- Volume 57, Issue 8, 2007

The taxonomic position of two actinomycete strains, LC2T and LC11T, isolated from a filtration substrate made from Japanese volcanic soil, was determined using a polyphasic approach. The strains grew at temperatures from 5 to 45 °C, on media of pH between 6 and 11 and in the presence of 7 % NaCl. The major menaquinone was MK-9(H4). The major fatty acid was iso-C16 : 0. A phylogenetic tree based on 16S rRNA gene sequences showed that the two strains formed a distinct evolutionary lineage within the genus Amycolatopsis. On the basis of their morphological, physiological and genotypic characteristics, the isolates are proposed to represent two novel species of the genus Amycolatopsis, for which the names Amycolatopsis echigonensis sp. nov. (type strain LC2T =IAM 15387T =CCTCC AB206019T), and Amycolatopsis niigatensis sp. nov. (type strain LC11T =IAM 15388T =CCTCC AB206020T) are proposed.

An actinomycete, designated strain GIMV4.0001T, was isolated from a forest soil sample in Vietnam. It produced white aerial mycelium and violet–blue diffusible pigment on Gause's synthetic agar. The substrate mycelium colour was not sensitive to pH. Micoscopic observations revealed that strain GIMV4.0001T produced long, straight chains of cylindrical spores, and chemotaxonomic data confirmed that it belongs to the genus Streptomyces. Melanin was produced, but no antibacterial activity was evident against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, Candida albicans or Penicillium citrinum. Analysis of the 16S rRNA gene sequence of strain GIMV4.0001T revealed that the highest similarity (99.4 %) was to Streptomyces bikiniensis ATCC 11062T. However, the DNA–DNA relatedness between strain GIMV4.0001T and S. bikiniensis ATCC 11062T was found to be 50.3 %. Strain GIMV4.0001T could also be differentiated from S. bikiniensis ATCC 11062T and other Streptomyces species showing high 16S rRNA gene sequence similarity (98–99 %) based on morphological, physiological and biochemical characteristics. On the basis of its physiological and molecular properties, it is evident that strain GIMV4.0001T represents a novel species of the genus Streptomyces, for which the name Streptomyces vietnamensis sp. nov. is proposed. The type strain is GIMV4.0001T (=CCTCC M 205143T=IAM 15340T).

A novel actinomycete, designated strain LDDC 2876-05T, was isolated from an equine placenta during the course of routine diagnostic tests for nocardioform placentitis. In a preliminary study, the strain was observed to be phylogenetically distinct from the genera Crossiella and Amycolatopsis and probably a member of the genus Lentzea. A polyphasic study of strain LDDC 2876-05T confirmed its identification as a member of Lentzea on the basis of its chemotaxonomic and morphological similarity to all of the known species of the genus. Moreover, the strain could be distinguished from other species with validly published names on the basis of its phylogenetic and physiological characteristics and its fatty acid profile. Therefore strain LDDC 2876-05T represents a novel species of the genus Lentzea, for which the name Lentzea kentuckyensis sp. nov. is proposed. The type strain is LDDC 2876-05T (=NRRL B-24416T =DSM 44909T).

Two bacterial strains, BBH6T and BBH9, were isolated from a deep-sea sediment sample collected from the Chagos Trench, Indian Ocean, at a depth of 5904 m. The two strains were closely related in their 16S rRNA gene sequences (99.7 %), belonged to one genomic species and were virtually identical at the phenotypic level. Microbacterium barkeri DSM 20145T was the nearest phylogenetic neighbour to the new isolates, with 16S rRNA gene sequence similarity levels of 97.2–97.4 %. The new isolates exhibited levels of DNA–DNA relatedness of 32–34 % to M. barkeri and differed from it in a number of phenotypic characteristics. Therefore, it is suggested that strains BBH6T and BBH9 represent a novel species of the genus Microbacterium, for which the name Microbacterium indicum sp. nov. is proposed. The type strain is BBH6T (=LMG 23459T=IAM 15355T).

A Gram-negative, yellow-coloured, non-motile, chemoheterotrophic, strictly aerobic, rod-shaped bacterium, designated IMCC1616T, was isolated from the marine polychaete Periserrula leucophryna inhabiting tidal flat sediment of the Yellow Sea, and characterized by a polyphasic approach. The temperature, pH and NaCl ranges for growth were 3–37 °C, pH 5.0–11.0 and 0.5–7.5 %. Based on 16S rRNA gene sequence similarity analyses, the strain was most closely related to members of the genera Lutibacter (90.7 %), Tenacibaculum (89.2–90.4 %) and Polaribacter (88.4–90.2 %). Phylogenetic analysis using three treeing algorithms based on 16S rRNA gene sequences indicated that the strain formed a distinct lineage within the family Flavobacteriaceae. The DNA G+C content of the strain was 40.1 mol% and the predominant cellular fatty acids were iso-C15 : 0 (16.5 %), anteiso-C15 : 0 (10.9 %), iso-C17 : 0 3-OH (8.8 %) and iso-C17 : 1 ω9c (8.2 %). The DNA G+C content, large amount of iso-C17 : 1 ω9c and several phenotypic characteristics, including growth temperature and catalase activity, differentiated the strain from other related genera in the family. Therefore, from the taxonomic evidence collected in this study, it is proposed that strain IMCC1616T represents a new genus and species named Lutimonas vermicola gen. nov., sp. nov. The type strain of Lutimonas vermicola is strain IMCC1616T (=KCCM 42379T =NBRC 102041T).

A novel bacterium designated Mok-1-85T was isolated from a marine sediment sample collected from Okinawa Island, Japan. Cells of strain Mok-1-85T stained Gram-negative, were catalase- and oxidase-positive and were non-motile. In a neighbour-joining tree based on 16S rRNA gene sequences, the novel strain clustered with the genus Flammeovirga, a member of the family ‘Flammeovirgaceae’. The novel isolate shared low 16S rRNA gene sequence similarities (≤86 %) with the members of the genus Flammeovirga and other related taxa. The major isoprenoid quinone was MK-7 and the predominant fatty acids of this organism were iso-C15 : 0, C16 : 1 ω5c and C16 : 0 3-OH. The G+C content of the DNA was 38 mol%. Combined phylogenetic and physiological data showed that strain Mok-1-85T represents a novel genus and species for which the name Sediminitomix flava gen. nov., sp. nov. is proposed. The type strain is Mok-1-85T (=NBRC 101625T=KCTC 12970T=CIP 109411T).

A novel strain, designated KP01T, belonging to the class Sphingobacteria (phylum Bacteroidetes) was isolated from soil in South Korea and was characterized taxonomically using a polyphasic approach. The strain was found to comprise Gram-negative, aerobic, non-motile, non-spore-forming rods. A phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belonged to the genus Chitinophaga but was clearly separated from established Chitinophaga species. The 16S rRNA gene sequence similarities between KP01T and type strains of established Chitinophaga species ranged from 90.3 to 95.7 %. Phenotypic and chemotaxonomic data (major menaquinone, MK-7; major fatty acids, iso-C15 : 0 and C16 : 1 ω5c; major hydroxy fatty acid, C17 : 0 iso 3-OH) supported the affiliation of strain KP01T with the genus Chitinophaga. Therefore strain KP01T represents a novel species, for which the name Chitinophaga terrae sp. nov. is proposed. The type strain is KP01T (=KCTC 12836T =LMG 24015T).

A strain isolated from pleural fluid of a patient with suppurative pleuritis (strain GTC 3021T) was characterized in terms of its phenotypic and biochemical features, cellular fatty acid profile and phylogenetic position based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the isolate was a member of the genus Prevotella. The isolate was related to Prevotella enoeca ATCC 51261T with about 92 % 16S rRNA gene sequence similarity. The strain was an obligately anaerobic, non-pigmenting, non-spore-forming, non-motile, Gram-negative rod. Although the phenotypic and biochemical characteristics of the strain were similar to those of P. enoeca JCM 12259T, the cellular fatty acid composition of the isolate was significantly different from that of P. enoeca JCM 12259T (C18 : 1 ω9c and anteiso-C15 : 0 fatty acid content). Based on these data, we propose a novel Prevotella species, Prevotella pleuritidis sp. nov., with the type strain GTC 3021T (=JCM 14110T =CCUG 54350T). The G+C content of the type strain is 45.4 mol%.

A Gram-negative, non-motile, rod-shaped and pink-pigmented bacterium, designated strain X2-1gT, was isolated from a mixture of sand samples collected from the desert of Xinjiang, China, after exposure of the sand to 8 kGy gamma radiation. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that this isolate represents a novel member of the genus Hymenobacter, with low sequence similarities (<97 %) to recognized Hymenobacter species. Biolog GN2 assays supported this conclusion. Optimum growth was observed at pH 7 and 28 °C. The strain contained MK-7 as the predominant menaquinone and the major fatty acids were iso-C15 : 0 (19.5 %), C16 : 1 ω7c/iso-C15 : 0 2-OH (20.2 %), C16 : 1 ω5c (10.6 %), C16 : 0 (6.2 %), anteiso-C17 : 1 B/iso-C17 : 1 I (8.5 %) and C18 : 0 (6.5 %). The DNA G+C content was 54 mol% (T m). On the basis of the polyphasic evidence presented, it is proposed that strain X2-1gT represents a novel species of the genus Hymenobacter, for which the name Hymenobacter xinjiangensis sp. nov. is proposed. The type strain is X2-1gT (=CCTCC AB 206080T =IAM 15452T).

A Gram-negative, non-motile, rod-shaped bacterial strain, designated CW-E 2T, was isolated from a polluted soil sample collected from Jiangsu Province, China. A taxonomic study of the isolate, including phylogenetic analysis based on 16S rRNA gene sequences and phenotypic characteristics, was carried out. The predominant menaquinone was MK-6 and the major fatty acids were i-C15 : 0, i-C17 : 0 3-OH, i-C17 : 1 ω9c and summed feature 4. The G+C content of the DNA was 37.2 mol%. Based on phenotypic and genotypic characteristics, strain CW-E 2T represents a novel species of the genus Chryseobacterium for which the name Chryseobacterium flavum sp. nov. is proposed. The type strain is CW-E 2T (=KCTC 12877T=CCTCC AB 206147T).

Two strictly anaerobic bacterial strains, KB7T and A42, were isolated from rice plant residue and living rice roots, respectively, from irrigated rice-field soil in Japan. These two strains were closely related to each other with 16S rRNA gene sequence similarity of 99.8 %. Both strains showed almost the same physiological properties. Cells were Gram-negative, non-motile, non-spore-forming rods. Growth was remarkably stimulated by the addition of haemin to the medium. The strains utilized various saccharides including xylan, xylose, pectin and carboxymethylcellulose and produced acetate and succinate with small amounts of formate and malate. The strains grew at 10–40 °C; optimum growth was observed at 30 °C and pH 5.7–6.7. Oxidase, catalase and nitrate-reducing activities were not detected. Aesculin was hydrolysed. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0, C15 : 0 and iso-C17 : 0 3-OH. Menaquinones MK-11 and MK-11(H2) were the major respiratory quinones and the genomic DNA G+C content was 39.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed both strains in the phylum Bacteroidetes. 16S rRNA gene sequence analysis showed that the most related species to both strains was Prevotella oulorum (92.8–92.9 % similarity). Prevotella veroralis and Prevotella melaninogenica were the next most closely related known species with sequence similarities of 91.9–92.4 %. Based on differences in the phylogenetic, ecological, physiological and chemotaxonomic characteristics between the two isolates and related species, it is proposed that strains KB7T and A42 represent a novel species, Prevotella paludivivens sp. nov. This is the first described Prevotella species derived from a natural habitat; all other Prevotella species are from mammalian sources. The type strain of Prevotella paludivivens is KB7T (=JCM 13650T=DSM 17968T).

A novel strain, designated Gsoil 664T, isolated from the soil of a ginseng field in South Korea, was characterized by a polyphasic approach to clarify its taxonomic position. The isolate was Gram-negative, strictly aerobic, heterotrophic, non-motile, non-spore-forming and possessed rod-shaped cells. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate formed a cluster with several uncultured bacterial clones and with the established genera Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes. However, the isolate was clearly separated from these genera: the gene sequence similarities with respect to the type strains of recognized species from closely related genera ranged from 86.7 to 90.7 %. The G+C content of the genomic DNA was 40.4 mol%. The predominant isoprenoid quinone was MK-7. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C15 : 1 and C16 : 1 ω5c. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain Gsoil 664T from recognized species of related genera. On the basis of the polyphasic evidence, Gsoil 664T represents a novel genus and species, for which the name Segetibacter koreensis gen. nov., sp. nov. is proposed. The type strain of S. koreensis is Gsoil 664T (=KCTC 12655T=DSM 18137T).

Two strains (Gsoil 492T and Gsoil 643T) isolated in Pocheon Province, South Korea, from soil used for ginseng cultivation were characterized using a polyphasic approach. Both isolates comprised Gram-negative, aerobic, non-motile, rod-shaped bacteria. They had similar chemotaxonomic characteristics, e.g. containing MK-7 as the major quinone, having a DNA G+C content in the range 42.5–43.3 mol% and possessing iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. A phylogenetic analysis based on 16S rRNA gene sequences indicated that the two isolates formed a tight cluster with several uncultured bacterial clones and with the established genera Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes but were clearly separate from these genera. The levels of 16S rRNA gene sequence similarity between the isolates and type strains of related genera ranged from 87.5 to 92.4 %. Furthermore, the results of physiological and biochemical tests allowed phenotypic differentiation of the isolates from phylogenetically closely related species with validly published names. The level of 16S rRNA gene sequence similarity between the two strains was 99.5 %, whereas the DNA–DNA relatedness value was 44 %, indicating that they represent separate species. On the basis of the polyphasic evidence, a novel genus, Flavisolibacter gen. nov., and two novel species, Flavisolibacter ginsengiterrae sp. nov. (type strain Gsoil 492T=KCTC 12656T=DSM 18136T) and Flavisolibacter ginsengisoli sp. nov. (type strain Gsoil 643T=KCTC 12657T=DSM 18119T), are proposed. Flavisolibacter ginsengiterrae is the type species of the genus.

Three isolates obtained from grass samples were investigated by means of a polyphasic taxonomic study and were shown to represent a novel species within the genus Chryseobacterium. Comparison of 16S rRNA gene sequences and phenotypic features indicated that the three isolates belonged to a single species. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic neighbours were Chryseobacterium shigense and Chryseobacterium vrystaatense, which formed a stable cluster with the isolates; this phylogeny was supported by a high bootstrap value and was obtained using different treeing methods. A DNA–DNA hybridization study with the closest neighbour, C. shigense DSM 17126T (98.3 % 16S rRNA gene sequence similarity), clearly demonstrated a separate species status for the grass isolate strain P 456/04T. Comparisons involving physiological properties and whole-cell fatty acid profiles confirmed this result at the phenotypic level. On the basis of these results, strain P 456/04T represents a novel species of the genus Chryseobacterium, for which the name Chryseobacterium luteum sp. nov. is proposed. The type strain is P 456/04T (=DSM 18605T =LMG 23785T).

A pink-coloured bacterial strain, 5516J-15T, was isolated from an air sample from Jeju Island, Republic of Korea. The organism was found to have resistance to UV radiation typical of members of the genus Deinococcus, and it was placed within the radiation of the Deinococcus on a phylogenetic tree based on 16S rRNA gene sequences. Strain 5516J-15T shared low 16S rRNA gene sequence similarity (84.5–87.8 %) with Deinococcus species, showing highest sequence similarity to Deinococcus deserti VCD115T (87.8 %) and Deinococcus indicus Wt/1aT (87.8 %). Strain 5516J-15T had type A3β peptidoglycan with l-ornithine, menaquinone 8 (MK-8) as the major quinone and iso-C12 : 0, anteiso-C13 : 0, iso-C16 : 0 and C16 : 0 as the major fatty acids. Its polar lipid profile contained three unknown aminophospholipids, two unknown polar lipids, one unknown phospholipid and one unknown glycolipid. The DNA G+C content of strain 5516J-15T was 61.3 mol%. Based on the phylogenetic and phenotypic data presented, it is proposed that the unknown strain should be classified within a novel species in the genus Deinococcus with the name Deinococcus cellulosilyticus sp. nov. The type strain is 5516J-15T (=KACC 11606T =DSM 18568T).

Three pink-pigmented, facultatively methylotrophic strains, designated MP1, MP2 and MRT, were isolated from seawater from southern China and characterized. Analysis of their complete 16S rRNA gene sequences revealed that they constituted three separate phylogenetic groups, showing the highest levels of similarity with respect to some members of the genus Methylobacterium. PCR amplification also showed the gene coding for the α-subunit of methanol dehydrogenase (mxaF) to be present in all strains, indicating a methylotrophic metabolism. All three strains utilized d-fructose, ethanol and nutrient agar as carbon sources, but did not utilize sucrose, citrate, acetate or formaldehyde. On the basis of the phenotypic, phylogenetic and genotypic analyses, strain MRT represents a novel species, for which the name Methylobacterium salsuginis sp. nov. is proposed, with MRT (=CGMCC 1.6474T =NCCB 100140T) as the type strain. Strains MP1 and MP2 respectively represent novel strains of the species Methylobacterium oryzae and Methylobacterium lusitanum.

An aerobic and heterotrophic, Gram-negative bacterial isolate, strain HY34T, was isolated from sediment of an oilfield in the South China Sea, China. The taxonomy of strain HY34T was studied by phenotypic and phylogenetic methods. Strain HY34T formed faint-pink colonies on marine agar 2216. Cells of strain HY34T were non-motile, ovoid or short rods. Strain HY34T was positive for catalase and oxidase, and nitrate was reduced to nitrite. The nearly complete 16S rRNA gene sequence of strain HY34T was obtained and sequence analysis showed that it, together with the genus Rubellimicrobium, formed a distinct clade close to some members of the Roseobacter clade in the family Rhodobacteraceae, and it showed highest sequence similarities to Oceanicola granulosus HTCC2516T (93.8 %), Silicibacter lacuscaerulensis ITI-1157T (93.3 %), Dinoroseobacter shibae DFL 12T (93.3 %) and Rubellimicrobium thermophilum C-lvk-R2A-2T (92.2 %). Bacteriochlorophyll a was not detected. The ubiquinone system was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. The major fatty acids (>10 %) were C18 : 1 ω7c and C16 : 0. The DNA G+C content of this strain was 69.4 mol%. A polyphasic analysis supported the conclusion that this strain represents a novel genus and species, which we designated Wenxinia marina gen. nov., sp. nov. The type strain of Wenxinia marina is HY34T (=CGMCC 1.6105T =JCM 14017T).

A novel strain, designated 5715S-12T, was isolated from an air sample collected from Suwon region, Republic of Korea, using R2A medium. The cells were strictly aerobic, Gram-negative, motile, short rods. Comparison of the 16S rRNA gene sequence of strain 5715S-12T showed the highest sequence similarities to Aurantimonas altamirensis S21BT (95.9 %) and Aurantimonas coralicida WP1T (95.4 %). Phylogenetic trees indicated that the strain formed a cluster with members of the family Aurantimonadaceae (A. altamirensis, A. coralicida and Fulvimarina pelagi). The major fatty acid was C18 : 1 ω7c. The predominant isoprenoid quinone was ubiquinone 10 (Q-10). Diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, phosphatidyldimethylethanolamine, phosphatidylglycerol, phosphatidylcholine and four unknown lipids were found as the polar lipid components. The DNA G+C content was 67.0 mol%. On the basis of the phenotypic and phylogenetic features studied, we propose that strain 5715S-12T be assigned to a novel species of the genus Aurantimonas, for which the name Aurantimonas ureilytica sp. nov. (type strain 5715S-12T =KACC 11607T =DSM 18598T) is proposed.