- Volume 62, Issue Pt_9, 2012
Volume 62, Issue Pt_9, 2012
- Validation List
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List of new names and new combinations previously effectively, but not validly, published
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors’ names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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- Notification List
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Notification that new names and new combinations have appeared in volume 62, part 6, 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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- Archaea
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Halobacterium piscisalsi Yachai et al. 2008 is a later heterotypic synonym of Halobacterium salinarum Elazari-Volcani 1957
Halobacterium piscisalsi was proposed by Yachai et al. (2008), with a single strain, HPC1-2T ( = BCC 24372T = JCM 14661T = PCU 302T), which was isolated from fermented fish (pla-ra) in Thailand. According to Yachai et al. (2008), the strain was closely related to Halobacterium salinarum based on 16S rRNA gene sequence comparisons and could be differentiated by low DNA–DNA relatedness values and different biochemical profiles compared with other species of the genus. The reanalysis of the 16S rRNA gene sequences and the DNA–DNA relatedness among H. piscisalsi JCM 14661T and H. salinarum strains JCM 8978T, R1 and NRC-1 revealed that they all had exactly the same 16S rRNA gene sequence and shared more than 70 % DNA–DNA relatedness. In addition, the full-length DNA-dependent RNA polymerase subunit B (RpoB) protein sequence of H. piscisalsi JCM 14661T (607 amino acids) was the same as that of H. salinarum JCM 8978T and showed 94.7 and 96.7 % similarities with those of Halobacterium noricense JCM 15102T and Halobacterium jilantaiense JCM 13558T, respectively. Despite the different biochemical properties described by Yachai et al. (2008), the characteristic phenotypic properties of H. piscisalsi agreed with those in the description of H. salinarum emended by Gruber et al. (2004). Therefore, H. piscisalsi Yachai et al. (2008) should be regarded as a later heterotypic synonym of H. salinarum Elazari-Volcani 1957.
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- Actinobacteria
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Microbacterium amylolyticum sp. nov., isolated from soil from an industrial waste site
More LessA Gram-staining-positive, heterotrophic, aerobic, non-motile, non-endospore-forming, yellow-coloured rod, designated strain N5T, was isolated from a soil sample collected at an industrial waste site in Noida, on the outskirts of Delhi, India. In phylogenetic analyses based on 16S rRNA gene sequences, strain N5T was most closely related to members of established species in the genus Microbacterium (with sequence similarities of approximately 94.0–97.6 %), particularly Microbacterium indicum LMG 23459T (97.59 %) and Microbacterium gubbeenense LMG 19263T (97.18 %). In DNA–DNA hybridization studies, however, none of the DNA–DNA relatedness values between strain N5T and members of the genus Microbacterium exceeded 11.3 %. The genomic DNA G+C content of the novel strain was 68 mol%. The chemotaxonomic characteristics of strain N5T, which had MK-11 and MK-10 as its major menaquinones and anteiso-C15 : 0 (45 %), anteiso-C17 : 0 (37 %), iso-C16 : 0 (8.5 %) and C16 : 0 (4.5 %) as its predominant fatty acids, were consistent with classification in the genus Microbacterium . Peptidoglycan in the novel strain, which contained ornithine, alanine, glycine, homoserine, glutamic acid, 3-hydroxyglutamic acid, muramic acid and traces of N-glycolyl residues, was of type B2β. The polar lipid profile of strain N5T comprised diphosphatidylglycerol, phosphatidylglycerol and an unknown glycolipid. The novel strain’s major cell-wall sugars were glucose and galactose. Based on the phylogenetic, DNA–DNA hybridization, chemotaxonomic and phenotypic data, strain N5T represents a novel species within the genus Microbacterium for which the name Microbacterium amylolyticum sp. nov. is proposed; the type strain is N5T ( = DSM 24221T = CCM 7881T).
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Promicromonospora thailandica sp. nov., isolated from marine sediment
More LessA novel actinomycete, strain S7F-02T, which produced primary branched hyphae and fragmented into V- and Y-shaped bacillary cells, was isolated from marine sediment collected in the Andaman Sea, Trang Province, Thailand. Lysine was found to be the diagnostic diamino acid in the cell-wall peptidoglycan. The whole-cell sugars of strain S7F-02T were ribose, arabinose and glucose. The characteristic phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinone was MK-9(H4). The predominant cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0. The G+C content of the genomic DNA of strain S7F-02T was 70.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain S7F-02T should be classified in the genus Promicromonospora . This strain formed a close association with Promicromonospora citrea DSM 43110T, with which it shared 99.2 % 16S rRNA gene sequence similarity. DNA–DNA hybridization data together with physiological and biochemical properties showed that strain S7F-02T could be readily distinguished from its closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain S7F-02T is considered to represent a novel species of the genus Promicromonospora , for which the name Promicromonospora thailandica sp. nov. is proposed. The type strain is S7F-02T ( = BCC 41922T = JCM 17130T).
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Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium
A Gram-positive, non-endospore-forming bacterium, designated strain SK 18T, was isolated from surface soil of a landfill site by dilution plating on trypticase soy broth agar. Preliminary characterization of strain SK 18T via biochemical tests, analysis of fatty acid methyl esters and partial 16S rRNA gene sequencing placed it within the genus Microbacterium . Analysis of the cell wall indicated that the peptidoglycan was of cross-linkage type B, containing the amino acids lysine and ornithine and with muramic acid in the N-glycolyl form. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unidentified phospholipid and an unidentified glycolipid. The major fatty acids of the cell membrane were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C16 : 0. These data further strengthened placement of the strain within the genus Microbacterium . Strain SK 18T shared highest 16S rRNA gene sequence similarity (97.2 %) with Microbacterium ulmi DSM 16931T. Levels of similarity with the type strains of all other recognized Microbacterium species were less than 97.0 %. DNA–DNA hybridization experiments with strain SK 18T and its closest relative, M. ulmi DSM 16931T, revealed a low reassociation value of 39.0 % (σ = 3.8 %). Moreover, strain SK 18T showed a number of differences in phenotypic characteristics (colony colour, catalase activity, hydrolysis of polymers, acid production from sugars and oxidation of various substrates), and its DNA G+C content was also higher than that of M. ulmi DSM 16931T. These data indicated that strain SK 18T represents a novel species of the genus Microbacterium , for which the name Microbacterium immunditiarum sp. nov. is proposed. The type strain is SK 18T ( = MTCC 7185T = JCM 14034T). An emended description of the genus Microbacterium is also provided.
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Corynebacterium epidermidicanis sp. nov., isolated from skin of a dog
A Gram-stain-positive, pleomorphic, oxidase-negative, non-motile isolate from the skin of a dog, designated strain 410T, was subjected to comprehensive taxonomic characterization. Comparison of the 16S rRNA gene sequences revealed that the novel isolate showed highest similarities to the type strains of Corynebacterium humireducens , Corynebacterium diphtheriae , Corynebacterium pseudotuberculosis and Corynebacterium ulcerans (96.1–96.8 %). The quinone system consisted predominantly of MK-8(H2) and MK-9(H2). The polar lipid profile of strain 410T contained the major compounds diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, two unidentified phospholipids and four unidentified glycolipids. The polyamine pattern was composed of the major amines spermidine and spermine. In the fatty acid profile, predominantly straight-chain, saturated and mono-unsaturated fatty acids were detected (C18 : 1ω9c, C16 : 1ω7c, C16 : 0). These chemotaxonomic traits are in agreement with those reported for representatives of the genus Corynebacterium . Strain 410T tested negative for diphtheria toxin. Physiological properties as well as unique traits in the polar lipid profile could be used to distinguish strain 410T from the most closely related species. These data suggest that strain 410T represents a novel species of the genus Corynebacterium , for which we propose the name Corynebacterium epidermidicanis sp. nov. The type strain is 410T ( = DSM 45586T = LMG 26322T = CCUG 60915T).
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Arcanobacterium canis sp. nov., isolated from otitis externa of a dog, and emended description of the genus Arcanobacterium Collins et al. 1983 emend. Yassin et al. 2011
A polyphasic taxonomic study was performed on an unidentified Arcanobacterium -like Gram-stain-positive bacterium isolated from otitis externa of a dog. Comparative 16S rRNA gene sequencing showed that the bacterium belonged to the genus Arcanobacterium and was most closely related to the type strains of Arcanobacterium haemolyticum (97.2 %), Arcanobacterium hippocoleae (96.5 %) and Arcanobacterium phocae (96.4 %). The presence of the major menaquinone MK-9(H4) supported the affiliation of this strain to the genus Arcanobacterium . The polar lipid profile contained the major lipids phosphatidylcholine, diphosphatidylglycerol, phosphatidylinositol mannoside and an unidentified phospholipid (PL2). Major fatty acids were C14 : 0, C16 : 0, C18 : 0, C18 : 1ω9c and C18 : 2ω6,9c/anteiso-C18 : 0 (detected as a summed feature). C10 : 0 and C12 : 0 were present in minor amounts. The results of physiological and biochemical testing clearly distinguished the unknown bacterium from other species of the genus Arcanobacterium . Based on these tests, it is proposed that the unknown bacterium should be classified in the novel species Arcanobacterium canis sp. nov. The type strain of Arcanobacterium canis is P6775T ( = CCM 7958T = CCUG 61573T = CIP 110339T). An emended description of the genus Arcanobacterium is also provided.
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- Firmicutes and Related Organisms
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Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis)
Three strains of lactic acid bacteria (LAB) were isolated from the faeces of apparently healthy wild Canada geese (Branta canadensis) in 2010 by cultivating faecal LAB on Rogosa SL agar under aerobic conditions. These three isolates were found to share 99.9 % gene sequence similarity of their 16S rRNA, their 16S–23S intergenic transcribed spacer region (ITS), partial 23S rRNA, rpoB, rpoC, rpoA and pheS gene sequences. However, the three strains exhibited lower levels of sequence similarity of these genetic targets to all known LAB, and the phylogenetically closest species to the geese strains were Lactobacillus casei , Lactobacillus paracasei , Lactobacillus rhamnosus and Lactobacillus saniviri . In comparison to L. casei ATCC 393T, L. paracasei ATCC 25302T, L. rhamnosus ATCC 7469T and L. saniviri DSM 24301T, the novel isolates reacted uniquely in tests for cellobiose, galactose, mannitol, citric acid, aesculin and dextrin, and gave negative results in tests for l-proline arylamidase and l-pyrrolydonyl-arylamidase, and in the Voges-Proskauer test. Biochemical tests for cellobiose, aesculin, galactose, gentiobiose, mannitol, melezitose, ribose, salicin, sucrose, trehalose, raffinose, turanose, amygdalin and arbutin could be used for differentiation between L. saniviri and the novel strains. On the basis of phenotypic and genotypic characteristics, and phylogenetic data, the three isolates represent a novel species of the genus Lactobacillus , for which the name Lactobacillus brantae sp. nov. is proposed. The type strain is SL1108T ( = ATCC BAA-2142T = LMG 26001T = DSM 23927T) and two additional strains are SL1170 and SL60106.
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Bacillus eiseniae sp. nov., a swarming, moderately halotolerant bacterium isolated from the intestinal tract of an earthworm (Eisenia fetida L.)
More LessA swarming and moderately halotolerant bacterium, designated strain A1-2T, was isolated from the intestinal tract of the earthworm Eisenia fetida L. Cells were endospore-forming rods that were facultatively anaerobic, catalase-positive, oxidase-negative and motile by peritrichous flagella. The isolate grew optimally at 30 °C and pH 7.0, and could grow with up to 9 % (w/v) NaCl. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain A1-2T belonged to the genus Bacillus and exhibited 16S rRNA gene sequence similarities of 96.8, 96.0, 96.0, 96.4 and 96.7 % with Bacillus drentensis LMG 21831T, B. horneckiae PT-45T, B. niacini BAC 1015, B. infantis SMC 4352-1T and B. shackletonii LMG 18435T, respectively. DNA–DNA relatedness values between the isolate and the reference strains were ≤38.3 %. The DNA G+C content of strain A1-2T was 38.5 mol%. The predominant menaquinone was MK-7 and the major polar lipids were diphosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were iso-C15 : 0 (51.5 %) and anteiso-C15 : 0 (29.6 %) and the cell-wall diamino acid was meso-diaminopimelic acid. On the basis of 16S rRNA gene sequence analysis and chemotaxonomic and phenotypic characteristics, it is concluded that strain A1-2T represents a novel species of the genus Bacillus , for which we propose the name Bacillus eiseniae sp. nov. The type strain is A1-2T ( = KCCM 90092T = JCM 16993T).
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Amphibacillus cookii sp. nov., a facultatively aerobic, spore-forming, moderately halophilic, alkalithermotolerant bacterium
More LessNovel strains of facultatively aerobic, moderately alkaliphilic and facultatively halophilic bacteria were isolated from a sediment sample taken from the Southern Arm of Great Salt Lake, Utah. Cells of strain JW/BP-GSL-QDT (and related strains JW/BP-GSL-RA and JW/BP-GSL-WB) were rod-shaped, spore-forming, motile bacteria with variable Gram-staining. Strain JW/BP-GSL-QDT grew under aerobic conditions between 14.5 and 47 °C (optimum 39 °C), in the pH37 °C range 6.5–10.3 (optimum pH37 °C 8.0), and between 0.1 and 4.5 M Na+ (optimum 0.9 M Na+). No growth was observed in the absence of supplemented Na+. Strain JW/BP-GSL-QDT utilized l-arabinose, d-fructose, d-galactose, d-glucose, inulin, lactose, maltose, mannitol, d-mannose, pyruvate, d-ribose, d-sorbitol, starch, trehalose, xylitol and d-xylose under both aerobic and anaerobic conditions, and used ethanol and methanol only under aerobic conditions. Strains JW/BP-GSL-WB and JW/BP-GSL-RA had the same profiles except that methanol was not used aerobically. During growth on glucose, the major organic compounds formed under aerobic conditions were acetate and lactate, and under anaerobic conditions, the fermentation products were formate, acetate, lactate and ethanol. Oxidase and catalase activities were not detected and cytochrome was absent. No respiratory quinones were detected. The main cellular fatty acids were iso-C15 : 0 (39.1 %) and anteiso-C15 : 0 (36.3 %). Predominant polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unknown phospholipid. Additionally, a small amount of an unknown glycolipid was detected. The DNA G+C content of strain JW/BP-GSL-QDT was 35.4 mol% (determined by HPLC). For strain JW/BP-GSL-QDT the highest degree of 16S rRNA gene sequence similarity was found with Amphibacillus jilinensis (98.6 %), Amphibacillus sediminis (96.7 %) and Amphibacillus tropicus (95.6 %). The level of DNA–DNA relatedness between strain JW/BP-GSL-QDT and A. jilinensis Y1T was 58 %. On the basis of physiological, chemotaxonomic and phylogenetic data, strain JW/BP-GSL-QDT represents a novel species of the genus Amphibacillus , for which the name Amphibacillus cookii sp. nov. is proposed. The type strain is JW/BP-GSL-QDT ( = ATCC BAA-2118T = DSM 23721T).
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Brevibacillus nitrificans sp. nov., a nitrifying bacterium isolated from a microbiological agent for enhancing microbial digestion in sewage treatment tanks
More LessA heterotrophic nitrifying bacterium, designated strain DA2T, was isolated from a microbiological agent for enhancing microbial digestion in sewage treatment tanks. Cells of strain DA2T were Gram-positive, facultatively anaerobic, sporulating rods that were motile by means of peritrichous flagella; they were able to grow at pH 5–8. The major isoprenoid quinone of strain DA2T was menaquinone-7 (MK-7) and its cellular fatty acid profile consisted mainly of iso-C15 : 0 (18.6 %) and anteiso-C15 : 0 (69.1 %). The DNA G+C content was 54.1 mol%. 16S rRNA gene sequence phylogeny suggested that strain DA2T is a member of the genus Brevibacillus , with highest sequence similarities (in parentheses) to the type strains of Brevibacillus choshinensis (99.7 %), B. formosus (99.4 %), B. brevis (99.4 %), B. agri (99.0 %), B. reuszeri (98.8 %), B. parabrevis (98.7 %), B. centrosporus (98.6 %), B. limnophilus (97.4 %), B. panacihumi (97.3 %) and B. invocatus (97.3 %). DNA–DNA hybridization showed less than 60 % relatedness between strain DA2T and type strains of the most closely related species given above. Given the significant differences in phenotypic and chemotaxonomic characteristics, and phylogenetic analysis based on the 16S rRNA sequence and DNA–DNA relatedness data, the isolate merits classification as a novel species, for which the name Brevibacillus nitrificans is proposed; the type strain of this species is DA2T ( = JCM 15774T = NCIMB 14531T).
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Salisediminibacterium halotolerans gen. nov., sp. nov., a halophilic bacterium from soda lake sediment
More LessAn orange-pigmented, Gram-reaction-positive, non-spore-forming, halophilic, alkali-tolerant rod, designated strain halo-2T, was isolated from sediment of Xiarinaoer soda lake, in China’s Inner Mongolia Autonomous Region. Strain halo-2T grew in a complex medium with 3–30 % (w/v) NaCl and at pH 5–10. The cell-wall peptidoglycan contained meso-diaminopimelic acid and the major respiratory isoprenoid quinone was MK-7. The predominant cellular fatty acids were anteiso-C15 : 0 (43.6 %), anteiso-C17 : 0 (14.8 %) and iso-C15 : 0 (6.8 %) and the polar lipids consisted of diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol. The genomic DNA G+C content of the novel strain was 48.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain halo-2T was most closely related to Bacillus agaradhaerens DSM 8721T (93.9 % sequence similarity). However, strain halo-2T could be clearly differentiated from its closest phylogenetic relatives on the basis of several phenotypic, genotypic and chemotaxonomic characteristics. Strain halo-2T therefore represents a novel species in a new genus for which the name Salisediminibacterium halotolerans gen. nov., sp. nov. is proposed. The type strain of the type species is halo-2T ( = CGMCC 1.7654T = NBRC 104935T).
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Pectinatus brassicae sp. nov., a Gram-negative, anaerobic bacterium isolated from salty wastewater
More LessA novel Gram-negative, non-spore-forming, strictly anaerobic, heterotrophic bacterium, strain TYT, was isolated from salty pickle wastewater. Cells were rod-shaped with comb-like flagella, slightly curved and very variable in length. Optimal growth occurred at 28 °C and pH 6.5. Cells were resistant to up to 50 g NaCl l−1. Strain TYT produced acid from glycerol, sucrose, glucose, fructose and mannitol. The main fermentation products from glucose were acetic and propionic acids. Tests for acid phosphatase and naphthol-AS-BI-phosphohydrolase activities were positive. The major fatty acids were C14 : 0 DMA (18.7 %), C15 : 0 (15.4 %), anteiso-C18 : 1 (15.2 %), C11 : 0 (13.3 %) and summed feature 5 (C17 : 1ω7c and/or C17 : 2) (11.0 %). The DNA G+C content was 35.9 mol%. 16S rRNA gene sequence-based phylogenetic analysis indicated that strain TYT represented a novel species of the genus Pectinatus (sequence similarity to other members of the genus ranged from 93.2 to 94.8 %). Based on its phenotypic, genotypic and phylogenetic characteristics, strain TYT is proposed to represent a novel species, named Pectinatus brassicae sp. nov. (type strain TYT = JCM 17499T = DSM 24661T).
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Exiguobacterium aquaticum sp. nov., a member of the genus Exiguobacterium
More LessA Gram-positive, motile, short rod-shaped, orange pigmented bacterium, designated strain IMTB-3094T, was isolated from a water sample collected from Tikkar Tal Lake, Haryana, and subjected to detailed polyphasic taxonomic analysis. Strain IMTB-3094T possessed most of the phenotypic and chemotaxonomic properties of the genus Exiguobacterium and, based on 16S rRNA gene sequence analysis, was assigned to this genus. Strain IMTB-3094T exhibited the highest 16S rRNA gene sequence similarity to Exiguobacterium mexicanum MTCC 7759T (99.5 %) followed by Exiguobacterium aurantiacum MTCC 6414T (99.1 %), Exiguobacterium aestuarii MTCC 7750T (98.0 %), Exiguobacterium profundum MTCC 10851T (98.0 %) and Exiguobacterium marinum MTCC 7751T (98.0 %). The G+C content of the genomic DNA of strain IMTB-3094T was 53.2 mol% and a DNA–DNA relatedness study confirmed that it represents a novel species. The major fatty acids of strain IMTB-3094T were iso-C17 : 0 (16.1 %), anteiso-C13 : 0 (19.0 %), iso-C13 : 0 (11.9 %), iso-C15 : 0 (9.8 %) and iso-C17 : 1 (12.7 %). The predominant quinones were MK-7 (55.0 %) and MK-6 (26.0 %) with minor amounts of MK-8 (12.0 %). Based on phenotypic, chemotaxonomic and phylogenetic analyses, strain IMTB-3094T represents a novel species of the genus Exiguobacterium , for which the name Exiguobacterium aquaticum sp. nov. is proposed. The type strain is IMTB-3094T ( = MTCC 10958T = JCM 17977T).
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Enterococcus rivorum sp. nov., from water of pristine brooks
A significant number of Enterococcus strains from pristine waters of two brooks in Finland formed a distinct cluster on the basis of whole-cell protein fingerprinting by one-dimensional SDS-PAGE. The strains shared the following characteristics. Cells were ovoid, Gram-positive-staining and non-spore-forming, appearing singly or in pairs or chains. They were facultatively anaerobic and catalase-negative. Growth in broth containing 6.5 % NaCl or at 45 °C was weak or absent. Production of D antigen was variable. The strains tolerated 60 °C for 30 min, 40 % bile and tellurite, hydrolysed aesculin strongly and gelatin weakly, produced no acid from hippurate and did not reduce it, grew weakly at 10 °C, showed a strong reaction for the Voges–Proskauer test and produced acid from methyl α-d-glucoside, mannitol, sorbitol and sucrose, with weak or no production of acid from methyl α-d-mannoside, l-arabinose, gluconate and l-xylose. Several of the strains were selected for identification on the basis of sequencing of almost the whole 16S rRNA gene and partial atpA and pheS genes and of (GTG)5-PCR fingerprints. Partial atpA and pheS gene sequencing was also performed for those type strains of Enterococcus species without available sequences in the database. The pristine brook isolates formed a novel species, for which the name Enterococcus rivorum sp. nov. (type strain S299T = HAMBI 3055T = LMG 25899T = CCM 7986T) is proposed. On the basis of 16S rRNA gene sequence similarity, E. rivorum sp. nov. is related to the Enterococcus faecalis genogoup. It is distinguished from described Enterococcus species on the basis of 16S rRNA, atpA and pheS gene sequences and whole-cell protein and (GTG)5-PCR fingerprints. It is most closely related to E. faecalis , but DNA–DNA hybridization confirms it to represent a novel species.
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- Proteobacteria
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Erythrobacter marinus sp. nov., isolated from seawater
More LessA Gram-negative, non-motile, ovoid to rod-shaped bacterium, designated strain HWDM-33T, was isolated from seawater of the Yellow Sea, Korea, and was subjected to a polyphasic taxonomic study. Strain HWDM-33T grew optimally at pH 7–8, at 25 °C and in the presence of 2–3 % (w/v) NaCl. Neighbour-joining, maximum-likelihood and maximum-parsimony phylogenetic trees based on 16S rRNA gene sequences showed that strain HWDM-33T clustered with Erythrobacter gangjinensis K7-2T, with which it shared 96.9 % sequence similarity. Strain HWDM-33T exhibited 94.2–95.8 % 16S rRNA gene sequence similarity to the type strains of other recognized species of the genus Erythrobacter . Strain HWDM-33T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c, C17 : 1ω6c, and C16 : 1ω7c and/or iso-C15 : 0 2-OH as the major fatty acids. The major polar lipids were sphingoglycolipid, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain HWDM-33T was 66.1 mol%. Differential phenotypic properties and phylogenetic distinctiveness demonstrated that strain HWDM-33T was separate from E. gangjinensis and other recognized species of the genus Erythrobacter . On the basis of the data presented here, strain HWDM-33T represents a novel species of the genus Erythrobacter , for which the name Erythrobacter marinus sp. nov. is proposed. The type strain is HWDM-33T ( = KCTC 23554T = CCUG 60528T).
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Pseudahrensia aquimaris gen. nov., sp. nov., isolated from seawater
More LessA Gram-negative, non-motile, ovoid to rod-shaped bacterium, designated HDW-32T, was isolated from seawater of the Yellow Sea, Korea. Strain HDW-32T grew optimally at pH 7–8, at 30 °C and with 2–3 % (w/v) NaCl. Strain HDW-32T exhibited 95.1 % 16S rRNA gene sequence similarity with Nitratireductor basaltis J3T, 94.8 % sequence similarity with Ahrensia kielensis IAM 12618T and <94.5 % with other members of the family Phyllobacteriaceae . In the neighbour-joining, maximum-likelihood and maximum-parsimony trees based on 16S rRNA gene sequences, strain HDW-32T clustered with A. kielensis IAM 12618T. Strain HDW-32T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c as the major fatty acid. Differences in polar lipids, DNA G+C content and other phenotypic properties distinguished strain HDW-32T from A. kielensis JCM 20689T. Strain HDW-32T could also be distinguished from representatives of the genera Nitratireductor and Hoeflea by differences in fatty acids and polar lipids. On the basis of phylogenetic, chemotaxonomic and phenotypic data, strain HDW-32T represents a novel species belonging to a novel genus of the family Phyllobacteriaceae of the class Alphaproteobacteria , for which the name Pseudahrensia aquimaris gen. nov., sp. nov. is proposed. The type strain of the type species is HDW-32T ( = KCTC 23345T = CCUG 60023T).
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Marinomonas hwangdonensis sp. nov., isolated from seawater
More LessA Gram-negative, motile, rod-shaped bacterial strain, designated HDW-15T, was isolated from seawater of the Yellow Sea, Korea, and subjected to a polyphasic taxonomic study. Strain HDW-15T grew optimally at pH 7.0–8.0, at 25 °C and in the presence of 2 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain HDW-15T fell within the clade comprising Marinomonas species, joining the type strain of Marinomonas arctica , with which it exhibited highest 16S rRNA gene sequence similarity (97.7 %). The 16S rRNA gene sequence similarity values between strain HDW-15T and the type strains of other Marinomonas species were in the range 93.7–97.2 %. Mean DNA–DNA relatedness values between strain HDW-15T and the type strains of M. arctica , Marinomonas polaris and Marinomonas pontica were 5.0–9.9 %. The DNA G+C content of the isolate was 48.7 mol%. Strain HDW-15T contained Q-8 as the predominant ubiquinone and C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C16 : 0 as the major fatty acids. The major polar lipids found in strain HDW-15T were phosphatidylglycerol and phosphatidylethanolamine. Differential phenotypic properties, together with phylogenetic and genetic distinctiveness, showed that strain HDW-15T can be differentiated from other Marinomonas species. On the basis of the data presented, strain HDW-15T is considered to represent a novel species of the genus Marinomonas , for which the name Marinomonas hwangdonensis sp. nov. is proposed. The type strain is HDW-15T ( = KCTC 23661T = CCUG 61321T).
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Candidimonas bauzanensis sp. nov., isolated from soil, and emended description of the genus Candidimonas Vaz-Moreira et al. 2011
A Gram-negative, facultatively anaerobic, psychrophilic, motile rod, designated BZ59T, was isolated from hydrocarbon-contaminated soil. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BZ59T belonged to the genus Candidimonas and had highest 16S rRNA gene sequence similarity with Candidimonas nitroreducens SC-089T (97.7 %) and Candidimonas humi SC-092T (97.6 %). The ubiquinone was Q-8 and the major fatty acids were C16 : 0, C17 : 0 cyclo and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The polar lipid profile contained the major compounds phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmonomethylethanolamine and diphosphatidylglycerol. The major polyamines were putrescine and spermidine; a minor amount of 2-hydroxyputrescine was present. The DNA G+C content of strain BZ59T was 61.6 mol%. Combined data from phenotypic, phylogenetic and DNA–DNA relatedness studies demonstrated that strain BZ59T represents a novel species of the genus Candidimonas , for which the name Candidimonas bauzanensis sp. nov. is proposed. The type strain is BZ59T ( = DSM 22805T = LMG 26046T = CGMCC 1.10190T). The description of the genus Candidimonas is emended.
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Desulfonatronobacter acidivorans gen. nov., sp. nov. and Desulfobulbus alkaliphilus sp. nov., haloalkaliphilic heterotrophic sulfate-reducing bacteria from soda lakes
More LessTwo types of heterotrophic sulfate-reducing bacteria (SRB) were isolated from anoxic sediments of hypersaline soda lakes in Kulunda Steppe (Altai, Russia). The isolates used propionate as an energy and carbon source. Strain APT2T was enriched and isolated with thiosulfate as the electron acceptor. Strains APS1T and ASS1 were isolated with sulfate. Strain APT2T was a short rod and motile with a single subpolar flagellum, while strains APS1T and ASS1 were lemon-shaped oval rods and motile with a single polar flagellum and thin flagella-like filaments. Strain APT2T grew by complete oxidation of C3–C8 fatty acids with thiosulfate or sulfate as the electron acceptor, while strains APS1T and ASS1 were much less versatile and utilized only propionate and pyruvate as the electron donor and carbon source with sulfate or sulfite as the electron acceptor. Furthermore, strains APS1T and ASS1 oxidized propionate incompletely to form acetate. All of the isolates were moderately halophilic and obligately alkaliphilic. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolates in the order Desulfobacterales of the class Deltaproteobacteria . Strain APT2T belonged to the family Desulfobacteraceae and clustered with a halophilic SRB, Desulfosalsimonas propionicica PropAT. Strains APS1T and ASS1 were closely related to each other and clustered with the genus Desulfobulbus of the family Desulfobulbaceae . On the basis of phenotypic and phylogenetic analysis, the isolates are proposed to represent two novel taxa, Desulfonatronobacter acidivorans gen. nov., sp. nov. (type strain of the type species APT2T = DSM 24257T = UNIQEM U853T) and Desulfobulbus alkaliphilus sp. nov. (type strain APS1T = DSM 24258T = UNIQEM U900T).
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Kerstersia similis sp. nov., isolated from human clinical samples
More LessAnalysis of gyrB gene sequences, (GTG)5-primed PCR fingerprinting and biochemical characteristics determined in the Biolog GEN III microtest system were used to differentiate an unnamed Kerstersia species from Kerstersia gyiorum , the type and only named species in this genus. The inability to oxidize d-galacturonic and d-glucuronic acids and the ability to oxidize d-serine, along with gyrB gene sequence analysis and (GTG)5-PCR fingerprints, readily differentiated the unnamed taxon from the type species. Therefore, we propose to formally classify this unnamed taxon as Kerstersia similis sp. nov. with strain LMG 5890T ( = CCUG 46999T), isolated from a leg wound in the USA in 1983, as the type strain.
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Salinisphaera halophila sp. nov., a moderately halophilic bacterium isolated from brine of a salt well
A Gram-stain-negative, moderately halophilic, strictly aerobic bacterium, designated YIM 95161T, was isolated from brine of a salt well in Yunnan province, China, and subjected to a taxonomic study using a polyphasic approach. Cells of strain YIM 95161T were short rods, approximately 0.9–1.4 µm long and 0.4–0.6 µm wide. Strain YIM 95161T grew at 15–40 °C (optimum, 25–30 °C), 6–29 % (w/v) NaCl (optimum, 14–19 %) and at pH 5.0–8.0 (optimum, pH 7.0). The predominant isoprenoid quinone was Q-8. The major fatty acids (>10 %) were summed feature 8 (C18 : 1ω6c and/or C18 : 1ω7c) and C14 : 0. The polar lipids consisted of diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, one unknown phosphoglycolipid and two unknown lipids. The DNA G+C content was 69.5 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 95161T was a member of the genus Salinisphaera and exhibited sequence similarities of 96.7 %, 95.6 % and 95.4 % to Salinisphaera shabanensis E1L3AT, Salinisphaera dokdonensis CL-ES53T and Salinisphaera hydrothermalis EPR70T, respectively. On the basis of phylogenetic, physiological and chemotaxonomic analysis, strain YIM 95161T represents a novel species of the genus Salinisphaera , for which the name Salinisphaera halophila sp. nov. is proposed. The type strain is YIM 95161T ( = CCTCC AB 2011132T = JCM 17431T).
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Mesorhizobium silamurunense sp. nov., isolated from root nodules of Astragalus species
Four rhizobial strains representing a previously defined novel group in the genus Mesorhizobium and isolated from Astragalus species in China were further characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that these Gram-negative bacteria belonged to the genus Mesorhizobium , with Mesorhizobium plurifarium LMG 11892T as the closest neighbour sharing a sequence similarity of 99.8 %. Comparative sequence analysis of the atpD, recA, glnII, rpoB, nodC and nifH genes, SDS-PAGE of whole-cell soluble proteins, DNA–DNA hybridization, fatty acid profiles and a series of phenotypic and physiological tests differentitated the novel group from all recognized species of the genus Mesorhizobium . Based on the data obtained in the present and previous studies, this group represents a novel species within the genus Mesorhizobium , for which the name Mesorhizobium silamurunense sp. nov. is proposed. The type strain is CCBAU 01550T ( = HAMBI 3029T = LMG 24822T), and could form effective nodules on Astragalus membranaceus, Astragalus adsurgens and Caragana intermedia, and ineffective nodules on Phaseolus vulgaris in cross-nodulation tests.
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Parasphingopyxis lamellibrachiae gen. nov., sp. nov., isolated from a marine annelid worm
More LessA Gram-stain-negative, aerobic, motile, orange-pigmented, slightly halophilic, rod-shaped bacterium, designated strain JAMH 0132T, was isolated from the trophosome of a tubeworm in Kagoshima Bay, Japan, and its taxonomic position was investigated using a polyphasic approach. The novel strain grew optimally at 28–30 °C and with about 2.0 % (w/v) NaCl. Chemotaxonomic analysis showed that Q-10 was the predominant respiratory quinone and that C18 : 1ω7c, C16 : 0 2-OH and C16 : 0 were the major fatty acids. Sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine were the major polar lipids. The genomic DNA G+C content was 60.1 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JAMH 0132T belonged to the family Sphingomonadaceae , within the class Alphaproteobacteria . The novel strain appeared most closely related to Sphingopyxis baekryungensis SW-150T (95.1 % 16S rRNA gene sequence similarity) and showed less sequence similarity with representatives of the genera Blastomonas , Sphingomonas , Sphingosinicella and Novosphingobium (<94.8 %). In having no detectable polyamine, strain JAMH 0132T differed from members of all genera currently in the family Sphingomonadaceae . On the basis of its phenotypic properties and phylogenetic distinctiveness, strain JAMH 0132T represents a novel species of a new genus in the family Sphingomonadaceae for which the name Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is proposed. The type strain of Parasphingopyxis lamellibrachiae gen. nov., sp. nov. is JAMH 0132T ( = JCM 15549T = NCIMB 14486T).
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Kangiella taiwanensis sp. nov. and Kangiella marina sp. nov., marine bacteria isolated from shallow coastal water
More LessTwo Gram-negative, heterotrophic, aerobic, marine bacteria, designated strains KT1T and KM1T, were isolated from seawater samples collected from the shallow coastal regions of northern Taiwan. Cells grown in broth cultures were non-flagellated rods. NaCl was required for growth. Optimal growth occurred with 2–5 % NaCl, at 25–30 °C and at pH 8. They grew aerobically and were not capable of anaerobic growth by fermenting d-glucose or other carbohydrates. Q-8 was the only isoprenoid quinone. The major polar lipid detected in strain KT1T was phosphatidylmonomethylethanolamine, whereas those detected in KM1T were phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine and an unidentified phospholipid. Cellular fatty acids were nearly all iso-branched, with iso-C15 : 0 as the most abundant component (54.6–57.2 % of the total). Strains KT1T and KM1T had DNA G+C contents of 43.9 and 46.3 mol%, respectively. The two strains shared 98.1 % 16S rRNA gene sequence similarity; levels of similarity with the type strains of species of the genus Kangiella were 95.6–98.4 %. Data from the present taxonomic study conducted using a polyphasic approach revealed that the isolates could be classified as representatives of two novel species of the genus Kangiella , for which the names Kangiella taiwanensis sp. nov. (type strain KT1T = BCRC 80330T = JCM 17727T) and Kangiella marina sp. nov. (type strain KM1T = BCRC 80329T = JCM 17728T) are proposed.
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Oceanicaulis stylophorae sp. nov., isolated from the reef-building coral Stylophora pistillata
More LessA bacterial strain designated GISW-4T was isolated from the reef-building coral Stylophora pistillata, collected from seawater off the coast of southern Taiwan, and was characterized in this taxonomic study using a polyphasic approach. Strain GISW-4T was Gram-stain-negative, aerobic, beige, rod-shaped, and dimorphic, either non-motile with stalks (or prosthecae), or non-stalked and motile by means of a single polar flagellum. 16S rRNA gene sequence studies showed that the novel strain clustered with Oceanicaulis alexandrii C116-18T (98.9 % 16S rRNA gene sequence similarity). Strain GISW-4T exhibited optimal growth at 35–40 °C, 1–2 % (w/v) NaCl and at pH 7–9. The predominant cellular fatty acids (>10 %) were C18 : 0, C18 : 1ω7c and C18 : 1ω7c 11-methyl. The predominant polar lipids were phosphatidylglycerol, sulfoquinovosyl diacylglycerol and two unknown phospholipids (PL1–2). The major respiratory quinones were ubiquinone Q-10 and Q-9, and the DNA G+C content was 61.6 mol%. The results of physiological and biochemical tests allowed clear phenotypic differentiation of strain GISW-4T from the type strain of O. alexandrii . It is evident from the genotypic, phenotypic and chemotaxonomic data that the isolate should be classified as a novel species of the genus Oceanicaulis . The name proposed for this taxon is Oceanicaulis stylophorae sp. nov., with the type strain GISW-4T ( = LMG 25723T = BCRC 80207T).
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Rhizobium grahamii sp. nov., from nodules of Dalea leporina, Leucaena leucocephala and Clitoria ternatea, and Rhizobium mesoamericanum sp. nov., from nodules of Phaseolus vulgaris, siratro, cowpea and Mimosa pudica
Two novel related Rhizobium species, Rhizobium grahamii sp. nov. and Rhizobium mesoamericanum sp. nov., were identified by a polyphasic approach using DNA–DNA hybridization, whole-genome sequencing and phylogenetic and phenotypic characterization including nodulation of Leucaena leucocephala and Phaseolus vulgaris (bean). As similar bacteria were found in the Los Tuxtlas rainforest in Mexico and in Central America, we suggest the existence of a Mesoamerican microbiological corridor. The type strain of Rhizobium grahamii sp. nov. is CCGE 502T ( = ATCC BAA-2124T = CFN 242T = Dal4T = HAMBI 3152T) and that of Rhizobium mesoamericanum sp. nov. is CCGE 501T ( = ATCC BAA-2123T = HAMBI 3151T = CIP 110148T = 1847T).
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Burkholderia symbiotica sp. nov., isolated from root nodules of Mimosa spp. native to north-east Brazil
Four strains, designated JPY-345T, JPY-347, JPY-366 and JPY-581, were isolated from nitrogen-fixing nodules on the roots of two species of Mimosa, Mimosa cordistipula and Mimosa misera, that are native to North East Brazil, and their taxonomic positions were investigated by using a polyphasic approach. All four strains grew at 15–43 °C (optimum 35 °C), at pH 4–7 (optimum pH 5) and with 0–2 % (w/v) NaCl (optimum 0 % NaCl). On the basis of 16S rRNA gene sequence analysis, strain JPY-345T showed 97.3 % sequence similarity to the closest related species Burkholderia soli GP25-8T, 97.3 % sequence similarity to Burkholderia caryophylli ATCC25418T and 97.1 % sequence similarity to Burkholderia kururiensis KP23T. The predominant fatty acids of the strains were C18 : 1ω7c (36.1 %), C16 : 0 (19.8 %) and summed feature 3, comprising C16 : 1ω7c and/or C16 : 1ω6c (11.5 %). The major isoprenoid quinone was Q-8 and the DNA G+C content of the strains was 64.2–65.7 mol%. The polar lipid profile consisted of a mixture of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and phospholipids. DNA–DNA hybridizations between the novel strain and recognized species of the genus Burkholderia yielded relatedness values of <51.8 %. On the basis of 16S rRNA and recA gene sequence similarities and chemotaxonomic and phenotypic data, the four strains represent a novel species in the genus Burkholderia , for which the name Burkholderia symbiotica sp. nov. is proposed. The type strain is JPY-345T ( = LMG 26032T = BCRC 80258T = KCTC 23309T).
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- Bacteroidetes
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Cyclobacterium qasimii sp. nov., a psychrotolerant bacterium isolated from Arctic marine sediment
A novel Gram-stain-negative, horseshoe-shaped, non-motile bacterium, designated strain M12-11BT, was isolated from a marine sediment sample collected at a depth of 200 m from Kongsfjorden, Svalbard. The colony colour was orangish red due to the presence of carotenoids. Fatty acids were dominated by branched and unsaturated fatty acids (90.8 %), with a high abundance of iso-C15 : 0 (14.9 %), anteiso-C15 : 0 (11.4 %), iso-C15 : 1 G (13.1 %), C15 : 1ω6c (5.4 %), C17 : 1ω6c (6.7 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 9.3 %) and summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1ω9c; 5.9 %). Strain M12-11BT contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid and three unidentified lipids. Based on 16S rRNA gene sequence similarities, the type strains of Cyclobacterium amurskyense , Cyclobacterium marinum and Cyclobacterium lianum were most closely related to M12-11BT with sequence similarities of 98.2, 96.8 and 93.3 %, respectively. Other members of the family Cyclobacteriaceae had sequence similarities of <92.0 %. However, DNA–DNA hybridization with Cyclobacterium amurskyense KCTC 12363T and Cyclobacterium marinum DSM 745T showed relatedness values of only 24.5 and 32.5 % with respect to strain M12-11BT. Based on the results of DNA–DNA hybridization experiments and phenotypic and chemotaxonomic data, it appears that strain M12-11BT represents a novel species of the genus Cyclobacterium , for which the name Cyclobacterium qasimii sp. nov. is proposed; the type strain is M12-11BT ( = KCTC 23011T = NBRC 106168T) and it has a DNA G+C content of 40.5 mol%.
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Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater
More LessA Gram-staining-negative, non-flagellated, non-gliding and pleomorphic bacterial strain, designated DPG-25T, was isolated from seawater in a seaweed farm in the South Sea in Korea and its taxonomic position was investigated by using a polyphasic approach. Strain DPG-25T grew optimally at 25 °C, at pH 7.0–7.5 and in the presence of 2 % (w/v) NaCl. Flexirubin-type pigments were not produced. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain DPG-25T formed a cluster with the type strains of Actibacter sediminis , Aestuariicola saemankumensis and Lutimonas vermicola . Strain DPG-25T exhibited 16S rRNA gene sequence similarity values of 95.3, 93.1 and 93.6 % to the type strains of Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola , respectively. Strain DPG-25T contained MK-6 as the predominant menaquinone and iso-C15 : 0 and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain DPG-25T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content was 39.9 mol%. Differential phenotypic properties and the phylogenetic distinctiveness of strain DPG-25T demonstrated that this strain is distinguishable from Actibacter sediminis , Aestuariicola saemankumensis and L. vermicola . On the basis of the data presented here, strain DPG-25T represents a novel species in a novel genus of the family Flavobacteriaceae , for which the name Namhaeicola litoreus gen. nov., sp. nov. is proposed. The type strain of Namhaeicola litoreus is DPG-25T ( = KCTC 23702T = CCUG 61485T).
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Mongoliicoccus roseus gen. nov., sp. nov., an alkaliphilic bacterium isolated from a haloalkaline lake
More LessTwo pink, non-motile, aerobic, alkaliphilic, halotolerant, Gram-negative cocci, designated MIM28T and MIM29, were isolated from the surface water of a haloalkaline lake on the Mongolia Plateau. The isolates grew optimally at 30–33 °C, at pH 8–9 and with 3–4 % (w/v) NaCl. The isolates were chemoheterotrophic and could assimilate carbohydrates, organic acids and amino acids. The major respiratory quinone was menaquinone MK-7. The major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The predominant cellular fatty acids were iso-C15 : 0 (13.8–17.5 %), anteiso-C15 : 0 (10.5–11.2 %), iso-C16 : 0 (9.9–13.0 %), C16 : 0 (4.3–4.6 %), iso-C17 : 0 (3.8–5.3 %), anteiso-C17 : 0 (3.7–7.1 %), C17 : 1ω6c (4.6–6.4 %), iso-C17 : 0 3-OH (4.6–5.8 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 4.0–6.4 %) and summed feature 9 (iso-C17 : 1ω9c and/or C16 : 0 10-methyl; 10.4–12.5 %). Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates were most closely related to Litoribacter ruber YIM CH208T (93.6 % 16S rRNA gene sequence similarity), the genus Echinicola (90.4–92 %) and other members of the family Cyclobacteriaceae (87.8–90 %). The DNA G+C contents of strains MIM28T and MIM29 were 62.8 and 62.2 mol%. On the basis of morphology, physiology, fatty acid composition, phylogeny and 16S rRNA gene sequence analysis, the isolates are assigned to a novel species of a new genus, for which we propose the name Mongoliicoccus roseus gen. nov., sp. nov.; the type strain of the type species is MIM28T ( = ACCC 05511T = KCTC 19808T).
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Fulvivirga imtechensis sp. nov., a member of the phylum Bacteroidetes
More LessA novel, Gram-staining-negative, yellow-coloured, rod-shaped, obligately aerobic, non-motile bacterium, designated strain AK7T, was isolated from seawater collected on the coast at Visakhapatnam, Andhra Pradesh, India. The predominant fatty acids of the novel strain were iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 1ω5c, iso-C17 : 0 3-OH and summed features 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) and 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The major respiratory quinone was MK-7 and the polar lipid profile comprised phosphatidylethanolamine, two unidentified aminolipids and four other unidentified lipids. In phylogenetic analysis based on 16S rRNA gene sequences, strain AK7T appeared most closely related to Fulvivirga kasyanovii KMM 6220T (95.9 % sequence similarity), a member of the family Flammeovirgaceae in the phylum Bacteroidetes . The genomic DNA G+C content of strain AK7T was 55.1 mol%. Based on the morphological, biochemical, physiological, chemotaxonomic and phylogenetic evidence, strain AK7T represents a novel species of the genus Fulvivirga for which the name Fulvivirga imtechensis sp. nov. is proposed. The type strain is AK7T ( = MTCC 11053T = JCM 17390T).
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Pricia antarctica gen. nov., sp. nov., a member of the family Flavobacteriaceae , isolated from Antarctic intertidal sediment
Yong Yu, Hui-Rong Li, Yin-Xin Zeng, Kun Sun and Bo ChenA yellow-coloured, rod-shaped, Gram-reaction- and Gram-staining-negative, non-motile and aerobic bacterium, designated strain ZS1-8T, was isolated from a sample of sandy intertidal sediment collected from the Antarctic coast. Flexirubin-type pigments were absent. In phylogenetic analyses based on 16S rRNA gene sequences, strain ZS1-8T formed a distinct phyletic line and the results indicated that the novel strain should be placed in a new genus within the family Flavobacteriaceae . In pairwise comparisons between strain ZS1-8T and recognized species, the levels of 16S rRNA gene sequence similarity were all <93.3 %. The strain required Ca2+ and K+ ions as well as NaCl for growth. Optimal growth was observed at pH 7.5–8.0, 17–19 °C and with 2–3 % (w/v) NaCl. The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), an unknown acid with an equivalent chain-length of 13.565 and iso-C17 : 0 3-OH. The major respiratory quinone was MK-6. The predominant polar lipid was phosphatidylethanolamine. The genomic DNA G+C content was 43.9 mol%. Based on the phylogenetic, phenotypic and chemotaxonomic data, strain ZS1-8T represents a novel species in a new genus in the family Flavobacteriaceae for which the name Pricia antarctica gen. nov., sp. nov. is proposed. The type strain of the type species is ZS1-8T ( = JCM 17291T = DSM 23421T).
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Salinirepens amamiensis gen. nov., sp. nov., a member of the family Cryomorphaceae isolated from seawater, and emended descriptions of the genera Fluviicola and Wandonia
More LessThe taxonomic position of bacterial strain AM11-6T, isolated from seawater in Japan, was determined by using a polyphasic taxonomic approach. The strain was a strictly aerobic and Gram-staining-negative slender rod, motile by gliding. The major respiratory quinone was menaquinone-6 and the predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C14 : 0 and iso-C15 : 1 G. The polar lipid pattern indicated the presence of an unidentified phospholipid, several glycolipids and an unidentified polar lipid. The G+C content of the genomic DNA was 36.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain AM11-6T clustered with members of the genera Wandonia and Fluviicola in the family Cryomorphaceae of the phylum Bacteroidetes . The strain required NaCl and MgCl2 for growth and could be differentiated from members of other genera in the family Cryomorphaceae by fatty acid composition and other phenotypic characters. On the basis of these results, we describe the novel genus and species, Salinirepens amamiensis gen. nov., sp. nov. The type strain of Salinirepens amamiensis is AM11-6T ( = NBRC 101268T = NCIMB 14607T). Emended descriptions of the genera Fluviicola and Wandonia are also proposed.
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Pseudarcicella hirudinis gen. nov., sp. nov., isolated from the skin of the medical leech Hirudo medicinalis
A pinkish-pigmented, Gram-stain-negative, rod-shaped, non-spore-forming bacterium, strain E92T, was isolated from the skin of the medical leech Hirudo medicinalis, on R2A agar. 16S rRNA gene sequence analysis of strain E92T showed a relatively low 16S rRNA gene sequence similarity (93.0–93.5 %) to representatives of the genus Arcicella and 91.5–92.0 % to members of the genus Flectobacillus . The polar lipid profile was composed of the major compounds phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified aminolipid and an unidentified polar lipid; glycolipids were not detected. The major quinone was menquinone MK-7, and the major compound in the polyamine pattern was spermidine. The predominant fatty acids were C16 : 1ω5c and C16 : 1ω7c and/or iso-C15 : 0 2-OH (detected as summed feature 3). The isolate did not contain C14 : 0 or the hydroxyl fatty acid iso-C17 : 0 3-OH found in all representatives of the genera Arcicella and Flectobacillus , but did produce C18 : 1ω7c and 11-methyl C18 : 1ω7c which are not found in these two genera. The DNA G+C content of strain E92T was 64.4 mol%. The unique 16S rRNA gene sequence, and specific chemotaxonomic and physiological data revealed that strain E92T represents a new genus in the family Cytophagaceae for which we propose the name Pseudarcicella hirudinis gen. nov., sp. nov., with the type strain of the type species as E92T ( = LMG 26720T = CCM 7988T).
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Cecembia lonarensis gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae , isolated from a haloalkaline lake and emended descriptions of the genera Indibacter , Nitritalea and Belliella
A novel Gram-staining-negative, rod-shaped, non-motile bacterium, designated strain LW9T, was isolated from a water sample collected from Lonar Lake of Buldhana district, Maharashtra, India. Colonies and broth cultures were reddish orange due to the presence of carotenoid pigments. Strain LW9T was positive for catalase, ornithine decarboxylase and lysine decarboxylase activities and negative for gelatinase, oxidase, urease and lipase activities. The predominant fatty acids were iso-C15 : 0 (31.3 %), iso-C16 : 0 (9.3 %), anteiso-C15 : 0 (7.3 %), iso-C16 : 1 H (6.1 %), summed feature 3 (comprising C16 : 1ω7c/C16 : 1ω6c; 5.9 %), iso-C17 : 1ω9c (5.4 %) and iso-C17 : 0 3-OH (5.0 %). Strain LW9T contained MK-7 as the major respiratory quinone. The polar lipids consisted of phosphatidylethanolamine, two unidentified aminolipids and seven unidentified lipids. The DNA G+C content of strain LW9T was 40.5 mol%. 16S rRNA gene sequence analysis indicated that the type strains of Indibacter alkaliphilus and Aquiflexum balticum , two members of the family Cyclobacteriaceae (phylum ‘ Bacteroidetes ’) were the most closely related strains with sequence similarities of 93.0 and 94.0 %, respectively. Other members of the family Cyclobacteriaceae showed sequence similarities <93.0 %. Based on these phenotypic characteristics and on phylogenetic inference, strain LW9T is proposed as the representative of novel species in a new genus, Cecembia lonarensis gen. nov., sp. nov. The type strain of the type species, Cecembia lonarensis, is LW9T ( = CCUG 58316T = KCTC 22772T). Emended descriptions of the genera Indibacter , Nitritalea and Belliella are also proposed.
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- Other Bacteria
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Granulicella arctica sp. nov., Granulicella mallensis sp. nov., Granulicella tundricola sp. nov. and Granulicella sapmiensis sp. nov., novel acidobacteria from tundra soil
More LessFour aerobic bacteria, designated MP5ACTX2T, MP5ACTX8T, MP5ACTX9T and S6CTX5AT, were isolated from tundra soil of north-western Finland (69° 03′ N 20° 50′ E). Cells of all isolates were Gram-negative, non-motile rods. Phylogenetic analysis indicated that they belonged to the genus Granulicella of subdivision 1 of the phylum Acidobacteria . 16S rRNA gene sequence similarity between the new isolates and the type strains of Granulicella aggregans , Granulicella paludicola , Granulicella pectinivorans and Granulicella rosea ranged from 94 to 99 %. Analysis of the RNA polymerase beta subunit (rpoB) gene sequence indicated that the isolates represented novel species of the genus Granulicella (<92 % rpoB sequence similarity between the isolates and members of the genus Granulicella ). This was also confirmed by low DNA–DNA relatedness (31 %) between strain S6CTX5AT and the type strain of G. pectinivorans , which exhibited 99.1 % 16S rRNA gene sequence similarity and 91.7 % rpoB gene sequence similarity. The isolates grew at pH 3.5–6.5 and at 4–26 °C. Sugars were the preferred growth substrates. The major cellular fatty acids were iso-C15 : 0, C16 : 1ω7c and C16 : 0 and the major isoprenoid quinone was MK-8. The DNA G+C content was 56–60 mol%. On the basis of phylogenetic analysis and chemotaxonomic and physiological data, the isolates represent four novel species of the genus Granulicella , for which the names Granulicella arctica MP5ACTX2T ( = ATCC BAA-1858T = DSM 23128T), Granulicella mallensis MP5ACTX8T ( = ATCC BAA-1857T = DSM 23137T), Granulicella tundricola MP5ACTX9T (ATCC BAA-1859T = DSM 23138T) and Granulicella sapmiensis S6CTX5AT ( = LMG 26174T = DSM 23136T) are proposed. An emended description of the genus Granulicella is also presented.
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Luteolibacter luojiensis sp. nov., isolated from Arctic tundra soil, and emended description of the genus Luteolibacter
A yellow-pigmented, Gram-reaction-negative, non-motile, aerobic bacterium, designated DR4-30T, was isolated from tundra soil near Ny-Ålesund, Svalbard Archipelago, Norway (78° 58′ N 12° 03′ E). Growth occurred at 4–28 °C (optimum 20–25 °C) and at pH 7–8 (optimum pH 7). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain DR4-30T belongs to the genus Luteolibacter in the family Verrucomicrobiaceae . The 16S rRNA gene sequence of this strain showed 95.4 and 94.7 % sequence similarity to those of Luteolibacter pohnpeiensis A4T-83T and Luteolibacter algae A5J-41-2T, respectively. The major respiratory quinones were MK-9 and MK-10; the predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 20.7 %), iso-C14 : 0 (20.3 %), C17 : 0 (10.7 %), C16 : 0 (8.0 %) and C14 : 0 (6.6 %). The DNA G+C content was 57.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain DR4-30T represents a novel species of the genus Luteolibacter , for which the name Luteolibacter luojiensis sp. nov. is proposed. The type strain is DR4-30T ( = CCTCC AB 2010415T = NRRL B-59669T). An emended description of the genus Luteolibacter is also provided.
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- Eukaryotic Micro-organisms
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Candida adriatica sp. nov. and Candida molendinolei sp. nov., two yeast species isolated from olive oil and its by-products
Thirteen strains isolated from virgin olive oil or its by-products in several Mediterranean countries were found to be phenotypically and genetically divergent from currently recognized yeast species. Sequence analysis of the large subunit (LSU) rDNA D1/D2 domain and internal transcribed spacer regions/5.8S rDNA revealed that the strains represented two novel species described as Candida adriatica sp. nov. (type strain ZIM 2334T = CBS 12504T = NCAIM Y.02001T) and Candida molendinolei sp. nov. (type strain DBVPG 5508T = CBS 12508T = NCAIM Y.02000T). Phylogenetic analysis based on concatenated sequences of the small subunit rRNA gene, the D1/D2 region of the LSU rDNA and the translation elongation factor-1α gene suggested that C. adriatica sp. nov. and C. molendinolei sp. nov. should be placed within the Lindnera and Nakazawaea clades, respectively.
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Candida borneonana sp. nov., a methanol-assimilating anamorphic yeast isolated from decaying fruit
More LessFive strains of a previously uncharacterized anamorphic, methanol-assimilating yeast species are described here, for which the name Candida borneonana is proposed. The strains were isolated from fruit waste collected in markets in Brunei, Borneo. The sequences of the D1/D2 domains of the large subunit rRNA genes, the internal transcribed spacer (ITS) regions and the 18S rRNA genes were identical between the isolates and differed from the corresponding sequences of all previously described yeast species. Phylogenetic analysis of these sequences showed that the new species formed a cluster with species of the genus Kuraishia, the closest related species being K. capsulata (6 % nucleotide substitutions in the D1/D2 domain). The type strain, 11-487T, has been deposited in the Centralbureau voor Schimmelcultures (Utrecht, The Netherlands) as CBS 12507T, the Culture Collection of Yeasts (Bratislava, Slovakia) as CCY 29-182-1T and the National Collection of Agricultural and Industrial Microorganisms (Budapest, Hungary) as NCAIM Y.02008. Mycobank no. MB563710.
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Candida kuoi sp. nov., an anamorphic species of the Starmerella yeast clade that synthesizes sophorolipids
More LessA novel strain of anamorphic yeast, designated strain NRRL Y-27208T, was isolated from concentrated grape juice in Cape Province, South Africa. Analysis of nuclear large subunit rRNA gene sequences from the D1/D2 domains separated the novel isolate from strains of Starmerella bombicola and Starmerella meliponinorum, as well as from species of the genus Candida that are members of the Starmerella clade. Compared to previously described species, strain NRRL Y-27208T is most closely related to S. bombicola but can be separated from this species by its ability to grow on d-ribose and erythritol. Strain NRRL Y-27208T produced sophorolipids that have an open chain structure similar to Candida batistae, Candida riodocensis and Candida stellata, which is in contrast to the closed chain sophorolipids produced by S. bombicola and Candida apicola. The analyses showed that NRRL Y-27208T ( = CBS 7267T) represents a novel species distinct from previously described species, for which the name Candida kuoi sp. nov. is proposed.
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- Evolution, Phylogeny and Biodiversity
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Differentiation and classification of phytoplasmas in the pigeon pea witches’-broom group (16SrIX): an update based on multiple gene sequence analysis
More LessThe pigeon pea witches’-broom phytoplasma group (16SrIX) comprises diverse strains that cause numerous diseases in leguminous trees and herbaceous crops, vegetables, a fruit, a nut tree and a forest tree. At least 14 strains have been reported worldwide. Comparative phylogenetic analyses of the highly conserved 16S rRNA gene and the moderately conserved rplV (rpl22)–rpsC (rps3) and secY genes indicated that the 16SrIX group consists of at least six distinct genetic lineages. Some of these lineages cannot be readily differentiated based on analysis of 16S rRNA gene sequences alone. The relative genetic distances among these closely related lineages were better assessed by including more variable genes [e.g. ribosomal protein (rp) and secY genes]. The present study demonstrated that virtual RFLP analyses using rp and secY gene sequences allowed unambiguous identification of such lineages. A coding system is proposed to designate each distinct rp and secY subgroup in the 16SrIX group.
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Phylogenetic multilocus sequence analysis identifies seven novel Ensifer genospecies isolated from a less-well-explored biogeographical region in East Africa
More LessThe diversity of 71 rhizobial strains belonging to the genus Ensifer , isolated from root nodules of woody legumes growing in southern Ethiopia, was studied using multilocus sequence analysis (MLSA) and phenotypic approaches. Phylogenetic analyses based on core genes revealed that 43 strains were clustered in seven distinct and consistent positions (genospecies I–VII), while another 25 strains were also distinct but were discrepant in their placement on the different gene trees. The remaining three strains occupied the same phylogenetic branches as defined Ensifer species and thus were not distinct. Irrespective of their chromosomal background, the majority of the test strains were highly related with respect to their nifH and nodC gene sequences, suggesting that these symbionts might have acquired these genes recently from a common origin. On the nifH phylogenetic tree, the branch containing the test strains and reference species isolated from woody legumes in Africa was clearly separate from those isolated outside the continent, suggesting that these symbionts have a long history of separate evolution within Ensifer for this gene. A cross-inoculation study showed that our strains were capable of eliciting effective nodulation on the homologous host and on other host species. This suggests a potential to improve nitrogen fixation by selecting for broad-host-range inoculants. Our study confirms the presence of a wide diversity of Ensifer in East Africa and, while contributing to the general knowledge of the biodiversity within the genus, also highlights the need to focus on previously less-well-explored biogeographical regions to unravel as-yet-unidentified rhizobial resources.
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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 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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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 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 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)