Nocardioides baculatus sp. Nov., a novel actinomycete isolated from the rhizosphere of tagetes patula

An aerobic, Gram-stain-positive, non-motile, dull-yellow, short rod-shaped actinomycete strain, designated G10^T, was isolated from Tagetes patula (marigold) roots collected from Goyang in the Republic of Korea. The isolate showed best growth on Reasoner's 2A agar at 25 °C, pH 6.5.0 and with 0% NaCl (w/v). The strain was negative for oxidase activity and positive for catalase activity. On the basis of 16S RNA gene sequence similarity, strain G10^T was affiliated to the genus Nocardioides and the closest species were Nocardioides glacieisoli HLT3-15^T (98.8%), Nocardioides zhouii HLT2-9^T (98.8%), Nocardioides ganghwensis JC2055^T (98.7%), Nocardioides cavernae YIM A1136^T (98.6%), Nocardioides flavus Y4^T (98.5%), Nocardioides oleivorans DSM 16090^T (98.3%), Nocardioides alpinus Cr7-14^T (98.2%), Nocardioides exalbidus DSM 22017^T (98.1%) and Nocardioides hwasunensis KCTC 19197^T (98.1%). Strain G10^T formed a monophyletic cluster with N. glacieisoli HLT3-15^T, N. zhouii HLT2-9^T and N. hwasunensis KCTC 19197^T in all phylogenetic trees. The cell-wall peptidoglycan of strain G10^T contained ll-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C_{16: 0} and C_{17: 1} ω8c. MK-8(H₄ ) was the major isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Average nucleotide identity and digital DNA–DNA hybridization values were 78.6–88.7% and 21.5– 36.2%, respectively, with the type strains of related species of the genus Nocardioides, suggesting that strain G10^T represents a novel species. The genome of strain G10^T is 4231000 bp long with a DNA G+C content of 71.5mol% and encodes 4071 predicted proteins, six rRNAs and 46 tRNAs. The genome of strain G10^T comprises the biosynthetic gene cluster for T3PKS, terpene, NRPS-like fragment and RRE-containing element as secondary metabolites. The results of taxonomic, phylogenetic, biochemical, chemotaxonomic and genomic analysis clearly supported that strain G10^T represent a novel species within the genus Nocardioides, for which the name Nocardioides baculatus sp. nov is proposed and the type strain is G10^T (=KCTC 49626^T=NBRC 114801^T).