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

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Abstract

A Gram-reaction-positive, strictly aerobic, catalase-positive, oxidase-negative, non-motile actinobacterium, designated C1-24T, 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(H2) 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 C16:0, C18:1 ω9c, C16:1 ω7c and/or C16:1 ω6c and 10-methyl C18:0. 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 C1-24T (=KACC 19964T=DSM 109484T) 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.

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Lee, S. D., Kim, I. S., Kim, Y. J., & Joung, Y. (2020). Rhodococcus cavernicola sp. nov., isolated from a cave, and rhodococcus degradans is a later heterosynonym of rhodococcus qingshengii. International Journal of Systematic and Evolutionary Microbiology, 70(7), 4409–4415. https://doi.org/10.1099/ijsem.0.004126

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