- Volume 62, Issue Pt_7, 2012

A Micromonospora -like strain, RtIII47T, was isolated from a mangrove swamp in Sanya, Hainan Province, China. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the strain had a close association with the genus Verrucosispora and shared the highest sequence similarity with Verrucosispora lutea YIM 013T (98.0 %). The strain also showed high 16S rRNA gene sequence similarities to Micromonospora olivasterospora DSM 43868T (97.9 %), Plantactinospora mayteni YIM 61359T (97.9 %), Salinispora tropica CNB-440T (97.8 %), Micromonospora peucetia DSM 43363T (97.7 %), Micromonospora auratinigra TT1-11T (97.7 %), Verrucosispora sediminis CGMCC 4.3550T (97.6 %) and Salinispora arenicola CNH-643T (97.5 %). Phylogenetic analysis based on the gyrB gene sequence supported the conclusion that strain RtIII47T should be assigned to the genus Verrucosispora . DNA–DNA relatedness between strain RtIII47T and the most closely related type strain, V. lutea YIM 013T, was less than 40 %. Chemotaxonomic results confirmed the taxonomic position of the isolate in the genus Verrucosispora , and revealed differences at the species level in polar lipids, whole-cell sugars and DNA G+C content. A combination of physiological and biochemical tests also distinguished this strain from other Verrucosispora species. Based on genotypic and phenotypic observations, strain RtIII47T ( = CGMCC 4.5826T  = NBRC 106684T) is proposed as the type strain of a novel species, Verrucosispora qiuiae sp. nov. An emended description of the genus Verrucosispora is also provided.

A straight-chain, spore-forming actinobacterium, strain YIM 120770T, was isolated from soil. Phylogenetic analysis on the basis of 16S rRNA gene sequence comparisons revealed that the isolate represents a distinct cluster within the clade comprising the genus Nonomuraea and is related most closely to Nonomuraea rhizophila YIM 67092T (96.5 % similarity). Cells of strain YIM 120770T grew in the presence of 0–3 % (w/v) NaCl, at 15–37 °C and at pH 7.0–8.0. The diagnostic amino acid was meso-diaminopimelic acid, cell hydrolysates contained madurose, glucose, mannose, ribose and galactose, the predominant cellular fatty acids were 10-methyl C17 : 0 and iso-C16 : 0, and the DNA G+C content was 66.4 mol%, data consistent with affiliation of strain YIM 120770T to the genus Nonomuraea . Strain YIM 120770T shared low levels of 16S rRNA gene sequence similarity (<97 %) with the type strains of recognized species of the genus Nonomuraea and could be differentiated from its closest phylogenetic relative based on phenotypic characteristics. These results suggested that strain YIM 120770T represents a novel species of the genus Nonomuraea , for which the name Nonomuraea soli sp. nov. is proposed. The type strain is YIM 120770T ( = DSM 45533T = JCM 17347T).

An actinobacterial strain, SCSIO 10427T, was isolated from a gorgonian coral sample collected from Weizhou Island, Guangxi province, China, and its taxonomic position was investigated using a polyphasic approach. The organism was found to have a range of chemical and morphological properties consistent with its classification in the genus Nocardiopsis . Phylogenetic analysis indicated that 16S rRNA gene sequence similarity between strain SCSIO 10427T and type strains of other recognized members of the genus Nocardiopsis was lower than 98.4 %. Furthermore, phenotypic characteristics revealed that the strain differed from the currently recognized species of the genus Nocardiopsis . Therefore, strain SCSIO 10427T represents a novel species of the genus Nocardiopsis , for which the name Nocardiopsis coralliicola sp. nov. is proposed. The type strain is SCSIO 10427T ( = CCTCC AA 2011010T = DSM 45611T).

A novel aerobic actinobacterium, strain EUM 273T, was isolated from the root of a Grey Box tree (Eucalyptus microcarpa Maiden). Cells were Gram-staining-positive with well-developed substrate mycelia which were non-motile and rod-like, with coccoid elements. Phylogenetic evaluation based on 16S rRNA gene sequence analysis placed the isolate as a member of the family Promicromonosporaceae that was most closely related to Promicromonospora xylanilytica YIM 61515T (98.2 %) and Promicromonospora vindobonensis V45T (98 %). Chemotaxonomic data including cell wall components, major menaquinone and major fatty acids confirmed the affiliation of strain EUM 273T to the genus Promicromonospora . The results of the phylogenetic analysis, including physiological and biochemical studies in combination with DNA–DNA hybridization, allowed the genotypic and phenotypic differentiation of strain EUM 273T from the closest related species with validly published names. The name proposed for the novel species is Promicromonospora endophytica sp. nov. The type strain is EUM 273T ( = DSM 23716T = NRRL B-24816T).

During screening for 4-chlorophenol-degrading micro-organisms in activated sludge from industrial wastewater treatment, a Gram-positive, rod-shaped, aerobic bacterial strain, designated 2C6-43T, was isolated and characterized taxonomically by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain 2C6-43T belongs to the family Bogoriellaceae , class Actinobacteria , and is related most closely to Georgenia soli CC-NMPT-T3T (98.8 % sequence similarity), Georgenia muralis 1A-CT (97.6 %), Georgenia thermotolerans TT02-04T (96.8 %), Georgenia ruanii YIM 004T (96.6 %) and Georgenia halophila YIM 93316T (96.0 %). The G+C content of the genomic DNA of strain 2C6-43T was 66.2 mol%. Sugars from whole-cell hydrolysates found in strain 2C6-43T were rhamnose, ribose and galactose. The menaquinone MK-8(H4) was detected as the predominant quinone. Polar lipid analysis of 2C6-43T revealed diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol and phosphatidylglycerol. An aromatic compound ring cleavage enzyme of catechol 1,2-dioxygenase was detected but catechol 2,3-dioxygenase was not detected in 2C6-43T. A fatty acid profile with anteiso-C15 : 0, iso-C15 : 0 and C16 : 0 as the major components supported the affiliation of strain 2C6-43T to the genus Georgenia . However, the DNA–DNA relatedness between strain 2C6-43T and the type strains of five species of the genus Georgenia ranged from 17 to 40 %, clearly showing that the isolate constitutes a new genospecies. Strain 2C6-43T could be clearly differentiated from its phylogenetic neighbours on the basis of some phenotypic, genotypic and chemotaxonomic features. Therefore, strain 2C6-43T is considered to represent a novel species of the genus Georgenia , for which the name Georgenia daeguensis sp. nov. is proposed; the type strain is 2C6-43T ( = KCTC 19801T = JCM 17459T).

Sixty-two strains of thermophilic aerobic endospore-forming bacteria were subjected to polyphasic taxonomic study including 16S rRNA gene sequence analysis, polar lipid and fatty acid analysis, phenotypic characterization, and DNA–DNA hybridization experiments. Distinct clusters of the species Geobacillus stearothermophilus , Geobacillus thermodenitrificans , Geobacillus toebii and Geobacillus thermoglucosidasius were formed, allowing their descriptions to be emended, and the distinctiveness of the poorly represented species Geobacillus jurassicus , Geobacillus subterraneus and Geobacillus caldoxylosilyticus was confirmed. It is proposed that the name Geobacillus thermoglucosidasius be corrected to Geobacillus thermoglucosidans nom. corrig. Bacillus thermantarcticus clustered between Geobacillus species on the basis of 16S rRNA gene sequence analysis, and its transfer to the genus Geobacillus as Geobacillus thermantarcticus comb. nov. (type strain LMG 23032T = DSM 9572T = strain M1T = R-35644T) is proposed. The above-mentioned species, together with Geobacillus thermoleovorans and Geobacillus thermocatenulatus , form a monophyletic cluster representing the genus Geobacillus . The distinctiveness of ‘Geobacillus caldoproteolyticus’ was confirmed and it is proposed that it be accommodated, along with Geobacillus tepidamans , in the genus Anoxybacillus as Anoxybacillus caldiproteolyticus sp. nov. (type strain DSM 15730T = ATCC BAA-818T = LMG 26209T = R-35652T) and Anoxybacillus tepidamans comb. nov. (type strain LMG 26208T = ATCC BAA-942T = DSM 16325T = R-35643T), respectively. The type strain of Geobacillus debilis was not closely related to any members of the genera Anoxybacillus and Geobacillus , and it is proposed that this species be placed in the new genus Caldibacillus as Caldibacillus debilis gen. nov. comb. nov. The type strain of the type species, Caldibacillus debilis, is LMG 23386T ( = DSM 16016T = NCIMB 13995T = TfT = R-35653T).

A novel filamentous bacterium, designated NariEXT, was isolated from soil collected from Chott Melghir salt lake, which is located in the south-east of Algeria. The strain was an aerobic, halotolerant, thermotolerant, Gram-positive bacterium that was able to grow in NaCl concentrations up to 21 % (w/v), at 37–60 °C and at pH 5.0–9.5. The major fatty acids were iso- and anteiso-C15 : 0. The DNA G+C content was 47.3 mol%. The major menaquinone was MK-7, but MK-6 and MK-8 were also present. The polar lipid profile consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylmonomethylethanolamine (methyl-PE). Results of molecular and phenotypic analysis led to the description of the strain as a new member of the family Thermoactinomycetaceae . The isolate was distinct from members of recognized genera of this family by morphological, biochemical and chemotaxonomic characteristics. Strain NariEXT showed 16S rRNA gene sequence similarities of 95.38 and 94.28 % with the type strains of Desmospora activa and Kroppenstedtia eburnea , respectively, but differed from both type strains in its sugars, polar lipids and in the presence of methyl-PE. On the basis of physiological and phylogenetic data, strain NariEXT represents a novel species of a new genus of the family Thermoactinomycetaceae for which the name Melghirimyces algeriensis gen. nov., sp. nov. is proposed. The type strain of Melghirimyces algeriensis, the type species of the genus, is NariEXT ( = DSM 45474T = CCUG 59620T).

Eight Gram-positive, catalase-negative bacterial strains were isolated during screening of enterococcal populations on plants. rep-PCR fingerprinting using the (GTG)5 primer showed that the isolates constituted a single cluster that was separate from all known enterococcal species. 16S rRNA gene sequence phylogenetic analysis of three representative strains showed that the isolates belonged to the genus Enterococcus and that they clustered with the Enterococcus faecalis species group. Sequencing of the genes for the phenylalanyl-tRNA synthase alpha subunit (pheS) and the RNA polymerase alpha subunit (rpoA) also revealed the isolates’ separate taxonomic position. Application of whole-cell protein fingerprinting, automated ribotyping and extensive phenotyping demonstrated the genetic and phenotypic homogeneity of the isolates and confirmed their separate position within the E. faecalis species group. The isolates represent a novel species of the genus Enterococcus , for which the name Enterococcus plantarum sp. nov. is proposed; the type strain is CCM 7889T ( = LMG 26214T = C27T).

A novel anaerobic, moderately thermophilic bacterium (strain SGL43T) was isolated from Severo-Stavropolskoye underground gas storage reservoir (Russia). Cells of strain SGL43T were motile straight rods, 0.4 µm in diameter and 2.0–3.0 µm in length. The temperature range for growth was 28–65 °C, with optimum growth at 50 °C. The pH range for growth was 5.5–8.0, with optimum growth at pH 7.0–7.5. Growth of strain SGL43T was observed at NaCl concentrations of 0–4.0 % (w/v) with optimum growth at 1.0 % (w/v) NaCl. Substrates utilized by strain SGL43T included peptone, yeast extract, glucose, fructose, maltose, galactose, pyruvate and citrate. Products of glucose or citrate fermentation were acetate, hydrogen and CO2. Thiosulfate was reduced to sulfide. The DNA G+C content of strain SGL43T was 43.1 mol%. 16S rRNA gene sequence analysis revealed that strain SGL43T belongs to the order Thermoanaerobacterales (phylum ‘ Firmicutes ’). The closest relative of strain SGL43T was Thermoanaerobacterium saccharolyticum (86.2 % 16S rRNA gene sequence similarity with the type strain). Based on the data presented here, strain SGL43T is considered to represent a novel species of a new genus, for which the name Caloribacterium cisternae gen. nov., sp. nov. is proposed. The type strain of Caloribacterium cisternae, the type species of the genus, is SGL43T ( = DSM 23830T = VKM B-2670T).

Strains LMG 8159 and LMG 11499 were reclassified by a polyphasic approach, including 16S rRNA gene sequence analysis, 16S–23S rRNA intergenic spacer (IGS) sequence analysis, (GTG)5-PCR fingerprinting, RAPD fingerprinting, fatty acid methyl ester analysis and an analysis of phenotypic features using API 50 CH. The two strains were closely related to the type strains of the three defined subspecies of Leuconostoc mesenteroides , showing 99.7–99.9 % 16S rRNA gene sequence similarity, 99.2 % 16S–23S rRNA gene intergenic spacer sequence similarity, 97.1–97.4 % pheS gene sequence similarity and 98.0–98.2 % rpoA gene sequence similarity. Low atpA gene sequence similarity (91.4–91.7 %), (GTG)5-PCR fingerprinting, RAPD fingerprinting, fatty acid compositions and phenotypic features allowed us to differentiate strains LMG 8159 and LMG 11499 from all established subspecies within L. mesenteroides . Based upon the data obtained in the present and previous studies, a novel subspecies is proposed within the species L. mesenteroides , Leuconostoc mesenteroides subsp. suionicum subsp. nov., with the type strain LMG 8159T ( = ATCC 9135T  = DSM 20241T  = NCIMB 6992T).

The first alkaliphilic obligately anaerobic hydrogenotrophic homoacetogenic bacterium, strain Z-7100T, was isolated from sediments of the soda-depositing soda lake Tanatar III (Altay, Russia). Cells were thin, flexible rods, motile, Gram-negative and spore-forming. The organism was an obligate alkaliphile, growing at pH 8.5 to 10.5, with optimum growth at pH 8.8–9.3, and it grew in soda brines containing 1.9–4.7 M total Na+ (optimum at 2.8–3.3 M). It exhibited an obligate dependence upon sodium carbonate but not upon chloride ions with an NaCl range for growth of 0–14 % (w/v) and an optimum at 7.0–8.5 % (w/v). The isolate was mesophilic and grew at temperatures from 25 to 45 °C, with an optimum at 40 °C. An H2+CO2 mixture, ethanol, pyruvate and lactate were utilized with the formation of acetate as the sole metabolic product. Carbohydrates and amino acids did not support growth. The isolate had a respiratory type of metabolism, reducing , SeO4 2− or anthraquinone-2,6-disulfonate (as electron acceptors with ethanol as an electron donor). It was able to grow chemolithotrophically on H2+CO2 in medium supplemented with a vitamin solution only. The major cellular fatty acids were the saturated fatty acids anteiso-C15, C14 : 0 and C16 : 0 and the aldehydes C16, C14 and anteiso-C15. The DNA G+C content of the isolate was 32.0 mol%. 16S rRNA gene sequence analysis showed that strain Z-7100T is a member of the order Halanaerobiales and represents a new branch within the family Halobacteroidaceae , clustering with the type strain of Selenihalanaerobacter shriftii (92.9 % gene sequence similarity). On the basis of its physiological characteristics and phylogenetic position, the isolate is considered to represent a novel species in a new genus within the family Halobacteroidaceae . The name Fuchsiella alkaliacetigena gen. nov., sp. nov. is proposed. The type strain of the type species is Z-7100T ( = DSM 24880T = VKM B-2667T).

A novel moderately thermophilic, anaerobic, ethanol-producing bacterial strain, 45BT, was isolated from a mixed sediment water sample collected from a hot spring at Potosi, Bolivia. The cells were straight to slightly curved rods approximately 2.5 µm long and 0.5 µm wide. The strain was Gram-stain-variable, spore-forming and monotrichously flagellated. Growth of the strain was observed at 45–65 °C and pH 5.5–8.0, with optima of 60 °C and pH 6.5. The substrates utilized by strain 45BT were xylose, cellobiose, glucose, arabinose, sucrose, lactose, maltose, fructose, galactose, mannose, glycerol, xylan, carboxymethylcellulose and yeast extract. The main fermentation product from xylose and cellobiose was ethanol (0.70 and 0.45 g ethanol per gram of consumed sugar, respectively). Acetate, lactate, propionate, carbon dioxide and hydrogen were also produced in minor quantities. 1,3-Propanediol was produced when glycerol-containing medium was supplemented with yeast extract. The major cellular fatty acids were anteiso-C15 : 0, C16 : 0, iso-C16 : 0, C15 : 1, iso-C14 : 0, C13 : 0 and C14 : 0. The polar lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an aminoglycolipid and 15 other unidentified lipids were predominant. The DNA G+C content of strain 45BT was 32.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarity revealed that strain 45BT is located within the Gram-type positive Bacillus – Clostridium branch of the phylogenetic tree. On the basis of morphological and physiological properties and phylogenetic analysis, strain 45BT represents a novel species, for which the name Caloramator boliviensis sp. nov. is proposed; the type strain is 45BT ( = DSM 22065T = CCUG 57396T).

A novel anaerobic, Fe(III)-reducing, hydrogenogenic, carboxydotrophic bacterium, designated strain Ug1T, was isolated from a volcanic acidic hot spring in southern Kyushu Island, Japan. Cells of the isolate were rod-shaped (1.0–3.0 µm long) and motile due to peritrichous flagella. Strain Ug1T grew chemolithoautotrophically on CO (100 % in the gas phase) with reduction of ferric citrate, amorphous iron (III) oxide, 9,10-anthraquinone 2,6-disulfonate, thiosulfate or elemental sulfur. No carboxydotrophic growth occurred with sulfate, sulfite, nitrate or fumarate as electron acceptor. During growth on CO, H2 and CO2 were produced. Growth occurred on molecular hydrogen as an energy source and carbon dioxide as a sole carbon source. Growth was observed on various organic compounds under an N2 atmosphere with the reduction of ferric iron. The temperature range for carboxydotrophic growth was 50–70 °C, with an optimum at 65 °C. The pH25 °C range for growth was 4.6–8.6, with an optimum between 6.0 and 6.5. The doubling time under optimum conditions using CO with ferric citrate was 1.5 h. The DNA G+C content was 42.2 mol%. Analysis of 16S rRNA gene sequences demonstrated that this strain belongs to the thermophilic carboxydotrophic bacterial genus Carboxydothermus , with sequence similarities of 94.1–96.6 % to members of this genus. The isolate can be distinguished from other members of the genus Carboxydothermus by its ability to grow with elemental sulfur or thiosulfate coupled to CO oxidation. On the basis of phylogenetic analysis and unique physiological features, the isolate represents a novel species of the genus Carboxydothermus for which the name Carboxydothermus pertinax sp. nov. is proposed; the type strain of the novel species is Ug1T ( = DSM 23698T = NBRC 107576T).

Several Gram-negative-staining, facultatively anaerobic bacterial isolates were obtained from Eucalyptus seedlings showing symptoms of bacterial blight and dieback in Colombia, Rwanda and South Africa. Partial 16S rRNA gene sequencing, together with partial gyrB sequencing, placed the isolates in the genus Pantoea and indicated that they constituted three novel species. Multilocus sequence analysis (MLSA) based on partial sequences of gyrB, rpoB, infB and atpD revealed Pantoea dispersa , Pantoea eucrina and Pantoea cypripedii as their closest phylogenetic relatives. DNA–DNA hybridization studies confirmed the classification of the new isolates as three novel species and phenotypic tests allowed them to be differentiated from their closest phylogenetic neighbours. The names Pantoea rodasii sp. nov. [type strain LMG 26273T = BD 943T (deposited with the Plant Pathogenic and Plant Protecting Bacteria Collection, South Africa) = BCC 581T (deposited with the Bacterial Culture Collection, Forestry and Agricultural Institute, South Africa)], Pantoea rwandensis sp. nov. (type strain LMG 26275T = BD 944T = BCC 571T) and Pantoea wallisii sp. nov. (type strain LMG 26277T = BD 946T = BCC 682T) are proposed.

Two novel acetic acid bacteria, strains G5-1T and I5-1, were isolated from traditional kaki vinegar (produced from fruits of kaki, Diospyros kaki Thunb.), collected in Kumamoto Prefecture, Japan. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains G5-1T and I5-1 formed a distinct subline in the genus Gluconacetobacter and were closely related to Gluconacetobacter swingsii DST GL01T (99.3 % 16S rRNA gene sequence similarity). The isolates showed 96–100 % DNA–DNA relatedness with each other, but <53 % DNA–DNA relatedness with closely related members of the genus Gluconacetobacter . The isolates could be distinguished from closely related members of the genus Gluconacetobacter by not producing 2- and 5-ketogluconic acids from glucose, producing cellulose, growing without acetic acid and with 30 % (w/v) d-glucose, and producing acid from sugars and alcohols. Furthermore, the genomic DNA G+C contents of strains G5-1T and I5-1 were a little higher than those of their closest phylogenetic neighbours. On the basis of the phenotypic characteristics and phylogenetic position, strains G5-1T and I5-1 are assigned to a novel species, for which the name Gluconacetobacter kakiaceti sp. nov. is proposed; the type strain is G5-1T ( = JCM 25156T = NRIC 0798T = LMG 26206T).

A bacterial strain designated SW15T was isolated from a sample of the reef-building coral Isopora palifera, collected in southern Taiwan. The novel strain was characterized using a polyphasic taxonomic approach. Cells of strain SW15T were Gram-negative, aerobic, light yellow, rod-shaped and motile by means of a single polar flagellum. In phylogenetic analyses based on 16S rRNA gene sequences, strain SW15T appeared to belong to the genus Idiomarina in the class Gammaproteobacteria and to be most closely related to Idiomarina homiensis PO-M2T (97.6 % sequence similarity). Strain SW15T exhibited optimal growth between 20 and 30 °C, with NaCl between 3 % and 4 % (w/v) and at a pH value between 7 and 8. Predominant cellular fatty acids were iso-C15 : 0 (31.1 %), iso-C17 : 0 (15.4 %), iso-C17 : 1ω9c (10.0 %) and C16 : 0 (8.8 %). The major respiratory quinone was ubiquinone Q-8. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylserine, an uncharacterized aminolipid and several uncharacterized phospholipids. The DNA G+C content was 51.1 mol%. The level of DNA–DNA relatedness between strain SW15T and Idiomarina homiensis PO-M2T was 42.6–56.5 %. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of the novel strain from established species of the genus Idiomarina . Based on the genotypic, phenotypic and chemotaxonomic data, strain SW15T represents a novel species in the genus Idiomarina , for which the name Idiomarina aquimaris sp. nov. is proposed, with SW15T ( = LMG 25374T = BCRC 80083T) as the type strain.