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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo - Volume 66, Issue 4, 2016

Volume 66, Issue 4

Volume 66, Issue 4, 2016

  • NEW TAXA
    • Other Bacteria

      • gen. nov., sp. nov., a member of the family isolated from guinea pigs ()

        https://doi.org/10.1099/ijsem.0.000922

        A pleomorphic, Gram-stain-negative, rod-shaped, indole-, oxidase- and catalase-negative, non-spore-forming, non-motile bacterium was originally isolated from the mandibular lymph node of a guinea pig and deposited as CCUG 39713 in 1998. A second strain, 151011837, was isolated from an identical lesion in a guinea pig in Germany in 2015. On the basis of 16S rRNA gene sequence analyses, these strains displayed highest sequence similarities with NTS65407 (93.4 %) and ‘’ Sn35 (93.2 %), followed by DSM 12112 (91.3 %), ‘’ OGS16 (91.2 %), AHL370-1 (91.0 %), HKU33 (90.9 %) and 131000547 (90.9 %). Levels of sequence similarity with all other members of the family were < 89 %. Results of phylogenetic analyses of strains CCUG 39713 and 151011837, based on , and nucleotide and deduced amino acid sequences, were highly similar, as the topologies of all trees were virtually identical. DNA relatedness values derived from average nucleotide identities calculated for comparisons between strain CCUG 39713 and the type strains of and , respectively, were 72.05 and 70.42 %. The genomes of CCUG39713 and 151011837 shared 99.57 % average nucletide identity. The chemotaxonomic and physiological data for strains CCUG 39713 and 151011837 were in congruence with other closely related members of the family , with highly similar enzyme activities and fatty acid profiles. Matrix-assisted laser desorption ionization time-of-flight MS analysis was capable of clearly discriminating strains CCUG 39713 and 151011837 from all taxa of the family with validly published names. On the basis of these data, the novel taxon gen. nov., sp. nov. is proposed. The type strain of is CCUG 39713 ( = DSM 101949); 151011837 (DSM 101950) is an additional strain of the species.

    • sp. nov., a sulfur-disproportionating bacterium isolated from a hot spring, and emended description of the genus

      https://doi.org/10.1099/ijsem.0.000947

      A novel autotrophic, thermophilic bacterium, strain TF1, was isolated from a hot spring in Japan. Cells of strain TF1 were motile, Gram-stain-negative, rod-shaped, 1.0–2.0 μm in length and 0.5–0.6 μm in width. Major components in the cellular fatty acid profile were C, C and anteiso-C. The temperature range for growth was 40–77 °C, and optimum temperature was 75 °C. The pH range for growth was 5.9–9.5, and the optimum pH was 7.5–8.8. Strain TF1 grew chemolithoautotrophically by disproportionation of sulfur, thiosulfate and sulfite. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strain belongs to the family . The closest cultivated relative was DS, with highest 16S rRNA gene sequence similarity of 96 %. The genome of strain TF1 consists of one circular chromosome, with a size of 1.8 Mbp and G+C content of 38.30 mol%. On the basis of its phylogenetic and phenotypic properties, strain TF1 ( = DSM 29380 = NBRC 110713) is proposed as the type strain of a novel species, sp. nov.

    • sp. nov. and sp. nov., two tremellaceous yeast species from Brazil

      https://doi.org/10.1099/ijsem.0.000945

      Two yeast species, sp. nov. and sp. nov., in the family Rhynchogastremataceae of the Tremellales are proposed. The two species are related to six species of the genus : , and . The novel species are proposed on the basis of the sequence-based phylogenetic species concept with analysis of the D1/D2 region of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region. A total of 16 strains of sp. nov. were obtained from freshwater and bromeliad leaves collected in Brazil. sp. nov. differs by 11, 12, 16, 14, 11 and 13 substitutions in the D1/D2 domain from the related species , and , respectively. Differences of 11 substitutions and 21 or more substitutions in ITS regions were found when the sequences of sp. nov. were compared with and its closest relatives. The type strain of sp. nov. is UFMG-CM-Y374 ( = CBS 13918). sp. nov. is represented by two strains isolated from a flower of sp. and a water sample in Brazil. sp. nov. differs from the related species and by eight substitutions, from and by 11 substitutions, from by 10 substitutions and from by 6 substitutions in the D1/D2 domain, and by 7 substitutions from and more than 19 substitutions in the ITS region from its closest relatives. The type strain of sp. nov. is CBS 8358 (ML 3666 = DBVPG-4492). The MycoBank numbers for sp. nov. and sp. nov. are MB 813594 and MB 814882, respectively.

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  • EVOLUTION, PHYLOGENY AND BIODIVERSITY

      • Multilocus sequence analysis supports the taxonomic position of symbionts based on DNA–DNA hybridization

        https://doi.org/10.1099/ijsem.0.000862

        In this study, the phylogenetic relationship and taxonomic status of six strains, representing different phenons and genomic groups of symbionts, originating from Poland, were established by comparative analysis of five concatenated housekeeping gene sequences (, , , and ), DNA–DNA hybridization and total DNA G+C content. Maximum-likelihood phylogenetic analysis of combined , , , and sequence data placed the studied bacteria into the clade comprising the genus . In the core gene phylograms, four nodule isolates (AG1, AG7, AG15 and AG27) formed a cluster common with , whereas the two other symbionts (AG17 and AG22) were grouped together with and . The species position of the studied bacteria was clarified by DNA–DNA hybridization. The DNA–DNA relatedness between isolates AG1, AG7, AG15 and AG27 and reference strain USDA 3383 was 76.4–84.2 %, and all these nodulators were defined as members of the genomospecies . DNA–DNA relatedness for isolates AG17 and AG22 and the reference strain ICMP 15022 was 77.5 and 80.1 %, respectively. We propose that the nodule isolates AG17 and AG22 belong to the genomic species . Additionally, it was found that the total DNA G+C content of the six test symbionts was 59.4–62.1 mol%, within the range for species of the genus .

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