- Volume 60, Issue 3, 2010

A Gram-positive, neutrophilic, non-motile and non-spore-forming actinobacterium, strain FS24T, was isolated from a bioreactor treating salt-containing wastewater. This isolate grew in the presence of 0–15 % (w/v) NaCl and at 10-37 °C. The optimum NaCl concentration for growth of FS24T was 5 % (w/v) at 37 °C or 1 % (w/v) at 25 °C. Chemotaxonomic analysis revealed MK-9(H2) as the predominant menaquinone and the major cellular polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, four unknown glycolipids, two unknown phospholipids and an unknown lipid. The major fatty acids were anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. The genomic DNA G+C content was 66.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain FS24T clustered with members of the genus Citricoccus, exhibiting high sequence similarity to the 16S rRNA gene sequences of the type strains of Citricoccus alkalitolerans (98.9 %) and Citricoccus muralis (98.8 %), respectively. The DNA–DNA relatedness values of strain FS24T to C. alkalitolerans DSM 15665T and C. muralis DSM 14442T were 54 and 39 %, respectively. On the basis of phenotypic and genotypic data, strain FS24T represents a novel species of the genus Citricoccus, for which the name Citricoccus zhacaiensis sp. nov. is proposed. The type strain is FS24T (=CGMCC 1.7064T =JCM 15136T).

A Gram-positive, yellow-pigmented, branched-hyphae-forming micro-organism, strain 09-Be-007T, was isolated from the wall of an indoor environment. Based on 16S rRNA gene sequence similarity studies, strain 09-Be-007T belonged to the genus Promicromonospora. The novel isolate showed sequence similarities of 98.8 % to Promicromonospora aerolata V54AT, 98.9 % to Promicromonospora vindobonensis V45T, 98.1 % to Promicromonospora sukumoe DSM 44121T, 98.2 % to Promicromonospora kroppenstedtii RS16T, 96.7 % to Promicromonospora flava CC 0387T and 97.8 % to Promicromonospora citrea DSM 43110T, the type strain of the type species of this genus. Cell wall sugars of strain 09-Be-007T were galactose, rhamnose and glucose. The diagnostic diamino acid of the cell-wall peptidoglycan was lysine. The major menaquinones detected were MK-9(H4) and MK-9(H6). Major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. Major fatty acids were iso-C15 : 0 and anteiso-C15 : 0; moderate amounts of anteiso-C17 : 0, iso-C16 : 0 and iso-C15 : 1 were also found. All these data supported the affiliation of strain 09-Be-007T to the genus Promicromonospora. DNA–DNA hybridization values and physiological and biochemical data enabled strain 09-Be-007T to be differentiated genotypically and phenotypically from the six recognized species of the genus Promicromonospora. For these reasons, strain 09-Be-007T represents a novel species, for which the name Promicromonospora umidemergens sp. nov. is proposed, with 09-Be-007T (=DSM 22081T=CCM 7634T) as the type strain.

A novel endophytic actinomycete, strain GMKU 931T, was isolated from the root of a wattle tree, Acacia auriculiformis A. Cunn. ex Benth., collected at Kasetsart University, Bangkok, Thailand. Strain GMKU 931T produced short spiral chains of smooth-surfaced spores on the aerial mycelium. Lysine and meso-diaminopimelic acid were present in the cell-wall peptidoglycan. Whole-cell hydrolysates contained galactose, madurose and mannose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major fatty acids were iso-C16 : 0 and iso-C16 : 1. The major phospholipids were phosphatidylinositol and phosphatidylglycerol. A phylogenetic analysis based on 16S rRNA gene sequences suggested that strain GMKU 931T forms a distinct phyletic line within the recently proposed genus Actinoallomurus. The significant differences in phenotypic and genotypic data indicate that strain GMKU 931T represents a novel species of the genus Actinoallomurus, for which the name Actinoallomurus acaciae sp. nov. is proposed. The type strain is GMKU 931T (=BCC 28622T =NBRC 104354T =NRRL B-24610T).

A novel actinobacterial strain, MN07-A0370T, was isolated from Mongolian soil and its taxonomic status was determined using a polyphasic approach. Comparative 16S rRNA gene sequence studies revealed that strain MN07-A0370T represented a novel lineage within the actinobacteria. Strain MN07-A0370T formed a distinct clade in the family Dermacoccaceae and was most closely related to the members of the genera Dermacoccus (16S rRNA gene sequence similarity, 96.2 %–96.4 %), Demetria (94.1 %) and Kytococcus (93.7 %). The cell-wall peptidoglycan of the novel strain contained l-lysine, alanine, aspartic acid, glutamic acid and serine and represented peptidoglycan type A4α. The menaquinones were MK-8(H4) and MK-8(H6). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol and the whole-cell sugars were galactose, mannose, rhamnose, ribose and glucose. Mycolic acids were absent. The fatty acid profile was characterized by the presence of large amounts of saturated iso- and anteiso-branched-chain fatty acids as well as smaller amounts of saturated straight-chain and unsaturated acids. The major fatty acids were iso-C16 : 0, anteiso-C17 : 0, iso-C16 : 1 H, C17 : 1 ω9c and C17 : 0 10-methyl. The G+C content of the DNA was 68.2 mol%. On the basis of chemotaxonomic, physiological and biochemical differences from other genera of the family Dermacoccaceae, strain MN07-A0370T should be classified as representing a novel species in a new genus, for which we propose the name Luteipulveratus mongoliensis gen. nov., sp. nov. The type strain is MN07-A0370T (=NBRC 105296T=VTCC D9-09T).

Two novel actinomycetes, designated DQS3-9A1T and DQS3-9A2, were isolated from a saline soil contaminated with crude oil in the Shengli Oilfield in China. On the basis of 16S rRNA gene sequence analysis, the two strains were most closely related to Mycobacterium species (92.7–94.9 % similarities), and formed a distinct lineage in the suborder Corynebacterineae. In addition, the major sugars in the cell wall, arabinose and galactose, supported the affiliation of strain DQS3-9A1T with members of the family Mycobacteriaceae. However, strain DQS3-9A1T did not contain mycolic acids and MK-8 (85.5 %) was the major menaquinone for both isolates. The major cellular fatty acids for strain DQS3-9A1T were C16 : 0 (20.5 %), 10-methyl C17 : 0 (19.3 %), 10-methyl C18 : 0 (16.1 %), summed feature 3 (11.4 %), C15 : 0 (11.3 %), C17 : 0 (5.0 %) and C17 : 1 ω8c (5.0 %). The polar lipids of strain DQS3-9A1T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unknown glucosamine-containing phospholipid. These chemotaxonomic data indicated that strain DQS3-9A1T differs from the present members of the suborder Corynebacterineae. Therefore, the creation of Amycolicicoccus subflavus gen. nov., sp. nov. is proposed, with DQS3-9A1T (=DSM 45089T=CGMCC 4.3532T) as the type strain.

Two actinomycete strains, JSM1-1T and JSM1-3, were isolated from sea sand collected in Thailand. Their taxonomic position was determined using a polyphasic approach. The chemotaxonomic characteristics of these strains coincided with those of the genus Micromonospora, i.e. the presence of meso-diaminopimelic acid and N-glycolyl muramic acid in the peptidoglycan, whole cell sugar pattern D, phospholipids type II, and cellular fatty acid type 3b. Phylogenetic analysis of 16S rRNA gene sequences revealed a close relationship between strains JSM1-1T and JSM1-3 (99.8 %), and between JSM1-1T and Micromonospora aurantiaca JCM 10878T (99.3 %), Micromonospora chalcea JCM 3031T (99.0 %), and Micromonospora coxensis JCM 13248 T (99.0 %). However, strains JSM1-1T and JSM1-3 could be clearly distinguished from these type strains by a low DNA–DNA relatedness and by phenotypic differences. On the basis of the data presented, a new species, Micromonospora marina sp. nov., is proposed. The type strain is JSM1-1T (=JCM 12870T =PCU 269T =TISTR 1566T).

A Gram-stain-positive, coccoid, non-motile, halotolerant actinobacterium, designated YIM 45900T, was found as a contaminant on an agar plate in the laboratory of Yunnan Institute of Microbiology, China. The peptidoglycan type was A4α with an l-Lys–l-Ser–d-Asp interpeptide bridge. The cell-wall sugars contained galactose and fucose. The predominant menaquinone was MK-8(H4). The major fatty acids were iso-C15 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The polar lipids contained diphosphatidylglycerol, phosphatidylinositol, a glucosamine-containing phospholipid and an unknown phospholipid. The DNA G+C content was 65.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the organism falls within the radius of the suborder Micrococcineae and its closest phylogenetic neighbours are the genera of the family Dermacoccaceae. Strain YIM 45900T showed 16S rRNA gene sequences similarity values of 93.1–95.9 % with members of the genera Dermacoccus, Demetria and Kytococcus. On the basis of the phylogenetic and phenotypic characteristics of the actinobacterium, a novel genus and species, Yimella lutea gen. nov., sp. nov., are proposed. The type strain of Yimella lutea is YIM 45900T (=DSM 19828T =KCTC 19231T =CCTCC AB 207007T).

Streptomyces griseus and related species form the biggest but least well-defined clade in the whole Streptomyces 16S rRNA gene tree. Multilocus sequence analysis (MLSA) has shown promising potential for refining Streptomyces systematics. In this investigation, strains of 18 additional S. griseus clade species were analysed and data from a previous pilot study were integrated in a larger MLSA phylogeny. The results demonstrated that MLSA of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) is better than the previous six-gene scheme, as it provides equally good resolution and stability and is more cost-effective; MLSA using three or four of the genes also shows good resolution and robustness for differentiating most of the strains and is therefore of value for everyday use. MLSA is more suitable for discriminating strains that show >99 % 16S rRNA gene sequence similarity. DNA–DNA hybridization (DDH) between strains with representative MLSA distances revealed a strong correlation between the data of MLSA and DDH. The 70 % DDH value for current species definition corresponds to a five-gene MLSA distance of 0.007, which could be considered as the species cut-off for the S. griseus clade. It is concluded that the MLSA procedure can be a practical, reliable and robust alternative to DDH for the identification and classification of streptomycetes at the species and intraspecies levels. Based on the data from MLSA and DDH, as well as cultural and morphological characteristics, 18 species and three subspecies of the S. griseus clade are considered to be later heterotypic synonyms of 11 genomic species: Streptomyces griseinus and Streptomyces mediolani as synonyms of Streptomyces albovinaceus; Streptomyces praecox as a synonym of Streptomyces anulatus; Streptomyces olivoviridis as a synonym of Streptomyces atroolivaceus; Streptomyces griseobrunneus as a synonym of Streptomyces bacillaris; Streptomyces cavourensis subsp. washingtonensis as a synonym of Streptomyces cyaneofuscatus; Streptomyces acrimycini, Streptomyces baarnensis, Streptomyces caviscabies and Streptomyces flavofuscus as synonyms of Streptomyces fimicarius; Streptomyces flavogriseus as a synonym of Streptomyces flavovirens; Streptomyces erumpens, ‘Streptomyces ornatus’ and Streptomyces setonii as synonyms of Streptomyces griseus; Streptomyces graminofaciens as a synonym of Streptomyces halstedii; Streptomyces alboviridis, Streptomyces griseus subsp. alpha, Streptomyces griseus subsp. cretosus and Streptomyces luridiscabiei as synonyms of Streptomyces microflavus; and Streptomyces californicus and Streptomyces floridae as synonyms of Streptomyces puniceus.

Strain 56T was isolated from a hypersaline soil in Aswan (Egypt). Cells were pleomorphic rods. The organism was neutrophilic, motile and required at least 1.7 M (10 % w/v) NaCl, but not MgCl2, for growth; optimal growth occurred at ≥3.8 M (≥22.5 %) NaCl. The strain was thermotolerant with an optimum temperature for growth of 40 °C, although growth was possible up to 55 °C. The G+C content of the DNA of the novel strain was 67.1 mol%.16S rRNA gene sequence analysis revealed that strain 56T was a member of the phyletic group defined by the family Halobacteriaceae, showing the highest similarity to Halopiger xanaduensis SH-6T (99 %) and the next highest similarity of 94 % to other members of the family Halobacteriaceae. DNA–DNA hybridization revealed 27 % relatedness between strain 56T and Hpg. xanaduensis SH-6T. Polar lipid analysis revealed the presence of the bis-sulfated glycolipid S2-DGD-1 as the sole glycolipid and the absence of the glycerol diether analogue phosphatidylglycerosulfate. Both C20 . 20 and C20 . 25 core lipids were present. Strain 56T accumulated large amounts of polyhydroxybutyrate and also secreted an exopolymer. Physiological and biochemical differences suggested that Hpg. xanaduanesis and strain 56T were sufficiently different to be separated into two distinct species. It is suggested that strain 56T represents a novel species of the genus Halopiger, for which the name Halopiger aswanensis sp. nov. is proposed. The type strain is strain 56T (=DSM 13151T=JCM 11628T).

Two anaerobic, pigmented, non-spore-forming, Gram-stain-negative, rod-shaped strains isolated from the human oral cavity, OMA31T and OMA130, were characterized by determining their phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the new isolates belonged to a single species of the genus Prevotella. The two isolates showed 100 % 16S rRNA gene sequence similarity with each other and were most closely related to Prevotella intermedia ATCC 25611T with 96.4 % 16S rRNA gene sequence similarity; the next most closely related strains to the isolates were Prevotella pallens AHN 10371T (96.1 %) and Prevotella falsenii JCM 15124T (95.3 %). Phenotypic and biochemical characteristics of the isolates were the same as those of P. intermedia JCM 12248T, P. falsenii JCM 15124T and Prevotella nigrescens JCM 12250T. The isolates could be differentiated from P. pallens JCM 11140T by mannose fermentation and α-fucosidase activity. Conventional biochemical tests were unable to differentiate the new isolates from P. intermedia, P. falsenii and P. nigrescens. However, hsp60 gene sequence analysis suggested that strain OMA31T was not a representative of P. intermedia, P. pallens, P. falsenii or P. nigrescens. Based on these data, a novel species of the genus Prevotella, Prevotella aurantiaca sp. nov., is proposed, with OMA31T (=JCM 15754T=CCUG 57723T) as the type strain.

A novel, strictly aerobic, Gram-stain-negative, yellow-orange-pigmented, rod-shaped bacterium was isolated from abalone (Haliotis discus) under aquaculture in seawater off the Wando coast, Southern Korea, and subjected to a polyphasic taxonomic study. Cells of strain Haldis-1T were catalase- and oxidase-positive rods with flexirubin pigments. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Haldis-1T formed a distinct lineage within the family Cryomorphaceae and could be distinguished from the related genera Lishizhenia and Fluviicola. Strain Haldis-1T shared 16S rRNA gene sequence similarities of 92.5 and 92.4 % with Lishizhenia caseinilytica UST040201-001T and Fluviicola taffensis RW262T, respectively. The DNA G+C content was 38.1 mol% and the major respiratory quinone was MK-7. The predominant cellular fatty acids were iso-C15 : 0 (38.6 %), C15 : 0 2-OH (20.3 %) and C15 : 0 (10.7 %). Growth was observed at 25–42 °C (optimum 30–37 °C) and at pH 6.5–9.5 (optimum pH 6.5–8.0). On the basis of polyphasic analysis of phenotypic, genotypic and phylogenetic data, strain Haldis-1T represents a novel genus and species within the family Cryomorphaceae in the phylum Bacteroidetes, for which the name Wandonia haliotis gen. nov., sp. nov. is proposed. The type strain is Haldis-1T (=KCTC 22610T =NBRC 105642T).

A novel bacterial strain, designated THYL-44T, was isolated from the soil of a Euphrates poplar (Populus euphratica) forest in Xinjiang, China. The cells were strictly aerobic, Gram-staining-negative, non-flagellated, non-motile and filamentous. Growth occurred at 17–37 °C (optimum 30 °C), at pH 5.0–8.0 (optimum pH 7.0) and with 0–1 % NaCl (w/v; optimum 0 %). Flexirubin pigments were not produced. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain THYL-44T was closely related to Niastella koreensis KACC 11465T (95.5 % sequence similarity). The major respiratory quinone was MK-7 and the predominant cellular fatty acids were iso-C15 : 0 (28.6 %), iso-C17 : 0 3-OH (23.9 %) and iso-C15 : 1 G (17.4 %). The DNA G+C content was 45.2 mol%. Therefore, the phylogenetic, physiological and chemotaxonomic data demonstrated that strain THYL-44T represents a novel species of the genus Niastella, for which the name Niastella populi sp. nov. is proposed. The type strain is THYL-44T (=CCTCC AB 208238T=KCTC 22560T). On the basis of new data, an emended description of the genus Niastella is also proposed.

An aerobic, Gram-reaction-negative, non-motile, catalase- and oxidase-positive bacterium, designated strain MDSW-25T, was isolated from seaweed collected in the vicinity of Mara Island in Jeju province, Republic of Korea. Colonies were smooth, circular and convex with entire edges and yellow in colour. Growth occurred at 10–30 °C, at pH 6.1–9.1 and in the presence of 1–12 % (w/v) NaCl. The major fatty acids were iso-C15 : 0 (25.6 %) and iso-C15 : 1 G (11.3 %), and the major menaquinone was MK-6. The DNA G+C content was 30.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain MDSW-25T belonged to the genus Mesonia, family Flavobacteriaceae. Sequence similarity with Mesonia mobilis and Mesonia algae was 97.5 and 95.4 %, respectively, but DNA relatedness between strain MDSW-25T and M. mobilis KCTC 12708T was only 47 %. A battery of phenotypic data, phylogenetic inference and DNA–DNA hybridization analyses supports the conclusion that strain MDSW-25T (=KCTC 22373T =DSM 21425T) represents a novel species of the genus Mesonia, for which the name Mesonia phycicola sp. nov. is proposed. On the basis of new data obtained in this study, an emended description of the genus Mesonia is also proposed.

A Gram-staining-negative, aerobic, non-motile, non-gliding, yellow-pigmented and rod-shaped bacterial strain, designated S7-2T, was isolated from a tidal flat sediment at Saemankum on the west coast of Korea and investigated using a polyphasic taxonomic approach. Strain S7-2T grew optimally at pH 7.0–8.0, at 25–30 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain S7-2T clustered with Lutibacter litoralis CF-TF09T, a member of the family Flavobacteriaceae, with which it showed 95.8 % 16S rRNA gene sequence similarity. It contained MK-6 as the predominant menaquinone and iso-C15 : 0 and C15 : 1 ω6c as the major fatty acids. The major polar lipids of strain S7-2T and L. litoralis JCM 13034T were phosphatidylethanolamine and three unidentified lipids. The DNA G+C content was 34.6 mol%. Differential phenotypic properties and phylogenetic distinctiveness suggested that strain S7-2T represents a novel species of the genus Lutibacter, for which the name Lutibacter maritimus sp. nov. is proposed. The type strain is S7-2T (=KCTC 22635T=CCUG 57524T).

A Gram-staining-negative, rod-shaped, oxidase-positive, aerobic, non-motile and yellow-pigmented bacterial strain containing flexirubin type pigments, designated H1T, was isolated from raw cow'smilk in Israel.16S rRNA gene sequence analysis indicated that the isolate should be placed in the genus Epilithonimonas (family Flavobacteriaceae, phylum Bacteroidetes). The level of 16S rRNA gene sequence similarity between strain H1T and the type strain of Epilithonimonas tenax was 97.6 %. Strain H1T grew at 5–33 °C and with 0–2.0 % NaCl. The dominant cellular fatty acids of strain H1T were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c), and the DNA G+C content was 38.0 mol%. On the basis of phenotypic properties and phylogenetic distinctiveness, the milk isolate is classified as a new species in the genus Epilithonimonas, for which the name Epilithonimonas lactis sp. nov. (type strain H1T =LMG 24401T =DSM 19921T) is proposed.

Two aerobic, Gram-positive, rod-shaped bacterial strains, 5YN10-14T and GR21-5T, were isolated from the Yongneup wetland and ginseng soil in Korea, respectively. The two strains formed ellipsoidal or oval spores positioned centrally or paracentrally in swollen sporangia. On the basis of 16S rRNA gene sequence analysis, these strains were related to members of the genus Cohnella. 16S rRNA gene sequence similarity between strains 5YN10-14T and GR21-5T was 95.9 %. Strains 5YN10-14T and GR21-5T showed, respectively, 94.3 and 95.2 % 16S rRNA gene sequence similarity to Cohnella thermotolerans CCUG 47242T, 94.6 and 94.4 % to Cohnella hongkongensis HKU3T, 94.7 and 94.7 % to Cohnella laeviribosi RI-39T, and 95.4 and 94.8 % to Cohnella phaseoli GSPC1T. The major fatty acids of strain 5YN10-14T were anteiso-C15 : 0 (51.1 %), iso-C16 : 0 (18.5 %) and C16 : 0 (13.2 %), and the major fatty acids of strain GR21-5T were anteiso-C15 : 0 (48.9 %), iso-C16 : 0 (15.0 %) and iso-C15 : 0 (12.2 %). The two strains contained menaquinone with seven isoprene units (MK-7) as the predominant quinone, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as major polar lipids; however, strain 5YN10-14T also contained lysylphosphatidylglycerol as a major polar lipid, whereas strain GR21-5T had an unknown aminophospholipid as another major polar lipid. The DNA G+C contents of strains 5YN10-14T and GR21-5T were 58.8 and 61.3 mol%, respectively. Based on the results of the phylogenetic and phenotypic data presented, it was concluded that the two strains represent two novel species of the genus Cohnella, for which the names Cohnella yongneupensis sp. nov. (type strain 5YN10-14T=KACC 11768T=DSM 18998T) and Cohnella ginsengisoli sp. nov. (type strain GR21-5T=KACC 11771T=DSM 18997T) are proposed.