- Volume 51, Issue 1, 2001
Volume 51, Issue 1, 2001
- Articles
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Genomic approaches to typing, taxonomy and evolution of bacterial isolates.
V Gürtler and B C MayallThe current literature on bacterial taxonomy, typing and evolution will be critically examined from the perspective of whole-genome structure, function and organization. The following three categories of DNA band pattern studies will be reviewed: (i) random whole-genome analysis; (ii) specific gene variation and (iii) mobile genetic elements. (i) The use of RAPD, PFGE and AFLP to analyse the whole genome will provide a skeleton of polymorphic sites with exact genomic positions as whole-genome sequence data become available. (ii) Different genes provide different levels of evolutionary information for determining isolate relatedness depending on whether they are highly variable (prone to recombination events and horizontal transfer), housekeeping genes with only a small number of single nucleotide differences between isolates or part of the rrn multigene family that is prone to intragenomic recombination and concerted evolution. Comparative analyses of these different gene classes can provide enhanced information about isolate relatedness. (iii) Mobile genetic elements such as insertion sequences, transposons, plasmids and bacteriophages integrate into the bacterial genome at specific (e.g. tRNA genes) or non-specific sites to alter band patterns produced by PFGE, RAPD or AFLP. From the literature it is not clear what level of genetic element duplication constitutes non-relatedness of isolates. A model is presented that incorporates all of the above genomic characteristics for the determination of isolate relatedness in taxonomic, typing and evolutionary studies.
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Azospirillum doebereinerae sp. nov., a nitrogen-fixing bacterium associated with the C4-grass Miscanthus.
More LessA new group of nitrogen-fixing Azospirillum sp. bacteria was isolated from the roots of the C4-gramineous plant Miscanthus. Polyphasic taxonomy was performed, including auxanography using API galleries, physiological tests and 16S rRNA sequence comparison. The ability of the isolates to fix dinitrogen was evaluated by amplification of the nifD gene, immunodetection of the dinitrogenase reductase and acetylene-reduction assay. On the basis of these results, the nitrogen-fixing isolates represent a new species within the genus Azospirillum. Its closest phylogenetic neighbours, as deduced by 16S rDNA-based analysis, are Azospirillum lipoferum, Azospirillum largimobile and Azospirillum brasilense with 96.6, 96.6 and 95.9% sequence similarity, respectively. Two 16S rRNA-targeting oligonucleotide probes were developed which differentiate the new species from the other Azospirillum species by whole-cell fluorescence hybridization. Strains of the new species are curved rods or S-shaped, 1.0-1.5 microm in width and 2,0-3.0 microm in length, Gram-negative and motile with a single polar flagellum. Optimum growth occurs at 30 degrees C and at pH values between 6.0 and 7.0. No growth takes place at 37 degrees C. They have a respiratory type of metabolism, grow well on arabinose, D-fructose, gluconate, glucose, glycerol, malate, mannitol and sorbitol. They differ from A. largimobile and A. lipoferum by their inability to use N-acetylglucosamine and D-ribose, from A. lipoferum by their ability to grow without biotin supplementation and from A. brasilense by their growth with D-mannitol and D-sorbitol as sole carbon sources. Nitrogen fixation occurs in microaerobic nitrogen-limited conditions. For this species, the name Azospirillum doebereinerae sp. nov. is suggested, with strain GSF71T as the type strain (= DSM 13131T; reference strain Ma4 = DSM 13400). Its G+C content is 70.7 mol%.
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Determination of the systematic position of the genus Asticcacaulis Poindexter by a polyphasic analysis.
More LessThe genus Asticcacaulis, to date, comprises two species of unicellular, stalked bacteria, developing a stalk at a site which is not coincidental with the centre of the pole of the cell. Multiplication is similar to that demonstrated by the prosthecate species of the genera Caulobacter, Brevundimonas and Maricaulis. A polyphasic approach, comprising 16S rRNA gene sequencing, lipid analysis and NaCl tolerance characterizations, was used to clarify the taxonomy of the two Asticcacaulis species. From the analysis of the 16S rRNA gene sequences, a close phylogenetic relationship between the species that comprise the genera Asticcacaulis, Caulobacter and Brevundimonas could be deduced wherein the three genera form three distinct branches. The individual genera could also be discerned by different characteristic polar lipids. The species of Asticcacaulis differed from species of Caulobacter and Brevundimonas by the lack of 1,2-diacyl-3-O-[6'-phosphatidyl-alpha-D-glucopyranosyl]glycerol. They also did not contain 1,2-di-O-acyl-3-O-[D-glucopyranosyl-(1-->4)-alpha-D-glucuronopyranosyl]glycerol, which is found in most Brevundimonas species but not in strains of the genus Caulobacter. The morphological differences seen between the two species Asticcacaulis excentricus and Asticcacaulis biprosthecium are mirrored by the observed 16S rDNA sequence similarity value of 95.3%, which is relatively low compared to the interspecies similarity values observed within the genera Brevundimonas or Caulobacter.
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Reclassification of bioindicator strains Bacillus subtilis DSM 675 and Bacillus subtilis DSM 2277 as Bacillus atrophaeus.
More LessOn the basis of high DNA-DNA reassociation values and confirmatory automated RiboPrint analysis, two aerobic spore-forming strains hitherto allocated to Bacillus subtilis and used as bioindicators (DSM 675, hot-air sterilization control; DSM 2277, ethylene oxide sterilization control) are reclassified as Bacillus atrophaeus.
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Clostridium hiranonis sp. nov., a human intestinal bacterium with bile acid 7alpha-dehydroxylating activity.
M Kitahara, F Takamine, T Imamura and Y BennoThe Clostridium-like organisms TO-931T and HD-17, isolated from human faeces, have high levels of bile acid 7alpha-dehydroxylating activity. Sequencing of their 16S rDNA demonstrated that they belong to cluster XI of the genus Clostridium and that they represent a new and distinct line of descent. Clostridium bifermentans and Clostridium sordellii in cluster XI also possess bile acid 7alpha-dehydroxylating activity. DNA-DNA hybridization experiments with the isolates, TO-931T and HD-17, and C bifermentans and C. sordellii revealed that the isolates are a single species distinct from C. bifermentans and C sordellii. On the basis of phylogenetic analysis, using 16S rDNA sequences, and DNA-DNA hybridization analysis, it is concluded that strains TO-931T and HD-17 are members of a new species of the genus Clostridium, for which the name Clostridium hiranonis is proposed. The type strain is strain TO-931T (= JCM 10541T = DSM 13275T).
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Lactobacillus cypricasei sp. nov., isolated from Halloumi cheese.
More LessFour strains of a hitherto unknown bacterium isolated from Halloumi cheese were compared by using phenotypic and phylogenetic studies. Comparative 16S rRNA gene sequencing demonstrated that the strains were identical to each other and represent a new subline within the genus Lactobacillus. The unknown bacterium was readily distinguished from other described Gram-positive catalase-negative taxa by means of biochemical tests and electrophoretic analysis of whole-cell proteins. On the basis of phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Lactobacillus cypricasei sp. nov. The type strain of L. cypricasei is CCUG 42961T (= CIP 106393T).
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Re-examining the 16S rDNA sequence of Halomonas salina.
More LessPrevious reports of 16S rDNA sequencing of members of the family Halomonadaceae Franzmann et al. 1989 include two different sequences that were both attributed to the type strain of Halomonas salina (Valderrama et al. 1991) Dobson and Franzmann 1996 (basonym Deleya salina Valderrama et al. 1991). The two sequences are sufficiently different for them to belong to two different species within the genus Halomonas. In order to determine which of the two sequences corresponded to that of the type strain of Halomonas salina, the designated type strains of this species were obtained from the ATCC and the DSMZ. It was possible to show that only one of the previous sequences corresponded to the sequences obtained from DSMZ 5928T and ATCC 49509T.
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Arcanobacterium pluranimalium sp. nov., isolated from porpoise and deer.
More LessTwo strains of a previously undescribed Arcanobacterium-like bacterium were isolated from a dead harbour porpoise and a dead sallow deer. Biochemical testing and PAGE analysis of whole-cell proteins indicated that the strains were phenotypically closely related to each other and distinct from previously described Actinomyces and Arcanobacterium species. Comparative 16S rRNA gene sequencing studies showed the bacterium to be a hitherto unknown subline within the genus Arcanobacterium. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as Arcanobacterium pluranimalium sp. nov. The type strain of Arcanobacterium pluranimalium is CCUG 42575T (= CIP 106442T).
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Vibrio cyclotrophicus sp. nov., a polycyclic aromatic hydrocarbon (PAH)-degrading marine bacterium.
More LessStrain P-2P44T was isolated from creosote-contaminated marine sediments by using a most-probable number procedure in which phenanthrene was the sole carbon and energy source. Growth experiments showed that P-2P44T utilized several two- and three-ring polycyclic aromatic hydrocarbons (PAHs) as substrates, including naphthalene, 2-methylnaphthalene and phenanthrene. Additionally, gas-chromatography experiments showed that P-2P44T degraded several other PAHs, though it was unable to use them as sole sources of carbon and energy. Phylogenetic analyses confirmed that strain P-2P44T is a member of the genus Vibrio, most closely related to Vibrio splendidus. However, strain P-2P44T shared only 98.3% 16S rDNA identity and 35% DNA-DNA reassociation with the type strain of V. splendidus. Strain P-2P44T differed phenotypically from V. splendidus. Together, these differences indicated that strain P-2P44T represents a novel species in the genus Vibrio, for which the name Vibrio cyclotrophicus sp. nov. is proposed; the type strain is P-2P44T (= ATCC 700982T = PICC 106644T).
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Reclassification of [Pseudomonas] doudoroffii (Baumann et al. 1983) into the genus Oceanomonas gen. nov. as Oceanomonas doudoroffii comb. nov., and description of a phenol-degrading bacterium from estuarine water as Oceanomonas baumannii sp. nov.
More LessA bacterium, isolate GB6T, capable of degrading phenol in the presence of elevated salinity was isolated from the estuary of the River Wear, UK. The bacterium was subjected to biochemical and molecular analysis to determine its taxonomic status. These studies indicated that the bacterium was a distinct species closely related to [Pseudomonas] doudoroffii. However, the phylogenetic analysis indicated that [Pseudomonas] doudoroffii was misclassified, as noted previously. Analysis of the characteristics of isolate GB6T and the type strain of [Pseudomonas] doudoroffii confirmed that these bacteria belonged to the same novel genus, which we have named Oceanomonas gen. nov. The type strain of Oceanomonas doudoroffii (Baumann et al. 1983) comb. nov. is ATCC 27123T (= DSM 7028T. The DNA-DNA homology between isolate GB6T and [Pseudomonas] doudoroffii is low and phenotypic differences between the two organisms are evident. Isolate GB6T (= ATCC 700832T = NCIMB 13685T) is therefore proposed as the type strain of a new species, Oceanomonas baumannii sp. nov.
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Sphingomonas alaskensis sp. nov., a dominant bacterium from a marine oligotrophic environment.
More LessSeven Gram-negative strains, isolated in 1990 from a 10(6)-fold dilution series of seawater from Resurrection Bay, a deep fjord of the Gulf of Alaska, were identified in a polyphasic taxonomic study. Analysis of 16S rDNA sequences and DNA-homology studies confirmed the phylogenetic position of all strains in the genus Sphingomonas and further indicated that all of the strains constitute a single homogeneous genomic species, distinct from all validly described Sphingomonas species. The ability to differentiate the species, both phenotypically and chemotaxonomically, from its nearest neighbours justifies the proposal of a new species name, Sphingomonas alaskensis sp. nov., for this taxon. Strain LMG 18877T (= RB2256T = DSM 13593T) was selected as the type strain.
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Ornithinimicrobium humiphilum gen. nov., sp. nov., a novel soil actinomycete with L-ornithine in the peptidoglycan.
More LessA Gram-positive bacterium originating from garden soil was taxonomically studied. Cells are non-motile, non-sporulating, irregular rods and cocci. The cell wall peptidoglycan contains L-ornithine as diagnostic diamino acid and an interpeptide bridge consisting of L-Orn<--L-Ala<--Gly<--D-Asp. The major menaquinone is MK-8(H4). 13-Methyl tetradecanoic acid and 14-methyl pentadecanoic acid are the predominant fatty acids. The polar lipids are phosphatidylinositol, phosphatidylglycerol, diphosphatidylglycerol, three unknown glycolipids and three unknown phospholipids. Mycolic acids are absent. The DNA G+C composition is 70 mol%. The acyl type of the glycan chain of peptidoglycan is acetyl. Glucose is the dominating whole cell sugar; arabinose, rhamnose and xylose are present in traces. Results of 16S rDNA sequence comparisons revealed that strain HKI 0124T represents a novel lineage within the suborder Micrococcineae of the order Actinomycetales adjacent to the recently described genus Ornithinicoccus. On the basis of the clearly pronounced morphological, physiological, chemotaxonomic and phylogenetic differences between strain HKI 0124T and all members of the suborder Micrococcineae, it is proposed to assign strain HKI 0124T to a new genus and species, Ornithinimicrobium humiphilum gen. nov., sp. nov. The type and only strain is HKI 0124T (= DSM 12362T = CIP 106634T).
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A revision of Rhizobium Frank 1889, with an emended description of the genus, and the inclusion of all species of Agrobacterium Conn 1942 and Allorhizobium undicola de Lajudie et al. 1998 as new combinations: Rhizobium radiobacter, R. rhizogenes, R. rubi, R. undicola and R. vitis.
More LessRhizobium, Agrobacterium and Allorhizobium are genera within the bacterial family Rhizobiaceae, together with Sinorhizobium. The species of Agrobacterium, Agrobacterium tumefaciens (syn. Agrobacterium radiobacter), Agrobacterium rhizogenes, Agrobacterium rubi and Agrobacterium vitis, together with Allorhizobium undicola, form a monophyletic group with all Rhizobium species, based on comparative 16S rDNA analyses. Agrobacterium is an artificial genus comprising plant-pathogenic species. The monophyletic nature of Agrobacterium, Allorhizobium and Rhizobium and their common phenotypic generic circumscription support their amalgamation into a single genus, Rhizobium. Agrobacterium tumefaciens was conserved as the type species of Agrobacterium, but the epithet radiobacter would take precedence as Rhizobium radiobacter in the revised genus. The proposed new combinations are Rhizobium radiobacter, Rhizobium rhizogenes, Rhizobium rubi, Rhizobium undicola and Rhizobium vitis.
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Thioflavicoccus mobilis gen. nov., sp. nov., a novel purple sulfur bacterium with bacteriochlorophyll b.
J F Imhoff and N PfennigA novel phototrophic purple sulfur bacterium was isolated from a flat, laminated microbial mat in a salt marsh near Woods Hole, Massachusetts, USA. The cells were monotrichously flagellated motile cocci with internal photosynthetic membranes of the tubular type. The main photosynthetic pigments were bacteriochlorophyll b and the carotenoid 3,4,3',4'-tetrahydrospirilloxanthin. The marine bacterium showed optimal growth in the presence of 2% salts. It was obligately phototrophic and strictly anaerobic. It grew photoautotrophically and photoassimilated acetate, pyruvate and ascorbate as the only organic substrates. In the presence of sulfide, elemental sulfur globules were formed inside the cells. Elemental sulfur was further oxidized to sulfate. The DNA base composition of the new bacterium was 66.5 mol% G+C. The 16S rDNA nucleotide sequence was most similar to strains of Thiococcus pfennigii, there being approximately 92-93% sequence similarity. The new bacterium is described as a new species and a new genus, and the name Thioflavicoccus mobilis is proposed; the type strain is 8321T (= ATCC 700959T).
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Phylogenetic and DNA-DNA hybridization analyses of Bradyrhizobium species.
More LessThe 16S rDNA sequence of Bradyrhizobium liaoningense was determined and analysed together with sequences of other Bradyrhizobium species and related taxa. In addition, DNA-DNA hybridizations were performed between representative strains of the three Bradyrhizobium species. Bradyrhizobium liaoningense is genotypically highly related to Bradyrhizobium japonicum, whereas Bradyrhizobium elkanii is more distantly related to these two species. The fact that Afipia, Agromonas, Blastobacter, Nitrobacter and Rhodopseudomonas are phylogenetically more closely related to Bradyrhizobium japonicum than to Bradyrhizobium elkanii is discussed.
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Hyphomicrobium chloromethanicum sp. nov. and Methylobacterium chloromethanicum sp. nov., chloromethane-utilizing bacteria isolated from a polluted environment.
More LessTwo chloromethane-utilizing facultatively methylotrophic bacteria, strains CM2T and CM4T, were isolated from soil at a petrochemical factory. On the basis of their morphological, physiological and genotypical properties, strain CM2T (= VKM B-2176T = NCIMB 13687T) is proposed as a new species of the genus Hyphomicrobium, Hyphomicrobium chloromethanicum, and strain CM4T (= VKM B-2223T = NCIMB 13688T) as a new species of the genus Methylobacterium, Methylobacterium chloromethanicum.
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Clostridium hungatei sp. nov., a mesophilic, N2-fixing cellulolytic bacterium isolated from soil.
More LessTwo strains of obligately anaerobic, mesophilic, cellulolytic, N2-fixing, spore-forming bacteria were isolated from soil samples collected at two different locations near Amherst, MA, USA. Single cells of both strains were slightly curved rods that measured between 2 and 6 microm in length and approximately 0.5 microm in diameter. The spores were spherical, terminally located, distended the sporangium and measured 0.8-1.0 microm in diameter. The cells of both isolates (designated strain ADT and strain B3B) stained Gram-negative, but did not have a typical Gram-negative cell wall structure as demonstrated by transmission electron microscope analysis. The cells of both strains were motile with subpolarly inserted flagella and exhibited chemotactic behaviour towards cellobiose and D-glucose. Both strains fermented cellulose, xylan, cellobiose, cellodextrins, D-glucose, D-xylose, D-fructose, D-mannose and gentiobiose. In addition, strain B3B fermented L-arabinose. For both strains, fermentation products from cellulose were acetate, ethanol, H2 and CO2, as well as small amounts of lactate and formate. The G+C content of strain AD was 40 mol% and that of strain B3B was 42 mol%. Based on their morphological, physiological and phylogenetic characteristics, it was concluded that the two isolates are representatives of a novel species of Clostridium. The name Clostridium hungatei is proposed for the new species. The type strain of Clostridium hungatei sp. nov. is strain ADT (= ATCC 700212T).
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Desulfosporosinus meridiei sp. nov., a spore-forming sulfate-reducing bacterium isolated from gasolene-contaminated groundwater.
More LessEight strains of spore-forming, sulfate-reducing bacteria, isolated from groundwater contaminated with motor fuel [mostly benzene, toluene ethylbenzene and xylene (BTEX) compounds] in sandy soil near Perth, Australia, were closely related to Desulfosporosinus (previously Desulfotomaculum) orientis DSM 765T (95.3-97.3% 16S rDNA sequence similarity). Whole-cell fatty acids were dominated by even-carbon, straight-chain saturated and mono-unsaturated fatty acids, in particular 16:0, 16:1cis9, 14:0 and 18:1cis11. The strains grew at temperatures between 4 and 42 degrees C and in medium containing up to 4% NaCl. The eight strains clustered into two main groups based on phylogeny, randomly amplified polymorphic DNA (RAPD)-PCR patterns and nutritional characteristics. Representatives of the two groups, strain S5 (group A) and strain S10T (group B) had 81% DNA-DNA homology with each other and therefore should be accommodated in the same species. Strain S10T had less than 38% homology with Desulfosporosinus orientis DSM 765T, the most closely phylogenetically related type strain available. The new strains were distinguished from Desulfosporosinus orientis DSM 765T by different banding patterns in a RAPD-PCR, and phenotypically by their inability to utilize fumarate as a carbon and energy source with sulfate as the electron acceptor and by their lower tolerance to NaCl. The DNA G+C contents were 46.8 and 46.9 mol% for strains S5 and S10T, respectively (Desulfosporosinus orientis DSM 765T 45.9 mol%). It is proposed that these new strains be placed in a new species of the genus Desulfosporosinus. The name Desulfosporosinus meridiei is proposed, with strain S10T as the type strain (= DSM 13257T = NCIMB 13706T).
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Carboxydobrachium pacificum gen. nov., sp. nov., a new anaerobic, thermophilic, CO-utilizing marine bacterium from Okinawa Trough.
A new anaerobic, thermophilic, CO-utilizing marine bacterium, strain JMT, was isolated from a submarine hot vent in Okinawa Trough. Cells of strain JMT were non-motile thin straight rods, sometimes branching, with a cell wall of the Gram-positive type, surrounded with an S-layer. Chains of three to five cells were often observed. The isolate grew chemolithotrophically on CO, producing equimolar quantities of H2 and CO2 (according to the equation CO+H2O-->CO2+H2) and organotrophically on peptone, yeast extract, starch, cellobiose, glucose, galactose, fructose and pyruvate, producing H2, acetate and CO2. Growth was observed from 50 to 80 degrees C with an optimum at 70 degrees C. The optimum pH was 6.8-7.1. The optimum concentration of sea salts in the medium was 20.5-25.5 g l(-1). The generation time under optimal conditions was 7.1 h. The DNA G+C content was 33 mol %. Growth of isolate JMT was not inhibited by penicillin, but ampicillin, streptomycin, kanamycin and neomycin completely inhibited growth. The results of 16S rDNA sequence analysis revealed that strain JMT belongs to the Thermoanaerobacter phylogenetic group within the Bacillus-Clostridium subphylum of Gram-positive bacteria but represents a separate branch of this group. On the basis of morphological and physiological features and phylogenetic data, this isolate should be assigned to a new genus, for which the name Carboxydobrachium is proposed. The type species is Carboxydobrachium pacificum; the type strain is JMT (= DSM 12653T).
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Actinomyces marimammalium sp. nov., from marine mammals.
More LessThree strains of a previously undescribed Actinomyces-like bacterium were isolated from samples taken from two dead seals and a porpoise. Biochemical testing and PAGE analysis of whole-cell proteins indicated the strains were phenotypically similar to each other but different from previously described Actinomyces and Arcanobacterium species. Comparative 16S rRNA gene sequencing studies showed the organisms from marine animals were genetically closely related and represent a hitherto unknown subline within the genus Actinomyces (sequence divergence values > 6% with recognized species). Based on phylogenetic and phenotypic evidence it is proposed that the unknown bacterium from the seals and a porpoise should be classified as Actinomyces marimammalium sp. nov. The type strain is CCUG 41710T.
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Herbaspirillum frisingense sp. nov., a new nitrogen-fixing bacterial species that occurs in C4-fibre plants.
More LessThe enrichment of nitrogen-fixing bacteria from the C4-fibre plants, Spartina pectinata, Miscanthus sinensis, Miscanthus sacchariflorus and Pennisetum purpureum, with nitrogen-free semi-solid media led to the isolation of Herbaspirillum-like strains among other diazotrophic bacteria. On the basis of physiological properties, phylogenetic analysis comparing 16S rDNA sequences and DNA-DNA hybridization experiments of chromosomal DNA the new isolates could be grouped together in a new species with the proposed name Herbaspirillum frisingense sp. nov. Morphological characteristics, such as cell size and shape, colony appearance, motility and flagellation are largely identical to the known species Herbaspirillum rubrisubalbicans and Herbaspirillum seropedicae. On the basis of utilization of adipate (-), N-acetyl-D-glucosamine (+), meso-erythritol (-), L-rhamnose (-) and meso-inositol (-) Herbaspirillum frisingense sp. nov. can be distinguished from other known Herbaspirillum spp. Nitrogen-fixing capability was examined by PCR amplification of the nifD gene and an acetylene reduction assay, and was found with all isolates tested. 16S rDNA sequence similarity to the other Herbaspirillum spp. is 98.5-99.1%. In genomic DNA-DNA hybridization experiments Herbaspirillum frisingense sp. nov. forms a homogeneous group with 70-100+/-10% similarity, clearly distinct from Herbaspirillum seropedicae and Herbaspirillum rubrisubalbicans with 1-34% similarity. 16S rRNA-targeted oligonucleotide probes, specific for the whole genus Herbaspirillum and for three Herbaspirillum species were designed and are suitable for fluorescence in situ hybridization. The DNA G+C content of Herbaspirillum frisingense sp. nov. is 63+/-2 mol%, in agreement with the values of 61-65% for the genus. PCR fingerprinting exhibits a consistent pattern for groups of strains isolated from the same plant, suggesting a low genomic diversity among bacteria inhabiting C4-gramineous plant tissues. Low genetic DNA diversity seems to be common between probable endophytic bacterial isolates of the same taxon. The type strain of Herbaspirillum frisingense sp. nov. is GSF30T (= DSM 13128T).
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Arthrobacter siderocapsulatus Dubinina and Zhdanov 1975AL is a later subjective synonym of Pseudomonas putida (Trevisan 1889) Migula 1895AL.
More LessThe taxonomic position of Arthrobacter siderocapsulatus Dubinina and Zhdanov 1975AL was investigated using 16S rDNA, fatty acid and phenotypic analyses. The type strain (NCIMB 11286T) showed 99.85% 16S rDNA similarity to the type strain of Pseudomonas putida. Phenotypic properties of the two strains were compared using API 20NE and BIOLOG kits. Identical reactions were recorded for all tests, except for assimilation of malonic acid. The two strains also showed almost identical cellular fatty acid profiles. On the basis of evidence presented in this and earlier studies, it is proposed that Arthrobacter siderocapsulatus is a later subjective synonym of Pseudomonas putida (Trevisan 1889) Migula 1895AL.
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Reclassification of Desulfobacterium phenolicum as Desulfobacula phenolica comb. nov. and description of strain SaxT as Desulfotignum balticum gen. nov., sp. nov.
J Kuever, M Könneke, A Galushko and O DrzyzgaA mesophilic, sulfate-reducing bacterium (strain SaxT) was isolated from marine coastal sediment in the Baltic Sea and originally described as a 'Desulfoarculus' sp. It used a large variety of substrates, ranging from simple organic compounds and fatty acids to aromatic compounds as electron donors. Autotrophic growth was possible with H2, CO2 and formate 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 CO2, but at high substrate concentrations acetate accumulated. CO dehydrogenase activity was observed, indicating the operation of the CO dehydrogenase pathway (reverse Wood pathway) for CO2 fixation and complete oxidation of acetyl-CoA. The rod-shaped cells were 0.8-1.0 microm wide and 1.5-2.5 microm long. Spores were not produced and cells stained Gram-negative. The temperature limits for growth were between 10 and 42 degrees C (optimum growth at 28-32 degrees C). Growth was observed at salinities ranging from 5 to 110 g NaCl l(-1), with an optimum at 10-25 g NaCl l(-1). The G+C content of the DNA was 62.4 mol%. Vitamins were required for growth. Based on the 16S rRNA gene sequence, strain SaxT represents a new genus within the delta-subclass of the Proteobacteria. The name Desulfotignum balticum gen. nov., sp. nov. is proposed. After the 16S rDNA sequences of all members of the genus Desulfobacterium were published (GenBank accession nos. AJ237601-AJ237604, AJ237606, AJ237607), the need to reclassify most members of the genus Desulfobacterium became obvious due to their strong phylogenetic affiliation to other genera. Here, we propose to reclassify Desulfobacterium phenolicum as Desulfobacula phenolica comb. nov. Desulfotignum balticum, Desulfobacterium phenolicum and Desulfobacula toluolica contain cellular fatty acids which have so far only been found in members of the genus Desulfobacter.
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Phylogenetic position of Bartonella vinsonii subsp. arupensis based on 16S rDNA and gltA gene sequences.
More LessThe nucleotide sequences of the genes encoding 16S rRNA and citrate synthase (gltA) from a recently described member of the genus Bartonella, Bartonella vinsonii subsp. arupensis, isolated from mice and from the blood of a patient suffering from bacteraemia, were determined and compared with sequences of the 16S rDNA and gltA genes of other members of the genus Bartonella in order to determine its relative phylogenetic position. B. vinsonii subsp. arupensis appeared to be closely related to B. vinsonii subsp. vinsonii, another rodent-associated taxon, and to B. vinsonii subsp. berkhoffii, which was described recently in dogs.
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Genotypic and chemotaxonomic evidence for the reclassification of Pseudomonas woodsii (Smith 1911) Stevens 1925 as Burkholderia andropogonis (Smith 1911) Gillis et al. 1995.
T Coenye, S Laevens, M Gillis and P VandammeIt was reported before that [Pseudomonas] woodsii and Burkholderia andropogonis are phenotypically indistinguishable and probably represent the same taxon, for which the name B. andropogonis has been proposed. In the present study, it was found that [P.] woodsii and B. andropogonis strains were indistinguishable by whole-cell protein electrophoresis and have a highly similar cellular fatty acid composition. A high DNA-DNA binding value of 95% was found between the type strains of both species. In addition, the 16S rDNA sequence of [P.] woodsii strain LMG 2362T was very similar to that of B. andropogonis LMG 2129T (99.0%). The chemotaxonomic and genotypic data confirm that [P.] woodsii and B. andropogonis represent the same species, for which it is proposed to retain the name B. andropogonis.
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Amycolatopsis sacchari sp. nov., a moderately thermophilic actinomycete isolated from vegetable matter.
More LessThe taxonomic position of a group of moderately thermophilic actinomycetes isolated from vegetable matter was determined using a suite of genotypic and phenotypic properties. The organisms were found to share a range of chemical and morphological markers typical of members of the genus Amycolatopsis. A representative of the group, strain K24T, formed a distinct phyletic line within the range of variation occupied by the genus Amycolatopsis in the 16S rDNA tree. The strains have many phenotypic properties in common and some of these distinguish the group from representatives of the validly described species of Amycolatopsis. It is clear from the combined datasets that the strains merit recognition as a new species of Amycolatopsis. The name proposed for the new species is Amycolatopsis sacchari; the type strain is K24T (= DSM 44468T = KCTC 9863T).
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Phylogeny of the filamentous bacterium 'Nostocoida limicola' III from activated sludge.
More LessFive strains of the filamentous bacterium 'Nostocoida limicola' III were successfully isolated into pure culture from samples of activated sludge biomass from five plants in Australia. 16S rRNA gene sequence analyses showed that all isolates were members of the Planctomycetales, most closely related to Isosphaera pallida, but they differed phenotypically from this species in that they did not glide and were not thermotolerant. The ultrastructure of these 'N. limicola' III isolates was also consistent with them being Planctomycetales, in that they possessed complex intracellular membrane systems compartmentalizing the cells. However, the arrangements of these intracellular membranes differed between isolates. These data confirm that 'N. limicola' III is phylogenetically unrelated to both 'N. limicola' I and 'N. limicola' II, activated sludge filamentous bacteria which share morphological features in common with 'N. limicola' III and which have been presumed historically to be the same or very similar bacteria.
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Molecular evolution of the Chlamydiaceae.
R M Bush and K D EverettPhylogenetic analyses of surface antigens and other chlamydial proteins were used to reconstruct the evolution of the Chlamydiaceae. Trees for all five coding genes [the major outer-membrane protein (MOMP), GroEL chaperonin, KDO-transferase, small cysteine-rich lipoprotein and 60 kDa cysteine-rich protein] supported the current organization of the family Chlamydiaceae, which is based on ribosomal, biochemical, serological, ecological and DNA-DNA hybridization data. Genetic distances between some species were quite large, so phylogenies were evaluated for robustness by comparing analyses of both nucleotide and protein sequences using a variety of algorithms (neighbour-joining, maximum-likelihood, maximum-parsimony with bootstrapping, and quartet puzzling). Saturation plots identified areas of the trees in which factors other than relatedness may have determined branch attachments. All nine species were clearly differentiated by distinctness ratios calculated for each gene. The distribution of virulence traits such as host and tissue tropism were mapped onto the consensus phylogeny. Closely related species were no more likely to share virulence characters than were more distantly related species. This phylogenetically disjunct distribution of virulence traits could not be explained by lateral transfer of the genes we studied, since we found no evidence for lateral gene transfer above the species level. One interpretation of this observation is that when chlamydiae gain access to a new niche, such as a new host or tissue, significant adaptation ensues and the virulence phenotype of the new species reflects adaptation to its environment more strongly than it reflects its ancestry.
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Taxonomic studies on the genus Cystofilobasidium: description of Cystofilobasidium ferigula sp. nov. and clarification of the status of Cystofilobasidium lari-marini.
J P Sampaio, M Gadanho and R BauerA new species of the genus Cystofilobasidium is described as Cystofilobasidium ferigula sp. nov. The new taxon represents the teleomorphic stage of Cryptococcus ferigula and was obtained in mating experiments using three strains deposited in the Portuguese Yeast Culture Collection (mating types A1) and a recent isolate (mating type A2). Cystofilobasidium ferigula is characterized using an integrated approach encompassing morphological studies, investigation of the ultrastructure of the septal pore, a comparative study of physiological traits, determination of the DNA base composition, DNA reassociation experiments and PCR fingerprinting. During the course of this study, a close similarity of microsatellite-primed PCR fingerprints was detected between Cystofilobasidium lari-marini and Cystofilobasidium capitatum. DNA-DNA reassociation experiments gave high homology values, which indicates that Cystofilobasidium lari-marini must be regarded as a synonym of Cystofilobasidium capitatum.
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Sporobolomyces yunnanensis sp. nov., a Q-10(H2)-containing yeast species with a close phylogenetic relationship to Erythrobasidium hasegawianum.
F Y Bai, M Takashima, M Hamamoto and T NakaseA ballistoconidia-forming yeast strain, CH 2.141T, isolated from a semi-dried leaf sample collected in Yunnan, China, was found to have Q-10(H2) as its major ubiquinone. Molecular phylogenetic analysis based on the nucleotide sequences of small subunit (18S) rDNA and the internal transcribed spacer region (including 5.8S rDNA) indicated that the strain was closely related to the two described Q-10(H2)-containing yeast species, Erythrobasidium hasegawianum and Sporobolomyces elongatus, with a closer relationship to the former. A DNA-DNA reassociation experiment showed that strain CH 2.141T represents a new yeast species, for which the name Sporobolomyces yunnanensis sp. nov. is proposed.
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Phylogenetic structure of the Sporopachydermia cereana species complex.
More LessA large number of isolates previously referred to as members of the 'Sporopachydermia cereana species complex' were examined by various DNA characterization methods, leading to the conclusion that the complex is in fact made up of 10 species, one of which contains three varieties. The sequences of the internal transcribed spacer (ITS) region and the D1/D2 divergent domains of the large subunit rDNA were determined for representatives of each taxon and specific primers based on differences in the ITS were designed for rapid identification of five of the taxa. Whereas the data provide additional elements for the calibration of the ITS as a criterion for species delineation, the emerging pattern is that the ITS region does not function as well as the D1/D2 domains as an evolutionary clock. Some taxa appear to be specific for the geographical regions where they were isolated, and the distribution of many taxa is mutually exclusive.
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Radical changes to chlamydial taxonomy are not necessary just yet.
J Schachter, R S Stephens, P Timms, C Kuo, P M Bavoil, S Birkelund, J Boman, H Caldwell, L A Campbell, M Chernesky, G Christiansen, I N Clarke, C Gaydos, J T Grayston, T Hackstadt, R Hsia, B Kaltenboeck, M Leinonnen, D Ojcius, D Ocjius, G McClarty, J Orfila, R Peeling, M Puolakkainen, T C Quinn, R G Rank, J Raulston, G L Ridgeway, P Saikku, W E Stamm, D T Taylor-Robinson, S P Wang and P B Wyrick
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A taxonomic note on the authorship and date of valid publication of Rhodococcus sputi.
More LessAuthorship of the name Rhodococcus sputi is variously attributed to Tsukamura 1978 or Tsukamura and Yano 1985. DNA-DNA binding data indicate that this species and Rhodococcus obuensis Tsukamura 1983 and Rhodococcus chubuensis Tsukamura 1983 are subjective (heterotypic) synonyms. Although these organisms have been placed in the genus Gordonia as Gordonia sputi, the correct name of the taxon created by unification of these three species is directly affected by the date of valid publication of these species as members of the genus Rhodococcus. Thus, the name R. sputi only has priority if the authorship is attributed to Tsukamura 1978. The question of authorship and priority is clarified in the present work.
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