- Volume 58, Issue 7, 2008
Volume 58, Issue 7, 2008
- 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 (i.e. documents certifying deposition and availability of type strains). 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 and in the volume author index. 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 58, part 4, 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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- List Of Changes In Taxonomic Opinion
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Notification of changes in taxonomic opinion previously published outside the IJSEM
The Bacteriological Code deals with the nomenclature of prokaryotes. This may include existing names (the Approved Lists of Bacterial Names) as well as new names and new combinations. In this sense the Code is also dealing indirectly with taxonomic opinions. However, as with most codes of nomenclature there are no mechanisms for formally recording taxonomic opinions that do not involve the creation of new names or new combinations. In particular, it would be desirable for taxonomic opinions resulting from the creation of synonyms or emended descriptions to be made widely available to the public. In 2004, the Editorial Board of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) agreed unanimously that it was desirable to cover such changes in taxonomic opinions (i.e. the creation of synonyms or the emendation of circumscriptions) previously published outside the IJSEM, and to introduce a List of Changes in Taxonomic Opinion [Notification of changes in taxonomic opinion previously published outside the IJSEM; Euzéby et al. (2004). Int J Syst Evol Microbiol 54, 1429–1430]. Scientists wishing to have changes in taxonomic opinion included in future lists should send one copy of the pertinent reprint or a photocopy or a PDF file thereof to the IJSEM Editorial Office or to the Lists Editor. It must be stressed that the date of proposed taxonomic changes is the date of the original publication not the date of publication of the list. Taxonomic opinions included in the List of Changes in Taxonomic Opinion cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. The names that are to be used are those that are the ‘correct names’ (in the sense of Principle 6) in the opinion of the bacteriologist, with a given circumscription, position and rank. A particular name, circumscription, position and rank does not have to be adopted in all circumstances. Consequently, the List of Changes in Taxonomic Opinion must be considered as a service to bacteriology and it has no ‘official character’, other than providing a centralized point for registering/indexing such changes in a way that makes them easily accessible to the scientific community.
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- New Taxa
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- Actinobacteria
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Micromonospora pattaloongensis sp. nov., isolated from a Thai mangrove forest
More LessAn actinomycete, designated strain TJ2-2T, was isolated from soil collected from a mangrove forest in Pattaloong Province, Thailand, and was subjected to morphological and chemotaxonomic analysis and phylogenetic investigation based on 16S rRNA gene sequences. The data from these analyses indicated that the novel strain should be classified as a member of the genus Micromonospora and that the closest relative was Micromonospora olivasterospora DSM 43868T (98.7 % gene sequence similarity). The DNA–DNA hybridization data and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from its closest phylogenetic relatives. On the basis of these phenotypic and genotypic data, strain TJ2-2T represents a novel species of the genus Micromonospora, for which the name Micromonospora pattaloongensis sp. nov. is proposed. The type strain is TJ2-2T (=JCM 12833T=TISTR 1559T).
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Fodinicola feengrottensis gen. nov., sp. nov., an actinomycete isolated from a medieval mine
More LessA filamentous, Gram-positive actinobacterium was isolated from acidic rocks in a medieval alum slate mine and was investigated by means of a polyphasic taxonomic approach. A 16S rRNA gene sequence similarity study indicated that strain HKI 0501T forms an individual line of descent and is related to certain members of the suborder Frankineae, order Actinomycetales (<95 % sequence similarity). Distance-matrix and neighbour-joining analyses set the branching point of the novel isolate between two clades, one being represented by members of the genus Cryptosporangium (family ‘Kineosporiaceae’) and the other by members of the genera Frankia and Acidothermus (family Frankiaceae and family Acidothermaceae, respectively). The organism had meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and xylose as the characteristic cell-wall sugar. The muramic acid in the peptidoglycan was found to be N-acetylated. The major menaquinones were MK-9(H4), MK-9(H6) and MK-9(H8) and the fatty acid profile was characterized by the predominance of iso-C16 : 0, 10-methyl C17 : 0, C17 : 1 cis9 and 10-methyl iso-C18 : 0. The polar lipids comprised diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol and several unknown phospholipids and glycolipids. Mycolic acids were absent. The DNA G+C content was 65 mol%. The distinct phylogenetic position and the phenotypic markers that clearly separate the novel organism from all other members of the suborder Frankineae indicate that strain HKI 0501T represents a novel genus and species, for which the name Fodinicola feengrottensis gen. nov., sp. nov. is proposed. The type strain of Fodinicola feengrottensis is HKI 0501T (=DSM 19247T =JCM 14718T).
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Nocardiopsis valliformis sp. nov., an alkaliphilic actinomycete isolated from alkali lake soil in China
More LessA strain (HBUM 20028T) isolated from alkali lake soil in China was studied by a polyphasic taxonomic approach. The strain produced abundant aerial and substrate mycelia. Long spore chains were borne on the aerial mycelium, and the substrate mycelium was often arranged in a shape like a fence or palisade. The special characteristic of strain HBUM 20028T was its abundant growth under alkaline conditions, at pH 8.0–14.0. The cell wall of strain HBUM 20028T contained meso-diaminopimelic acid but no diagnostic sugar. Major phospholipids included diphosphatidylglycerol and phosphatidylcholine. The major menaquinones were MK-10(H2), MK-10(H4) and MK-10(H6). The major cellular fatty acids were iso-C16 : 0 (31.66 %), anteiso-C17 : 0 (14.85 %) and C18 : 1 ω9c (14.73 %). All of these characters consistently indicated that strain HBUM 20028T belongs to the genus Nocardiopsis. DNA–DNA hybridization between the strain and type strains of related species gave relatedness values far below 70 %. Based on 16S rRNA gene sequence analysis, DNA relatedness and phenotypic characteristics, a novel species with the name Nocardiopsis valliformis sp. nov. is proposed. The type strain is HBUM 20028T (=DSM 45023T =CGMCC 4.2135T).
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Humibacillus xanthopallidus gen. nov., sp. nov.
More LessStrain KV-663T was isolated from a soil sample collected from a paddy field in Japan by using GPM agar plates. Strain YM21-029 was obtained from a lake sediment sample by using HSV agar. The two novel strains were Gram-positive, catalase-positive, rod-shaped bacteria with ll-diaminopimelic acid as the diagnostic diamino acid of the cell-wall peptidoglycan. The major menaquinone was MK-8(H4). Mycolic acids were not detected. The G+C content of the DNA was 69–70 mol%. 16S rRNA gene sequence analysis revealed that these strains represent a novel lineage within the family Intrasporangiaceae, order Actinomycetales, and are related to members of the genera Intrasporangium and Terracoccus. Based on morphological, biochemical and chemotaxonomic properties, together with phylogenetic analysis based on 16S rRNA gene sequences, the two new strains are considered to represent a novel species of a new genus, for which the name Humibacillus xanthopallidus gen. nov., sp. nov. is proposed. The type strain of the type species, Humibacillus xanthopallidus, is KV-663T (=NRRL B-24471T=NBRC 101803T).
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Catenulispora subtropica sp. nov. and Catenulispora yoronensis sp. nov.
More LessThree strains of actinomycetes that formed spore chains were isolated from a paddy field and forest soil and subjected to a polyphasic taxonomic characterization study. The cell wall peptidoglycan contained ll-diaminopimelic acid and glycine. The major isoprenoid quinones were MK-9(H8) and MK-9(H6), and the major cellular fatty acids were iso-C16 : 0 and anteiso-C17 : 0. Phylogenetic analysis based on 16S rRNA gene sequences showed that these organisms belonged in a monophyletic cluster with members of the genus Catenulispora. According to the physiological, biochemical and chemotaxonomic data, the novel organisms could be differentiated from recognized members of the genus Catenulispora. Based on the phenotypic and genotypic data, the three strains are considered to represent two novel species of the genus Catenulispora, for which the names Catenulispora subtropica sp. nov. for strains TT 99-48T (type strain; =NBRC 103395T=KCTC 19328T) and TT 01-19 (=NBRC 103396), and Catenulispora yoronensis sp. nov. (type strain TT N02-20T=NBRC 103397T=KCTC 19327T) are proposed. An emended description of the genus Catenulispora is given.
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Streptomonospora halophila sp. nov., a halophilic actinomycete isolated from a hypersaline soil
More LessAn actinomycete strain, designated YIM 91355T, was isolated from a soil sample collected from a hypersaline soil in Xinjiang Province, China, and its taxonomic position was investigated by using a polyphasic approach. The strain grew well on most media tested and no diffusible pigment was produced. The aerial mycelium of this organism was well developed but not fragmented and, at maturity, formed short chains of spores. Substrate mycelium was branched with non-fragmenting hyphae and single, oval to round spores were formed, borne on sporophores. Strain YIM 91355T contained meso-diaminopimelic acid as the diagnostic amino acid. The purified cell-wall hydrolysate contained galactose. The predominant menaquinones were MK-10(H8) (43.2 %), MK-10(H6) (17.7 %) and MK-11(H8) (10.4 %). Phospholipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylcholine, phosphatidylinositol and an unidentified phospholipid. The major fatty acids were i-C16 : 0, ai-C17 : 0, 10-methyl C17 : 0 and 10-methyl C18 : 0. The G+C content of the genomic DNA was 72.1 mol%. Phylogenetic analysis indicated that the isolate belongs to the genus Streptomonospora of the family Nocardiopsaceae. Based on phenotypic and genotypic data, it is concluded that strain YIM 91355T represents a novel species of the genus Streptomonospora, for which the name Streptomonospora halophila sp. nov. (type strain YIM 91355T =DSM 45075T =KCTC 19236T) is proposed.
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Streptacidiphilus anmyonensis sp. nov., Streptacidiphilus rugosus sp. nov. and Streptacidiphilus melanogenes sp. nov., acidophilic actinobacteria isolated from Pinus soils
More LessThe taxonomic positions of 22 spore-forming, extensively branched actinobacteria isolated from Pinus soils were examined using a polyphasic approach. Analysis of the 16S rRNA gene sequences indicated that all of the isolates fell into three distinctive phylogenetic clusters within the genus Streptacidiphilus of the family Streptomycetaceae, and also that Streptacidiphilus jiangxiensis was the species closest to the three phyloclusters, with 16S rRNA gene sequence similarities ranging from 98.0 to 99.2 %. However, the low DNA–DNA relatedness values between representatives of the three clusters and S. jiangxiensis clearly differentiated them from one another. Representative isolates were also found to have chemotaxonomic features typical of the genus Streptacidiphilus and were distinguishable from all established species of Streptacidiphilus on the basis of a combination of phenotypic properties. It is evident from this study that each of the three phyloclusters should be equated with three novel Streptacidiphilus species, for which the following names are proposed: Streptacidiphilus anmyonensis sp. nov. (type strain AM11T =NBRC 103185T =KCTC 19278T), Streptacidiphilus rugosus sp. nov. (type strain AM16T =NBRC 103186T =KCTC 19279T) and Streptacidiphilus melanogenes sp. nov. (type strain SB-B34T =NBRC 103184T =KCTC 19280T).
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Microbacterium aquimaris sp. nov., isolated from seawater
More LessStrains JS54-2T and JS63-1 were isolated from seawater at Jeju, Korea. Cells of these strains were Gram-positive, non-motile, non-spore-forming, short rods and formed yellow-pigmented colonies on tryptic soy agar. The strains had chemotaxonomic markers that were consistent with their classification in the genus Microbacterium, i.e. MK-11, MK-12 and MK-10 as the major menaquinones, fatty acids that were predominantly iso- and anteiso-branched, galactose and glucose as the cell-wall sugars, peptidoglycan-type B2β with glycolyl residues and DNA G+C contents of 69.3–69.6 mol%. A phylogenetic analysis based on 16S rRNA gene sequences showed that the strains were closely related to Microbacterium oleivorans DSM 16091T and Microbacterium halophilum IFO 16062T (with 97.7 and 97.4 % sequence similarity, respectively) and formed a separate lineage with M. halophilum in the genus Microbacterium. Data from DNA–DNA hybridization and phenotypic analyses supported the conclusion that strains JS54-2T and JS63-1 represent a novel species in the genus Microbacterium, for which the name Microbacterium aquimaris sp. nov. is proposed. The type strain is JS54-2T (=KCTC 19124T =DSM 19713T).
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Pseudosporangium ferrugineum gen. nov., sp. nov., a new member of the family Micromonosporaceae
More LessAn actinomycete strain 3-44-a(19)T was isolated from sandy soil collected in Bangladesh. The strain formed irregular pseudosporangia directly from aggregated spore chains above the rudimentary aerial mycelium. The pseudosporangia developed singly. Each pseudosporangium contained many small, non-motile, spherical, smooth-surfaced spores in chains. Strain 3-44-a(19)T contained meso- and 3-hydroxydiaminopimelic acid in the cell wall and MK-9(H6) as the major menaquinone and arabinose, galactose, glucose, mannose, ribose and xylose were present in the whole-cell hydrolysate. The diagnostic phospholipid was phosphatidylethanolamine and iso-C15 : 0 (24.6 %), C18 : 1 ω9c (15.5 %), C16 : 0 (10.6 %), C18 : 0 (9.4 %), iso-C16 : 0 (8.6 %) and anteiso-C15 : 0 (6.0 %) were detected as the major cellular fatty acids. The acyl type of the peptidoglycan was glycolyl and mycolic acids were not detected. The G+C content of the DNA was 73.6 mol%. The chemotaxonomic data indicated that the strain belonged to the family Micromonosporaceae. Phylogenetic analysis based on 16S rRNA gene sequence data also suggested that strain 3-44-a(19)T fell within the family Micromonosporaceae. On the basis of phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides as well as morphological and chemotaxonomic data, this strain should be classified as a member of a new genus and species, Pseudosporangium ferrugineum gen. nov., sp. nov., in the family Micromonosporaceae. The type strain of Pseudosporangium ferrugineum is 3-44-a(19)T (=JCM 14710T =MTCC9007T).
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Actinomadura bangladeshensis sp. nov. and Actinomadura chokoriensis sp. nov.
More LessThe taxonomic position of two soil isolates, 3-46-b(3)T and 3-45-a(11)T, was clarified based on data from a polyphasic study. The organisms showed a combination of chemotaxonomic and morphological properties typical of the genus Actinomadura. They formed distinct phyletic lines in the Actinomadura 16S rRNA gene tree and were closely associated with the type strains of Actinomadura meyerae (sequence similarity of 98.3–98.5 %), Actinomadura napierensis (98.1–98.3 %) and Actinomadura latina (96.4–96.8 %). The level of 16S rRNA gene sequence similarity between the new isolates was 99.1 %. The level of DNA–DNA hybridization between strains 3-46-b(3)T and 3-45-a(11)T was 43.6 % and levels of relatedness between the two new isolates and the type strains of A. meyerae and A. napierensis were 21.0–27.3 %. On the basis of phenotypic and genotypic properties, the new isolates could be differentiated from each other and from their closest phylogenetic relatives. It is proposed that the organisms be classified as representing two novel species of the genus Actinomadura. The names proposed for these taxa are Actinomadura bangladeshensis sp. nov. [type strain 3-46-b(3)T =JCM 13933T =MTCC8057T] and Actinomadura chokoriensis sp. nov. [type strain 3-45-a(11)T =JCM 13932T =MTCC8056T].
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Microbacterium luticocti sp. nov., isolated from sewage sludge compost
More LessStrain SC-087BT, isolated from sewage sludge compost during a study of bacterial diversity in composts, was characterized. The isolate was a Gram-positive, short rod that was motile, catalase- and oxidase-negative and able to grow at 27–45 °C, pH 5.5–9.7 and in up to 10 % NaCl. The peptidoglycan was of the B2β type, containing the characteristic amino acids ornithine, homoserine and hydroxyglutamic acid. The muramic acid residues of the peptidoglycan were partially glycolylated. The major cell-wall sugar was mannose; traces of xylose were also detected. The predominant fatty acids, comprising more than 70 % of the total, were anteiso-C17 : 0 and anteiso-C15 : 0, the major respiratory quinone was menaquinone-12 (MK-12) and the G+C content of the genomic DNA was 72 mol%. Based on analysis of the 16S rRNA gene sequence, the closest phylogenetic neighbours of strain SC-087BT were members of the family Microbacteriaceae, showing sequence similarity values of around 96 % with members of the species Microbacterium barkeri (96.0 %), Microbacterium gubbeenense (95.6 %) and Microbacterium indicum (95.7 %). The chemotaxonomic and phenotypic traits analysed supported the inclusion of this strain within the genus Microbacterium and the proposal of a novel species. The name Microbacterium luticocti sp. nov. is proposed and the type strain is SC-087BT (=DSM 19459T=CCUG 54537T).
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- Archaea
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Halorubrum luteum sp. nov., isolated from Lake Chagannor, Inner Mongolia, China
More LessA novel halophilic archaeon, strain CGSA15T, was isolated from water of Lake Chagannor in China. The strain grew optimally at 33–37 °C, pH 9.5–10.0 and 4.0–4.3 M NaCl. The major polar lipids were phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester. The genomic DNA G+C content of strain CGSA15T was 60.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CGSA15T was a member of the genus Halorubrum and was related most closely to Halorubrum alkaliphilum AS 1.3528T (96.1 % similarity) and Halorubrum tibetense AS 1.3239T (96.9 %). Levels of DNA–DNA relatedness between strain CGSA15T and Hrr. alkaliphilum AS 1.3528T and Hrr. tibetense AS 1.3239T were 36.7 and 28.9 %, respectively. According to the phenotypic and genotypic data presented, strain CGSA15T is considered to represent a novel species of the genus Halorubrum, for which the name Halorubrum luteum sp. nov. is proposed. The type strain is CGSA15T (=CGMCC 1.6783T =CECT 7303T).
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- Bacteroidetes
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Sphingobacterium kitahiroshimense sp. nov., isolated from soil
A novel exopolysaccharide-degrading bacterium, designated strain 10CT, was isolated from soil from Kitahiroshima city, Hokkaido, Japan. The novel isolate was Gram-negative, strictly aerobic and chemoheterotrophic. The DNA G+C content was 36.9 mol%. Major fatty acids were C16 : 1 ω7c, iso-C15 : 0 2-OH, iso-C15 : 0 and iso-C17 : 0 3-OH. 16S rRNA gene sequence analysis and chemotaxonomic and morphological data indicated that the novel strain clearly belonged to the genus Sphingobacterium. Based on phenotypic properties and DNA–DNA hybridization data, the new isolate was assigned to the genus Sphingobacterium as Sphingobacterium kitahiroshimense sp. nov. The type strain is 10CT (=JCM 14970T=NCIMB 14398T).
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Muricauda lutimaris sp. nov., isolated from a tidal flat of the Yellow Sea
More LessA Gram-negative, non-motile, rod-shaped bacterial strain, SMK-108T, was isolated from a tidal flat of the Yellow Sea in Korea and was subjected to a polyphasic taxonomic investigation. Strain SMK-108T grew optimally at pH 7.0–8.0 and at 30 °C. It contained MK-6 as the predominant menaquinone. The major fatty acids were iso-C17 : 0 3-OH, iso-C15 : 1 and iso-C15 : 0. The DNA G+C content was 41.1 mol%. Comparative 16S rRNA gene sequence analysis showed that strain SMK-108T was related most closely to members of the genus Muricauda, exhibiting 96.6–98.8 % sequence similarity to the type strains of recognized Muricauda species. Strain SMK-108T was distinguishable from recognized Muricauda species on the basis of differential phenotypic characteristics, levels of DNA–DNA relatedness and phylogenetic distinctiveness. This organism is thus considered to represent a novel species of the genus Muricauda, for which the name Muricauda lutimaris sp. nov. is proposed. The type strain is SMK-108T (=KCTC 22173T =CCUG 55324T).
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Pedobacter agri sp. nov., from soil
A Gram-negative strain, PB92T, which belongs to the family Sphingobacteriaceae, was isolated from soil (Daejeon, Korea). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PB92T was associated with the genus Pedobacter and was most closely related to the type strains Pedobacter sandarakinus DS-27T (97.7 %), Pedobacter roseus CL-GP80T (97.5 %) and Pedobacter suwonensis 15-52T (97.5 %). The major cellular fatty acid components of strain PB92T were C16 : 1 ω7c (21.4 %), iso-C15 : 0 (30.8 %), iso-C17 : 0 3-OH (9.3 %) and iso-C15 : 0 2-OH (11.2 %). The G+C content of the genomic DNA from strain PB92T was 41.4 mol%. Analysis of 16S rRNA gene sequences, as well as physiological and biochemical tests, indicated that strain PB92T could be differentiated genotypically and phenotypically from reference species of the genus Pedobacter. Strain PB92T (=KCTC 12511T=DSM 19486T) is proposed as the type strain of a novel species, Pedobacter agri sp. nov.
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Robiginitalea myxolifaciens sp. nov., a novel myxol-producing bacterium isolated from marine sediment, and emended description of the genus Robiginitalea
More LessA marine, Gram-negative, deep-orange-coloured, rod/coccoid-shaped, strictly aerobic, non-motile, oxidase- and catalase-positive bacterial strain, designated YM6-073T, was isolated from sediment collected in Okinawa, Japan. Strain YM6-073T produced the carotenoid (3R,2′S)-myxol. A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain YM6-073T belonged to a distinct lineage in the family Flavobacteriaceae, the closest relative being Robiginitalea biformata HTCC2501T (93.7 % sequence similarity). Strain YM6-073T could be distinguished from other members of the family Flavobacteriaceae by means of a number of phenotypic characteristics. The DNA G+C content was 50.1 mol%. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 1 ω10c, iso-C17 : 0 3-OH and C15 : 0, and menaquinone-6 was the only respiratory quinone. DNA–DNA hybridization between strain YM6-073T and R. biformata DSM 15991T showed less than 10 % DNA–DNA relatedness. On the basis of phenotypic, genotypic and phylogenetic features, strain YM6-073T represents a novel species of the genus Robiginitalea, for which the name Robiginitalea myxolifaciens sp. nov. is proposed. The type strain is YM6-073T (=MBIC 06409T=KCTC 22216T=DSM 21019T).
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Flavobacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil
More LessA Gram-negative, non-spore-forming, cream–yellow-pigmented bacterial strain, IP-10T, was isolated from soil samples from a waste site highly contaminated with hexachlorocyclohexane in Ummari village, India. The organism showed the highest 16S rRNA gene sequence similarity of 92.7 % with Flavobacterium soli KCTC 12542T and levels of 87–92 % with the type strains of other recognized species of the genus Flavobacterium. The DNA G+C content of strain IP-10T was 31 mol%. The predominant fatty acids were iso-C15 : 0 (22.1 %), iso-C17 : 0 3-OH (18.5 %) and summed feature 3 (comprising C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 13.2 %). Strain IP-10T could be differentiated from recognized species of the genus Flavobacterium based on a number of phenotypic features. Strain IP-10T is therefore considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium lindanitolerans sp. nov. is proposed. The type strain is IP-10T (=MTCC 8597T=CCM 7424T).
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Fulvibacter tottoriensis gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from marine sediment
More LessA novel bacterium, MTT-39T, was isolated from a sample of marine sediment collected at Tottori on the coast of the Sea of Japan. Cells were Gram-negative, rod-shaped and non-motile. The bacterium formed yellowish brown colonies on marine agar 2216. Although the 16S rRNA gene sequence of strain MTT-39T classified this strain as a member of the family Flavobacteriaceae, the maximum sequence similarity obtained was only 91.5 % (with Kordia algicida OT-1T). In the maximum-likelihood tree based on 16S rRNA gene sequences, the novel bacterium clustered with the type strains of Kordia algicida, Lutibacter litoralis, Tenacibaculum maritimum and Polaribacter filamentus. The novel strain exhibited the following characteristics: the predominant fatty acids in cells grown on artificial seawater-based tryptic soya agar were iso-C15 : 1, iso-C15 : 0 and iso-C15 : 0 3-OH, the major respiratory quinone was MK-6 and the DNA G+C content was 35 mol%. On the basis of its distinct phenotypic traits and the phylogenetic distance between this marine isolate and other recognized taxa, strain MTT-39T represents a novel genus and species of the family Flavobacteriaceae, for which the name Fulvibacter tottoriensis gen. nov., sp. nov. is proposed. The type strain of the type species is MTT-39T (=NBRC 102624T=KCTC 22214T=CGMCC 1.7058T).
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- Other Bacteria
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Prosthecobacter fluviatilis sp. nov., which lacks the bacterial tubulin btubA and btubB genes
Leptothrix cholodnii is a sheathed bacterium often found in metal-rich and oligotrophic aquatic environments. A bacterial strain that is able to degrade the NaOH-treated sheath of L. cholodnii was isolated. The isolate was a Gram-negative, aerobic and prosthecate bacterium. The optimum growth temperature and pH were 30 °C and pH 7.0, respectively. The DNA G+C content was 62.9 mol%. The major respiratory quinone was MK-6. A phylogenetic analysis based on the 16S rRNA gene indicated that the isolate is a member of the genus Prosthecobacter. The nearest relative was the type strain of Prosthecobacter vanneervenii, with a similarity of 97.1 %. However, the isolate does not possess the bacterial tubulin genes, btubA and btubB, unique to known species of the genus Prosthecobacter. It is proposed that the isolate represents a novel species, Prosthecobacter fluviatilis sp. nov. The type strain is HAQ-1T (=JCM 14805T =KACC 12649T =KCTC 22182T).
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Calditerrivibrio nitroreducens gen. nov., sp. nov., a thermophilic, nitrate-reducing bacterium isolated from a terrestrial hot spring in Japan
More LessA moderately thermophilic, nitrate-reducing bacterium, strain Yu37-1T, was isolated from hot spring water from Yumata, Nagano, Japan. Cells of strain Yu37-1T were strictly anaerobic, Gram-negative, non-sporulating, motile by means of a single polar flagellum, vibrio-shaped and 1.4–2.0 μm long. The temperature and pH for optimum growth were 55 °C and pH 7.0–7.5, respectively. Strain Yu37-1T grew best in basal medium without the addition of NaCl. Acetate, pyruvate, lactate, fumarate, succinate, malate, yeast extract, peptone and Casamino acids were utilized as electron donors, with nitrate as the only electron acceptor. Ammonium was the end product from nitrate. The G+C content of the genomic DNA was 35.1 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that strain Yu37-1T could be accommodated in the family Deferribacteraceae and that its closest neighbours were members of the five genera of the family Deferribacteraceae, namely Deferribacter, Denitrovibrio, Flexistipes, Geovibrio and Mucispirillum, with similarities of only 83.2–86.2 %. The growth temperature and salinity range for growth of strain Yu37-1T differed from those of the phylogenetically related organisms. On the basis of phenotypic features and phylogenetic position, a novel genus and species are proposed, Calditerrivibrio nitroreducens gen. nov., sp. nov. Strain Yu37-1T (=NBRC 101217T =DSM 19672T) is the type strain of Calditerrivibrio nitroreducens.
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- Proteobacteria
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Kaistia soli sp. nov., isolated from a wetland in Korea
A bacterial strain, 5YN9-8T, was isolated from a peat layer in Yongneup, Republic of Korea. It was strictly aerobic, Gram-negative, non-motile, short rod- or coccus-shaped and produced ivory-pigmented colonies. Results of 16S rRNA gene sequence analyses indicated a close relationship between this isolate and Kaistia granuli Ko04T (97.2 % similarity) and Kaistia adipata Chj404T (96.2 % similarity), members of the order Rhizobiales within the Alphaproteobacteria. Predominant cellular fatty acids of strain 5YN9-8T were C18 : 1 ω7c, C18 : 0, C19 : 0 ω8c cyclo and C16 : 0. The DNA G+C content was 67.0 mol%. Phylogenetic, phenotypic and chemotaxonomic data accumulated in this study revealed that the isolate represents a novel species of the genus Kaistia, for which the name Kaistia soli sp. nov. is proposed; strain 5YN9-8T (=KACC 12605T =DSM 19436T) is the type strain.
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Polaromonas jejuensis sp. nov., isolated from soil in Korea
A Gram-negative, rod-shaped, non-motile bacterial strain, designated JS12-13T, was isolated from soil from Halla Mountain on Jeju Island, Korea. Analysis of the 16S rRNA gene sequence of strain JS12-13T revealed that it was a member of the genus Polaromonas, sharing 96.9–98.4 % sequence similarity with type strains of the genus Polaromonas and being most closely related to Polaromonas aquatica CIP 108776T. The major fatty acids of strain JS12-13T were summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH; 38.3 %), C16 : 0 (28.4 %), C17 : 0 cyclo (15.9 %) and C18 : 1 ω7c (9.1 %). The major quinone found was ubiquinone-8. The G+C content of the genomic DNA of strain JS12-13T was 63.7 mol%. On the basis of phenotypic and genotypic characteristics, strain JS12-13T represents a novel species of the genus Polaromonas, for which the name Polaromonas jejuensis sp. nov. is proposed. The type strain is JS12-13T (=KACC 12508T =DSM 19351T).
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Pseudoxanthobacter soli gen. nov., sp. nov., a nitrogen-fixing alphaproteobacterium isolated from soil
A Gram-type negative or variable, aerobic, rod-shaped, nitrogen-fixing bacterium, designated strain CC4T, was isolated on nutrient agar from a soil sample collected at a regional agricultural research field station located in Kaohsiung County, Taiwan. 16S rRNA gene sequence analysis demonstrated that this isolate is unique, showing <92.5 % similarity with respect to species of the genera Xanthobacter (maximum of 92.2 % similarity), Prosthecomicrobium (92.0 %), Devosia (91.9 %), Kaistia (91.9 %) and Methylocystis (91.9 %). The organism utilized acetic acid, formic acid, β-hydroxybutyric acid, dl-lactic acid, succinic acid, bromosuccinic acid, l-alaninamide, l-alanine, l-alanyl glycine, l-glutamic acid and l-proline as substrates, but not methanol or methylamine. Chemotaxonomic data revealed that strain CC4T contains ubiquinone Q-10 as the major respiratory quinone. The characteristic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, an unknown lipid and an unknown aminolipid. The fatty acid profile differed from those of members of the genera Xanthobacter, Prosthecomicrobium, Devosia and Kaistia. The predominant fatty acids were C18 : 1 ω7c, C19 : 0 cyclo and C16 : 0. On the basis of 16S rRNA gene sequence analysis in combination with chemotaxonomic and physiological data, strain CC4T represents a novel genus and species, for which we propose the name Pseudoxanthobacter soli gen. nov., sp. nov. The type strain of Pseudoxanthobacter soli is CC4T (=DSM 19599T =CIP 109513T).
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Burkholderia latens sp. nov., Burkholderia diffusa sp. nov., Burkholderia arboris sp. nov., Burkholderia seminalis sp. nov. and Burkholderia metallica sp. nov., novel species within the Burkholderia cepacia complex
The taxonomic position of five recA gene clusters of Burkholderia cepacia complex (Bcc) isolates was determined using a polyphasic taxonomic approach. The levels of 16S rRNA and recA gene sequence similarity, multilocus sequence typing (MLST) data and the intermediate DNA–DNA binding values demonstrated that these five clusters represented five novel species within the Bcc. Biochemical identification of these species is difficult, as is the case for most Bcc species. However, identification of these novel species can be accomplished through recA gene sequence analysis, MLST and BOX-PCR profiling and by recA RFLP analysis. For diagnostic laboratories, recA gene sequence analysis offers the best combination of accuracy and simplicity. Based on these results, we propose five novel Bcc species, Burkholderia latens sp. nov. (type strain FIRENZE 3T =LMG 24064T =CCUG 54555T), Burkholderia diffusa sp. nov. (type strain AU1075T =LMG 24065T =CCUG 54558T), Burkholderia arboris sp. nov. (type strain ES0263AT =LMG 24066T =CCUG 54561T), Burkholderia seminalis sp. nov. (type strain AU0475T =LMG 24067T =CCUG 54564T) and Burkholderia metallica sp. nov. (type strain AU0553T =LMG 24068T =CCUG 54567T). In the present study, we also demonstrate that Burkholderia ubonensis should be considered a member of the Bcc.
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Cucumibacter marinus gen. nov., sp. nov., a marine bacterium in the family Hyphomicrobiaceae
More LessA Gram-negative, rod-shaped, strictly aerobic micro-organism, designated strain CL-GR60T, was isolated from coastal seawater from the East Sea, Korea. A 16S rRNA gene sequence analysis revealed a clear affiliation with the family Hyphomicrobiaceae. Phylogenetic analyses showed that strain CL-GR60T formed a robust cluster with the species of the genus Devosia at sequence similarity levels of 91.1–93.1 %; no other species in the family Hyphomicrobiaceae shared more than 90 % sequence similarity with strain CL-GR60T. The strain grew optimally in the presence of 3–4 % sea salts at 30–35 °C and pH 7. The major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, two unidentified glycolipids, an unidentified phospholipid and an unidentified lipid. The strain contained C18 : 1 ω7c (54.7 %), 11-methyl C18 : 1 ω7c (19.3 %), C18 : 0 (14.4 %) as the predominant fatty acids. Ubiquinone-10 was the major quinone. The DNA G+C content was 62.9 mol%. On the basis of physiological data, fatty acid composition and results of phylogenetic analysis of the 16S rRNA gene sequence, strain CL-GR60T represents a novel genus and species within the family Hyphomicrobiaceae, for which the name Cucumibacter marinus gen. nov., sp. nov. is proposed. The type strain of Cucumibacter marinus is CL-GR60T (=KCCM 90027T =DSM 18995T).
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Nautilia profundicola sp. nov., a thermophilic, sulfur-reducing epsilonproteobacterium from deep-sea hydrothermal vents
More LessA thermophilic, strictly anaerobic, sulfur-reducing epsilonproteobacterium (strain AmHT) isolated from deep-sea hydrothermal vents is described. Cells were motile, Gram-negative rods. Growth was observed at 30–55 °C, pH 6.0–9.0 and 2–5 % (w/v) NaCl. Chemolithoautotrophic growth occurred with molecular hydrogen or formate as the electron donor and elemental sulfur as the electron acceptor, producing hydrogen sulfide. Heterotrophic and mixotrophic growth occurred with formate as a source of carbon. The dominant phospholipid fatty acids were C18 : 1 ω7c (73.26 % of the total), C16 : 1 ω7c (12.70 %) and C16 : 0 (12.27 %). The genomic DNA G+C content was 33.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain AmHT within the family Nautiliaceae of the Epsilonproteobacteria. DNA–DNA hybridization experiments between strain AmHT and Nautilia lithotrophica DSM 13520T revealed a level of relatedness of 34.6 % between the two strains. Based on physiological and phylogenetic characteristics, strain AmHT is considered to represent a novel species of the genus Nautilia, for which the name Nautilia profundicola sp. nov. is proposed. The type strain is AmHT (=ATCC BAA-1463T =DSM 18972T).
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Vibrio porteresiae sp. nov., a diazotrophic bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka)
More LessTwo facultatively anaerobic, nitrogen-fixing bacteria (strains MSSRF30T and MSSRF31) were isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka). These strains were determined to be nitrogen-fixers using the acetylene reduction assay and by PCR detection of a nifH gene amplicon. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the novel strains were most closely related to Vibrio fluvialis LMG 7894T (96.8 % gene sequence similarity), Vibrio furnissii LMG 7910T (96.8 % sequence similarity) and Vibrio tubiashii CIP 102760T (96.7 % sequence similarity). Further multilocus sequence analysis using recA, pyrH, rpoA and nifH genes also showed low levels of sequence similarities (83–93 %) with all species of the genus Vibrio with validly published names. A multigene phylogenetic tree using concatenated sequences of the four genes (16S rRNA, rpoA, recA and pyrH) showed that strains MSSRF30T and MSSRF31 occupied a distinct phylogenetic position, forming a long branching that was not clustered with any other recognized Vibrio species. The fatty acid profile also suggested that the novel strains belonged to the genus Vibrio. The results of physiological and biochemical tests, genomic fingerprinting and DNA–DNA hybridization analyses clearly differentiated both novel strains from their closest phylogenetic neighbours, Vibrio cholerae IID6019, Vibrio mimicus LMG 7896T, V. fluvialis LMG 7894T and V. furnissii LMG 7910T. Several phenotypic traits enabled the differentiation of strain MSSRF30T from other species of the genus Vibrio. The DNA G+C content of strain MSSRF30T was 44.4±3.1 mol%. Based on genotypic, phenotypic, chemotaxonomic, phylogenetic and DNA–DNA hybridization analyses, the name Vibrio porteresiae sp. nov. (type strain MSSRF30T=LMG 24061T=DSM 19223T) is proposed for this novel taxon.
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Vibrio sinaloensis sp. nov., isolated from the spotted rose snapper, Lutjanus guttatus Steindachner, 1869
Nine bacterial strains were studied by means of rep-PCR, 16S rRNA gene sequence analysis, DNA–DNA hybridization and physiological characterization. Typing analysis by means of rep-PCR showed that all nine strains were highly homogeneous, with similarities above 94 %. The strains were isolated from the same geographical area (Mazatlán, Sinaloa state, Mexico) and the same type of host (cultured rose snapper, Lutjanus guttatus), although from different individuals and organs. Comparison of the almost-complete 16S rRNA gene sequences of five strains showed that they belonged to the genus Vibrio and are closely related to the type strains of Vibrio brasiliensis and Vibrio hepatarius, with similarity values ranging from 97.9 to 98.1 % and from 97.4 to 97.8 %, respectively. The DNA–DNA hybridization value of strain CAIM 797T with the type strain of V. brasiliensis (CAIM 495T) was 47.5 %, with a reciprocal value of 44.7 %. The main phenotypic features of the strains were in agreement with the phylogenetic and genomic data. The results presented here support the description of a novel species, for which the name Vibrio sinaloensis sp. nov. is proposed, with strain CAIM 797T (=CECT 7298T) as the type strain.
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Rickettsia raoultii sp. nov., a spotted fever group rickettsia associated with Dermacentor ticks in Europe and Russia
We describe the characterization of a novel Rickettsia species cultivated from Dermacentor ticks collected in Russia and France, for which we propose the name Rickettsia raoultii sp. nov. Using multigene sequencing, we demonstrated that five rickettsial isolates from Dermacentor silvarum, Dermacentor reticulatus, Dermacentor marginatus and Dermacentor nuttalli ticks were classified within this novel spotted fever rickettsia species. This rickettsia also exhibited a serotype distinct from previously described Rickettsia species. The type strain of Rickettsia raoultii sp. nov. is strain KhabarovskT (=CSUR R3T =ATCC VR-1596T).
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Naxibacter varians sp. nov. and Naxibacter haematophilus sp. nov., and emended description of the genus Naxibacter
More LessSix Gram-negative, rod-shaped, non-spore-forming bacteria isolated from clinical specimens and water samples were investigated for their taxonomic allocation. On the basis of 16S rRNA gene sequence similarities, these strains (CCUG 35299T, CCUG 24677A, CCUG 48018, CCUG 49054, CCUG 48700A and CCUG 38318T) were shown to belong to the Betaproteobacteria, closely related to Naxibacter alkalitolerans (97.9–98.8 % sequence similarity to the type strain). Chemotaxonomic data (major ubiquinone Q-8; major polyamines hydroxyputrescine and putrescine; major polar lipids phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; major fatty acids C16 : 1 ω7c and C16 : 0, with 3-OH C10 : 0 and 2-OH C12 : 0 as hydroxylated fatty acids) supported the affiliation of the isolates to the genus Naxibacter. The results of DNA–DNA hybridization and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolates from the described Naxibacter species. Isolates CCUG 35299T, CCUG 24677A, CCUG 48018, CCUG 49054 and CCUG 48700A were closely related on the basis of DNA–DNA reassociation experiments and therefore represent a single novel species, for which the name Naxibacter varians sp. nov. is proposed, with the type strain CCUG 35299T (=CCM 7478T). Strain CCUG 38318T represents a second novel Naxibacter species, for which we propose the name Naxibacter haematophilus sp. nov. (type strain CCUG 38318T =CCM 7480T).
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Thiohalospira halophila gen. nov., sp. nov. and Thiohalospira alkaliphila sp. nov., novel obligately chemolithoautotrophic, halophilic, sulfur-oxidizing gammaproteobacteria from hypersaline habitats
More LessA previously unknown ecotype of obligately chemolithoautotrophic, sulfur-oxidizing bacteria was discovered in sediments of various inland hypersaline lakes and a solar saltern. The salt requirements for these bacteria were similar to those of haloarchaea, representing the first example of extreme halophiles occurring among the chemolithoautotrophs. They were enriched and isolated at 4 M NaCl under aerobic conditions with thiosulfate or tetrathionate as the electron donor or under micro-oxic conditions with sulfide. In total, 20 strains were obtained from hypersaline inland lakes in central Asia, central Russia and Crimea and a sea saltern of the Adriatic Sea. The isolates were thin, motile spirilla, some of which possessed a yellow, membrane-bound pigment. They were obligately aerobic, chemolithoautotrophic, sulfur-oxidizing bacteria that used thiosulfate, sulfide, sulfur and tetrathionate as electron donors. The characteristic feature of the group was the production of large amounts of tetrathionate as an intermediate during the oxidation of thiosulfate to sulfate. All but one of the strains grew within the pH range 6.5–8.2 (optimally at pH 7.3–7.8) and at NaCl concentrations from 2.0 to 5 M (optimally at 3.0 M). A single strain, designated ALgr 6spT, obtained (by enrichment) from the hypersaline alkaline lakes of the Wadi Natrun valley, was found to be moderately halophilic and facultatively alkaliphilic (capable of growth at pH 10). The predominant cellular fatty acids were quite unusual, with 10-methyl C16 : 0 and C16 : 0 predominating. Cells grown at 4 M NaCl accumulated extremely high concentrations of glycine betaine as a compatible solute. The 20 neutrophilic isolates contained three genospecies (on the basis of DNA–DNA relatedness data) but could not be discriminated phenotypically. On the basis of the phenotypic and genotypic analyses, the isolates constitute a novel genus and species, for which the name Thiohalospira halophila gen. nov., sp. nov. is proposed. The type strain of Thiohalospira halophila is HL 3T (=DSM 15071T=UNIQEM U219T). The haloalkaliphilic strain ALgr 6spT represents a second species of the new genus, for which the name Thiohalospira alkaliphila sp. nov. is proposed. The type strain of Thiohalospira alkaliphila is ALgr 6spT (=DSM 17116T=UNIQEM U372T).
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Rhizobium multihospitium sp. nov., isolated from multiple legume species native of Xinjiang, China
Thirty-one rhizobial strains isolated from nodules of legumes native of Xinjiang, China, were characterized. These strains were classified as belonging to the genus Rhizobium based on amplified 16S rDNA restriction analysis (ARDRA). The strains were distinguished from recognized Rhizobium species using analysis of 16S–23S rDNA intergenic spacers (IGS-RFLP), SDS-PAGE analysis of whole proteins and BOX-PCR; the test strains always formed a distinct cluster with patterns that were quite different from those of the reference rhizobial strains used. According to the phylogenetic analysis based on the 16S rRNA gene, the test strains belonged to the genus Rhizobium, with Rhizobium tropici, Rhizobium rhizogenes and Rhizobium lusitanum as the closest related species, with 99.6, 99.2 and 99.4 % sequence similarities, respectively, between the type strains of the three Rhizobium species and strain CCBAU 83401T. Phylogenetic analyses of the representative strains using IGS and atpD, recA and glnII genes all confirmed the phylogenetic arrangements obtained using the 16S rRNA gene. The DNA–DNA relatedness values between strain CCBAU 83401T and strains CCBAU 83364, CCBAU 83345 and CCBAU 83523 ranged from 80.8 to 100 %, showing that they belong to the same species. The DNA–DNA relatedness between strain CCBAU 83401T and R. tropici IIB CIAT 899T, R. tropici IIA CFN 299, R. rhizogenes LMG 150T and R. lusitanum P1-7T were 26.9, 27.7, 38.2 and 22.6 %, respectively, clearly indicating that strain CCBAU 83401T represents a novel species. Phenotypic characterization of four representative strains, CCBAU 83401T, CCBAU 83364, CCBAU 83345 and CCBAU 83523, showed several distinctive features that differentiated them from closely related species. The 31 strains had identical nodD and nifH genes, which were very similar to those of the bean-nodulating R. lusitanum, Devosia neptuniae and R. tropici IIB. Based upon these results, the strains from this study are considered to represent a novel species, for which the name Rhizobium multihospitium sp. nov. is proposed. The DNA G+C content ranged from 65.3 to 66.0 mol% (T m). The type strain is CCBAU 83401T (=LMG 23946T=HAMBI 2975T), which nodulates Robinia pseudoacacia, but not Leucaena leucocephala, Phaseolus vulgaris, Pisum sativum or Medicago sativa.
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Psychromonas japonica sp. nov., Psychromonas aquimarina sp. nov., Psychromonas macrocephali sp. nov. and Psychromonas ossibalaenae sp. nov., psychrotrophic bacteria isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan
More LessFour novel species of psychrotrophic bacteria were isolated from sediment adjacent to sperm whale carcasses off Kagoshima, Japan, at a depth of 228–250 m. Cells of the five isolated strains, JAMM 0394T, JAMM 0404T, JAMM 0415T, JAMM 0700 and JAMM 0738T, were Gram-negative, rod-shaped, non-sporulating and motile by means of a single polar flagellum. The novel strains were able to produce isoprenoid quinone Q-8 as the major component. The predominant fatty acids were C16 : 0 and C16 : 1. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strains represent a separate lineage within the genus Psychromonas. The G+C contents of the novel strains were 38.8–42.8 mol%. DNA–DNA hybridization values between these strains and reference strains of the genus Psychromonas were significantly lower than that generally accepted as the threshold for the phylogenetic definition of species. The names Psychromonas japonica sp. nov. (type strain JAMM 0394T=JCM 14783T=ATCC BAA-1525T), Psychromonas aquimarina sp. nov. (type strain JAMM 0404T=JCM 14784T=ATCC BAA-1526T), Psychromonas macrocephali sp. nov. (two strains, type strain JAMM 0415T=JCM 14785T=ATCC BAA-1527T) and Psychromonas ossibalaenae sp. nov. (type strain JAMM 0738T=JCM 14786T=ATCC BAA-1528T) are proposed.
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Marinomonas arctica sp. nov., a psychrotolerant bacterium isolated from the Arctic
A novel psychrotolerant, Gram-negative, motile bacterium, designated strain 328T, was isolated from sea-ice samples collected off the Canadian Basin of the Arctic Ocean (7 ° 23′ 14″ N 14 ° 06′ 55″ W). Strain 328T was able to grow at 0–37 °C, with optimum growth at 25–27 °C. It possessed phosphatidylethanolamine and phosphatidylglycerol as major phospholipids and C10 : 0 3-OH (31.78 %), C18 : 1 ω7c (27.50 %) and iso-C15 : 0 2-OH and/or C16 : 1 ω7c (19.22 %) as predominant cellular fatty acids. The DNA G+C content of strain 328T was 45.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 328T was a member of the genus Marinomonas (92.7–96.0 % 16S rRNA gene sequence similarity). On the basis of phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain 328T was considered to represent a novel species of the genus Marinomonas. The name Marinomonas arctica sp. nov. is proposed, with strain 328T (=CGMCC 1.6498T=JCM 14976T) as the type strain.
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Rhodobacter maris sp. nov., a phototrophic alphaproteobacterium isolated from a marine habitat of India
More LessDuring investigations into the diversity of anoxygenic phototrophic bacteria in marine habitats, an ovoid to rod-shaped purple non-sulfur bacterium, designated strain JA276T, was isolated from enrichments under photoheterotrophic conditions from a marine sediment sampled from the seashore of Cochin, India. Strain JA276T is a Gram-negative, motile, chain-forming bacterium that shows optimum growth under photoheterotrophic conditions and is also able to grow chemoorganotrophically. Thiamine is required as a growth factor. Strain JA276T contains vesicular intracytoplasmic membranes, bacteriochlorophyll a and the carotenoids spheroidene and spheroidenone. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JA276T belongs to the genus Rhodobacter and is closely related to the type strain of Rhodobacter capsulatus (96.2 % sequence similarity). On the basis of the results of 16S rRNA gene sequence analysis and morphological and physiological data, strain JA276T is significantly different from other species of the genus Rhodobacter and represents a novel species of the genus, for which the name Rhodobacter maris sp. nov. is proposed. The type strain is JA276T (=JCM 14794T =ATCC BAA-1549T =CCUG 55129T).
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Rhodovulum kholense sp. nov.
More LessA yellowish brown bacterium was isolated from photoheterotrophic enrichment cultures obtained from a mud sample collected from a mangrove forest located in Khola, India. Enrichment and isolation in medium containing 2 % NaCl (w/v) yielded strain JA297T, cells of which were ovoid and motile. Cells of strain JA297T contained vesicular internal membranes and bacteriochlorophyll a and carotenoids of the spheroidene series. Strain JA297T grew optimally at 30 °C and at pH 6.0–7.0. Photo-organoheterotrophy was the preferred mode of growth. Strain JA297T was also able to grow photolithoautotrophically and chemo-organotrophically but not by chemolithoautotrophy or by fermentation. Strain JA297T was able to utilize sulfide, sulfite, sulfate, thiosulfate, thioglycolate and cysteine as sulfur sources. Biotin, niacin and thiamine were required as growth factors. On the basis of 16S rRNA gene sequence analysis, strain JA297T was shown to belong to the class Alphaproteobacteria and was closely related to the type strains of Rhodovulum marinum (96.72 % similarity), Rhodovulum visakhapatnamense (96.42 %) and Rhodovulum sulfidophilum (96.32 %). The DNA G+C composition was 63 mol%. Based on 16S rRNA gene sequence analysis and morphological and physiological characteristics, strain JA297T could be distinguished from all recognized species of the genus Rhodovulum. This strain is therefore suggested to represent a novel species of the genus Rhodovulum, for which the name Rhodovulum kholense sp. nov. is proposed. The type strain is JA297T (=ATCC BAA-1544T=JCM 14888T=CCUG 55397T).
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- Eukaryotic Micro-Organisms
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Two novel species of Aspergillus section Nigri from Thai coffee beans
More LessTwo novel species of Aspergillus section Nigri from Thai coffee beans are described as Aspergillus aculeatinus sp. nov. and Aspergillus sclerotiicarbonarius sp. nov. Their taxonomic status was determined using a polyphasic taxonomic approach with phenotypic (morphology and extrolite profiles) and molecular (β-tubulin, internal transcribed spacer and calmodulin gene sequences) characteristics. A. aculeatinus sp. nov. is a uniseriate species with a similar morphology to Aspergillus aculeatus and Aspergillus japonicus, but producing smaller conidia (2–5 μm). A. aculeatinus sp. nov. produced neoxaline, secalonic acid D and F, and aculeacins. A. sclerotiicarbonarius sp. nov. is a biseriate species similar to Aspergillus carbonarius and Aspergillus ibericus, but produces abundant sclerotia and some unique indol-alkaloids. The type strain of Aspergillus sclerotiicarbonarius sp. nov. is CBS 121057T (=IBT 28362T) and the type strain of Aspergillus aculeatinus sp. nov. is CBS 121060T (=IBT 29077T).
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- Other Gram-Positive Bacteria
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Salinicoccus halodurans sp. nov., a moderate halophile from saline soil in China
More LessA moderately halophilic, Gram-positive coccus, designated strain W24T, was isolated from saline soil in Qinghai province, China. The isolate was able to grow at salinities of 0–24 % (w/v) NaCl (optimally at 8 %, w/v), at pH 5.5–9.0 (optimally at pH 7.5) and at 8–43 °C (optimally at 28 °C). The genomic DNA G+C content of strain W24T was 45.8 mol%. The predominant isoprenoid quinone was MK-6 and the cell wall contained lysine and glycine as diagnostic diamino acids. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The major cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0 and C16 : 0. Based on 16S rRNA gene sequence analysis, strain W24T was found to be a member of the genus Salinicoccus and was related most closely to Salinicoccus hispanicus DSM 5352T (96.5 % sequence similarity). Based on data from the current polyphasic study, strain W24T is considered to represent a novel species of the genus Salinicoccus, for which the name Salinicoccus halodurans sp. nov. is proposed. The type strain is W24T (=CGMCC 1.6501T=DSM 19336T).
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Lactobacillus senmaizukei sp. nov., isolated from Japanese pickle
More LessThe taxonomic position of a lactic acid bacterium, strain L13T, isolated from senmaizuke, a Japanese traditional pickle, was studied. This strain was a heterofermentative, facultatively anaerobic, Gram-positive, non-spore-forming, non-motile, rod-shaped bacterium. It produced dl-lactic acid from glucose. Phylogenetic analysis of its 16S rRNA gene sequence and physiological and biochemical characteristics indicated that the strain was a member of the genus Lactobacillus. Based on 16S rRNA gene sequence similarity, strain L13T was closely related to Lactobacillus hammesii CIP 108387T (98.9 %) and Lactobacillus parabrevis ATCC 53295T (98.5 %). In addition, the rpoA gene sequence of strain L13T was closely related to those of L. hammesii CIP 108387T (92.2 %) and L. parabrevis ATCC 53295T (92.0 %). However, DNA–DNA hybridization of strain L13T with these two strains revealed that strain L13T represents a separate genomic species. The DNA G+C content of strain L13T was 46 mol% and the peptidoglycan was of the A4α l-Lys–d-Asp type. Thus, these data indicate that strain L13T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus senmaizukei is proposed. The type strain is L13T (=NBRC 103853T=TISTR 1847T).
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Enterococcus thailandicus sp. nov., isolated from fermented sausage (‘mum’) in Thailand
More LessA Gram-positive and catalase-negative coccus that formed chains, designated strain FP48-3T, isolated from fermented sausage (‘mum’), was studied systematically. Strain FP48-3T was facultatively anaerobic and produced l-lactic acid from glucose. Straight-chain fatty acids C18 : 1 and C16 : 0 were the dominant components. The DNA G+C content of strain FP48-3T was 37.9 mol%. On the basis of 16S rRNA and RNA polymerase α-subunit (rpoA) gene sequence analysis, strain FP48-3T was closely related to Enterococcus hirae LMG 6399T, Enterococcus durans LMG 10746T and Enterococcus faecium LMG 11423T, with 99.3–99.6 and 95.1–96.9 % sequence similarities, respectively. Strain FP48-3T could be clearly distinguished from E. hirae LMG 6399T, E. durans LMG 10746T and E. faecium LMG 11423T by low DNA–DNA relatedness (≤14 %) and phenotypic characteristics. Therefore, this strain represents a novel species of the genus Enterococcus, for which the name Enterococcus thailandicus sp. nov. is proposed. The type strain is FP48-3T (=KCTC 13134T=NBRC 101867T=NRIC 0107T=TISTR 933T=PCU 282T).
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- International Committee On Systematics Of Prokaryotes
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- Minutes
- Opinions
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Rejection of the genus name Methanothrix with the species Methanothrix soehngenii Huser et al. 1983 and transfer of Methanothrix thermophila Kamagata et al. 1992 to the genus Methanosaeta as Methanosaeta thermophila comb. nov. Opinion 75
The Judicial Commission of the International Committee on Systematics of Prokaryotes has decided to place the genus Methanothrix with the species Methanothrix soehngenii Huser et al. 1983 on the list of nomina rejicienda, based on the fact that it is not represented by an axenic culture and contravenes Rule 31a of the International Code of Nomenclature of Bacteria. The species Methanothrix thermophila is transferred to the genus Methanosaeta as Methanosaeta thermophila ( Kamagata et al. 1992 ) Boone and Kamagata 1998 comb. nov.
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Status of strains that contravene Rules 27 (3) and 30 of the International Code of Nomenclature of Bacteria. Opinion 81
Based on a list of 205 names proposed in original articles in the International Journal of Systematic and Evolutionary Microbiology or cited in Validation Lists from January 2001 that are not in accordance with Rules 27(3) and 30 of the International Code of Nomenclature of Bacteria (the Code), the Judicial Commission rules that names contained in lists 2–4 are to be considered to be validly published and that deposit in more than one collection in different countries is documented. Names included in list 1 are only to be considered validly published if evidence is presented that the strains have been deposited in additional collections, as laid down by Rules 27 (3) and 30 of the Code.
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The type strain of Lactobacillus casei is ATCC 393, ATCC 334 cannot serve as the type because it represents a different taxon, the name Lactobacillus paracasei and its subspecies names are not rejected and the revival of the name ‘Lactobacillus zeae’ contravenes Rules 51b (1) and (2) of the International Code of Nomenclature of Bacteria. Opinion 82
The Judicial Commission affirms that typification of Lactobacillus casei is based on ATCC 393, that ATCC 334 is a member of a different taxon and that the publication rejecting the name Lactobacillus paracasei (and its included subspecies) together with the revival of the name ‘Lactobacillus zeae’ contravenes Rules 51b (1) and (2) of the International Code of Nomenclature of Bacteria.
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The subgenus names Moraxella subgen. Moraxella and Moraxella subgen. Branhamella and the species names included within these taxa should have been included on the Approved Lists of Bacterial Names and a ruling on the proposal to make changes to Rule 34a. Opinion 83
The Judicial Commission of the International Committee for Systematics of Prokaryotes rules that the following names should have been included on the Approved Lists of Bacterial Names, Moraxella (subgen. Branhamella Bøvre 1979), Moraxella (subgen. Moraxella Lwoff 1939), Moraxella (subgen. Branhamella Bøvre 1979) catarrhalis, Moraxella (subgen. Branhamella Bøvre 1979) caviae, Moraxella (subgen. Branhamella Bøvre 1979) ovis, Moraxella (subgen. Moraxella Lwoff 1939) atlantae, Moraxella (subgen. Moraxella Lwoff 1939) bovis, Moraxella (subgen. Moraxella Lwoff 1939) lacunata, Moraxella (subgen. Moraxella Lwoff 1939) nonliquefaciens, Moraxella (subgen. Moraxella Lwoff 1939) osloensis, Moraxella (subgen. Moraxella Lwoff 1939) phenylpyruvica. Proposals to alter Rule 34a were rejected.
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- Request For Opinion
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Proposal of a neotype strain (A1-86) for Eubacterium rectale. Request for an Opinion
More LessEubacterium rectale is one of the most abundant bacterial species recovered from human faeces. E. rectale ( Hauduroy et al. 1937 ) appears in the ‘List of Bacterial Names with Standing in Nomenclature’, but it is noted that the originally proposed type strain, VPI 0989T, has been lost and its possible replacement by another strain (VPI 0990) from the same faecal sample has never been formally proposed. It is therefore proposed that strain A1-86 (=DSM 17629=NCIMB 14373), isolated from human adult faeces, be formally recognized as the neotype strain of Eubacterium rectale.
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- Taxonomic Notes
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Challenging Opinion 75
More LessOpinion 75 issued by the Judicial Commission is based on an interpretation of the Rules of the International Code of Nomenclature of Bacteria (the Code) that failed to take into consideration changes made to the Code by the Judicial Commission prior to consideration of the original Request for an Opinion. Furthermore, closer examination of the Request indicates a number of contradictions that have been carried over into the published Opinion. The Judicial Commission is therefore requested to re-examine Opinion 75.
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Challenging Opinion 83
More LessThe Judicial Commission has ruled that subgenus names within the genus Moraxella should be considered to have been included on the Approved Lists, together with the corresponding species names within these subgenera. Closer examination of the facts, including the wording of the relevant passages in the Code and the original publication in which these names are included, together with information that has subsequently come to light, indicates that there is good cause to re-examine the facts on which this Opinion is based.
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Rule 15 of the International Code of Nomenclature of Bacteria: a current source of confusion
More LessThere is some degree of confusion surrounding Rule 15 of the International Code of Nomenclature of Bacteria and the fact that it appears to contradict the general principle of priority, which is central to codes of nomenclature. The present overview attempts to highlight the problem and also to provide a basis for discussion towards a solution.
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Clarifying Rule 24a of the International Code of Nomenclature of Bacteria
More LessNote 1 of Rule 24a of the International Code of Nomenclature of Bacteria can be interpreted in an ambiguous fashion, because the wording is not sufficiently clear. It is proposed that the wording of this note be modified to clarify this point.
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- Errata
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 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 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 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)