Rhodococcus aromaticivorans sp. nov., an o-xylene degrading bacterium, and evidence supporting reclassification of Rhodococcus jostii RHA1

Abstract

A Gram-positive, aerobic, non-motile bacterium with a rod-coccus shape, designated DK17(T), was isolated from a crude oil-contaminated soil and identified as a member of the genus Rhodococcus based on 16S rRNA gene analysis, showing highest similarity (99.93%) to Rhodococcus jostii DSM 44719(T). However, average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain DK17(T) and type strains within the genus Rhodococcus were below the species delineation thresholds of 95% and 70%, respectively. In contrast, DK17(T) exhibited ANI and dDDH values over 99% and 92%, respectively, with R. jostii RHA1. Comparative genomic analysis revealed that DK17(T) and RHA1 shared 93.5% of genes, while RHA1 and R. jostii NBRC 16295T shared only 78.6%, indicating a closer relationship between DK17(T) and RHA1. Both strains possess large genomes (similar to 9.5-9.7 Mb) comprising a linear chromosome and multiple plasmids, and encode multiple dioxygenases and secondary metabolite biosynthetic gene clusters. In vitro assays confirmed o-xylene degradation by both DK17(T) and R. jostii RHA1, consistent with the presence of the akb gene cluster. Both strains shared C16:0 as a major fatty acid and menaquinone-8 (H2) as the dominant quinone. Based on genomic, phenotypic, and chemotaxonomic data, DK17(T) (=KCCM 90599(T) = InaCC B1662(T)) is proposed as a novel species, Rhodococcus aromaticivorans sp. nov., and R. jostii RHA1 is reclassified as a member of the same species.