Nocardioides baculatus sp. nov., a novel actinomycete isolated from the rhizosphere of Tagetes patula

Abstract

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 degrees 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 Cr7-14T (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 iota iota-diaminopimelic acid as the diagnostic amino acid. The predominant fatty acids were iso-C-16:0 and C-17:1 omega 8c. MK-8(H-4) 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 4 231 000 bp long with a DNA G+C content of 71.5 mol% 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)).