Rhodococcus subtropicus sp. nov., a new actinobacterium isolated from a cave

A novel Gram-stain-positive actinobacterial strain, designated C9-28 T , was isolated from soil sampled in a natural cave on Jeju Island, Republic of Korea. Strain C9-28 T morphologically exhibited a rod-coccus life cycle and grew at 10-37 °C (optimum, 30 °C), pH 6-9 (optimum, pH 7) and 0-3 % (optimum, absence of NaCl). In the maximum-likelihood tree based on 16S rRNA gene sequences, strain C9-28 T formed a sublineage between a Rhodococcus equi-Rhodococcus soli-Rhodococcus agglutinans clade and the type strain of Rhodococcus defluvii . The closest relatives of strain C9-28 T were the type strains of R. defluvii (98.88 % 16S rRNA gene sequence similarity), R. equi (98.88 %) and R. soli (98.60 %). The phylogenomic tree based on whole genome sequences supported the distinct position of the novel strain within the genus Rhodococcus . The following chemotaxonomic characteristics also supported the assignment to the genus: meso -diaminopimelic acid; arabinose and galactose in whole-cell hydrolysates; the predominant menaquinone of MK-8(H 2 ); and polar lipids including diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified glycolipids and two unidentified lipids. The predominant cellular fatty acids were C 16 : 0 , summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ), C 18 : 1 ω9 c and C 14 : 0 . Based on the values of average nucleotide identity and digital DNA-DNA hybridization from whole genome sequences, and in vitro DNA-DNA hybridization between the isolate and the closest relatives, strain C9-28 T (=KACC 19823 T =DSM 107559 T ) represents a novel species of the genus Rhodococcus , for which the name Rhodococcussubtropicus sp. nov. is proposed.