Clostridium omnivorum sp. nov., isolated from anoxic soil under the treatment of reductive soil disinfestation

Reductive soil disinfestation (RSD), also known as biological soil disinfestation, is a bioremediation method used to suppress soil-borne plant pathogens by stimulating the activity of indigenous anaerobic bacteria in the soil. An anaerobic bacterial strain (E14 T ) was isolated from an anoxic soil sample subjected to RSD treatment and then comprehensively characterized. Cells of the strain were Gram-stain-positive, curved to sigmoid, and spore-forming rods. Cells were motile with a polar flagellum. Strain E14 T grew in peptone–yeast extract broth, indicating that it utilized proteinous compounds. Strain E14 T was also saccharolytic and produced acetate, isobutyrate, butyrate, isovalerate and gases (H 2 and CO 2 ) as fermentation products. The strain did not decompose any of examined polysaccharides except for starch. The major cellular fatty acids of strain E14 T were iso-C 15:0 and iso-C 15:0 DMA. The closest relative to strain E14 T , based on 16S rRNA gene sequences, was Clostridium thermarum SYSU GA15002 T (96.2 %) in the Clostridiaceae . Whole-genome analysis of strain E14 T showed that its genome was 4.66 Mb long with a genomic DNA G+C content of 32.5 mol%. The average nucleotide identity (ANIb) between strain E14 T and C. thermarum SYSU GA15002 T was 69.0 %. The presence of the genes encoding glycolysis and butyrate production via the acetyl–CoA pathway was confirmed through genome analysis. Based on the obtained phylogenetic, genomic and phenotypic data, we propose that strain E14 T should be assigned to the genus Clostridium in the family Clostridiaceae as Clostridium omnivorum sp. nov. The type strain is E14 T (=NBRC 115133 T =DSM 114974 T ).