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 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).

Nocardioides dongxiaopingii sp. nov., isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau

Two novel Gram-stain-positive, irregular rod-shaped actinomycetes, S-1144^T and 4053, were isolated from leaves of Lamiophlomis rotata on the Qinghai-Tibet Plateau, PR China. Cells were aerobic, catalase-positive and oxidase-negative. Colonies on Reasoner's 2A agar were light yellow, circular, shiny, smooth and convex after 2 days of incubation. The isolates grew optimally at 25 °C, pH 7.5 and with 0 % (w/v) NaCl. The results of polyphasic analyses indicated that strain S-1144^T belonged to the genus Nocardioides and its close phylogenetic neighbours (16S rRNA gene sequence similarity) were Nocardioides litoris DSM 103718^T (98.4 %), Nocardioides rubriscoriae DSM 23986^T (98.2%) and Nocardioides plantarum DSM 11054^T (97.8 %). The genome of strain S-1144^T showed less than 70 % digital DNA-DNA hybridization and < 95-96 % average nucleotide identity values to the above reference strains. The DNA G+C content of strain S-1144^T was 73.5 mol%. MK-8(H₄) was the predominant respiratory quinone (96.0 %) and llLL-2,6-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The polar lipid profile of strain S-1144^T consisted of diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids, one unidentified glycolipid and one unidentified lipid. The major cellular fatty acids were iso-C_16 : 0, C_17 : 1  ω8c, C_17 : 0 and C_18 : 1  ω9c. On the basis of obtained data, strain S-1144^T represented a novel species of the genus Nocardioides, for which the name Nocardioides dongxiaopingii sp. nov. is proposed. The type strain is S-1144^T (=CGMCC 4.7568^T=JCM 33469^T).

Nocardioides jejuensis sp. nov., isolated from soil

A Gram-stain positive, asporogenous, aerobic, white -coloured bacterium, designated 18JY15-6^T, was isolated from soil from Jeju Island, Korea. Pairwise analysis of the 16S rRNA gene sequence of strain 18JY15-6^T indicated high similarity to Nocardioides phosphati DSM 104026^T (97.4%), Marmoricola terrae KACC 17308^T (96.7%) and Nocardioides jensenii KCTC 0074BP^T (96.6%). Phylogenetic analysis revealed that strain 18JY15-6^T formed a distinct lineage within the family Nocardioidaceae and is closely related to members of the genus Nocardioides. Genome sequencing of strain 18JY15-6^T revealed 3221 total genes, including 3162 protein coding genes, 59 RNA and 31 pseudogenes. Growth was observed at 18-37 °C (optimal 30 °C) in R2A medium at pH 7.0. The major cellular fatty acids of strain 18JY15-6^T were identified as C_16:0, C_18:1ω9c, C_18:0 10-methyl, tuberculostearic and C_17:0. The fatty acid profile of strain 18JY15-6^T was more dissimilar when compared with M. terrae. The only respiratory quinone present was found to be MK-8(H₄). The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. The results of phylogenetic, biochemical and chemotaxonomic characterisation allow the differentiation of strain 18JY15-6^T from N. phosphati WYH11-7^T, M. terrae JOS5-1^T and N. jensenii NBRC 14755^T which supports the conclusion that this strain represents a novel species of the genus Nocardioides, for which we propose the name Nocardioides jejuensis sp. nov. The type strain of Nocardioides jejuensis is 18JY15-6^T (= KCTC 49105^T = JCM 33182^T).

Nocardioides cavernae sp. nov., an actinobacterium isolated from a karst cave

A novel actinobacterial strain, designated YIM A1136T, was isolated from a soil sample collected from a karst cave in Xingyi county, Guizhou province, south-western China. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of the strain were aerobic, Gram-staining-positive and rod-shaped. Colonies of the strain were circular, convex, opaque and yellowish-white in colour. On the basis of 16S rRNA gene sequence analysis, strain YIM A1136T was most closely related to the type strains Nocardioides ganghwensis JC2055T (98.3 % sequence similarity), Nocardioides exalbidus RC825T (98.2 %), Nocardioides alpinus Cr7-14T (98.2 %), Nocardioides hwasunensis HFW-21T (98.0 %), Nocardioides oleivorans DSM 16090T (97.9 %) and Nocardioides furvisabuli SBS-26T (97.8 %) and is therefore considered to represent a member of the genus Nocardioides. DNA-DNA hybridization values between strain YIM A1136T and related type strains of the genus Nocardioides were less than 70 %. ll-Diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars were galactose, glucose, mannose, rhamnose and ribose. The major isoprenoid quinone was MK-8(H4), while the major fatty acids (>10 %) were C16 : 0, summed feature 3 and summed feature 8. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. The genomic DNA G+C content was 71.4 mol%. On the basis of phenotypic, genotypic and phylogenetic data, strain YIM A1136T merits representation of a novel species of the genus Nocardioides, for which the name Nocardioides cavernae sp. nov. is proposed. The type strain is YIM A1136T (=KCTC 39551T=DSM 29950T).