- Volume 59, Issue 5, 2009

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.