- Volume 50, Issue 3, 2000
Volume 50, Issue 3, 2000
- Articles
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Methylocella palustris gen. nov., sp. nov., a new methane-oxidizing acidophilic bacterium from peat bogs, representing a novel subtype of serine-pathway methanotrophs.
A new genus, Methylocella, and a new species, Methylocella palustris, are proposed for three strains of methane-oxidizing bacteria isolated from acidic Sphagnum peat bogs. These bacteria are aerobic, Gram-negative, colourless, non-motile, straight and curved rods that utilize the serine pathway for carbon assimilation, multiply by normal cell division and contain intracellular poly-beta-hydroxybutyrate granules (one at each pole). These strains use methane and methanol as sole sources of carbon and energy and are moderately acidophilic organisms with growth between pH 4.5 and pH 7.0, the optimum being at pH 5.0-5.5. The temperature range for growth is 10-28 degrees C with the optimum at 15-20 degrees C. The intracytoplasmic membrane system is different from those of type I and II methanotrophs. Cells contain an extensive periplasmic space and a vesicular membrane system connected to the cytoplasmic membrane. The strains grew only on media with a low salt content (0.2-0.5 g l(-1)). All three strains were found to possess soluble methane monooxygenase and are able to fix atmospheric nitrogen via an oxygen-sensitive nitrogenase. No products were observed in a PCR with particulate methane monooxygenase-targeted primers; hybridization with a pmoA probe was also negative. The major phospholipid fatty acids are 18:1 acids. The G+C content of the DNA is 61.2 mol%. The three strains share identical 16S rRNA gene sequences and represent a novel lineage of methane-oxidizing bacteria within the alpha-subclass of the class Proteobacteria and are only moderately related to type II methanotrophs of the Methylocystis-Methylosinus group. The three strains are most closely related to the acidophilic heterotrophic bacterium Beijerinckia indica subsp. indica (96.5% 16S rDNA sequence similarity). Collectively, these strains comprise a new species and genus Methylocella palustris gen. nov., sp. nov.; strain KT (= ATCC 700799T) is the type strain.
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Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7alpha-dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces.
M Kitahara, F Takamine, T Imamura and Y BennoUnknown Eubacterium-like organisms VPI 12708 and five strains (Y-1113, I-10, M-18, TH-82 and 36S) had high bile acid 7alpha-dehydroxylating activity; the unknown Clostridium-like organisms TN-271T and TN-272 also had the same activity. Analysis of their 16S rDNA sequences demonstrated that all strains belong to cluster XIVa of the genus Clostridium (Collins et al., 1994). Strain VPI 12708 and five other strains (Y-1113, I-10, M-18, TH-82 and 36S) formed a single cluster and strains TN-271T and TN-272 formed another single cluster. Clostridium scindens JCM 6567T was the most closely related species for two clusters in the phylogenetic tree. Values for DNA-DNA similarities among C. scindens JCM 6567T, strain VPI 12708 and the other five strains were greater than 70%, showing that these micro-organisms were a single species. Therefore, we identified strain VPI 12708 and the five other strains as C. scindens. In addition, DNA-DNA similarities among C. scindens JCM 6567T, strain TN-271T and strain N-272 revealed that strains TN-271T and TN-272 were distinct from C. scindens JCM 6567T. On the basis of phylogenetic analysis and DNA-DNA similarity data, it was concluded that strains TN-271T and TN-272 are members of a new species of the genus Clostridium, for which the name Clostridium hylemonae is proposed. The type strain is strain TN-271T (= JCM 10539T).
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Bulleidia extructa gen. nov., sp. nov., isolated from the oral cavity.
More LessFive strains of anaerobic non-sporing Gram-positive bacilli isolated from advanced periodontitis (four strains) and a dentoalveolar abscess (one strain) that did not correspond to existing species were subjected to phenotypic and genetic characterization. Following 16S rDNA sequence analysis, they were found to constitute a novel branch of the low G+C Gram-positive division of the phylogenetic tree related to Erysipelothrix rhusiopathiae and Holdemania filiformis. A new genus Bulleidia, and the species Bulleidia extructa, are proposed. Growth of B. extructa in broth media was poor but was enhanced by the addition of fructose, glucose or maltose together with Tween 80. Glucose and maltose were fermented and arginine was hydrolysed. Acetate, lactate and trace amounts of succinate were the end products of glucose fermentation. The G+C content of the DNA of the type strain is 38 mol%. The type strain of Bulleidia extructa is DSM 13220T.
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Rhodopseudomonas rhenobacensis sp. nov., a new nitrate-reducing purple non-sulfur bacterium.
More LessDuring the course of isolating and identifying purple non-sulfur bacteria, one nitrate-reducing strain was isolated which did not fit the description of any other purple non-sulfur bacterium known to date. The isolate had rod-shaped cells that contained lamellar intracytoplasmic membranes and produced red cultures. Absorption maxima of photosynthetically grown cell homogenates were at 376, 471, 503, 540, 591, 805 and 878 nm. The new isolate grew anaerobically in the light or aerobically in the dark. Various organic compounds served as carbon sources and electron donors. The predominant quinone was ubiquinone 10, the predominant fatty acid was 18:1omega7c. The polar lipids comprised diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine and phosphatidyl choline. Analysis of the 16S rDNA gene sequences revealed that the new isolate was closely related to Rhodopseudomonas palustris. A DNA-DNA- hybridization study differentiated the new isolate and Rhodopseudomonas palustris at the species level. Therefore, the name Rhodopseudomonas rhenobacensis sp. nov. is proposed for the new isolate.
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Cellulomonas persica sp. nov. and Cellulomonas iranensis sp. nov., mesophilic cellulose-degrading bacteria isolated from forest soils.
Two newly described species of mesophilic, cellulose-degrading, aerobic bacteria were isolated from forest humus soils along the southern border of the Caspian Sea. Cellulomonas persica and Cellulomonas iranensis are proposed as new specific epithets based on comparative sequence analyses of 16S rDNA, DNA-DNA hybridization and phenotypic characteristics. Formal species descriptions are provided.
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Ferroplasma acidiphilum gen. nov., sp. nov., an acidophilic, autotrophic, ferrous-iron-oxidizing, cell-wall-lacking, mesophilic member of the Ferroplasmaceae fam. nov., comprising a distinct lineage of the Archaea.
An isolate of an acidophilic archaeon, strain YT, was obtained from a bioleaching pilot plant. The organism oxidizes ferrous iron as the sole energy source and fixes inorganic carbon as the sole carbon source. The optimal pH for growth is 1.7, although growth is observed in the range pH 1.3 to 2.2. The cells are pleomorphic and without a cell wall. 16S rRNA gene sequence analysis showed this strain to cluster phylogenetically within the order 'Thermoplasmales' sensu Woese, although with only 89.9 and 87.2% sequence identity, respectively, to its closest relatives, Picrophilus oshimae and Thermoplasma acidophilum. Other principal differences from described species of the 'Thermoplasmales' are autotrophy (strain YT is obligately autotrophic), the absence of lipid components typical of the ' Thermoplasmales' (no detectable tetraethers) and a lower temperature range for growth (growth of strain YT occurs between 15 and 45 degrees C). None of the sugars, amino acids, organic acids or other organic compounds tested was utilized as a carbon source. On the basis of the information described above, the name Ferroplasma acidiphilum gen. nov., sp. nov. is proposed for strain YT within a new family, the Ferroplasmaceae fam. nov. Strain YT is the type and only strain of F. acidiphilum. This is the first report of an autotrophic, ferrous-iron-oxidizing, cell-wall-lacking archaeon.
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Analysis of the actinobacterial insertion in domain III of the 23S rRNA gene of uncultured variants of the bacterium associated with Whipple's disease using broad-range and 'Tropheryma whippelii'-specific PCR.
More LessHeterogeneity in the 16S-23S rDNA spacer of uncultured 'Tropheryma whippelii' has previously been reported. In this study, the hypervariable insertion in the 23S rDNA domain III characteristic for actinobacteria was analysed. The finding of a unique sequence virtually identical among the subtypes supports the classification of 'T. whippelii' among the actinobacteria and the concept of three subtypes rather than three subspecies, and provides an alternative target for diagnostic assays.
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Application of AFLP for taxonomic and epidemiological studies of Photobacterium damselae subsp. piscicida.
More LessA collection of 106 Photobacterium damselae subsp. piscicida strains and 19 Photobacterium damselae subsp. damselae strains, including reference and type strains, were genetically characterized using AFLP. The total genomic DNA of each bacterial strain was digested using restriction endonucleases HindIII and TaqI. Using numerical analysis, six clusters were recognized. The largest cluster (n = 106) contained the majority of the strains tested and consisted exclusively of Photobacterium damselae subsp. piscicida. The Photobacterium damselae subsp. damselae strains fell outside this cluster. DNA-DNA hybridization experiments showed 77% DNA binding between the two subspecies, indicating a close genetic relationship. This clearly demonstrates the applicability of AFLP in studying the taxonomic position of Photobacterium damselae subsp. piscicida. In addition, AFLP proved to be a useful genotypic technique for epidemiological surveys of the pathogen, since it was able to discriminate between Mediterranean and Japanese Photobacterium damselae subsp. piscicida isolates.
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Protein-coding genes as molecular markers for ecologically distinct populations: the case of two Bacillus species.
More LessBacillus globisporus and Bacillus psychrophilus are one among many pairs of ecologically distinct taxa that are distinguished by very few nucleotide differences in 16S rRNA gene sequence. This study has investigated whether the lack of divergence in 16S rRNA between such species stems from the unusually slow rate of evolution of this molecule, or whether other factors might be preventing neutral sequence divergence at 16S rRNA as well as every other gene. B. globisporus and B. psychrophilus were each surveyed for restriction-site variation in two protein-coding genes. These species were easily distinguished as separate DNA sequence clusters for each gene. The limited ability of 16S rRNA to distinguish these species is therefore a consequence of the extremely slow rate of 16S rRNA evolution. The present results, and previous results involving two Mycobacterium species, demonstrate that there exist closely related species which have diverged long enough to have formed clearly separate sequence clusters for protein-coding genes, but not for 16S rRNA. These results support an earlier argument that sequence clustering in protein-coding genes could be a primary criterion for discovering and identifying ecologically distinct groups, and classifying them as separate species.
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Cellular fatty acid composition of cyanobacteria assigned to subsection II, order Pleurocapsales.
More LessThe cellular fatty acid composition of five of the six genera of unicellular cyanobacteria in subsection II, Pleurocapsales (Dermocarpa, Xenococcus, Dermocarpella, Myxosarcina and the Pleurocapsa assemblage) contained high proportions of saturated straight-chain fatty acids (26-41% of the total) and unsaturated straight chains (40-67%). Isomers of 16:1 were the main monounsaturated acid component (11-59%). Polyunsaturated acids were present at trace levels (0-1% or less) in Xenococcus and Myxosarcina, at concentrations of less than 7% in Dermocarpa, Dermocarpella, Pleurocapsa and CCMP 1489, and at high concentrations (35% or more) in Chroococcidiopsis. Chroococcidiopsis was also different in terms of the percentage of 16:1 isomers (10-12%) compared to other genera (30-59%), and in terms of total 16-carbon and 18-carbon fatty acids. In general, the composition and heterogeneity of fatty acids in the order Pleurocapsales was similar to that reported for the unicellular cyanobacteria of subsection I, order Chroococcales.
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Reductively debrominating strains of Propionigenium maris from burrows of bromophenol-producing marine infauna.
More LessTwo novel strains of Propionigenium maris able to reductively debrominate 2,4,6-tribromophenol (TBP) to monobromophenols were isolated from marine hemichordate and polychaete burrows. These two strains, DSL-1 and ML-1, were anaerobic, non-motile rods that stained Gram-negative and required 0.05% yeast extract for growth. Strain DSL-1 fermented pyruvate and succinate to predominantly butyrate and strain ML-1 fermented glucose and succinate primarily to propionate. No inorganic terminal electron acceptors were identified. The pH and temperature optima for growth were 7.6 and 30 degrees C for strain DSL-1 and 7.0 and 32 degrees C for strain ML-1, respectively; doubling times for strains DSL-1 and ML-1 were 0.32 h and 0.30 h, respectively. Both strains required 2-3% (w/v) NaCl for optimal growth. Morphological and physiological features, as well as the results of 16S rDNA sequence analysis, showed these to be new strains of Propionigenium maris. Because they differ from the P. maris type strain (DSM 9537T) in a number of respects, including their ability to rapidly debrominate di- and tribromophenols, and in their specific habitats, the species description is amended to include these ecologically important properties.
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Characterization of Nodularia strains, cyanobacteria from brackish waters, by genotypic and phenotypic methods.
An investigation was undertaken of the genetic diversity of Nodularia strains from the Baltic Sea and from Australian waters, together with the proposed type strain of Nodularia spumigena. The Nodularia strains were characterized by using a polyphasic approach, including RFLP of PCR-amplified 16S rRNA genes, 16S rRNA gene sequencing, Southern blotting of total DNA, repetitive extragenic palindromic- and enterobacterial repetitive intergenic consensus-PCR, ribotyping and phenotypic tests. With genotypic methods, the Nodularia strains were grouped into two clusters. The genetic groupings were supported by one phenotypic property: the ability to produce nodularin. In contrast, the cell sizes of the strains were not different in the two genetic clusters. 16S rRNA gene sequences indicated that all the Nodularia strains were closely related, despite their different origins. According to this study, two genotypes of Nodularia exist in the Baltic Sea. On the basis of the taxonomic definitions of Komarek et al. (Algol Stud 68, 1-25, 1993), the non-toxic type without gas vesicles fits the description of Nodularia sphaerocarpa, whereas the toxic type with gas vesicles resembles the species N. spumigena and Nodularia baltica.
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Taxonomy of Antarctic Flavobacterium species: description of Flavobacterium gillisiae sp. nov., Flavobacterium tegetincola sp. nov., and Flavobacterium xanthum sp. nov., nom. rev. and reclassification of [Flavobacterium] salegens as Salegentibacter salegens gen. nov., comb. nov.
More Less16S rRNA phylogenetic analysis of a number of yellow- and orange-pigmented strains isolated from a variety of Antarctic habitats including sea ice, lakewater and cyanobacterial mats indicated a close relationship to the genus Flavobacterium but distinct from known Flavobacterium species. Phenotypic properties, DNA G+C content and whole-cell fatty acid profiles of the Antarctic strains were consistent with those of the genus Flavobacterium. DNA-DNA hybridization analysis indicated the presence of two distinct and novel genospecies each isolated from a different Antarctic habitat. From polyphasic taxonomic data it is proposed that the two groups represent new species with the following proposed names: Flavobacterium gillisiae (ACAM 601T) and Flavobacterium tegetincola (ACAM 602T). In addition polyphasic analysis of the species '[Cytophaga] xantha' (Inoue and Komagata 1976), isolated from Antarctic mud, indicated it was a distinct member of the genus Flavobacterium and was thus revived as Flavobacterium xanthum. Phylogenetic and fatty acid analyses also indicate that the species [Flavobacterium] salegens (Dobson et al. 1993), from Organic Lake, Antarctica, is misclassified at the genus level. It is proposed that this species belongs to a new genus, Salegentibacter salegens gen. nov., comb. nov.
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Haloterrigena thermotolerans sp. nov., a halophilic archaeon from Puerto Rico.
More LessAn extremely halophilic Archaeon belonging to the order Halobacteriales was isolated from the solar salterns of Cabo Rojo, Puerto Rico. The organism, designated strain PR5T, is rod-shaped, non-motile and requires at least 12% (w/v) NaCl to grow. The strain is highly thermotolerant: its temperature optimum is 50 degrees C and growth is possible up to 60 degrees C. Polar lipid analysis revealed the presence of the bis-sulfated glycolipid S2-DGD-1 as sole glycolipid and the absence of the glycerol diether analogue of phosphatidylglycerosulfate. Both C20,C20 and C20,C25 core lipids are present. The G+C content of the DNA is 63.3 mol%. According to 16S rDNA sequence data, strain PR5T is closely related to the representatives of the genera Haloterrigena and Natrinema, but on the basis of its phenotypic properties, 16S rDNA sequence and DNA-DNA hybridization studies, strain PR5T cannot be assigned to any of the recognized species within these genera. On the basis of its polar lipid composition, the isolate has been assigned to the genus Haloterrigena. The creation of a new species, Haloterrigena thermotolerans, is therefore proposed to accommodate this isolate. The type strain is strain PR5T (= DSM 11552T = ATCC 700275T).
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The Streptococcus anginosus species comprises five 16S rRNA ribogroups with different phenotypic characteristics and clinical relevance.
More LessA collection of 267 consecutively isolated Streptococcus anginosus strains was screened for the prevalence of previously described 'motile' strains by hybridization with oligonucleotide probes in a reverse line blot assay. The motile strains represented 101 (37.8%) of the S. anginosus strains. The vast majority of these strains fermented mannitol and raffinose, whereas most other S. anginosus strains did not (P<0.001). Most (83/101) of the motile strains were recovered from the urogenital tract (including five strains from neonatal surveillance cultures) and only a minority (36) of them were associated with infection-related samples (P<0.001). Strains that hybridized with the same oligonucleotide probes as the type strain S. anginosus ATCC 33397T (= NCTC 10713T) were designated ATCC-like strains. They accounted for 74 (27.7%) of the strains examined, were commonly distributed among the different body parts and were significantly more associated with infection-related samples. Three other hybridization patterns were recognized in the reverse line blot assay, ribogroup I (n = 51), ribogroup II (n = 21) and ribogroup III (n = 19). Ribogroup II strains were significantly more frequently recovered from the abdominal cavity and were associated with infection-related samples. Ribogroup I included the majority of the S. anginosus strains that carried Lancefield group C. Comparison of the nearly complete 16S rRNA sequence of two representative strains of each ribogroup revealed that all five ribogroups were closely related (>97% sequence similarities), and that most sequence divergences between the ribogroups occurred in the 1024-1064 bp region of the 16S rRNA gene. The present data confirm the heterogeneity within the S. anginosus species.
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Phylogenetic analysis of the genus Thermoactinomyces based on 16S rDNA sequences.
More LessThe almost complete 16S rDNA sequences of the type strains of eight validly described species and two invalid species of the genus Thermoactinomyces were determined and phylogenetically analysed. The validly described Thermoactinomyces species formed phylogenetic lineages related to the family Bacillaceae, as shown previously. However, the available strains of 'Thermoactinomyces glaucus' and 'Thermoactinomyces monosporus' exhibited their closest phylogenetic affinities not to the genus Thermoactinomyces but to the genus Saccharomonospora. Some Thermoactinomyces species were shown to be closely related from 16S rDNA sequence analysis. Particularly, Thermoactinomyces vulgaris KCTC 9076T and Thermoactinomyces candidus KCTC 9557T had the same 16S rDNA sequences and Thermoactinomyces thalpophilus KCTC 9789T and Thermoactinomyces sacchari KCTC 9790T showed 16S rDNA similarity value of almost 100%. From phylogenetic analysis based on 16S rDNA sequences, it is suggested that the genus Thermoactinomyces should be taxonomically re-evaluated using other useful taxonomic markers.
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Rapid identification of Staphylococcus epidermidis.
More LessDuring the collection of airborne bacteria in a museum in England some bacterial strains were isolated which due to their fatty acid profiles were clearly identified as members of the genus Staphylococcus. As fatty acid compositions of coagulase-negative staphylococci are very similar, differing only in quantities but not in qualities, further identification at the species level without a fatty acid database was not achieved. Investigation of the isolates using the Staph ID 32 API system resulted in an identification of the isolates as Staphylococcus epidermidis (probabilities of 79.7-95.5%). For further genotypic characterization of these isolates, some Staphylococcus epidermidis strains from different sources and the type strains of Staphylococcus aureus, Staphylococcus capitis, Staphylococcus epidermidis, Staphylococcus gallinarum, Staphylococcus haemolyticus, Staphylococcus hominis, Staphylococcus warneri and Staphylococcus xylosus were subjected to repetitive-sequence PCR, including enterobacterial repetitive intergenic consensus (ERIC) PCR, BOX-PCR and repetitive extragenic palindromic unit sequence (REP) PCR. ERIC- and BOX-PCR yielded a species-specific banding pattern for all Staphylococcus epidermidis strains. Furthermore, all staphylococcal reference strains investigated exhibited distinct banding patterns, clearly distinguishable from that of Staphylococcus epidermidis. No species-specific banding patterns could be observed after REP-PCR. As species identification of coagulase-negative staphylococci by fatty acid analyses and biochemical tests is known to be difficult ERIC- and BOX-PCR seem to be excellent tools for the identification of Staphylococcus epidermidis isolates.
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DNA-DNA hybridization determined in micro-wells using covalent attachment of DNA.
More LessThe present study was aimed at reducing the time and labour used to perform DNA-DNA hybridizations for classification of bacteria at the species level. A micro-well-format DNA hybridization method was developed and validated. DNA extractions were performed by a small-scale method and DNA was sheared mechanically into fragments of between 400 and 700 bases. The hybridization conditions were calibrated according to DNA similarities obtained by the spectrophotometric method using strains within the family Pasteurellaceae. Optimal conditions were obtained with 300 ng DNA added per well and bound by covalent attachment to NucleoLink. Hybridization was performed with 500 ng DNA, 5% (w/w) of which was labelled with photo-activatable biotin (competitive hybridization) for 2.5 h at 65 degrees C in 2 x SSC followed by stringent washing with 2 x SSC at the same temperature. The criteria for acceptance of results were a maximum of 15% standard deviation, calculated as a percentage of the mean for four replicate micro-wells, and that DNA similarities were not significantly different in at least two independent experiments. The relationship between DNA similarities obtained by the micro-well method (y) and by the spectrophotometric method (x) was y = 0.534x+30.6, when these criteria had been applied to 23 pairs of strains of Actinobacillus species, avian [Pasteurella] haemolytica-like bacteria and Mannheimia species. The correlation (Pearson) between DNA similarities obtained by interchange of strains used for covalent binding and hybridization was 0.794. Significantly lower DNA similarities were observed by the spectrophotometric compared with the micro-well method for three pairs of hybridizations. After removal of these data, the relationship between DNA similarities obtained by the micro-well and spectrophotometric methods improved to y = 0.855x + 11.0. It was found that the accuracy and precision of the micro-well method was at the same level as that of the spectrophotometric method, but the labour and analysis time were reduced significantly. The use of hybridization in the micro-well format will allow DNA-DNA hybridizations to be carried out between all strains selected for a particular taxonomic study, in order to construct complete data matrices and improve species definition.
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Catellatospora koreensis sp. nov., a novel actinomycete isolated from a gold-mine cave.
More LessA new actinomycete strain, LM 042T, which was isolated from a gold-mine cave in Kongju, Republic of Korea, is described by phenotypic and genotypic characters. The organism formed short chains of non-motile spores and globose bodies from substrate mycelium. An aerial mycelium was absent. This organism was chemotaxonomically characterized by the presence of meso-diaminopimelic acid, rhamnose, xylose, glucose, mannose and ribose in whole-cell hydrolysates (a type II cell wall and a variant of sugar pattern D), a glycolyl type of muramic acid, DNA G+C content of 70.4 mol%, a type PII phospholipid pattern (phosphatidylethanolamine as a diagnostic nitrogenous phospholipid), a tetrahydrogenated menaquinone with 10 isoprene units as a major menaquinone, and fatty acid profiles predominated by iso-branched hexadecanoic acid, iso-branched pentadecanoic acid and heptadcenoic acid. A comparative analysis of 16S rDNA sequences indicated that this organism formed a distinct clade within the evolutionary radiation of the family Micromonosporaceae and clustered with members of the genus Catellatospora. The 16S rDNA similarity values between the isolate and its phylogenetic neighbours, the two subspecies of Catellatospora citrea and Catellatospora tsunoense, were 95.0-95.2% and 94.9%, respectively. An equidistant relationship was observed among the isolate, Catellatospora ferruginea and all other members of the Micromonosporaceae genera (levels of similarity 93.0-94.0%). The combination of physiological, chemotaxonomic and DNA-DNA hybridization data supported that this organism is a novel species of the genus Catellatospora, for which the name Catellatospora koreensis sp. nov. is proposed. The type strain is LM 042T (= IMSNU 50729T).
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Emendation of the description of Blastomonas natatoria (Sly 1985) Sly and Cahill 1997 as an aerobic photosynthetic bacterium and reclassification of Erythromonas ursincola Yurkov et al. 1997 as Blastomonas ursincola comb. nov.
More LessPhotosynthetic properties of Blastomonas natatoria (Sly 1985) Sly and Cahill 1997, which had been recognized as being non-photosynthetic, were examined and compared with those of its close relative, the aerobic photosynthetic bacterium, Erythromonas ursincola Yurkov et al. 1997. HPLC experiments demonstrated that bacteriochlorophyll a was present in a detectable amount in the lipid extract from B. natatoria DSM 3183T as well as that from E. ursincola DSM 9006T. The puf genes, encoding the proteins of the photosynthetic reaction centre and core light-harvesting complexes, were detected by PCR from both the organisms. 16S rDNA sequence comparisons and DNA-DNA hybridization studies confirmed that B. natatoria and E. ursincola were closely related genetically in a single genus. On the basis of phenotypic, chemotaxonomic and phylogenetic data, it is proposed that the description of B. natatoria is emended as a species of aerobic photosynthetic bacteria and that E. ursincola is reclassified as Blastomonas ursincola comb. nov.
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Aeromonas salmonicida subsp. pectinolytica subsp. nov., a new pectinase-positive subspecies isolated from a heavily polluted river.
More LessAeromonas strains which phenotypically and genetically belong to the Aeromonas salmonicida species but that according to their phenotypic properties constitute a new subspecies have been isolated from the water of a heavily polluted river, the Matanza river, situated near the central district of Buenos Aires city. These strains were ascribed to the A. salmonicida species by using 65 biochemical tests and by DNA-DNA hybridization. They produce acid from -sorbitol, an unusual biochemical property found in a few members of the A. salmonicida species. They also utilize urocanic acid and do not ferment L-rhamnose or utilize LD-lactate, and are elastase- and gluconate-negative. The DNA relatedness was over 70%, the current limit accepted for the phylogenetic definition of a species, to the described A. salmonicida subspecies and nearly 100% within the new group of Aeromonas strains. Phenotypic differentiation from other A. salmonicida subspecies was readily achieved using the following characteristics: growth at 37 degrees C, melanin production, indole and Voges-Proskauer assays, growth on KCN broth, mannitol and sucrose fermentation and gas from glucose. A remarkable property of the strains of the new group was their ability to degrade polypectate, an unusual feature among Aeromonas species in general. The complete 16S rRNA gene of one strain of the new group was sequenced. Comparison with rDNA sequences of Aeromonas members available in databases revealed a close relationship between this strain and strains belonging to A. salmonicida subsp. salmonicida, masoucida and achromogenes, in agreement with the biochemical data. Since the new A. salmonicida strains constitute a tight genomic group that can be identified by phenotypic properties it was concluded that they represent a new subspecies for which the name Aeromonas salmonicida subsp. pectinolytica is proposed. The type strain of A. salmonicida subsp. pectinolytica is 34melT (= DSM 12609T).
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Acholeplasma vituli sp. nov., from bovine serum and cell cultures.
Organisms isolated from commercial foetal bovine serum and from cell culture lines containing such serum supplements were found to consist of non-helical, non-motile, pleomorphic coccoid forms. One strain (FC 097-2T) cultivated directly from foetal bovine serum was selected for characterization. In ultrastructural examination, individual round cells lacked cell wall structures and cells varied in size, with a mean diameter of about 700 nm. However, variable numbers of cells were filterable through membranes of 300 nm. Optimum growth occurred between 30 and 37 degrees C. The organism fermented glucose, fructose and mannose, but did not hydrolyse arginine. The strain was insensitive to 500 U penicillin ml(-1) and was capable of growing in the absence of serum or cholesterol. The organism was serologically distinct from all 13 currently described species in the genus Acholeplasma and from other sterol-requiring species in the genus Mycoplasma, using growth inhibition, immunoperoxidase and immunofluorescence tests. Strain FC 097-2T was found to have a DNA G+C composition between 37.6 +/- 1 mol% and 38.3 +/- 1 mol%. The genome size was determined to be 2095 kbp. The 16S rDNA sequence of strain FC 097-2T was compared to 16S rDNA sequences of other mollicutes in nucleotide databases. No deposited sequence was found to be identical; the closest relatives were several members of the genus Acholeplasma. On the basis of these findings and other similarities to acholeplasmas in morphology and growth, the absence of a sterol requirement for growth, and similar genomic characteristics, the organism was assigned to the genus Acholeplasma. Strain FC 097-2T is designated the type strain (ATCC 700667T) of a new species, Acholeplasma vituli.
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Polyphasic taxonomic approach in the description of Alishewanella fetalis gen. nov., sp. nov., isolated from a human foetus.
More LessA taxonomically unique bacterium is described on the basis of a physiological and biochemical characterization, fatty acid profiling and sequence analyses of 16S rRNA and gyrase B (gyrB) genes. This non-motile, non-fermentative bacterium was isolated from a human foetus in Uppsala, Sweden, and originally misidentified as a Shewanella putrefaciens by conventional biochemical testing. The bacterium grew well at mesophilic temperatures with optimum growth at 37 degrees C. It was facultatively anaerobic and utilized various electron acceptors (trimethylamine oxide, nitrate, nitrite and thiosulphate). The dominant fatty acids were 17:1B, 16:1 cis9, 17:0 and 16:0. Fatty acids 13:0 iso and 15:0 iso, which have been found to be typical of Shewanella species were not detected. The G+C content of the DNA was 50.6 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed a clear affiliation with members of the gamma subclass of the Proteobacteria. No relationship was seen with any of the established genera in the gamma subclass of the Proteobacteria, although a distinct relationship with Vibrionaceae was observed. That the bacterium represents a novel bacterial genus distinct from Vibrionaceae was also supported by gyrB sequence analysis. Considering the source and close proximity to the genus Shewanella, the name Alishewanella fetalis gen. nov., sp. nov. is proposed, for which the type strain is strain CCUG 30811T.
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Lactobacillus algidus sp. nov., a psychrophilic lactic acid bacterium isolated from vacuum-packaged refrigerated beef.
More LessLactobacillus algidus sp. nov. is described on the basis of 40 strains isolated as one of the predominant bacteria from five specimens of vacuum-packaged beef collected from different meat shops and stored at 2 degrees C for 3 weeks. These strains were quite uniform in the overall characteristics examined. They are facultatively anaerobic, psychrophilic, Gram-positive, non-spore-forming, non-motile, lactic acid-homofermentative rods. The cells occurred singly and in pairs on agar media and in rather long chains in broth media. They differed in several cultural and biochemical characteristics from the authentic meso-diaminopimelic acid-positive or psychrophilic lactic acid bacteria in the genera Lactobacillus, Carnobacterium and Brochothrix. The SDS-PAGE whole-cell protein pattern was clearly distinctive. DNA-DNA hybridization and phylogenetic analysis of 16S rDNA also failed to associate these strains closely with any of the validly described organisms used. The phylogenetic analysis showed that these strains are rather remotely but most closely related to Lactobacillus mali (93% sequence similarity), which belongs to the Lactobacillus casei/Pediococcus group. Therefore, these strains should be included in the genus Lactobacillus and considered to represent a new species, Lactobacillus algidus sp. nov. The type strain is M6A9T (= JCM 10491T).
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Vagococcus fessus sp. nov., isolated from a seal and a harbour porpoise.
More LessA polyphasic taxonomic study was performed on two strains of an unknown Gram-positive, catalase-negative, coccus-shaped bacterium isolated from a dead seal and a harbour porpoise. Comparative 16S rRNA gene sequencing demonstrated that the unknown bacterium represents a new subline within the genus Vagococcus close to, but distinct from, Vagococcus fluvialis, Vagococcus lutrae and Vagococcus salmoninarum. The unknown bacterium was readily distinguished from the three currently recognized Vagococcus species by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as a new species, Vagococcus fessus. The type strain of Vagococcus fessus is CCUG 41755T.
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Caloramator coolhaasii sp. nov., a glutamate-degrading, moderately thermophilic anaerobe.
More LessAn obligately anaerobic, moderately thermophilic, glutamate-degrading bacterium (strain ZT) was isolated from an enrichment culture obtained from anaerobic thermophilic granular sludge. The cells were rod-shaped to filamentous and showed no motility or spore formation. The cell wall had a Gram-positive structure, which was revealed by electron microscopy. Optimum growth of the strain was observed under neutrophilic conditions at 50-55 degrees C. The doubling time of strain ZT grown in rich medium was approximately 1 h at optimal pH and temperature. Strain ZT was able to grow on a variety of organic compounds. Most carbon sources were converted to acetate, CO2, H2, and traces of propionate and lactate. Strain ZT oxidized glutamate to acetate, CO2, NH4+, traces of propionate and H2. The doubling time on this substrate was 1-6 d. The strain fermented glutamate syntrophically in co-culture with Methanobacterium thermoautotrophicum Z-245T to the same products, but the co-culture had a fourfold higher growth rate. 16S rDNA sequence analysis revealed a relationship with Thermobrachium celere, Caloramator indicus and Caloramator proteoclasticus. The G+C content was 31.7 mol%. Based on its morphological, phylogenetic and physiological characteristics, it is proposed that strain ZT should be classified in the genus Caloramator as a new species, Caloramator coolhaasii.
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Acrocarpospora gen. nov., a new genus of the order Actinomycetales.
More LessThe taxonomic position of two actinomycete strains isolated from soil was studied. The isolates contained glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and menaquinone MK-9(H4) and madurose in the whole-cell hydrolysate. Phylogenetic analysis revealed that the isolates belonged to the family Streptosporangiaceae, but not to any known genus, and formed a monophyletic cluster with Streptosporangium corrugatum. On the basis of morphological characteristics, phylogenetic analysis and DNA-DNA hybridization, the name Acrocarpospora gen. nov. is proposed for a new genus containing the isolates and Streptosporangium corrugatum, and Acrocarpospora pleiomorpha sp. nov. R-31T (= IFO 16267T), Acrocarpospora macrocephala sp. nov. R-55T (=IFO 16266T) and Acrocarpospora corrugata comb. nov. IFO 13972T are described.
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An unusual Streptococcus from human urine, Streptococcus urinalis sp. nov.
More LessBiochemical, molecular chemical and molecular genetic studies were performed on an unknown Gram-positive, catalase-negative, chain-forming coccus isolated from the urine of a patient suffering from cystitis. Comparative 16S rRNA gene sequencing showed that the organism is a member of the 'pyogenic subgroup' of the genus Streptococcus and has a close affinity with Streptococcus pyogenes and Streptococcus canis. The unknown coccus was, however, readily distinguished from these species and other streptococci by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phenotypic and phylogenetic evidence, it is proposed that the unknown bacterium be classified as a new species of the genus Streptococcus, Streptococcus urinalis sp. nov. The type strain of Streptococcus urinalis is CCUG 41590T.
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Relationships of bradyrhizobia from Platypodium and Machaerium (Papilionoideae: tribe Dalbergieae) on Barro Colorado Island, Panama.
M A Parker and A LunkEnzyme electrophoresis and rRNA sequencing indicated that root nodule bacteria from the canopy tree Platypodium elegans and the lianas Machaerium milleflorum and Machaerium arboreum on Barro Colorado Island, Panama, were highly diverse on a local scale. A total of 11 distinct multilocus genotypes [ETs (electrophoretic types)] was found among the 33 isolates analysed. On average, ETs differed from one another at 74% of the 11 enzyme loci assayed, and separate nodules on a single host individual were often occupied by genetically divergent ETs. Certain ETs were sampled multiple times from both Platypodium and Machaerium, suggesting a lack of specificity toward the two legume genera. Within the intervening sequence (IVS) region in the 5' end of 23S rRNA, seven ETs had a length variant similar to that of Bradyrhizobium japonicum USDA 110, and the other four ETs had an IVS region 26-28 bp shorter. Parsimony analysis of both partial 23S rRNA and nearly full-length 16S rRNA sequences indicated that all Platypodium and Machaerium isolates were related to B. japonicum rather than Bradyrhizobium elkanii. The 16S rRNA sequence of one isolate was >99% similar to that of B. japonicum USDA 110, and the closest known relatives for other isolates were Philippine bradyrhizobia from the legumes Stylosanthes and Samanea.
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Sequence analysis of domains III and IV of the 23S rRNA gene of verticillate streptomycetes.
More LessDomains III and IV of the 23S rRNA gene of 25 strains of verticillate streptomycetes were sequenced. None of the sequences was identical to any other, with regions of variability being restricted to parts of helices 54 and 64. No relationships were detected between the similarities in the sequence and the assignment to phenetic clusters as defined by the numerical taxonomy studies. Limited agreement was also found between similarity of the sequences and DNA-DNA homology values. However, species (> 70% DNA-DNA homology values)-specific diagnostic oligonucleotides generally could be defined, except for Streptomyces baldaccii. Therefore the determination of the 23S rRNA sequence may be of greater value for fingerprinting individual strains than for taxonomic or identification purposes.
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Rhodococcus koreensis sp. nov., a 2,4-dinitrophenol-degrading bacterium.
More LessA 2,4-dinitrophenol-degrading bacterial strain, DNP505T, which was isolated from an industrial wastewater, was taxonomically studied by a polyphasic approach using phenotypic, chemotaxonomic and genetic methods. Strain DNP505T has a cell wall of chemotype IV containing meso-diaminopimelic acid, arabinose and galactose. The predominant menaquinone is MK-8(H2). Mycolic acids contain 43-53 carbon atoms. Strain DNP505T has a cellular fatty acid profile containing straight-chain saturated, unsaturated and 10-methyl-branched fatty acids and has C16:0 as the major fatty acid. The DNA G+C content is 66 mol%. Strain DNP505T formed a coherent cluster with Rhodococcus species in a phylogenetic inference based on 16S rDNA sequences. Interestingly, strain DNP505T was found to have two types of 16S rDNA sequence, which showed 10 bp sequence differences (99.3% nucleotide similarity). Its differences in some phenotypic characteristics and its genetic distinctiveness indicate that strain DNP505T is separate from Rhodococcus species described previously. It is therefore proposed that strain DNP505T should be placed in the genus Rhodococcus as a new species, Rhodococcus koreensis. The type strain of the new species is strain DNP505T (= KCTC 0569BPT = JCM 10743T).
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Gordonia nitida sp. nov., a bacterium that degrades 3-ethylpyridine and 3-methylpyridine.
More LessA bacterial strain, LE31T, which is capable of degrading 3-ethylpyridine and 3-methylpyridine, was isolated from an industrial wastewater and was taxonomically studied by using a polyphasic approach. Strain LE31T was identified as a member of the genus Gordonia on the basis of chemotaxonomic characteristics and phylogenetic inference-based 16S rDNA sequence. The cell wall contained meso-diaminopimelic acid, arabinose and galactose (wall chemotype IV). The predominant menaquinone was MK-9(H2). The mycolic acids contained 47-55 carbon atoms. The major fatty acids were C16:0, C18:1 omega9c, 10-methyl-C18:0 (TBSA). The G+C content of DNA was 67 mol%. The 16S rDNA sequence of strain LE31T was most similar to that of the type strain of Gordonia rubropertincta. The differences in some phenotypic characteristics and the genetic distinctiveness distinguish strain LE31T from the Gordonia species described previously. Therefore it is proposed that strain LE31T should be placed in the genus Gordonia as a new species. The name Gordonia nitida is proposed for strain LE31T. The type strain of the new species is strain LE31T (= KCTC 0605BPT = KCCM 80004T).
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Systematic analysis of xanthomonads (Xanthomonas spp.) associated with pepper and tomato lesions.
The taxonomy and evolutionary relationships among members of the genus Xanthomonas associated with tomato and pepper have been a matter of considerable controversy since their original description in 1921. These bacteria, which are a major affliction of tomato and pepper crops in warm and humid regions, were originally described as a single species, but subsequent research has shown the existence of at least two genetic groups differentiated by physiological, biochemical and pathological characteristics. This work synthesizes the findings from several approaches, including pathogenicity tests, enzymic activity, restriction fragment analysis of the entire genome, DNA-DNA hybridization and RNA sequence comparisons based on a 2097 base sequence comprising the 16S rRNA gene, the intergenic spacer located between the 16S and 23S rRNA genes and a small region of the 23S rRNA gene. Within the group of xanthomonads pathogenic on pepper and tomato four distinct phenotypic groups exist, of which three form distinct genomic species. These include Xanthomonas axonopodis pv. vesicatoria (A and C group), Xanthomonas vesicatoria (B group) and Xanthomonas gardneri (D group). On the basis of phenotypic and genotypic differences between A- and C-group strains, the C strains should be considered as a subspecies within Xanthomonas axonopodis pv. vesicatoria.
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Papillibacter cinnamivorans gen. nov., sp. nov., a cinnamate-transforming bacterium from a shea cake digester.
More LessA new, strictly anaerobic, Gram-positive, non-sporulating, mesophilic bacterium, designated strain CIN1T (T=type strain) was isolated from an anaerobic digester fed with shea cake rich in tannins and aromatic compounds. Cells of strain CIN1T were rod-shaped, had characteristically pointed ends (1.3-3.0 x 0.5-0.6 microm) and occurred singly, in pairs and sometimes in chains of up to six. The pH range for growth was 6.9-8.5 and the temperature growth range was 15-40 degrees C. Optimum growth occurred with yeast extract and cinnamate at 37 degrees C and a pH of 7.5. The isolate transformed cinnamate by degrading the aliphatic side chain to produce acetate and benzoate rather than by aromatic ring cleavage or demethoxylation. The position of the methoxyl group appears to be important in the degradation of the aliphatic side chain of cinnamate; consequently, 3-methoxycinnamate and 4-methoxycinnamate, but not 2-methoxycinnamate, are transformed to produce acetate and methoxybenzoates, namely 3-methoxybenzoate and 4-methoxybenzoate, respectively. Crotonate is degraded to acetate and butyrate. The G+C content of the DNA is 56 mol%. Phylogenetic analysis of the 16S rRNA gene of strain CIN1T indicated that it was a member of the low-G+C-containing Gram-positive branch with a specific relationship to Sporobacter termitidis (sequence identity of 88%). The phylogenetic results concur with the phenotypic data which reveals that the isolate is a novel bacterium and, based on these findings, strain CIN1T (= DSM 12816T = ATCC 700879T) has been designated Papillibacter cinnamivorans gen. nov., sp. nov.
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Halothiobacillus kellyi sp. nov., a mesophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium isolated from a shallow-water hydrothermal vent in the Aegean Sea, and emended description of the genus Halothiobacillus.
S M Sievert, T Heidorn and J KueverA new mesophilic, chemolithoautotrophic, sulfur-oxidizing bacterium, strain Milos-BII1T, was isolated from a sediment sample taken from a shallow-water hydrothermal vent in the Aegean Sea with thiosulfate as electron donor and CO2 as carbon source. Based on the almost complete sequence of the 16S rRNA gene, strain Milos-BII1T forms a phylogenetic cluster with Thiobacillus hydrothermalis, Thiobacillus neapolitanus, Thiobacillus halophilus and Thiobacillus sp. W5, all of which are obligately chemolithoautotrophic bacteria. Because of their phylogenetic relatedness and their physiological similarities it is proposed to transfer these organisms to a newly established genus within the gamma-subclass of the Proteobacteria, Halothiobacillus gen. nov. (Kelly and Wood 2000). Strain Milos-BII1T represents a new species of this genus, named Halothiobacillus kellyi. Cells were Gram-negative rods and highly motile. The organism was obligately autotrophic and strictly aerobic. Nitrate was not used as electron acceptor. Chemolithoautotrophic growth was observed with thiosulfate, tetrathionate, sulfur and sulfide. Growth was observed between pH values of 3.5 and 8.5, with an optimum at pH 6.5. The temperature limits for growth were 3.5 and 49 degrees C, with an optimum between 37 and 42 degrees C. Growth occurred between 0 and 2 M NaCl, with an optimum NaCl concentration between 400 and 500 mM. The mean maximum specific growth rate on thiosulfate was 0.45 h(-1).
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Desulfacinum hydrothermale sp. nov., a thermophilic, sulfate-reducing bacterium from geothermally heated sediments near Milos Island (Greece).
S M Sievert and J KueverA thermophilic, sulfate-reducing bacterium, strain MT-96T, was isolated from an active, marine, shallow-water hydrothermal vent system. It used a large variety of substrates, ranging from simple organic compounds to long-chain fatty acids, as electron donors. Autotrophic growth was possible with H2 and CO2 in the presence of sulfate. Sulfate, thiosulfate and sulfite were used as electron acceptors. Sulfur and nitrate were not reduced. Fermentative growth was obtained with pyruvate, but not with fumarate or malate. Substrate oxidation was usually complete, leading to production of CO2, but at high substrate concentrations acetate accumulated. The oval-shaped cells were 0.8-1.0 microm in width and 1.5-2.5 microm in length. Cells were motile during the early-exponential-growth phase, but motility rapidly declined during later growth phases. Spores were not produced and cells stained Gram-negative. The temperature limits for growth were between 37 and 64 degrees C, with an optimum at 60 degrees C. Growth was observed at salinities ranging from 15 to 78 g NaCl l(-1), with optimum growth in the presence of 32-36 g NaCl l(-1). This might reflect an adaptation to the elevated salinity of the hydrothermal fluid. The G+C content of the DNA was 59.5 mol%. Vitamins or other supplements were not required. Based on the 16S rRNA gene sequence, strain MT-96T belonged in the delta-subclass of the Proteobacteria. Strain MT-96T was found to be phenotypically and phylogenetically related to Desulfacinum infernum (< 95.3% sequence identity) and represents a new member of the genus Desulfacinum. The name Desulfacinum hydrothermale is proposed for this strain; the type strain is MT-96T (= DSM 13146).
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Characterization of a Rothia-like organism from a mouse: description of Rothia nasimurium sp. nov. and reclassification of Stomatococcus mucilaginosus as Rothia mucilaginosa comb. nov.
More LessAn unknown, Gram-positive, ovoid-shaped bacterium isolated from the nose of a mouse was subjected to a polyphasic taxonomic analysis. Comparative 16S rRNA gene sequencing demonstrated that the unknown organism was a member of the family Micrococcaceae and possessed a specific phylogenetic association with Rothia dentocariosa and Stomatococcus mucilaginosus. Phenotypically, the bacterium closely resembled R. dentocariosa and S. mucilaginosus but could be distinguished from these species by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified in the genus Rothia, as Rothia nasimurium sp. nov. In addition, it is proposed that S. mucilaginosus be reclassified in the genus Rothia, as Rothia mucilaginosa comb. nov.
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Lactobacillus fornicalis sp. nov., isolated from the posterior fornix of the human vagina.
More LessTwelve strains isolated from the posterior fornix fluid of the human vagina were identified as Lactobacillus johnsonii, Lactobacillus acidophilus, Lactobacillus gallinarum and Lactobacillus crispatus based on numerical analyses of total soluble cell protein profiles and randomly amplified polymorphic DNA (RAPD)-PCR banding patterns. Five strains grouped with the type strains of Lactobacillus gasseri (DSM 20077T) and Lactobacillus jensenii (DSM 20557T) at r > or = 0.83 in one protein profile cluster, well separated from the other species included in this study. However, numerical analysis of the RAPD-PCR banding patterns of representative strains selected from the L. gasseri-L. jensenii protein cluster clearly indicated that they belong to two different species. Four strains (TV 1010, TG 1013, TV 1018T and TV 1045) grouped into another well separated protein profile cluster at r > or = 0.87. Strains selected from this cluster displayed very similar RAPD-PCR banding patterns and clustered at R2 > or = 0.78, separate from the other strains examined. Sequencing of the 16S rRNA of two representative strains, TV 1018T and TG 1013, of this group indicated that it represents a new member of rRNA group I Lactobacillus, which includes Lactobacillus delbrueckii, the type of the genus, and close relatives Lactobacillus acetotolerans, Lactobacillus kefiranofaciens, Lactobacillus iners, L. jensenii, L. crispatus, L. acidophilus, Lactobacillus helveticus, Lactobacillus amylovorus, Lactobacillus hamsteri, L. johnsonii, L. gasseri and Lactobacillus amylolyticus. The name Lactobacillus fornicalis sp. nov. is proposed for strains TV 1010 (DSM 13172), TG 1013, TV 1018T and TV 1045, with strain TV 1018T (= DSM 13171T = ATCC 700934T) as the type.
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Clostridium peptidivorans sp. nov., a peptide-fermenting bacterium from an olive mill wastewater treatment digester.
More LessA new peptide-degrading, strictly anaerobic bacterium, designated strain TMC4T, was isolated from an olive mill wastewater treatment digester. Cells of strain TMC4T were motile, rod-shaped (5-10 x 0.6-1.2 microm), stained Gram-positive and formed terminal to subterminal spores that distended the cells. Optimal growth occurred at 37 degrees C and pH 7 in an anaerobic basal medium containing 0.5% Casamino acids. Arginine, lysine, cysteine, methionine, histidine, serine, isoleucine, yeast extract, peptone, Biotrypcase, gelatin and crotonate also supported growth, but not carbohydrates, organic acids or alcohols. The end-products of degradation were: acetate and butyrate from lysine and crotonate; acetate, butyrate, H2 and CO2 from Biotrypcase, gelatin and peptone; acetate, alanine, H2 and CO2 from cysteine; acetate, H2 and CO2 from serine, cysteine and yeast extract; acetate and formate from histidine; propionate from methionine; methyl 2-butyrate, H2 and CO2 from isoleucine; acetate and ethanol from arginine; and acetate, propionate, butyrate, methyl 2-butyrate, H2 and CO2 from Casamino acids. The DNA G+C content of strain TMC4T was 31 mol%. Phylogeny based on 16S rRNA sequence analysis showed that strain TMC4T was a member of the low-G+C-content Gram-positive genus Clostridium, with the closest relative being Clostridium pascui (sequence similarity of 96 %). Due to considerable differences in genomic and phenotypic properties between strain TMC4T and those of its nearest relative, strain TMC4T is proposed as a new species of the genus Clostridium, Clostridium peptidivorans sp. nov. Strain TMC4T has been deposited in the DSMZ as strain DSM 12505T.
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The halotolerance and phylogeny of cyanobacteria with tightly coiled trichomes (Spirulina Turpin) and the description of Halospirulina tapeticola gen. nov., sp. nov.
More LessThe morphologies, halotolerances, temperature requirements, pigment compositions and 16S rRNA gene sequences of five culture collection strains and six novel isolates of cyanobacteria with helical, tightly coiled trichomes were investigated. All strains were very similar morphologically and could be assigned to the genus Spirulina (or section Euspirulina sensu Geitler), according to traditional classification. However, the isolates showed significantly different requirements for salinity and temperature, which were in accordance with their respective environmental origins. The genetic divergence among the strains investigated was large. The results indicate the drastic underestimation of the physiological and phylogenetic diversity of these cyanobacteria by the current morphology-based classification and the clear need for new taxa. Three of the isolates originated from hypersaline waters and were similar with respect to their high halotolerance, broad euryhalinity and elevated temperature tolerance. By phylogenetic analyses, they were placed in a tight monophyletic cluster apart from all other cyanobacteria. Thus it is proposed to reclassify highly halotolerant cyanobacteria with tightly coiled trichomes in Halospirulina gen. nov., with the type species Halospirulina tapeticola sp. nov.
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Description of Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. and emendation of some families of the suborder Micrococcineae.
More LessThe hierarchic taxonomic framework described recently for the phylogenetic structure of the suborder Micrococcineae, class Actinobacteria, on the basis of 16S rDNA sequences and signature nucleotides was modified and extended. With the recent addition of novel taxa into the suborder, the phylogenetic coherence of some families was disrupted, leading to the emergence of novel lineages that, as judged by the depth of their branching points, were equivalent to those of described families. Bogoriellaceae fam. nov., Dermacoccaceae fam. nov., Rarobacteraceae fam. nov. and Sanguibacteraceae fam. nov. are proposed for these lineages. As a consequence of the restructuring process, some families have had to be emended, i.e. Dermatophilaceae, Cellulomonadaceae and Intrasporangiaceae.
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Thermanaerovibrio velox sp. nov., a new anaerobic, thermophilic, organotrophic bacterium that reduces elemental sulfur, and emended description of the genus Thermanaerovibrio.
More LessA moderately thermophilic, organotrophic bacterium with vibrioid cells was isolated from a sample of a cyanobacterial mat from caldera Uzon, Kamchatka, Russia, and designated strain Z-9701T. Cells of strain Z-9701T were curved, Gram-negative rods, 0.5-0.7 x 2.5-5.0 microm in size, with tapering ends and with fast, wavy movement by means of lateral flagella located on the concave side of the cell. Colonies were small, white, irregular or round, 0.2 mm in diameter, and with even edges. Strain Z-9701T was an obligate anaerobe with a temperature optimum at 60-65 degrees C and a pH optimum at 7.3. It fermented glucose, fructose, mannose, N-acetyl-D-glucosamine, adonite, arginine, serine, peptone, yeast extract and Casamino acids. The fermentation products formed during growth on glucose were acetate, lactate, H2, CO2 and ethanol. Strain Z-9701T reduced elemental sulfur to H2S during organotrophic growth with glucose or peptides as energy and carbon sources. In the presence of S0, strain Z-9701T was capable of lithotrophic growth with molecular hydrogen as energy substrate and 0.1 g yeast extract l(-1) as carbon source. Sulfate, thiosulfate, nitrate, Fe(III) and sulfite were not reduced and did not stimulate growth. The G+C content of strain Z-9701T DNA was 54.6 mol%. The results of 16S rDNA sequence analyses revealed that strain Z-9701T belongs to the cluster within the Clostridium group formed by Thermanaerovibrio acidaminovorans, Dethiosulfovibrio peptidovorans, Anaerobaculum thermoterrenum and Aminobacterium colombiense, but the level of sequence similarity with the members of this cluster was not very high (87.6-92.2%). Among these organisms, Thermanaerovibrio acidaminovorans is phenotypically close to strain Z-9701T. However, the two organisms showed a relatively low level of similarity of their 16S rRNA sequences (92.2%) and of DNA-DNA hybridization (15 +/- 1%). Nevertheless, on the basis of the similar morphology and physiology of the new isolate and Thermanaerovibrio acidaminovorans, strain Z-9701T was placed in the genus Thermanaerovibrio and a new species, Thermanaerovibrio velox, proposed for it. The type strain is Z-9701T (= DSM 12556T).
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Natrinema versiforme sp. nov., an extremely halophilic archaeon from Aibi salt lake, Xinjiang, China.
More LessA novel extremely halophilic archaeon, strain XF10T, was isolated from a salt lake in China. This organism was neutrophilic, non-motile and pleomorphic, and was rod, coccus or irregularly shaped. It required at least 1.5 M NaCl for growth and grew in a wide range of MgCl2 concentrations (0.005-0.5 M). Lipid extract of whole cells contained two glycolipids with the same chromatographic properties as two unidentified glycolipids found in the two described Natrinema species, Natrinema pellirubrum and Natrinema pallidum. Phylogenetic analysis based on 16S rDNA sequence comparison revealed that strain XF10T clustered with the two described Natrinema species and several other strains (strains T5.7, GSL-11 and Haloterrigena turkmenica JCM 9743) with more than 98.1% sequence similarities, suggesting that strain XF1OT belongs to the genus Natrinema. Comparative analysis of phenotypic properties and DNA-DNA hybridization between strain XF10T and the Natrinema species supported the conclusion that strain XF10T is a novel species within the genus Natrinema. The name Natrinema versiforme sp. nov. is proposed for this strain. The type strain is XF10T (=JCM 10478T=AS 1.2365T=ANMR 0149T).
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New psychrophilic and psychrotolerant Bacillus marinus strains from tropical and polar deep-sea sediments and emended description of the species.
More LessIn contrast to the current view that psychrophily combined with an absolute requirement for NaCl is connected with the Gram-negative cell wall type, psychrophilic and psychrotolerant, NaCl-requiring, Gram-positive bacteria have been isolated from tropical Atlantic, Arctic and Antarctic deep-sea sediments. Some of the isolates are even extremely psychrophilic, having maximum growth temperatures of 4 degrees C. On the basis of phenotypic characteristics, DNA base analyses, DNA-DNA hybridizations and partial and complete 16S rRNA gene sequence analyses, the strains from the three distinct geographical regions have been allocated to the obligately marine species Bacillus marinus. The distribution and origin of B. marinus are discussed and an emended description of the species is presented.
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Saccharothrix violacea sp. nov., isolated from a gold mine cave, and Saccharothrix albidocapillata comb. nov.
More LessThe generic position of two isolates from soils inside a gold mine cave in Kongju, Korea, was determined by 16S rDNA sequencing and chemotaxonomic characteristics. Phylogenetic analysis indicated that both of the isolates formed a clade with Lentzea albidocapillata and members of the genus Saccharothrix of the family Pseudonocardiaceae. The chemical composition of the isolates and of Lentzea albidocapillata was consistent with that of the genus Saccharothrix, which is characterized by a type III cell wall (the meso-isomer of diaminopimelic acid, and galactose and rhamnose as characteristic whole-cell sugars), MK-9(H4) as the major menaquinone, and a phospholipid type PII pattern (phosphatidylethanolamine as a diagnostic phospholipid). The combination of morphological features, chemotaxonomic characters and phylogenetic data supported the proposal that Lentzea albidocapillata, the only and type strain of the genus Lentzea, should be transferred to the genus Saccharothrix. On the basis of physiological properties, cellular fatty acid composition and DNA-DNA hybridization data, two new species within the genus Saccharothrix are proposed: Saccharothrix violacea sp. nov., type strain LM 036T (= IMSNU 50388T), and Saccharothrix albidocapillata comb. nov., type strain DSM 44073T (=IMSNU 21253T).
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Comparison of the 16S-23S rRNA intergenic spacer regions among strains of the Mycoplasma mycoides cluster, and reassessment of the taxonomic position of Mycoplasma sp. bovine group 7.
R Harasawa, H Hotzel and K SachseNucleotide sequence analysis of the 16S-23S rRNA intergenic spacer regions of six type or reference strains belonging to the Mycoplasma mycoides cluster and of Mycoplasma putrefaciens suggested the presence of two subclusters. One subcluster comprised M. mycoides subsp. mycoides small colony (SC) type, M. mycoides subsp. mycoides large colony (LC) type and M. mycoides subsp. capri, whereas the second subcluster comprised Mycoplasma capricolum subsp. capricolum, M. capricolum subsp. capripneumoniae and Mycoplasma sp. bovine group 7. The type strains from M. mycoides subsp. mycoides SC and M. mycoides subsp. capri had identical spacer sequences. The existence of two subclusters was supported by predicted secondary structures of the analysed region. The nucleotide variations in the loop domains of the secondary structures might be a useful genetic marker to distinguish between the two subclusters. The secondary structure differences delineated the differences between the two subclusters more clearly than the nucleotide sequence alignments, which only showed a small number of differences, and some of these were common to both clusters. The data also provided evidence in favour of a reclassification of Mycoplasma sp. bovine group 7 as another subspecies of M. capricolum.
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Bacillus thermodenitrificans sp. nov., nom. rev.
More LessA polyphasic study was performed on 10 soil isolates of thermophilic denitrifying Bacillus strains from different geographical areas. The presence of two main characteristic bands following amplification of the internal transcribed spacer (ITS) region of rrn operons suggests a close relatedness to 'Bacillus thermodenitrificans'. The isolates cluster around two strains of 'B. thermodenitrificans' in riboprint and fatty acid analyses, though differences occur at the strain level. Subsequent DNA-DNA reassociation studies including the 10 isolates, 'B. thermodenitrificans' DSM 465T and DSM 466, and Bacillus stearothermophilus ATCC 12980T and Bacillus thermoleovorans ATCC 43513T revealed such a high level of genomic relatedness between the isolates and the DSM strains (> 73% similarity) that they must be considered strains of the same taxon. The degree of DNA-DNA similarity between the 12 strains of 'B. thermodenitrificans' and the type strains of the other two phylogenetically neighbouring Bacillus species was significantly lower (21-43% similarity). Based upon phylogenetic, chemotaxonomic and phenotypic evidence, the designation of B. thermodenitrificans sp. nov., nom. rev. is proposed. The type strain of B. thermodenitrificans is DSM 465T.
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Photobacterium histaminum Okuzumi et al. 1994 is a later subjective synonym of Photobacterium damselae subsp. damselae (Love et al. 1981) Smith et al. 1991.
B Kimura, S Hokimoto, H Takahashi and T FujiiThe type strain of Photobacterium histaminum, JCM 8968T (= ATCC 51805T), and that of Photobacterium damselae subsp. damselae, ATCC 33539T, exhibit 100% identity in their 16S rRNA sequence, more than 80% DNA-DNA homology and only one phenotypic difference. Also, like P. histaminum, P. damselae subsp. damselae was shown to excrete a large amount of histamine when cells were grown on medium containing excessive histidine under acidic conditions. Therefore, the name P. histaminum should be considered to be a later subjective synonym of P. damselae subsp. damselae.
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