- Volume 50, Issue 1, 2000
Volume 50, Issue 1, 2000
- Articles
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Phylogenetic analysis of Saccharothrix and related taxa: proposal for Actinosynnemataceae fam. nov.
More LessPartial sequences for 16S rDNA were determined for strains of the genus Saccharothrix, including most described species, as well as strains of the described species of the related genera Kutzneria, Actinokineospora and Actinosynnema. These were aligned with published sequences for other species of these genera, as well as those of the genera 'Actinoalloteichus', 'Asiosporangium', Lentzea, Kutzneria, Streptoalloteichus and representative taxa from other actinomycete families. Phylogenetic analysis of the sequence data showed that species of the genera Actinokineospora, Actinosynnema, Lentzea and Saccharothrix are members of the same clade, and distinct from the Pseudonocardiaceae. It is proposed that a new family be created within the class Actinobacteria for these genera, to be called the Actinosynnemataceae on the basis of the oldest described genus within this family, Actinosynnema Hasegawa et al. The chemotaxonomic properties of all the genera to be placed within the new family have similar cell wall type (type III), whole-cell sugars (generally galactose although mannose and rhamnose may be present), phospholipid type (PII) and menaquinones [MK-9(H4) predominant].
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Modestobacter multiseptatus gen. nov., sp. nov., a budding actinomycete from soils of the Asgard Range (Transantarctic Mountains).
More LessOligotrophic PYGV medium, inoculated with soils from Linnaeus Terrace (1600 m, Antarctica), yielded four aerobic actinomycetes with short rods, multiple and irregular septa and often motile buds. Cells were 1.0-2.8 x 1.0-3.0 microm and colonies were beige to pink. The isolates were nearly identical in physiological and biochemical tests. Three strains grew from 0 degrees C to 25-28 degrees C, but one was psychrophilic with a maximum growth temperature of 20 degrees C. Carbon sources utilized were D-glucose, D-galactose, lactose, sucrose or mannitol; malate, succinate, fumarate, pyruvate or glutarate were decarboxylated aerobically. Peptone and yeast extract were the preferred nitrogen sources. Nitrate was reduced aerobically or anaerobically. Cell walls contained meso-diaminopimelic acid, glutamate, alanine, glycine, galactose, glucose and ribose. Major fatty acids of strains AA-802, -824, -825 and -826T were n18:1, i16:0 and ai17:0. Major respiratory quinones were MK-9(H4) and MK-8(H4). Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. Phosphatidylglycerol was found in most strains. The DNA G+C contents were 68-70 mol%. In 16S rDNA analyses, similarity values obtained for 500 nucleotides from the 5' terminus were > 99.5%. Almost complete sequences from AA-826T and -825 were 99.9% similar. Strain AA-826T belonged to a novel cluster of desert soil and rock isolates within the Geodermatophilaceae and was equidistantly related to members of Geodermatophilus and to a Blastococcus lineage. The four isolates represent a new genus, Modestobacter gen. nov., with Modestobacter multiseptatus sp. nov. as the type species. The type strain, Modestobacter multiseptatus AA-826T, was deposited in the DSMZ as DSM 44406T.
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Corynebacterium simulans sp. nov., a non-lipophilic, fermentative Corynebacterium.
P Wattiau, M Janssens and G WautersThree coryneform strains isolated from clinical samples were analysed. These strains fitted the biochemical profile of Corynebacterium striatum by conventional methods. However, according to recently described identification tests for fermenting corynebacteria, the strains behaved rather like Corynebacterium minutissimum. The three isolates could be distinguished from C. minutissimum by a positive nitrate and nitrite reductase test and by not fermenting maltose; from C. striatum by their inability to acidify ethylene glycol and to grow at 20 degrees C. Genetic studies based on 16S rRNA showed that the three strains were in fact different from C. minutissimum and C. striatum (96.9 and 98% similarity, respectively) and from other corynebacteria. They represent a new species for which the name Corynebacterium simulans sp. nov. is proposed. The type strain is DSM 44415T (= UCL 553T = Co 553T).
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Frigoribacterium faeni gen. nov., sp. nov., a novel psychrophilic genus of the family Microbacteriaceae.
The taxonomic position of five actinobacterial strains isolated from dust, an animal shed, the air inside a museum and soil was investigated using a polyphasic approach. The growth characteristics were unusual for actinomycetes. Optimal growth was at temperatures ranging from 2 to 10 degrees C. After small-step adaptation (5 degrees C steps) to higher temperatures, the strains were also able to grow at 20 degrees C. Cell wall analyses revealed that the organisms showed a hitherto undescribed, new group B-type peptidoglycan [type B2beta according to Schleifer & Kandler (1972), but with lysine instead of ornithine]. All strains contained menaquinone MK-9. Mycolic acids were not detected. Diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid were detected in the polar lipid extracts. The main fatty acids were 12-methyl-tetradecanoic acid (15:0 anteiso), 12-methyl-tetradecenoic acid (15:1 anteiso), 14-methyl-pentadecanoic acid (16:0 iso) and 14-methyl-hexadecanoic acid (17:0 iso), as well as an unusual compound identified as 1,1-dimethoxy-anteiso-pentadecane (15:0 anteiso-DMA). The G+C content of DNA was approximately 71 mol%. The results of 16S rRNA gene sequence comparisons revealed that the strains represent a new lineage in the suborder Micrococcineae and the family Microbacteriaceae of the order Actinomycetales. On the basis of these results the new genus Frigoribacterium gen. nov. is proposed, harbouring the new species Frigoribacterium faeni sp. nov. (type strain = 801T = DSM 10309T).
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The genus Abiotrophia (Kawamura et al.) is not monophyletic: proposal of Granulicatella gen. nov., Granulicatella adiacens comb. nov., Granulicatella elegans comb. nov. and Granulicatella balaenopterae comb. nov.
More LessThe genus Abiotrophia currently includes four species, Abiotrophia defectiva, Abiotrophia adiacens, Abiotrophia balaenopterae and Abiotrophia elegans. Recent 16S rRNA gene sequencing studies have demonstrated that the genus is not monophyletic and is in need of taxonomic revision. Phylogenetically, the genus Abiotrophia consists of two distinct lines, A. defectiva, the type species of the genus, and a robust group consisting of A. adiacens, A. balaenopterae and A. elegans. Therefore, it is formally proposed that the genus Abiotrophia should be restricted to A. defectiva and that A. adiacens, A. balaenopterae and A. elegans should be reclassified in a new genus, Granulicatella, as Granulicatella adiacens comb. nov., Granulicatella balaenopterae comb. nov. and Granulicatella elegans comb. nov.
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Leifsonia poae gen. nov., sp. nov., isolated from nematode galls on Poa annua, and reclassification of 'Corynebacterium aquaticum' Leifson 1962 as Leifsonia aquatica (ex Leifson 1962) gen. nov., nom. rev., comb. nov. and Clavibacter xyli Davis et al. 1984 with two subspecies as Leifsonia xyli (Davis et al. 1984) gen. nov., comb. nov.
More LessThe new genus Leifsonia gen. nov. with two new species, Leifsonia poae sp. nov. (type strain VKM Ac-1401T) and Leifsonia aquatica (ex Leifson 1962) nom. rev., comb. nov. (the type species, with VKM Ac-1400T = DSM 20146T = JCM 1368T as type strain), is proposed to accommodate bacteria found in Poa annua root gall, induced by the nematode Subanguina radicicola, and 'Corynebacterium aquaticum' Leifson 1962. Further, it is proposed to reclassify Clavibacter xyli Davis et al. 1984 with two subspecies in the new genus as Leifsonia xyli (Davis et al. 1984) comb. nov., Leifsonia xyli subsp. xyli (Davis et al. 1984) comb. nov. and Leifsonia xyli subsp. cynodontis (Davis et al. 1984) comb. nov. Members of the proposed genus are characterized by coryneform morphology, peptidoglycans based upon 2,4-diaminobutyric acid, the major menaquinone MK-11, phosphatidylglycerol and diphosphatidylglycerol as principal phospholipids, the high content of anteiso- and iso-branched saturated fatty acids, and a DNA G+C base composition of 66-73 mol%. They form a distinct phylogenetic branch attached to the line of descent of Agromyces spp. The new and reclassified species of the new genus clearly differ from each other phylogenetically and phenetically and can be recognized by their morphologies, the cell wall sugar composition, the requirement of complex media for growth, and numerous physiological characteristics, including the oxidase reaction.
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Trichosporon veenhuisii sp. nov., an alkane-assimilating anamorphic basidiomycetous yeast.
More LessA morphological and physiological description of an alkane-assimilating anamorphic basidiomycetous yeast species, named Trichosporon veenhuisii, is presented. The ability to assimilate several aliphatic and aromatic compounds as sole source of carbon and energy is reported. The phylogenetic position within the genus, based on nuclear base sequencing of the D1/D2 region of the large subunit of rDNA, is discussed. The type strain is CBS 7136T.
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Candida tartarivorans sp. nov., an anamorphic ascomycetous yeast with the capacity to degrade L(+)- and meso-tartaric acid.
More LessAn undescribed anamorphic yeast species of ascomycetous affinity, for which the name Candida tartarivorans is proposed, was isolated from dried wine lees in Portugal using a selective medium with L(+)-tartaric acid as the sole source of carbon and energy. The single isolate (IGC 4854T) showed the following characteristics: sympodial holoblastic conidiogenesis, absence of asci with ascospores, a negative colour reaction with Diazonium Blue B, production of elaborate pseudomycelium and ability to grow with inositol as sole source of carbon. Analysis of the physiological data pointed to a close relationship with other inositol-assimilating taxa, namely the genera Arxula, Stephanoascus, Sympodiomyces, Zygoascus and selected Candida species. Comparative analysis of the D1/D2 variable domain of the 26S rRNA gene of all available sequences for ascomycetous yeasts showed that strain IGC 4854T did not match with any other species in the database. The closest relative was Candida auringiensis Santa Maria, but the two species differed in 24 nucleotide positions. A description of the new species is given.
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Four new yeasts in the Pichia anomala clade.
More LessFour new yeasts are described that were recognized as novel from nucleotide substitutions in domain D1/D2 of 26S rDNA, a region that is sufficiently divergent to allow resolution of most ascomycetous yeast species. The new species and their type strains are as follows: Pichia maclurae NRRL Y-5377T (= CBS 8671T); Pichia misumaiensis NRRL Y-17389T (= CBS 8062T); Candida mycetangii NRRL Y-6843T (= CBS 8675T); and Candida ulmi NRRL YB-2694T (= CBS 8670T). The two Pichia species form spherical ascospores and are heterothallic. Phylogenetic analysis of domain D1/D2 sequences placed the four new species in the Pichia anomala clade.
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Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene.
C Belloch, A Querol, M D García and E BarrioA phylogenetic analysis of 17 species belonging to the genus Kluyveromyces and 12 reference and outgroup species was performed using mitochondrial cytochrome-c oxidase II gene sequences. The genus Kluyveromyces appears as a polyphyletic taxon formed by species included within the following four main groups. The Kluyveromyces phaffii group encompasses the species Kluyveromyces blattae, K. phaffii and Kluyveromyces yarrowii. The Kluyveromyces marxianus group is a monophyletic group consisting of the species Kluyveromyces aestuarii, Kluyveromyces dobzhanskii, Kluyveromyces lactis, K. marxianus and Kluyveromyces wickerhamii. The monophyletic Kluyveromyces thermotolerans group is formed by K. thermotolerans, Kluyveromyces waltii and Saccharomyces kluyveri (which appears in the mitochondrial tree as the sister clade of the K. marxianus group). Finally, the Saccharomyces cerevisiae group contains the remaining Kluyveromyces species, as well as the reference Saccharomyces species (sensu lato and sensu stricto) and Candida glabrata (the phylogenetic relationships within this group are unclear according to the bootstrap test). The phylogenetic relationships obtained for this mitochondrial gene are, for the most part, congruent with previous trees based on nuclear rRNA sequences, except for the position of K. yarrowii and the close relationship between the K. marxianus and K. thermotolerans groups. These differences, as well as the existence of these groups, are discussed in the context of previous studies based on phenotypic, genetic and molecular data. Although additional studies are required to decipher the phylogenetic relationships between the genus Kluyveromyces and the closely related genera Saccharomyces, Torulaspora and Zygosaccharomyces, future changes to their taxonomic status should take account of the existence of these four groups of Kluyveromyces species.
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Taxonomic relationships among the taxa in the Candida guilliermondii complex, as revealed by comparative electrophoretic karyotyping.
More LessElectrophoretic karyotypes of 15 type strains of the taxa in the Candida guilliermondii complex including Candida fukuyamaensis Nakase et al. and Candida xestobii Yarrow et S. A. Meyer were comparatively analysed by using the CHEF (contour-clamped homogeneous electric field) method of PFGE. Eighteen strains (isolated from various natural sources in China) which were originally identified as C. guilliermondii by conventional methods were also included. Six electrophoretic karyotype groups were recognized among the strains compared. The following type strains were grouped together with the type strains of C. guilliermondii (Castellani) Langeron et Guerra and Pichia guilliermondii Wickerham: Blastodendrion arztii Ota, Blastodendrion krausi Ota, Candida amidovorans Balloni et al., C. guilliermondii var. japonica Sugiyama et Goto, Candida mamillae S. Goto, Candida parapsilosis (Ashford) Langeron et Talice var. tokyoensis Suzuki et al., C. parapsilosis var. tuxtlensis Herrera et al. and six Chinese strains. The type strain of Torulopsis kestonii Scarr et Rose was classified into the group together with the type strain of Candida fermentati (Saito) Bai and seven Chinese strains. The group represented by the type strain of C. fukuyamaensis included five other strains isolated in China. The type strains of Candida xestobii, C. guilliermondii var. carpophila Phaff et M. W. Miller and Trichosporon appendiculare Batista et al. were separated into three different groups, respectively. Taxonomic relationships among the taxa studied are discussed.
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Volumes and issues
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Volume 74 (2024)
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