A Gram-stain-positive, non-spore-forming bacterium (strain RV113T) was isolated from the marine sponge Aplysina aerophoba. 16S rRNA gene sequence analysis showed that strain RV113T belongs to the genus Rubrobacter , and is related most closely to Rubrobacter bracarensis VF70612_S1T (96.9 % similarity) and more distantly related (<93 %) to all other species of the genus Rubrobacter . The peptidoglycan diamino acid was lysine. Strain RV113T exhibited a quinone system with menaquinone MK-8 as the predominant compound. The polar lipid profile of strain RV113T consisted of the major compounds phosphatidylglycerol and two unidentified phosphoglycolipids. The major fatty acid was anteiso-C17 : 0ω9c. These chemotaxonomic traits are in agreement with those of other speciesof the genus Rubrobacter . The results of physiological and biochemical tests allowed the clear phenotypic differentiation of strain RV113T from all recognized Rubrobacter species. Strain RV113T is thus considered to represent a novel species, for which the name Rubrobacter aplysinae sp. nov. is proposed. The type strain is RV113T ( = DSM 27440T = CECT 8425T).
A Gram-stain-positive, aerobic actinomycete, designated strain YIM M13141T, was isolated from a marine sediment sample from the South China Sea, and its taxonomic position was determined using a polyphasic approach. The strain produced branched substrate mycelium and aerial hyphae, but no diffusible pigments were produced on the media tested. At maturity, substrate mycelium was fragmented and spore chains were formed on aerial hyphae and substrate mycelium. Optimum growth occurred at 28 °C, 1–3 % (w/v) NaCl and pH 7.0. Comparative analysis of the 16S rRNA gene sequence showed that the isolate belongs to the genus Pseudonocardia , showing highest levels of similarity with respect to Pseudonocardia sichuanensis KLBMP 1115T (97.1 %), Pseudonocardia tetrahydrofuranoxydans K1T (97.1 %) and Pseudonocardia kunmingensis YIM 63158T (97.0 %). Whole-organism hydrolysates of the strain contained meso-diaminopimelic acid and the sugars galactose, glucose, mannose and arabinose. The predominant menaquinone was MK-8(H4). The polar lipids detected were diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol, phosphatidylmethylethanolamine, phosphatidylethanolamine, two unknown phosphoglycolipids and two glycolipids. The major fatty acid was iso-C16 : 0. The G+C content of the genomic DNA was 73.1 mol%. DNA–DNA relatedness with P. tetrahydrofuranoxydans DSM 44239T was 42.8±3.5 % (mean±sd). Based on phylogenetic analysis, phenotypic and genotypic data, it is concluded that the isolate represents a novel species of the genus Pseudonocardia , for which the name Pseudonocardia sediminis sp. nov. is proposed. The type strain is YIM M13141T ( = DSM 45779T = JCM 18540T).
A novel actinomycete, strain N1286T, isolated from a lung transplant patient with a pulmonary infection, was provisionally assigned to the genus Nocardia . The strain had chemotaxonomic and morphological properties typical of members of the genus Nocardia and formed a distinct phyletic line in the Nocardia 16S rRNA gene tree. Isolate N1286T was most closely related to Nocardia farcinica DSM 43665T (99.8 % gene sequence similarity) but could be distinguished from the latter by the low level of DNA–DNA relatedness. These strains were also distinguishable on the basis of a broad range of phenotypic properties. It is concluded that strain N1286T represents a novel species of the genus Nocardia for which the name Nocardia kroppenstedtii sp. nov. is proposed. The type strain is N1286T ( = DSM 45810T = NCTC 13617T).
A Gram-stain-positive, non-endospore-forming rod-shaped bacterium, strain Ca11T, was isolated from a bioreactor with extensive phosphorus removal and was studied in detail for its taxonomic allocation. 16S rRNA gene sequence analysis revealed closest sequence similarity of the strain to type strains of [ Corynebacterium hoagii ] and Rhodococcus equi (98.9 %), Rhodococcus koreensis and Rhodococcus wratislaviensis (both 98.4 %), Rhodococcus opacus and Rhodococcus canchipurensis (both 98.0 %) followed by Rhodococcus kunmingensis and Rhodococcus imtechensis (97.7 %). Phylogenetic trees showed a distinct clustering of strain Ca11T with the type strains of [ C. hoagii ], R. equi , and R. kunmingensis separate to all other species of the genus Rhodococcus . The quinone system of strain Ca11T was composed of dihydrogenated menaquinones with 8 (major amount) as well as 7 and 6 isoprenoid units [MK-8(H2), MK-7(H2), MK-6(H2)]. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol mannoside, one unknown phospholipid and an unidentified glycolipid. The fatty acid profile was similar to that reported for R. equi and contained major amounts of C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0, supporting the allocation of the strain to the genus Rhodococcus . Physiological and biochemical characterization and DNA–DNA hybridization with type strains of the most closely related species allowed clear phenotypic and genotypic differentiation of the isolate. On the basis of these results, strain Ca11T ( = DSM 45893T = LMG 27563T) represents a novel species of the genus Rhodococcus , with the proposed name Rhodococcus defluvii sp. nov. In addition, a polyphasic taxonomic analysis of [ Corynebacterium hoagii ] DSM 20295T and Rhodococcus equi DSM 20307T indicated that the two strains belong to the same species, for which the name Rhodococcus hoagii comb. nov. takes priority, according to the Rules of the Bacteriological Code.
A novel actinobacterium, strain S1412T, was isolated from a deep sediment sample, collected from the southern Black Sea coast of Turkey, and was examined using a polyphasic approach. The organism had chemical and morphological features typical of the genus Streptomyces . The cell wall of the novel strain contained ll-diaminopimelic acid. Whole-cell hydrolysates contained galactose, glucose and traces of xylose. The polar lipid profile of S1412T consisted of the predominant compound diphosphatidylglycerol, moderate amounts of phosphatidylethanolamine and phosphatidylinositol, and minor amounts of phosphatidylglycerol. Strain S1412T exhibited an unusual quinone system, with the predominant compounds MK-10(H8), MK-9(H8) and MK-10(H6) and small amounts of MK-9(H6) and MK-10(H4). Major fatty acids were iso-C16 : 0, iso-C16 : 1 H and anteiso-C17 : 0. The 16S rRNA gene sequence similarities for strain S1412T with respect to the most closely related type strains of species of the genus Streptomyces were less than 97.0 %. Phenotypic data clearly distinguished the isolate from its closest relatives, Streptomyces specialis GW 41-1564T, Streptomyces mayteni YIM 60475T, Streptomyces hainanensis YIM 47672T, Streptomyces avicenniae MCCC1A01535T and Streptomyces sedi YIM 65188T. Based on chemotaxonomic, phenotypic and genotypic characteristics, strain S1412T is considered to represent a novel species of the genus Streptomyces , for which the name Streptomyces hoynatensis sp. nov. is proposed. The type strain is S1412T ( = KCTC 29097T = DSM 42069T).
A novel actinobacteria, designated strain K413T, was isolated from soil collected from Karpaz National Park, Magusa, Northern Cyprus, and characterized to determine its taxonomic position. The isolate was found to have chemical and morphological properties associated with members of the genus Streptomyces . Phylogenetic analyses based on almost-complete 16S rRNA gene sequences indicated that the isolate was closely related to members of the genus Streptomyces , and was shown to form a distinct phyletic line in the Streptomyces phylogenetic tree. Strain K413T was most closely related to Streptomyces marinus DSM 41968T (98.01 %). Sequence similarities with other strains of the genus Streptomyces were below 98.0 %. The cell wall of the novel strain contained ll-diaminopimelic acid. The predominant menaquinone was MK-9(H8) (45.0 %). The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine and phosphatidylinositol. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Based on 16S rRNA gene sequence analysis, DNA–DNA relatedness, phenotypic characteristics and chemotaxonomic data, strain K413T represents a novel species of the genus Streptomyces , for which the name Streptomyces karpasiensis sp. nov. is proposed. The type strain is K413T ( = KCTC 29096T = DSM 42068T).
Three novel Gram-stain-positive bacteria, designated IY07-20T, IY07-56T and IY07-113, were isolated from soil samples from Iriomote Island, Okinawa, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the three isolates were closely related to the members of the genus Agromyces , with similarity range of 95.6–98.7 %. The isolates contained l-2,4-diaminobutylic acid, d-alanine, d-glutamic acid and glycine in their peptidoglycans. The predominant menaquinone was MK-12 and the major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C contents were 70.9–72.9 mol%. The chemotaxonomic characteristics of the isolates matched those described for members of the genus Agromyces . The results of phylogenetic analysis and DNA–DNA hybridization, along with differences in phenotypic characteristics between strains IY07-20T, IY07-56T and IY07-113 and the species of the genus Agromyces with validly published names, indicate that the three isolates merit classification as representatives of two novel species of the genus Agromyces , for which the names Agromyces iriomotensis sp. nov. and Agromyces subtropica sp. nov. are proposed; the type strains are IY07-20T ( = NBRC 106452T = DSM 26155T) and IY07-56T ( = NBRC 106454T = DSM 26153T), respectively.
A Gram-staining-positive, strictly aerobic, rod-shaped, non-motile, non-spore-forming bacterial strain, designated GTGR-8T, which formed white colonies, was isolated from roots of Phytolacca acinosa Roxb. collected from Taibai Mountain in Shaanxi Province, north-west China. Strain GTGR-8T grew optimally at 28–30 °C, at pH 7.0–8.0 and in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain GTGR-8T was a member of the genus Solirubrobacter and was closely related to Solirubrobacter pauli B33D1T (98.9 % similarity), Solirubrobacter ginsenosidimutans BXN5-15T (97.0 %) and Solirubrobacter soli Gsoil 355T (96.9 %). No other recognized bacterial species showed more than 94.2 % 16S rRNA gene sequence similarity to the novel isolate. The only respiratory quinone of strain GTGR-8T was MK-7(H4) and the major fatty acids (>5 %) were iso-C16 : 0, C18 : 1ω9c, C17 : 1ω8c, C18 : 3ω6c (6,9,12) and C17 : 1ω6c. The DNA G+C content was 71.0 mol%. DNA–DNA relatedness for strain GTGR-8T with respect to its closest relatives, S. pauli KCTC 9974T and S. ginsenosidimutans KCTC 19420T, was 52.5 and 24.5 %, respectively. Based on phenotypic, phylogenetic and genotypic data, strain GTGR-8T is considered to represent a novel species in the genus Solirubrobacter , for which the name Solirubrobacter phytolaccae sp. nov. is proposed. The type strain is GTGR-8T ( = CCTCC AB 2013011T = KCTC 29190T).
An actinobacterial strain was isolated from a sediment sample from Chorao Island, in Goa province, India, and subjected to a taxonomic investigation. The isolate, designated NIO-1021T, was a Gram-stain positive, aerobic, non-motile and coccoid. Strain NIO-1021T was identified as a member of the genus Kocuria by a polyphasic approach. Strain NIO-1021T could be differentiated from other members of the genus Kocuria on the basis of physiology and 16S rRNA gene sequence analysis. The 16S rRNA gene sequence similarity of strain NIO-1021T to the most closely related species, Kocuria marina KCTC 9943T, was 98.6 % with 19 nt differences). Furthermore, DNA–DNA hybridization analysis revealed that the novel strain had lower relatedness with the type strains of other members of the genus Kocuria . The strain formed a monophyletic clade with K. marina with 100 % bootstrap values. The major phospholipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified lipids. The predominant menaquinone was MK-7(H2). The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The DNA G+C content of strain NIO-1021T was 60.5 mol%. Chemotaxonomic and phylogenetic properties of the strain were consistent with its classification as representing a member of the genus Kocuria . On the basis of phenotypic, chemotypic and molecular characteristics, strain NIO-1021T is considered to represent a novel species of the genus Kocuria , for which the name Kocuria indica sp. nov. is proposed, with strain NIO-1021T ( = NCIM 5455T = DSM 25126T = CCTCC AA 209050T) as the type strain.
In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp . albus NRRL B-1811T forms a cluster with five other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these other species, including Streptomyces almquistii NRRL B-1685T, Streptomyces flocculus NRRL B-2465T, Streptomyces gibsonii NRRL B-1335T and Streptomyces rangoonensis NRRL B-12378T are quite similar. This cluster is of particular taxonomic interest because Streptomyces albus is the type species of the genus Streptomyces . The related strains were subjected to multilocus sequence analysis (MLSA) utilizing partial sequences of the housekeeping genes atpD, gyrB, recA, rpoB and trpB and confirmation of previously reported phenotypic characteristics. The five strains formed a coherent cluster supported by a 100 % bootstrap value in phylogenetic trees generated from sequence alignments prepared by concatenating the sequences of the housekeeping genes, and identical tree topology was observed using various different tree-making algorithms. Moreover, all but one strain, S. flocculus NRRL B-2465T, exhibited identical sequences for all of the five housekeeping gene loci sequenced, but NRRL B-2465T still exhibited an MLSA evolutionary distance of 0.005 from the other strains, a value that is lower than the 0.007 MLSA evolutionary distance threshold proposed for species-level relatedness. These data support a proposal to reclassify S. almquistii , S. flocculus , S. gibsonii and S. rangoonensis as later heterotypic synonyms of S. albus with NRRL B-1811T as the type strain. The MLSA sequence database also demonstrated utility for quickly and conclusively confirming that numerous strains within the ARS Culture Collection had been previously misidentified as subspecies of S. albus and that Streptomyces albus subsp. patho cidicus should be redescribed as a novel species, Streptomyces pathocidini sp. nov., with the type strain NRRL B-24287T.
A Gram-staining-positive, aerobic, non-motile, irregular coccus, designated strain YIM M13146T, was isolated from a sediment sample collected from the South China Sea at a depth of 2439 m, and its taxonomic position was determined by a polyphasic approach. Optimal growth of the strain was observed at 30 °C (range 5–40 °C), pH 7.0 (pH 6.0–9.0) and 0–1 % NaCl (0–6 %, w/v) on/in tryptic soy agar/broth. Strain YIM M13146T had the major cellular fatty acid anteiso-C15 : 0, the predominant respiratory menaquinone MK-9(H4), peptidoglycan type A3γ (ll-DAP–Gly) containing alanine, glycine, glutamic acid and ll-diaminopimelic acid (ll-DAP) and the polar lipids phosphatidylcholine, diphosphatidylglycerol, one unknown phospholipid and several glycolipids. The G+C content of the DNA was 67.2 mol%. Phenotypic and chemotaxonomic characteristics together with 16S rRNA gene sequence analyses showed that strain YIM M13146T was distinct from its close phylogenetic relatives in the genera Propioniferax and Granulicoccus of the family Propionibacteriaceae . Hence, a new genus and species, Mariniluteicoccus flavus gen. nov., sp. nov., is proposed. The type strain of Mariniluteicoccus flavus is YIM M13146T ( = DSM 25892T = CCTCC AB 2012055T).