- Volume 61, Issue 2, 2011
Volume 61, Issue 2, 2011
- Notification List
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Notification that new names and new combinations have appeared in volume 60, part 11, 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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- New Taxa
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- Actinobacteria
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Auritidibacter ignavus gen. nov., sp. nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of the members of the family Yaniellaceae Li et al. 2008 to the family Micrococcaceae and emended description of the suborder Micrococcineae
More LessA Gram-reaction-positive, aerobic, catalase-positive, non-spore-forming, rod-shaped bacterium designated IMMIB L-1656T was isolated from an ear swab of a man and characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain IMMIB L-1656T is related to members of the family Micrococcaceae (<95.1 % sequence similarity). Anaylsis using different phylogenetic algorithms consistently grouped strain IMMIB L-1656T with members of the genus Yaniella. The organism posessed a cell-wall murein based on l-lysine (variation A4α, type l-Lys–Gly–l-Glu), MK-10 as the predominant menaquinone and long-chain cellular fatty acids of straight-chain and branched-chain saturated types (with iso-C15 : 0 and anteiso-C17 : 0 predominating). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol in addition to unknown glycolipids. The DNA G+C content was 59.7 mol%. Based on its distinctive genotypic and phenotypic characteristics, strain IMMIB L-1656T represents a novel species in a novel genus, for which the name Auritidibacter ignavus gen. nov., sp. nov. is proposed. We also propose that members of the family Yaniellaceae be transferred to the family Micrococcaceae with amendments to the description of the suborder Micrococcineae. The type strain of Auritidibacter ignavus is IMMIB L-1656T (=DSM 45359T =CCUG 57943T).
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Allocatelliglobosispora scoriae gen. nov., sp. nov., isolated from volcanic ash
More LessA novel actinomycete, designated strain Sco-B14T, was isolated from volcanic ash collected near Darangshi Oreum (a parasitic or satellite volcano) in Jeju, Republic of Korea. The organism formed well-developed, branched substrate mycelium, on which short chains of non-motile spores were arranged singly or in clusters. Aerial mycelium was not produced. Globose bodies were observed. The reverse colour of colonies was light brown to brown. Diffusible pigments were produced on ISP medium 3 and oatmeal-nitrate agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain Sco-B14T formed a lineage within the family Micromonosporaceae and was distinct from established genera. The 16S rRNA gene sequence similarity of strain Sco-B14T to members of related genera of the family was 95.0–95.7 % to type strains of Catellatospora species, 94.7 % to Hamadaea tsunoensis IMSNU 22005T, 94.7 % to Longispora albida K97-0003T and 94.0 % to Catelliglobosispora koreensis LM 042T. 3-Hydroxydiaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. Whole-cell sugars were glucose, rhamnose, ribose, xylose, arabinose, galactose and mannose. The polar lipids included diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol. The menaquinone profile contained MK-10(H4) (49 %), MK-9(H4) (24 %), MK-10(H6) (18 %) and MK-9(H6) (9 %). The predominant fatty acids were iso-C15 : 0 and C17 : 0. The DNA G+C content was 70.1 mol%. The combination of chemotaxonomic and phylogenetic data clearly separated the isolate from the type strains of all genera in the family Micromonosporaceae. On the basis of the phylogenetic and chemotaxonomic data presented in this paper, strain Sco-B14T is considered to represent a novel species of a new genus in the family Micromonosporaceae, for which the name Allocatelliglobosispora scoriae gen. nov., sp. nov. is proposed. The type strain of Allocatelliglobosispora scoriae is Sco-B14T (=KCTC 19661T =DSM 45362T).
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Kocuria salsicia sp. nov., isolated from salt-fermented seafood
Strain 104T was isolated from a traditional salt-fermented seafood in Korea. It was a Gram-positive, non-motile, coccus-shaped bacterium. It formed lemon–yellow, opaque colonies that were circular with entire margins. Optimal growth occurred at 30–37 °C, pH 7–8 and in the presence of 0–2 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences from strain 104T and reference species of the genus Kocuria indicated that strain 104T formed an independent line. The G+C content of the chromosomal DNA was 60.6 mol%. MK-7 was the major menaquinone and the predominant fatty acids were anteiso-C15 : 0 (76.7 %), anteiso-C17 : 0 (10.9 %) and iso-C16 : 0 (4.5 %). Strain 104T was most closely related to Kocuria rhizophila TA68T (98.9 % 16S rRNA gene sequence similarity). The DNA–DNA hybridization value between strain 104T and K. rhizophila TA68T was 14.1±3.4 %. On the basis of this polyphasic taxonomic analysis, strain 104T appears to represent a novel species in the genus Kocuria. The name Kocuria salsicia sp. nov. is proposed. The type strain is 104T (=KACC 21128T=JCM 16361T).
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Reclassification of ‘Dactylosporangium variesporum’ as Saccharothrix variisporea corrig. (ex Tomita et al. 1977) sp. nov., nom. rev.
More LessIn the course of a polyphasic study it was observed that ‘Dactylosporangium variesporum’ NRRL B-16296 is misclassified in the genus Dactylosporangium as it exhibits properties consistent with its assignment to the genus Saccharothrix. Phylogenetic analyses based on 16S rRNA gene sequences show that the strain falls within the evolutionary radiation of the genus Saccharothrix, a result which is supported by corresponding chemotaxonomic and morphological markers. The strain is phylogenetically most closely, albeit loosely, related to Saccharothrix espanaensis, but can be readily distinguished from this and other species of the genus Saccharothrix with validly described names by using a range of phenotypic properties. The combined genotypic and phenotypic data demonstrate conclusively that this strain should be classified as a new species in the genus Saccharothrix for which the name Saccharothrix variisporea sp. nov. is proposed. The type strain is NRRL B-16296T (=ATCC 31203T =DSM 43911T =JCM 3273T =NBRC 14104T).
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Micromonospora rhizosphaerae sp. nov., isolated from mangrove rhizosphere soil
Strain 211018T was isolated from mangrove Excocaria agallocha rhizosphere soil. 16S rRNA gene sequence analysis showed the highest similarity to the type strains of Micromonospora olivasterospora DSM 43868T (98.6 %) and Micromonospora pattaloongensis TJ2-2T (98.4 %). gyrB gene sequence analysis also indicated that strain 211018T should be assigned to the genus Micromonospora. The characteristic whole-cell sugars are xylose, mannose and arabinose. The predominant menaquinone is MK-9(H4) and the major fatty acids are iso-C15 : 0 (27.5 %), 10-methyl C17 : 0 (14.2 %), C17 : 1 ω8c (12.8 %), iso-C16 : 0 (12.6 %), anteiso-C15 : 0 (6.1 %), iso-C17 : 0 (4.1 %) and anteiso-C17 : 0 (4.0 %). The phospholipid profile comprises phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannosides. The DNA G+C content is 70.8 mol%. The chemotaxonomic data of the strain coincided with those of the genus Micromonospora. Furthermore, a combination of DNA–DNA hybridization results and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from the closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain 211018T represents a novel species of the genus Micromonospora, for which the name Micromonospora rhizosphaerae sp. nov. is proposed. The type strain is 211018T (=CGMCC 4.5599T =DSM 45431T).
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Microbacterium mitrae sp. nov., isolated from salted turban shell
More LessA novel bacterium (strain M4-8T) belonging to the genus Microbacterium was isolated from salted turban shell, which is a traditional fermented food in Korea. Its morphology, physiology, biochemical features and 16S rRNA gene sequence were characterized. Cells of this strain were Gram-positive, non-motile, non-spore-forming rods that formed yellow-pigmented colonies. It grew in 0–8 % (w/v) NaCl and at 15–37 °C, with optimal growth occurring in 1 % (w/v) NaCl and at 30 °C. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M4-8T is associated with members of the genus Microbacterium. Within the phylogenetic tree, this novel strain shared a branching point with Microbacterium hominis IFO 15708T (97.8 % similarity). The DNA G+C content was 71.3 mol% and DNA–DNA hybridization experiments showed a low level (<29 %) of DNA–DNA relatedness between M4-8T and its closest relatives. The major fatty acids were iso-C15 : 0 and anteiso-C15 : 0 and the major cell-wall diamino acid was ornithine. Data obtained from DNA–DNA hybridization and chemotaxonomic phenotypic analysis support the conclusion that strain M4-8T represents a novel species within the genus Microbacterium. The name Microbacterium mitrae sp. nov. is proposed, with M4-8T (=KACC 21129T =JCM 16363T) as the type strain.
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Nocardia niwae sp. nov., isolated from human pulmonary sources
Members of the genus Nocardia are responsible for cutaneous, pulmonary and disseminated human infections. From 2003 to 2008, four nocardioform strains (W8027, W8681, W9071 and W9241T) were isolated from patients in the state of Florida, USA. Ribosomal gene sequencing analysis suggested that a novel species of the genus Nocardia had been isolated. These strains were subjected to a taxonomic analysis using a polyphasic approach. Phenotypic analyses included morphological examination, biochemical profiling and antimicrobial susceptibility testing. Molecular studies included 16S rRNA and DNA gyrase B subunit (gyrB) gene sequence analyses and DNA–DNA hybridization. Phylogenetic neighbours were determined through 16S rRNA and gyrB gene sequence analyses. Phenotypic characteristics that differentiated the novel isolates from phylogenetically related species were growth at 45 °C, and three of the four novel strains utilized l-rhamnose. The antimicrobial profiles could not reliably distinguish the novel species from related nocardiae. Analysis showed that the 16S rRNA gene sequences of the four novel isolates were identical. The blast analysis of the near full-length 16S rRNA gene showed 99.2 % sequence similarity to Nocardia araoensis DSM 44729T, Nocardia arthritidis DSM 44731T and Nocardia beijingensis JCM 10666T, 98.7 % to Nocardia amamiensis DSM 45066T, 98.2 % to Nocardia pneumoniae JCM 12119T and 97.8 % to Nocardia takedensis JCM 13313T. Analysis of partial gyrB gene sequences showed that the novel isolates had 95.4 % similarity to N. arthritidis DSM 44731T, 95.3 % to Nocardia gamkensis DSM 44956T, 94.4 % to N. pneumoniae JCM 12119T, 93.8 % to Nocardia asiatica DSM 44668T, 93.5 % to N. amamiensis DSM 45066T, 93.4 % to N. beijingensis JCM 10666T and 93.2 % to N. araoensis DSM 44729T. The DNA–DNA relatedness values between the four novel strains were 86–89 %; the relatedness value for strain W9241T compared with N. beijingensis JCM 10666T was 47 % and 46 % with N. araoensis DSM 44729T, 44 % with N. arthritidis DSM 44731T, 32 % with N. amamiensis DSM 45066T and 20 % with N. asiatica DSM 44668T. The results of the taxonomic analysis suggested that the new isolates represent a novel species of the genus Nocardia for which the name Nocardia niwae sp. nov. is proposed. The type strain is W9241T (=DSM 45340T=CCUG 57756T).
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- Archaea
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Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov., isolated from salt in Thai fish sauce
More LessTwo red-pigmented, strictly aerobic, pleomorphic rod-shaped and extremely halophilic archaea, designated strains HST01-2RT and HST03T, were isolated from salt in a fish sauce sample from Thailand. The novel strains grew optimally at 37 °C, pH 7.0, and in the presence of 20–25 % (w/v) NaCl. The DNA G+C contents of the isolates were 61.6–62.2 mol%. Phylogenetic analysis based on a comparison of 16S rRNA gene sequences revealed that strains HST01-2RT and HST03T were placed in the radiation of species of the genus Haloarcula. The chemotaxonomic properties of the two strains, i.e. the presence of MK-8 and MK-8(H2) as the major menaquinone components and C20C20 derivatives of phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a triglycosyl diether as major polar lipids, supported the assignment of the two strains to the genus Haloarcula. Nevertheless, several phenotypic features and the low DNA–DNA relatedness between the two strains and related species of the genus Haloarcula (13.4–46.9 %) enabled the strains to be distinguished from each other and from recognized species. Therefore, strains HST01-2RT and HST03T represent two novel species in the genus Haloarcula, for which the names Haloarcula salaria sp. nov. and Haloarcula tradensis sp. nov. are proposed, respectively. The type strains are HST01-2RT (=BCC 40029T=JCM 15759T=PCU 313T) and HST03T (=BCC 40030T=JCM 15760T=PCU 314T).
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- Bacteroidetes
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Gangjinia marincola gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae
A novel strictly aerobic, orange-pigmented, Gram-stain-negative bacterium, designated strain GJ16T, was isolated from coastal seawater of Gangjin Bay, the southernmost part of the Korean peninsula, and subjected to a polyphasic taxonomic study. It grew optimally at 25–30 °C, at pH 7.0–8.0 and in the presence of 3 % NaCl. Comparative 16S rRNA gene sequence analysis revealed that strain GJ16T formed a distinct lineage within the family Flavobacteriaceae and shared less than 91.2 % 16S rRNA gene sequence similarity with members of the genera Leptobacterium, Zhouia, Winogradskyella, Dokdonia and Krokinobacter. The predominant cellular fatty acids were iso-C15 : 0 (40.2 %), iso-C15 : 1 G (12.8 %), iso-C17 : 0 3-OH (11.2 %) and C15 : 0 (6.6 %). The G+C content of the genomic DNA was 39.4 mol% and the major respiratory isoprenoid quinone was MK-6. On the basis of phenotypic and genotypic data, strain GJ16T represents a novel species in a new genus in the family Flavobacteriaceae, for which the name Gangjinia marincola gen. nov., sp. nov. is proposed; the type strain is GJ16T (=KCTC 22649T =JCM 16082T).
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Formosa spongicola sp. nov., isolated from the marine sponge Hymeniacidon flavia
More LessA Gram-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, oxidase- and catalase-positive, marine bacterium, designated A2T, was isolated from a marine sponge, Hymeniacidon flavia, collected from the coast of Jeju Island, South Korea. Phylogenetic analysis based on nearly complete 16S rRNA gene sequences revealed that strain A2T was a member of the family Flavobacteriaceae. Its closest relatives were Formosa agariphila KMM 3901T and Formosa algae KMM 3553T (96.99 and 96.98 % 16S rRNA gene sequence similarity, respectively). DNA–DNA relatedness between strain A2T and F. agariphila KMM 3901T and F. algae KMM 3553T was 14.1 and 26.8 %, respectively. The dominant fatty acids (>5 %) of strain A2T were iso-C15 : 0 (33.9 %), iso-C17 : 0 3-OH (20.8 %), iso-C15 : 1 G (10.5 %) and iso-C15 : 0 3-OH (6.1 %). The DNA G+C content of strain A2T was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of phenotypic and phylogenetic analysis, strain A2T represents a novel species of the genus Formosa, for which the name Formosa spongicola sp. nov. is proposed. The type strain is A2T (=KCTC 22662T =DSM 22637T).
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Flavobacterium dongtanense sp. nov., isolated from the rhizosphere of a wetland reed
More LessTwo strains of Gram-reaction-negative, rod-shaped, non-spore-forming, non-motile, aerobic bacteria, designated LW30T and LW29, were isolated from the rhizosphere of a wetland reed in Dongtan, Chongming Island, China. The strains formed pale-yellow colonies on R2A plates. Growth occurred at 4–37 °C (optimum 30 °C), at pH 6–9 (optimum pH 7–8) and in the presence of 0–3 % (w/v) NaCl (optimum 0–1 %). Oxidase and catalase activities and flexirubin-type pigments were absent. MK-6 was the major respiratory quinone. The major fatty acids were iso-C15 : 0, C15 : 0, iso-C15 : 1 G and iso-C17 : 1 ω9c. Strains LW30T and LW29 could be differentiated from related species by several phenotypic characteristics. Phylogenetic analyses based on 16S rRNA gene sequences placed strains LW30T and LW29 in the genus Flavobacterium with high sequence similarity to Flavobacterium cheniae NJ-26T (94.0 %) and Flavobacterium indicium GPTSA 100-9T (93.9 %). Together with F. indicium GPTSA 100-9T, strains LW30T and LW29 formed a distinct group in the phylogenetic tree. The DNA G+C content was 30 mol%. On the basis of the phylogenetic and phenotypic evidence, strains LW30T and LW29 represent a novel species of the genus Flavobacterium, for which the name Flavobacterium dongtanense sp. nov. is proposed. The type strain is LW30T (=KCTC 22671T =CCTCC AB 209201T).
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Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro
More LessA Gram-stain-negative, yellow-pigmented, rod-shaped, strictly aerobic, non-flagellated, non-gliding and oxidase- and catalase-positive bacterium, designated A6T, was isolated from a marine sponge, Halichondria oshoro, collected on the coast of Jeju Island, South Korea. Phylogenetic analysis based on the nearly complete 16S rRNA gene sequence revealed that strain A6T was a member of the family Flavobacteriaceae. The closest relatives were Aquimarina intermedia LMG 23204T, A. latercula ATCC 23177T, A. brevivitae SMK-19T and A. muelleri KMM 6020T, with which strain A6T shared 95.7, 95.1, 94.7 and 94.6 % 16S rRNA gene sequence similarity, respectively. The dominant fatty acids of strain A6T were iso-C15 : 0 (32.2 %), iso-C17 : 0 3-OH (20.0 %), iso-C15 : 0 3-OH (12.3 %), iso-C15 : 1 G (7.2 %) and summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 6.8 %). The DNA G+C content of strain A6T was 36.0 mol% and the major respiratory quinone was MK-6. On the basis of combined phenotypic and phylogenetic analyses, strain A6T represents a novel species of the genus Aquimarina, for which the name Aquimarina spongiae sp. nov. is proposed. The type strain is A6T (=KCTC 22663T =DSM 22623T).
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Bacteroides paurosaccharolyticus sp. nov., isolated from a methanogenic reactor treating waste from cattle farms
More LessA strictly anaerobic bacterial strain (WK042T) was isolated from rice-straw residue in a methanogenic reactor treating waste from cattle farms in Japan. Cells were Gram-staining-negative, non-motile, non-spore-forming rods. Growth was stimulated well by haemin, and was enhanced by cobalamin (vitamin B12). Strain WK042T utilized arabinose, xylose, glucose, mannose and aesculin as preferred substrates. Maltose, dextrin, glycogen, starch and pectin were also utilized, although growth on these substrates was much slower. The strain produced acetate, propionate and succinate from these saccharides. The strain was slightly alkaliphilic, with optimum growth at pH 7.7. The temperature range for growth was 10–40 °C, the optimum being 35 °C. The strain was sensitive to bile. The major cellular fatty acids were anteiso-C15 : 0, iso-C17 : 0 3-OH and C15 : 0. Menaquinone 11 (MK-11) was the major respiratory quinone and the genomic DNA G+C content was 41.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed the strain in the phylum Bacteroidetes. Strain WK042T was related distantly to the type strains of species in the cluster including Bacteroides massiliensis, Bacteroides vulgatus and Bacteroides dorei (91–92 % 16S rRNA gene sequence similarity). Based on data from the present phylogenetic, physiological and chemotaxonomic analyses, strain WK042T is considered to represent a novel species of the genus Bacteroides, for which the name Bacteroides paurosaccharolyticus sp. nov. is proposed. The type strain is WK042T (=JCM 15092T =DSM 21004T).
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- Firmicutes And Related Organisms
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Jeotgalicoccus coquinae sp. nov. and Jeotgalicoccus aerolatus sp. nov., isolated from poultry houses
More LessTwo Gram-stain-positive, non-motile, non-spore-forming cocci (strains MK-7T and MPA-33T) were isolated from poultry houses. Strain MK-7T was isolated on marine broth agar from coquina, a food supplement for female ducks used in a duck-fattening farm. Strain MPA-33T was isolated from the air of a turkey house on TSA after filter sampling. On the basis of 16S rRNA gene sequence similarity studies, both strains were shown to belong to the genus Jeotgalicoccus; MK-7T was most closely related to Jeotgalicoccus psychrophilus YKJ-115T (99.3 % similarity) and MPA-33T was most closely related to Jeotgalicoccus halotolerans YKJ-101T (98.8 %). The quinone system of MK-7T was composed of equal amounts of menaquinones MK-7 and MK-6 and that of MPA-33T contained 76 % MK-7 and 24 % MK-6. The polar lipid profile of strain MK-7T consisted of the major compounds diphosphatidylglycerol and phosphatidylglycerol and six unidentified lipids present in minor to moderate amounts. In strain MPA-33T, diphosphatidylglycerol was the single predominant lipid, whereas phosphatidylglycerol was detected in moderate amounts. In addition, one unidentified phospholipid and four unidentified lipids were detected. Fatty acid profiles with iso-15 : 0 and anteiso-15 : 0 as major fatty acids supported the affiliation of the strains to the genus Jeotgalicoccus. The results of physiological and biochemical tests as well as DNA–DNA hybridizations allowed clear phenotypic differentiation of strains MK-7T and MPA-33T from the most closely related species. Strains MK-7T and MPA-33T therefore represent novel species, for which the names Jeotgalicoccus coquinae sp. nov. (type strain MK-7T =DSM 22419T =CCM 7682T =CCUG 57956T) and Jeotgalicoccus aerolatus sp. nov. (type strain MPA-33T =DSM 22420T =CCM 7679T =CCUG 57953T) are proposed.
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Virgibacillus soli sp. nov., isolated from mountain soil
More LessA Gram-positive bacterium (strain CC-YMP-6T) was isolated from soil samples collected from Yang-Ming Mountain, Taiwan. On the basis of 16S rRNA gene sequence analysis, strain CC-YMP-6T clearly belonged to the genus Virgibacillus and was most closely related to the type strains of Virgibacillus halophilus (96.2 % similarity) and Virgibacillus kekensis (96.3 %). The predominant isoprenoid quinone was menaquinone MK-7 and the polar lipid profile was composed of the major components diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and one unidentified phospholipid plus moderate amounts of two unidentified aminophospholipids and a phospholipid. The polyamine pattern comprised spermidine as the single major component with spermine and putrescine present in minor amounts. The major fatty acids of strain CC-YMP-6T were iso-C15 : 0 and anteiso-C15 : 0. The results of physiological and biochemical tests allowed the clear phenotypic differentiation of strain CC-YMP-6T from all recognized species of the genus Virgibacillus. Strain CC-YMP-6T is therefore considered to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus soli sp. nov. is proposed. The type strain is CC-YMP-6T (=DSM 22952T=CCM 7714T).
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Paenibacillus chungangensis sp. nov., isolated from a tidal-flat sediment
More LessA Gram-stain-positive, rod-shaped, endospore-forming bacterium, strain CAU 9038T, was isolated from a tidal-flat sediment of DaeYiJac Island, Republic of Korea, and its taxonomic position was investigated using a polyphasic approach. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol, the major isoprenoid quinone was MK-7 and the dominant cellular fatty acid was anteiso-C15 : 0. The DNA G+C content was 51.6 mol%. 16S rRNA gene sequence analysis showed that the strain belonged to the genus Paenibacillus, with <96.1 % sequence similarity to type strains of Paenibacillus species with validly published names. The most closely related type strains to CAU 9038T were Paenibacillus thailandensis S3-4AT (96.1 % similarity) and Paenibacillus agaridevorans DSM 1355T (95.3 %). The phenotypic, chemotaxonomic and genotypic data clearly indicated that strain CAU 9038T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus chungangensis sp. nov. is proposed. The type strain is CAU 9038T (=KCTC 13717T =CCUG 59129T).
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Fontibacillus panacisegetis sp. nov., isolated from soil of a ginseng field
More LessA facultatively anaerobic, endospore-forming bacterium, designated strain P11-6T, was isolated from soil of a ginseng field located in Geumsan County, Republic of Korea. Cells of strain P11-6T were Gram-stain-negative, catalase-negative, motile rods and produced semi-translucent, circular, white colonies on tryptic soy agar. The isolate contained MK-7 as the only menaquinone and anteiso-C15 : 0 as the major fatty acid. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown aminophosphoglycolipid, an unknown aminophospholipid, two unknown phospholipids, three unknown glycolipids and three unknown lipids were detected in the polar lipid profile. The DNA G+C content of strain P11-6T was 41.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing showed that strain P11-6T was most closely related to Fontibacillus aquaticus GPTSA 19T (97.2 % sequence similarity) and that it formed a separate lineage with F. aquaticus in the family Paenibacillaceae. Combined phenotypic and DNA–DNA hybridization data supported the conclusion that strain P11-6T represents a novel species in the genus Fontibacillus, for which the name Fontibacillus panacisegetis sp. nov. is proposed; the type strain is P11-6T (=KCTC 13564T =CECT 7605T).
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- Other Bacteria
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Borrelia carolinensis sp. nov., a novel species of the Borrelia burgdorferi sensu lato complex isolated from rodents and a tick from the south-eastern USA
More LessA group of 16 isolates with genotypic characteristics different from those of known species of the Borrelia burgdorferi sensu lato complex were cultured from ear biopsies of the rodents Peromyscus gossypinus and Neotoma floridana trapped at five localities in South Carolina, USA, and from the tick Ixodes minor feeding on N. floridana. Multilocus sequence analysis of members of the novel species, involving the 16S rRNA gene, the 5S–23S (rrf–rrl) intergenic spacer region and the flagellin, ospA and p66 genes, was conducted and published previously and was used to clarify the taxonomic status of the novel group of B. burgdorferi sensu lato isolates. Phylogenetic analysis based on concatenated sequences of the five analysed genomic loci showed that the 16 isolates clustered together but separately from other species in the B. burgdorferi sensu lato complex. The analysed group therefore represents a novel species, formally described here as Borrelia carolinensis sp. nov., with the type strain SCW-22T (=ATCC BAA-1773T =DSM 22119T).
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- Proteobacteria
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Aeromonas rivuli sp. nov., isolated from the upstream region of a karst water rivulet
Two freshwater isolates (WB4.1-19T and WB4.4-101), sharing 99.9 % 16S rRNA gene sequence similarity, were highly related to Aeromonas sobria (99.7 % similarity; 6 bp differences). A phylogenetic tree derived from a multi-locus phylogenetic analysis (MLPA) of the concatenated sequences of five housekeeping genes (gyrB, rpoD, recA, dnaJ and gyrA; 3684 bp) revealed that both strains clustered as an independent phylogenetic line next to members of Aeromonas molluscorum and Aeromonas bivalvium. The DNA–DNA reassociation value between the two new isolates was 89.3 %. Strain WB4.1-19T had a DNA–DNA relatedness value of <70 % with the type strains of the other species tested. Phenotypic characterization differentiated the two novel strains from all other type strains of species of the genus Aeromonas. It is concluded that the two new strains represent a novel species of the genus Aeromonas, for which the name Aeromonas rivuli sp. nov. is proposed, with the type strain WB4.1-19T (=CECT 7518T=DSM 22539T=MDC 2511T).
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Burkholderia oxyphila sp. nov., a bacterium isolated from acidic forest soil that catabolizes (+)-catechin and its putative aromatic derivatives
A novel bacterium, designated strain OX-01T, was isolated from acidic soil, taxonomically investigated and identified as an agent that catabolizes (+)-catechin into taxifolin. Strain OX-01T is a Gram-reaction-negative, aerobic, non-sporulating, non-motile and rod-shaped bacterium. 16S rRNA gene sequence analysis identified this strain as a member of the genus Burkholderia and occupying a phylogenetic position closest to, but clearly distinct from, Burkholderia sacchari. Strain OX-01T does not have any nif genes, which are required for N2-fixation, in its genome, a feature that is similar to B. sacchari, which lacks nifH, but is distinct from the N2-fixing features of many other phylogenetically related taxa, such as Burkholderia ferrariae, B. heleia, B. mimosarum, B. nodosa, B. silvatlantica, B. tropica and B. unamae. Strain OX-01T has the following chemotaxonomic characteristics: the major ubiquinone is Q-8, the DNA G+C content is 64 mol% and the major fatty acids are C16 : 0, C17 : 0 cyclo and C18 : 1 ω7c. It also has a unique profile of carbohydrate utilization among other species of the genus Burkholderia. The strain cannot assimilate many pentoses, hexoses and oligosaccharides, whereas it can catabolize (+)-catechin and its putative aromatic derivatives, such as 4-hydroxy-3-methoxycinnamic acid, protocatechuic acid, p-hydroxybenzoic acid, trans-p-coumaric acid and vanillic acid. Based on its morphological, physiological and chemotaxonomic characteristics, together with DNA–DNA relatedness values and 16S rRNA gene sequence comparison data, we show that strain OX-O1T represents a novel species of the genus Burkholderia, for which the name Burkholderia oxyphila sp. nov. is proposed. The type strain is OX-01T (=NBRC 105797T =DSM 22550T).
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Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil
More LessA bacterial strain, designated BF-3T, was isolated from phenol-contaminated soil and investigated using a polyphasic taxonomic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BF-3T formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Comamonas; it showed highest sequence similarities to Comamonas aquatica LMG 2370T (96.8 %), C. nitrativorans DSM 13191T (96.4 %), C. odontotermitis LMG 23579T (96.4 %), C. kerstersii LMG 3475T (96.3 %), C. koreensis KCTC 12005T (96.1 %) and C. terrigena LMG 1253T (96.0 %). The major cellular fatty acids were C16 : 0, C18 : 1/C18 : 1 ω7c, C17 : 0 cyclo and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition and biochemical characteristics, strain BF-3T was clearly distinct from type strains of other recognized species of the genus Comamonas and, as such, represents a novel species of the genus Comamonas, for which the name Comamonas zonglianii sp. nov. is proposed. The type strain is BF-3T (=CCTCC AB 209170T =DSM 22523T).
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Novosphingobium soli sp. nov., isolated from soil
A yellow-pigmented, Gram-negative, rod-shaped, non-spore-forming bacterium, strain CC-TPE-1T, was isolated from oil-contaminated soil near an oil refinery located in Kaohsiung County, Taiwan. 16S rRNA gene sequence analysis of strain CC-TPE-1T showed highest sequence similarity to Novosphingobium naphthalenivorans TUT562T (98.1 %), N. panipatense SM16T (97.9 %) and N. mathurense SM117T (97.6 %) and lower (<97 %) sequence similarity to all other Novosphingobium species. DNA–DNA hybridizations of strain CC-TPE-1T with N. naphthalenivorans DSM 18518T, N. panipatense SM16T and N. mathurense SM117T showed low relatedness of 30 % (reciprocal 35 %), 29.1 % (reciprocal 30.6 %) and 35 % (reciprocal 23.6 %), respectively. The major respiratory quinone was ubiquinone Q-10, the predominant fatty acid was C18 : 1 ω7c (49.9 %) and three 2-hydroxy fatty acids, C14 : 0 2-OH (8.2 %), C15 : 0 2-OH (2.45 %) and C16 : 0 2-OH (1.05 %), were detected. Polar lipids consisted mainly of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phosphatidyldimethylethanolamine, two sphingoglycolipids, phosphatidylmonomethylethanolamine and several unidentified lipids, and a yellow pigment was also detected. The polyamine pattern contained the single major compound spermidine. Characterization by 16S rRNA gene sequence analysis, physiological parameters, pigment analysis and polyamine, ubiquinone, polar lipid and fatty acid compositions revealed that strain CC-TPE-1T represents a novel species of the genus Novosphingobium, for which we propose the name Novosphingobium soli sp. nov., with the type strain CC-TPE-1T (=DSM 22821T =CCM 7706T =CCUG 58493T).
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Parvibaculum indicum sp. nov., isolated from deep-sea water
More LessA taxonomic study was carried out on strain P31T, which was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium enriched with deep-sea water of the Indian Ocean. The isolate was Gram-reaction-negative, rod-shaped, motile by means of a polar flagellum and incapable of reducing nitrate to nitrite. Growth was observed at 0.5–8 % NaCl and at 10–41 °C. Strain P31T was unable to degrade Tween 80 or gelatin. The major respiratory quinone was ubiquinone 11 (Q-11). The dominant fatty acids were C18 : 1 ω7c (39.79 %), 11-methyl C18 : 1 ω7c (17.84 %), C19 : 0 cyclo ω8c (12.05 %) and C18 : 0 (6.09 %). The G+C content of the chromosomal DNA was 62.1 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain P31T and Parvibaculum lavamentivorans DS-1T formed a distinct lineage in the family Phyllobacteriaceae; these two strains showed 95.7 % sequence similarity, while similarities between P31T and other members of the genus Parvibaculum were below 93 %. Based on the genotypic and phenotypic data, strain P31T represents a novel species of the genus Parvibaculum, for which the name Parvibaculum indicum sp. nov. is proposed. The type strain is P31T (=CCTCC AB 208230T =LMG 24712T =MCCC 1A01132T).
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Hydrogenophilus islandicus sp. nov., a thermophilic hydrogen-oxidizing bacterium isolated from an Icelandic hot spring
More LessA novel chemolithotrophic bacterium, strain 16CT, was isolated from a hot spring in Graendalur, south-west Iceland. Cells of this organism were Gram-negative, rod-shaped and motile. The isolate was aerobic and capable of chemolithotrophic growth on hydrogen and carbon dioxide, heterotrophic growth on butyrate and several other organic compounds, and mixotrophic growth on butyrate, hydrogen and carbon dioxide. Heterotrophic growth was generally enhanced in the presence of yeast extract. Autotrophic growth on hydrogen was observed at pH values between 6.0 and 10.0 and temperatures between 35 and 60 °C; optimum growth conditions were pH 7.0 and 55 °C. The DNA G+C content was 63.9 mol%. 16S rRNA gene sequence analysis showed that strain 16CT was a member of a distinct species belonging to the class Betaproteobacteria and was most closely related to Hydrogenophilus thermoluteolus NBRC 14978T and Hydrogenophilus hirschii DSM 11420T. The major cellular fatty acids were straight-chain C16 : 0 (44.98 %) and C18 : 1 ω7c (17.93 %), as well as cyclic C17 : 0 (13.90 %) and C19 : 0 ω8c (4.67 %) fatty acids. Based on its physiological and molecular properties, it is concluded that strain 16CT represents a novel species within the genus Hydrogenophilus, for which the name Hydrogenophilus islandicus is proposed; the type strain is 16CT (=DSM 21442T=JCM 16106T).
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Nitratireductor indicus sp. nov., isolated from deep-sea water
More LessA taxonomic study was carried out on a novel bacterial strain, designated C115T, isolated from a crude-oil-degrading consortium, enriched from deep-sea water of the Indian Ocean. Cells were Gram-negative short rods, mobile by means of a monopolar flagellum. Growth was observed at salinities of 0–7 % and at 10–43 °C. It was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence analysis showed that strain C115T was related most closely to Nitratireductor aquibiodomus NL21T (96.5 % similarity), Nitratireductor kimnyeongensis KY 101T (96.4 %) and Nitratireductor basaltis J3T (96.2 %). The predominant fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c, 81.8 %) and C18 : 0 (7.0 %). The G+C content of the chromosomal DNA of strain C115T was 59 mol%. Based on its morphology, physiology and fatty acid composition together with 16S rRNA gene sequence comparisons, the novel strain most appropriately belongs to the genus Nitratireductor, but can be distinguished readily from recognized species of the genus. Strain C115T is therefore considered to represent a novel species of the genus Nitratireductor, for which the name Nitratireductor indicus sp. nov. is proposed. The type strain is C115T (=RC92-7T =CCTCC AB 209298T =LMG 25540T =MCCC 1A01260T).
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Photobacterium swingsii sp. nov., isolated from marine organisms
Six Gram-negative coccobacilli were isolated from Pacific oysters (Crassostrea gigas) from Mexico and haemolymph of spider crabs (Maja brachydactyla) from Spain. All of the isolates grew as small green colonies on thiosulphate-citrate-bile salts-sucrose (TCBS) agar and were facultatively anaerobic, oxidase-positive and sensitive to the vibriostatic agent O/129. Repetitive palindromic PCR analysis revealed a high degree of genomic homogeneity among the isolates. Several phenotypic traits differentiated the isolates from the type strains of species of the genus Photobacterium. DNA–DNA relatedness between two representative isolates and their closest phylogenetic neighbours by 16S rRNA gene sequence similarity, Photobacterium aplysiae CAIM 14T and Photobacterium frigidiphilum CAIM 20T, was 44.01–53.85 %. We propose a novel species of the genus Photobacterium to accommodate the six isolates, with the name Photobacterium swingsii sp. nov. The type strain is CAIM 1393T (=CECT 7576T).
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Ruegeria marina sp. nov., isolated from Marine Sediment
More LessA Gram-negative, neutrophilic and rod-shaped bacterium, strain ZH17T, was isolated from a marine sediment of the East China Sea and subjected to a polyphasic taxonomic characterization. The isolate grew in the presence of 0–7.5 % (w/v) NaCl and at pH 6.5–9.0; optimum growth was observed with 0.5–3.0 % (w/v) NaCl and at pH 7.5. Chemotaxonomic analysis showed ubiquinone-10 as predominant respiratory quinone and C18 : 1 ω7c, 11-methyl C18 : 1 ω7c, C16 : 0, C12 : 0 3-OH and C16 : 0 2-OH as major fatty acids. The genomic DNA G+C content was 63.5 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolate belongs to the genus Ruegeria. Strain ZH17T exhibited the closest phylogenetic affinity to the type strain of Ruegeria pomeroyi, with 97.2 % sequence similarity, and less than 97 % sequence similarity with respect to other described species of the genus Ruegeria. The DNA–DNA reassociation value between strain ZH17T and R. pomeroyi DSM 15171T was 50.7 %. On the basis of phenotypic and genotypic data, strain ZH17T represents a novel species of the genus Ruegeria, for which the name Ruegeria marina sp. nov. (type strain ZH17T =CGMCC 1.9108T =JCM 16262T) is proposed.
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Pseudoalteromonas donghaensis sp. nov., isolated from seawater
More LessA Gram-negative, rod-shaped, motile and aerobic bacterium, designated strain HJ51T, was isolated from a seawater sample from the East Sea, near South Korea. The isolate grew slowly at 4 °C, was able to grow at 40 °C, required NaCl and grew optimally at pH 6.5–7.0. The G+C content of the genomic DNA was 41.8 mol%. The major fatty acids were summed feature 4 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and summed feature 7 (C18 : 1 ω7c, C18 : 1 ω9t and/or C18 : 1 ω12t). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain HJ51T belonged to the genus Pseudoalteromonas and had 91.7–98.9 % 16S rRNA gene sequence similarity with type strains of species of the genus Pseudoalteromonas. Strain HJ51T had 7.2 % DNA–DNA relatedness with Pseudoalteromonas mariniglutinosa DSM 15203T and 12.9 % with Pseudoalteromonas prydzensis DSM 14232T. On the basis of the phenotypic, phylogenetic and genomic data, strain HJ51T represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas donghaensis sp. nov. is proposed. The type strain is HJ51T (=KCTC 22219T=LMG 24469T).
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Arcobacter trophiarum sp. nov., isolated from fattening pigs
More LessIn the course of a longitudinal study elucidating the dynamics of Arcobacter populations in pigs, 16 isolates of Gram-reaction-negative, rod-shaped, slightly curved, non-spore-forming bacteria were grouped by amplified fragment length polymorphism analysis into a distinct phenon within the genus Arcobacter. Fragments were generated for all isolates in a genus-specific PCR assay, but no amplicon was obtained in a species-specific multiplex-PCR test. Numerical analysis of the whole-cell protein profiles also showed that all isolates clustered in a single group that was distinct from related members of the genus Arcobacter. DNA–DNA hybridizations between two representative strains, designated 64T and 122, of the isolates obtained exhibited a mean DNA–DNA relatedness of 72 %. DNA–DNA hybridizations between strains 64T and 122 and reference strains of other animal-related bacteria of the genus Arcobacter revealed binding values of 47 % or less. The DNA G+C contents of the two representative strains were 28.5 and 28.4 mol%, respectively, and analysis of three marker genes identified Arcobacter cryaerophilus, A. thereius, A. cibarius and A. skirrowii as their closest phylogenetic neighbours. Strains 64T and 122 could be distinguished from other members of the genus Arcobacter by means of biochemical tests for catalase and urease activities, nitrate reduction, indoxyl acetate hydrolysis, lack of growth at 37 °C, growth in 2 % (w/v) NaCl, growth on 0.1 % sodium deoxycholate and non-supplemented Campylobacter charcoal-deoxycholate base medium and resistance to cephalothin (32 mg l−1) and cefoperazone (64 mg l−1). Additionally, a PCR assay was developed for the detection and identification of strains 64T and 122, which represent a novel species of the genus Arcobacter, for which the name Arcobacter trophiarum sp. nov. is proposed. The type strain is strain 64T (=LMG 25534T =CCUG 59229T).
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Vibrio communis sp. nov., isolated from the marine animals Mussismilia hispida, Phyllogorgia dilatata, Palythoa caribaeorum, Palythoa variabilis and Litopenaeus vannamei
Eight Vibrio isolates originating from the marine corals Mussismilia hispida and Phyllogorgia dilatata and the zoanthids Palythoa caribaeorum and Palythoa variabilis in Brazil and the Pacific white shrimp (Litopenaeus vannamei) in Ecuador were studied by means of a polyphasic approach. The novel isolates formed a tight monophyletic group in the genus Vibrio and were closely related to species of the Vibrio harveyi group, to which they showed more than 99 % 16S rRNA gene sequence similarity. Analysis based on concatenated sequences of the following seven genes, 16S rRNA, gyrB, recA, rpoA, topA, pyrH and mreB (5633 bp in length), showed clear separation between the isolates and species of the V. harveyi group. Amplified fragment length polymorphism (AFLP) analysis, performed previously, revealed that a representative isolate of this group, LMG 20370, was clearly separate from known Vibrio species (it belonged to the so-called AFLP cluster A31). DNA–DNA hybridization (DDH) experiments with representative isolates and type strains of the V. harveyi species group revealed high DDH between the novel isolates (more than 74 %) and less than 70 % DDH towards type strains of related Vibrio species, proving the novel species status of the isolates. Phenotypically, the novel species belongs to the arginine dihydrolase (A)-negative, lysine decarboxylase (L)-positive and ornithine decarboxylase (O)-positive (A−/L+/O+) cluster reported previously. Most species of the V. harveyi group (i.e. Vibrio rotiferianus, V. harveyi, V. parahaemolyticus and V. alginolyticus) also belong to this A−/L+/O+ cluster. However, several phenotypic features can be used for the identification of the novel species. In contrast to its closest phylogenetic neighbours, the novel species exhibits esterase (C4) and N-acetyl-β-glucosaminidase activities, but it does not produce acetoin, does not use citrate, α-ketoglutaric acid or propionic acid and does not ferment melibiose. The novel species can also be differentiated on the basis of the presence of the fatty acids C17 : 0, C17 : 1 ω8c, iso-C17 : 0 and iso-C13 : 0 and the absence of the fatty acid C18 : 0. The name Vibrio communis sp. nov. is proposed for this taxon. Strain R-40496T (=LMG 25430T =CAIM 1816T) is the type strain.
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Oleibacter marinus gen. nov., sp. nov., a bacterium that degrades petroleum aliphatic hydrocarbons in a tropical marine environment
Three Gram-negative, motile, mesophilic, aerobic, rod-shaped bacterial strains, designated 2O1T, 1O14 and 1O18, were isolated from Indonesian seawater after enrichment with crude oil and a continuous supply of supplemented seawater. The strains exhibited high n-alkane-degrading activity, which indicated that the strains were important degraders of petroleum aliphatic hydrocarbons in tropical marine environments. Phylogenetic analyses based on 16S rRNA gene sequences of members of the Gammaproteobacteria showed that the isolates formed a coherent and distinct cluster in a stable lineage containing Oceanobacter kriegii IFO 15467T (96.4–96.5 % 16S rRNA gene sequence similarity) and Thalassolituus oleivorans MIL-1T. DNA G +C content was 53.0–53.1 mol%. The major fatty acids were C16 : 0, C16 : 1 ω7 and C18 : 1 ω9 and the hydroxy fatty acids were C12 : 0 3-OH and C10 : 0 3-OH. The polar lipids were phosphatidylglycerol, a ninhydrin-positive phospholipid(s) and glycolipids. The major quinone was Q-9 (97–99 %), which distinguished the isolates from Oceanobacter kriegii NBRC 15467T (Q-8; 91 %). On the basis of phenotypic, genotypic and chemotaxonomic data, including DNA–DNA hybridization, the isolates represent a novel genus and species, for which the name Oleibacter marinus gen. nov., sp. nov. is proposed. The type strain of Oleibacter marinus is 2O1T (=NBRC 105760T =BTCC B-675T).
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Description of Undibacterium oligocarboniphilum sp. nov., isolated from purified water, and Undibacterium pigrum strain CCUG 49012 as the type strain of Undibacterium parvum sp. nov., and emended descriptions of the genus Undibacterium and the species Undibacterium pigrum
A Gram-negative, oxidase- and catalase-positive, flagellated, rod-shaped bacterium, designated strain EM 1T, was isolated from purified water. 16S rRNA gene sequence analysis indicated that the novel strain belonged to the family Oxalobacteraceae within the class Betaproteobacteria; the closest phylogenetic relative was Undibacterium pigrum DSM 19792T (96.7 % gene sequence similarity). The new isolate could be distinguished from the type strain of U. pigrum DSM 19792T (=CCUG 49009T=CIP 109318T) and from strain CCUG 49012T, which has been described as a second genomovar of this species, on the basis of genotypic data and several phenotypic properties. An S-layer was present in the cell envelope in U. pigrum DSM 19792T, but was absent in strains EM 1T and CCUG 49012T. Test conditions were established that enabled strain CCUG 49012T to be distinguished from U. pigrum DSM 19792T. As found for U. pigrum, the main fatty acids of strains EM 1T and CCUG 49012T were summed feature 3 (including unsaturated C16 : 1 ω7c), straight-chain C16 : 0 and unsaturated C18 : 1 ω7c (low percentage in strain CCUG 49012T), and C10 : 0 3-OH was the sole hydroxylated fatty acid. The polar lipid profile consisted of the predominant lipids phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The polyamine profile was mainly composed of the major compound putrescine and moderate amounts of 2-hydroxyputrescine. In contrast to U. pigrum and strain CCUG 49012T, where ubiquinone Q8 was reported as the sole quinone component, the quinone system of strain EM 1T consisted of ubiquinone Q-8 (64 %) and Q-7 (36 %). The 16S rRNA gene sequence similarity, the polar lipid profile and the absence of C12-hydroxylated fatty acids all indicated that strain EM 1T was affiliated with the genus Undibacterium. 16S rRNA gene sequence similarity values lower than 97.0 % and several differentiating phenotypic traits demonstrated that strain EM 1T represents a novel species for which the name Undibacterium oligocarboniphilum sp. nov. is proposed (type strain EM 1T=DSM 21777T=CCUG 57265T). In addition, based on previously published results and this study, a separate species, Undibacterium parvum sp. nov., is proposed with strain CCUG 49012T (=DSM 23061T=CIP 109317T) as the type strain.
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Dyella thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soil of sunflower (Helianthus annuus L.)
A Gram-negative, aerobic, motile, rod-shaped, thiosulfate-oxidizing bacterium, designated ATSB10T, was isolated from rhizosphere soil of sunflower (Helianthus annuus L.). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ATSB10T was closely related to members of the genera Dyella (96.4–98.1 % 16S rRNA gene sequence similarity) and Luteibacter (96.4–97.0 %) and Fulvimonas soli LMG 19981T (96.7 %) and Frateuria aurantia IFO 3245T (97.8 %). The predominant fatty acids were iso-C16 : 0, iso-C17 : 1 ω9c and iso-C15 : 0. The major quinone was Q-8. The G+C content of the genomic DNA was 66.0 mol%. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidyldimethylethanolamine, an unknown phospholipid, unknown aminophospholipids and an unknown aminolipid. On the basis of phenotypic properties, phylogenetic distinctiveness and DNA–DNA relatedness, strain ATSB10T represents a novel species in the genus Dyella, for which the name Dyella thiooxydans sp. nov. is proposed. The type strain is ATSB10T (=KACC 12756T =LMG 24673T).
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Limnobacter litoralis sp. nov., a thiosulfate-oxidizing, heterotrophic bacterium isolated from a volcanic deposit, and emended description of the genus Limnobacter
More LessA Gram-negative, aerobic, heterotrophic bacterium, designated KP1-19T, was isolated from a 22-year-old volcanic deposit at a site lacking vegetation on the island of Miyake, Japan. Strain KP1-19T was able to use thiosulfate (optimum concentration 10 mM) as an additional energy source. 16S rRNA gene sequence analysis indicated that strain KP1-19T was closely related to Limnobacter thiooxidans CS-K2T within the class Betaproteobacteria (97.7 % 16S rRNA gene sequence similarity). The cellular fatty acid profile was characteristic of the genus Limnobacter: the major fatty acids (>5 %) were C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c and minor amounts of C10 : 0 3-OH were also found. DNA–DNA relatedness between strain KP1-19T and L. thiooxidans LMG 19593T was 18 %. Therefore, strain KP1-19T represents a novel species, for which the name Limnobacter litoralis sp. nov. is proposed. The type strain is KP1-19T (=LMG 24869T =NBRC 105857T =CIP 109929T).
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Hydrocarboniphaga daqingensis sp. nov., isolated from a freshwater lake
More LessA Gram-negative bacterium, designated B2-9T, was isolated from water of a slightly alkaline lake, Longhu Lake in Daqing, north-east China. Strain B2-9T was an aerobic rod, heterotrophic, catalase- and oxidase-positive and motile by means of a single polar flflagellum. The isolate grew well on n-alkanes C9–C17 and weakly on C6–C8, C18 and C19. Growth occurred at 10–37 °C (optimum 20–25 °C), at pH 5.5–9.5 (optimum pH 7.0) and with ≤1.0 % (w/v) NaCl. The major fatty acids were C18 : 1 ω7c (41.4 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω7c; 18.5 %) and C16 : 0 (10.9 %). Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain B2-9T belonged to the genus Hydrocarboniphaga of the class Gammaproteobacteria and shared 97.0 % 16S rRNA gene sequence similarity with Hydrocarboniphaga effusa AP103T. DNA–DNA relatedness between strain B2-9T and H. effusa DSM 16095T was 24 %. The DNA G+C content of strain B2-9T was 66 mol%. Strain B2-9T is considered to represent a novel species of the genus Hydrocarboniphaga, for which the name Hydrocarboniphaga daqingensis sp. nov. is proposed. The type strain is B2-9T (=CGMCC 1.7049T =NBRC 104238T).
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Cocleimonas flava gen. nov., sp. nov., a gammaproteobacterium isolated from sand snail (Umbonium costatum)
More LessA Gram-stain-negative, aerobic, yellow-pigmented, heterotrophic, sulfur-oxidizing, non-motile, rod-shaped bacterium, designated KMM 3898T, was isolated from an internal tissue of the sand snail Umbonium costatum, collected from the shallow sediments of the Sea of Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain KMM 3898T formed a distinct phylogenetic lineage within the class Gammaproteobacteria and was most closely related to Leucothrix mucor DSM 2157T (89.2 % 16S rRNA gene sequence similarity) and members of the genus Thiothrix (86.7–88.5 %). Chemotaxonomically, strain KMM 3898T contained the isoprenoid quinone Q-8, the polar lipids phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and an unknown phospholipid and the fatty acids C18 : 1 ω7c, C16 : 1 ω7c and C16 : 0 as predominant components (>10 %). The DNA G+C content of strain KMM 3898T was 43.4 mol%. On the basis of phenotypic features and phylogenetic analysis, strain KMM 3898T represents a novel genus and species, for which the name Cocleimonas flava gen. nov., sp. nov. is proposed. The type strain is KMM 3898T (=NRIC 0757T =JCM 16494T).
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Kordiimonas lacus sp. nov., isolated from a ballast water tank, and emended description of the genus Kordiimonas
More LessA Gram-negative, motile, rod-shaped bacterial strain, designated S3-22T, was isolated from a sediment sample collected from a ballast water tank of a commercial ship and subjected to a polyphasic taxonomic characterization. The isolate formed small, light-yellow, semi-translucent and circular colonies on solid complex media. The strain was oxidase- and catalase-positive and metabolized a large number of carbon sources. Chemotaxonomic analysis showed ubiquinone Q-10 as predominant respiratory quinone, phosphatidylglycerol and an unidentified glycolipid as major polar lipids and iso-C17 : 1 ω9c, iso-C15 : 0, C16 : 1 ω7c and/or iso-C15 : 0 2-OH, C16 : 0, iso-C17 : 0 and C18 : 1 ω7c as major fatty acids and the hydroxy fatty acids iso-C17 : 0 3-OH and C16 : 0 3-OH. The genomic DNA G+C content was 54.9 mol%. 16S rRNA gene sequence analysis revealed that the isolate has 96.1 % similarity to the type strain of Kordiimonas gwangyangensis, the sole described species within the order Kordiimonadales, and less than 91.0 % similarity to other recognized species. On the basis of phenotypic and genotypic data, strain S3-22T represents a novel species of the genus Kordiimonas, for which the name Kordiimonas lacus sp. nov. is proposed, with the type strain S3-22T (=CGMCC 1.9109T =JCM 16261T). An emended description of the genus Kordiimonas is also presented.
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Roseovarius marinus sp. nov., isolated from seawater
More LessA Gram-stain-negative, non-motile, ovoid- to rod-shaped bacterium, designated HDW-9T, belonging to the class Alphaproteobacteria, was isolated from seawater of the Yellow Sea, Korea. Strain HDW-9T grew optimally at pH 7.0–8.0, at 30 °C and with 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HDW-9T clustered with Roseovarius crassostreae CV919-312T, with which it exhibited 95.5 % 16S rRNA gene sequence similarity. Strain HDW-9T exhibited 92.5–94.7 % 16S rRNA gene sequence similarity with the other type strains of species of the genus Roseovarius. Strain HDW-9T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The DNA G+C content was 58.3 mol%. Differential phenotypic properties distinguished strain HDW-9T from the other members of the genus Roseovarius. Strain HDW-9T is considered to represent a novel species of the genus Roseovarius, for which the name Roseovarius marinus sp. nov. is proposed. The type strain is HDW-9T (=KCTC 22805T =CCUG 58403T).
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Lysobacter xinjiangensis sp. nov., a moderately thermotolerant and alkalitolerant bacterium isolated from a gamma-irradiated sand soil sample
More LessA yellow-pigmented bacterial strain, designated RCML-52T, was isolated from an abandoned gold mine in the desert in Xinjiang, China. Strain RCML-52T was Gram-negative, aerobic and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain RCML-52T was affiliated with the genus Lysobacter. Strain RCML-52T exhibited <95.6 % 16S rRNA gene sequence similarity to the type strains of all species of the genus Lysobacter. The major fatty acids were iso-C16 : 0 (27.6 %), iso-C15 : 0 (19.1 %), iso-C17 : 1 ω9c (16.4 %), iso-C11 : 0 3-OH (6.5 %) and iso-C11 : 0 (5.3 %). The DNA G+C content was 69.7 mol%. The major isoprenoid quinone was Q-8. On the basis of phylogenetic, phenotypic and chemotaxonomic analysis, strain RCML-52T should be assigned to a novel species of the genus Lysobacter, for which the name Lysobacter xinjiangensis sp. nov. is proposed. The type strain is RCML-52T (=CCTCC AB 208194T =KCTC 22558T).
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Frateuria terrea sp. nov., isolated from forest soil, and emended description of the genus Frateuria
More LessA bacterial strain, designated VA24T, was isolated from forest soil of the Changbai Mountains, Heilongjiang province, China. Cells of strain VA24T were Gram-reaction-negative, aerobic, non-spore-forming, long rods, 0.3–0.5×2.0–3.0 μm in size and were motile by means of a subpolar flagellum. Strain VA24T was oxidase-positive and catalase-negative. Growth occurred at 21–36 °C, pH 5–10 and in 0–2 % (w/v) NaCl but did not occur at 37 °C. The predominant respiratory quinone was Q-8, the major polar lipids were phosphatidylethanolamine and phosphatidylmonomethylethanolamine and the major cellular fatty acids were iso-C15 : 0 (14.9 %), iso-C17 : 1 ω9c (14.1 %), iso-C17 : 0 (10.8 %) and iso-C16 : 0 (10.3 %). The DNA G+C content was 67.4 mol% (T m). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain VA24T was closely related to Frateuria aurantia IFO 13300T with 96.9 % sequence similarity. DNA–DNA relatedness of strain VA24T to F. aurantia DSM 6220T was 15.8 %. Based on its phenotypic and genotypic features, strain VA24T represents a novel species of the genus Frateuria, for which the name Frateuria terrea sp. nov. is proposed. The type strain is VA24T (=CGMCC 1.7053T =NBRC 104236T).
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- Eukaryotic Micro-Organisms
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Candida andamanensis sp. nov., Candida laemsonensis sp. nov. and Candida ranongensis sp. nov., anamorphic yeast species isolated from estuarine waters in a Thai mangrove forest
More LessFive strains (RV5T, RV140, R31T, RS17 and RS28T) representing three novel anamorphic ascomycetous yeast species were isolated by membrane filtration from estuarine waters collected from a mangrove forest in Laem Son National Park, Ranong Province, Thailand, on different occasions. On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 domain of the large-subunit rRNA gene and the internal transcribed spacer region and phylogenetic analysis, three strains were found to represent two novel Candida species. Two strains (RV5T and RV140) represented a single novel species, for which the name Candida laemsonensis sp. nov. is proposed. The type strain is RV5T (=BCC 35154T =NBRC 105873T =CBS 11419T). Strain R31T was assigned to a novel species that was named Candida andamanensis sp. nov. (type strain R31T =BCC 25965T =NBRC 103862T =CBS 10859T). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics, sequence analysis of the D1/D2 domain of the large-subunit rRNA gene and phylogenetic analysis, strains RS17 and RS28T represented another novel species of Candida, for which the name Candida ranongensis sp. nov. is proposed. The type strain is RS28T (=BCC 25964T =NBRC 103861T =CBS 10861T).
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Candida saraburiensis sp. nov. and Candida prachuapensis sp. nov., xylose-utilizing yeast species isolated in Thailand
Four strains of two novel xylose-utilizing yeast species were obtained from samples collected in Thailand from decaying corncobs (strains KU-Xs13T and KU-Xs18), a decaying grass (KU-Xs20) and estuarine water from a mangrove forest (WB15T). On the basis of morphological, biochemical, physiological and chemotaxonomic characteristics and sequence analysis of the D1/D2 domain of the large subunit rRNA gene, the four strains were found to represent two novel species of the genus Candida in the Candida albicans/Lodderomyces elongisporus clade. Three strains (KU-Xs13T, KU-Xs18 and KU-Xs20) were assigned as a single novel species, which was named Candida saraburiensis sp. nov. The type strain is KU-Xs13T (=CBS 11696T=NBRC 106721T=BCC 39601T). Strain WB15T represented another novel species of the genus Candida that was named Candida prachuapensis sp. nov. The type strain is WB15T (=CBS 11024T=NBRC 104881T=BCC 29904T).
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Sympodiomycopsis kandeliae sp. nov., a basidiomycetous anamorphic fungus from mangroves, and reclassification of Sympodiomycopsis lanaiensis as Jaminaea lanaiensis comb. nov.
More LessThree ustilaginomycetous anamorphic strains were isolated from flowers of Kandelia candel in mangrove forests of Taiwan. Phylogenetic analyses based on the combined sequences of internal transcribed spacer 1 (ITS1)-5.8S-ITS2 and the D1/D2 domain of the large-subunit (LSU) rDNA indicated that the closest recognized species was Sympodiomycopsis paphiopedili. The results of a DNA–DNA hybridization experiment and the physiological characteristics showed that the three strains represent a novel species within the genus Sympodiomycopsis. The name Sympodiomycopsis kandeliae sp. nov. is proposed, with FIRDI 007T (=BCRC 23165T =CBS 11676T) as the type strain. In addition, based on phenotypic characteristics and the phylogenetic analyses of the combined sequences of the ITS region and D1/D2 domain of the LSU rDNA, Sympodiomycopsis lanaiensis was clustered with the genus Jaminaea. A new combination, Jaminaea lanaiensis comb. nov. (type strain LM418T =DSM 18755T =ATCC MYA-4092T =NRRL Y-48466T =CBS 10858T =BCRC 23177T), is proposed.
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- Evolution, Phylogeny And Biodiversity
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Genetic characterization of root-nodule bacteria associated with Acacia salicina and A. stenophylla (Mimosaceae) across south-eastern Australia
More LessSymbiotic relationships between legumes and nitrogen-fixing soil micro-organisms are of ecological importance in plant communities worldwide. For example, nutrient-poor Australian soils are often dominated by shrubby legumes (e.g. species of Acacia). However, relatively few studies have quantified patterns of diversity, host-specificity and effectiveness of these ecologically important plant–microbe interactions. In this study, 16S rRNA gene sequence and PCR-RFLP analyses were used to examine bacterial strains isolated from the root nodules of two widespread south-eastern Australian legumes, Acacia salicina and Acacia stenophylla, across nearly 60 sites. The results showed that there was extensive genetic diversity in microbial populations, including a broad range of novel genomic species. While previous studies have suggested that most native Australian legumes nodulate primarily with species of the genus Bradyrhizobium, our results indicate significant associations with members of other root-nodule-forming bacterial genera, including Rhizobium, Ensifer, Mesorhizobium, Burkholderia, Phyllobacterium and Devosia. Genetic analyses also revealed a diverse suite of non-nodulating bacterial endophytes, only a subset of which have been previously recorded. Although the ecological roles of these endosymbionts are not well understood, they may play both direct and indirect roles in promoting plant growth, nodulation and disease suppression.
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Phylogenetic relationships and diversity of β-rhizobia associated with Mimosa species grown in Sishuangbanna, China
More LessIn order to investigate the genetic diversity of rhizobia associated with various exotic and invasive species in tropical mainland China, 116 bacterial isolates were obtained from Mimosa root nodules collected from Sishuangbanna and Yuanjiang districts of Yunnan province. Isolated rhizobia were characterized by RFLP analysis of 16S rRNA genes, SDS-PAGE of whole-cell proteins and BOX-PCR. Most of the isolated strains were identified as β-rhizobia belonging to diverse populations of Burkholderia and Cupriavidus, and the phylogenetic relationships of their 16S rRNA gene sequences showed that they were closely related to one of four β-rhizobia species: Burkholderia phymatum, B. mimosarum, B. caribensis or Cupriavidus taiwanensis. Additionally, among the 116 isolates, 53 different whole-cell SDS-PAGE profiles and 30 distinct BOX-PCR genotypic patterns were detected, which demonstrated the genetic and phenotypic diversity found within these Burkholderia and Cupriavidus strains. To the best of our knowledge, this is the first report that β-rhizobia are extant and possibly widespread on the Chinese mainland and nodulate easily with Mimosa plants. We also find it especially interesting that this appears to be the first report from mainland China of Cupriavidus symbionts of Mimosa. These records enrich our knowledge and understanding of the geographical distribution and diversity of these bacteria.
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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 72 (2022 - 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 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)