- Volume 52, Issue 5, 2002
Volume 52, Issue 5, 2002
- Articles
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Phyllobacterium myrsinacearum (subjective synonym Phyllobacterium rubiacearum) emend.
More LessThe taxonomic relationships between Phyllobacterium myrsinacearum LMG 2t2T, Phyllobacterium rubiacearum LMG 1t1T and two Phyllobacterium strains representing a collection of isolates from sugar-beet roots were investigated by means of fatty acid analysis and DNA-DNA hybridization. The strains showed very similar fatty acid compositions and more than 96% DNA reassociation to each other. On the basis of these results and available data from the literature, it is proposed that P. rubiacearum be classified as a junior subjective synonym of P. myrsinacearum, and that the sugar-beet isolates be included in the latter species. An emended description of P. myrsinacearum is given.
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Nocardia pseudovaccinii sp. nov.
More LessComparative 16S rDNA studies of Nocardia type and reference strains revealed that strain DSM 43406T, identified as Nocardia vaccinii, was wrongly classified. The strain was aerobic, gram-positive and produced scarce, white, branched aerial mycelium and a beige-red substrate mycelium. The reverse side of the colonies was yellow-orange. It showed chemotaxonomic markers that were consistent with its classification in the genus Nocardia. The mycolic acids had chain lengths from 50 to 58 carbon atoms. The 16S rDNA sequence showed the highest similarity to Nocardia nova (97.7%) and N. vaccinii (97.6%), but the strain could be clearly separated from these species and other members of the N. vaccinii cluster by significant differences in biochemical test results and unique fatty acid and mycolic acid patterns. These data led to the conclusion that the isolate represents a novel species within the genus Nocardia, for which the name Nocardia pseudovaccinii sp. nov. is proposed. The type strain is strain AR 368,38366-20T (= DSM 43406T = NRRL B-24154T).
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Halomicrobium mukohataei gen. nov., comb. nov., and emended description of Halomicrobium mukohataei.
More LessHaloarcula mukohataei, previously isolated from soils of salt flats in Argentina, was originally placed in the genus Haloarcula on the basis of 16S rRNA gene sequence comparison. However, its morphology and polar lipid composition differs from that of the other Haloarcula species. In addition, its phylogenetic distance from other Haloarcula species is rather large, and the 16S rDNA sequence does not contain many of the signature bases characteristic of the genus. Transfer of the species to a new genus was therefore recommended by the International Committee on Systematic Bacteriology Subcommittee on the taxonomy of Halobacteriaceae. A full description of the isolate, proposed as a member of a new genus, Halomicrobium, as Halomicrobium mukohataei comb. nov., is presented. The type strain is strain arg-2T (= JCM 9738T = DSM 12286T = ATCC 700874T = NCIMB 13541T).
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Development of fluorescent adjacent hybridization probes and their application in real-time PCR for the simultaneous detection and identification of Fervidobacterium and Caloramator.
More LessA stretch of nucleotides consisting of a conserved region and an adjacent upstream variable region in the 16S rDNA of members of domain Bacteria was identified as a suitable target site for developing a real-time PCR adjacent hybridization assay. A single universal fluorogenic cyanin 5-labelled probe, CY5 1046+, targeting the conserved region, and two FITC-labelled probes, Calo and Fervi, targeting the variable region were designed and synthesized for the identification and differentiation of the thermophilic anaerobes Caloramator and Fervidobacterium. The simultaneous hybridization of probes CY5 1046+ and Fervi to the 16S rDNA target sites of Fervidobacterium species during PCR amplification resulted in an increase in fluorescence emission that was monitored continuously in a LightCycler. The differences in the temperature of disassociation of the hybridization probes (Tm) due to compositional variation in the nucleotide bases of the probe and target sequences enabled Fervidobacterium islandicum DSM 5733T to be differentiated from Fervidobacterium gondwanense ACM 5017T and Fervidobacterium nodosum ATCC 35602T. The simultaneous hybridization of probes CY5 1046+ and Calo to the 16S rDNA target sequence of Caloramator indicus ACM 3982T during PCR amplification also resulted in an increase in fluorescence emission. However, as the target sequence of C. indicus ACM 3982T is identical to those of the other three Caloramator species, Caloramator fervidus ATCC 43204T (formerly Clostridium fervidus), Caloramator proteoclasticus DSM 10124T and Caloramator coolhaasii DSM 12679T, further species discrimination on the basis of Tm will not be possible, making probe Calo a useful genus-specific probe. The devised method was subsequently used to detect and identify Fervidobacterium and Caloramator isolates from our previously uncharacterized culture collection and from enrichment cultures. The assay is cheap and flexible, as only a battery of inexpensive FITC probes for differentiating other members of domain Bacteria needs to be synthesized and DNA templates prepared by a simple lyse-boil method, in addition to purified DNA, can also be used.
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Kineosphaera limosa gen. nov., sp. nov., a novel Gram-positive polyhydroxyalkanoate-accumulating coccus isolated from activated sludge.
More LessA high-G+C gram-positive, motile, non-spore-forming coccus capable of accumulating significant amounts of polyhydroxyalkanoate (PHA) was isolated from an inefficient biological phosphorus removal activated sludge reactor. The cell wall of strain Lpha5T was characterized by the presence of meso-diaminopimelic acid, menaquinone MK-8(H4) and a complex fatty-acid pattern consisting of C16:0 and at least five other major straight-chain saturated and unsaturated fatty acids. Strain Lpha5T also had a high G+C content (71.3 mol%). The nearest phylogenetic relative of strain Lpha5T, based on 16S rDNA sequence analysis, was the high-G+C gram-positive bacterium Dermatophilus congolensis (similarity value of 94%), of the family Dermatophilaceae, class Actinobacteria. As strain Lpha5T was distinct from D. congolensis in its morphological, phenotypical (i.e. its PHA-accumulating ability and fatty-acid profile) and genetic traits (phylogeny and G+C content), it is proposed that strain Lpha5T be designated as the type species of a novel genus within the Dermatophilaceae. The name Kineosphaera limosa is proposed for strain Lpha5T (= JCM 11399T = DSM 14548T).
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Rheinheimera baltica gen. nov., sp. nov., a blue-coloured bacterium isolated from the central Baltic Sea.
More LessA set of taxonomically unique, blue-coloured bacterial isolates are described on the basis of physiological and biochemical characterization, fatty acid profiling and analyses of 16S rDNA sequences. The flagellated, non-fermentative strains were isolated in 1986, 1987 and 1998 from different layers of the water column of the central Baltic Sea. According to 16S rDNA sequences, all strains are very closely related to each other and to strains from several other marine environments, including the deep sea. Thus, the described species seems to be widespread in marine habitats. According to DNA-DNA hybridization, the strains described can be considered to belong to the same species. The bacteria grew at temperatures from 4 to 30 degrees C, with an optimum around 20-25 degrees C. Growth was observed at salinities from 0 to 30, with an optimum between 10 and 30 and no growth at high salinities. The dominant fatty acids were 16:1omega7c, 16:0 and 18:1omega7c. The G+C content of the DNA ranged from 47.8 to 48.9 mol%. Phylogenetic analyses of the 16S rDNA sequences revealed a clear affiliation with members of the gamma-Proteobacteria. The closest relationship was seen with Alishewanella fetalis but, in terms of physiology, colour and fatty acids, the bacteria described are rather distant from A. fetalis. To honour the marine microbiologist Gerhard Rheinheimer, the name Rheinheimera baltica gen. nov., sp. nov., is suggested for the Baltic isolates, with the type strain OSBAC1T (= DSM 14885T = LMG 21511T).
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Thermovibrio ruber gen. nov., sp. nov., an extremely thermophilic, chemolithoautotrophic, nitrate-reducing bacterium that forms a deep branch within the phylum Aquificae.
More LessA novel, extremely thermophilic, chemolithoautotrophic bacterium was isolated from the submarine hydrothermal system off the beach of Lihir Island, Papua New Guinea. Cells of the organism were curved rods of about 1.5-3 microm in length and 0.5-0.8 microm in width. The bacterium grew within the temperature range 50-80 degrees C (optimum around 75 degrees C) and was an obligate anaerobe. Molecular hydrogen was used as the sole electron donor by the bacterium, and nitrate or elemental sulfur served as electron acceptors, producing ammonium or H2S, respectively. Complex organic substrates stimulated growth of the bacterium, but they could not be used as the sole energy source. Based on 16S-rDNA-based phylogenetic analyses and on physiological, biochemical and structural characteristics, the novel organism was found to represent a novel genus for which the name Thermovibrio is proposed. This novel genus, together with Desulfurobacterium thermolithotrophum, may represent a new order within the phylum Aquificae. Since cell pellets of the novel bacterium had an intense red colour, the name Thermovibrio ruber is proposed for the novel organism. The type strain of Thermovibrio ruber gen. nov., sp. nov. is ED11/3LLKT (= DSM 14644T = JCM 11468T).
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Phylogenetic comparison of the cyanobacterial genera Anabaena and Aphanizomenon.
Morphological analysis and sequencing of the 165 rRNA gene, the spacer region of the ribosomal operon (ITS1) and the rbcLX (RubisCO) region was performed on 26 Anabaena strains and 14 Aphanizomenon strains isolated from several lakes in Denmark, Finland and France. Based on their morphology, Anabaena strains differed from strains of Aphanizomenon: the vegetative cells, heterocysts and akinetes were significantly wider in Anabaena than in Aphanizomenon. Phylogenetic trees based on the 16S rDNA, ITS1 and rbcLX regions showed that the planktic Anabaena strains were not distinguishable from Aphanizomenon strains. The results of the clustering of Anabaena and Aphanizomenon strains based on 16S rDNA sequences showed that these two genera are not monophyletic. Sequence analysis of the 16S rDNA, ITS1-S and rbcLX regions of the planktic Anabaena strains showed that this genus is heterogeneous. In all methods, Anabaena strains that produced different toxic compounds (e.g. anatoxin-a, microcystin and an unknown neurotoxin) were clustered separately from each other but were grouped either with non-toxic Anabaena and/or Aphanizomenon strains. Our data suggest that the planktic Anabaena and Aphanizomenon isolates belong to the same genus, regardless of their morphological differences. Thus, a taxonomic revision of the two genera is required.
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Carnobacterium viridans sp. nov., an alkaliphilic, facultative anaerobe isolated from refrigerated, vacuum-packed bologna sausage.
More LessA facultatively anaerobic, non-spore-forming, psychrophilic, gram-positive, non-aciduric but alkaliphilic, rod-shaped bacterium (MPL-11T) was found to be responsible for green discoloration of refrigerated vacuum-packaged bologna upon opening of the package. Although Aerococcus viridans, which had been implicated earlier in causing the same problem, was also found, this is the first report of discoloration caused by an organism shown to be a species of Carnobacterium. Bacterial discoloration was caused by H2O2 production upon exposure of the meat to air. Strain MPL-11T is catalase- and oxidase-negative. It is not motile and does not reduce nitrate to nitrite or produce ammonia from arginine. It does not grow in acetate-containing broth or agar (Rogosa) or produce H2S. The peptidoglycan is of the meso-diaminopimelic acid type and it produces predominantly L(+)-lactic acid from glucose. It grows from at least 2 to 30 degrees C over a pH range from 5.5 to 9.1. Ribotyping suggested that strain MPL-11T could be a species of either Lactobacillus or Carnobacterium, but analysis using DNA sequences from the 16S rRNA gene showed conclusively that the organism belonged to the genus Carnobacterium. Since acid is not produced from amygdalin, inulin, mannitol, methyl alpha-D-glucoside or D-xylose, the organism differs from the seven described species of Carnobacterium. In addition, strain MPL-11T is the first member of the genus found that does not produce acid from ribose. It is capable of acid production/growth on galactose, glucose, fructose, mannose, N-acetylglucosamine, aesculin, cellobiose, maltose, lactose, sucrose, trehalose and tagatose. Although extremely salt tolerant, it does not grow in > or = 4% NaCl. On the basis of phenotypic and genotypic data, it is concluded that this isolate represents a separate, novel species. Accordingly, the name Carnobacterium viridans sp. nov. is proposed. The type strain is strain MPL-11T (= ATCC BAA-336T = DSM 14451T).
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Udeniomyces pannonicus sp. nov., a ballistoconidium-forming yeast isolated from leaves of plants in Hungary.
More LessFifteen ballistoconidium-forming yeasts, isolated from the leaves of plants in Hungary, showed morphological, physiological and biochemical characteristics similar to those of Udeniomyces pyricola. The identical sequences of internal transcribed spacer regions for selected strains (HY-16T, HY-29, HY-111 and HY-186) indicated that they should be classified as one species. Although a representative strain, HY-16T, showed a closer relationship to Itersonilia perplexans than to known Udeniomyces species in phylogenetic trees constructed using 18S rDNA and the D1/D2 region of the 26S rDNA sequence, this species was placed in the genus Udeniomyces on the basis of its morphological and chemotaxonomic characteristics. Udeniomycespannonicus sp. nov. (type strain HY-16T = JCM 11145T = NCAIM Y 01556T = CBS 9123T) is proposed.
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Lateral gene transfers and the evolution of eukaryotes: theories and data.
More LessVertical transmission of heritable material, a cornerstone of the Darwinian theory of evolution, is inadequate to describe the evolution of eukaryotes, particularly microbial eukaryotes. This is because eukaryotic cells and eukaryotic genomes are chimeric, having evolved through a combination of vertical (parent to offspring) and lateral (trans-species) transmission. Observations on widespread chimerism in eukaryotes have led to new and revised hypothesis for the origin and diversification of eukaryotes that provide specific predictions on the tempo (early vs continuous transfers) and mode (nature of donor and recipient lineages) of lateral gene transfers (LGTs). Analyses of available data indicate that LGTs in eukaryotes largely fall into two categories: (1) LGTs from organelles to the nucleus, only a few of which appear to have occurred at the time of the origin of eukaryotes, and (2) anomalous LGTs involving diverse donor and recipient lineages. Further testing of hypotheses on the origin and diversification of eukaryotes will require complete genome sequences from a number of diverse eukaryotes and prokaryotes combined with sequences of targeted genes from a broad phylogenetic sample.
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Insights into the diversity of choreotrich and oligotrich ciliates (Class: Spirotrichea) based on genealogical analyses of multiple loci.
More LessTo examine relationships among spirotrich ciliates using multi-locus sequence analyses and to provide preliminary insights into molecular diversity within species, we sequenced the small subunit rDNA (SSU rDNA), 5.8S rDNA, alpha-tubulin and the internally transcribed spacer regions (ITS1 and ITS2) of the rDNA genes from seven choreotrich (Class: Spirotrichea) and three oligotrich (Class: Spirotrichea) taxa. Genealogies constructed from SSU rDNA and ITS sequences are concordant and broadly support current classifications based on morphology. The one exception is the freshwater oligotrich Halteria grandinella, which, as has been previously noted, falls outside of the clade containing the other oligotrichs. In contrast, analyses of alpha-tubulin sequences are discordant with traditional taxonomy and rDNA genealogies. These analyses also indicate that considerably more genetic variation exists among choreotrich and oligotrich genera than among stichotrich genera. To explore the level of genetic variation among individuals in temporally isolated populations, we collected additional samples of a subset of planktonic choreotrichs and oligotrichs and characterized polymorphisms in ITS1, ITS2 and 5.8S rDNA. Analyses of these data indicate that, at least for some ciliate lineages, DNA polymorphisms vary temporally, and that genetic heterogeneity underlies some very similar morphological types.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 69 (2019)
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Volume 68 (2018)
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