- Volume 61, Issue 3, 2011

Strain M1-8T was isolated from jeotgal, a Korean salt-fermented food. Cells were aerobic, non-motile, Gram-reaction-positive and rod-shaped. Colonies were cream-coloured and circular with entire margins. Strain M1-8T exhibited optimal growth at 25–30 °C and pH 7.0–8.0 and in 0–4 % (w/v) NaCl. The strain tolerated up to 10.0 mM Cr(VI). Phylogenetic analyses of 16S rRNA gene sequences indicated that strain M1-8T represents a novel species in the genus Leucobacter. The 16S rRNA gene sequence of M1-8T exhibited 98.1 % similarity to that of Leucobacter chromiireducens subsp. chromiireducens L-1T. The new isolate was clustered with Leucobacter species on a 16S rRNA gene sequence-based phylogenetic tree. The chromosomal DNA G+C content of strain M1-8T was 62.8 mol%. Its cell-wall peptidoglycan contained 2,4-diaminobutyric acid, glutamic acid, alanine, glycine and γ-aminobutyric acid. The major menaquinone was MK-11 and the predominant fatty acids were anteiso-C15 : 0 (63.6 %), anteiso-C17 : 0 (16.7 %) and iso-C16 : 0 (14.2 %). The polar lipid profile of strain M1-8T contained diphosphatidylglycerol and one unknown glycolipid. Significant genotypic and phenotypic differences were found between strain M1-8T and other Leucobacter species. These differentiating characteristics indicate that strain M1-8T represents a novel species of the genus Leucobacter, for which the name Leucobacter salsicius sp. nov. is proposed. The type strain is M1-8T (=KACC 21127T =JCM 16362T).

An actinomycete, designated strain GIMN4.002T, was isolated from a tomato rhizosphere soil sample in Guangzhou, China. The strain produces white aerial mycelium and dark blue diffusible pigment on Gause's synthetic agar, and microscopic observation revealed that it produces looped chains of spiny spores. Morphological and chemotaxonomic characteristics of the strain are typical of the genus Streptomyces. Melanin was produced and antibacterial activity was detected against Gram-positive micro-organisms, such as Bacillus subtilis, Micrococcus luteus and Staphylococcus aureus. The 16S rRNA gene sequence of strain GIMN4.002T had highest similarity (99.4 %) to Streptomyces lincolnensis B91; however, DNA–DNA relatedness between strain GIMN4.002T and S. lincolnensis NBRC 13054T was only 32.17 %. Further, the morphological, physiological and biochemical characteristics of strain GIMN4.002T are distinct from S. lincolnensis and other species of the genus Streptomyces with which this strain has high 16S rRNA gene sequence similarity (98–99 %). On the basis of the physiological and molecular properties observed, it is proposed that strain GIMN4.002T represents a novel species of the genus Streptomyces, for which the name Streptomyces caeruleatus sp. nov. is proposed, with GIMN4.002T (=CCTCC M 208213T =NRRL B-24802T) as the type strain.

A Gram-positive, non-motile, non-spore-forming, aerobic, coccoid-shaped bacterium, designated BXN5-13T, was isolated from the soil of a ginseng field from Baekdu Mountain in Jilin district, China. Strain BXN5-13T grew optimally at 30 °C and pH 6.5–7.5 with 0–2 % (w/v) NaCl. Strain BXN5-13T had β-glucosidase activity that was connected with ginsenoside-converting ability, so that it was able to convert ginsenoside Rb1 to ginsenoside F2. On the basis of 16S rRNA gene sequence analysis, the closest phylogenetic relatives of strain BXN5-13T were Phycicoccus aerophilus 5516T-20T (98.4 % 16S rRNA gene sequence similarity), P. bigeumensis MSL-03T (98.3 %), P. dokdonensis DS-8T (97.9 %) and P. jejuensis KSW2-15T (96.9 %). Lower sequence similarity (<97.0 %) was found with the type strains of other recognized species of the family Intrasporangiaceae. The predominant quinone was MK-8(H4). The major fatty acids (>10 %) were iso-C15 : 0, C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The chemotaxonomic data and the high genomic DNA G+C content of strain BXN5-13T (70.8 mol%) supported its affiliation with the genus Phycicoccus. DNA–DNA relatedness between strain BXN5-13T and its closest phylogenetic neighbours was below 16 %. Strain BXN5-13T represents a novel species within the genus Phycicoccus, for which the name Phycicoccus ginsenosidimutans sp. nov. is proposed. The type strain is BXN5-13T (=KCTC 19419T=DSM 21006T=LMG 24462T).

An orange bacterial strain, designated G5T, was isolated during the study of the bacterial diversity of a coal mine. The cell wall of strain G5T contained peptidoglycan type A4α (l-Lys–Gly–l-Glu) and the sugars xylose and mannose. The major menaquinones were MK-8 (45.0 %) and MK-9 (34.0 %) and minor amounts of MK-7 and MK-8(H2) were also found. The major fatty acids were anteiso-C15 : 0 (44.9 %) and iso-C15 : 0 (44.2 %). The main cellular polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. 16S rRNA gene sequence analysis showed that strain G5T was closely related to Yaniella halotolerans YIM 70085T and Yaniella flava YIM 70178T (both 96.7 % 16S rRNA gene sequence similarity). The genomic DNA G+C content of strain G5T was 61.6 mol%. These data and other phenotypic characteristics clearly indicated that strain G5T represents a novel species of the genus Yaniella, for which the name Yaniella fodinae sp. nov. is proposed. The type strain is G5T (=MTCC 9846T=DSM 22966T).

Three Gram-positive, rod-shaped bacterial strains were isolated from the drinking water supply system of the Hungarian capital, Budapest. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparison revealed that the isolates represented a distinct cluster within the clade of the genus Nocardioides and were most closely related to Nocardioides pyridinolyticus OS4T, Nocardioides aquiterrae GW-9T, Nocardioides sediminis MSL-01T and N. hankookensis DS-30T. The peptidoglycan based on ll-2,6-diaminopimelic acid, the major menaquinone MK-8(H4), the cellular fatty acid profile with iso-C16 : 0 and anteiso-C17 : 0 as predominating components and the DNA G+C content of 71.4 mol% (strain 1RaM5-12T) were consistent with the affiliation of the isolates to the genus Nocardioides. Because of differences in physiological characteristics, matrix-assisted laser-desorption/ionization time-of-flight mass spectra of protein extracts, PvuII RiboPrinter patterns and 96.1 % 16S rRNA gene sequence similarity between strain 1RaM5-12T and its closest phylogenetic neighbour, N. pyridinolyticus OS4T, a novel species, Nocardioides hungaricus sp. nov., is proposed. The type strain is 1RaM5-12T (=DSM 21673T =NCAIM 02330T).

A Gram-positive, aerobic, non-motile actinobacterium, designated strain 6014T, was isolated from a soil sample collected from Qinghai province, north-west China, and subjected to a polyphasic taxonomic study. The isolate formed elementary branching hyphae and abundant aerial mycelia with globose sporangia on ISP 4 and R2A media. Whole-cell hydrolysates of strain 6014T contained arabinose, galactose and ribose as diagnostic sugars and meso-diaminopimelic acid as the diagnostic diamino acid. The polar lipids consisted of phosphatidylmethylethanolamine, phosphatidylethanolamine, hydroxy-phosphatidylethanolamine, N-acetylglucosamine-containing phospholipids, two unknown phospholipids and an unknown glycolipid. The menaquinone system contained MK-9(H2) and MK-9(H4). The major fatty acids were C14 : 0, i-C15 : 0, C16 : 0 and 10-methyl-C16 : 1. The genomic DNA G+C content of the isolate was 69.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 6014T fell within the radius of the suborder Streptosporangineae, in which the strain formed a distinct lineage next to genera of the family Streptosporangiaceae. Based on data from this polyphasic study, strain 6014T can be readily distinguished from previously described organisms and represents a member of a novel species within a new genus in the suborder Streptosporangineae. The name Sinosporangium album gen. nov., sp. nov. is proposed with 6014T (=DSM 45181T =KCTC 19655T) as the type strain.

Two actinomycete strains, CM9-9T and AK2-48, which produced straight rod-shaped, non-motile cells, were isolated from soils in Chiang Mai and Phuket provinces, respectively, Thailand. The morphological and chemotaxonomic characteristics of the isolates coincided with those of the genus Agromyces. Phylogenetic analysis using 16S rRNA gene sequences also indicated that the isolates were clearly separated from their closest relative, Agromyces aurantiacus YIM 21741T, and should be classified in the genus Agromyces. Furthermore, a combination of DNA–DNA hybridization results and physiological and biochemical properties indicated that the isolates could be distinguished from all recognized members of the genus Agromyces. The isolates therefore represent a novel species, for which the name Agromyces tropicus sp. nov. is proposed. The type strain is CM9-9T (=JCM 15672T =BCC 34764T).

A filamentous actinomycete, designated strain CCNWNQ 0016T, was isolated from soil from a zinc and copper mine in Shaanxi province, north-western China. A polyphasic taxonomic study was carried out to establish the status of strain CCNWNQ 0016T. Chemical and morphological properties of the isolate were similar to those of species of the genus Streptomyces. Analysis of the almost complete 16S rRNA gene sequence placed strain CCNWNQ 0016T in the genus Streptomyces where it formed a distinct phyletic line with recognized species of this genus. The strain exhibited highest sequence similarities to Streptomyces niveoruber NBRC 15428T (98.8 %), Streptomyces griseoviridis NBRC 12874T (98.7 %) and Streptomyces aurantiogriseus NBRC 12842T (98.7 %). Furthermore, DNA–DNA hybridization studies between the novel isolate and these three strains showed relatedness values of 49.6±0.6, 47.2±0.9 and 46.9±1.1 %, respectively. A number of phenotypic properties also enabled the isolate to be differentiated from related species of the genus Streptomyces. Therefore, it is proposed that strain CCNWNQ 0016T (=K42T =ACCC 41871T =HAMBI 3107T) should be classified as the type strain of a novel species in the genus Streptomyces, Streptomyces zinciresistens sp. nov. The maximum level of resistance to Zn2+ for strain CCNWNQ 0016T is 35 mM.

A thermotolerant, Gram-stain-positive, aerobic, sporangium-forming actinomycete, strain RA45T, was isolated from a desert region in Xinjiang Uigur Autonomous Region, north-western China. Comparative analysis of the 16S rRNA gene sequence and phenotypic characterization revealed that strain RA45T belonged phylogenetically to the family Pseudonocardiaceae of the suborder Pseudonocardineae. Strain RA45T showed more than 5 % 16S rRNA gene sequence divergence from recognized species of genera in the family Pseudonocardiaceae, forming a distinct lineage within the evolutionary radiation occupied by the genera Amycolatopsis, Prauserella, Thermocrispum, Saccharomonospora, Saccharopolyspora and Sciscionella, but distinct from each of them. The affiliation to the family was supported by the presence of suborder- and family-specific 16S rRNA signature nucleotides, a DNA G+C content of 69.9 mol%, the presence of meso-diaminopimelic acid, ribose, arabinose, glucose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes, the presence of menaquinone MK-9(H4) as the major respiratory lipoquinone, a lack of mycolic acids and the presence of an N-acetylated type of muramic acid. However, strain RA45T differed from known genera of the family in its polar lipid composition: the major phospholipids were phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylmethylethanolamine, diphosphatidylglycerol, phospholipids of unknown structure and phospholipids of unknown structure containing glucosamine (phospholipid type IV). Based on its morphological, chemotaxonomic and phylogenetic characteristics, strain RA45T is considered to represent a novel species of a new genus in the family Pseudonocardiaceae, for which the name Yuhushiella deserti gen. nov., sp. nov. is proposed. The type strain of Yuhushiella deserti is RA45T (=CGMCC 4.5579T =JCM 16584T).

A novel strain of the class Actinobacteria was isolated from a seawater sample collected in the South China Sea using modified R2A agar plates. The strain was a Gram-stain-positive, non-motile, non-spore-forming, catalase-positive, irregular rod-shaped bacterium. The strain grew at 4–45 °C and pH 5.0–10.2, and tolerated 5 % (w/v) NaCl. Based on its 16S rRNA gene sequence, the organism was related phylogenetically to members of the genera Fodinibacter (96.7 % similarity), Lapillicoccus (96.5 %), Knoellia (95.0–95.8 %), Oryzihumus (95.6 %) and Humibacillus (95.6 %). The cell-wall contained l-ornithine as the major diagnostic diamino acid in the peptidoglycan. MK-8(H4) was the predominant menaquinone. Major cellular fatty acids were iso-C18 : 1 ω9c, iso-C16 : 0, iso-C15 : 0 and C17 : 0. The G+C content of the DNA was 69.6 mol%. Phenotypic and phylogenetic data revealed that this strain represents a novel species in a new genus of the family Intrasporangiaceae, for which the name Ornithinibacter aureus gen. nov., sp. nov. is proposed; the type strain of Ornithinibacter aureus is HB09001T (=CGMCC 1.10341T =DSM 23364T).

Two bacterial strains, designated Sa 1147-06T and Sa 1143-06, were isolated from Atlantic salmon (Salmo salar) farmed in Lake Chapo, Chile, and were studied using a polyphasic approach. Both isolates were very similar; cells were rod-shaped, formed yellow-pigmented colonies and were Gram-reaction-negative. Based on 16S rRNA gene sequence analysis, strains Sa 1147-06T and Sa 1143-06 shared 100 % sequence similarity and showed 98.9 and 97.5 % sequence similarity to Chryseobacterium jeonii AT1047T and Chryseobacterium antarcticum AT1013T, respectively. Sequence similarities to all other members of the genus Chryseobacterium were below 97.3 %. The major fatty acids of strain Sa 1147-06T were iso-C13 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 1 ω9c, with iso-C15 : 0 3-OH, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH constituting the major hydroxylated fatty acids. DNA–DNA hybridizations with C. jeonii JMSNU 14049T and C. antarcticum JMNSU 14040T gave relatedness values of 20.7 % (reciprocal 15.1 %) and 15.7 % (reciprocal 25.7 %), respectively. Together, the DNA–DNA hybridization results and differentiating biochemical properties showed that strains Sa 1147-06T and Sa 1143-06 represent a novel species, for which the name Chryseobacterium chaponense sp. nov. is proposed. The type strain is Sa 1147-06T (=DSM 23145T =CCM 7737T).

Three bacterial strains, designated CCUG 51397T, CCUG 53736 and CCUG 53920, isolated from water samples taken at different locations in southern Sweden were studied to determine their taxonomic position using a polyphasic approach. Comparative analysis of 16S rRNA gene sequences showed that these bacteria had <93 % sequence similarity to all described species of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Chitinophaga. The three organisms grouped most closely with Sediminibacterium salmoneum NJ-44T but showed only 92.5 % sequence similarity to this strain, the only recognized species of this genus. The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G with smaller amounts of iso-C15 : 0 3-OH, iso-C16 : 0 3-OH and other fatty acids, which differentiated the novel strains from related genera. Biochemical tests performed on strains CCUG 51397T, CCUG 53736 and CCUG 53920 also gave different results from those of Sediminibacterium salmoneum NJ-44T and other related genera. Based on this evidence, strains CCUG 51397T, CCUG 53736 and CCUG 53920 represent a novel species of a new genus, for which the name Hydrotalea flava gen. nov., sp. nov. is proposed. The type strain of Hydrotalea flava is CCUG 51397T (=CCM 7760T). A formal allocation of the genera Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Chitinophaga to the family Chitinophagaceae fam. nov. is also proposed.

A rod-shaped, endospore-forming, Gram-reaction-variable bacterial strain, designated WPCB173T, was isolated from freshwater collected from the Woopo wetland, Republic of Korea. Based on its phenotypic characteristics and phylogenetic position inferred from 16S rRNA gene sequence analysis, the isolate was identified as being a member of the genus Paenibacillus. Major polar lipids present in strain WPCB173T included phosphatidylethanolamine and several unidentified phospholipids. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C15 : 0 (65.2 %). The DNA G+C content was 48.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WPCB173T clustered with species of the genus Paenibacillus, its closest neighbours being Paenibacillus chinjuensis WN9T (96.7 %) and Paenibacillus soli DCY03T (96.4 %). DNA–DNA hybridization of strain WPCB173T with P. soli DCY03T and P. chinjuensis WN9T showed relatedness values of only 10 and 19 %, respectively. On the basis of the phenotypic and phylogenetic evidence, strain WPCB173T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus rigui sp. nov. is proposed. The type strain of the novel species is WPCB173T (=KCTC 13282T =JCM 16352T).

Two novel thermophilic micro-organisms, designated YMO81T and YMO722T, were isolated from a high-temperature compost (internal temperature >95 °C). The isolates were able to grow at 80 °C in a nutrient broth and in a synthetic medium. Cells were aerobic, Gram-negative rods (0.3×4.0 μm). Spore formation was not observed. Strain YMO81T grew at 83 °C and pH 6.9–8.9 and grew optimally at 78 °C and pH 7.5 with 2 % NaCl. For growth in a synthetic minimal medium at 70 °C, the vitamins biotin, folic acid and thiamine and the amino acids glutamine and methionine were essential for growth of both strains; at 80 °C, strain YMO81T also required histidine, isoleucine, leucine, lysine, phenylalanine, serine, tryptophan and valine. Cellular fatty acids of the isolates comprised mainly iso-C17 : 0 and anteiso-C17 : 0. The DNA G+C contents of strains YMO81T and YMO722T were 70 and 64 mol%, respectively. When the 16S rRNA gene sequences of the isolates were compared with those of other bacteria, highest similarity was observed with Planifilum yunnanense LA5T (90 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain YMO722T and strain YMO81T was 55 %. N 4-Aminopropylspermine was identified as a major polyamine, which suggested that the isolates were distinct from other related taxa. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, we propose a new genus, Calditerricola gen. nov., and two novel species, the type species Calditerricola satsumensis sp. nov., with type strain YMO81T (=ATCC BAA-1462T =JCM 14719T =DSM 45223T), and Calditerricola yamamurae sp. nov., with type strain YMO722T (=ATCC BAA-1461T =JCM 14720T =DSM 45224T).

A strictly thermophilic anaerobe, designated strain VF08T, was isolated from a water sample collected from a Great Artesian Basin bore (registered bore number 22981) situated at Mitchell, QLD, Australia. Cells of isolate VF08T were slightly curved, non-sporulating rods (1.5–3.5×0.4–0.8 μm), which stained Gram-negative but possessed a Gram-positive cell-wall ultrastructure. The strain grew optimally in tryptone-yeast extract-glucose (TYEG) medium at 55 °C (temperature growth range between 37 and 60 °C) and a pH of 7 (pH growth range, 6.0–9.0). Yeast extract or tryptone was required for growth on glucose, fructose, xylose, maltose, sucrose, raffinose, cellobiose, ribose, pyruvate, tryptone, peptone, Casamino acids, amyl media and serine, but could also support growth as the sole carbon source. End products from glucose fermentation were acetate, ethanol, CO2 and H2. The strain reduced vanadium(V), but not iron(III), manganese(IV), elemental sulfur, sulfate, thiosulfate, sulfite, nitrate or nitrite in the presence of 0.2 % yeast extract, peptone, tryptone, glucose, sucrose and Casamino acids, but an increase in the growth rate or cell yield was not observed. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin and ≥2 % NaCl (w/v). The G+C content of the DNA was 38.4±0.8 mol% as determined by the thermal denaturation (T m) method. 16S rRNA gene sequence analysis revealed that isolate VF08T was a member of the genus Caloramator with Caloramator australicus and Caloramator fervidus (formerly Clostridium fervidus) being the closest relatives with similarity values of 85.0 and 86.1 %, respectively, when helix 6 nucleotides were included in the analysis, and 95.2 % and 94 %, respectively, when these nucleotides were masked from the analysis. Further analysis revealed that strain VF08T formed an individual cluster (cluster II) within the genus Caloramator and could be distinguished from other species within the genus Caloramator (clusters I, III and IV) on the basis of signature nucleotides and differences in phenotypic traits. These data suggest that strain VF08T is a novel species of the genus Caloramator, for which the name Caloramator mitchellensis sp. nov. is proposed. The type strain is VF08T (=JCM 15828T=KCTC 5735T). An emended description of the genus Caloramator is also provided.

Strain S5T, a novel bacterium that was isolated for its capability to respire selenate to elemental selenium, is described. In addition to selenate respiration, it was also capable of dissimilatory selenite, arsenate and nitrate reduction with short-chain organic acids such as pyruvate, lactate and acetate as the carbon sources and electron donors. The isolate was unable to grow fermentatively. Strain S5T was isolated from sediment of an estuarine canal in Chennai, India. Phylogenetic analysis of the 16S rRNA gene of this novel isolate revealed that it belonged to the family Chrysiogenaceae with sequence similarities of 92 and 98 %, respectively, with the type strains of Chrysiogenes arsenatis and Desulfurispirillum alkaliphilum, its closest known relatives. Strain S5T and D. alkaliphilum were closely related in terms of their 16S rRNA gene phylogeny; however, they varied greatly in their genomic DNA G+C content (56 mol% versus 45 mol%) and cellular fatty acid compositions, as well as in many metabolic capabilities. Strain S5T represents a novel species for which the name Desulfurispirillum indicum sp. nov. is proposed; the type strain is S5T (=DSM 22839T =ATCC BAA-1389T).

The taxonomic position of a Gram-stain-positive, rod-shaped, endospore-forming, facultatively anaerobic bacterial strain, CAU 9324T, isolated from a grassy sandbank was investigated by using a polyphasic approach. Strain CAU 9324T grew optimally at 30 °C and pH 6.0. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major isoprenoid quinone was menaquinone-7 (MK-7). The polar lipid profile consisted of diphosphatidylglycerol as the major component. The predominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content of strain CAU 9324T was 48.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain belonged to the genus Paenibacillus, showing <96.4 % similarity to the type strains of all recognized Paenibacillus species. On the basis of phenotypic, chemotaxonomic and genotypic data, strain CAU 9324T was considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus puldeungensis sp. nov. is proposed. The type strain is CAU 9324T (=KCTC 13718T =CCUG 59189T).