- Volume 59, Issue 5, 2009

A Gram-positive-staining, filamentous bacterial strain that developed cylindrical sporangia containing four oval- to rod-shaped spores at the ends of short sporangiophores on branched aerial mycelium was isolated from tropical rainforest soil near a hot spring. The cell-wall peptidoglycan contained meso-diaminopimelic acid, glutamic acid and alanine as cell-wall amino acids; the whole-cell hydrolysate contained rhamnose, madurose, glucose, galactose and 3-O-methylmannose as whole-cell sugars. The predominant menaquinone was MK-9(H4). Mycolic acids were not detected. The diagnostic phospholipid was phosphatidylethanolamine. The predominant cellular fatty acids were iso-C16 : 0 and 10-methylated C17 : 0. The G+C content of the DNA was 71.1 mol%. The phenotypic and chemotaxonomic analyses showed that the isolate had characteristics typical of members of the genus Planotetraspora. Furthermore, 16S rRNA gene sequence analysis also indicated that this strain belongs to the genus Planotetraspora, but as a putative novel species. Following phenotypic, chemotaxonomic and genotypic studies, the isolate is proposed to be a representative of a novel species, to be named Planotetraspora thailandica sp. nov. The type strain is BCC 21825T (=NBRC 104271T). An emended description of the genus Planotetraspora is also presented.

The taxonomic position of the cholesterol-degrading strain Chol-3T, isolated from a sewage sludge sample, was clarified using a polyphasic taxonomic approach. Phylogenetic analysis of its 16S rRNA gene sequence, whole-cell fatty acid profile and mycolic acid composition revealed that this isolate is a member of the genus Gordonia with the species Gordonia sihwensis, G. hydrophobica and G. shandongensis being the nearest phylogenetic neighbours. The results of DNA–DNA hybridization against its phylogenetically closest neighbours as well as the results of physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain Chol-3T from the other Gordonia species with validly published names. Strain Chol-3T therefore merits recognition as a member of a novel species within the genus Gordonia, for which the name Gordonia cholesterolivorans sp. nov. is proposed. The type strain is Chol-3T (=CECT 7408T =DSM 45229T).

Two strains of non-spore-forming, rod-shaped, Gram-positive bacteria, CIP 101303T and CIP 102116, were isolated from human blood in 1976 and 1977, respectively. These strains had chemotaxonomic markers that were consistent with classification in the genus Microbacterium, i.e. MK-10, MK-11 and MK-12 as the major menaquinones, predominant iso- and anteiso-branched cellular fatty acids, galactose, mannose and rhamnose as the cell-wall sugars and ornithine as the diamino acid in the cell-wall peptidoglycan. The DNA G+C content was 70–72 mol%. Comparative 16S rRNA gene sequence studies revealed that strains CIP 101303T and CIP 102116 belonged to the genus Microbacterium and that they were related closely to Microbacterium halotolerans. The level of DNA–DNA relatedness showed that the two isolates represented a separate genomic species. Based on phenotypic and genotypic results, it is proposed that strains CIP 101303T and CIP 102116 be assigned to a novel species, Microbacterium binotii sp. nov. The type strain is CIP 101303T (=DSM 19164T).

Two actinomycete strains, designated YIM 56256T and YIM 61331T, were isolated from the roots of Scoparia dulcis and Maytenus austroyunnanensis, two Chinese medicinal plants, and their taxonomic status was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Glycomyces. 16S rRNA gene sequence analysis showed that they were closely related to each other and to Glycomyces sambucus E71T. A battery of physiological characteristics and levels of DNA–DNA relatedness indicated that strains YIM 56256T and YIM 61331T represent two novel species, clearly different from the related known Glycomyces species. On the basis of the data presented, it is evident that each of these strains represents a novel species of the genus Glycomyces, for which the names Glycomyces scopariae sp. nov. (type strain YIM 56256T =KCTC 19158T =DSM 44968T) and Glycomyces mayteni sp. nov. (type strain YIM 61331T =KCTC 19527T =CCTCC AA 208004T) are proposed.

A non-chromogenic, slowly growing Mycobacterium strain was isolated from a maxillary sinus lavage from a symptomatic patient in Riyadh, Saudi Arabia. It was initially identified as a member of the Mycobacterium tuberculosis complex by a commercial line-probe assay. Its 16S rRNA, hsp65 and rpoB gene and 16S–23S internal transcribed spacer sequences were unique; phylogenetic analysis based on the 16S rRNA gene sequence groups this organism close to Mycobacterium szulgai and Mycobacterium malmoense. Its unique biochemical properties and mycolic acid profile support separate species status. We propose the name Mycobacterium riyadhense sp. nov. to accommodate this strain. The type strain is NLA000201958T (=CIP 109808T =DSM 45176T).

A Gram-positive bacterial strain, designated YIM 56238T, was isolated from plant roots (Aquilaria sinensis), and characterized by using a polyphasic approach. Strain YIM 56238T grew optimally at pH 7.0–8.0 and at 28 °C. Analysis of the 16S rRNA gene sequence of strain YIM 56238T indicated that it belongs to the genus Micrococcus. Chemotaxonomic data strongly supported the classification of this strain within the genus Micrococcus: the cell-wall peptidoglycan contained lysine, glutamic acid, alanine and glycine; the predominant menaquinones were MK-8(H2) (63.6 %) and MK-7(H2) (21.1 %); the phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unknown ninhydrin-negative phospholipid; and the major cellular fatty acids were iso-C15 : 0 (30.95 %) and anteiso-C15 : 0 (53.75 %). The G+C content of the genomic DNA was 72.9 mol%. A number of physiological features were found that clearly distinguished strain YIM 56238T from recognized species of the genus Micrococcus. DNA–DNA hybridization studies suggested that the novel strain represents a separate genomic species. On the basis of the data, therefore, strain YIM 56238T represents a novel species of the genus Micrococcus, for which the name Micrococcus endophyticus sp. nov. is proposed. The type strain is YIM 56238T (=DSM 17945T=KCTC 19156T).

An actinomycete isolated from soil from a field of grass was analysed using a polyphasic taxonomic approach. The organism, designated strain W12T, was found to have a range of chemical and morphological properties consistent with its classification in the genus Saccharopolyspora. An almost-complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences for representatives of the genus Saccharopolyspora, using two tree-making algorithms. The novel organism formed a monophyletic clade with the type strain of Saccharopolyspora antimicrobica, but the DNA–DNA relatedness value was low. Strain W12T also had a phenotypic profile that readily distinguished it from recognized representatives of the genus Saccharopolyspora. It is evident from the combined genotypic and phenotypic data that the new organism should be classified as a novel species of the genus Saccharopolyspora. The name proposed for this new taxon is Saccharopolyspora jiangxiensis sp. nov., with strain W12T (=CGMCC 4.3529T=JCM 14613T) as the type strain.

Two novel extremely acidophilic, iron-oxidizing actinobacteria were isolated, one from a mine site in North Wales, UK (isolate T23T), and the other from a geothermal site in Yellowstone National Park, Wyoming, USA (Y005T). These new actinobacteria belong to the subclass Acidimicrobidae, and in contrast to the only other classified member of the subclass (Acidimicrobium ferrooxidans), both isolates were obligate heterotrophs. The mine site isolate was mesophilic and grew as small rods, while the Yellowstone isolate was a moderate thermophile and grew as long filaments, forming macroscopic flocs in liquid media. Both isolates accelerated the oxidative dissolution of pyrite in yeast extract-amended cultures, but neither was able to oxidize reduced forms of sulfur. Ferrous iron oxidation enhanced growth yields of the novel mesophilic actinobacterium T23T, though this was not confirmed for the Yellowstone isolate. Both isolates catalysed the dissimilatory reduction of ferric iron, using glycerol as electron donor, in oxygen-free medium. Based on comparative analyses of base compositions of their chromosomal DNA and of their 16S rRNA gene sequences, the isolates are both distinct from each other and from Acidimicrobium ferrooxidans, and are representatives of two novel genera. The names Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov. are proposed for the mesophilic and moderately thermophilic isolates, respectively, with the respective type strains T23T (=DSM 19497T=ATCC BAA-1647T) and Y005T (=DSM 19514T=ATCC BAA-1645T).

A brown–orange-pigmented, non-spore-forming, coccus-shaped actinomycete, designated S2-20T, was isolated from desert sand from Xinjiang Province in China. The isolate stains Gram-positive, is motile and produces a brownish diffusible pigment. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain S2-20T was phylogenetically affiliated to the genus Kineococcus, and the sequence similarity to the type strains of Kineococcus species was less than 96 %, making it clear that strain S2-20T represents a species that is separate from recognized Kineococcus species. Its major fatty acid was anteiso-C15 : 0. The major menaquinone was MK-9(H2). Whole-cell hydrolysates of strain S2-20T contained meso-diaminopimelic acid, arabinose and galactose. The DNA G+C content was 77.8 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain S2-20T should be classified within a novel species of the genus Kineococcus, for which the name Kineococcus xinjiangensis sp. nov. is proposed. The type strain is S2-20T (=CCTCC AB 207179T =KCTC 19474T).

Three Gram-positive, rod-shaped, oxidase-negative, non-spore-forming, non-motile bacteria (KSS-3SeT, KSS-4Se and KSS-10Se) were isolated from a coolant lubricant. 16S rRNA gene sequence analyses revealed almost identical sequences, with only a few (<10 positions) differences for these three isolates. Comparisons showed the highest similarities to Corynebacterium pilosum NCTC 11862T (97.6 % similarity with strain KSS-3SeT). Similarities with other established Corynebacterium species were lower than 97.0 %. Chemotaxonomic data studied for strain KSS-3SeT [polar lipids – major compounds phosphatidylglycerol and an unknown glycolipid, moderate amounts of phosphatidylinositol and diphosphatidylglycerol; polyamines (small amounts) – major compounds spermidine and spermine; quinones – significant amounts of menaquinones MK-9(H2), MK-8(H2) and MK-7(H2); and major fatty acids – tuberculostearic acid (10-methyl C18 : 0), C16 : 0 and C18 : 1 ω9c] were congruent with those reported for Corynebacterium. The strain showed differences in phenotype from C. pilosum. DNA–DNA hybridizations between KSS-3SeT and C. pilosum DSM 20521T yielded a relatedness of 22.9 % (20.4 % in the reciprocal assay). From these results, it is evident that the organisms represent a novel species, for which the name Corynebacterium lubricantis sp. nov. is proposed (type strain KSS-3SeT =DSM 45231T =CCUG 56567T =CCM 7546T).

The taxonomic status of a bacterium isolated from a patient with bronchial carcinoma was established using a polyphasic taxonomic approach. The strain had morphological and chemotaxonomic characteristics consistent with those of members of the genus Saccharopolyspora. The generic assignment was confirmed by comparative analysis of the 16S rRNA gene sequence, which showed that the strain constituted a distinct phyletic line, displaying 93.5–96.9 % sequence similarity with respect to members of the genus Saccharopolyspora. The isolate was distinguished from the type strains of recognized members of the genus Saccharopolyspora by means of various biochemical tests. The genotypic and phenotypic data obtained demonstrated that strain IMMIB L-1070T represents a novel species of the genus Saccharopolyspora, for which the name Saccharopolyspora rosea sp. nov. is proposed. The type strain is IMMIB L-1070T (=DSM 45226T=CCUG 56401T).

Peatlands are important sources of CH4 emissions to the atmosphere and molecular surveys have identified a diverse, but mainly uncultured, euryarchaeal community in them. Characterization of a strain, E1-9cT, associated with uncultured group E1, from a minerotrophic fen is reported. Cells were regular cocci, usually found in pairs, that stained Gram-positive and were resistant to lysis by 0.1 % SDS. Multiple flagella were observed, but motility was not observed in wet mounts. Optimal growth was obtained at moderate temperatures (28–30 °C) and slightly acidic pH (5.5). Total Na+ and NaCl were only tolerated at concentrations less than 100 mM and 0.5 %, respectively, and Na2S concentrations above 0.1 mM were inhibitory. H2/CO2 and formate were the only methanogenic substrates used by E1-9cT; formate concentrations above 50 mM were inhibitory for growth. Vitamins, coenzyme M and acetate (4 mM) were required for growth and the doubling time was about 19 h. Phylogenetic analysis of the 16S rRNA gene and inferred McrA amino acid sequences showed that E1-9cT represented an independent lineage within the order Methanomicrobiales. Physiological and phylogenetic comparisons with different members of the order supported classification of E1-9cT in a new genus in the Methanomicrobiales. The name Methanosphaerula palustris gen. nov., sp. nov. is proposed; strain E1-9cT (=ATCC BAA-1565T =DSM 19958T) is the type strain of Methanosphaerula palustris.

A methanogenic organism from the domain Archaea (SD1T) was isolated from saline water released from a coal seam located 926 m below the surface via a methane-producing well near Monroe, Louisiana, USA. Growth and methanogenesis were supported with methanol, monomethylamine, dimethylamine or trimethylamine, but not with dimethylsulfide, formate, acetate or H2/CO2. Cells grew in high-salt minimal medium but growth was stimulated with yeast extract or tryptone. Cells were single, non-motile, irregular coccoids 0.5–1.0 μm in diameter and the cell wall contained protein. Conditions for the maximum rate of growth were 40–50 °C, 0.2–0.6 M NaCl, 100–≥200 mM MgCl2, and pH 7.0–8.0. The G+C content of the genomic DNA was 42±1mol %. A comparison of 16S rRNA gene sequences indicated that strain SD1T was most closely related to Methanolobus oregonensis DSM 5435T with 96 % gene sequence similarity. It is proposed that strain SD1T represents a novel species, Methanolobus zinderi sp. nov. The type strain is SD1T (=ATCC BAA-1601T=DSM 21339T).

A novel strain, designated Jip 10T, isolated from dried rice straw, was characterized by a polyphasic approach to clarify its taxonomic position. The isolate was Gram-negative, facultatively aerobic, heterotrophic, non-motile, non-spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate clustered with the genus Mucilaginibacter in the phylum Bacteroidetes. 16S rRNA gene sequence similarities between strain Jip 10T and the type strains of Mucilaginibacter gracilis and Mucilaginibacter paludis were 93.7 and 93.6 %, respectively. The G+C content of the genomic DNA was 48.1 mol%. Chemotaxonomic data [major menaquinone MK-7 and major fatty acids iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c)] supported the affiliation of strain Jip 10T to the genus Mucilaginibacter. However, the results of physiological and biochemical tests allowed phenotypic differentiation of strain Jip 10T from other Mucilaginibacter species with validly published names. Therefore, strain Jip 10T (=KCTC 12639T =LMG 23488T) was classified in the genus Mucilaginibacter as the type strain of a novel species, for which the name Mucilaginibacter daejeonensis sp. nov. is proposed.

A Gram-negative, strictly aerobic, motile, filamentous and viscous exopolymer-producing bacterium, designated strain YT21T, was isolated from fresh water. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain YT21T lies within a cluster containing the established genera Segetibacter, Terrimonas, Niastella and Chitinophaga in the phylum Bacteroidetes. However, the isolate represented a lineage distinct from these genera, with sequence similarities ranging from 88.9 to 91.8 %. The genomic G+C content was 45.2 mol%. The predominant isoprenoid quinone was MK-7. The major fatty acids were 15 : 0 iso, 17 : 0 iso 3-OH and 15 : 1 iso G. On the basis of morphological features and phenotypic and phylogenetic data, strain YT21T represents a novel genus and species, for which the name Filimonas lacunae gen. nov., sp. nov. is proposed. The type strain of Filimonas lacunae is strain YT21T (=NBRC 104114T =DSM 21054T).

A novel strain, NJ-8T, was isolated from sediment of the eutrophic Taihu Lake (China) and was subjected to a taxonomic study by using a polyphasic approach. The novel strain was aerobic and formed orange-pigmented colonies on R2A agar. Cells were Gram-negative single rods that were motile by means of gliding. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain NJ-8T belonged to the phylum Bacteroidetes, with Niastella yeongjuensis DSM 17621T (92.3 % gene sequence similarity) and Niastella koreensis DSM 17620T (92.0 % similarity) as its closest relatives. The major fatty acids (>5 % of the total) were iso-C15 : 0 (27.8 %), iso-C15 : 1 G (15.4 %), iso-C17 : 0 3-OH (14.5 %) and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 13.9 %). The genomic DNA G+C content was 46.6 mol%. Based on molecular and phenotypic data, strain NJ-8T is considered to represent a novel species of a new genus, for which the name Lacibacter cauensis gen. nov., sp. nov. is proposed. The type strain of the type species of the genus, Lacibacter cauensis, is NJ-8T (=CGMCC 1.7271T=NBRC 104930T).

A Gram-negative, rod-shaped bacterium, designated strain YC6274T, was isolated from a stream (Sasang) carrying wastewater polluted with heavy metals in Busan, Korea. Growth was observed at 10–35 °C (optimum, 30 °C) and pH 6.0–9.5 (optimum, pH 7.5–8.0). Comparative 16S rRNA gene sequence analyses showed that the strain was most closely related to Flavobacterium cucumis R2A45-3T (96.6 % similarity), F. aquatile ATCC 11947T (93.7 %), F. croceum EMB47T (93.3 %), F. indicum GPTSA100-9T (93.3 %) and F. terrigena DS-20T (93.2 %). Sequence similarities with strains of other Flavobacterium species with validly published names were lower than 93.0 %. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain YC6274T formed a distinct phyletic lineage within the genus Flavobacterium. The predominant fatty acids of strain YC6274T were iso-C15 : 0, iso-C16 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH and iso-C15 : 0 3-OH. The G+C content of the genomic DNA was 32.5 mol% and the major quinone was MK-6. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain YC6274T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium sasangense sp. nov. is proposed. The type strain is YC6274T (=KCTC 22246T =DSM 21067T).

An irregular, long, rod-shaped marine bacterium, designated CL-CB462T, was isolated from a Synechococcus culture, which was established from surface water from the tropical Pacific Ocean. The physiological and biochemical features, fatty acid profile and phylogenetic position based on 16S rRNA gene sequences were investigated for the novel strain. Phylogenetic analysis of the 16S rRNA gene sequence showed that the closest relatives of strain CL-CB462T were Balneola vulgaris and Balneola alkaliphila. Strain CL-CB462T formed a robust clade with members of the genus Balneola in all phylogenetic trees constructed by three different methods. However, the 16S rRNA gene sequence similarity was very low (91.3–91.5 % similarity) and phenotypic and physiological features could clearly differentiate strain CL-CB462T from the genus Balneola. Cells of the novel strain were non-motile and spore-forming. The strain was able to grow at 1–20 % (w/v) (optimum of 3–6 %) sea salt concentration, at temperatures of 20–40 °C and between pH 6 and 10. The fatty acids were dominated by 15 : 0 iso (41.2 %) and 17 : 1ω9c iso (21.4 %). The DNA G+C content was 42.7 mol%. Based on polyphasic evidence, strain CL-CB462T was considered to represent a new genus. The name Gracilimonas tropica gen. nov., sp. nov. is proposed for the type strain of the type species (CL-CB462T=KCCM 90063T=DSM 19535T).

A Gram-negative, strictly aerobic, non-spore-forming, rod-shaped, red–pink bacterium, designated strain Dae14T, was isolated from stream sediment collected near Daecheong Dam, South Korea, and its taxonomic position was investigated by using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that strain Dae14T belonged to the genus Hymenobacter. Sequence similarities between strain Dae14T and the type strains of Hymenobacter species with validly published names ranged from 91.3 to 94.3 %. The predominant cellular fatty acids of strain Dae14T were iso-C15 : 0, C16 : 1 ω5c, summed feature 5 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and iso-C16 : 0. The DNA G+C content was 62.2 mol%. Results of phylogenetic, chemotaxonomic and phenotypic characterization indicated that strain Dae14T can be distinguished from all known Hymenobacter species and represents a novel species, for which the name Hymenobacter daecheongensis sp. nov. is proposed, with Dae14T (=KCTC 22258T=LMG 24498T) as the type strain.

A novel strain, designated MRN461T, was isolated from a marine sponge in Micronesia. The 16S rRNA gene sequence of the isolate showed 95.6 % similarity with that of ‘Microscilla furvescens’ IFO (now NBRC) 15994. Phylogenetic analysis revealed that the isolate and ‘Microscilla furvescens’ IFO 15994 formed a distinct phyletic line within the family ‘Flexibacteraceae’. Cells of strain MRN461T were Gram-negative, long filamentous rods, motile by gliding. Growth was observed at 15–40 °C (optimum, 33 °C), at pH 5.0–9.5 (optimum, pH 7.5) and in the presence of 0.5–7.0 % sea salts (optimum, 2.5 %). The major isoprenoid quinone was MK-7. The dominant fatty acids were summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 34.8 %), C16 : 1 ω5c (21.6 %) and iso-C16 : 1 (19.8 %). The DNA G+C content was 41.5 mol%. On the basis of evidence from our polyphasic taxonomic study, strain MRN461T is classified within a novel genus and species in the family ‘Flexibacteraceae’, for which the name Marinoscillum pacificum gen. nov., sp. nov. is proposed. The type strain of Marinoscillum pacificum is strain MRN461T (=KCCM 42325T =JCM 14064T). The misclassified species ‘[Microscilla] furvescens’ is transferred to the new genus as Marinoscillum furvescens (ex Lewin 1969) nom. rev., comb. nov., with LMG 13023T (=DSM 4134T =ATCC 23129T =NBRC 15994T) as the type strain.

A novel lactic acid bacterium, strain TMW 2.694T, was isolated among other lactic acid bacteria from palm wine, an alcoholic beverage produced from the sap of various palm tree species. Strain TMW 2.694T is a Gram-positive, facultatively anaerobic, catalase-negative, non-spore-forming coccus, occurring in long chains. Phylogenetic analysis based on 16S rRNA gene sequencing positioned strain TMW 2.694T in a distinct line of descent within the genus Leuconostoc, with the closest neighbours being Leuconostoc lactis JCM 6123T (98.7 % sequence similarity) and Leuconostoc citreum DSM 5577T (98.8 % sequence similarity). Comparative sequencing of the additional phylogenetic markers dnaK and recA confirmed the 16S rRNA gene tree topology. Genomic DNA–DNA similarities of strain TMW 2.694T to L. lactis DSM 20202T and L. citreum DSM 5577T were 45.1 and 17.7 %, respectively. The DNA G+C content is 36.4 mol%. Thus, we propose a novel species within the genus Leuconostoc, with the name Leuconostoc palmae sp. nov. and the type strain TMW 2.694T (=DSM 21144T =LMG 24510T).

A taxonomic study was performed on strain HR1T, which was isolated from a desert soil sample collected from Xinjiang Province (China). Cells were aerobic, Gram-positive-staining, pink-pigmented, sporulating rods with a single lateral flagellum. The organism can grow at 15–42 °C and pH 5.0–10.0, optimally at 30–37 °C and pH 6.0–8.0. Growth is inhibited by 6 % NaCl. Analysis of almost-complete 16S rRNA gene sequence revealed that the isolate represents a distinct taxon within the genus Saccharibacillus; Saccharibacillus sacchari LMG 24085T was the nearest relative (97.9 % sequence similarity). DNA–DNA hybridization showed 29.6 % genetic relatedness between strain HR1T and S. sacchari LMG 24085T. The major isoprenoid quinone was MK-7 and the predominant fatty acid was anteiso-C15 : 0 (50.3 %). The G+C content of the DNA was 50.5 mol%. Therefore, based on phenotypic criteria and the phylogenetic position, strain HR1T belongs to a previously unidentified species of the genus Saccharibacillus, for which the name Saccharibacillus kuerlensis sp. nov. is proposed. The type strain is HR1T (=KCTC 13182T =JCM 14865T =CGMCC 1.6964T).

A strictly anaerobic, thermophilic bacterium, designated strain B2-1T, was isolated from microbial mats colonizing a runoff channel formed by free-flowing thermal water from a Great Artesian Basin, Australia, bore well (registered number 17263). The cells of strain B2-1T were slightly curved rods (3.0–3.5×0.6–0.7 μm) which stained Gram-negative. The strain grew optimally in tryptone-yeast extract-glucose medium at 50 °C (temperature growth range 30–55 °C) and a pH of 8 (pH growth range 6.5–9). Strain B2-1T grew poorly on yeast extract (0.2 %) and/or tryptone (0.2 %), which were obligately required for growth on other energy sources, including a range of other carbohydrates and organic acids, but not amino acids. The end-products of glucose fermentation were ethanol and acetate. In the presence of 0.2 % yeast extract, iron(III), manganese(IV) and elemental sulfur were reduced but sulfate, thiosulfate, sulfite, nitrate and nitrite were not reduced. Growth was inhibited by chloramphenicol, streptomycin, tetracycline, penicillin, ampicillin, sodium azide and by NaCl concentrations greater than 4 % (w/v). The DNA G+C content was 48±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis indicated that strain B2-1T was a member of the family Clostridiaceae, class Clostridia, phylum Firmicutes and was most closely related to Geosporobacter subterraneus DSM 17957T (89.9 % similarity). On the basis of 16S rRNA gene sequence comparisons and physiological characteristics, strain B2-1T is considered to represent a novel species of a new genus, for which the name Thermotalea metallivorans gen. nov., sp. nov. is proposed. The type strain is B2-1T (=KCTC 5625T=JCM 15105T=DSM 21119T).

A strictly anaerobic, mesophilic, cellulolytic bacterial strain, designated CDT-1T, was isolated from rice-straw residue from a methanogenic reactor treating waste from cattle farms. The isolation was performed using enrichment culture with filter paper as a substrate. Cells stained Gram-negative, but reacted Gram-positively in the KOH test. Cells were slightly curved rods and were motile by means of peritrichous flagella. The strain produced yellow pigment when grown on filter-paper fragments. Although spore formation was not confirmed microscopically, thermotolerant cells were produced when the strain was grown on filter paper. The optimum temperature for growth was 33 °C and the optimum pH was 7.4. Oxidase, catalase and nitrate-reducing activities were absent. The strain utilized xylose, fructose, glucose, cellobiose, xylooligosaccharide, cellulose (filter-paper fragments and ball-milled filter paper) and xylan. The major fermentation products were acetate, ethanol, H2 and CO2. The major cellular fatty acids were iso-C15 : 0, iso-C14 : 0 and C16 : 0 DMA. The cell-wall peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. The genomic DNA G+C content was 40.7 mol%. On the basis of 16S rRNA gene sequence similarities, strain CDT-1T could be placed in cluster III of the genus Clostridium, being closely related to type strains of Clostridium hungatei (96.6 % sequence similarity), Clostridium termitidis (96.2 %) and Clostridium papyrosolvens (96.1 %). On the basis of the cellular, physiological and phylogenetic differences between CDT-1T and its close relatives, this strain represents a novel species of the genus Clostridium, for which the name Clostridium sufflavum sp. nov. is proposed. The type strain is CDT-1T (=JCM 14807T=DSM 19573T).

Pu'er tea is a fermented drink made from the leaves of the tea plant, Camellia sinensis. Two novel bacteria, designated strains b09i-3T and b13i-1, were isolated during the process of fermentation of this tea. These isolates were Gram-positive, endospore-forming, motile rods that grew at 25–42 °C and pH 5.5–10.4. The DNA G+C content was 56.6–58.4 mol%, the predominant isoprenoid quinone was MK-7 and the predominant cellular fatty acid was anteiso-C15 : 0 (49.0–50 % of the total). Phylogenetic analysis based on 16S rRNA gene sequences showed that strains b09i-3T and b13i-1 shared 99.9 % similarity and were affiliated with a cluster within the family Paenibacillaceae. Strains b09i-3T and b13i-1 were related most closely to Paenibacillus ginsengihumi DCY16T (97 % 16S rRNA gene sequence similarity). Levels of DNA–DNA relatedness between the two novel isolates and P. ginsengihumi DCY16T were below 56 %. The phylogenetic and phenotypic characteristics of these novel isolates allowed them to be distinguished clearly from recognized species of the genus Paenibacillus. Based on these data, strains b09i-3T and b13i-1 are considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus pueri sp. nov. is proposed. The type species is b09i-3T (=KCTC 13223T=CECT 7360T).

A Gram-positive, coccus-shaped, lactic acid bacterium, strain NGRI 0510QT, was isolated from ryegrass silage produced in Okinawa Prefecture, Japan. The cell is non-spore-forming, non-motile, and occurs in pairs or tetrads. The strain is homofermentative and produces d- and l-lactic acid from glucose. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain NGRI 0510QT belongs to the genus Pediococcus and clusters within the Pediococcus acidilactici and Pediococcus pentosaceus group, with 98.2 and 96.9 % sequence identity, respectively. DNA–DNA relatedness between strain NGRI 0510QT and P. acidilactici JCM 8797T and P. pentosaceus JCM 5890T was 19.3 and 17.3 %, respectively. Based on its phenotypic characteristics, phylogenetic relationship and DNA–DNA relatedness, NGRI 0510QT (=JCM 15055T=DSM 19927T) represents the type strain of a novel species, for which the name Pediococcus lolii sp. nov. is proposed.

Following the transfer of three of the six species enclosed in the original definition of rRNA group 2 of Bacillus to the genus Sporosarcina and two to Lysinibacillus, other species of this group, some of which were added later, still await taxonomic revision. In a recent publication, a set of ‘core’ characteristics was proposed for species to be included in the genus Bacillus ( Kämpfer et al., 2006 ). Except for Bacillus silvestris, however, several or none of these properties are available for members of rRNA group 2. According to our analysis of data including the ‘core’ characteristics, Bacillus silvestris should not be a member of the genus Bacillus. We therefore propose the establishment of a new genus, Solibacillus gen. nov., and transfer Bacillus silvestris to this genus as Solibacillus silvestris comb. nov., with the type strain HR3-23T (=DSM 12223T=ATCC BAA-269T=CIP 106059T).

Strains of aerobic, Gram-positive, rod-shaped, round-spore-forming bacteria were isolated from different geographical locations and a subsequent polyphasic study was undertaken to clarify the taxonomic position of the round-spore-forming isolates strain KSC-SF6gT, strain M32 and strain NBRC 12622. 16S rRNA gene sequence similarities demonstrated that these strains were most closely affiliated with Bacillus pycnus NRRL NRS-1691T (98 %), with species of Kurthia (96 %) and Viridibacillus (94–96 %) as the next nearest relatives. However, while DNA–DNA hybridization studies showed approx. 70 % reassociation among strains KSC-SF6gT, M32 and NBRC 12622, DNA–DNA hybridization values between these strains and B. pycnus NRRL NRS-1691T never exceeded 13 %. Differences in the molecular structure of the cell-wall peptidoglycan could not differentiate these strains sufficiently from other closely related genera (Viridibacillus and Kurthia). However, Lys–Asp was present in strains KSC-SF6gT, M32 and NBRC 12622, whereas l-Lys–d-Glu was reported in B. pycnus NRRL NRS-1691T. The menaquinone MK-7 was dominant in strains KSC-SF6gT, M32 and NBRC 12622 and members of the genus Kurthia, whereas MK-8 was abundant in Viridibacillus species. Strains KSC-SF6gT, M32 and NBRC 12622 exhibited fatty acid profiles consisting of major amounts of anteiso-C15 : 0 (∼50 %) and iso-C15 : 0 (∼25 %) and moderate amounts of anteiso-C17 : 0 (∼7 %), which discriminated them from closely related B. pycnus NRRL NRS-1691T and species of Viridibacillus (iso-C15 : 0; 46–74 %). The authors propose that strains KSC-SF6gT, M32 and NBRC 12622 and B. pycnus NRRL NRS-1691T be reclassified into a separate genus based on clear-cut differences in discriminative taxonomic markers and the distant placement of B. pycnus and the novel strains described herein from other species of this clade according to current 16S rRNA gene sequence-based relatedness (∼4 % difference in sequence). We propose the placement of these isolates into the novel genus Rummeliibacillus gen. nov. For the new taxon comprising strains KSC-SF6gT, M32 and NBRC 12622, we propose the name Rummeliibacillus stabekisii gen. nov., sp. nov. (the type species of Rummeliibacillus), represented by the type strain KSC-SF6gT (=NRRL B-51320T =NBRC 104870T). In addition, Bacillus pycnus, which bears traits distinct from other round-spore-forming species [i.e. absence of growth at high NaCl (7 %), positive reaction for gelatin liquefaction], is reclassified as Rummeliibacillus pycnus comb. nov. (type strain JCM 11075T =NRRL NRS-1691T) based on phylogenetic affiliations and phenotypic characterization.

A strictly anaerobic, thermophilic bacterium, designated strain Y170T, was isolated from a microbial mat colonizing thermal waters of a run-off channel created by the free-flowing waters of a Great Artesian Basin (GAB) bore well (New Lorne bore; registered number 17263). Cells of strain Y170T were slightly curved rods (1.2–12×0.8–1.1 μm) and stained Gram-negative. The strain grew optimally in tryptone-yeast extract-glucose medium at 70 °C (temperature range for growth was 55–80 °C) and pH 7 (pH range for growth was 5–9). Strain Y170T grew poorly on yeast extract as a sole carbon source, but not on tryptone (0.2 %). Yeast extract could not be replaced by tryptone and was obligately required for growth on tryptone, peptone, glucose, fructose, galactose, cellobiose, mannose, sucrose, xylose, mannitol, formate, pyruvate, Casamino acids and threonine. No growth was observed on arabinose, lactose, maltose, raffinose, chitin, xylan, pectin, starch, acetate, benzoate, lactate, propionate, succinate, myo-inositol, ethanol, glycerol, amyl media, aspartate, leucine, glutamate, alanine, arginine, serine and glycine. End products detected from glucose fermentation were acetate, ethanol and presumably CO2 and H2. Iron(III), manganese(IV), thiosulfate and elemental sulfur, but not sulfate, sulfite, nitrate or nitrite, were used as electron acceptors in the presence of 0.2 % yeast extract. Iron(III) in the form of amorphous Fe(III) oxhydroxide and Fe(III) citrate was also reduced in the presence of tryptone, peptone and Casamino acids, but not with chitin, xylan, pectin, formate, starch, pyruvate, acetate, benzoate, threonine, lactate, propionate, succinate, inositol, ethanol, glycerol, mannitol, aspartate, leucine, glutamate, alanine, arginine, serine or glycine. Strain Y170T was not able to utilize molecular hydrogen and/or carbon dioxide in the presence or absence of iron(III). Chloramphenicol, streptomycin, tetracycline, penicillin and ampicillin and NaCl concentrations greater than 2 % inhibited growth. The G+C content of the DNA was 48±1 mol% [sd (n=3); T m]. 16S rRNA gene sequence analysis indicated that strain Y170T is a member of the family Syntrophomonadaceae, class Clostridia, phylum Firmicutes and was most closely related to members of the genus Thermosediminibacter (mean similarity of 93.6 %). On the basis of the 16S rRNA gene sequence comparisons and physiological characteristics, strain Y170T is considered to represent a novel species of a new genus, for which the name Fervidicola ferrireducens gen. nov., sp. nov. is proposed. The type strain is Y170T (=KCTC 5610T=JCM 15106T=DSM 21121T).

We describe 10 new strains of marine lactic acid bacteria isolated from decaying marine algae, decaying seagrass, raw fish, salted fish and salted and fermented shrimp paste (‘ka-pi’) collected from a temperate area of Japan and Thailand. The isolates are Gram-positive and non-sporulating. They have motility with peritrichous flagella depending on the strains. They lack catalase and quinones. Under anaerobic conditions, lactate yields were 64–93 % of the glucose consumed; residual products were formate, acetate and ethanol with a molar ratio of approximately 2 : 1 : 1. The pH of the fermentation medium markedly affected the product composition; at higher pH, the yield of lactate decreased (15–48 % at pH 9.0) and yields of other products increased, retaining the molar ratio. Under aerobic conditions, acetate and lactate were produced from carbohydrates and related compounds. The isolates were slightly halophilic, highly halotolerant and alkaliphilic. The optimum NaCl concentration for growth ranged between 0.5 and 4.0 % (w/v), depending on the strain, with a growth range of between 0 and 17–21 % (11 % for one isolate). The optimum pH for growth ranged between 8.0 and 9.5, with a growth range of 6.0–11.0, depending on the strains. Comparative sequence analysis of the 16S rRNA genes revealed that the isolates occupied three phylogenetic positions within the genus Alkalibacterium, showing 97.1–99.8 % similarity to Alkalibacterium indicireducens. DNA–DNA hybridization values (<46 %) among the 10 isolates and phylogenetically related taxa resulted in the identification of four genomic species (designated groups GS1–GS4). The G+C contents of the DNA were 41.7 mol% (group GS1), 42.2 mol% (group GS2), 41.0–43.0 mol% (group GS3) and 38.4–39.4 mol% (group GS4). The cell-wall peptidoglycan was type A4β, Orn–d-Asp, for three genomic species (groups GS1, GS2 and GS3), and type A4β, Orn–d-Glu, for the remaining species (group GS4). The major components of cellular fatty acids were C16 : 0, C16 : 1 ω9c and C18 : 1 ω9c (oleic acid). On the bases of phenotypic characteristics, genetic distinctiveness and phylogenetic affiliations, the four genomic species, groups GS1, GS2, GS3 and GS4, were classified as four novel species within the genus Alkalibacterium, for which the names Alkalibacterium thalassium sp. nov., Alkalibacterium pelagium sp. nov., Alkalibacterium putridalgicola sp. nov. and Alkalibacterium kapii sp. nov., respectively, are proposed. The respective type strains are T117-1-2T (=DSM 19181T=NBRC 103241T=NRIC 0718T), T143-1-1T (=DSM 19183T=NBRC 103242T=NRIC 0719T), T129-2-1T (=DSM 19182T=NBRC 103243T=NRIC 0720T) and T22-1-2T (=DSM 19180T=NBRC 103247T=NRIC 0724T).

Two Gram-positive-staining, endospore-forming, rod-shaped, motile bacteria, strains DCY35T and C17, were isolated from soil of a ginseng field in South Korea and were characterized in order to determine their taxonomic positions. 16S rRNA gene sequence analysis revealed that the two strains belonged to the family Paenibacillaceae; strain DCY35T showed highest levels of similarity to strain C17 (99.9 %), Brevibacillus invocatus LMG 18962T (98.9 %), B. centrosporus DSM 8445T (98.0 %), B. borstelensis DSM 6347T (97.6 %), B. formosus DSM 9885T (97.4 %), B. agri DSM 6348T (97.3 %), B. brevis DSM 30T (97.3 %) and B. levickii LMG 22481T (97.0 %). Chemotaxonomic analyses revealed that strains DCY35T and C17 possess menaquinone MK-7, common to members of the genus Brevibacillus, and that the predominant fatty acids were iso-C15 : 0 (37.3 % of the total), anteiso-C15 : 0 (32.9 %), iso-C14 : 0 (11.8 %) and iso-C16 : 0 (6.5 %). The results of physiological and biochemical tests clearly demonstrated that strains DCY35T and C17 represent a distinct species. Based on these data, the two strains are considered to represent a novel species of the genus Brevibacillus, for which the name Brevibacillus panacihumi sp. nov. is proposed. The type strain is DCY35T (=KCTC 13206T =JCM 15085T).

Four strains of anaerobic, Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise a homogeneous group distinct from any species with validly published names. 16S rRNA and 23S rRNA gene sequence analyses and DNA–DNA reassociation data revealed that the strains constituted a novel group within the phylum ‘Synergistetes’ and were most closely related to Jonquetella anthropi. Two libraries of randomly cloned DNA were prepared from strain W5455T and were sequenced to provide a genome survey as a resource for metagenomic studies. A new genus and novel species, Pyramidobacter piscolens gen. nov., sp. nov., is proposed to accommodate these strains. The genus Pyramidobacter comprises strains that are anaerobic, non-motile, asaccharolytic bacilli that produce acetic and isovaleric acids and minor to trace amounts of propionic, isobutyric, succinic and phenylacetic acids as end products of metabolism. P. piscolens gen. nov., sp. nov. produced hydrogen sulphide but was otherwise largely biochemically unreactive. Growth was stimulated by the addition of glycine to broth media. The G+C content of the DNA of the type strain was 59 mol%. The type strain of Pyramidobacter piscolens sp. nov. is W5455T (=DSM 21147T=CCUG 55836T).

Bovine digital dermatitis (BDD) is a debilitating infection that is being increasingly recognized in livestock worldwide. Several treponeme phylotypes have been identified in BDD lesions, although only a single BDD-associated treponeme taxon (Treponema brennaborense) has been proposed thus far. In a previous study, we observed that four BDD-associated spirochaete isolates formed a distinct phylogenetic cluster on the basis of 16S rRNA gene sequence analysis and shared less than 97 % sequence similarity with recognized treponeme species. Further characterization of these isolates on the basis of growth characteristics, flaB2 gene sequences, enzyme profiles and cell morphology confirmed that they formed a coherent taxonomic group displaying marked genotypic and phenotypic differences with respect to recognized treponeme species. The four novel isolates displayed a novel 3 : 6 : 3 flagellar pattern rather than the 2 : 4 : 2 pattern shown by their closest relatives and exhibited esterase C4, esterase lipase C8, trypsin and chymotrypsin enzyme activities. Therefore these four new isolates represent a novel species of the genus Treponema, for which the name Treponema pedis sp. nov. is proposed. The type strain is T3552BT (=DSM 18691T=NCTC 13403T).

The number of bacterial phyla has greatly increased in the past decade. Among them, a candidate division named ‘Synergistes’ was proposed in a phylogenetic study on the global diversity of bacteria. We previously described the genus Jonquetella and suggested that it belonged to this not yet well-delineated candidate phylum. 16S rRNA gene based-phylogeny studies were conducted using four reconstruction methods and 599 sequences forming five datasets were used in an alternative treeing approach. These analyses indicated that the genera Aminiphilus, Aminobacterium, Aminomonas, Anaerobaculum, Dethiosulfovibrio, Jonquetella, Synergistes, Thermanaerovibrio and Thermovirga should be grouped in the same high-level taxon. This taxon was shown to be a phylum-rank lineage in the domain Bacteria and, because of the prior use of the name Synergistes for a genus, the name ‘Synergistetes’ is proposed for this candidate phylum. We also propose an emended delineation of the phylum ‘Deferribacteres’, which is now only represented by the family Deferribacteriaceae. The emended family Syntrophomonadaceae is limited to the genera Pelospora, Syntrophomonas, Syntrophothermus and Thermosyntropha.

An extremely thermophilic, strictly anaerobic, facultatively chemolithoautotrophic bacterium designated strain DST was isolated from Treshchinnyi Spring, one of the hottest springs of the Uzon Caldera (Kamchatka, Russia). Cells of the novel organism were Gram-negative rods, about 1.0–1.2 μm long and 0.5 μm wide. The temperature range for growth was 52–82 °C, with an optimum at 75 °C. Growth was observed at pH 6.8–7.4, and the optimum pH was 7.0–7.2. Strain DST was able to grow lithoautotrophically with hydrogen in the presence of CO2 as a carbon source and thiosulfate or elemental sulfur as an electron acceptor. It also grew well with ethanol, fumarate, succinate or malate in the presence of thiosulfate. Yeast extract was not required for growth and did not stimulate growth. The genomic DNA G+C content was 35.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that the novel organism was a member of the family Thermodesulfobacteriaceae. On the basis of phylogenetic and physiological considerations, it is proposed that strain DST represents a new genus and species, Caldimicrobium rimae gen. nov., sp. nov. The type strain of Caldimicrobium rimae is DST (=DSM 19393T =VKM B-2460T).

A novel weakly halotolerant, sulfate-reducing bacterium, designated strain RB22T, was isolated from exhaust water of a Tunisian oil refinery. Cells of strain RB22T were Gram-negative, motile, vibrio-shaped or sigmoid and non-spore-forming, and occurred singly or in chains. Strain RB22T grew between 15 and 45 °C (optimum, 37 °C) and at pH 4.5 to 9 (optimum, pH 7). NaCl was not required for growth, but the strain tolerated high NaCl concentrations (up to 70 g l−1) with an optimum of 40 g l−1. Sulfate, thiosulfate, sulfite and elemental sulfur served as electron acceptors, but not fumarate. Nitrate and nitrite were not reduced. Strain RB22T utilized lactate, formate, fumarate, succinate, glycerol, H2+CO2 and methanol as substrates. The DNA G+C content was found to be 59.6 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the isolate was a member of the genus Desulfovibrio, with no close relatives at the species level (16S rRNA gene sequence similarity of less than 95 %). Strain RB22T exhibited levels of 16S rRNA gene sequence similarity of 94.6 and 94.12 % to the type strains of the closely related species Desulfovibrio aespoeensis and Desulfovibrio dechloracetivorans, respectively. On the basis of genotypic and phylogenetic characteristics, and significant phenotypic differences, we suggest that strain RB22T represents a novel species, for which the name Desulfovibrio tunisiensis sp. nov. is proposed. The type strain is RB22T (=NCIMB 14400T=JCM 15076T=DSM 19275T).

It has been recognized that there is heterogeneity among Leptospira isolates in culture collections worldwide, causing confounding results for researchers utilizing these organisms; one such culture is Leptospira meyeri serovar Perameles. The serovar reference strain Bandicoot 343 was previously identified to the species level by DNA–DNA hybridization; however, subsequent published studies demonstrated results that contradicted the initial speciation. In this study, initial serological testing was performed with isolates from the culture collections of the Centers for Disease Control (CDC), Atlanta, USA (strain Lepto0214), and the WHO/FAO/OIE Collaborating Centre for Reference and Research on Leptospirosis, Brisbane, Australia (strain Bandicoot 343), and the original serovar Perameles hyperimmune antiserum produced in 1964. The results indicated that strain Lepto0214 was not serologically reactive to the antiserum. However, further investigations revealed an alternative serovar Perameles strain held in the CDC collection (Lepto0213) that yielded titres against the antiserum. 16S rRNA gene sequencing of the three strains revealed that Lepto0214 had significant sequence similarity with previously sequenced L. meyeri strains; however, strains Lepto0213 and Bandicoot 343 had significant similarity with Leptospira interrogans strains. 16S rRNA gene sequencing results were confirmed by pulsed-field gel electrophoresis; Lepto0214 had a pattern similar to that of L. meyeri serovar Hardjo strain Went 5, and the pattern differed significantly from those of Lepto0213 and Bandicoot 343. This research provides evidence for the reclassification of serovar Perameles from L. meyeri to L. interrogans. This reclassification highlights a need for changes to how reference Leptospira serovars are identified, disseminated and stored, with the aim of reducing heterogeneity of reference strains between culture collections.

A novel mesophilic sulfate-reducing bacterium, EMSSDQ4 T, was isolated from olive mill wastewater in the semi-arid region of Morocco (Marrakech). Cells were Gram-negative, catalase-positive, straight rods that were non-motile and non-spore-forming and contained cytochrome c 3 and desulfoviridin. The DNA G+C content was 65.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate was a member of the genus Desulfovibrio with Desulfovibrio carbinoliphilus D41T, Desulfovibrio alcoholivorans SPSNT, Desulfovibrio fructosivorans JJT and Desulfovibrio carbinolicus EDK82T as the most closely related strains with validly published names. In addition to the classical substrates used by Desulfovibrio species, the isolate oxidized 1,4-tyrosol, one of the most abundant phenolic compounds occurring in olive mill wastewater, to 4-hydroxyphenylacetate without ring cleavage. D. alcoholivorans SPSNT was also found to carry out this reaction. Under air, strain EMSSDQ4 T exhibited limited growth on lactate and yeast extract in the absence of sulfate. On the basis of genotypic and phenotypic characteristics, it is proposed that the isolate represents a novel species, Desulfovibrio marrakechensis sp. nov. The type strain is EMSSDQ4 T (=DSM 19337T =ATCC BAA-1562T).

A Gram-negative, aerobic, rod-shaped, non-spore-forming bacterial strain, designated Gsoil 068T, was isolated from soil of a ginseng field in Pocheon Province (South Korea), and was characterized to determine its taxonomic position by using a polyphasic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 068T belonged to the family Xanthomonadaceae, class Gammaproteobacteria, and was related most closely to Lysobacter brunescens ATCC 29482T and Lysobacter gummosus ATCC 29489T (96.1 % sequence similarity). The G+C content of the genomic DNA of strain Gsoil 068T was 67.0 mol%. The detection of a quinone system with ubiquinone Q-8 as the predominant component and a fatty acid profile with iso-C15 : 0, iso-C17 : 1 ω9c, iso-C17 : 0 and iso-C11 : 0 3-OH as the major components supported the affiliation of strain Gsoil 068T to the genus Lysobacter. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil 068T is considered to represent a novel species of the genus Lysobacter, for which the name Lysobacter panaciterrae sp. nov. is proposed. The type strain is Gsoil 068T (=KCTC 12601T =DSM 17927T).

Strain CC-MMS-1T, a motile, Gram-negative, orange-pigmented bacterium, was isolated from water samples collected from a rare coastal hot spring at Lutao, an island off the eastern coast of Taiwan. 16S rRNA gene sequence studies showed that the novel strain was closely related to Parvularcula bermudensis HTCC2503T (95.1 % sequence similarity). The fatty acid profile was slightly different from P. bermudensis HTCC2503T. The results of physiological and biochemical tests allowed clear phenotypic differentiation of the novel isolate from P. bermudensis HTCC2503T. It is evident from the genotypic and phenotypic data that the strain should be classified as a novel species in the genus Parvularcula. The name proposed for this taxon is Parvularcula lutaonensis sp. nov. The type strain is CC-MMS-1T (=BCRC 17814T=KCTC 22245T).

An aerobic, Gram-negative, catalase-positive, oxidase-positive bacterium was isolated from a dried seaweed sample collected from Kimnyeong Beach in Jeju, Republic of Korea. The cells of the organism, designated strain KY 101T, were rods (0.4–0.5×1.2–2.7 μm) and motile by means of flagella. The colonies of the cells were 0.5–1 mm in diameter, smooth, circular, convex and light yellow in colour. The isolate showed growth at 10–40 °C, pH 6.1–12.1 and in the presence of 7 % NaCl. The major fatty acid was summed feature C18 : 1 ω7c/C18 : 1 ω9c/C18 : 1 ω12t and the DNA G+C content was 60.4 mol%. 16S rRNA gene sequence studies showed that the organism was phylogenetically related to the family Phyllobacteriaceae, with Nitratireductor aquibiodomus (99.1 % sequence similarity) as the closest neighbour. The level of DNA–DNA relatedness between strain KY 101T and N. aquibiodomus DSM 15645T was 18.4–23.2 % (duplicate measurements). The combination of phenotypic differences and DNA–DNA hybridization data supports the suggestion that the isolate represents a novel species of the genus Nitratireductor, for which the name Nitratireductor kimnyeongensis sp. nov. is proposed. The type strain is strain KY 101T (=KACC 11904T=JCM 14851T).

A novel bacterium, designated strain 5YN1-3T, was isolated from wetland peat collected from Yongneup, Korea. The bacterium was facultatively anaerobic, Gram-negative, yellow-coloured, rod-shaped, mesophilic and motile with one polar flagellum. The strain grew optimally at 30 °C, at pH 6.0–9.0 and with 0–1 % NaCl (w/v). 16S rRNA gene sequence analysis showed the highest similarity to the sequence from Aquitalea magnusonii TRO-001DR8T, with 98.7 % sequence similarity. However, strain 5YN1-3T showed DNA–DNA relatedness of 43 % (40 % in a reciprocal experiment) with A. magnusonii LMG 23054T. The strain contained summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c) and C16 : 0 as major cellular fatty acids. On the basis of DNA–DNA relatedness and physiological and biochemical characterization, strain 5YN1-3T should be assigned to a novel species of the genus Aquitalea, for which the name Aquitalea denitrificans sp. nov. is proposed. The type strain is 5YN1-3T (=KACC 12729T =DSM 21300T).

Multiple isolates of the genus Providencia were obtained from the haemolymph of wild-caught Drosophila melanogaster fruit flies. Sixteen isolates were distinguished from the six previously described species based on 16S rRNA gene sequences. These isolates belonged to two distinct groups, which we propose each comprise previously undescribed species. Two isolates, designated AT and BT, were characterized by DNA sequences of the fusA, lepA, leuS, gyrB and ileS housekeeping genes, whole-genome DNA–DNA hybridizations with their nearest relatives and utilization of substrates for metabolism. The closest phylogenetic relatives of strain AT are strain BT (86.9 % identity for the housekeeping genes) and Providencia stuartii DSM 4539T (86.0 % identity). The closest phylogenetic relatives of strain BT are strain AT (86.9 % identity) and P. stuartii DSM 4539T (86.6 % identity). The type strains of described species in this genus shared between 84.1 and 90.1 % identity for these sequences. DNA–DNA hybridization between the strain pairs AT–BT, AT–P. stuartii DSM 4539T and BT–P. stuartii DSM 4539T all resulted in less than 25 % relatedness. In addition, patterns of utilization of amygdalin, arbutin, aesculin, salicin, d-sorbitol, trehalose, inositol, d-adonitol and d-galactose distinguish strains AT and BT from other members of this genus. Strains AT and BT therefore represent novel species, for which the names Providencia sneebia sp. nov. (type strain AT =DSM 19967T =ATCC BAA-1589T) and Providencia burhodogranariea sp. nov. (type strain BT =DSM 19968T =ATCC BAA-1590T) are proposed.

An aerobic, Gram-negative, ovoid to rod-shaped bacterial isolate, strain 81-2T, was isolated from deep-sea sediment of the Western Pacific Ocean. Strain 81-2T was motile, formed faint pink colonies, and was catalase-positive, weakly positive for oxidase and required NaCl for growth. It did not synthesize bacteriochlorophyll a and its DNA G+C content was 62.3 mol%. The 16S rRNA gene sequence of strain 81-2T indicated that it was a member of the Roseobacter clade of the class Alphaproteobacteria, with moderate bootstrap support for inclusion in the genus Roseovarius. Its closest phylogenetic neighbour was the type strain of Roseovarius nubinhibens, which shared 95.8 % 16S rRNA gene sequence similarity; strain 81-2T was <95.0 % similar to strains of other related species and genera. Phenotypic, chemotaxonomic and phylogenetic data support assignment of this strain to the genus Roseovarius as a representative of a novel species. The name Roseovarius pacificus sp. nov. is proposed, with strain 81-2T (=MCCC 1A00293T=CGMCC 1.7083T=LMG 24575T) as the type strain.

A polyphasic study was undertaken to clarify the taxonomic position of Campylobacter lari-like strains isolated from shellfish and humans. The diversity within the strain collection was initially screened by means of fluorescent amplified fragment length polymorphism analysis and whole-cell protein electrophoresis, revealing the existence of two clusters distinct from C. lari and other Campylobacter species. The divergence of these clusters was confirmed by phenotypic analysis and by 16S rRNA and hsp60 gene sequence analysis. Phylogenetic analysis identified C. lari, Campylobacter jejuni, Campylobacter coli and Campylobacter insulaenigrae as the closest phylogenetic neighbours of both taxa. DNA–DNA hybridizations revealed that one cluster, comprising 10 strains, represented a novel Campylobacter species, for which the name Campylobacter peloridis sp. nov. is proposed, with 2314BVAT (=LMG 23910T =CCUG 55787T) as the type strain. The second cluster, comprising six strains, represents a novel subspecies within the species C. lari, for which the name Campylobacter lari subsp. concheus subsp. nov. is proposed, with 2897RT (=LMG 21009T =CCUG 55786T) as the type strain. The description of C. lari subsp. concheus has the effect of automatically creating the subspecies Campylobacter lari subsp. lari subsp. nov. (type strain LMG 8846T=NCTC 11352T).

An ovoid to rod-shaped, phototrophic, purple non-sulfur bacterium was isolated from a brown-coloured microbial mat from the brackish water of Bhitarkanika mangrove forest, Dangmal, Orissa, India. Cells of strain JA296T were Gram-negative and motile, forming chains of four to eight cells. The colour of the cell suspension grown under anaerobic conditions in the light was yellowish green. Bacteriochlorophyll a and the carotenoids spheroidene and spheroidenone of the spirilloxanthin series were present as photosynthetic pigments. The bacterium was a facultative anaerobe and was able to grow photo-organoheterotrophically and chemo-organoheterotrophically. Thiamine was required as a growth factor. C18 : 1 ω7c was the dominant fatty acid. Internal cytoplasmic membranes were of the vesicular type. Strain JA296T did not require NaCl for growth. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA296T was most closely related to Rhodobacter capsulatus ATCC 11166T (95.5 % sequence similarity) and clustered with species of the genus Rhodobacter of the family Rhodobacteraceae, class Alphaproteobacteria. On the basis of 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA296T represents a novel species of the genus Rhodobacter, for which the name Rhodobacter aestuarii sp. nov. is proposed; the type strain is JA296T (=JCM 14887T =CCUG 55130T).

A Gram-negative, ovoid rod-shaped bacterium that lacked bacteriochlorophyll a, designated strain Y-2T, was isolated from seawater of the Taiwan Strait, China. The strain was oxidase- and catalase-positive, and reduced nitrate to nitrite. Optimal growth occurred at around pH 7.0 and 25 °C in the presence of 1–3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Y-2T belonged to the class Alphaproteobacteria and formed a coherent cluster with Donghicola eburneus SW-277T (96.2 % sequence similarity). The major whole-cell fatty acid was C18 : 1 ω7c (75.42 %). Other characteristic fatty acids were C18 : 0 (9.16 %) and C16 : 0 (7.32 %). The DNA G+C content of strain Y-2T was 62.4 mol%. Therefore, based on phenotypic properties, phylogeny and genomic data, strain Y-2T should be placed in the genus Donghicola as representing a novel species, for which the name Donghicola xiamenensis sp. nov. is proposed. The type strain is Y-2T (=MCCC 1A00107T=LMG 24574T=CGMCC 1.7081T).

A taxonomic study was carried out on a Gram-negative, rod-shaped, non-motile, halophilic bacterium, designated strain W11-2BT, which was isolated from a pyrene-degrading consortium that was enriched from sediment from the Pacific Ocean. Growth was observed at salinities of 0.5–10 % and at temperatures of 10–41 °C. Strain W11-2BT was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence comparisons showed that strain W11-2BT was related most closely to Oceanicola nanhaiensis SS011B1-20T (95.8 % similarity) and Oceanicola batsensis HTCC2597T (95.7 %); levels of 16S rRNA gene sequence similarity between strain W11-2BT and the type strains of other species tested were below 95.2 %. The dominant fatty acids of strain W11-2BT were C18 : 1 ω7c (32.1 % of the total), C19 : 0 cyclo (20.9 %), C18 : 1 ω7c 11-methyl (19.5 %), C18 : 0 (7.3 %), C17 : 0 (6.6 %) and C16 : 0 (3.8 %). The G+C content of the chromosomal DNA was 64.6 mol%. The above data were in good agreement with those of members of the genus Oceanicola. Based on morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain W11-2BT is considered to represent a novel species of the genus Oceanicola, for which the name Oceanicola pacificus sp. nov. is proposed. The type strain is W11-2BT (=CCTCC AB 208224T=LMG 24619T=MCCC 1A01034T).

Two strains, CN44T and CN47T, isolated from marine sediment of the East China Sea, were characterized by using a polyphasic approach. The isolates were Gram-negative, strictly aerobic, non-spore-forming rods. The chemotaxonomic characteristics of these isolates included the presence of C18 : 1 ω7c, C16 : 0, iso-C15 : 0 2-OH and/or C16 : 1 ω7c and C10 : 0 3-OH as the major cellular fatty acids and Q-8 as the predominant ubiquinone. The DNA G+C contents of strains CN44T and CN47T were 62.5 and 56.3 mol%, respectively. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CN44T was related to members of the genus Marinobacterium. The most closely related described organism was the type strain of Marinobacterium rhizophilum (95.3 % sequence similarity). Strain CN47T showed the highest sequence similarity to the type strain of Marinobacterium stanieri (97.8 %) and <97 % similarity to other type strains of described Marinobacterium species. The level of DNA–DNA relatedness between strain CN47T and M. stanieri DSM 7027T was 46 %. On the basis of phenotypic and genotypic properties, strains CN44T and CN47T represent two novel species within the genus Marinobacterium, for which the names Marinobacterium nitratireducens sp. nov. (type strain, CN44T =CGMCC 1.7286T =JCM 15523T) and Marinobacterium sediminicola sp. nov. (type strain, CN47T =CGMCC 1.7287T =JCM 15524T) are proposed.

A Sphingomonas-like bacterium, strain KC7T, was isolated from a marine crustacean specimen obtained from the Sea of Japan and subjected to a polyphasic study. Comparative 16S rRNA gene sequence analysis positioned the novel strain in the genus Sphingomonas as an independent lineage adjacent to a subclade containing Sphingomonas trueperi LMG 2142T, Sphingomonas pituitosa EDIVT and Sphingomonas azotifigens NBRC 15497T. Strain KC7T shared highest 16S rRNA gene sequence similarity (96.1 %) with S. trueperi LMG 2142T, Sphingomonas dokdonensis DS-4T and S. azotifigens NBRC 15497T; similarities to strains of other recognized Sphingomonas species were lower (96.0–93.9 %). The strain contained sphingoglycolipid and the predominant fatty acids were C16 : 1, C16 : 0 and C18 : 1; 2-OH C14 : 0 was the major 2-hydroxy fatty acid. Previously, these lipids have been found to be characteristic of members of the genus Sphingomonas sensu stricto. On the basis of phylogenetic analysis and physiological and biochemical characterization, strain KC7T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas japonica sp. nov. is proposed. The type strain is KC7T (=KMM 3038T =NRIC 0738T =JCM 15438T).

A novel aerobic, Gram-negative bacterium, designated strain CM41_15aT, was isolated from the surface of coastal waters of the north-western Mediterranean Sea. Cells were non-motile straight rods that formed red colonies on marine agar medium. The G+C content of the genomic DNA was 65 mol %. Phylogenetic analysis of the 16S rRNA gene sequence placed the strain in the genus Haliea within the class Gammaproteobacteria. On the basis of the 16S rRNA gene sequence comparison and physiological and biochemical characteristics, strain CM41_15aT represents a novel species, for which the name Haliea rubra sp. nov. is proposed. The type strain is CM41_15aT (=DSM 19751T=CIP 109758T=MOLA 104T).

Phylogenetic analyses based on 16S rRNA gene sequences revealed that Teichococcus ludipueritiae and Muricoccus roseus are closely related to the species of the genus Roseomonas. The type strain of Teichococcus ludipueritiae, 170/96T, exhibited 16S rRNA gene sequence similarity levels of 96.4 % to Roseomonas cervicalis ATCC 49957T, 95.0 % to Roseomonas aquatica TR53T, 94.5 % to Muricoccus roseus 173/96T, 93.4 % to Roseomonas mucosa ATCC BAA-692T and 93.5 % to Roseomonas gilardii subsp. gilardii ATCC 49956T, while Muricoccus roseus 173/96T showed 16S rRNA gene sequence similarity values of 95.7 % to R. mucosa ATCC BAA-692T, 95.7 % to R. aquatica TR53T and 95.3 % to R. gilardii subsp. gilardii ATCC 49956T and R. gilardii subsp. rosea ATCC BAA-691T. Different phylogenetic analysis methods (neighbour-joining, maximum-likelihood and maximum-parsimony) confirmed that both species are within the Roseomonas branch. Neither polyamine patterns (spermidine predominant) nor major characteristics in the polar lipid profiles distinguished the two species from representatives of the genus Roseomonas. The fatty acid composition of the two species exhibited alphaproteobacterial characteristics but, like Roseomonas species, they also showed considerable amounts of the rarely encountered C18 : 1 2-OH. On the other hand, they showed some phenotypic differences, but their features are compatible with the transfer of these two species to the genus Roseomonas. We propose the reclassification of Teichococcus ludipueritiae and Muricoccus roseus as Roseomonas ludipueritiae comb. nov. (type strain 170/96T =CIP 107418T =DSM 14915T) and Roseomonas rosea comb. nov. (type strain 173/96T =CIP 107419T =DSM 14916T), respectively. Emended descriptions of the genus Roseomonas and the species Roseomonas gilardii (and its subspecies Roseomonas gilardii subsp. gilardii and Roseomonas gilardii subsp. rosea), Roseomonas aquatica, Roseomonas cervicalis, Roseomonas mucosa and Roseomonas lacus are provided.

Three isolates (LMG 24369T, LMG 24370 and R-26156) obtained from a marine electroactive biofilm that was grown on a cathodically polarized electrode were investigated by using a polyphasic taxonomic approach. Whole-cell fatty acid methyl ester and 16S rRNA gene sequence analyses indicated that the isolates were members of the genus Phaeobacter, class Alphaproteobacteria. Genotypic and phenotypic analyses demonstrated that the three isolates represent a novel species of the genus Phaeobacter, for which the name Phaeobacter caeruleus sp. nov. is proposed. The type strain is LMG 24369T (=CCUG 55859T). The DNA G+C content of strain LMG 24369T is 63.6 mol%.

Two novel yeast species, Wickerhamomyces queroliae sp. nov. and Candida jalapaonensis sp. nov., were isolated, respectively, from larvae of Anastrepha mucronata (Diptera: Tephritidae) collected from ripe fruit of Peritassa campestris (‘Bacupari’, Hippocrateaceae) and from flowers of Centropogon cornutus (Campanulaceae) in the Cerrado ecosystem of the state of Tocantins, Brazil. Analysis of the D1/D2 large-subunit rRNA gene sequences placed W. queroliae in the Wickerhamomyces clade near Wickerhamomyces ciferri and Candida silvicultrix. Candida jalapaonensis belongs to the Wickerhamiella clade and is related to Candida drosophilae. The type strain of Wickerhamomyces queroliae is UFMG-05-T200.1T (=CBS 10936T=NRRL Y-48478T) and the type strain of Candida jalapaonensis is UFMG-03-T210T (=CBS 10935T=NRRL Y-48477T).

A metsulfuron-methyl-resistant yeast strain, JHLT, was isolated from metsulfuron-methyl-contaminated soil collected in Jiangsu Province, China. Through morphological and physiological analysis as well as a molecular phylogenetic analysis based on the 26S rRNA gene D1/D2 region and internal transcribed spacer (ITS), this strain, which forms a clade with Candida vartiovaarae and a teleomorphic species, Williopsis saturnus, was revealed to represent a novel species in the genus Candida. The name Candida mengyuniae sp. nov. (type strain JHLT=CGMCC 2.3681T=CBS 10845T) is proposed for this novel species.

The delineation of species among strains assigned to Debaryomyces hansenii was examined using a gene genealogies-based approach in order to compare spliceosomal intron sequences found in four housekeeping genes (ACT1, TUB2, RPL31 and RPL33). This revealed four distinct groups of strains containing, respectively, D. hansenii var. hansenii CBS 767T, D. hansenii var. fabryi CBS 789T, Candida famata var. flareri CBS 1796T (the anamorph of D. hansenii var. fabryi CBS 789T) and Debaryomyces tyrocola CBS 766T, whose species status was no longer accepted. The sequence divergence between these groups, reaching in some cases over 20 %, unambiguously isolated the groups as separate taxa, leading to a proposal for the reinstatement of the originally described species D. hansenii CBS 767T and D. tyrocola CBS 766T. The variety D. hansenii var. fabryi was further subdivided into two taxa, Debaryomyces fabryi CBS 789T and Candida flareri CBS 1796T (previously C. famata var. flareri and Blastodendrion flareri). The comparison of intron sequences therefore exposed cryptic species whose phenotypic traits are not distinguishable from known species, but which have significantly diverged from the genetic point of view. Hence, we describe the new taxon Debaryomyces macquariensis sp. nov. CBS 5571T is related to, but clearly distinct from, the Debaryomyces species mentioned above. The approach used in this work has also revealed the existence of populations within the newly delineated species D. hansenii and genetic exchanges between these populations, indicating an unexpected genetic diversity within this part of the genus Debaryomyces.