 %, respectively. C5S11<jats:sup>T</jats:sup> had a gene encoding cold shock protein (RNA chaperone) in the genome, homologues of which have been found in psychrophilic species of the genus <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.3878" xlink:type="simple">Clostridium</jats:ext-link> </jats:named-content> </jats:italic>. On the basis of the differences in the phylogenetic, genomic and phenotypic characteristics of C5S11<jats:sup>T</jats:sup> from those of the closely related species, a novel species, <jats:italic>Clostridium gelidum</jats:italic> sp. nov., is proposed to accommodate the strain. The type strain is C5S11<jats:sup>T</jats:sup> (=NBRC 114689<jats:sup>T</jats:sup> = DSM 112608<jats:sup>T</jats:sup>).</jats:p>

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