Rhodococcus cavernicola sp. nov., isolated from a cave, and Rhodococcus degradans is a later heterosynonym of Rhodococcus qingshengii

A Gram-reaction-positive, strictly aerobic, catalase-positive, oxidase-negative, non-motile actinobacterium, designated C1-24 T , was isolated from a soil sample collected inside a natural cave. The organism exhibited a rod–coccus developmental cycle during its growth phase. Results of 16S rRNA gene-based phylogenetic analysis showed that the novel strain belonged to the genus Rhodococcus and formed a distinct sublineage at the base of the radiation including a Rhodococcus enclensis–Rhodococcus kroppenstedtii–Rhodococcus corynebacterioides–Rhodococcus trifoli cluster. In the results of phylogenomic analysis, the novel strain was loosely associated to Rhodococcus corynebacterioides . The closest relatives were Rhodococcus qingshengii (98.01 % 16S rRNA gene sequence similarity) and Rhodococcus degradans (98.01 %). The genome size was 5.66 Mbp and the DNA G+C content was 64.30 mol%. Whole-cell hydrolysates contained meso -diaminopimelic acid, arabinose and galactose as the diagnostic diamino acid and sugars. MK-8(H 2 ) was the predominant menaquinone. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid and three unidentified phospholipids. Mycolic acids were present. The major fatty acids were C 16 : 0 , C 18 : 1   ω9 c , C 16 : 1   ω7 c and/or C 16 : 1   ω6 c and 10-methyl C 18 : 0 . Digital DNA–DNA hybridization and average nucleotide identity values revealed that the novel strain should be assigned to a different species. Based on the combined data obtained here, strain C1-24 T (=KACC 19964 T =DSM 109484 T ) represents a new species of the genus Rhodococcus , for which Rhodococcus cavernicola sp. nov. is proposed. Also, it is proposed that R. degradans is a later heterosynonym of R. qingshengii based on analyses of 16S rRNA gene and whole-genome sequences.