- Volume 48, Issue 4, 1998
Volume 48, Issue 4, 1998
- Systematic Bacteriology
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Streptomyces thermogriseus, a new species of the genus Streptomyces from soil, lake and hot-spring
More LessMany thermophilic actinomycetes were isolated from samples collected from a hot-spring, lake and soil in Yunnan, China. Chemical and molecular classification of four selected strains of thermophilic Streptomyces with an upper limited growth temperature of 65-68 °C and autolytic characteristics was carried out. A new species, Streptomyces thermogriseus sp. nov. is described. The type strain is Y-14046T (= CCTCC AA97014T).
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Description of Saccharomonospora xinjiangensis sp. nov. based on chemical and molecular classification
More LessComparative studies of morphology, physiology, biochemistry and chemical composition of cells, and phylogenetic analysis based on 16S rRNA gene sequences were carried out with strains XJ-54Tand XJ-58 of the genus Saccharomonospora and type strains of related genera. The results indicated that the two strains are different from known members of the genus Saccharomonospora. A new species with the name Saccharomonospora xinjiangensis sp. nov. is proposed. The new species is characterized by the presence of longitudinal pairs of spores on both the aerial and the vegetative hyphae and contains phosphatidyl ethanolamine, phosphatidyl choline and unknown glucosamine-containing phospholipids, and the major menaquinones MK-9(H2), MK-9(H4) and MK-7(H4).
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Lactobacillus manihotivorans sp. nov., a new starch-hydrolysing lactic acid bacterium isolated during cassava sour starch fermentation
More LessTwo Lactobacillus strains were isolated from sour cassava starch fermentation. The cells were Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They produced only l(+)lactate and were homofermentative. Growth occurred at pH values of 5·0-7·0 and optimum growth occurred at pH 6·0. Growth was positive at 15 and 45 °C. The DNA G+C content was 48·4±0·2 mol%. Sequence analysis of the 16S rRNA gene revealed that strains OND 32T and YAM 1 clustered with, but were separate from Lactobacillus casei- related taxa. Protein pattern and sequence analyses of the 16S rRNA gene confirmed that the two new isolates represent a new Lactobacillus species, for which the name Lactobacillus manihotivorans is proposed; strain OND 32T is the type strain of this species.
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Methanoculleus palmolei sp. nov., an irregularly coccoid methanogen from an anaerobic digester treating wastewater of a palm oil plant in North-Sumatra, Indonesia
More LessStrain INSLUZT(= DSM 4273T) was isolated from a biogas-producing bioreactor treating wastewater of a palm oil mill on North-Sumatra (Indonesia). Cells of strain INSLUZT were highly irregularly coccoid, 1·25–2·0 in diameter, had a cell envelope consisting of the cytoplasmic membrane and an S-layer of hexagonally arranged glycoprotein subunits with an M r of 120 000, and were flagellated (motility was not observed). Cells were mesophilic and grew most rapidly at 40 °C on H2/CO2, formate, 2-propanol/CO2, 2-butanol/CO2 and cyclopentanol/CO2 to give methane. Tungstate promoted growth on H2/CO2 with acetate as the solely required organic medium supplement. The G+C content of DNA was 59 mol% (T m method) and 59·5 mol% (HPLC method). 16S rDNA analysis revealed a phylogenetic relationship to Methanoculleus species; the name Methanoculleus palmolei sp. nov. is therefore proposed for strain INSLUZT (= DSM 4273T).
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Verrucosispora gifhornensis gen. nov., sp. nov., a new member of the actinobacterial family Micromonosporaceae
More LessA Gram-positive, aerobic, spore-forming actinomycete strain, HR1-2T, was isolated from a peat bog near Gifhorn, Lower Saxony, Germany. Comparative analysis of the 16S rDNA sequence indicated that HR1-2Twas phylogenetically related to members of the family Micromonosporaceae, branching adjacent to Spirilliplanes yamanashiensis, Couchioplanes caeruleus, Catenuloplanes japonicus and members of the genus Micromonospora. The affiliation to the family was supported by the presence of family-specific 16S rDNA signature nucleotides, DNA G+C content of 70 mol%, peptidoglycan of type A1γ′ (directly crossed-linked, presence of glycine, alanine, glutamic acid and meso-diaminopimelic acid in the peptide side-chain), menaquinone MK-9(H4) as the major respiratory lipoquinone, polar lipid composition PII (phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylserine and phosphatidylinositolmannosides) and a glycolyl type of muramic acid. It differed from genera of the family by the lack of arabinose in whole-cell sugars and a unique nucleotide signature stretch between positions 1132 and 1143 (Escherichia coli numbering), 5’ CAAUUCGGUUG 3’. Morphologically strain HR1-2T resembles Micromonospora species but can be distinguished from them by the lack of arabinose in whole-cell sugars, the presence of 10-methyl C17:0 fatty acids and a distinct 16S rDNA sequence. Based on the unique combination of morphological, chemotaxonomic and phylogenetic properties a new genus, Verrucosispora gen. nov., is proposed. The type species of this genus is Verrucosispora gifhornensis sp. nov., and the type strain of V. gifhornensis is strain HR1-2T(= DSM 44337T).
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Phylogenetic relationships among the Chromatiaceae, their taxonomic reclassification and description of the new genera Allochromatium, Halochromatium, Isochromatium, Marichromatium, Thiococcus, Thiohalocapsa and Thermochromatium
More LessSequences of the 16S rDNA from all available type strains of Chromatium species have been determined and were compared to those of other Chromatiaceae, a few selected Ectothiorhodospiraceae and Escherichia coli. The clear separation of Ectothiorhodospiraceae and Chromatiaceae is confirmed. Most significantly the sequence comparison revealed a genetic divergence between Chromatium species originated from freshwater sources and those of truly marine and halophilic nature. Major phylogenetic branches of the Chromatiaceae contain (i) marine and halophilic species, (ii) freshwater Chromatium species together with Thiocystis species and (iii) species of the genera Thiocapsa and Amoebobacter as recently reclassif ied [Guyoneaud, R. & 6 other authors (1998). Int J Syst Bacteriol 48, 957–964], namely Thiocapsa roseopersicina, Thiocapsa pendens (formerly Amoebobacter pendens). Thiocapsa rosea (formerly Amoebobacter roseus), Amoebobacter purpureus and Thiolamprovum pedioforme (formerly Amoebobacter pedioformis). The genetic relationships between the species and groups are not in congruence with the current classification of the Chromatiaceae and a reclassification is proposed on the basis of 16S rDNA sequence similarity supported by selected phenotypic properties. The proposed changes include the transfers of Chromatium minus and Chromatium violascens to Thiocystis minor comb. nov. and Thiocystis violascens comb, nov., of Chromatium vinosum, Chromatium minutissimum and Chromatium warmingii to the new genus Allochromatium as Allochromatium vinosum comb. nov., Allochromatium minutissimum comb. nov., and Allochromatium warmingii comb. nov., of Chromatium tepidum to the new genus Thermochromatium as Thermochromatium tepidum comb, nov., of Chromatium salexigens and Chromatium glycolicum to the new genus Halochromatium as Halochromatium salexigens comb. nov. and Halochromatium glycolicum comb, nov., of Chromatium gracile and Chromatium purpuratum to the new genus as Marichromatium gracile comb. nov. and Marichromatium purpuratum comb, nov., of Thiocapsa pfennigii to Thiococcus pfennigii gen. nom. rev., of Thiocapsa halophila to the new genus Thiohalocapsa as Thiohalocapsa halophila comb, nov., and of Chromatium buderi to the new genus Isochromatium as Isochromatium buderi comb. nov.
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Phenotypic characterization of the marine pathogen Photobacterium damselae subsp. piscicida
More LessThe taxonomic position of Photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis, is controversial as this organism has also been described as ‘pasteurella piscicida’. To clarify the taxonomic position of the pathogen, a total of 113 P. damselae subsp. piscicida strains and 20 P. damselae subsp. damselae strains, isolated from different geographical areas and from the main affected fish species, were analysed using 129 morphological and biochemical tests, including the commercial API 20E and API CH50 test systems. For comparison, the type strains of other Photobacterium species (i.e. Photobacterium leiognathi and Photobacterium angustum) were included in the analyses. The results were statistically analysed by unweighted pair group average clustering and the distance between the different clusters was expressed as the percentage disagreement. The analyses showed that, based on morphological and biochemical identification tests, P. damselae subsp. piscicida is related to other Photobacterium species. However, it is clearly distinguishable from P. damselae subsp. damselae and no phenotypic evidence was found to include P. damselae subsp. piscicida as a subspecies in the species P. damselae.
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Revised Classification Scheme of Phytoplasmas based on RFLP Analyses of 16S rRNA and Ribosomal Protein Gene Sequences
More LessRFLP analyses of 16S rDNA nested PCR products from 34 phytoplasma strains with 17 restriction enzymes delineated distinct pattern types. Based on similarity coefficients derived from RFLP analyses, the 34 representative phytoplasma strains were differentiated into 14 major groups (termed 16Sr groups) and 32 sub-groups. The similarity coefficients of RFLP patterns between distinct groups were 90% or below. By including additional groups and sub-groups from which RFLP analyses were not performed but for which 16S rDNA sequence data were available to predict restriction sites, a total of 14 groups and 41 sub-groups were proposed. By combined RFLP analyses of 16S rRNA and ribosomal protein gene sequences, thus far, a total of 46 subgroups have been recognized. The phytoplasma 16Sr groups were consistent with the phylogenetic groups (subclades) defined by phylogenetic analysis of near-full-length 16S rRNA gene sequences, indicating that the RFLP-based groups are phylogenetically valid. The approach using RFLP analyses of PCR-amplified 16S rDNA (and ribosomal protein gene sequences) provides a simple, reliable and rapid means for differentiation and classification of unknown phytoplasmas.
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Colwellia demingiae sp. nov., Colwellia hornerae sp. nov., Colwellia rossensis sp. nov. and Colwellia psychrotropica sp. nov.: psychrophilic Antarctic species with the ability to synthesize docosahexaenoic acid (22:6ω3)
As part of a general survey of the biodiversity and inherent ecophysiology of bacteria associated with coastal Antarctic sea-ice diatom assemblages, eight strains were identified by 16S rRNA sequence analysis as belonging to the genus Colwellia. The isolates were non-pigmented, curved rod-like cells which exhibited psychrophilic and facultative anaerobic growth and possessed an absolute requirement for sea water. One isolate was able to form gas vesicles. All strains synthesized the ω3 polyunsaturated fatty acid (PUFA) docosahexaenoic acid (22:6ω3, DHA) (0·7–8·0% of total fatty acids). Previously, DHA has only been detected in strains isolated from deep-sea benthic and faunal habitats and is associated with enhanced survival in permanently cold habitats. The G+C content of the DNA from the Antarctic Colwellia strains ranged from 35 to 42 mol% and DNA-DNA hybridization analyses indicated that the isolates formed five genospecies, including the species Colwellia psychrerythraea (ACAM 550T). 16S rRNA sequence analysis indicated that the strains formed a cluster in the γ-subclass of the Proteobacteria with Colwellia psychrerythraea. Sequence similarities ranged from 95·2 to 100% between the various Antarctic Colwellia isolates. Phenotypic characterization confirmed distinct differences between the different genospecies. These studies indicate that the DHA-producing Antarctic isolates consist of five different Colwellia species: Colwellia psychrerythraea and four novel species with the proposed names Colwellia demingiae sp. nov. (ACAM 459T), Colwellia psychrotropica sp. nov. (ACAM 179T), Colwellia rossensis sp. nov. (ACAM 608T) and Colwellia hornerae sp. nov. (ACAM 607T).
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Thermococcus guaymasensis sp. nov. and Thermococcus aggregans sp. nov., two novel thermophilic archaea isolated from the Guaymas Basin hydrothermal vent site
More LessThermococcus strains TYST and TYT isolated from the Guaymas Basin hydrothermal vent site and previously described were compared by DNA-DNA hybridization analysis with the closest Thermococcus species in terms of physiology and nutritional aspects. On the basis of the new data and taking into consideration the molecular, physiological and morphological traits published previously, it is proposed that strains TYT and TYST should be classified as new species named Thermococcus aggregans sp. nov. and Thermococcus guaymasensis sp. nov., respectively. The type strain of T. aggregans is strain TYT (= DSM 10597T) and the type strain of T. guaymasensis is strain TYST (= DSM 11113T).
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Proposal of a new halobacterial genus Natrinema gen. nov., with two species Natrinema pellirubrum nom. nov. and Natrinema pallidum nom. nov.
More LessA phylogenetic analysis of 69 halobacterial 16S rRNA gene sequences has been carried out, integrating data from new isolates, previously described halobacteria and cloned sequences from uncultivated halobacteria. Halobacterium halobium NCIMB 777, Halobacterium trapanicum NCIMB 784 and Halobacterium salinarium NCIMB 786, together with several other strains (strains T5.7, L11 and Halobacterium trapanicum NCIMB 767) constitute a distinct lineage with at least 98·2% sequence similarity. These strains have been incorrectly assigned to the genus Halobacterium. Therefore, based on a variety of taxonomic criteria, it is proposed that Halobacterium salinarium NCIMB 786 is renamed as Natrinema pellirubrum nom. nov., the type species of the new genus Natrinema gen. nov., and that Halobacterium halobium NCIMB 777 and Halobacterium trapanicum NCIMB 784 are renamed as a single species, Natrinema pallidum nom. nov. It was notable that halobacteria closely related to the proposed new genus have been isolated from relatively low-salt environments.
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Entomoplasma freundtii sp. nov., a new species from a green tiger beetle (Coleoptera: Cicindelidae)
A mollicute (strain BARC 318T) isolated from gut tissue of a green tiger beetle (Coleoptera: Cicindelidae) was found by dark-field microscopy to consist of non-helical, non-motile, pleomorphic coccoid forms of various sizes. In ultrastructural studies, individual cells varied in diameter from 300 to 1200 nm, were surrounded by a cytoplasmic membrane and showed no evidence of cell wall. The organisms were readily filterable through membrane filters with mean pore diameters of 450 and 300 nm, with unusually large numbers of organisms filterable through 200 nm pore membrane filters. Growth occurred over a temperature range of 15–32 °C with optimum growth at 30 °C. The organism fermented glucose and hydrolysed arginine but did not hydrolyse urea. Strain BARC 318T was insensitive to 500 U penicillin ml–1 and required serum or cholesterol for growth. It was serologically distinct from all currently described sterol-requiring, fermentative Mycoplasma species and from 12 non-sterol-requiring Mesoplasma species, 13 non-sterol-requiring Acholeplasma species and 5 previously described sterol-requiring Entomoplasma species. Strain BARC 318T was shown to have a G+C content of 34 mol% and a genome size of 870 kbp. The 16S rDNA sequence of strain BARC 318T was compared to 16S rDNA sequences of several other Entomoplasma species and to other representative species of the genera Spiroplasma and Mycoplasma, and to other members of the class Mollicutes. These comparisons indicated that strain BARC 318T had close phylogenetic relationships to other Entomoplasma species. On the basis of these findings and other similarities in morphology, growth and temperature requirements and genomic features, the organism was assigned to the genus Entomoplasma. Strain BARC 318T (ATCC 51999T) is designated the type strain of Entomoplasma freundtii sp. nov.
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Pseudoalteromonas tunicata sp. nov., a bacterium that produces antifouling agents
More LessA dark-green-pigmented marine bacterium, previously designated D2, which produces components that are inhibitory to common marine fouling organisms has been characterized and assessed for taxonomic assignment. Based on direct double-stranded sequencing of the 16S rRNA gene, D2T was found to show the highest similarity (93%) to members of the genus Pseudoalteromonas. The G+C content of D2T is 42 mol%, and it is a facultatively anaerobic rod and oxidase-positive. D2T is motile by a sheathed polar flagellum, exhibited non-fermentative metabolism and required sodium ions for growth. The strain was not capable of using citrate, fructose, sucrose, sorbitol and glycerol but it utilizes mannose and maltose and hydrolyses gelatin. The molecular evidence, together with phenotypic characteristics, showed that this bacterium which produces an antifouling agent constitutes a new species of the genus Pseudoalteromonas. The name Pseudoalteromonas tunicata is proposed for this bacterium, and the type strain is D2T (= CCUG 26757T).
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Glaciecola punicea gen. nov., sp. nov. and Glaciecola pallidula gen. nov., sp. nov.: psychrophilic bacteria from Antarctic sea-ice habitats
More LessA group of pigmented, psychrophilic, strictly aerobic chemoheterotrophs isolated from sea-ice cores collected from coastal areas of eastern Antarctica was found to represent a novel 16S rRNA lineage within the gamma subclass of the Proteobacteria, adjacent to the genus Alteromonas. The isolates are motile. Gram-negative, rod-shaped cells, which are psychrophilic and slightly halophilic, and possess an absolute requirement for seawater. Differences in phenotypic characteristics and DNA–DNA hybridization indicated the isolates formed two distinct taxa which have DNA G+C contents of 44–46 mol% and 40 mol%, respectively. Whole-cell fatty acid profiles of the isolates were however very similar and included 16:1ω7c, 18:1ω7c, 16:0 and 17:1ω8c as the major fatty acid components. Overall, sufficient differences exist to distinguish the sea-ice strains from currently recognized bacterial genera. It is proposed the sea-ice strains represent a new genus, Glaciecola, which contains two species, Glaciecola punicea gen. nov., sp. nov. (ACAM 611T) and Glaciecola pallidula gen. nov., sp. nov. (ACAM 615T).
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Application of the Ribonuclease P (RNase P) RNA Gene Sequence for Phylogenetic Analysis of the Genus Saccharomonospora
More LessSequences of the RNase P RNA gene were investigated for the phylogenetic analysis of the genus Saccharomonospora. Aligned nucleotide sequences, determined from the PCR-amplified RNase P RNA gene of representative strains of the genus Saccharomonospora, displayed 94·2±1·3% interspecific variances. The intraspecific similarity value was 99·7–100% in all species tested. Saccharomonospora azurea K161Tand “Saccharomonospora caesia” K76Tdisplayed identical RNase P RNA gene sequences in the region that was determined and Saccharomonospora sp. K180 showed sequences distinct from validly described species with a similarity value of 94·6±1·0%. The phylogenetic trees constructed by aligning the sequences either within the genus Saccharomonospora or with other Gram-positive bacteria were similar to the ones derived using sequences of the 16S rDNA gene. Advantageous features of this gene for application as a molecular phyletic marker are discussed.
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Genetic relationships among the different phenotypes of Streptococcus dysgalactiae strains
The species Streptococcus dysgalactiae was proposed to accommodate a heterogeneous group of streptococci associated with infections in animals and human beings. This taxon is now considered to include animal isolates of α-haemolytic group C streptococci, previously called S. dysgalactiae; animal and human isolates of β-haemolytic group C streptococci, previously called ‘S. equisimilis’; β-haemolytic group L strains associated with infections in animals and, rarely, in humans; and β-hiaemolytic group G strains isolated from humans. DNA-DNA reassociation experiments (hydroxyapatite method) and multilocus enzyme electrophoresis (MEE) were performed on reference strains and clinical isolates to determine the genetic relationships among these different phenotypic categories. DNA-DNA hybridization tests showed that they were related at the species level, despite the phenotypic and host heterogeneity. Both genotypic and phenotypic characterization indicated that S. dysgalactiae could be separated into two major sub-groups. The first subgroup contained α-haemolytic strains that showed levels of DNA relatedness with the type strain of S. dysgalactiae ranging from 84 to 90% and from 82 to 88% under optimal (55 °C) and stringent (70 °C) conditions, respectively. The second sub-group contained βhaemolytic strains showing levels of relatedness ranging from 71 to 79% (55 °C) and from 62 to 73% (70 °C). Percentage divergence varied from 0·5 to 1·0% (α-haemolytic group) and from 20 to 3·5% (α-haemolytic group). A dendrogram based on phenotypic similarity between the enzyme bands produced by MEE showed a Jaccard similarity coefficient of 0·45 between the subclusters formed by the two sub-groups. The results of phenotypic and genotypic characterization were consistent with a published proposal to divide S. dysgalactiae into two subspecies, S. dysgalactiae subsp. dysgalactiae and S. dysgalactiae subsp. equisimilis, with a few modifications.
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Description of four new species of the genus Kineosporia: Kineosporia succinea sp. nov., Kineosporia rhizophila sp. nov., Kineosporia mikuniensis sp. nov. and Kineosporia rhamnosa sp. nov., isolated from plant samples, and amended description of the genus Kineosporia
More LessEleven motile spore-bearing actinomycetes were isolated from various plant samples and were studied to determine their taxonomic positions. The isolates showed colony appearance and morphology similar to those of the ‘sporedome actinomycetes’ previously described by L. G. Willoughby in 1969. Although the isolates showed variety in composition of isomers of 2,6-diaminopimelic acid in the cell walls and in whole-cell sugar patterns, all of the isolates were classified in the genus Kineosporia Pagani and Parenti 1978 emend. Itoh et al. 1989 on the basis of their morphological and other chemotaxonomic characteristics, i.e. menaquinone, phospholipid and cellular fatty acid compositions. This assignment to the genus was also supported by a phylogenetic analysis using the 16S rRNA gene sequences. By DNA-DNA hybridization experiment, five genospecies were recognized among the isolates, and one of them showed high levels with the type strain of the type species, Kineosporia aurantiaca, which is the sole member of the genus. These genospecies can be distinguished from each other by their cultural, physiological and biochemical characteristics, and the other four genospecies should be placed into four new species for which the names Kineosporia succinea (type strain 1-273T= JCM 9957T), Kineosporia rhizophila (type strain l-449T= JCM 9960T). Kineosporia mikuniensis (type strain l-463T= JCM 9961T) and Kineosporia rhamnosa (type strain l-132T= JCM 9954T) are proposed.
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Variation amongst human isolates of Brachyspira (Serpulina) pilosicoli based on biochemical characterization and 16S rRNA gene sequencing
More LessBrachyspira pilosicoli (formerly Serpulina pilosicoli) causes swine spirochaetosis and can also be isolated from human faeces, although its role in human disease remains unclear. The genetic and biochemical variations amongst 19 isolates of human spirochaetes from five different countries were evaluated and compared to those found amongst swine isolates of B. pilosicoli. All isolates were negative for β-glucosidase and all but one were positive for hippurate hydrolysis, which are characteristics typical of B. pilosicoli. The isolates showed variation in indole production and α-galactosidase and α-glucosidase activity, other characteristics which can be used to identify B. pilosicoli. The DNA sequences of part of the 16S rRNA gene differed from each other and from that of B. pilosicoli by 0–3 bp out of 283 bp. It is concluded that there is considerable variation amongst human intestinal spirochaetes. Since few of the isolates reported here match the current criteria for B. pilosicoli, it is concluded that this species is more heterogeneous than previously appreciated. However, it cannot be excluded that some isolates may belong to uncharacterized related BrachyspiralSerpulina species.
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Grouping of Frankia strains on the basis of susceptibility to antibiotics, pigment production and host specificity
More LessThirty-nine selected Frankia strains belonging to different genomic species were clustered on the basis of their in vitro susceptibility to 17 antibiotics, pigment production and ability to nodulate plants of the genus Alnus and/or the family Elaeagnaceae, or the family Casuarinaceae. The majority of the strains studied fell into three cluster groups, A, E and C, corresponding to the three host-specificity groups, Alnus, Elaeagnus and Casuarina. Within the groups, eight composite clusters, consisting of at least two strains, and five single-member clusters were recovered at the 0·74 distance level, in good agreement with levels of genetic relatedness between the strains. In addition, five strains were recovered as single-member clusters not in the cluster groups, four of them representing single-member genospecies and one strain not assigned to any known genospecies. The concordance between the phenotypic clusters and the genospecies described previously shows that the grouping may reflect the taxonomic structure of the genus Frankia. For some clusters, differentiating phenotypic characters were found which may be useful for species definition.
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Allorhizobium undicola gen. nov., sp. nov., nitrogen-fixing bacteria that efficiently nodulate Neptunia natans in Senegal
A group of nodule isolates from Neptunia natans, an indigenous stemnodulated tropical legume found in waterlogged areas of Senegal, was studied. Polyphasic taxonomy was performed, including SDS-PAGE of total proteins, auxanography using API galleries, host-plant specificity, PCR-RFLP of the internal transcribed spacer region between the 16S and the 23S rRNA coding genes, 16S rRNA gene sequencing and DNA-DNA hybridization. It was demonstrated that this group is phenotypically and phylogenetically separate from the known species of Rhizobium, Sinorhizobium, Mesorhizobium, Agrobacterium, Bradyrhizobium and Azorhizobium. Its closest phylogenetic neighbour, as deduced by 16S rRNA gene sequencing, is Agrobacterium vitis (96·2% sequence homology). The name Allorhizobium undicola gen. nov., sp. nov., is proposed for this group of bacteria, which are capable of efficient nitrogen-fixing symbiosis with Neptunia natans, and the type strain is ORS 992T (= LMG 11875T).
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Corynebacterium confusum sp. nov., isolated from human clinical specimens
More LessThree strains of a previously unknown coryneform bacterium were isolated from two patients with foot infections and from a blood culture of a third patient. The three non-lipophilic strains exhibited very slow fermentative acid production from glucose but not from maltose or sucrose, nitrate reductase activity, no tyrosinase activity and the presence of small amounts of tuberculostearic acid as the most significant phenotypic features. Differentiation of these strains from all other presently defined coryneform bacteria was readily achieved. Chemotaxonomic investigations revealed that the three strains unambiguously belonged to the genus Corynebacterium. Comparative 16S rRNA gene sequence analysis demonstrated that the isolates were almost identical and represented a new subline within the genus Corynebacterium, for which the designation Corynebacterium confusum sp. nov. is proposed. The type strain of Corynebacterium confusum is CCUG 38267T.
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Coprothermobacter platensis sp. nov., a new anaerobic proteolytic thermophilic bacterium isolated from an anaerobic mesophilic sludge
More LessA new anaerobic, proteolytic, moderately thermophilic bacterium, strain 3RT, was isolated from a methanogenic mesophilic reactor treating protein-rich wastewater. The cells were Gram-negative, non-spore-forming, non-motile rods. The DNA base composition was 43 mol% G+C. The optimum pH and temperature for growth were 7·0 and 55 °C respectively. The bacterium fermented gelatin, casein, bovine albumin, peptone and yeast extract. Glucose, fructose, sucrose, maltose and starch were poorly fermented. The major fermentation products from glucose were acetate, CO2 and H2 and, from gelatin, propionate was also detected. Growth on glucose was stimulated by thiosulfate, which was reduced to sulfide. Sulfate and nitrate were not reduced. 16S rRNA gene analysis revealed that the isolated bacterial strain was phylogenetically related to Coprothermobacter proteolyticus (96·3% sequence similarity), the only known species within the genus. DNA-DNA hybridization analysis demonstrated a very low level of homology, indicating that the isolated strain and C. proteolyticus were not related at species level. Therefore, it is proposed to classify the described strain in the genus Coprothermobacter as a new species, Coprothermobacter platensis. The type strain of C. platensis is strain 3RT (= DSM 11748T).
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Halogeometricum borinquense gen. nov., sp. nov., a novel halophilic archaeon from Puerto Rico
A novel extremely halophilic archaeon was isolated from the solar salterns of Cabo Rojo, Puerto Rico. The organism is very pleomorphic motile and requires at least 8% (w/v) NaCI to grow. Polar lipid composition revealed the presence of a novel non-sulfate-containing glycolipid and the absence of the glycerol diether analogue of phosphatidylglycerosulfate. The G+C content of the DNA is 59 mol%. On the basis of 16S rRNA sequence data, the new isolate cannot be classified in one of the recognized genera, but occupies a position that is distantly related to the genus Haloferax. All these features justify the creation of a new genus and a new species for the family Halobacteriaceae, order Halobacteriales. The name Halogeometricum borinquense gen. nov., sp. nov. is proposed. The type strain is ATCC 700274T.
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Methylopila capsulata gen. nov., sp. nov., a novel non-pigmented aerobic facultatively methylotrophic bacterium
A new genus, Methylopila, and one new species are described for a group of seven strains of facultatively methylotrophic bacteria with the serine pathway of C1 assimilation. These bacteria are aerobic. Gram-negative, non-spore-forming, motile, colourless rods that multiply by binary fission. Their DNA base content ranges from 66 to 70 mol % G+C. Their cellular fatty acid profile consists primarily of C18:1ω7 cis-vaccenic and C19:0 cyclopropane acids. The major hydroxy acid is 3-OH C14:0. The main ubiquinone is Q-10. The dominant cellular phospholipids are phosphatidylethanolamine and phosphatidylcholine. The new isolates have a low level of DNA-DNA homology (5–10%) with the type strains of the serine pathway methylobacteria belonging to the genera Methylobacterium, Aminobacter, Hyphomicrobium and Methylorhabdus. Another approach, involving 16S rRNA gene sequence analysis of strain IM1T, has shown that the new isolates represent a separate branch within the a-2 subclass of the Proteobacteria. The type species of the new genus is Methylopila capsulata sp. nov., with the type strain IM1T (= VKM B-1606T).
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The phylogeny of Ureaplasma urealyticum based on the mba gene fragment
More LessSequencing of mba gene fragments of reference strains of Ureaplasma urealyticum serovars 1, 3, 6, 14 and 8, in addition to 33 clinical U. urealyticum isolates is reported. A phylogenetic tree deduced from alignment of these sequences clearly demonstrates two major clusters (confidence limit 100%), which equate to the parvo and T960 biovars, and five types, which have been designated mba 1, 3, 6, 8 and X. These relationships are supported by bootstrap analysis. Polymorphisms within the mba fragment of types mba 1, 3 and 6 were used to define nine subtypes (mba 1a, 1b, 3a, 3b, 3c, 3d, 3e, 6a and 6b), thus facilitating high resolution typing of U. urealyticum. Inclusion of reference strains for serovars 1, 3, 6 and 8 in the mba typing scheme showed that the results of this analysis are broadly consistent with currently accepted serotyping. In addition, a ure gene fragment from nine of the clinical isolates was amplified and sequenced. Comparisons of the sequences clearly distinguished the two biovars of U. urealyticum; however, this fragment was invariant within the parvo biovar. This study has shown that the mba sequence can reveal the fine details of the relationships between U. urealyticum isolates and also supports the significant evolutionary gap between the two biovars.
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Bartonella tribocorum sp. nov., a new Bartonella species isolated from the blood of wild rats
Two Bartonella strains from blood of two wild rats (Rattus norvegicus) living in a rural environment were isolated. These strains were distinct from all previously known Bartonella species based on phenotypic and genotypic characteristics. This new species is distinguished by its trypsin-like activity, the absence of the ability to hydrolyse proline and tributyrin, its 16S rRNA and citrate synthase gene sequences and by whole-DNA hybridization data. This new species, for which the name Bartonella tribocorum sp. nov. is proposed, seems to be genetically related to Bartonella elizabethae, an agent isolated in a case of human endocarditis. The type strain of Bartonella tribocorum sp. nov. is IBS 506T (CIP 105476T).
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Marinospirillum gen. nov., with descriptions of Marinospirillum megaterium sp. nov., isolated from kusaya gravy, and transfer of Oceanospirillum minutulum to Marinospirillum minutulum comb. nov.
More LessTwo strains of helical, halophilic, Gram-negative, heterotrophic bacteria were isolated from kusaya gravy which is a traditional Japanese fermented brine. These strains were motile by means of a single polar or bipolar tuft flagellum. They had a large cell size, were helical, formed coccoid bodies, were microaerophilic and had quinone type Q-8. The DNA G+C content of the strains was 44–45 mol%. A detailed investigation of the phenotypic, chemotaxonomic and phylogenetic characteristics of the strains revealed that they represent a new species of halophilic helical bacteria. The sequence of the 16S rRNA gene of strain H7T, designated the type strain of the new isolates, and all of the Oceanospirillum species except for Oceanospirillum linum were determined. Phylogenetic analysis indicated that these strains were closely related to Oceanospirillum minutulum, with enough distance to separate the O. minutulum/new isolate H7Tcluster from Oceanospirillum sensu stricto on the genus level. It is proposed that a new genus, Marinospirillum, be created; this genus should include Marinospirillum minutulum ATCC 19193T(formerly Oceanospirillum minutulum) as the type species, as well as Marinospirillum megaterium JCM 10129T(=H7T).
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Mycobacterium bohemicum sp. nov., a new slow-growing scotochromogenic mycobacterium
A new, slow-growing, scotochromogenic mycobacterium was isolated from sputum of a 53-year-old patient with Down’s syndrome suffering from tuberculosis. Growth occurred at temperatures between 25 and 40°C with an optimum at 37°C. This strain had surprisingly few enzymic activities (only positive for 68°C heat-stable catalase and weakly positive for urease) and was sensitive to prothionamide, cycloserine, clarithromycin, gentamicin and amikacin but showed resistance to isoniazid, streptomycin, ethambutol, rifampin and ciprofloxacin. These characteristics assign this organism to a novel mycobacterial species characterized by a unique 16S rDNA nucleotide sequence. The name Mycobacterium bohemicum sp. nov. is proposed for this new, slow-growing, scotochromogenic mycobacterium. The type strain is DSM 44277T.
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Assignment of Vibrio sp. strain ABE-1 to Colwellia maris sp. nov., a new psychrophilic bacterium
More LessA psychrophilic bacterium, previously described as Vibrio sp. strain ABE-1T, has been reassigned by phenotypic characterization, chemotaxonomic analysis and 16S rRNA phylogenetic analysis. The organism was curved rods and it could reduce nitrate to nitrite and hydrolyse gelatin and DNA, but not chitin. NaCl was required for growth. This strain was susceptible to the vibriostatic compound 0/129. The major isoprenoid quinone was ubiquinone-8 and the DNA G+C content was 39·4 mol%. The whole-cell fatty acids comprised saturated and monounsaturated fatty acids with 10–18 C atoms; saturated and monounsaturated C16 fatty acids were predominant. Strain ABE-1T contained the unique trans-unsaturated fatty acid, 9-trans-hexadecenoic acid. Although strain ABE-1T has been identified as a Vibrio species, the strain did not ferment glucose. Phylogenetic analysis based on 16S rRNA sequencing indicated that strain ABE-1T was more closely related to Colwellia species than to Vibrio species. However, strain ABE-1T differed from other reported Colwellia species in terms of phylogenetic position, some phenotypic characteristics, chemotaxonomic analysis and relatedness by DNA–DNA hybridization. Accordingly, the name Colwellia maris is proposed. The type strain is ABE-1T ( = JCM 10085T).
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Antarctobacter heliothermus gen. nov., sp. nov., a budding bacterium from hypersaline and heliothermal Ekho Lake
Four Gram-negative, aerobic, pointed and budding bacteria were isolated from various depths of the hypersaline, heliothermal and meromictic Ekho Lake (Vestfold Hills, East Antarctica). The cells contained storage granules and formed rosettes. Daughter cells may be motile. Growth required sodium ions. Nitrate was reduced to nitrite, and dissimilatory reduction of nitrite was possible. DNase and gelatinase were produced. Glutamate was metabolized with and without an additional source of combined nitrogen. The most abundant fatty acid was C18:1; other fatty acids present in lower concentrations were C12:1 3-OH, C16:1, C16:0, C18:0 and C19:0 eye. The main polar lipids were phosphatidylglycerol and phosphatidylcholine. The DNA base composition was 62·3–62·8 mol% G+C. 16S rDNA sequence comparisons showed the isolates to be phylogenetically related to the genera Sagittula and Roseobacter. Morphological, physiological and genotypic differences to these and distinct characteristics supported the description of a new genus and a new species, Antarctobacter heliothermus gen. nov., sp. nov. The type strain is EL-219T (= DSM 11445T).
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Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group
The Bacillus cereus group comprises the four valid species Bacillus cereus, Bacillus mycoides, Bacillus thuringiensis and Bacillus anthracis. Some isolates of B. cereus are known to be psychrotolerant (growth at 7 °C or below). Here, specific sequence differences are described between the 16S rDNA, the 23S rDNA, the 16S–23S rDNA spacer region and the genes of the major cold-shock protein homologue cspA in a variety of psychrotolerant and mesophilic B. cereus and B. mycoides strains. Randomly amplified polymorphic DNA analysis using three different primers clearly separated psychrotolerant strains of both species from the rest of the B. cereus group, as did inverse PCR patterns of the rDNA operons. These data strongly support a hitherto unrecognized fifth sub-group within the B. cereus species group comprising psychrotolerant, but not mesophilic, B. cereus strains. Despite the latter finding, the DNA sequences investigated exhibited a high degree of sequence similarity indicating a close relationship between the species of the B. cereus group. Considering the unusual importance of B. cereus in both food poisoning and food spoilage and to avoid merging all species of the group, a new species, Bacillus weihenstephanensis sp. nov., comprising psychrotolerant ‘cereus’ strains, is proposed. Isolates of the new species grow at 4–7°C but not at 43°C and can be identified rapidly using rDNA or cspA targeted PCR. The type strain is B. weihenstephanensis WSBC 10204T(= DSM 11821T).
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Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium
A syntrophic propionate-oxidizing bacterium, strain MPOBT, was isolated from a culture enriched from anaerobic granular sludge. It oxidized propionate syntrophically in co-culture with the hydrogen- and formate-utilizing Methanospirillum hungateii, and was able to oxidize propionate and other organic compounds in pure culture with sulfate or fumarate as the electron acceptor. Additionally, it fermented fumarate. 16S rRNA sequence analysis revealed a relationship with Syntrophobacter wolinii and Syntrophobacter pfennigii. The G+C content of its DNA was 60·6 mol %, which is in the same range as that of other Syntrophobacter species. DNA-DNA hybridization studies showed less than 26% hybridization among the different genomes of Syntrophobacter species and strain MPOBT. This justifies the assignment of strain MPOBT to the genus Syntrophobacter as a new species. The name Syntrophobacter fumaroxidans is proposed; strain MPOBT (= DSM 10017T) is the type strain.
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Phylogeny and photosynthetic features of Thiobacillus acidophilus and related acidophilic bacteria: its transfer to the genus Acidiphilium as Acidiphilium acidophilum comb. nov.
Phylogenetic analyses based on 16S rDNA sequences and genomic DNA-DNA relatedness showed that the sulphur-oxidizing facultative chemolithotroph Thiobacillus acidophilus was closely related to members of the genus Acidiphilium, which is a group of strictly aerobic, heterotrophic acidophiles now categorized into aerobic photosynthetic bacteria. Lipophilic pigment analyses revealed that zinc-chelated bacteriochlorophyll a and carotenoids occurred in appreciable amounts in T. acidophilus and all established species of the genus Acidiphilium. PCR experiments showed that T. acidophilus as well as Acidiphilium species contained puf genes, encoding the photosynthetic reaction centre proteins and the core light-harvesting complex of the purple bacteria. There were high similarities between T. acidophilus and Acidiphilium species in the primary structure of their reaction centre proteins deduced from the nucleotide sequence data. The phylogenetic tree of the reaction centre proteins was in agreement with the 16S rDNA sequence-based phylogenetic tree in the relationship between T. acidophilus and Acidiphilium species and between the Acidiphilium cluster and other purple photosynthetic bacteria. Based on these results, together with previous phylogenetic and phenotypic information, it is proposed to reclassify T. acidophilus (Guay and Silver) Harrison 1983 as Acidiphilium acidophilum comb. nov. The type strain is ATCC 27807T(= DSM 700T).
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Rickettsia honei sp. nov., the aetiological agent of Flinders Island spotted fever in Australia
More LessThe name Rickettsia honei, strain RBT, has been proposed for a unique spotted fever group (SFG) agent which is pathogenic for humans. This agent has previously been compared to the other SFG agents and was shown to be distinct in protein structure by SDS-PAGE and by immunoblotting. Genetic comparisons of the 16S rRNA, rompA, gltA and the 17 kDa antigen genes with the other SFG rickettsiae confirmed the phylogenetic distance between R. honei and the previously described species. Genetically, Rickettsia honei is more closely related to the Thai tick typhus (TT-118) rickettsia than to any other member of the SFG. Indeed, it is proposed that TT-118 is a strain of R. honei which was previously isolated in Thailand. These results elucidate the presence of a unique SFG rickettsial species in Australasia.
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Flavobacterium hibernum sp. nov., a lactose-utilizing bacterium from a freshwater Antarctic Lake
Four freshwater Antarctic lakes were examined for the presence of β-galactosidase-producing bacteria using mineral medium enrichments and lactose. Enrichments from only one of the lakes produced growth and two strains were isolated that were very similar in phenotype and fatty acid profile, and shared considerable homology in their DNA (DNA–DNA hybridization = 93±7%). The strains were psychrotrophic with theoretical T max, T min and T opt of 30–31, –7 ° and 26 °C, respectively. The β-galactosidase in cell extracts had an optimal activity at 39 C. The strains were Gram-negative rods, showed gliding motility, contained branched and hydroxy fatty acids, and menaquinone 6 as the major respiratory quinone. The strains did not form microcysts and utilized lactose while using ammonium ions as a source of nitrogen, and a range of other sugars. The G+C content of the DNA was 34 mol%. Phylogenetic analysis of one of the strains, by comparison of 16S rDNA sequences, showed that it was most similar, but not identical to, Flavobacterium columnare and ‘[Sporocytophaga] cauliformis’. Both species could be differentiated phenotypically from the Antarctic isolates. DNA–DNA hybridization of the Antarctic isolate with six different members of the Flavobacterium 16S rDNA cluster showed no strain with greater than 18% relatedness. The nearest type species to the Antarctic isolate in the phylogenetic analysis was Flavobacterium aquatile. The name Flavobacterium hibernum is proposed for the Antarctic strains, and the type strain is ATCC 51468T(= ACAM376T).
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Note: Transfer of Pseudomonas nautica to Marinobacter hydrocarbonoclasticus
More LessA combination of genotypic and phenotypic properties (a polyphasic taxonomic approach) was used to determine the relatedness between the type strains of Pseudomonas nautica Bauman et al. 1982 and Marinobacter hydrocarbonoclasticus Gauthier et al. 1992 , which were originally found to be highly related by partial 16S rDNA sequence analysis. Analysis of genotypic properties, such as comparison of the almost complete 16S rDNA sequences, base composition of the total genomic DNA and DNA-DNA hybridization revealed that the two strains were highly similar and should be considered members of the same species. The phenotypic properties, such as the physiology and chemotaxonomic data (i.e. fatty acid composition, polar lipid patterns and respiratory lipoquinone content), confirmed the genotypic evaluation, and has lead to the proposal for a unification of the two species, Pseudomonas nautica (DSM 50418T) and Marinobacter hydrocarbonoclasticus (DSM 8798T) as Marinobacter hydrocarbonoclasticus.
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Note: Corynebacterium kroppenstedtii sp. nov., a novel corynebacterium that does not contain mycolic acids
More LessA strain of a hitherto undescribed coryneform bacterium from human clinical material was characterized by phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequence analysis demonstrated the strain represents a novel and deep lineage within the genus Corynebacterium sensu stricto. Chemical analyses revealed the unidentified strain was unusual in that it lacked mycotic acids. Based on the phylogenetic and phenotypic distinctiveness of the unknown isolate, it is proposed that the bacterium be classified as a new Corynebacterium species, for which the name Corynebacterium kroppenstedtii sp. nov. is proposed. The type strain is CCUG 35717T.
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Note: Rickettsia slovaca sp. nov., a member of the spotted fever group rickettsiae
More LessThe name Rickettsia slovaca sp. nov. (type strain is strain B) is proposed for a member of the spotted fever group (SFG) rickettsiae which was isolated from Dermacentor marginatus ticks in Slovakia in 1968, and was recently implicated in human febrile illness. This rickettsia can be phenotypically distinguished from other SFG rickettsiae by microimmunofluorescence serotyping, SDS-PAGE, Western blotting and mAbs. Genotypic differences between R. slovaca and the other SFG representatives can be demonstrated by PCR-RFLP analysis, pulsed-field gel electrophoresis and sequencing of 16S rRNA, gltA and ompA genes.
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- Validation List
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- Notification List
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- Systematics Of Yeasts
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The yeast genus Starmerella gen. nov. and Starmerella bombicola sp. nov., the teleomorph of Candida bombicola (Spencer, Gorin & Tullock) Meyer & Yarrow
More LessSeven strains of a heterothallic haploid yeast species were isolated from flowers of Calystegia sepium (hedge bindweed, Convolvulaceae) and associated sap beetles of the genus Conotelus. Conjugation was observed between some of the isolates and the type strain of Candida bombicola, resulting in evanescent asci with one ascospore with a convoluted surface. The sequences of the D1/D2 variable domain of the large subunit of the rDNAs of three strains differed by only one or two bases from that of the type strain. The new genus Starmerella, with the single species Starmerella bombicola. is proposed to accommodate the teleomorph of C. bombicola. The designated isotype is strain UWO(PS)97–1181(h-; CBS 84511).
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Debaryomyces prosopidis sp. nov., a yeast from exudates of mesquite trees
More LessNine strains were studied of a new haploid species of the genus Debaryomyces Lodder & Kreger-van Rij that had been isolated from exudates of mesquite (Prosopis juliflora) trees in southern Arizona and from Drosophila carboneria that breeds in these exudates. Their physiological characteristics, life cycle, and nuclear DNA base composition (approx. 37·5 mol% G+C) led to their original classification as Debaryomyces hansenii (Zopf) Kreger-van Rij. However, the two taxa are, at most, distantly related based on DNA reassociation values that indicated low base sequence complementarity. The two taxa also have distinctly different electrophoretic karyotypes. Debaryomyces hansenii has two varieties, D. hansenii var. hansenii and D. hansenii var. fabryi. Debaryomyces prosopidis can be differentiated phenotypically from both varieties by lack of growth on cellobiose after 2 weeks incubation and from the variety hansenii by a higher maximum temperature for growth. The type strain of Debaryomyces prosopidis sp. nov. is strain UCD-FST 84-100T (= DBVPG 7010T = CBS 8450T = ATCC 201611T).
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Trichosporon japonicum sp. nov. isolated from the air
More LessA yeast strain isolated from the air in Japan was found to represent a new species, and was named Trichosporon japonicum. This species produced arthroconidia and appressoria. T. japonicum formed a cluster with the appressorium-forming species Trichosporon inkin and Trichosporon ovoides in a phylogenetic tree constructed using small-subunit rDNA sequences. However, they had low relatedness to each other in DNA–DNA hybridization experiments. T. japonicum is distinguished from both T. inkin and T. ovoides by its ability to assimilate inulin, and its inability to assimilate L-rhamnose. JCM 8357T is the type strain of the species.
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Wickerhamiella australiensis, Wickerhamiella cacticola, Wickerhamiella occidentalis, Candida drosophilae and Candida lipophila, five new related yeast species from flowers and associated insects
Five new yeast species, Wickerhamiella australiensis, Wickerhamiella cacticola, Wickerhamiella occidentalis, Candida drosophilae and Candida lipophila, are described to accommodate isolates recovered from flowers and floricolous insects of Australian Hibiscus trees, cosmopolitan morning glories (Ipomoea spp.) and Brazilian cereoid cacti. The new Wickerhamiella species are heterothallic, occur in the haploid condition and are clearly separated reproductively from one another. Although they exhibit little physiological variation, they are easily delineated from Wickerhamiella domercqiae, the only species known previously, by their resistance to cycloheximide and the production of strong extracellular lipases. C. drosophilae and C. lipophila share the latter property, but unlike the Wickerhamiella species, they fail to utilize nitrate as sole nitrogen source. PFGE indicates that these yeasts have an unusually low number of chromosomes. The large-subunit rDNA (D1/D2) sequences demonstrate a close relationship between the five species and Candida vanderwaltii and Candida azyma. Their relationship with W. domercqiae is more distant, but all share, with some other Candida species, a single monophyletic clade. The type and isotype strains are as follows: W. australiensis strains UWO(PS)95–604.3T(h+; CBS 8456T) and UWO(PS)95–631.31(h+; CBS 84571); W. cacticola strains UFMG96–267T(h+; CBS 84540 and UFMG96–3811(h-; CBS 84551); W. occidentalis strains UWO(PS)91–698.4T(h+; CBS 8452T) and UFMG96–2121 (h-; CBS 84531); C. drosophilae UWO(PS)91–716.3T(CBS 8459T); and C. lipophila UWO(PS)91–681.3T(CBS 8458T).
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Note: DNA hybridization and electrokaryotype study of some Candida species
More LessSome Candida species which were si to each other in phenotypic characteristics were studied by chemotraxonomic and molecular taxonomic comparison including the ubiquinone systems, electrophoretic karyotypes, DNA base composition and DNA relatedness. Candida viswanathii and Candida lodderae showed similar electrophoretic karyotypes and DNA base composition and demonstrated 89 to 90 % DNA relatedness, confirming their synonymy.
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- International Committee On Systematic Bacteriology
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