- Volume 65, Issue Pt_1, 2015

An extremely halophilic archaeon, strain IC35T, was isolated from a mud sample of the Aran-Bidgol salt lake in Iran. The novel strain was cream, non-motile, rod-shaped and required at least 2.5 M NaCl, but not MgCl2, for growth. Optimal growth was achieved with 3.4 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.0 (grew over a pH range of 6.5–9.0) and 40 °C (grew over a temperature range of 30–50 °C), respectively. Analysis of 16S rRNA gene sequences revealed that strain IC35T clustered with species of the genus Halovivax , with sequence similarities of 97.3 %, 96.6 % and 96.3 %, respectively, to Halovivax limisalsi IC38T, Halovivax asiaticus EJ-46T and Halovivax ruber XH-70T. The rpoB′ gene similarities between the novel strain and Halovivax limisalsi IBRC-M 10022T, Halovivax ruber JCM 13892T and Halovivax asiaticus JCM 14624T were 90.2 %, 90.2 % and 89.9 %, respectively. The polar lipid pattern of strain IC35T consisted of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester; six unknown glycolipids and two minor phospholipids were also observed. The only quinone present was MK-8 (II-H2). The G+C content of the genomic DNA was 63.2 mol%. DNA–DNA hybridization studies (29 % hybridization with Halovivax limisalsi IBRC-M 10022T), as well as biochemical and physiological characterization, allowed strain IC35T to be differentiated from other species of the genus Halovivax . A novel species, Halovivax cerinus sp. nov., is therefore proposed to accommodate this strain. The type strain is IC35T ( = IBRC-M 10256T = KCTC 4050T).

An anaerobic, rod-shaped, hyperthermophilic and acidophilic crenarchaeon, designated strain CBA1501T, was isolated from solfataric soil of the Mayon volcano in the Republic of the Philippines. Phylogenetic analysis showed that strain CBA1501T is affiliated with the genus Vulcanisaeta in the phylum Crenarchaeota . DNA sequence similarities between the 16S rRNA gene of strain CBA1501T and those of Vulcanisaeta distributa IC-017T and Vulcanisaeta souniana IC-059T were 98.5 and 97.4 %, respectively. Strain CBA1501T grew between 75–90 °C, over a pH range of 4.0–6.0 and in the presence of 0–1.0 % (w/v) NaCl, with optimal growth occurring at 85 °C, pH 5.0, and with 0 % (w/v) NaCl. Fumarate, malate, oxidized glutathione, sulfur and thiosulfate were used as final electron acceptors, but FeCl3, nitrate and sulfate were not. The DNA G+C content of strain CBA1501T was 43.1 mol%. On the basis of polyphasic taxonomic analysis, strain CBA1501T represents a novel species of the genus Vulcanisaeta in the phylum Crenarchaeota , for which we propose the name Vulcanisaeta thermophila sp. nov. The type strain is CBA1501T ( = ATCC BAA-2415T = JCM 17228T).

Strain TS-56T was isolated from the gut of a wood-feeding termite, Reticulitermes chinensis Snyder. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain represented a member of the genus Gryllotalpicola of the family Microbacteriaceae , with sequence similarities to other species of the genus ranging from 96.6 % to 97.8 %. The isolate was Gram-stain-positive, non-motile, with light yellow colonies and irregular short rod-shaped cells (0.4–0.6 µm in diameter, 0.6–1.0 µm in length). Growth of TS-56T occurred at 20–35 °C (optimum, 30 °C) and at pH 4.0–8.0 (optimum, pH 5.0). The peptidoglycan of TS-56T contained ornithine, glutamic acid, alanine, homoserine and glycine. The acyl type was acetyl. The most abundant cellular fatty acid of TS-56T was cyclohexyl-C17 : 0 (88.79 %). The respiratory menaquinone was MK-11. The polar lipid profile contained disphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and two unknown glycolipids. DNA of the type strain had a G+C content of 67.4 mol%. On the basis of the phylogenetic properties and phenotypic distinctiveness, TS-56T represents a novel species of the genus Gryllotalpicola , for which the name Gryllotalpicola reticulitermitis sp. nov. is proposed. The type strain is TS-56T ( = CGMCC 1.10363T = NBRC 109838T).

A strain of a species of the genus Corynebacterium , designated AJ 3170T, was isolated during the 1980s from putrefied bananas. Since then, there have been no further updates on the description of the strain or its phylogenetic classification. However, phylogenetic analysis of this strain using 16S rRNA and in silico DNA–DNA hybridization has confirmed that it is a member of the genus Corynebacterium and that strain AJ 3170T clusters with Corynebacterium variabile DSM 44702T, Corynebacterium terpenotabidum Y-11T and Corynebacterium nuruki S6-4T in one subgroup. Furthermore, a combination of enzymatic, chemical, and morphological characterization techniques was applied in order to describe strain AJ 3170T further. The strain grew well at pH values of 6–10 and at temperatures of 30–41 °C. The major fatty acids were C16 : 0 (42.15 %), C18 : 1ω9c (41.6 %) and C18 : 0 10-methyl (TBSA) (8.56 %). The whole-cell sugars were determined to comprise galactose, arabinose and ribose. On the basis of this phenotypic, chemotaxonomic and phylogenetic characterization, it is proposed that strain AJ 3170T represents a novel species, for which the name Corynebacterium glyciniphilum sp. nov. is proposed; the type strain is AJ 3170T ( = DSM 45795T = ATCC 21341T).

A novel actinomycete, designated strain CA15-2T, was isolated from a soil sample collected from the rhizosphere of tamarisk in the Lop Nor region, Xinjiang, China, and was characterized by using a polyphasic taxonomic approach. Optimal growth occurred at 37 °C and pH 7.5–8.0 and with 5 % (w/v) NaCl. Strain CA15-2T formed white to pale-yellow branched substrate mycelium without fragmentation and sparse aerial mycelium with wavelike curves. Whole-cell hydrolysates of the isolate contained meso-diaminopimelic acid as the diagnostic diamino acid of the cell wall but no diagnostic sugars. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmethylethanolamine, phosphatidylethanolamine, one unidentified glycolipid, one unidentified phospholipid and other unidentified lipids. MK-9(H8), MK-10(H8) and MK-10(H6) were the predominant menaquinones. The major fatty acids were iso-C16 : 0 and C16 : 0. The G+C content of the genomic DNA was 69.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CA15-2T formed a distinct subclade in the family Nocardiopsaceae , with less than 95 % 16S rRNA gene sequence similarity to all known members of the family Nocardiopsaceae . On the basis of the evidence from our polyphasic study, a novel genus, Allosalinactinospora gen. nov., is proposed, with the type species Allosalinactinospora lopnorensis gen. nov., sp. nov. The type strain of Allosalinactinospora lopnorensis is strain CA15-2T ( = DSM 45697T = CGMCC 4.7074T).

We define two novel species of the genus Staphylococcus that are phenotypically similar to and have near identical 16S rRNA gene sequences to Staphylococcus aureus . However, compared to S. aureus and each other, the two species, Staphylococcus argenteus sp. nov. (type strain MSHR1132T = DSM 28299T = SSI 89.005T) and Staphylococcus schweitzeri sp. nov. (type strain FSA084T = DSM 28300T = SSI 89.004T), demonstrate: 1) at a whole-genome level considerable phylogenetic distance, lack of admixture, average nucleotide identity <95 %, and inferred DNA–DNA hybridization <70 %; 2) different profiles as determined by MALDI-TOF MS; 3) a non-pigmented phenotype for S. argenteus sp. nov.; 4) S. schweitzeri sp. nov. is not detected by standard nucA PCR; 5) distinct peptidoglycan types compared to S. aureus ; 6) a separate ecological niche for S. schweitzeri sp. nov.; and 7) a distinct clinical disease profile for S. argenteus sp. nov. compared to S. aureus .

A Gram-reaction-positive, catalase-negative, facultatively anaerobic, rod-shaped lactic acid bacterium, designated strain S215T, was isolated from fermented soybean meal. The organism produced d-lactic acid from glucose without gas formation. 16S rRNA gene sequencing results showed that strain S215T had 98.74–99.60 % sequence similarity to the type strains of three species of the genus Lactobacillus ( Lactobacillus farciminis BCRC 14043T, Lactobacillus futsaii BCRC 80278T and Lactobacillus crustorum JCM 15951T). A comparison of two housekeeping genes, rpoA and pheS, revealed that strain S215T was well separated from the reference strains of species of the genus Lactobacillus . DNA–DNA hybridization results indicated that strain S215T had DNA related to the three type strains of species of the genus Lactobacillus (33–66 % relatedness). The DNA G+C content of strain S215T was 36.2 mol%. The cell walls contained peptidoglycan of the d-meso-diaminopimelic acid type and the major fatty acids were C18 : 1ω9c, C16 : 0 and C19 : 0 cyclo ω10c/C19 : 1ω6c. Phenotypic and genotypic features demonstrated that the isolate represents a novel species of the genus Lactobacillus , for which the name Lactobacillus formosensis sp. nov. is proposed. The type strain is S215T ( = NBRC 109509T = BCRC 80582T).

A Gram-stain-variable, rod-shaped and endospore-forming bacterium, designated strain L7-75, was isolated from duckweed (Lemna aequinoctialis). Cells were motile with a monopolar flagellum. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain L7-75T belonged to the genus Paenibacillus , and the closest phylogenetically related species were Paenibacillus uliginis N3/975T (98.5 % 16S rRNA gene sequence similarity), Paenibacillus purispatii ES_M17T (98.5 %), Paenibacillus lactis MB 1871T (98.2 %), Paenibacillus campinasensis 324T (97.7 %), Paenibacillus glucanolyticus S93T (97.7 %) and Paenibacillus lautus ATCC 43898T (97.4 %). Growth of strain L7-75T was observed at pH 7–10 and at 20–40 °C, and NaCl concentrations up to 5 % (w/v) were tolerated. Major cellular fatty acids included anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0 that were present at 36.0 %, 14.2 % and 10.0 % of the total cellular fatty acid profile, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidyl-N-methylethanolamine. MK-7 was the predominant menaquinone. The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. The DNA G+C content was 49.1 mol% (T m). DNA–DNA relatedness values between strain L7-75T and its closest relatives ranged from 4.4 to 47.8 %. These results indicate that strain L7-75T represents a novel species of the genus Paenibacillus , for which the name Paenibacillus lemnae sp. nov. is proposed. The type strain is L7-75T ( = BCC 67838T = NBRC 109972T).

Strain LTF Kr01T, a novel mesophilic, anaerobic, halotolerant, rod-shaped bacterium, was isolated from a drain at the bottom of a corroded kerosene storage tank of the Société Tunisienne des Industries de Raffinage (STIR), Bizerte, northern Tunisia. Cells were Gram-positive-staining rods, occurred singly or in pairs, and were motile by one lateral flagellum. Strain LTF Kr01T grew at temperatures between 15 and 40 °C (optimum 30 °C), between pH 5.5 and 8.2 (optimum pH 7.2) and at NaCl concentrations between 0 and 50 g l−1 (optimum 5 g l−1). It reduced thiosulfate and elemental sulfur into sulfide, but did not reduce sulfate or sulfite. It utilized a wide range of carbohydrates (cellobiose, d-glucose, d-fructose, d-mannitol, d-ribose, sucrose, d-xylose, maltose, d-galactose, starch and trehalose) and produced acetate, CO2 and H2 as end products from glucose fermentation. The DNA G+C content was 37.4 mol%. The predominant cellular fatty acids were C14 : 0 and C16 : 0. Phylogenetic analysis of the 16S rRNA gene sequence suggested that Fusibacter tunisiensis was the closest relative of strain LTF Kr01T (gene sequence similarity of 94.6 %). Based on phenotypic, phylogenetic and genotypic taxonomic characteristics, strain LTF Kr01T is proposed to represent a novel species of the genus Fusibacter , order Clostridiales , for which the name Fusibacter bizertensis sp. nov. is proposed. The type strain is LTF Kr01T ( = DSM 28034T = JCM 19376T).

A Gram-stain-positive, moderately halophilic, motile, strictly aerobic, endospore-forming, rod-shaped bacterium, strain MY11T, was isolated from a sediment sample collected from the Western Pacific. This isolate grew in the presence of 0.5–18 % (w/v) NaCl and at pH 6.0–10.0 and 15–45 °C; optimum growth was observed with 3.5 % (w/v) NaCl and at pH 8.0–9.0 and 35–37 °C. Strain MY11T had menaquinone 7 (MK-7) as the predominant respiratory quinone and anteiso-C15 : 0 and anteiso-C17 : 0 as major fatty acids. Major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C content was 34.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that strain MY11T was a member of the genus Virgibacillus , exhibiting sequence similarities of 95.3–97.6 % to the type strains of recognized Virgibacillus species. Strain MY11T could be differentiated from recognized species of the genus Virgibacillus based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and DNA–DNA hybridization data. On the basis of the data presented, strain MY11T is considered to represent a novel species of the genus Virgibacillus , for which the name Virgibacillus oceani sp. nov. is proposed. The type strain is MY11T ( = LMG 28105T = CGMCC 1.12754T = MCCC 1A09973T).

A Gram-reaction-positive, endospore-forming, aerobic bacterium, designated strain CY1T, was isolated from iron mineral soil of Hunan Province, China. The isolate was rod-shaped and motile by means of peritrichous flagella. The major cellular fatty acids were anteiso-C15 : 0 and iso-C16 : 0 and the major quinone was menaquinone 7. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol phosphatidylethanolamine. The genomic DNA G+C content was 50.5 mol% and the major diagnostic diamino acid in cell-wall peptidoglycan was meso-diaminopimelic acid. Phylogenetic analyses based on the 16S rRNA gene sequence indicated that strain CY1T is most closely related to Paenibacillus chondroitinus DSM 5051T (97.7 % 16S rRNA gene sequence similarity), Paenibacillus pocheonensis Gsoil 1138T (97.4 %) and Paenibacillus frigoriresistens YIM 016T (97.0 %). DNA–DNA hybridization dissociation values were lower than 49 % with the most closely related species. On the basis of phenotypic, chemotaxonomic and phylogenetic evidence, strain CY1T is affiliated to the genus Paenibacillus , but could be distinguished from the species of this genus. A novel species with the name Paenibacillus ferrarius sp. nov. is proposed. The type strain is CY1T ( = KCTC 33419T = CCTCC AB 2013369T).

Sampling of seafood and dairy processing facilities in the north-eastern USA produced 18 isolates of Listeria spp. that could not be identified at the species-level using traditional phenotypic and genotypic identification methods. Results of phenotypic and genotypic analyses suggested that the isolates represent two novel species with an average nucleotide blast identity of less than 92 % with previously described species of the genus Listeria . Phylogenetic analyses based on whole genome sequences, 16S rRNA gene and sigB gene sequences confirmed that the isolates represented by type strain FSL M6-0635T and FSL A5-0209 cluster phylogenetically with Listeria cornellensis . Phylogenetic analyses also showed that the isolates represented by type strain FSL A5-0281T cluster phylogenetically with Listeria riparia . The name Listeria booriae sp. nov. is proposed for the species represented by type strain FSL A5-0281T ( = DSM 28860T = LMG 28311T), and the name Listeria newyorkensis sp. nov. is proposed for the species represented by type strain FSL M6-0635T ( = DSM 28861T = LMG 28310T). Phenotypic and genotypic analyses suggest that neither species is pathogenic.

A novel thermophilic bacterial strain, CBS-ZT, was isolated from a terrestrial hot spring in the Changbai Mountains, PR China. Cells of strain CBS-ZT were short straight rods without flagella and had Gram-positive cell walls. Growth was observed at 40–90 °C (optimum 75 °C) and at pH 5.6–8.6 (optimum pH 7.8). The primary end-products from the fermentation of filter paper by strain CBS-ZT were acetate, lactate, H2, and CO2. The main cellular fatty acids were iso-C17 : 0, iso-C14 : 0 3-OH and C16 : 0. The G+C content of the genomic DNA was 36.08 mol%. Multiple sequence alignment of the 16S rRNA gene sequence and phylogenetic analyses indicated that strain CBS-ZT belongs to the genus Caldicellulosiruptor and the most similar micro-organism was Caldicellulosiruptor saccharolyticus DSM 8903T (96.36 % 16S rRNA gene sequence similarity); the 16S rRNA gene sequence similarity of strain CBS-ZT to other species was below 95 %. Based on its phylogenetic and phenotypic characteristics, strain CBS-ZT represents a novel species of the genus Caldicellulosiruptor , for which the name Caldicellulosiruptor changbaiensis sp. nov. is proposed. The type strain is CBS-ZT ( = DSM 26941T = CGMCC 1.5180T).

An aerobic, Gram-stain-negative, non-motile coccus, designated strain GVCNT2T, was isolated from the tonsils of a healthy adult female. Cells were oxidase- and catalase-positive, positive for the production of esterase (C4), esterase lipase (C8) and leucine arylamidase, and weakly positive for naphthol-AS-BI-phosphohydrolase and alkaline phosphatase. Cells were also capable of hydrolysing DNA. Growth was observed at 20–37 °C and in the presence of up to 1.5 % NaCl. Phylogenetic analysis of near full-length 16S rRNA gene sequences indicated that the strain exhibited closest sequence similarity to Moraxella boevrei ATCC 700022T (94.68 %) and an uncultured, unspeciated bacterial clone (strain S12-08; 99 %). The major fatty acids were C18 : 1ω9c, C18 : 0, C16 : 0 and C16 : 1ω6c/C16 : 1ω7c. The DNA G+C content of strain GVCNT2T was 40.7 mol%. The major respiratory quinone identified was Q-8. Strain GVCNT2T exhibited a comparable phenotypic profile to other members of the genus Moraxella but could be distinguished based on its ability to produce acid (weakly) from d-glucose, melibiose, l-arabinose and rhamnose and on its ability to hydrolyse DNA. On the basis of phenotypic and phylogenetic differences from other members of the family Moraxellaceae , strain GVCNT2T is considered to represent a novel species of a new genus, for which the name Faucicola mancuniensis gen. nov., sp. nov. is proposed. The type strain of Faucicola mancuniensis is GVCNT2T ( = DSM 28411T = NCIMB 14946T).

Six isolates recovered from coffee seeds giving off a potato-like flavour were studied. Gene sequencing (rrs and rpoB) showed they belong to the genus Pantoea . By DNA–DNA hybridization, the isolates constituted a genomic species with less than 17 % relatedness to 96 strains representing enterobacterial species. Multilocus sequence analysis (gyrB, rpoB, atpD and infB genes) showed the isolates to represent a discrete species of the genus Pantoea . Nutritional versatility of the novel species was poor. The novel species is proposed as Pantoea coffeiphila sp.nov. and its type strain is Ca04T ( = CIP 110718T = DSM 28482T).

Several strains of aerobic, acidophilic, chemo-organotrophic bacteria belonging to the genus Acidiphilium were isolated from an acid mine drainage (AMD) (pH 2.2) treatment plant. 16S rRNA gene sequence comparisons showed that most of the novel isolates formed a phylogenetically coherent group (designated Group Ia) distinguishable from any of the previously established species of the genus Acidiphilium at <98 % similarity. This was supported by genomic DNA–DNA hybridization assays. The Group Ia isolates were characterized phenotypically by an oval cell morphology, non-motility, growth in the range pH 2.0–5.5 (optimum pH 3.5), lack of photosynthetic pigment and the presence of C19 : 0 cyclo ω8c as the main component of the cellular fatty acids and ubiquinone-10 as the major quinone. On the basis of these data, the name Acidiphilium iwatense sp. nov. is proposed to accommodate the Group Ia isolates, and the description of the genus Acidiphilium is emended. The type strain of Acidiphilium iwatense sp. nov. is MS8T ( = NBRC 107608T = KCTC 23505T).