Rhodococcus pseudokoreensis sp. nov. isolated from the rhizosphere of young M26 apple rootstocks

The Gram-positive strain R79(T), isolated from the rhizosphere of young M26 apple rootstocks, was investigated by a polyphasic taxonomic approach. Phylogenetic identification based on the full-length 16S rRNA gene sequence revealed highest 16S rRNA gene sequence similarity to the type strains of Rhodococcus wratislaviensis (99.6%) and Rhodococcus opacus (99.2%) followed by Rhodococcus imtechensis (98.9%). All other 16S rRNA gene sequence similarities were below 98.65%. A phylogenomic tree calculated based on a whole-genome sequence also showed a distinct clustering with the type strain of Rhodococcus koreensis. Average nucleotide identity (ANI) values between whole-genome sequences of R79(T) and the closest related type strains were below 95% supported the novel species status. The DNA G + C content of R79(T) was 67.24% mol. Predominant fatty acids were C(16:0,) C(15:0) and C(17:1ω8c). The strain contained MK8-H(2) as the major respiratory quinone. The polar lipid profile consists of diphosphatidylglycerol and phosphatidylethanolamine, as well as of some unidentified lipids. The peptidoglycan type of the strain is A1γ meso-diaminopimelic acid. Based on the obtained genotypic and phenotypic, including chemotaxonomic data, we conclude that R79(T) represents a novel species of the genus Rhodococcus, for which the name Rhodococcus pseudokoreensis sp. nov. is proposed. The type strain is R79(T) (= DSM 113102(T) = LMG 32444(T) = CCM 9183(T)). SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00203-022-03079-2.