- Volume 63, Issue Pt_8, 2013
Volume 63, Issue Pt_8, 2013
- New Taxa
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- Proteobacteria
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Proposal for a new class within the phylum Proteobacteria , Acidithiobacillia classis nov., with the type order Acidithiobacillales , and emended description of the class Gammaproteobacteria
More LessThe order Acidithiobacillales was previously assigned to the class Gammaproteobacteria . Recent analyses have indicated that this order actually lies outside all the proteobacterial classes, as a sister group to the combined classes Betaproteobacteria and Gammaproteobacteria . We now confirm this result with multiprotein phylogenetic analysis of all the available genomes of members of the order Acidithiobacillales and representatives of all available bacterial orders, and propose the new proteobacterial class, Acidithiobacillia, with the type order Acidithiobacillales , comprising the families Acidithiobacillaceae and Thermithiobacillaceae with the type genus Acidithiobacillus .
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Martelella endophytica sp. nov., an antifungal bacterium associated with a halophyte
More LessA Gram-staining-negative, non-spore-forming endophytic bacterium, designated strain YC6887T, was isolated from a root sample of a halophyte, Rosa rugosa, collected from a tidal flat area of Namhae Island, located at the southern end of Korea. Strain YC6887T was found to exhibit inhibitory activity against oomycete plant pathogens. The cells were non-motile and aerobic rods. The strain was able to grow at 4–40 °C (optimum 28–30 °C) and at pH 5.0–9.0 (optimum pH 7.0–8.5). Strain YC6887T was able to grow at NaCl concentrations of 0–9 % (w/v) with optimum growth at 4–5 % (w/v) NaCl, but NaCl is not essential for growth. Comparison of 16S rRNA gene sequences showed that the strain was a member of the genus Martelella , a member of order Rhizobiales , exhibiting highest similarity with Martelella mediterranea (98.6 %). The DNA–DNA relatedness between strain YC6887T and M. mediterranea MACL11T was 19.8±6.8. Chemotaxonomically, strain YC6887T contained C19 : 0 cyclo ω8c (28.0 %) and C18 : 1ω7c (17.9 %) as predominant fatty acids, confirming the affiliation of strain YC6887T with the genus Martelella . The major respiratory quinone was Q-10 and the DNA G+C content was 62.1 mol%. On the basis of phylogenetic analysis, physiological and biochemical characterization and DNA–DNA hybridization data, strain YC6887T should be classified as representing a novel species of the genus Martelella , for which the name Martelella endophytica sp. nov. is proposed. The type strain is YC6887T ( = KCCM 43011T = NBRC 109149T).
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Acinetobacter puyangensis sp. nov., isolated from the healthy and diseased part of Populus ×euramericana canker bark
Two Gram-negative, non-motile, rod-shaped strains, BQ4-1T and NHI3-2, isolated respectively from the healthy and diseased part of Populus ×euramericana canker bark, were characterized using a polyphasic approach. Chemotaxonomic characterization supported the inclusion of the two strains in the genus Acinetobacter , with genomic DNA G+C contents (42.5–43 mol%) within the range observed for this genus (38–47 mol%) and 9-octadecenoic acid (C18 : 1ω9c, 39.87 %), hexadecanoic acid (C16 : 0, 11.26 %) and summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c, 18.90 %) as major fatty acids. Phylogenetic analysis based on 16S rRNA, rpoB and gyrB gene sequences revealed that strains BQ4-1T and NHI3 did not cluster with any species with validly published names, and formed a distinct cluster with 99–100 % bootstrap support on three phylogenetic trees within the genus Acinetobacter . Acid was not produced from d-glucose, and haemolysis was not observed on agar media supplemented with sheep erythrocytes. On the basis of phenotypic, genotypic and phylogenetic characteristics, the two strains are considered to represent a novel species of the genus Acinetobacter , for which the name Acinetobacter puyangensis sp. nov. is proposed. The type strain is BQ4-1T ( = CFCC 10780T = JCM 18011T).
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Thioclava dalianensis sp. nov., isolated from surface seawater
More LessA taxonomic study was carried out on strain DLFJ1-1T, which was isolated from an oil-degrading bacterial consortium, enriched by the surface seawater from around the Dalian Peninsula. The isolate was Gram-reaction-negative, oxidase- and catalase-positive, short-rod-shaped and non-motile. Growth was observed at salinities from 0.5 to 15 % and at temperatures from 4 to 37 °C; the strain was unable to degrade gelatin or to reduce nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DLFJ1-1T belonged to the genus Thioclava , with the highest sequence similarity (96.4 %) to Thioclava pacifica TL 2T, while the similarities to other species examined were all below 95.0 %. The principal fatty acids were C19 : 0ω8c cyclo and summed feature 8 (C18 : 1ω7c/ω6c). The major quinone of strain DLFJ1-1T was Q10. The major polar lipids of strain DLFJ1-1T were phosphatidylethanolamine and phosphatidylglycerol. The G+C content of the chromosomal DNA was 62.5 mol%. The combined genotypic and phenotypic data show that strain DLFJ1-1T represents a novel species of the genus Thioclava , for which the name Thioclava dalianensis sp. nov. is proposed, with the type strain DLFJ1-1T ( = CGMCC 1.12325T = LMG 27290T = MCCC 1A03957T). An emended description of the genus Thioclava is also proposed.
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Vogesella fluminis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella
More LessA bacterial strain designated Npb-07T was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Strain Npb-07T was Gram-negative, aerobic, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 10–37 °C (optimum, 20–30 °C), at pH 6.0–9.0 (optimum, pH 6.0–7.0) and with 0–1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain Npb-07T belonged to the genus Vogesella and its most closely related neighbour was Vogesella indigofera ATCC 19706T with sequence similarity of 98.4 %. The major fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c, 44.4 %) and C16 : 0 (31.9 %). The major respiratory quinone was Q-8. The DNA G+C content of the genomic DNA was 65.3 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two uncharacterized aminophospholipids and an uncharacterized phospholipid. The DNA–DNA relatedness of strain Npb-07T with respect to V. indigofera ATCC 19706T was less than 70 %. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain Npb-07T represents a novel species in the genus Vogesella , for which the name Vogesella fluminis sp. nov. is proposed. The type strain is Npb-07T ( = LMG 26669T = BCRC 80377T = KCTC 23713T).
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Rhodospirillum oryzae sp. nov., a phototrophic bacterium isolated from rhizosphere soil of paddy
More LessA reddish-brown bacterium, designated strain JA318T, was purified from a photoheterotrophic enrichment culture obtained from the rhizosphere soil of paddy. Cells of strain JA318T are spiral shaped, Gram-stain-negative and motile by means of amphitrichous flagella. Strain JA318T has no NaCl requirement for growth but can tolerate up to 1.5 % (w/v) NaCl. Internal photosynthetic membranes are present as lamellar stacks. Photoorganoheterotrophy is the only growth mode observed. Strain JA318T contains bacteriochlorophyll a, lycopene and rhodopin as major carotenoids. Thiamine, niacin and para-aminobenzoic acid (PABA) are required as growth factors. Major fatty acids are C18 : 1ω7c and C16 : 0. Ubiquinone-8 and rhodoquinone-8 are the observed quinones. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified aminolipid are the major polar lipids in strain JA318T. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain JA318T clustered with species of the genus Rhodospirillum which belongs to the class Alphaproteobacteria . The highest sequence similarity of strain JA318T was found with Rhodospirillum sulfurexigens JA143T (99.9 %). The DNA–DNA reassociation values of strain JA318T with Rsp. sulfurexigens JA143T and Rhodospirillum photometricum DSM 122T were 52±2 % and 45±1 %, respectively. The genomic DNA G+C content of strain JA318T was 60.2 mol%. Based on the morphological, physiological, chemotaxonomical and molecular evidence, strain JA318T is significantly different from the type strains of species of the genus Rhodospirillum , of the family Rhodospirillaceae , and it is proposed that the strain be classified as a representative of a novel species for which the name Rhodospirillum oryzae sp. nov. is proposed. The type strain is JA318T ( = KCTC 5960T = NBRC 107573T).
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Devosia submarina sp. nov., isolated from deep-sea surface sediments
More LessThe taxonomic status of two aerobic, Gram-stain-negative, orange–reddish pigmented, motile, rod-shaped bacteria, designated KMM 9415T and KMM 9416, isolated from a deep surface-sediment sample from the Sea of Japan, was defined. Comparative 16S rRNA gene sequence analysis of strains KMM 9415T and KMM 9416 revealed their affiliation to the genus Devosia with a high sequence similarity of 98.5 % to both Devosia psychrophila DSM 22950T and Devosia glacialis LMG 26051T. The novel strains were characterized by the predominance of the fatty acid C18 : 1ω7c followed by C16 : 1 and C16 : 0. The major isoprenoid quinone was Q-10 and the polar lipids comprised phosphatidylglycerol, phosphatidic acid and unknown glycolipids. The DNA–DNA hybridization value of 88 % between the novel strains KMM 9415T and KMM 9416 confirmed their assignment to the same species. The values of DNA relatedness determined for strain KMM 9415T and the closely related strains D. psychrophila DSM 22950T and D. glacialis LMG 26051T were 21 % and 23 %, respectively. Based on distinctive phenotypic characteristics, phylogenetic analysis and DNA–DNA relatedness, it can be concluded that the novel strains KMM 9415T and KMM 9416 represent a novel species within the genus Devosia , for which the name Devosia submarina sp. nov. is proposed. The type strain is the strain KMM 9415T ( = NRIC 0884T = JCM 18935T).
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- Errata
- Taxonomic Note
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Multilocus sequence analysis and 16S rRNA gene sequencing reveal that Yersinia frederiksenii genospecies 2 is Yersinia massiliensis
More LessSince Yersinia frederiksenii was first described in 1980, it has been recognized genotypically as a heterogeneous species, comprising three phenotypically indistinguishable genospecies. In this study, the sequence of the 16S rRNA gene and the concatenated sequences of six housekeeping genes (glnA, gyrB, hsp60, recA, rpoB and sodA) of all the currently known species of the genus Yersinia were used to determine the phylogenetic position of Y. frederiksenii genospecies 2 in the genus Yersinia . The phylogenetic analyses grouped the Y. frederiksenii genospecies 2 strains in a monophyletic group together with representative strains of Yersinia massiliensis . Moreover, the Y. frederiksenii genospecies 2 strains were also grouped apart from the other species of the genus Yersinia and far from the other two genospecies of Y. frederiksenii . All of the observations made in this study support the conclusion that Y. frederiksenii genospecies 2 should be reclassified as Y. massiliensis .
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Volumes and issues
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Volume 74 (2024)
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Volume 69 (2019)
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