- Volume 61, Issue 1, 2011

Six strains of anaerobic, pleomorphic Gram-positive bacilli, isolated from the human oral cavity and an infected arm wound, were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group. 16S rRNA gene sequence analysis revealed that the isolates were most closely related to Scardovia inopinata CCUG 35729T (94.8–94.9 % 16S rRNA gene sequence similarity). The isolates were saccharolytic and produced acetic and lactic acids as end products of fermentation. The major fatty acids were C16 : 0 (49.8 %) and C18 : 1 ω9c (35.8 %). Polar lipid analysis revealed a variety of glycolipids, diphosphatidylglycerol, an unidentified phospholipid and an unidentified phosphoglycolipid. No respiratory quinones were detected. The peptidoglycan was of the type A4α l-Lys–Thr–Glu, with l-lysine partially replaced by l-ornithine. The DNA G+C content of one of the strains, C1A_55T , was 55 mol%. A novel species, Scardovia wiggsiae sp. nov., is proposed to accommodate the six isolates, with the type strain C1A_55T (=DSM 22547T=CCUG 58090T).

A novel actinomycete, designated strain GIMN4.001T, was isolated from the rhizosphere of tomato plants grown in Guangzhou, China. The strain produced greyish white aerial mycelia, lactic acid and a large quantity of double diamond-shaped crystals on potato dextrose agar and yeast extract-malt extract agar. The colour of the substrate mycelium was not sensitive to pH. Microscopic observations revealed that strain GIMN4.001T produced verticillate chains of cylindrical spores. Chemotaxonomic data confirmed that strain GIMN4.001T belonged to the genus Streptomyces. Melanin pigments were not produced. No antibacterial activity was observed against Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis or Candida albicans, but inhibitory activity was observed against Penicillium citrinum. 16S rRNA gene sequence analysis revealed that strain GIMN4.001T was related most closely to Streptomyces morookaense ATCC 19166T (98.9 % similarity) and Streptomyces lavenduligriseus ATCC 13306T (98.7 %). Levels of DNA–DNA relatedness between strain GIMN4.001T and the type strains of these species were low (14–20 %). Furthermore, strain GIMN4.001T could be differentiated from S. morookaense, S. lavenduligriseus and other closely related species of the genus Streptomyces based on morphological, physiological and biochemical characteristics. On the basis of its physiological and molecular properties, strain GIMN4.001T is considered to represent a novel species of the genus Streptomyces, for which the name Streptomyces lacticiproducens sp. nov. is proposed. The type strain is GIMN4.001T (=CCTCC M208214T=NRRL B-24800T).

A Gram-stain-positive, non-endospore-forming actinobacterium (CC-12301T) was isolated from soil attached to a spawn used in the laboratory to grow the edible mushroom Agaricus brasiliensis. Based on 16S rRNA gene sequence similarities, strain CC-12301T was shown to belong to the genus Gordonia and was most closely related to the type strains of Gordonia hydrophobica (97.6 % similarity), Gordonia terrae (97.5 %), Gordonia amarae (97.5 %) and Gordonia malaquae (97.4 %). The quinone system was determined to consist predominantly of menaquinone MK-9(H2), minor amounts of MK-8(H2) and MK-7(H2). The polar lipid profile consisted of the major compounds diphosphatidylglycerol and phosphatidylethanolamine, moderate amounts of two phosphatidylinositol mannosides and phosphatidylinositol and minor amounts of phosphatidylglycerol, three unidentified glycolipids, two phosphoglycolipids and a phospholipid. Mycolic acids were present. These chemotaxonomic traits and the major fatty acids, which were C16 : 1 cis9, C16 : 0, C18 : 1 and tuberculostearic acid (10-methyl C18 : 0), supported the affiliation of strain CC-12301T to the genus Gordonia. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain CC-12301T from the most closely related Gordonia species. Strain CC-12301T therefore represents a novel species, for which the name Gordonia humi sp. nov. is proposed, with the type strain CC-12301T (=DSM 45298T =CCM 7727T).

A bacterial strain, designated V2M29T, was isolated from forest soil collected in the Changbai Mountains, Heilongjiang Province, China. Cells of strain V2M29T were Gram-positive, rod-shaped (0.5–0.8 μm in diameter and 1.5–2.0 μm in length), strictly aerobic and non-motile. Colonies produced on R2A agar plates were creamy, smooth, circular and 0.3–0.8 mm in diameter. Strain V2M29T grew at 14–35 °C (optimum, 29 °C), at pH 4.1–10.0 (optimum, pH 7.0–8.0) and in the presence of 0–7.0 % (w/v) NaCl (optimum, 0–2.0 %). Strain V2M29T contained MK-8(H4) as the major respiratory quinone and iso-C15 : 0 (20.9 %), iso-C16 : 0 (18.5 %), C17 : 1 ω8c (16.7 %) and 10-methyl-C17 : 0 (9.2 %) as the major cellular fatty acids. The cell-wall peptidoglycan type was based on meso-2,6-diaminopimelic acid and the acyl type of the muramic acid was acetyl. Diphosphatidylglycerol, phosphatidylinositol and six unknown glycolipids were the major polar lipids. The G+C content of the DNA was 72.0 mol% (T m). 16S rRNA gene sequence analysis indicated that strain V2M29T was phylogenetically related to members of the genus Phycicoccus, with sequence similarities ranging from 96.6–97.8 %. The DNA–DNA relatedness values of strain V2M29T to Phycicoccus dokdonensis DS-8T and Phycicoccus bigeumensis DSM 19264T were 32.5±3.3 % and 29.2±2.3 %, respectively. Based on these results, it is concluded that strain V2M29T represents a novel species of the genus Phycicoccus, for which the name Phycicoccus cremeus sp. nov. is proposed, with V2M29T (=CGMCC 1.6963T =NBRC 104261T) as the type strain.

A novel actinomycete, designated strain OU-40T, was isolated from farm soil collected from the Hyderabad region of Andhra Pradesh, southern India. The strain was found to have morphological and chemotaxonomic characteristics typical of species of the genus Streptomyces. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain OU-40T belonged to the genus Streptomyces, and was related most closely to Streptomyces pactum NBRC 13433T (99.0 % sequence similarity), Streptomyces olivaceus NBRC 12805T (99.0 %) and Streptomyces parvulus NBRC 13193T (98.8 %). Strain OU-40T could be distinguished from the type strains of its closest phylogenetic relatives based on levels of DNA–DNA relatedness and comparison of morphological and phenotypic data. It is therefore concluded that strain OU-40T represents a novel species of the genus Streptomyces, for which the name Streptomyces hyderabadensis sp. nov. is proposed. The type strain is OU-40T (=CCTCC AA 209024T =PCM 2692T).

A thermophilic, Gram-positive bacterium that formed a branched vegetative mycelium was isolated from compost. The strain, designated I3T, grew at temperatures between 35 and 62 °C, with optimum growth at 50–55 °C. No growth was observed below 29 °C or above 65 °C. The pH range for growth was 5.7–10.0, the pH for optimum growth was 7.0 and no growth was observed below pH 5.6 or above pH 10.8. The DNA G+C content of strain I3T was 69.2 mol%. The major fatty acids found were C15 : 0 iso (14.2 %), C15 : 0 anteiso (12.1 %), C17 : 0 iso (16.3 %) and C17 : 0 anteiso (21.7 %). The major menaquinones were MK-9(H4), MK-10(H4) and MK-11(H4). The cell wall contained glutamic acid, glycine, alanine and ll-diaminopimelic acid in a molar ratio of 1.0 : 3.9 : 0.6 : 0.5. The polar lipids consisted of ninhydrin-positive phosphoglycolipids, phosphatidylglycerol, diphosphatidylglycerol and an unknown glycolipid. The cell-wall sugars were rhamnose and arabinose. 16S rRNA gene sequence analysis assigned this actinomycete to the family Nocardioidaceae, but its 16S rRNA gene sequence shared no more than 95.5 % similarity with those of other members of the family. The chemotaxonomic and phenotypic characteristics of strain I3T differed in some respects from those of members of the genus Actinopolymorpha, the most closely related genus. Therefore, strain I3T represents a novel species in a new genus of the family Nocardioidaceae, for which the name Thermasporomyces composti gen. nov., sp. nov. is proposed. The type strain of the type species is I3T (=JCM 16421T=DSM 22891T).

A Gram-staining-positive, coccoid to rod-shaped bacterium, designated strain YC6903T, was isolated from a halophytic plant (Carex scabrifolia Steud.) collected from sand dunes at Namhae Island, Korea, and its taxonomic position was investigated by using a polyphasic approach. Strain YC6903T grew optimally at 30 °C and at pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YC6903T belongs to the genus Nocardioides in the family Nocardioidaceae. Strain YC6903T was related most closely to Nocardioides pyridinolyticus OS4T (97.0 % 16S rRNA gene sequence similarity), Nocardioides dokdonensis FR1436T (96.6 %), Nocardioides aquiterrae GW-9T (96.6 %) and Nocardioides hankookensis DS-30T (96.6 %). The cell-wall peptidoglycan contained ll-diaminopimelic acid and MK-8(H4) was the major respiratory quinone. The mean (±sd) level of DNA–DNA relatedness between strain YC6903T and N. pyridinolyticus OS4T was 53.5±5.5 %. The predominant cellular fatty acid of strain YC6903T was iso-C16 : 0 (28.9 %). The DNA G+C content was 71.7 mol%. Phenotypic, phylogenetic and chemotaxonomic data indicated that strain YC6903T represents a novel species of the genus Nocardioides, for which the name Nocardioides caricicola sp. nov. is proposed. The type strain is YC6903T (=KACC 13778T =DSM 22177T).

A Gram-positive, non-motile, coccoid- to rod-shaped, non-spore-forming bacterium, designated strain YM18-15T, was isolated from sea sand and studied using a polyphasic taxonomic approach. Strain YM18-15T grew under both aerobic and anaerobic conditions. The cell-wall peptidoglycan type was A4β and ornithine was the diagnostic diamino acid. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unknown phospholipid, MK-8(H4) was the major menaquinone and the predominant fatty acids were anteiso-C15 : 0 and C16 : 0. The DNA G+C content was 74.2 mol%. High 16S rRNA gene sequence similarities (96.3–97.3 %) were found with the sequences of the type strains of the three genera of the family Beutenbergiaceae. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YM18-15T formed a clade with Serinibacter salmoneus, Salana multivorans and Beutenbergia cavernae. Strain YM18-15T differed from these three type strains in chemotaxonomic characteristics and in 16S rRNA gene signature nucleotides. Based on genetic and chemotaxonomic evidence, it is suggested that strain YM18-15T represents a novel species of a new genus within the family Beutenbergiaceae, for which the name Miniimonas arenae gen. nov., sp. nov. is proposed. The type strain of the type species is YM18-15T (=NBRC 106267T=KCTC 19750T=MBIC 08348T).

A Gram-stain-positive, non-spore-forming actinobacterium, designated 15-Je-017T, was isolated from wall material of an indoor environment. The isolate formed a rudimentary substrate mycelium that fragmented into rod-shaped cells. On the basis of 16S rRNA gene sequence analysis, strain 15-Je-017T was shown to belong to the genus Jiangella and was most closely related to Jiangella alba YIM 61503T (99.7 % 16S rRNA gene sequence similarity), Jiangella alkaliphila D8-87T (99.0 %) and Jiangella gansuensis YIM 002T (99.0 %). The predominant menaquinone was MK-9(H4). Whole-cell hydrolysates contained ll-diaminopimelic acid as the diagnostic diamino acid in the cell wall and rhamnose and glucose as the main sugars. Mycolic acids were absent. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and seven unknown phospholipids. The fatty acid profile contained major amounts (>5 %) of anteiso-C15 : 0, iso-C16 : 0, iso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0 and C17 : 1 ω8c, which supported the affiliation of strain 15-Je-017T to the genus Jiangella. DNA–DNA relatedness and physiological and biochemical tests allowed the differentiation of strain 15-Je-017T from the type strains of the three known Jiangella species. Strain 15-Je-017T represents a novel Jiangella species, for which we propose the name Jiangella muralis sp. nov., with type strain 15-Je-017T (=DSM 45357T =CCM 7680T).

A Gram-positive, non-motile bacterium, designated KSL51201-037T, was isolated from Anyang stream, Republic of Korea, and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain KSL51201-037T belonged to the family Microbacteriaceae of the class Actinobacteria and exhibited 96.9 % gene sequence similarity to Labedella gwakjiensis KSW2-17T, 96.0 % to Leifsonia ginsengi wged11T and 95.9 % to Microterricola viridarii KV-677T. The G+C content of the genomic DNA was 72.7 mol%. Strain KSL51201-037T had l-2,4-diaminobutyric acid as the diagnostic cell-wall diamino acid, MK-11 and MK-12 as the major menaquinones, anteiso-C15 : 0 (47.8 %) and iso-C16 : 0 (24.0 %) as the major fatty acids and phosphatidylglycerol and three unknown phospholipids as the major polar lipids. On the basis of phenotypic and genotypic properties and phylogenetic distinctiveness, it is suggested that strain KSL51201-037T represents a novel species of a new genus in the family Microbacteriaceae for which the name Amnibacterium kyonggiense gen. nov., sp. nov. is proposed. The type strain of the type species is KSL51201-037T (=KEMC 51201-037T=JCM 16463T).

A cholesterol side-chain-cleaving bacterial strain, AD-6T, was isolated from fresh faeces of a clouded leopard (Neofelis nebulosa) and was studied using a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that the novel strain formed a distinct subline within the genus Gordonia, its closest neighbours being the type strains of Gordonia cholesterolivorans, Gordonia sihwensis and Gordonia hydrophobica, with sequence similarity values of 98.2, 97.8 and 97.6 %, respectively. The gyrB gene sequence of strain AD-6T exhibited similarities of 77–91 % with those of the type strains of recognized species of the genus Gordonia, being most similar to the type strains of G. sihwensis, G. hydrophobica and Gordonia hirsuta (91, 87 and 84 % similarity, respectively). The results of whole-cell fatty acid analyses and DNA–DNA relatedness data readily distinguished the new isolate from its nearest neighbours. Strain AD-6T is therefore considered to represent a novel species of the genus Gordonia, for which the name Gordonia neofelifaecis sp. nov. is proposed. The type strain is AD-6T (=NRRL B-59395T=CCTCC AB-209144T).

A novel actinobacterial strain, designated CPCC 201356T, was isolated from a rhizosphere soil sample of the medicinal plant Astragalus membranaceus and subjected to a polyphasic taxonomic analysis. Good growth occurred at 20–32 °C, at pH 7.0–7.5 and with 0–1 % (w/v) NaCl. Colonies on R2A and ISP 2 agar were light red to red, round and lacked aerial mycelium; cells adhered to the agar. The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The predominant menaquinones were MK-9(H4) and MK-9. Polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and two unknown phospholipids. The major cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and C17 : 1 ω8c. The G+C content of the genomic DNA was 72.8 mol%. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain CPCC 201356T belonged to the family Geodermatophilaceae and consistently formed a distinct sub-branch with Geodermatophilus obscurus DSM 43160T. The organism showed 16S rRNA gene sequence similarity of 97.7 % with G. obscurus DSM 43160T. DNA–DNA hybridization between strain CPCC 201356T and G. obscurus DSM 43160T was 17.4 %. On the basis of evidence from this polyphasic taxonomic study, a novel species, Geodermatophilus ruber sp. nov., is proposed; the type strain is CPCC 201356T (=DSM 45317T =CCM 7619T).

A halophilic, filamentous actinomycete strain, designated YIM 93246T, was isolated from a salt lake in Xinjiang province, north-west China, and subjected to polyphasic taxonomic characterization. The isolate grew in the presence of 7–23 % (w/v) NaCl, but not in the absence of NaCl. Strain YIM 93246T had particular morphological properties, forming aerial mycelium that had long spore chains and pseudosporangium-like, rhiziform spore aggregates at maturity. ll-DAP was the cell-wall diamino acid and glucosamine, mannose, glucose, arabinose and galactose were the cell-wall sugars. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. MK-9 (H4) was the predominant menaquinone and the genomic DNA G+C content was 70.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93246T clustered with the genus Jiangella. The sequence similarities between strain YIM 93246T and Jiangella alba, Jiangella gansuensis and Jiangella alkaliphila were 96.9, 96.9 and 96.6 %, respectively. Based on morphological, physiological and chemotaxonomic differences, and phylogenetic analysis, a novel genus and species, Haloactinopolyspora alba gen. nov., sp. nov., is proposed. The type strain of the species is YIM 93246T (=DSM 45211T=KCTC 19409T). Additionally, phylogenetic analysis placed the genus Jiangella together with strain YIM 93246T within the order Actinomycetales as an independent lineage, clearly distinguished from other described suborders of the class Actinobacteria. Hence, based on phylogenetic characteristics, the genus Jiangella together with the newly proposed genus Haloactinopolyspora are proposed to be classified as Jiangellaceae fam. nov. and Jiangellineae subord. nov.

A novel acidiphilic, hydrogenotrophic methanogen, designated strain 6A8T, was isolated from an acidic (pH 4.0–4.5) and ombrotrophic (rain-fed) bog located near Ithaca, NY, USA. Cultures were dimorphic, containing thin rods (0.2–0.3 μm in diameter and 0.8–3.0 μm long) and irregular cocci (0.2–0.8 μm in diameter). The culture utilized H2/CO2 to produce methane but did not utilize formate, acetate, methanol, ethanol, 2-propanol, butanol or trimethylamine. Optimal growth conditions were near pH 5.1 and 35 °C. The culture grew in basal medium containing as little as 0.43 mM Na+ and growth was inhibited completely by 50 mM NaCl. To our knowledge, strain 6A8T is one of the most acidiphilic (lowest pH optimum) and salt-sensitive methanogens in pure culture. Acetate, coenzyme M, vitamins and yeast extract were required for growth. It is proposed that a new genus and species be established for this organism, Methanoregula boonei gen. nov., sp. nov. The type strain of Methanoregula boonei is 6A8T (=DSM 21154T =JCM 14090T).