- Volume 59, Issue 12, 2009
Volume 59, Issue 12, 2009
- Notification List
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Notification that new names and new combinations have appeared in volume 59, part 9, of the IJSEM
This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission.
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- Taxonomic Note
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Falsibacillus pallidus to replace the homonym Bacillus pallidus Zhou et al. 2008
More LessThe prokaryotic species name Bacillus pallidus Zhou et al. 2008 is illegitimate because it is a later homonym of the name Bacillus pallidus Scholz et al. 1988 (Bacteria, Firmicutes, Bacillales, Bacillaceae, Bacillus). Although Bacillus pallidus Scholz et al. 1988 was transferred to the genus Geobacillus as Geobacillus pallidus comb. nov. in 2004, the species name Bacillus pallidus Scholz et al. 1988 remains validly published and has priority at that position [Principle 8 of the Bacteriological Code (1990 Revision)]. In order to solve this problem, a new name was sought for this taxon, represented by the type strain CW 7T. In addition, the placement of this species in the genus Bacillus was reassessed. The data collected were re-examined as part of a taxonomic study using a polyphasic approach. It was concluded, primarily based on the chemotaxonomic data, that strain CW 7T did not belong to the genus Bacillus, but should be placed in a new genus, for which the name Falsibacillus gen. nov. is proposed. The genus currently comprises a single species, Falsibacillus pallidus comb. nov. represented by the type strain CW 7T (=KCTC 13200T=CCTCC AB 207188T=LMG 24451T).
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- New Taxa
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- Actinobacteria
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Prauserella salsuginis sp. nov., Prauserella flava sp. nov., Prauserella aidingensis sp. nov. and Prauserella sediminis sp. nov., isolated from a salt lake
More LessStrains YIM 90625T, YIM 90630T, YIM 90636T and YIM 90694T were isolated from a salt lake in Xinjiang province, north-west China, and were subjected to a polyphasic analysis to determine their taxonomic positions. All isolates were moderately halophilic and were able to grow at NaCl concentrations up to 15 or 20 % (w/v). The genomic DNA G+C contents of the strains ranged from 69.1 to 70.1 mol%. Based on the results of 16S rRNA gene sequence analysis, DNA–DNA relatedness, phenotypic characteristics and chemotaxonomic data, the isolates are proposed to represent four novel species of the genus Prauserella for which the names Prauserella salsuginis sp. nov. (type strain YIM 90625T=CCTCC AA 208051T=DSM 45264T), Prauserella flava sp. nov. (type strain YIM 90630T=CCTCC AA 208052T=DSM 45265T), Prauserella aidingensis sp. nov. (type strain YIM 90636T=CCTCC AA 208053T=DSM 45266T) and Prauserella sediminis sp. nov. (type strain YIM 90694T=CCTCC AA 208054T=DSM 45267T).
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Saccharopolyspora tripterygii sp. nov., an endophytic actinomycete isolated from the stem of Tripterygium hypoglaucum
More LessAn endophytic actinomycete, designated strain YIM 65359T, was isolated from a surface-sterilized stem sample of Tripterygium hypoglaucum collected from Yunnan province, south-west China. The morphological and chemotaxonomic properties of the new isolate were consistent with those of members of the genus Saccharopolyspora. Analysis of 16S rRNA gene sequences revealed that the new isolate was most closely related to ‘Saccharopolyspora endophytica’ YIM 61095 (98.6 %), Saccharopolyspora flava AS4.1520T (97.6 %) and Saccharopolyspora spinosa DSM 44228T (97.0 %). The results of DNA–DNA hybridizations (57.5 %, 44.9 % and 48.5 %, respectively) with the above micro-organisms, in combination with differences in the biochemical and physiological characteristics, suggested that strain YIM 65359T should be classified as a novel species of the genus Saccharopolyspora. The name Saccharopolyspora tripterygii sp. nov. is proposed for this novel species, with YIM 65359T (=CCTCC AA 208062T=DSM 45269T) as the type strain.
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Nocardioides ginsengisoli sp. nov., isolated from soil of a ginseng field
More LessA Gram-positive, rod-shaped, non-spore-forming bacterium (Gsoil 1124T) was isolated from soil of a ginseng field of Pocheon province in South Korea, and was characterized in order to determine its taxonomic position. On the basis of 16S rRNA gene sequence similarity, strain Gsoil 1124T was shown to belong to the family Nocardioidaceae and related to Nocardioides simplex (98.2 % 16S rRNA gene sequence similarity), Nocardioides aromaticivorans (98.1 %), Nocardioides nitrophenolicus (97.7 %) and Nocardioides kongjuensis (97.5 %). The sequence similarity with any other species with validly published names within the genus Nocardioides was less than 94.5 %. Strain Gsoil 1124T was characterized chemotaxonomically as having ll-2,6-diaminopimelic acid in the cell-wall peptidoglycan, MK-8(H4) as the predominant menaquinone and iso-C16 : 0, C18 : 0, C16 : 0, and C18 : 1 ω9c as the major fatty acids. The G+C content of the genomic DNA was 70.2 mol%. The chemotaxonomic properties and phenotypic characteristics supported the affiliation of strain Gsoil 1124T to the genus Nocardioides. The results of physiological and biochemical tests, and the low level of DNA–DNA relatedness allowed genotypic differentiation of strain Gsoil 1124T from recognized Nocardioides species. Therefore, strain Gsoil 1124T is considered to represent a novel species, for which the name Nocardioides ginsengisoli sp. nov. is proposed, with the type strain Gsoil 1124T (=KCTC 19135T=CCUG 52478T=DSM 17921T).
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Streptomyces thinghirensis sp. nov., isolated from rhizosphere soil of Vitis vinifera
A novel actinomycete, strain S10T, was isolated from rhizosphere soil of wild Vitis vinifera in Thinghir, Ouarzazate Province, Southern Morocco. The taxonomic status of this strain was established using a polyphasic approach. Strain S10T had white–grey aerial mycelium with long, spiral spore chains bearing smooth surfaced spores and produced a yellow diffusible pigment. Chemotaxonomic analyses showed that the cell wall of strain S10T contained ll-diaminopimelic acid and glycine. Phylogenetic analysis based on the almost complete 16S rRNA gene sequence indicated that strain S10T belonged to the Group I streptomycetes, branching off next to Streptomyces marokkonensis LMG 23016T from the Streptomyces violaceoruber group. DNA–DNA relatedness and phenotypic data distinguished strain S10T from the phylogenetically closest related type strains. It is therefore proposed that strain S10T (=CCMM B35T=DSM 41919T) represents the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces thinghirensis sp. nov. is proposed.
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Actinocatenispora rupis sp. nov., isolated from cliff soil, and emended description of the genus Actinocatenispora
More LessA novel actinomycete, designated strain CS5-AC17T, was isolated from cliff soil in the Republic of Korea. Cells of the organism were aerobic and catalase- and oxidase-negative. Substrate mycelium was well developed and was pale to strong yellow. Spore chains were borne on rudimentary aerial mycelium. The spores (0.4–0.5×0.9–1.6 μm) were smooth surfaced and cylindrical. Growth occurred at 25–42 °C, at pH 5.1–12.1 and in the presence of up to 4 % NaCl. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the isolate was closely related to members of the genus Actinocatenispora in the family Micromonosporaceae. The phylogenetic neighbours were Actinocatenispora thailandica TT2-10T (97.7 % 16S rRNA gene sequence similarity) and Actinocatenispora sera KV-744T (97.6 %). The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. The major respiratory quinones were MK-9(H4), MK-9(H6) and MK-9(H8). The polar lipids contained phosphatidylethanolamine and phosphatidylinositol with a small amount of phosphatidylglycerol. The DNA G+C content was 74.3 mol%. DNA–DNA relatedness values between strain CS5-AC17T and its phylogenetically closest relatives were 6.1–7.1 % (A. thailandica DSM 44816T) and 21.5–27.6 % (A. sera NRRL B-24477T). On the basis of the phenotypic features and the DNA–DNA hybridization data, strain CS5-AC17T (=DSM 45178T=NRRL B-24660T) represents a novel species of the genus Actinocatenispora, for which the name Actinocatenispora rupis sp. nov. is proposed.
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Hoyosella altamirensis gen. nov., sp. nov., a new member of the order Actinomycetales isolated from a cave biofilm
A novel actinomycete, strain OFN S31T, was isolated from a complex biofilm in the Altamira Cave, Spain. A polyphasic study was carried out to clarify the taxonomic position of this strain. Phylogenetic analysis with 16S rRNA gene sequences of representatives of the genera Corynebacterium, Dietzia, Gordonia, Millisia, Mycobacterium, Nocardia, Rhodococcus, Segniliparus, Skermania, Tsukamurella and Williamsia indicated that strain OFN S31T formed a distinct taxon in the 16S rRNA gene tree that was more closely associated with the Mycobacterium clade. The type strain of Mycobacterium fallax was the closest relative of strain OFN S31T (95.6 % similarity). The cell wall contained meso-diaminopimelic acid, arabinose and galactose, which are characteristic components of cell-wall chemotype IV of actinomycetes. The sugars of the peptidoglycan were acetylated. The polar lipid pattern was composed of phosphatidylinositol, phosphatidylglycerol, phosphatidylethanolamine and diphosphatidylglycerol. Strain OFN S31T is characterized by the absence of mycelium and mycolic acids. Strain OFN S31T had MK-8 as the major menaquinone. The DNA G+C content was 49.3 mol%, the lowest found among all taxa included in the suborder Corynebacterineae. Based on morphological, chemotaxonomic, phenotypic and genetic characteristics, strain OFN S31T is considered to represent a novel species of a new genus, for which the name Hoyosella altamirensis gen. nov., sp. nov. is proposed. The type strain of Hoyosella altamirensis is strain OFN S31T (=CIP 109864T =DSM 45258T).
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Herbidospora osyris sp. nov., isolated from surface-sterilized tissue of Osyris wightiana Wall. ex Wight
More LessAn endophytic actinomycete, strain YIM 65070T, was isolated from surface-sterilized tissue of Osyris wightiana Wall. ex Wight collected from Yunnan province, south-west China, and characterized by using a polyphasic approach. Strain YIM 65070T had morphological and chemotaxonomic markers that were consistent with its classification in the genus Herbidospora. Phylogenetic analysis based on almost complete 16S rRNA gene sequences indicated that strain YIM 65070T was phylogenetically very closely related to Herbidospora cretacea IFO 15474T. DNA–DNA hybridization experiments confirmed the separate genomic status of strains YIM 65070T and H. cretacea DSM 44071T. Moreover, strain YIM 65070T could be distinguished from H. cretacea DSM 44071T by differences in several phenotypic characteristics such as tolerance to NaCl, degradation activity, utilization of sole carbon and nitrogen sources and the cellular fatty acid contents. On the basis of phenotypic and phylogenetic evidence, strain YIM 65070T was identified as a novel species of the genus Herbidospora, for which the name Herbidospora osyris sp. nov. is proposed, with YIM 65070T (=CCTCC AA 208019T=DSM 45214T) as the type strain.
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Microbispora siamensis sp. nov., a thermotolerant actinomycete isolated from soil
More LessAn actinomycete, strain DMKUA 245T, isolated from soil, was investigated using a polyphasic approach. The isolate formed longitudinally paired spores on the tips of short sporophores that branched alternately from aerial hyphae. The morphological and chemotaxonomic properties clearly demonstrated that the new isolate belonged to the genus Microbispora. 16S rRNA gene sequence analysis supported the assignment of the novel strain to the genus Microbispora. The gene sequence similarity values between the novel strain and the closely related species Microbispora corallina, Microbispora rosea subsp. rosea, Microbispora rosea subsp. aerata and Microbispora amethystogenes were 98.4 %, 97.4 %, 97.0 % and 96.9 %, respectively. The DNA–DNA hybridization values and some physiological and biochemical properties indicated that strain DMKUA 245T could be distinguished from its phylogenetically closest relatives. Based on these genotypic and phenotypic data, strain DMKUA 245T represents a novel species in the genus Microbispora for which the name Microbispora siamensis sp. nov. is proposed. The type strain is strain DMKUA 245T (=BCC 14407T=NBRC 104113T). In addition, DNA–DNA relatedness values in reciprocal hybridization experiments showed that M. amethystogenes was a separate genomic species from M. rosea subsp. rosea. A combination of genotypic and phenotypic data supported the classification of M. amethystogenes as a separate species.
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Kineosporia mesophila sp. nov., isolated from surface-sterilized stems of Tripterygium wilfordii
More LessAn endophytic actinomycete strain, designated YIM 65293T, was isolated from a surface-sterilized stem sample of Tripterygium wilfordii collected from Yunnan province, south-west China, and its taxonomic position was investigated. The chemical and morphological properties of the organism were consistent with those of the genus Kineosporia. Phylogenetic analysis indicated that the levels of 16S rRNA gene sequence similarity between strain YIM 65293T and other type strains of recognized members of the genus Kineosporia were 97.0–98.2 %. However, the DNA–DNA hybridization values, in combination with differences in phenotypic characteristics, revealed that the strain differed from recognized species of the genus Kineosporia. Therefore, strain YIM 65293T represents a novel species of the genus Kineosporia, for which the name Kineosporia mesophila sp. nov. is proposed. The type strain is YIM 65293T (=CCTCC AA 208061T=DSM 45271T).
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Gordonia hankookensis sp. nov., isolated from soil
More LessA Gram-positive, aerobic and non-motile bacterial strain, designated ON-33T, was subjected to a study based on a polyphasic approach to determine its exact taxonomic position. Strain ON-33T grew optimally at pH 7.0–7.5 and 30 °C. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain ON-33T fell within the clade comprising Gordonia species, clustering with Gordonia soli CC-AB07T, with which it exhibited 16S rRNA gene sequence similarity of 98.5 %. The chemotaxonomic properties of strain ON-33T were consistent with those shared by members of the genus Gordonia. The peptidoglycan type was based on meso-diaminopimelic acid and the whole-cell sugars were arabinose and galactose. The predominant menaquinone was MK-9(H2). The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside. The major fatty acids were C16 : 0, iso-C15 : 0 2-OH and/or C16 : 1 ω7c, 10-methyl C18 : 0 and C18 : 1 ω9c. The DNA G+C content was 66.9 mol%. Strain ON-33T exhibited a DNA–DNA relatedness value of 13 % to G. soli DSM 44995T and could be differentiated from G. soli by differences in phenotypic characteristics. On the basis of the data obtained, strain ON-33T is considered to represent a novel species of the genus Gordonia, for which the name Gordonia hankookensis sp. nov., is proposed. The type strain is ON-33T (=KCTC 19599T=CCUG 57507T).
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- Archaea
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Isolation of the anaerobic thermoacidophilic crenarchaeote Acidilobus saccharovorans sp. nov. and proposal of Acidilobales ord. nov., including Acidilobaceae fam. nov. and Caldisphaeraceae fam. nov.
An anaerobic acidophilic, hyperthermophilic archaeon, designated strain 345-15T, was isolated from an acidic hot spring of Kamchatka (Russia). Cells of strain 345-15T were regular or irregular cocci, 1–2 μm in diameter, with flagella. Strain 345-15T grew optimally at 80–85 °C and pH 3.5–4.0 and fermented a wide range of carbohydrates, including polysaccharides. Acetate, ethanol and lactate were the fermentation products. Growth was stimulated by elemental sulfur and thiosulfate, which were reduced to hydrogen sulfide. The G+C content of the DNA was 54.5 mol%. The 16S rRNA gene sequence analysis indicated that strain 345-15T belonged to the genus Acidilobus. The level of DNA–DNA hybridization between strain 345-15T and Acidilobus aceticus 1904T was 61 %. Thus, strain 345-15T was considered as representing a novel species of the genus Acidilobus, with the name Acidilobus saccharovorans sp. nov. (type strain, 345-15T=DSM 16705T=VKM B-2471T), which shared the main morphological and physiological properties of the genus but differed by the presence of flagella and the spectrum of substrates utilized. Phylogenetic analysis showed that the genus Acidilobus, with its species Acidilobus aceticus, Acidilobus saccharovorans sp. nov. and ‘Acidilobus sulfurireducens’, and the genus Caldisphaera, represented by Caldisphaera lagunensis and ‘Caldisphaera draconis’, formed a separate cluster that adjoins the cluster formed by the species of the order Desulfurococcales. Members of the Acidilobus–Caldisphaera cluster are thermophilic, organotrophic anaerobic cocci that can be distinguished from all species of the order Desulfurococcales on the basis of acidophily. Based on these considerations, we propose a new family, Acidilobaceae fam. nov., to accommodate the subcluster of hyperthermophiles represented by the genus Acidilobus, a new family, Caldisphaeraceae fam. nov., for the subcluster of extreme thermophiles represented by the genus Caldisphaera, and a new order, Acidilobales ord. nov., to accommodate the two new families.
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- Bacteroidetes
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Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish
More LessEight bacterial strains isolated from diseased rainbow trout (n=5) and Atlantic salmon (n=3) were characterized by phenotypic and molecular taxonomic methods. The isolates were negative for the Gram-reaction, non-motile, rod-shaped and catalase- and oxidase-positive. Colonies on solid media were yellow, smooth, shiny and circular with regular edges. Growth occurred at 4–28 °C (optimum, 15 °C) and with 0–3 % NaCl (optimum, 0.5 %). Analysis of the 16S rRNA gene sequence allocated the micro-organisms to the genus Chryseobacterium, with Chryseobacterium soldanellicola PSD1-4T and Chryseobacterium soli JS6-6T as their closest relatives (96.9 and 97.1 % sequence similarity, respectively). The levels of DNA–DNA hybridization towards these nearest phylogenetic neighbours were below 17.1 %. The DNA G+C contents of strains VQ-6316sT and VQ-4836s were 32.5 and 32.3 mol%, respectively. The predominant menaquinone was MK-6 and the major fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C17 : 1 ω9c, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω7t and/or iso-C15 : 0 2-OH). The eight isolates were classified as representatives of a novel species, Chryseobacterium piscicola sp. nov., with strain VQ-6316sT (=CECT 7357T=DSM 21068T) as the type strain.
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Parasegetibacter luojiensis gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from a forest soil
A novel golden-yellow-coloured strain, designated RHYL-37T, was isolated from a soil sample from a forest of Euphrates poplar (Populus euphratica) in Xinjiang, China. The cells were strictly aerobic, Gram-staining-negative, heterotrophic, non-spore-forming rods that were motile by gliding. Growth occurred at 17–37 °C (optimum, 30 °C), at pH 5.0–9.0 (optimum, pH 7.0) and with 0–1 % NaCl (w/v; optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate formed a cluster with members of the genera Segetibacter, Terrimonas, Niastella, Niabella and Chitinophaga in the family ‘Chitinophagaceae’ in the phylum Bacteroidetes. Sequence similarities with the type strains of recognized species ranged from 90.6 to 94.0 %. The predominant isoprenoid quinone was MK-7 and the major cellular fatty acids were iso-C15 : 0, iso-C15 : 1, C16 : 0 and iso-C17 : 0 3-OH. The DNA G+C content was 39.7 mol%. On the basis of the phylogenetic, physiological and chemotaxonomic data, strain RHYL-37T represents a novel genus and species in the family ‘Chitinophagaceae’, for which the name Parasegetibacter luojiensis gen. nov., sp. nov. is proposed. The type strain of Parasegetibacter luojiensis is RHYL-37T (=CCTCC AB 208240T=KCTC 22561T).
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Leeuwenhoekiella palythoae sp. nov., a new member of the family Flavobacteriaceae
The taxonomic status of a novel, heterotrophic, strictly aerobic, gliding and yellow–orange-pigmented bacterium (strain KMM 6264T), associated with the coral Palythoa, was determined. The 16S rRNA gene sequence analysis indicated that strain KMM 6264T clustered with the recognized species of the genus Leeuwenhoekiella of the family Flavobacteriaceae with 96.4–98.2 % sequence similarity. DNA–DNA reassociation levels between the isolate and the type strains of Leeuwenhoekiella species were 15–22 %. The DNA G+C content was 41.2 mol%. The phylogenetic evidence and the results of genomic and phenotypic analyses showed that the isolate should be classified as a member of a novel species of the genus Leeuwenhoekiella, for which the name Leeuwenhoekiella palythoae sp. nov. is proposed. The type strain is KMM 6264T (=KCTC 22020T=LMG 24856T).
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- Firmicutes And Related Organisms
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Planomicrobium flavidum sp. nov., isolated from a marine solar saltern, and transfer of Planococcus stackebrandtii Mayilraj et al. 2005 to the genus Planomicrobium as Planomicrobium stackebrandtii comb. nov.
More LessA Gram-positive to Gram-variable, motile and coccoid- or short rod-shaped bacterial strain, ISL-41T, was subjected to a polyphasic study to investigate its exact taxonomic position. Strain ISL-41T grew optimally at pH 7.0–8.0 and 30 °C. It contained MK-8 and MK-7 as the predominant menaquinones and anteiso-C15 : 0, iso-C16 : 0, anteiso-C17 : 0 and C16 : 1 ω7c alcohol as the major fatty acids. The DNA G+C content was 45.9 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that strain ISL-41T belonged to the genus Planomicrobium. The levels of similarity between the 16S rRNA gene sequence of strain ISL-41T and those of the type strains of recognized Planomicrobium species and Planococcus stackebrandtii were 97.4–98.6 %. Mean DNA–DNA relatedness values between strain ISL-41T and the type strains of Planomicrobium species and Planococcus stackebrandtii were 13–25 %. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, showed that strain ISL-41T could be differentiated from recognized Planomicrobium species and Planococcus stackebrandtii. On the basis of the phenotypic, phylogenetic and genetic data, strain ISL-41T is considered to represent a novel species within the genus Planomicrobium, for which the name Planomicrobium flavidum sp. nov. is proposed. The type strain is ISL-41T (=KCTC 13261T=CCUG 56756T). It is also proposed that Planococcus stackebrandtii be transferred to the genus Planomicrobium as Planomicrobium stackebrandtii comb. nov. (type strain K22-03T=MTCC 6226T=DSM 16419T=JCM 12481T).
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Janibacter hoylei sp. nov., Bacillus isronensis sp. nov. and Bacillus aryabhattai sp. nov., isolated from cryotubes used for collecting air from the upper atmosphere
Three novel bacterial strains, PVAS-1T, B3W22T and B8W22T, were isolated from cryotubes used to collect air samples at altitudes of between 27 and 41 km. Based on phenotypic characteristics, chemotaxonomic features, DNA–DNA hybridization with the nearest phylogenetic neighbours and phylogenetic analysis based on partial 16S rRNA gene sequences (PVAS-1T, 1196 nt; B3W22T, 1541 nt; B8W22T, 1533 nt), the three strains were identified as representing novel species, and the names proposed are Janibacter hoylei sp. nov. (type strain PVAS-1T =MTCC 8307T =DSM 21601T =CCUG 56714T), Bacillus isronensis sp. nov. (type strain B3W22T =MTCC 7902T =JCM 13838T) and Bacillus aryabhattai sp. nov. (type strain B8W22T =MTCC 7755T =JCM 13839T).
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Bacillus neizhouensis sp. nov., a halophilic marine bacterium isolated from a sea anemone
A novel Gram-stain-positive, slightly halophilic, facultatively alkaliphilic, non-motile, catalase- and oxidase-positive, endospore-forming, rod-shaped, aerobic bacterium, strain JSM 071004T, was isolated from a sea anemone collected from Neizhou Bay in the South China Sea. Growth occurred with 0.5–10 % (w/v) total salts (optimum 2–4 %) and at pH 6.5–10.0 (optimum pH 8.5) and 4–30 °C (optimum 25 °C). meso-Diaminopimelic acid was present in the cell-wall peptidoglycan. The predominant respiratory quinone was menaquinone 7 (MK-7) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The genomic DNA G+C content was 39.8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 071004T belongs to the genus Bacillus, being related most closely to the type strain of Bacillus agaradhaerens (sequence similarity 97.3 %), followed by the type strains of Bacillus cellulosilyticus (96.2 %), Bacillus clarkii (96.1 %) and Bacillus polygoni (96.0 %). The combination of phylogenetic analysis, DNA–DNA hybridization, phenotypic characteristics and chemotaxonomic data support the proposal that strain JSM 071004T represents a novel species of the genus Bacillus, for which the name Bacillus neizhouensis sp. nov. is proposed, with JSM 071004T (=CCTCC AB 207161T =DSM 19794T =KCTC 13187T) as the type strain.
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Virgibacillus salinus sp. nov., a moderately halophilic bacterium from sediment of a saline lake
More LessA novel, moderately halophilic, Gram-positive bacterium, designated strain XH-22T, was isolated from sediment of a saline lake located near Xilinhot, Inner Mongolia Autonomous Region, China. Cells were rod-shaped, endospore-forming and motile. The isolate was able to grow in the presence of 3–20 % (w/v) total salts (optimum, 10 %, w/v), and at 15–40 °C (optimum, 37 °C) and pH 6.0–10.0 (optimum, pH 7.5). Strain XH-22T had diaminopimelic acid in the cell-wall peptidoglycan, MK-7 as the predominant menaquinone, and anteiso-C15 : 0, C16 : 0 and iso-C14 : 0 as major fatty acids. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, a glycolipid and two unidentified phospholipids. The DNA G+C content of strain XH-22T was 38.8 mol%. 16S rRNA gene sequence analysis revealed that the novel strain was affiliated with the genus Virgibacillus. Levels of 16S rRNA gene sequence similarity between strain XH-22T and the type strains of recognized Virgibacillus species ranged from 97.6 % (with Virgibacillus carmonensis) to 94.9 % (with Virgibacillus koreensis). Levels of DNA–DNA relatedness between strain XH-22T and V. carmonensis DSM 14868T and Virgibacillus necropolis DSM 14866T were 32 and 28 %, respectively. Strain XH-22T could be differentiated from recognized Virgibacillus species based on phenotypic characteristics, chemotaxonomic differences, phylogenetic analysis and genotypic features. On the basis of these results, strain XH-22T is considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus salinus sp. nov. is proposed. The type strain is XH-22T (=CCM 7562T=CECT 7439T=DSM 21756T).
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Piscibacillus halophilus sp. nov., a moderately halophilic bacterium from a hypersaline Iranian lake
More LessA Gram-positive, moderately halophilic bacterium, designated strain HS224T, was isolated from the hypersaline lake Howz-Soltan in Iran. Cells of strain HS224T were rod-shaped, motile and produced oval endospores. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain HS224T was affiliated to the genus Piscibacillus, exhibiting 98.5 % sequence similarity to the type strain of Piscibacillus salipiscarius. Strain HS224T was also related closely to the type strains of Aquisalibacillus elongatus (98.0 % 16S rRNA gene sequence similarity), Filobacillus milosensis (97.9 %) and Tenuibacillus multivorans (97.0 %). Strain HS224T was able to grow at NaCl concentrations of 1–20 % (w/v), with optimum growth occurring at 10 % (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.5. Major polar lipids were phosphatidylglycerol and diphosphatidylglycerol, the isoprenoid quinone was MK-7 and the peptidoglycan type was A1γ, with meso-diaminopimelic acid as the diagnostic diamino acid; these characteristics were shared with P. salipiscarius. The major cellular fatty acids of strain HS224T were anteiso-C15 : 0, iso-C15 : 0, anteiso-C17 : 0 and iso-C16 : 0. The G+C content of the DNA was 37.5 mol%. The level of DNA–DNA relatedness between strain HS224T and P. salipiscarius JCM 13188T was 30.8 %. It is evident from the genotypic, chemotaxonomic and phenotypic data presented that strain HS224T represents a novel species of the genus Piscibacillus, for which the name Piscibacillus halophilus sp. nov. is proposed. The type strain is HS224T (=CCM 7596T=DSM 21633T=JCM 15721T=LMG 24786T).
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Anaerosphaera aminiphila gen. nov., sp. nov., a glutamate-degrading, Gram-positive anaerobic coccus isolated from a methanogenic reactor treating cattle waste
More LessA strictly anaerobic, mesophilic and aminolytic strain (WN036T) was isolated from a methanogenic reactor treating waste from cattle farms. Cells were Gram-positive cocci, often occurred in pairs and were non-motile. Although spore formation was not confirmed by microscopic observation of cells, the strain produced thermotolerant cells. The optimum temperature for growth was 35–37 °C and the optimum pH was 6.7. Oxidase, catalase and nitrate-reducing activities were negative. The novel strain did not ferment carbohydrates and grew in PY medium without additional substrates. The strain utilized l-glutamate, l-glutamine, l-histidine and l-arginine as growth substrates. Major fermentation products were acetate and butyrate with a small amount of propionate. The genomic DNA G+C content was 32.5 mol%. The major cellular fatty acids were C17 : 1 ω8, C18 : 1 ω7 DMA and C16 : 0. The diagnostic diamino acid of the cell-wall peptidoglycan was lysine. Glutamic acid, glycine, alanine and aspartic acid were also detected in the cell-wall peptidoglycan. On the basis of 16S rRNA gene sequences, the most closely related species to strain WN036T were Peptoniphilus asaccharolyticus ATCC 14965T (89.8 %) and Peptoniphilus indolicus ATCC 29427T (89.6 %). Based on the differences in the phenotypic and phylogenetic characteristics of strain WN036T compared with those of closely related species, a novel genus and species, Anaerosphaera aminiphila gen. nov., sp. nov., is proposed. The type strain is WN036T (=JCM 15094T=DSM 21120T).
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Carnobacterium jeotgali sp. nov., isolated from a Korean traditional fermented food
More LessA Gram-positive, facultatively anaerobic bacterium, designated strain MS3T, was isolated from a traditional Korean fermented food made with freshwater shrimp. Strain MS3T was able to grow at 4–37 °C, at pH 5.5–9.0 and in the presence of 0–5 % (w/v) NaCl. Optimal growth occurred at 30 °C, at pH 8.5 and in the presence of 2 % NaCl. The strain was catalase- and oxidase-negative. It was able to metabolize various carbohydrates as energy sources. 16S rRNA gene sequence analysis showed that strain MS3T was most closely related to Carnobacterium pleistocenium FTR1T (98.95 % similarity), but the level of DNA–DNA relatedness between the two taxa was less than 16.0 %. The genomic G+C content of strain MS3T was 43.9 mol% and the major fatty acid components were C16 : 0, C16 : 1 ω9c and C18 : 1 ω9c. On the basis of its genotypic, physiological and biochemical characteristics, strain MS3T is considered to represent a novel species of the genus Carnobacterium, for which the name Carnobacterium jeotgali sp. nov. is proposed. The type strain is MS3T (=KCTC 13251T=JCM 15539T).
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- Other Bacteria
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Thermus islandicus sp. nov., a mixotrophic sulfur-oxidizing bacterium isolated from the Torfajokull geothermal area
Strains PRI 2268 and PRI 3838T were isolated from two separate hot springs in the Torfajokull geothermal area of South Iceland. The cells were non-motile rods, approximately 0.3 μm in width and 1.5–2.5 μm in length. Electron microscopy revealed a Gram-negative cell-wall structure. The strains grew at 45–79 °C (optimum, 65 °C) and pH 5.5–10.5 (optimum, pH 6.0–7.0). 16S rRNA gene sequence analysis indicated that they formed a separate branch within the genus Thermus with ‘Thermus kawarayensis’ KW11 as their closest cultured relative (96.5 % similarity). The gene sequence similarities of both new isolates to Thermus aquaticus YT-1T and Thermus igniterrae RF-4T were 96.1 % and 95.5 %, respectively. DNA–DNA relatedness between strain PRI 3838T and ‘T. kawarayensis’ was 46.1 %. The DNA G+C content of strain PRI 3838T was 69.0 mol%. The predominant menaquinones, pigmentation, fatty acid profiles and phospholipid profiles of the novel strains were similar to those of other members of the genus Thermus. However, the new strains could be differentiated from the type strains of all other species of the genus Thermus by their lack of catalase activity and their utilization of only a few carbon sources. Furthermore, the novel strains exhibited mixotrophic growth with sulfur oxidation. On the basis of 16S rRNA gene sequence comparisons, DNA–DNA hybridization and physiological and biochemical characteristics, the new isolates represent a novel species. Since the species appears to be ubiquitous in Icelandic hot springs, the name Thermus islandicus sp. nov. is proposed. The type strain is PRI 3838T (=DSM 21543T=ATCC BAA-1677T).
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Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid
A novel thermophilic, heterotrophic bacterium, strain TBF 19.5.1T, was isolated from oil production fluid at the Troll B oil platform in the North Sea. Cells of strain TBF 19.5.1T were non-motile rods with a sheath-like structure, or toga. The strain was Gram-negative and grew at 20–80 °C (optimum 65 °C), pH 5.5–8.0 (optimum pH 6.8) and NaCl concentrations of 10–60 g l−1 (optimum 25–30 g l−1). For a member of the order Thermotogales, the novel isolate is capable of unprecedented growth at low temperatures, with an optimal doubling time of 175 min (specific growth rate 0.24 h−1) and a final optical density of >1.4 when grown on pyruvate at 37 °C. Various carbohydrates, proteinaceous compounds and pyruvate served as growth substrates. Thiosulfate, but not elemental sulfur, enhanced growth of the isolate. Sulfate also enhanced growth, but sulfide was not produced. The strain grew in the presence of up to approximately 15 % oxygen, but only if cysteine was included in the medium. Growth of the isolate was inhibited by acetate, lactate and propionate, while butanol and malate prevented growth. The major fermentation products formed on maltose were hydrogen, carbon dioxide and acetic acid, with traces of ethanol and propionic acid. The G+C content of the genomic DNA was 42.5 mol%. Phylogenetic analyses of the 16S and 23S rRNA gene sequences as well as 29 protein-coding ORFs placed the strain within the bacterial order Thermotogales. Based on the phylogenetic analyses and the possession of a variety of physiological characteristics not previously found in any species of this order, it is proposed that the strain represents a novel species of a new genus within the family Thermotogaceae, order Thermotogales. The name Kosmotoga olearia gen. nov., sp. nov. is proposed. The type strain of Kosmotoga olearia is TBF 19.5.1T (=DSM 21960T =ATCC BAA-1733T).
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- Proteobacteria
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Ponticaulis koreensis gen. nov., sp. nov., a new member of the family Hyphomonadaceae isolated from seawater
More LessAn obligately halophilic, stalked bacterium, designated strain GSW-23T, was isolated from seawater that had been collected on the coast of Jeju, Korea. Cells of the strain were characteristically Gram-negative, aerobic, chemo-organotrophic, non-budding, motile rods or vibrioids that possessed prosthecae and holdfasts. Multiplication occurred by means of binary fission. The major ubiquinone was Q-10. The dominant cellular fatty acids were summed feature 7 (one or more of C18 : 1 ω9c, C18 : 1 ω12t and C18 : 1 ω7c; 37.1 %), C16 : 0 (25.5 %) and C18 : 0 (14.1 %). The DNA G+C content was 53.3 mol%. 16S rRNA gene sequence analyses showed that the organism was related to members of the family Hyphomonadaceae and formed a distinct clade between members of the genus Hyphomonas and Hirschia baltica DSM 5838T. Strain GSW-23T was most closely related to the genus Hyphomonas (92.5–93.9 % sequence similarity), but differed from members of the genus by reproduction by binary fission, some physiological properties (gelatin liquefaction and tolerance of 6 % NaCl) and chemotaxonomic features (major fatty acids, major quinones and DNA G+C content). The other genera of the family can be readily differentiated from the isolate by a battery of cultural, physiological and chemotaxonomic characteristics. On the basis of the phenotypic and phylogenetic data presented here, strain GSW-23T represents a novel genus and species in the family Hyphomonadaceae, for which the name Ponticaulis koreensis gen. nov., sp. nov. is proposed. The type strain of Ponticaulis koreensis is strain GSW-23T (=KCTC 22146T =DSM 19734T =JCM 14975T).
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Bartonella rattaustraliani sp. nov., Bartonella queenslandensis sp. nov. and Bartonella coopersplainsensis sp. nov., identified in Australian rats
More LessA total of 11 Bartonella isolates were recovered from the blood of Melomys, Uromys and Rattus species in Australia and were characterized using phenotypic and genotypic methods. Comparison of 16S rRNA gene, ftsZ, gltA and 16S–23S rRNA internal transcribed spacer region sequences from the isolates indicated that they formed three sequence similarity groups that were distinct from one another and from the currently recognized Bartonella species. Phylogenetic analysis based on alignment of concatenated sequences inferred distinct evolutionary lineages for each of the three groups within the genus Bartonella. On the basis of these data, we propose the isolates be accommodated in three novel Bartonella species, namely Bartonella rattaustraliani sp. nov. (type strain AUST/NH4T =CIP 109051T =CCUG 52161T =CSUR B609T), Bartonella queenslandensis sp. nov. (type strain AUST/NH12T =CIP 109057T =CCUG 52167T =CSUR B617T) and Bartonella coopersplainsensis sp. nov. (type strain AUST/NH20T =CIP 109064T =CCUG 52174T =CSUR B619T).
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Arenimonas oryziterrae sp. nov., isolated from a field of rice (Oryza sativa L.) managed under a no-tillage regime, and reclassification of Aspromonas composti as Arenimonas composti comb. nov.
More LessThe taxonomic position of a novel bacterial strain, YC6267T isolated from a field of rice (Oryza sativa L.) managed under a no-tillage regime in Jinju, Korea, was studied using a polyphasic taxonomic approach. Cells of the strain were Gram-stain-negative, rod-shaped and aerobic. It grew at 15–37 °C (optimum at 28 °C). Growth of the strain occurred between pH 5.0 and 10.0, with an optimum of pH 7.0–8.0. The G+C content of the total DNA was 65.8 mol%. The 16S rRNA gene sequence of the strain was most closely related to species of the genera Arenimonas (95.6–94.4 %) and Aspromonas (95.1 %), with <95.0 % similarity to species of the genus Lysobacter and other genera of the family Xanthomonadaceae. Chemotaxonomic data (major quinone Q-8; major polar lipids phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; and major fatty acids iso-C15 : 0, iso-C14 : 0, iso-C16 : 0, and iso-C17 : 1 ω9c) supported the affiliation of strain YC6267T to the genus Arenimonas. Phylogenetic analysis based on 16S rRNA gene sequences and biochemical and physiological characteristics strongly supported the genotypic and phenotypic differentiation of strain YC6267T from described species of the genus Arenimonas. Strain YC6267T, therefore, represents a novel species, for which the name Arenimonas oryziterrae sp. nov. is proposed. The type strain is YC6267T (=KCTC 22247T =DSM 21050T). In addition, the reclassification of Aspromonas composti as Arenimonas composti comb. nov. is proposed (type strain TR7-09T =KCTC 12666T =DSM 18010T). A common line of descent and a number of shared phenotypic traits support this reclassification.
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Altererythrobacter marinus sp. nov., isolated from deep seawater
More LessA taxonomic study was carried out on strain H32T, which was isolated from a crude-oil-degrading consortium enriched from deep seawater of the Indian Ocean. The 16S rRNA gene sequence of strain H32T showed highest similarity to that of Altererythrobacter luteolus SW-109T (96.7 %); lower similarities were observed with other members of the genus Altererythrobacter (94.7–95.7 %) and with members of the genera Erythrobacter (94.5–96.3 %), Erythromicrobium (94.9 %) and Porphyrobacter (94.3–95.3 %). Phylogenetic analyses of all members of the family Erythrobacteraceae and several members of the family Sphingomonadaceae revealed that strain H32T formed a clade within the genus Altererythrobacter. The dominant fatty acids were C16 : 0 (6.7 %), C18 : 1 ω7c (44.3 %) and 11-methyl C18 : 1 ω7c (25.4 %). The major respiratory quinone was ubiquinone 10. The DNA G+C content was 66.5 mol%. Strain H32T did not contain bacteriochlorophyll a. These characteristics are in good agreement with those of members of the genus Altererythrobacter. Therefore, according to its morphology, physiology, fatty acid composition and 16S rRNA gene sequence data, strain H32T belongs to the genus Altererythrobacter, but can be readily distinguished from known Altererythrobacter species. It is therefore proposed that strain H32T represents a novel species, Altererythrobacter marinus sp. nov., with H32T (=CCTCC AB 208229T =LMG 24629T =MCCC 1A01070T) as the type strain.
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Gilvimarinus chinensis gen. nov., sp. nov., an agar-digesting marine bacterium within the class Gammaproteobacteria isolated from coastal seawater in Qingdao, China
A taxonomic study was performed on strain QM42T, which was isolated from coastal seawater from an aquaculture site near Qingdao, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QM42T was a member of the class Gammaproteobacteria. Cells of strain QM42T were Gram-negative, yellow, aerobic and rod-shaped. The strain formed a distinct phyletic line with less than 91 % 16S rRNA gene sequence similarity to its closest relatives with validly published names within the class Gammaproteobacteria. The genomic DNA G+C content was 51.9 mol%. The major fatty acids were C16 : 1 ω7c/iso-C15 : 0 2-OH, C18 : 1 ω7c and C16 : 0. Based on data from a polyphasic chemotaxonomic, physiological and biochemical study, strain QM42T is considered to represent a novel genus and species, for which the name Gilvimarinus chinensis gen. nov., sp. nov., is proposed. The type strain is QM42T (=CGMCC 1.7008T=DSM 19667T).
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Rhizobium alkalisoli sp. nov., isolated from Caragana intermedia growing in saline-alkaline soils in the north of China
More LessThree rhizobial strains (CCBAU 01393T, CCBAU 01389 and CCBAU 03239) isolated from nodules of Caragana intermedia grown in saline-alkaline soils in the north of China had identical 16S rRNA genes that showed 99.7 and 99.5 % sequence similarities with those of Rhizobium huautlense SO2T and Rhizobium galegae USDA 4128T, respectively. Phylogenies of the housekeeping genes atpD, recA and glnII confirmed their distinct position, differing from recognized Rhizobium species. SDS-PAGE of whole-cell soluble proteins and a series of phenotypic and physiological tests allowed us to differentiate the novel group from all closely related recognized Rhizobium species. The levels of DNA–DNA relatedness between strain CCBAU 01393T and R. huautlense SO2T and R. galegae USDA 4128T were 34.9 and 20.5 %, respectively. Therefore, we propose that strains CCBAU 01393T, CCBAU 01389 and CCBAU 03239 represent a novel species, Rhizobium alkalisoli sp. nov., with strain CCBAU 01393T (=LMG 24763T=HAMBI 3051T) as the type strain. This strain could form effective nodules on Caragana microphylla, Phaseolus vulgaris and Vigna radiata.
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Mesorhizobium shangrilense sp. nov., isolated from root nodules of Caragana species
More LessFive strains of bacteria isolated from nodules of Caragana bicolor and Caragana erinacea in Yunnan Province of China were classified within the genus Mesorhizobium in the class Alphaproteobacteria. The highest degree of 16S rRNA gene sequence similarity was determined to be to Mesorhizobium loti LMG 6125T (99.7 %) and Mesorhizobium ciceri UPM-Ca7T (99.7 %). Polyphasic taxonomic methods including SDS-PAGE of whole-cell soluble proteins, comparative housekeeping sequence analysis of atpD, glnII and recA, fatty acid profiles and a series of phenotypic and physiological tests allowed us to cluster the five strains into a coherent group while differentiating them from all previously established Mesorhizobium species. The DNA–DNA relatedness between the representative strain CCBAU 65327T and the type strains of M. loti and M. ciceri was 26.5 and 23.4 %, respectively, clearly indicating that strain CCBAU 65327T represents a novel species for which we propose the name Mesorhizobium shangrilense sp. nov. Strain CCBAU 65327T (=LMG 24762T =HAMBI 3050T) is designated as the type strain, and could nodulate Caragana microphylla, Caragana intermedia, Glycyrrhiza uralensis, Astragalus adsurgens, Vigna unguiculata, Vigna radiata and Phaseolus vulgaris in cross-nodulation tests.
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Pseudomonas pelagia sp. nov., isolated from a culture of the Antarctic green alga Pyramimonas gelidicola
More LessTwo Gram-negative, strictly aerobic bacterial strains, designated CL-AP6T and CL-AP22, were isolated from a culture of a green alga, Pyramimonas gelidicola, established from the Antarctic. Cells of the strains were straight rods and motile by means of a single polar flagellum. The strains grew with 0.5–8 % (w/v) NaCl (optimum, 1–2 %) and at 4–33 °C (optimum, 25 °C) and pH 6.5–9.1 (optimum, pH 7.5–8.1). The two strains shared 98.8 % 16S rRNA gene sequence similarity. Analysis of the 16S rRNA gene sequences of strains CL-AP6T and CL-AP22 revealed that they were members of the genus Pseudomonas and were most closely related to Pseudomonas xiamenensis C10-2T (95.5–95.8 % sequence similarity) and next to Pseudomonas pertucinogena NBRC 14163T (95.1–95.5 % sequence similarity) and to other members of the genus Pseudomonas (<95.2 % sequence similarity). Phylogenetic analyses based on the 16S rRNA gene sequences showed that strain CL-AP6T formed a robust clade with strain CL-AP22, and that this clade clustered tightly with the nearest clade containing P. xiamenensis and P. pertucinogena. The major isoprenoid quinone of strains CL-AP6T and CL-AP22 was Q-9 and the major cellular fatty acids were C18 : 1 ω7c (40.2–41.6 %), summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 26.3–26.8 %), C16 : 0 (13.7–13.9 %) and C12 : 0 (5.8–6.2 %). The genomic DNA G+C contents of strains CL-AP6T and CL-AP22 were 59.1 and 57.2 mol%, respectively. DNA–DNA hybridization experiments revealed high relatedness values (98.5±0.5 %; mean±sem, n=2) between strains CL-AP6T and CL-AP22, indicating that the two strains constituted a single species. However, the two strains differed phenotypically from P. xiamenensis by their inability to grow without NaCl, temperature range for growth, hydrolysis of starch and production of certain enzymes. The phylogenetic analysis and physiological and biochemical data showed that strains CL-AP6T and CL-AP22 should be classified as representing a novel species in the genus Pseudomonas, for which the name Pseudomonas pelagia sp. nov. is proposed. The type strain is CL-AP6T (=KCCM 90073T=JCM 15562T).
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Brachymonas chironomi sp. nov., isolated from a chironomid egg mass, and emended description of the genus Brachymonas
More LessA Gram-negative, aerobic, chemo-organotrophic, catalase- and oxidase-positive strain, designated AIMA4T, was isolated from a chironomid (Diptera; Chironomidae) egg mass which was sampled from a waste stabilization pond in northern Israel. Phylogenetic analysis based on the 16S rRNA gene placed strain AIMA4T in the genus Brachymonas (class Betaproteobacteria). Strain AIMA4T shared 16S rRNA gene sequence similarity values of 96.9 % with Brachymonas denitrificans JCM 9216T and <95.7 % with the type strains of other genera. Strain AIMA4T was found to be a non-motile coccobacillus or rod that did not grow under anaerobic conditions and did not produce acid from carbohydrates. Growth was observed at salinities from 0 to 2.5 % (w/v) NaCl, at pH values from 5.0 to 9.0 and at temperatures from 18 to 37 °C. The major fatty acids (>10 %) of strain AIMA4T were C16 : 1 ω7c, C16 : 0 and C18 : 1 ω7c. Phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine were the predominant components of the polar lipids. The major ubiquinone was Q-8. On the basis of phenotypic properties and phylogenetic distinctiveness, strain AIMA4T (=LMG 24400T=DSM 19884T) was classified in the genus Brachymonas as the type strain of a novel species for which the name Brachymonas chironomi sp. nov. is proposed.
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Marinobacterium maritimum sp. nov., a marine bacterium isolated from Arctic sediment
A Gram-negative, aerobic, rod-shaped, motile, marine bacterium, strain AR11T, was isolated from Arctic marine sediment. Strain AR11T grew with 0.5–7 % NaCl and at 7–37 °C and pH 5.5–9.0. It utilized propionate, 3-hydroxybenzoate, l-proline, acetate, d- and l-lactate, l-alanine, malate and phenylacetic acid. Alkaline phosphatase, esterase lipase (C8), leucine arylamidase and acid phosphatase activity tests were positive. Acid was produced from 5-ketogluconate and aesculin. Strain AR11T possessed C16 : 0 (22.0 %), summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 28.1 %) and summed feature 7 (one or more of C18 : 1 ω7c, ω9t and ω12t; 34.0 %) as the major cellular fatty acids. The major ubiquinone was Q-8. Comparative 16S rRNA gene sequence studies showed that strain AR11T belonged to the Gammaproteobacteria and was most closely related to Marinobacterium stanieri DSM 7027T, Marinobacterium halophilum mano11T and Marinobacterium georgiense KW-40T (97.8, 97.0 and 96.7 % similarity, respectively). The G+C content of the genomic DNA of strain AR11T was 57.9 mol%. DNA–DNA relatedness data indicated that strain AR11T represented a distinct species that was separated from M. stanieri DSM 7027T, M. halophilum KCTC 12240T and M. georgiense JCM 21667T. On the basis of evidence from this polyphasic study, it is proposed that strain AR11T (=KCTC 22254T=JCM 15134T) represents the type strain of a novel species, Marinobacterium maritimum sp. nov.
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Rhizobium tibeticum sp. nov., a symbiotic bacterium isolated from Trigonella archiducis-nicolai (Širj.) Vassilcz.
Isolated from root nodules of Trigonella archiducis-nicolai (Širj.) Vassilcz. grown in Tibet, China, cells of the bacterial strains CCBAU 85039T and CCBAU 85027 were Gram-negative, aerobic, motile, non-spore-forming rods that formed colonies that were semi-translucent and opalescent on yeast extract-mannitol agar. In numerical taxonomy, SDS-PAGE analysis of whole-cell proteins and DNA–DNA hybridization, the two strains were very similar and were different from reference strains of defined Rhizobium species. In the phylogeny based on 16S rRNA gene sequences, they were most similar to Rhizobium etli CFN 42T (98.2 % similarity) and R. leguminosarum USDA 2370T (97.6 %). Sequence analyses of the housekeeping genes recA, atpD and glnII and the 16S–23S rRNA intergenic spacer, phenotypic characteristics and cellular fatty acid profiles strongly suggested that these two strains represented a novel species within Rhizobium. Cross-nodulation tests and sequencing of nifH and nodA genes showed that these two strains were symbiotic bacteria that nodulated Trigonella archiducis-nicolai, Medicago lupulina, Medicago sativa, Melilotus officinalis, Phaseolus vulgaris and Trigonella foenum-graecum. Based on the results, the novel species Rhizobium tibeticum sp. nov. is described to accommodate the two strains. The type strain is CCBAU 85039T (=LMG 24453T =CGMCC 1.7071T). The DNA G+C content of this strain is 59.7 mol% (T m).
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Maribaculum marinum gen. nov., sp. nov., isolated from deep seawater
More LessA taxonomic study was carried out on strain P38T, which was isolated from an enriched polycyclic aromatic hydrocarbon-degrading consortium from a deep seawater sample collected from the Indian Ocean. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain P38T formed a distinct evolutionary lineage within the family Hyphomonadaceae. Strain P38T was most closely related to members of the genera Hyphomonas (92.3–93.5 % 16S rRNA gene sequence similarity), Hirschia (88.8 %), Maricaulis (88.3–88.6 %), Hellea (87.5 %), Oceanicaulis (87.4 %) and Robiginitomaculum (86.7 %) of the family Hyphomonadaceae. The DNA G+C content of strain P38T was 61.0 mol% and the predominant cellular fatty acids were C16 : 0 (20 %), C17 : 0 (5.7 %), C18 : 1 ω7c (37.7 %), C18 : 0 (6.3 %) and C18 : 1 ω7c 11-methyl (7.1 %). Strain P38T was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of the phenotypic and phylogenetic data, strain P38T represents a novel species of a new genus, for which the name Maribaculum marinum gen. nov., sp. nov. is proposed. The type strain of Maribaculum marinum is P38T (=CCTCC AB 208227T=LMG 24711T=MCCC 1A01086T).
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Aidingimonas halophila gen. nov., sp. nov., a moderately halophilic bacterium isolated from a salt lake
More LessTwo Gram-negative, facultatively anaerobic, catalase-positive, oxidase-negative, non-motile, rod-shaped and moderately halophilic bacterial strains, designated YIM 90637T and BH 017, were isolated from a salt lake in Xinjiang province, north-west China, and subjected to a polyphasic taxonomic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the two novel isolates were affiliated with the family Halomonadaceae; the two strains shared 100 % sequence similarity, but showed similarities of 94.7 % with the type strain of Modicisalibacter tunisiensis, 93.2–94.7 % with members of the genus Chromohalobacter, 93.2–95.0 % with members of the genus Halomonas and less than 92.0 % with other members of the family Halomonadaceae. However, DNA–DNA relatedness data and phenotypic properties demonstrated that strains YIM 90637T and BH 017 were representatives of the same species. The major fatty acids were C19 : 0 cyclo ω8c and C16 : 0. The relative amount of C19 : 0 cyclo ω8c was notably higher than that found in most species of the family Halomonadaceae for which fatty acid composition has been determined. The genomic DNA G+C content was 57.2–57.5 mol% and the only respiratory quinone was ubiquinone 9. Based on evidence from the polyphasic taxonomic study, it was concluded that the two strains should be classified as representatives of a novel species in a new genus, for which name Aidingimonas halophila gen. nov., sp. nov. is proposed; the type strain of Aidingimonas halophila is YIM 90637T (=KCTC 12885T=CCTCC AB 207002T).
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Desulfocurvus vexinensis gen. nov., sp. nov., a sulfate-reducing bacterium isolated from a deep subsurface aquifer
A novel anaerobic, chemo-organotrophic bacterium, designated VNs36T, was isolated from a well that collected water from a deep saline aquifer used for underground gas storage at a depth of 830 m in the Paris Basin, France. Cells were curved motile rods or vibrios (3.0–5.0×0.5 μm). Strain VNs36T grew at temperatures between 20 and 50 °C (optimum 37 °C) and at pH values between 5.0 and 9.0 (optimum 6.9). It did not require salt for growth, but tolerated up to 20 g NaCl l−1 (optimum 2 g l−1). In the presence of sulfate, strain VNs36T used lactate, formate and pyruvate as carbon and energy sources. The main fermentation products from lactate were acetate, H2 and CO2. Sulfate, thiosulfate and sulfite were used as electron acceptors, but not sulfur. The genomic DNA G+C content of strain VNs36T was 67.2 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain VNs36T was affiliated with the family Desulfovibrionaceae within the class Deltaproteobacteria. On the basis of 16S rRNA gene sequence comparisons, DNA G+C content and the absence of desulfoviridin in cell extracts, it is proposed that strain VNs36T be assigned to a new genus, Desulfocurvus gen. nov., as a representative of a novel species, Desulfocurvus vexinensis sp. nov. The type species of this genus is Desulfocurvus vexinensis with the type strain VNs36T (=DSM 17965T=JCM 14038T).
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Shewanella chilikensis sp. nov., a moderately alkaliphilic gammaproteobacterium isolated from a lagoon
More LessA Gram-negative, motile, rod-shaped, facultatively anaerobic bacterium was isolated from sediment of Chilika Lagoon, a brackish water lagoon in India. The strain, designated JC5T, was able to grow in the presence of 0–8.0 % NaCl and at pH 7.0–10.0. The isolate was positive for oxidase and catalase and exhibited α-haemolysis. The major fatty acids were iso-C15 : 0 (18.3 %), C16 : 0 (11.3 %), C17 : 1 ω8c (13.1 %) and a summed feature, C16 : 1 ω7c and/or C16 : 1 ω6c (15.1 %). The genomic DNA G+C content was 54.6 mol%. A phylogenetic tree based on the 16S rRNA gene sequences showed that strain JC5T forms a lineage within the genus Shewanella and is closely related to Shewanella haliotis DW01T (98.0 %), Shewanella algae ATCC 51192T (97.6 %) and Shewanella marina C4T (95.8 %). Further, genomic DNA–DNA hybridization of strain JC5T with S. haliotis DW01T and S. algae ATCC 51192T showed relatedness of only 42 and 23 %, respectively. On the basis of phenotypic and molecular genetic evidence, strain JC5T represents a novel species of the genus Shewanella, for which the name Shewanella chilikensis sp. nov. is proposed. The type strain is JC5T (=CCUG 57101T =NBRC 105217T =KCTC 22540T).
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Thiothrix caldifontis sp. nov. and Thiothrix lacustris sp. nov., gammaproteobacteria isolated from sulfide springs
Five strains of filamentous, sulfur-oxidizing bacteria were isolated from sulfur mats of different sulfide springs from various regions of the Northern Caucasus, Russia. A phylogenetic analysis based on 16S rRNA gene sequence comparison showed that all of the isolates are affiliated with the filamentous, colourless, sulfur-oxidizing bacteria of the genus Thiothrix within the Gammaproteobacteria and are closely related to Thiothrix fructosivorans. All strains are capable of growing heterotrophically, lithoautotrophically with thiosulfate or sulfide as the sole energy source and mixotrophically. Strains G1T, G2, P and K2 are able to fix molecular nitrogen, but strain BLT is not. Randomly amplified polymorphic DNA (RAPD)-PCR analysis was used to assess the level of genetic relationships among the Thiothrix isolates. The Nei and Li similarity index revealed high genetic similarity among strains G1T, G2, P and K2 (above 75 %), indicating that they are closely related. In combination with physiological and morphological data, strains G1T, G2, P and K2 can be considered as members of the same species. The lowest genetic similarity (approx. 20 %) was reached between strain BLT and the other isolated Thiothrix strains. Strains BLT and G1T shared 35 % DNA–DNA relatedness and showed 51 and 53 % relatedness, respectively, to Thiothrix fructosivorans ATCC 49749. On the basis of this polyphasic analysis, strains G1T, G2, P and K2 represent a novel species within the genus Thiothrix, for which the name Thiothrix caldifontis sp. nov. is proposed, with strain G1T (=DSM 21228T =VKM B-2520T) as the type strain. In addition, strain BLT represents a second novel species, Thiothrix lacustris sp. nov., with strain BLT (=DSM 21227T =VKM B-2521T) as the type strain.
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Sphingobium chinhatense sp. nov., a hexachlorocyclohexane (HCH)-degrading bacterium isolated from an HCH dumpsite
More LessA yellow-pigmented, hexachlorocyclohexane (HCH)-degrading bacterium, strain IP26T, was isolated from an HCH dumpsite and subjected to a polyphasic analysis in order to determine its taxonomic position. Strain IP26T showed maximum 16S rRNA gene sequence similarity with Sphingobium francense Sp+T (98.5 %), Sphingobium japonicum UT26T (98.4 %) and Sphingobium indicum B90AT (98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences also showed that strain IP26T formed a cluster with these three HCH-degrading strains. Chemotaxonomic data (major polyamine, spermidine; major quinone, ubiquinone with ten isoprene units; major polar lipids, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, diphosphatidylglycerol, phosphotidylcholine; and presence of 2-hydroxy fatty acid) supported inclusion of strain IP26T in the genus Sphingobium. However, the results of DNA–DNA hybridization and morphological and biochemical tests clearly allowed phenotypic and genotypic differentiation of strain IP26T from recognized species of the genus Sphingobium. Strain IP26T thus represents a novel species of the genus Sphingobium for which the name Sphingobium chinhatense sp. nov. is proposed. The type strain is IP26T (=MTCC8598T =CCM 7432T).
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Sphingobium vermicomposti sp. nov., isolated from vermicompost
Strain VC-230T was isolated from homemade vermicompost produced from kitchen waste. The isolate was a Gram-negative-staining, catalase- and oxidase-positive, motile rod-shaped bacterium able to grow at 15–37 °C and pH 6–8. On the basis of 16S rRNA gene sequence analysis, strain VC-230T was determined to belong to the family Sphingomonadaceae by its clustering with type strains of the genus Sphingobium, with Sphingobium chlorophenolicum ATCC 33790T (97.7 %) and Sphingobium herbicidovorans DSM 11019T (97.4 %) as its closest neighbours. The polar lipid pattern, the presence of spermidine and ubiquinone 10, the predominance of the cellular fatty acids C18 : 1 ω7c/9t/12t, C16 : 1 ω7c and C16 : 0 and the G+C content of the genomic DNA supported the affiliation of this organism to the genus Sphingobium. The phylogenetic, chemotaxonomic, phenotypic and DNA–DNA hybridization analyses verify that strain VC-230T represents a novel species, for which the name Sphingobium vermicomposti sp. nov. is proposed. The type strain is VC-230T (=CCUG 55809T =DSM 21299T).
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Brevundimonas naejangsanensis sp. nov., a proteolytic bacterium isolated from soil, and reclassification of Mycoplana bullata into the genus Brevundimonas as Brevundimonas bullata comb. nov.
More LessA Gram-negative, motile and rod-shaped bacterial strain, BIO-TAS2-2T, of the class Alphaproteobacteria, was isolated from a soil in Korea and studied using a polyphasic taxonomic approach. Strain BIO-TAS2-2T grew optimally at pH 7.5–8.5 and 30 °C and in the presence of 0–1.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain BIO-TAS2-2T fell within the clade comprising species of the genus Brevundimonas, forming a coherent cluster with Brevundimonas terrae KSL-145T and Brevundimonas diminuta LMG 2089T. It exhibited 16S rRNA gene sequence similarity values of 96.0–98.7 % to members of the genus Brevundimonas and Mycoplana bullata IAM 13153T. Strain BIO-TAS2-2T contained Q-10 as the predominant ubiquinone and cyclo-C18 : 1 ω7c and C16 : 0 as the major fatty acids. The DNA G+C content was 67.0 mol%. Strain BIO-TAS2-2T exhibited DNA–DNA relatedness levels of 12–19 % with the type strains of phylogenetically related Brevundimonas species and M. bullata. The novel strain could be differentiated from Brevundimonas species and M. bullata by differences in phenotypic characteristics. On the basis of phenotypic, phylogenetic and genetic data, strain BIO-TAS2-2T is considered to represent a novel species of the genus Brevundimonas, for which the name Brevundimonas naejangsanensis sp. nov. is proposed. The type strain is BIO-TAS2-2T (=KCTC 22631T=CCUG 57609T). In this study, it is also proposed that Mycoplana bullata be transferred to the genus Brevundimonas as Brevundimonas bullata comb. nov. (type strain TK0051T=ATCC 4278T=DSM 7126T=JCM 20846T=LMG 17157T).
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- Evolution, Phylogeny And Biodiversity
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Phylogeny and taxonomy of a diverse collection of Bradyrhizobium strains based on multilocus sequence analysis of the 16S rRNA gene, ITS region and glnII, recA, atpD and dnaK genes
More LessThe genus Bradyrhizobium encompasses a variety of bacteria that can live in symbiotic and endophytic associations with legumes and non-legumes, and are characterized by physiological and symbiotic versatility and broad geographical distribution. However, despite indications of great genetic variability within the genus, only eight species have been described, mainly because of the highly conserved nature of the 16S rRNA gene. In this study, 169 strains isolated from 43 different legumes were analysed by rep-PCR with the BOX primer, by sequence analysis of the 16S rRNA gene and the 16S–23S rRNA intergenic transcribed spacer (ITS) and by multilocus sequence analysis (MLSA) of four housekeeping genes, glnII, recA, atpD and dnaK. Considering a cut-off at a level of 70 % similarity, 80 rep-PCR profiles were distinguished, which, together with type strains, were clustered at a very low level of similarity (24 %). In both single and concatenated analyses of the 16S rRNA gene and ITS sequences, two large groups were formed, with bootstrap support of 99 % in the concatenated analysis. The first group included the type and/or reference strains of Bradyrhizobium japonicum, B. betae, B. liaoningense, B. canariense and B. yuanmingense and B. japonicum USDA 110, and the second group included strains related to Bradyrhizobium elkanii USDA 76T, B. pachyrhizi PAC48T and B. jicamae PAC68T. Similar results were obtained with MLSA of glnII, recA, atpD and dnaK. Greatest variability was observed when the atpD gene was amplified, and five strains related to B. elkanii revealed a level of variability never reported before. Another important observation was that a group composed of strains USDA 110, SEMIA 5080 and SEMIA 6059, all isolated from soybean, clustered in all six trees with high bootstrap support and were quite distinct from the clusters that included B. japonicum USDA 6T. The results confirm that MLSA is a rapid and reliable way of providing information on phylogenetic relationships and of identifying rhizobial strains potentially representative of novel species.
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- Minutes
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- Errata
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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 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 1 (1951)