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

Abstract

A cold-adapted or psychrotrophic anaerobic bacterial strain (C5S11T) was isolated from rice field soil in Japan using an enrichment culture incubated at 5 °C. C5S11T grew at 0 °C and optimum growth was observed at 10 °C. Cells of C5S11T were Gram-stain-positive, motile, spore-forming rods with peritrichous flagella. C5S11T was assigned to a large branch consisted of various mesophilic species of the genus Clostridium in the phylogenetic trees reconstructed using the 16S rRNA gene sequences. The most closely related species of the strain was Clostridium chromiireducens DSM 23318T (98.5 % sequence similarity). C5S11T fermented various carbohydrates, including polysaccharides (starch, inulin, pectin and xylan), and produced acetate, butyrate and H2 as major products. The major cellular fatty acids were C16 : 0, C16 : 1ω9c, C14 : 0 and C16 : 1ω7c. The diagnostic diamino acid of the cell wall peptidoglycan was meso-diaminopimelic acid. The genome size of C5S11T was 6.04 Mb and the genomic DNA G+C content was 29.0 mol%. Average nucleotide identity by blast (ANIb), avaerage amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values between the genomes of C5S11T and C. chromiireducens DSM 23318T were 80.0, 75.2 and 26.4 %, respectively. C5S11T had a gene encoding cold shock protein (RNA chaperone) in the genome, homologues of which have been found in psychrophilic species of the genus Clostridium . On the basis of the differences in the phylogenetic, genomic and phenotypic characteristics of C5S11T from those of the closely related species, a novel species, Clostridium gelidum sp. nov., is proposed to accommodate the strain. The type strain is C5S11T (=NBRC 114689T = DSM 112608T).