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-Rhodoc-occus 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 diphosphatidylg-lycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified glycolipid and three unidentified phospholipids. Mycolic acids were present. The major fatty acids were C-16:0, C18:1 omega 9c, C-16:1 omega 7c and/or C-16:1 omega 6c 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.