- Volume 59, Issue 12, 2009

An endophytic actinomycete, designated strain YIM 65359T, was isolated from a surface-sterilized stem sample of Tripterygium hypoglaucum collected from Yunnan province, south-west China. The morphological and chemotaxonomic properties of the new isolate were consistent with those of members of the genus Saccharopolyspora. Analysis of 16S rRNA gene sequences revealed that the new isolate was most closely related to ‘Saccharopolyspora endophytica’ YIM 61095 (98.6 %), Saccharopolyspora flava AS4.1520T (97.6 %) and Saccharopolyspora spinosa DSM 44228T (97.0 %). The results of DNA–DNA hybridizations (57.5 %, 44.9 % and 48.5 %, respectively) with the above micro-organisms, in combination with differences in the biochemical and physiological characteristics, suggested that strain YIM 65359T should be classified as a novel species of the genus Saccharopolyspora. The name Saccharopolyspora tripterygii sp. nov. is proposed for this novel species, with YIM 65359T (=CCTCC AA 208062T=DSM 45269T) as the type strain.

A Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 1124T) was isolated from soil of a ginseng field of Pocheon province in South Korea, and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 1124T was shown to belong to the family Nocardioidaceae and related to Nocardioides simplex (98.2 % 16S rRNA gene sequence similarity), Nocardioides aromaticivorans (98.1 %), Nocardioides nitrophenolicus (97.7 %) and Nocardioides kongjuensis (97.5 %). The sequence similarity with any other species with validly published names within the genus Nocardioides was less than 94.5 %. Strain Gsoil 1124T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C18 : 0, C16 : 0, and C18 : 1 ω9c as the major fatty acids. The G+C content of the genomic DNA was 70.2 mol%. The chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain Gsoil 1124T to the genus Nocardioides. The results of physiological and biochemical tests, and the low level of DNA–DNA relatedness allowed genotypic differentiation of strain Gsoil 1124T from recognized Nocardioides species. Therefore, strain Gsoil 1124T is considered to represent a novel species, for which the name Nocardioides ginsengisoli sp. nov. is proposed, with the type strain Gsoil 1124T (=KCTC 19135T=CCUG 52478T=DSM 17921T).

A novel actinomycete, strain S10T, was isolated from rhizosphere soil of wild Vitis vinifera in Thinghir, Ouarzazate Province, Southern Morocco. The taxonomic status of this strain was established using a polyphasic approach. Strain S10T had white–grey aerial mycelium with long, spiral spore chains bearing smooth surfaced spores and produced a yellow diffusible pigment. Chemotaxonomic analyses showed that the cell wall of strain S10T contained ll-diaminopimelic acid and glycine. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence indicated that strain S10T belonged to the Group I streptomycetes, branching off next to Streptomyces marokkonensis LMG 23016T from the Streptomyces violaceoruber group. DNA–DNA relatedness and phenotypic data distinguished strain S10T from the phylogenetically closest related type strains. It is therefore proposed that strain S10T (=CCMM B35T=DSM 41919T) represents the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces thinghirensis sp. nov. is proposed.

A novel actinomycete, designated strain CS5-AC17T, was isolated from cliff soil in the Republic of Korea. Cells of the organism were aerobic and catalase- and oxidase-negative. Substrate mycelium was well developed and was pale to strong yellow. Spore chains were borne on rudimentary aerial mycelium. The spores (0.4–0.5×0.9–1.6 μm) were smooth surfaced and cylindrical. Growth occurred at 25–42 °C, at pH 5.1–12.1 and in the presence of up to 4 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate was closely related to members of the genus Actinocatenispora in the family Micromonosporaceae. The phylogenetic neighbours were Actinocatenispora thailandica TT2-10T (97.7 % 16S rRNA gene sequence similarity) and Actinocatenispora sera KV-744T (97.6 %). The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major respiratory quinones were MK-9(H4), MK-9(H6) and MK-9(H8). The polar lipids contained phosphatidylethanolamine and phosphatidylinositol with a small amount of phosphatidylglycerol. The DNA G+C content was 74.3 mol%. DNA–DNA relatedness values between strain CS5-AC17T and its phylogenetically closest relatives were 6.1–7.1 % (A. thailandica DSM 44816T) and 21.5–27.6 % (A. sera NRRL B-24477T). On the basis of the phenotypic features and the DNA–DNA hybridization data, strain CS5-AC17T (=DSM 45178T=NRRL B-24660T) represents a novel species of the genus Actinocatenispora, for which the name Actinocatenispora rupis sp. nov. is proposed.

A novel actinomycete, strain OFN S31T, was isolated from a complex biofilm in the Altamira Cave, Spain. A polyphasic study was carried out to clarify the taxonomic position of this strain. Phylogenetic analysis with 16S rRNA gene sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Millisia, Mycobacterium, Nocardia, Rhodococcus, Segniliparus, Skermania, Tsukamurella and Williamsia indicated that strain OFN S31T formed a distinct taxon in the 16S rRNA gene tree that was more closely associated with the Mycobacterium clade. The type strain of Mycobacterium fallax was the closest relative of strain OFN S31T (95.6 % similarity). The cell wall contained meso-diaminopimelic acid, arabinose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes. The sugars of the peptidoglycan were acetylated. The polar lipid pattern was composed of phosphatidylinositol, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain OFN S31T is characterized by the absence of mycelium and mycolic acids. Strain OFN S31T had MK-8 as the major menaquinone. The DNA G+C content was 49.3 mol%, the lowest found among all taxa included in the suborder Corynebacterineae. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain OFN S31T is considered to represent a novel species of a new genus, for which the name Hoyosella altamirensis gen. nov., sp. nov. is proposed. The type strain of Hoyosella altamirensis is strain OFN S31T (=CIP 109864T =DSM 45258T).

An endophytic actinomycete, strain YIM 65070T, was isolated from surface-sterilized tissue of Osyris wightiana Wall. ex Wight collected from Yunnan province, south-west China, and characterized by using a polyphasic approach. Strain YIM 65070T had morphological and chemotaxonomic markers that were consistent with its classification in the genus Herbidospora. Phylogenetic analysis based on almost complete 16S rRNA gene sequences indicated that strain YIM 65070T was phylogenetically very closely related to Herbidospora cretacea IFO 15474T. DNA–DNA hybridization experiments confirmed the separate genomic status of strains YIM 65070T and H. cretacea DSM 44071T. Moreover, strain YIM 65070T could be distinguished from H. cretacea DSM 44071T by differences in several phenotypic characteristics such as tolerance to NaCl, degradation activity, utilization of sole carbon and nitrogen sources and the cellular fatty acid contents. On the basis of phenotypic and phylogenetic evidence, strain YIM 65070T was identified as a novel species of the genus Herbidospora, for which the name Herbidospora osyris sp. nov. is proposed, with YIM 65070T (=CCTCC AA 208019T=DSM 45214T) as the type strain.

An actinomycete, strain DMKUA 245T, isolated from soil, was investigated using a polyphasic approach. The isolate formed longitudinally paired spores on the tips of short sporophores that branched alternately from aerial hyphae. The morphological and chemotaxonomic properties clearly demonstrated that the new isolate belonged to the genus Microbispora. 16S rRNA gene sequence analysis supported the assignment of the novel strain to the genus Microbispora. The gene sequence similarity values between the novel strain and the closely related species Microbispora corallina, Microbispora rosea subsp. rosea, Microbispora rosea subsp. aerata and Microbispora amethystogenes were 98.4 %, 97.4 %, 97.0 % and 96.9 %, respectively. The DNA–DNA hybridization values and some physiological and biochemical properties indicated that strain DMKUA 245T could be distinguished from its phylogenetically closest relatives. Based on these genotypic and phenotypic data, strain DMKUA 245T represents a novel species in the genus Microbispora for which the name Microbispora siamensis sp. nov. is proposed. The type strain is strain DMKUA 245T (=BCC 14407T=NBRC 104113T). In addition, DNA–DNA relatedness values in reciprocal hybridization experiments showed that M. amethystogenes was a separate genomic species from M. rosea subsp. rosea. A combination of genotypic and phenotypic data supported the classification of M. amethystogenes as a separate species.

An endophytic actinomycete strain, designated YIM 65293T, was isolated from a surface-sterilized stem sample of Tripterygium wilfordii collected from Yunnan province, south-west China, and its taxonomic position was investigated. The chemical and morphological properties of the organism were consistent with those of the genus Kineosporia. Phylogenetic analysis indicated that the levels of 16S rRNA gene sequence similarity between strain YIM 65293T and other type strains of recognized members of the genus Kineosporia were 97.0–98.2 %. However, the DNA–DNA hybridization values, in combination with differences in phenotypic characteristics, revealed that the strain differed from recognized species of the genus Kineosporia. Therefore, strain YIM 65293T represents a novel species of the genus Kineosporia, for which the name Kineosporia mesophila sp. nov. is proposed. The type strain is YIM 65293T (=CCTCC AA 208061T=DSM 45271T).

A Gram-positive, aerobic and non-motile bacterial strain, designated ON-33T, was subjected to a study based on a polyphasic approach to determine its exact taxonomic position. Strain ON-33T grew optimally at pH 7.0–7.5 and 30 °C. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain ON-33T fell within the clade comprising Gordonia species, clustering with Gordonia soli CC-AB07T, with which it exhibited 16S rRNA gene sequence similarity of 98.5 %. The chemotaxonomic properties of strain ON-33T were consistent with those shared by members of the genus Gordonia. The peptidoglycan type was based on meso-diaminopimelic acid and the whole-cell sugars were arabinose and galactose. The predominant menaquinone was MK-9(H2). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were C16 : 0, iso-C15 : 0 2-OH and/or C16 : 1 ω7c, 10-methyl C18 : 0 and C18 : 1 ω9c. The DNA G+C content was 66.9 mol%. Strain ON-33T exhibited a DNA–DNA relatedness value of 13 % to G. soli DSM 44995T and could be differentiated from G. soli by differences in phenotypic characteristics. On the basis of the data obtained, strain ON-33T is considered to represent a novel species of the genus Gordonia, for which the name Gordonia hankookensis sp. nov., is proposed. The type strain is ON-33T (=KCTC 19599T=CCUG 57507T).

An anaerobic acidophilic, hyperthermophilic archaeon, designated strain 345-15T, was isolated from an acidic hot spring of Kamchatka (Russia). Cells of strain 345-15T were regular or irregular cocci, 1–2 μm in diameter, with flagella. Strain 345-15T grew optimally at 80–85 °C and pH 3.5–4.0 and fermented a wide range of carbohydrates, including polysaccharides. Acetate, ethanol and lactate were the fermentation products. Growth was stimulated by elemental sulfur and thiosulfate, which were reduced to hydrogen sulfide. The G+C content of the DNA was 54.5 mol%. The 16S rRNA gene sequence analysis indicated that strain 345-15T belonged to the genus Acidilobus. The level of DNA–DNA hybridization between strain 345-15T and Acidilobus aceticus 1904T was 61 %. Thus, strain 345-15T was considered as representing a novel species of the genus Acidilobus, with the name Acidilobus saccharovorans sp. nov. (type strain, 345-15T=DSM 16705T=VKM B-2471T), which shared the main morphological and physiological properties of the genus but differed by the presence of flagella and the spectrum of substrates utilized. Phylogenetic analysis showed that the genus Acidilobus, with its species Acidilobus aceticus, Acidilobus saccharovorans sp. nov. and ‘Acidilobus sulfurireducens’, and the genus Caldisphaera, represented by Caldisphaera lagunensis and ‘Caldisphaera draconis’, formed a separate cluster that adjoins the cluster formed by the species of the order Desulfurococcales. Members of the Acidilobus–Caldisphaera cluster are thermophilic, organotrophic anaerobic cocci that can be distinguished from all species of the order Desulfurococcales on the basis of acidophily. Based on these considerations, we propose a new family, Acidilobaceae fam. nov., to accommodate the subcluster of hyperthermophiles represented by the genus Acidilobus, a new family, Caldisphaeraceae fam. nov., for the subcluster of extreme thermophiles represented by the genus Caldisphaera, and a new order, Acidilobales ord. nov., to accommodate the two new families.

Eight bacterial strains isolated from diseased rainbow trout (n=5) and Atlantic salmon (n=3) were characterized by phenotypic and molecular taxonomic methods. The isolates were negative for the Gram-reaction, non-motile, rod-shaped and catalase- and oxidase-positive. Colonies on solid media were yellow, smooth, shiny and circular with regular edges. Growth occurred at 4–28 °C (optimum, 15 °C) and with 0–3 % NaCl (optimum, 0.5 %). Analysis of the 16S rRNA gene sequence allocated the micro-organisms to the genus Chryseobacterium, with Chryseobacterium soldanellicola PSD1-4T and Chryseobacterium soli JS6-6T as their closest relatives (96.9 and 97.1 % sequence similarity, respectively). The levels of DNA–DNA hybridization towards these nearest phylogenetic neighbours were below 17.1 %. The DNA G+C contents of strains VQ-6316sT and VQ-4836s were 32.5 and 32.3 mol%, respectively. The predominant menaquinone was MK-6 and the major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1 ω9c, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω7t and/or iso-C15 : 0 2-OH). The eight isolates were classified as representatives of a novel species, Chryseobacterium piscicola sp. nov., with strain VQ-6316sT (=CECT 7357T=DSM 21068T) as the type strain.

A novel golden-yellow-coloured strain, designated RHYL-37T, was isolated from a soil sample from a forest of Euphrates poplar (Populus euphratica) in Xinjiang, China. The cells were strictly aerobic, Gram-staining-negative, heterotrophic, non-spore-forming rods that were motile by gliding. Growth occurred at 17–37 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl (w/v; optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate formed a cluster with members of the genera Segetibacter, Terrimonas, Niastella, Niabella and Chitinophaga in the family ‘Chitinophagaceae’ in the phylum Bacteroidetes. Sequence similarities with the type strains of recognized species ranged from 90.6 to 94.0 %. The predominant isoprenoid quinone was MK-7 and the major cellular fatty acids were iso-C15 : 0, iso-C15 : 1, C16 : 0 and iso-C17 : 0 3-OH. The DNA G+C content was 39.7 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic data, strain RHYL-37T represents a novel genus and species in the family ‘Chitinophagaceae’, for which the name Parasegetibacter luojiensis gen. nov., sp. nov. is proposed. The type strain of Parasegetibacter luojiensis is RHYL-37T (=CCTCC AB 208240T=KCTC 22561T).

The taxonomic status of a novel, heterotrophic, strictly aerobic, gliding and yellow–orange-pigmented bacterium (strain KMM 6264T), associated with the coral Palythoa, was determined. The 16S rRNA gene sequence analysis indicated that strain KMM 6264T clustered with the recognized species of the genus Leeuwenhoekiella of the family Flavobacteriaceae with 96.4–98.2 % sequence similarity. DNA–DNA reassociation levels between the isolate and the type strains of Leeuwenhoekiella species were 15–22 %. The DNA G+C content was 41.2 mol%. The phylogenetic evidence and the results of genomic and phenotypic analyses showed that the isolate should be classified as a member of a novel species of the genus Leeuwenhoekiella, for which the name Leeuwenhoekiella palythoae sp. nov. is proposed. The type strain is KMM 6264T (=KCTC 22020T=LMG 24856T).

A Gram-positive to Gram-variable, motile and coccoid- or short rod-shaped bacterial strain, ISL-41T, was subjected to a polyphasic study to investigate its exact taxonomic position. Strain ISL-41T grew optimally at pH 7.0–8.0 and 30 °C. It contained MK-8 and MK-7 as the predominant menaquinones and anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and C16 : 1 ω7c alcohol as the major fatty acids. The DNA G+C content was 45.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-41T belonged to the genus Planomicrobium. The levels of similarity between the 16S rRNA gene sequence of strain ISL-41T and those of the type strains of recognized Planomicrobium species and Planococcus stackebrandtii were 97.4–98.6 %. Mean DNA–DNA relatedness values between strain ISL-41T and the type strains of Planomicrobium species and Planococcus stackebrandtii were 13–25 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, showed that strain ISL-41T could be differentiated from recognized Planomicrobium species and Planococcus stackebrandtii. On the basis of the phenotypic, phylogenetic and genetic data, strain ISL-41T is considered to represent a novel species within the genus Planomicrobium, for which the name Planomicrobium flavidum sp. nov. is proposed. The type strain is ISL-41T (=KCTC 13261T=CCUG 56756T). It is also proposed that Planococcus stackebrandtii be transferred to the genus Planomicrobium as Planomicrobium stackebrandtii comb. nov. (type strain K22-03T=MTCC 6226T=DSM 16419T=JCM 12481T).

Three novel bacterial strains, PVAS-1T, B3W22T and B8W22T, were isolated from cryotubes used to collect air samples at altitudes of between 27 and 41 km. Based on phenotypic characteristics, chemotaxonomic features, DNA–DNA hybridization with the nearest phylogenetic neighbours and phylogenetic analysis based on partial 16S rRNA gene sequences (PVAS-1T, 1196 nt; B3W22T, 1541 nt; B8W22T, 1533 nt), the three strains were identified as representing novel species, and the names proposed are Janibacter hoylei sp. nov. (type strain PVAS-1T =MTCC 8307T =DSM 21601T =CCUG 56714T), Bacillus isronensis sp. nov. (type strain B3W22T =MTCC 7902T =JCM 13838T) and Bacillus aryabhattai sp. nov. (type strain B8W22T =MTCC 7755T =JCM 13839T).

A novel Gram-stain-positive, slightly halophilic, facultatively alkaliphilic, non-motile, catalase- and oxidase-positive, endospore-forming, rod-shaped, aerobic bacterium, strain JSM 071004T, was isolated from a sea anemone collected from Neizhou Bay in the South China Sea. Growth occurred with 0.5–10 % (w/v) total salts (optimum 2–4 %) and at pH 6.5–10.0 (optimum pH 8.5) and 4–30 °C (optimum 25 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 071004T belongs to the genus Bacillus, being related most closely to the type strain of Bacillus agaradhaerens (sequence similarity 97.3 %), followed by the type strains of Bacillus cellulosilyticus (96.2 %), Bacillus clarkii (96.1 %) and Bacillus polygoni (96.0 %). The combination of phylogenetic analysis, DNA–DNA hybridization, phenotypic characteristics and chemotaxonomic data support the proposal that strain JSM 071004T represents a novel species of the genus Bacillus, for which the name Bacillus neizhouensis sp. nov. is proposed, with JSM 071004T (=CCTCC AB 207161T =DSM 19794T =KCTC 13187T) as the type strain.

A novel, moderately halophilic, Gram-positive bacterium, designated strain XH-22T, was isolated from sediment of a saline lake located near Xilinhot, Inner Mongolia Autonomous Region, China. Cells were rod-shaped, endospore-forming and motile. The isolate was able to grow in the presence of 3–20 % (w/v) total salts (optimum, 10 %, w/v), and at 15–40 °C (optimum, 37 °C) and pH 6.0–10.0 (optimum, pH 7.5). Strain XH-22T had diaminopimelic acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone, and anteiso-C15 : 0, C16 : 0 and iso-C14 : 0 as major fatty acids. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, a glycolipid and two unidentified phospholipids. The DNA G+C content of strain XH-22T was 38.8 mol%. 16S rRNA gene sequence analysis revealed that the novel strain was affiliated with the genus Virgibacillus. Levels of 16S rRNA gene sequence similarity between strain XH-22T and the type strains of recognized Virgibacillus species ranged from 97.6 % (with Virgibacillus carmonensis) to 94.9 % (with Virgibacillus koreensis). Levels of DNA–DNA relatedness between strain XH-22T and V. carmonensis DSM 14868T and Virgibacillus necropolis DSM 14866T were 32 and 28 %, respectively. Strain XH-22T could be differentiated from recognized Virgibacillus species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and genotypic features. On the basis of these results, strain XH-22T is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus salinus sp. nov. is proposed. The type strain is XH-22T (=CCM 7562T=CECT 7439T=DSM 21756T).