- Volume 67, Issue 1, 2017
Volume 67, Issue 1, 2017
- Validation List
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- Notification List
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- List of Changes in Taxonomic Opinion
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- New taxa
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- Actinobacteria
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Streptomyces krungchingensis sp. nov., isolated from soil
More LessA novel actinomycete, designated strain KC-035T, was isolated from soil collected from Krung Ching Waterfall National Park, Nakhon Si Thammarat Province, Thailand. Its taxonomic position was determined using a polyphasic approach. The strain had morphological and chemotaxonomic properties typical of members of the genus Streptomyces : flexuous spore chain; ll-diaminopimelic acid in the cell-wall peptidoglycan; MK-9(H8), MK-9(H6) and MK-9(H4) as menaquinones; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside as phospholipids; anteiso-C15 : 0, C16 : 0, iso-C16 : 0, iso-C15 : 0 and iso-C14 : 0 as major cellular fatty acids; and DNA G+C content of 72 mol%. 16S rRNA gene sequence analysis revealed that strain KC-035T showed high similarity to Streptomyces albiflavescens n20T (99.16 %) and Streptomyces siamensis KC-038T (98.43 %) as well as formed a monophyletic clade with them in the phylogenetic tree. On the basis of comparison of phenotypic properties and the low level of DNA–DNA relatedness, strain KC-035T could be distinguished from its closely related Streptomyces species and is considered to represent a novel species of the genus Streptomyces , for which the name Streptomyces krungchingensis sp. nov. is proposed. The type strain is KC-035T (=NBRC 110087T=KCTC 29503T=TISTR 2402T).
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Streptomyces fuscichromogenes sp. nov., an actinomycete from soil
More LessA novel actinomycete, designated strain m16T, was isolated from a soil sample collected from the tropical rain forest of Xishuangbanna, a prefecture in Yunnan Province, south-west China, and characterized by using polyphasic taxomomy. Cells were aerobic and Gram-reaction-positive, and spore chains were observed to be of the helical type, with elliptical spores and smooth spore surfaces. The novel strain grew over a temperature range of 15–35 °C, at pH 5.0–11.0 and in the presence of 0–3 % (w/v) NaCl. The DNA G+C content of strain m16T was 70.0 mol%. The main fatty acids were iso-C16 : 0 (29.3 %), iso-C15: 0 (15.4 %) and anteiso-C15:0 (14.6 %), and the predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). Comparative 16S rRNA gene sequence analysis showed that strain m16T was most closely related to Streptomyces jiujiangensis KCTC 29262T (98.7 %), Streptomyces panaciradicis KACC 17632T (98.7 %), Streptomyces rhizophilus NBRC 108885T (98.5 %), Streptomyces shenzhenensis DSM 42034T (98.4 %), Streptomyces graminisoli JR-19T (98.4 %) and Streptomyces gramineus JR-43T (98.3 %). Phylogenetic, chemotaxonomic and phenotypic analyses indicated that strain m16T represents a novel species within the genus Streptomyces , for which the name Streptomyces fuscichromogenes is proposed. The type strain is m16T (=CGMCC 4.7110T=KCTC 29195T).
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Kibdelosporangium metalli sp. nov., isolated from a rare earth mine
More LessA Gram-stain-positive, oxidase-negative, catalase-positive isolate forming sporangium-like globular bodies, isolated from the rare earth mine of Bayan Obo in China and designated strain KC 266T, was subjected to a comprehensive taxonomic study. Comparative 16S rRNA gene sequence analysis revealed that strain KC 266T represented a novel lineage within the genus Kibdelosporangium and showed highest 16S rRNA gene similarities to Kibdelosporangium philippinense (98.5 %), Kibdelosporangium aridum subsp. largum (98.2 %), Kibdelosporangium aridum subsp. aridum (98.2 %) and Kibdelosporangium phytohabitans (98.0 %). The DNA–DNA relatedness between strain KC 266T and the four species of the genus Kibdelosporangium was less than 60 %. The DNA G+C content of strain KC 266T was 67.9 mol%. The quinone system consisted of major amounts of MK-9(H4) and MK-9(H2), minor amounts of MK-8(H2) and traces of MK-10(H4). The diamino acid of the peptidoglycan was meso-diaminopimelic acid. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol, two unknown phospholipids and one unidentified aminophospholipid. The major cellular fatty acids were iso-C16 : 0, C17 : 1 ω6c, iso-C15 : 0 and iso-C14 : 0. Physiological traits as well as unique traits of the polar lipid profile and the fatty acid pattern distinguished strain KC 266T from the most closely related species. All these results indicate that strain KC 266T represents a novel species of the genus Kibdelosporangium , for which the name Kibdelosporangium metalli sp. nov. is proposed. The type strain is KC 266T (=KCTC 39719T=CCTCC AA 2016002T).
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Streptomyces capparidis sp. nov., a novel endophytic actinobacterium isolated from fruits of Capparis spinosa L.
A novel endophytic actinobacterial strain, designated EGI 6500195T, was isolated from fruits of Capparis spinosa. Growth occurred at 10–45 °C (optimum 30 °C), at pH 6–8 (optimum pH 7) and in the presence of 0–1 % (w/v) NaCl. Strain EGI 6500195T shared highest 16S rRNA gene sequence similarity (97.74 %) with Streptomyces vitaminophilus DSM 41686T and less than 97 % sequence similarity with other members of the genus Streptomyces . The diagnostic amino acid in the peptidoglycan was ll-diaminopimelic acid. Whole-cell hydrolysates contained glucose, ribose, fructose and mannose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The polar lipid profile of strain EGI 6500195T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylcholine, three unknown phospholipids, an unknown aminophospholipid and an unknown aminolipid. The cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C15 : 0, iso-C16 : 0, anteiso-C17 : 1 ω9c, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B) and iso-C17 : 1 ω9c. The DNA G+C content of strain EGI 6500195T was 74.1 mol%. The level of DNA–DNA relatedness between strain EGI 6500195T and Streptomyces. vitaminophilus DSM 41686T was 14.1±3.5 %. On the basis of the phenotypic, phylogenetic, chemotaxonomic and DNA–DNA hybridization data, strain EGI 6500195T represents a novel species of the genus Streptomyces , for which the name Streptomyces capparidis sp. nov. is proposed. The type strain is EGI 6500195T (=DSM 42145T=JCM 30089T).
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Kocuria oceani sp. nov., isolated from a deep-sea hydrothermal plume
More LessThree strains, FXJ8.095T, FXJ8.057 and H201, were isolated from deep-sea hydrothermal plume water collected at the Southwest Indian Ridge at a depth of 2800 m. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates formed a closely related subcluster within the genus Kocuria . The 16S rRNA gene sequence of strain FXJ8.095T shared 99.90 and 99.60 % similarity with those of strains FXJ8.057 and H201, respectively, and 98.81, 98.75, 98.68 and 98.10 % with those of ‘ Kocuria sediminis ’ JCM 17929, Kocuria flava HO-9041T, Kocuria turfanensis HO-9042T and Kocuria rosea JCM 11614T, respectively. DNA–DNA hybridization values among the three new isolates were higher than 70 %, while the values between each of the isolates and the closely related type strains were well below 70 %. Random amplified polymorphic DNA fingerprint patterns and a combination of physiological and biochemical properties also distinguished the isolates from the related species. The major cellular fatty acids of the isolates were anteiso-C15 : 0 and iso-C15 : 0, the predominant menaquinones were MK-7(H2) and MK-8(H2), and the main polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The DNA G+C contents of strains FXJ8.095T, FXJ8.057 and H201 were 75.6, 72.8 and 70.4 mol%, respectively. Based on the phylogenetic, phenotypic and chemotaxonomic data, we propose to classify the three strains in a novel species named Kocuria oceani sp. nov., with FXJ8.095T (=CGMCC 4.6946T=DSM 24949T) as the type strain.
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- Archaea
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Haloprofundus marisrubri gen. nov., sp. nov., an extremely halophilic archaeon isolated from a brine–seawater interface
We isolated a Gram-stain-negative, pink-pigmented, motile, pleomorphic, extremely halophilic archaeon from the brine–seawater interface of Discovery Deep in the Saudi Arabian Red Sea. This strain, designated SB9T, was capable of growth within a wide range of temperatures and salinity, but required MgCl2. Cells lysed in distilled water, but at 7.0 % (w/v) NaCl cell lysis was prevented. The major polar lipids from strain SB9T were phosphatidylglycerol, phosphatidylglycerolphosphate methyl ester, sulfated mannosyl glucosyl diether, mannosyl glucosyl diether, an unidentified glycolipid and two unidentified phospholipids. The major respiratory quinones of strain SB9T were menaquinones MK8 (66 %) and MK8 (VIII-H2) (34 %). Analysis of the 16S rRNA gene sequence revealed that strain SB9T was closely related to species in the genera Halogranum and Haloplanus ; in particular, it shared highest sequence similarity with the type strain of Halogranum rubrum (93.4 %), making it its closest known relative. The unfinished draft genome of strain SB9Twas 3 931 127 bp in size with a total G+C content of 62.53 mol% and contained 3917 ORFs, 50 tRNAs and eight rRNAs. Based on comparisons with currently available genomes, the highest average nucleotide identity value was 83 % to Halogranum salarium B-1T (GenBank accession no. GCA_000283335.1). These data indicate that this new isolate cannot be classified into any recognized genera of the family Haloferacaceae, and therefore strain SB9T is considered to be a representative of a novel species of a new genus within this family, for which the name Haloprofundus marisrubri gen. nov., sp. nov. is proposed. The type strain of Haloprofundus marisrubri is SB9T (=JCM 19565T=CGMCC 1.14959T).
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- Bacteroidetes
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Flavobacterium eburneum sp. nov., isolated from reclaimed saline land soil
More LessA novel Gram-stain-negative, motile by gliding, and aerobic bacterial strain, designated SA31T, was isolated from reclaimed saline land soil near a lake in Taean-gun, South Korea. Cells of the isolate formed ivory-coloured colonies. Growth occurred at 10–35 °C (optimum 25–30 °C), pH 6.0–9.0 (optimum pH 7.0–7.5), and 0–2.0 % (w/v) NaCl (optimum 0 %). Based on similarities of 16S rRNA gene sequences, strain SA31T was mostly affiliated with the genus Flavobacterium , exhibiting the highest sequence similarities with Flavobacterium palustre S44T (96.0 %), Flavobacterium glycines Gm-149T (95.9 %), Flavobacterium defluvii EMB117T (95.7 %) and Flavobacterium daejeonense GH1-10T (95.6 %). Phylogenetic analysis based on 16S rRNA gene sequences also indicated that strain SA31T was clustered with Flavobacterium daejeonense GH1-10T and Flavobacterium glycines Gm-149T. The predominant fatty acids (>7 % of total) of strain SA31T were iso-C15 : 0, summed feature 3 (C16 : 1 ω7с and/or C16 : 1 ω6с), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The major polar lipids of the isolate comprised phosphatidylethanolamine, one unknown aminolipid, one unknown glycolipid, one unknown aminophospholipid and three unknown lipids. The major respiratory quinone was MK-6. The genomic DNA G+C content of strain SA31T was 33.5 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic analyses, strain SA31T represents a novel species the genus Flavobacterium , for which the name Flavobacterium eburneum sp. nov. is proposed. The type strain is SA31T (=KACC 18743T=JCM 31221T).
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Flavobacterium inkyongense sp. nov., isolated from an artificial freshwater pond
More LessA Gram-stain-negative, non-motile, yellow-pigmented bacterium, designated strain IMCC27201T, was isolated from an artificial freshwater pond (Inkyong) in Korea. Growth of strain IMCC27201T occurred at 10–37 °C (optimum, 30 °C), at pH 7.0–8.0 (optimum, pH 7.0) and with 0–0.25 % (w/v) NaCl (optimum, 0 %). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain IMCC27201T belonged to the genus Flavobacterium and was related most closely to Flavobacterium columnare IFO 15943T (97.8 % sequence similarity), Flavobacterium terrae R2A1-13T (97.2 %) and Flavobacterium vireti THG-SM1T (96.4 %). Strain IMCC27201T exhibited low DNA–DNA relatedness with F. columnare KCTC 42885T (34.9–40.6 %). The DNA G+C content of strain IMCC27201T was 32.1 mol%. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G and iso-C15 : 0 3-OH. Strain IMCC27201T contained menaquinone-6 (MK-6) as the sole isoprenoid quinone. The polar lipids of strain IMCC27201T consisted of phosphatidylethanolamine, three unidentified aminolipids and two unidentified lipids. Based on 16S rRNA gene phylogeny, phenotypic characterization and DNA–DNA relatedness, strain IMCC27201Trepresents a novel species of the genus Flavobacterium , for which the name Flavobacterium inkyongense sp. nov. is proposed. The type strain is IMCC27201T (=KCTC 52244T=JCM 31385T).
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Flavobacterium orientale sp. nov., isolated from lake water
More LessTwo Gram-stain-negative, obligately aerobic, non-motile, rod-shaped bacterial strains, designated SP3T and SP38, were isolated from a cold-water lake in the west of China. A polyphasic taxonomic study was performed for the strains. Alignment of 16S rRNA gene sequences indicated that strains SP3T and SP38 were associated with the genus Flavobacterium and were most closely related to Flavobacterium lacus NP180T (96.4 % sequence similarity), Flavobacterium ponti GSW-R14T (95.6 %) and Flavobacterium yanchengense hgT (95.3 %). The genomic DNA G+C contents of strains SP3T and SP38 were 34.9 and 34.6 mol%, respectively. The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, summed feature 9 (iso-C17 : 1 ω9c and/or 10-methyl C16 : 0), iso-C17 : 0 3-OH and iso-C15 : 0 3-OH. The unique respiratory quinone was menaquinone 6 (MK-6). The polar lipid profile consisted of phosphatidylethanolamine, one unidentified aminolipid and several unidentified polar lipids. Based on physiological, biochemical and phylogenetic data for these isolates, it was confirmed that strains SP3T and SP38 were affiliated to the genus Flavobacterium and represented a novel species, for which the name Flavobacterium orientale sp. nov. is proposed. The type strain is SP3T (=CGMCC 1.12506T=NBRC 109717T).
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Soortia roseihalophila gen. nov., sp. nov., a new taxon in the order Balneolales isolated from a travertine spring, and description of Soortiaceae fam. nov.
A novel Gram-stain-negative, slightly halophilic, motile, curved rod with a horseshoe shape, designated strain Bsw-2bT, was isolated from Badab-Soort travertine spring in Iran. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain Bsw-2bT belongs to the order Balneolales , showing 84.6 % sequence similarity to Gracilimonas tropica DSM 19535T and 84.4 % and 83.9 % sequence similarity to Gracilimonas rosea CL-KR2T and Balneola vulgaris DSM 17893T, respectively. In addition, phenotypic and physiological features could clearly differentiate strain Bsw-2bT from species of the most closely related genera, Gracilimonas , Balneola , Aliifodinibius and Fodinibius . The strain was able to grow with 1–3 % (w/v) (optimum at 2 %) NaCl, at temperatures of 28–34 °C (optimum at 30 °C) and between pH 6.0 and 8.0 (optimum at pH 7.0). The major cellular fatty acids of strain Bsw-2bT were iso-C15 : 0, iso-C13 : 0 and iso-C14 : 0. The polar lipid profile of strain Bsw-2bT was composed predominantly of phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, an unknown glycolipid and four unknown phospholipids. The DNA G+C content was 40.5 mol%. Based on the evidence from the polyphasic study, strain Bsw-2bT represents a novel species in a novel genus within a new family, for which the name Soortia roseihalophila gen. nov., sp. nov. is proposed, within the new family Soortiaceae fam. nov. The type strain is strain Bsw-2bT (=IBRC-M 10915T=LMG 28547T).
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Nonlabens halophilus sp. nov., isolated from reclaimed land
More LessA Gram-stain-negative, orange-pigmented, non-spore-forming, non-motile, aerobic, rod-shaped bacterial strain, designated CAU 1131T, was isolated from reclaimed land. Strain CAU 1131T grew optimally at 30 °C and at pH 6.5 in the presence of 4 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1131T was grouped into the genus Nonlabens , and was most closely related to Nonlabens. marinus S1-08T (95.9 % 16S rRNA gene sequence similarity). The strain possessed+ MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C15:0 3-OH, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major cellular fatty acids. The polar lipid profile was determined to comprise phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid, an unidentified glycolipid and two unidentified lipids. The DNA G+C content was 38.7 mol%. On the basis of data from phenotypic, chemotaxonomic and phylogenetic inference, strain CAU 1131T represents a novel species of the genus Nonlabens , for which the name Nonlabens halophilus sp. nov. is proposed. The type strain is CAU 1131T (=KCTC 52177T=NBRC 111996T).
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Polaribacter vadi sp. nov., isolated from a marine gastropod
More LessA Gram-reaction-negative, non-motile, yellow-pigmented, NaCl-requiring bacterial strain, designated LPB0003T, was isolated from a marine gastropod, the granulated dogwhelk (Thais luteostoma). The complete genome sequence of strain LPB0003T (GenBank accession number CP017477), sized 3.81 Mb, had 3296 protein-coding genes. 16S rRNA gene sequence analysis indicated that strain LPB0003T belongs to the genus Polaribacter within the family Flavobacteriaceae with sequence similarities of 95.3–97.8 % to other species of the genus Polaribacter . The average nucleotide identities with closely related species were not higher than 80 %. The isoprenoid quinone (MK-6) and DNA G+C content (29.6 mol%) of strain LPB0003T fell within the expected ranges for the genus Polaribacter . The major polar lipids of the isolate were phosphatidylethanolamine, two unidentified aminolipids, an unidentified phospholipid, an unidentified glycolipid, and two unidentified lipids. The predominant cellular fatty acids were iso-C15 : 0, iso-C15 : 0 3-OH, C16 : 1 ω7c and/or C16 : 1 ω6c (summed feature 3), and C15 : 1 ω6c. Based on phylogenetic, genomic and phenotypic data presented in this study, strain LPB0003T should be classified as a novel species of the genus Polaribacter , for which the name Polaribacter vadi sp. nov. is proposed. The type strain is LPB0003T (=KACC 18704T=JCM 31217T).
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Olivibacter composti sp. nov., isolated from compost collected at a greenhouse
More LessA polyphasic approach was used to characterize a presumably novel bacterium, designated strain CC-KYC063T, isolated from a compost sample collected at a greenhouse facility within Taiwan. Strain CC-KYC063T was Gram-stain-negative and aerobic, able to grow at 15–37 °C (optimal 30 °C), at pH 7.0–9.0 (optimal pH 7.0) and with 0–2 % (w/v) NaCl. The 16S rRNA gene sequence of strain CC-KYC063T showed highest similarity to Olivibacter ginsengisoli Gsoil 060T (96.2 %) and Olivibacter terrae Jip13T (95.5 %). The DNA G+C content was 43.0 mol% and the predominant quinone system was menaquinone-7 (MK-7). The polyamine pattern showed a predominance of sym-homospermidine. The major fatty acids found in strain CC-KYC063T were iso-C15 : 0, iso-C17 : 0 3-OH and C16 : 1 ω6c/C16 : 1 ω7c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-KYC063T is considered to represent a novel species of the genus Olivibacter , for which the name Olivibacter composti sp. nov. is proposed. The type strain is CC-KYC063T (=BCRC 80939T=JCM 31198T).
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Flavobacterium gilvum sp. nov., isolated from stream water
More LessA cream-coloured, non-gliding, aerobic Flavobacterium strain, designated EM1308T, was isolated from stream water. 16S rRNA gene sequence analysis indicated that this isolate is closely related to Flavobacterium glycines NBRC 105008T (97.3 % similarity) and Flavobacterium piscis CCUG 60099T (97.2 %). To evaluate the genomic relatedness of the isolate with its neighbours, the whole genome sequences of strain EM1308T and the type strains of F. glycines and F. piscis were determined. Average nucleotide identities revealed that strain EM1308T is independent from other Flavobacterium species. The properties of major cellular fatty acids, polar lipids, menaquinone and DNA G+C content of the isolate were within the general range for the genus Flavobacterium , but many biochemical and physiological characteristics distinguished the isolate from previously known species. Thus, strain EM1308T represents a novel species of the genus Flavobacterium , for which the name Flavobacterium gilvum sp. nov. is proposed. The type strain is EM1308T (=KACC 18113T=JCM 30144T).
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- Firmicutes and Related Organisms
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Bacillus maritimus sp. nov., a novel member of the genus Bacillus isolated from marine sediment
The taxonomic position of a Gram-stain-positive, endospore-forming bacterium, strain KS16-9T, isolated from a marine sediment sample collected from Kovalam, Kanyakumari coastal region of the Indian Ocean, India, was analysed by a polyphasic approach. Strain KS16-9T had typical phenotypic characteristics and chemotaxonomic features (menaquinones, fatty acids and lipids) that were consistent with the genus Bacillus . omparative analysis of the 16S rRNA gene sequence of the strain with previously published Bacillus type strains confirmed that it belongs to the genus Bacillus and is moderately related to Bacillus persicus B48T (98.42 % similarity), followed by Bacillus foraminis CV53T (97.67 %) and Bacillus rigiliprofundi (97.61 %). Other species in the genus Bacillus shared <97.6 % 16S rRNA gene sequence similarity. Strain KS16-9T contained MK-7 as the predominant menaquinone, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, iso-C15 : 0 and anteiso-C15 : 0 as major fatty acids, and diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine as the major phospholipids. The DNA G+C content of strain KS16-9T was 45.4 mol%. Based on data from this polyphasic taxonomic study, strain KS16-9T represents a novel species of the genus Bacillus , for which the name Bacillus maritimus sp. nov. is proposed. The type strain is KS16-9T (=MTCC 12305T=DSM 100413T=KCTC 33834T).
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Lysinibacillus alkalisoli sp. nov., isolated from saline–alkaline soil
More LessA Gram-stain-positive, aerobic bacterial strain, designated Y2A20T, with peritrichous flagella was isolated from the top layer saline–alkaline soil, Hangjin Banner, Inner Mongolia, northern China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Y2A20T formed a stable clade with ‘ Lysinibacillus jejuensis ’ N2-5T. Strain Y2A20T shared highest 16S rRNA gene sequence similarity with ‘ L. jejuensis ' N2-5T (97.4 %), but lower 16S rRNA gene sequence similarities with all other type strains (<97.0 %). The major polar lipids of strain Y2A20T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidyethanolamine, two unknown aminophospholipids and three unknown phospholipids. Menaquinone-7 was the predominant menaquinone, while iso-C15 : 0, iso-C16 : 0 and iso-C17 : 0 were the major cellular fatty acids. Its genomic DNA G+C content was 39.0 mol%. DNA–DNA hybridization revealed that strain Y2A20T showed 26±5 % genomic DNA relatedness with its closest relative, ‘ L. jejuensis ’ N2-5T. The results of physiological and biochemical tests allowed the discrimination of strain Y2A20T from its phylogenetic relatives. Lysinibacillus alkalisoli sp. nov. is therefore proposed with Y2A20T (=CGMCC 1.15760T=KCTC 33825T) as the type strain.
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Virgibacillus jeotgali sp. nov., isolated from Myeolchi-jeotgal, a traditional Korean high-salt-fermented anchovy
More LessA Gram-staining-positive, motile, endospore-forming, rod-shaped bacterium, designated NS3012T, was isolated from Myeolchi-jeotgal, a traditional Korean high-salt-fermented anchovy and was characterized using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain NS3012T belongs to the genus Virgibacillus in the family Bacillaceae of the phylum Firmicutes . The 16S rRNA gene sequence analysis showed that strain NS3012T was closely related to Virgibacillus halotolerans WS-4627T (98.1 %), Virgibacillus oceani MY11T (96.6 %) and Virgibacillus byunsanensis ISL-24T (96.5 %). The chemotaxonomic properties of strain NS3012T were consistent with those of the genus Virgibacillus : the quinone system with MK-7 as the predominant menaquinone and anteiso-C15 : 0 and anteiso C17 : 0 as the major cellular fatty acids; the cell-wall peptidoglycan type was based on meso-diaminopimelic acid. The major polar lipid was diphosphatidylglycerol. The G+C content of the genomic DNA was 36.8 mol%. On the basis of phylogenetic inference, and chemotaxonomic and other phenotypic properties, strain NS3012T is clearly differentiated from closely related species of the genus Virgibacillus and represents a novel species in this genus, for which the name Virgibacillus jeotgali sp. nov. is proposed. The type strain is NS3012T (=KEMB 9001-125T=JCM 16522T).
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- Other Bacteria
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Deinococcus ruber sp. nov., a radiation-resistant bacterium isolated from soil
Two gamma- and UVC-resistant bacterial strains, designated JSH3-1T and 9-2-2, were isolated from garden soil in South Korea. Cells were Gram-stain-positive, aerobic, non-motile and spherical. A polyphasic approach was used to study the taxonomic properties of strains JSH3-1T and 9-2-2. Phylogenetic analysis based on nearly full-length 16S rRNA gene sequences of strains JSH3-1T and 9-2-2 indicated highest similarity with Deinococcus radiomollis PO-04-20-132T (94.7 and 94.9 %, respectively); levels of sequence similarity with the type strains of other Deinococcus species were less than 94.0 %. Strains JSH3-1T and 9-2-2 shared relatively high 16S rRNA gene sequence similarity (98.7 %) and had a high DNA reassociation value of 81±0.5 %. Meanwhile, they showed low levels of DNA reassociation (<25 %) with other closely related species of the genus Deinococcus . The two strains showed chemotaxonomic features typical of the genus Deinococcus , with the presence of menaquinone 8 as the respiratory quinone. The predominant fatty acids were iso-C17 : 0, iso-C13 : 0 and anteiso-C13 : 0. The polar lipids comprised phosphoglycolipid, aminophospholipid, glycolipid and unknown aminolipids. The DNA G+C contents of strains JSH3-1T and 9-2-2 were 62.0 and 61.9 mol%, respectively. On the basis of their phenotypic and genotypic characteristics, and phylogenetic distinction, strains JSH3-1T (=KCTC 33790T=JCM 31311T) and 9-2-2 (=KCTC 33789=JCM 31310) should be classified within a novel species of the genus Deinococcus , for which the name Deinococcus ruber sp. nov. is proposed.
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- Proteobacteria
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Formosimonas limnophila gen. nov., sp. nov., a new member of the family Burkholderiaceae isolated from a freshwater lake
More LessStrain AHQ-12T, isolated from a freshwater lake in Taiwan, was characterized using a polyphasic taxonomy approach. Cells of strain AHQ-12T were Gram-staining-negative, aerobic, non-motile, non-spore forming, straight rods and formed translucent white-coloured colonies. Optimal growth occurred at 20 °C, pH 6.0 and with 0 % NaCl. The predominant fatty acids were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major isoprenoid quinone was Q-8, and the DNA G+C content was 50.4 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several uncharacterized aminophospholipids and lipids. The major polyamine was cadaverine. 16S rRNA gene sequence analysis demonstrated that this isolate was unique, showing less than 91 % sequence similarity to its closest relatives, including members of the genera Ralstonia (89.7–90.8 %), Cupriavidus (88.8–90.3 %), Polynucleobacter (88.2–89.5 %), Burkholderia (86.6–90.3 %) and Pandoraea (89.2–90.1 %). Phylogenetic analyses demonstrated that strain AHQ-12T formed a distinct clade closely related to species of the family Burkholderiaceae . On the basis of the phylogenetic inference and phenotypic data, strain AHQ-12T should be classified as a novel species of a new genus in the family Burkholderiaceae , for which the name Formosimonas limnophila gen. nov., sp. nov. is proposed. The type strain is AHQ-12T (=BCRC 80690T=LMG 27847T=KCTC 32501T).
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Roseovarius aestuariivivens sp. nov., isolated from a tidal flat
More LessA Gram-stain-negative, non-motile, aerobic and coccoid, ovoid or rod-shaped bacterium, designated GHTF-24T, was isolated from a tidal flat on the South Sea, South Korea, and subjected to polyphasic taxonomic study. The novel strain grew optimally at 30 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. In the neighbour-joining phylogenetic tree based on 16S rRNA gene sequences, strain GHTF-24T fell within the clade comprising the type strains of species of the genus Roseovarius . Strain GHTF-24T exhibited 16S rRNA gene sequence similarity values of 97.0 % to each of Roseovarius halotolerans HJ50T and Roseovarius pacificus 81-2T and of 91.6–96.5 % to the type strains of the other species of the genus Roseovarius . Strain GHTF-24T contained Q-10 as the predominant ubiquinone and C18 : 1 ω7c as the major fatty acid. The major polar lipids of strain GHTF-24T were phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminolipid and one unidentified lipid. The DNA G+C content of strain GHTF-24T was 62.3 mol%, and its mean DNA–DNA relatedness values with the type strains of R. halotolerans and R. pacificus were 13–16 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain GHTF-24T is separated from other recognized species of the genus Roseovarius . On the basis of the data presented, strain GHTF-24T is considered to represent a novel species of the genus Roseovarius , for which the name Roseovarius aestuariivivens sp. nov. is proposed. The type strain is GHTF-24T (=KCTC 52454T=NBRC 112420T).
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Colwellia mytili sp. nov., isolated from mussel Mytilus edulis
A Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated RA2-7T, was isolated from a mussel (Mytilus edulis) collected from the South Sea, South Korea, and subjected to a taxonomic study using a polyphasic approach. Strain RA2-7T grew optimally at 20 °C, at pH 7.0–8.0 and in the presence of 2.0–3.0 % (w/v) NaCl. The phylogenetic trees based on 16S rRNA gene sequences showed that strain RA2-7T belonged to the genus Colwellia . Strain RA2-7T exhibited 16S rRNA gene sequence similarity values of 98.3, 98.0 and 97.5 % to the type strains of Colwellia sediminilitoris , Colwellia aestuarii and Colwellia polaris , respectively, and of 94.5–96.5 % to the type strains of the other species of the genus Colwellia . Strain RA2-7T contained Q-8 as the predominant ubiquinone and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major polar lipids detected in strain RA2-7T were phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content of strain RA2-7T was 39.0±0.04 mol% and its DNA–DNA relatedness values with the type strains of C . sediminilitoris , C. aestuarii and C. polaris were 14–19 %. Differential phenotypic properties, together with its phylogenetic and genetic distinctiveness, revealed that strain RA2-7T is separated from recognized species of the genus Colwellia . On the basis of the data presented, strain RA2-7T is considered to represent a novel species of the genus Colwellia , for which the name Colwellia mytili sp. nov. is proposed. The type strain is RA2-7T (=KCTC 52417T=NBRC 112381T).
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Achromobacter aloeverae sp. nov., isolated from the root of Aloe vera (L.) Burm.f.
Two Gram-staining-negative, strictly aerobic, rod-shaped bacteria, designated strains AVA-1T and AVA-2, were isolated from the root of Aloe vera (L.) Brum.f. derived from Chachoengsao Province, Thailand. The strains contained cytochrome oxidase and catalase activities. They grew in 4 % (w/v) NaCl, at a pH range of 6.0–9.0 (optimally at pH 7) and at 20–42 °C (optimally at 30–37 °C). The major isoprenoid quinone was ubiquinone with eight isoprene units (Q-8). The major fatty acids were C16 : 0 and C17 : 0 cyclo. On the basis of 16S rRNA gene sequence analysis, the strains represent a species belonging to the genus Achromobacter and are closely related to Achromobacter xylosoxidans NBRC 15126T (98.80 %), Achromobacter insolitus LMG 6003T (98.64 %), Achromobacter aminicus LMG 26690T (98.59 %), Achromobacter pulmonis LMG 26696T (98.58 %) and Achromobacter insuavis LMG 26845T (98.58 %). The DNA G+C content of strain AVA-1T was 66.5 mol%. The novel strains had low DNA–DNA relatedness values with related type strains. On the basis of the phenotypic and genotypic data obtained, the strains clearly represent a novel species, for which the name Achromobacter aloeverae sp. nov. is proposed. The type strain is strain AVA-1T (=LMG 29108T=NBRC 111463T=PCU 352T=TISTR 2383T).
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Halodesulfovibrio spirochaetisodalis gen. nov. sp. nov. and reclassification of four Desulfovibrio spp.
More LessAn antibiotic-producing, obligate anaerobic, Gram-stain-negative, catalase- and oxidase-negative strain (JC271T) was isolated from a marine habitat and identified, based on 16S rRNA gene sequence analysis, as a novel member of the family Desulfovibrionaceae . The closest phylogenetic relatives of strain JC271T were found to be Desulfovibrio marinisediminis C/L2T (99.2 %), Desulfovibrio acrylicus W218T (98.7 %), Desulfovibrio desulfuricans subsp. aestuarii (98.6 %), Desulfovibrio oceani subsp. oceani (98.0 %), Desulfovibrio oceani subsp. galatae (98.0 %) and other members of the genus Desulfovibrio (≤91.9 %). To resolve its full taxonomic position, the genomic sequence of strain JC271T was compared to available genomes of the most closely related phylogenetic members. Average Nucleotide Identity scores and DNA–DNA hybridization values confirmed that strain JC271T represents a novel genomic species. Iso-C17 : 0, iso-C17 : 1ω9c, and iso-C15 : 0 were found to be the major (comprising >10 % of the total present) fatty acids of strain JC271T. Phosphatidylglycerol, phosphatidylethanolamine and unidentified lipids (L1-8) were the polar lipids identified. The G+C content of strain JC271T was 46.2 mol%. Integrated genomic and phenotypic data supported the classification of strain JC271T as a representative of a novel genus, for which the name Halodesulfovibrio spirochaetisodalis gen. nov., sp. nov. is proposed. The type strain is JC271T (=KCTC 15474T=DSM 100016T). It is also proposed that Desulfovibrio acrylicus W218T is the latter heterotypic synonym of Desulfovibrio desulfuricans subsp. aestuarii Sylt 3T. Desulfovibrio desulfuricans subsp. aestuarii Sylt 3T should also be elevated as Halodesulfovibrio aestuarii comb. nov. and Desulfovibrio marinisediminis reclassified as Halodesulfovibrio marinisediminis comb. nov. Desulfovibrio oceani subsp. oceani should be reclassified as Halodesulfovibrio oceani subsp. oceani comb. nov. and Desulfovibrio oceani subsp. galateae as Halodesulfovibrio oceani subsp. galateae comb. nov.
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Microvirga ossetica sp. nov., a species of rhizobia isolated from root nodules of the legume species Vicia alpestris Steven
Gram-stain-negative strains V5/3MT, V5/5K, V5/5M and V5/13 were isolated from root nodules of Vicia alpestris plants growing in the North Ossetia region (Caucasus). Sequencing of the partial 16S rRNA gene (rrs) and four housekeeping genes (dnaK, gyrB, recA and rpoB) showed that the isolates from V. alpestris were most closely related to the species Microvirga zambiensis (order Rhizobiales , family Methylobacteriaceae ) which was described for the single isolate from root nodule of Listia angolensis growing in Zambia. Sequence similarities between the Microvirga -related isolates and M. zambiensis WSM3693T ranged from 98.5 to 98.7 % for rrs and from 79.7 to 95.8 % for housekeeping genes. Cellular fatty acids of the isolates V5/3MT, V5/5K, V5/5M and V5/13 included important amounts of C18 : 1ω7c (54.0–67.2 %), C16 : 0 (6.0–7.8 %), C19 : 0 cyclo ω8c (3.1–10.2 %), summed feature 2 (comprising one or more of iso-C16 : 1 I, C14 : 0 3-OH and unknown ECL 10.938, 5.8–22.5 %) and summed feature 3 (comprising C16 : 1ω7c and/or iso-C15 : 02-OH, 2.9–4.0 %). DNA–DNA hybridization between the isolate V5/3MT and M. zambiensis WSM3693T revealed DNA–DNA relatedness of 35.3 %. Analysis of morphological and physiological features of the novel isolates demonstrated their unique phenotypic profile in comparison with reference strains from closely related species of the genus Microvirga . On the basis of genotypic and phenotypic analysis, a novel species named Microvirga ossetica sp. nov. is proposed. The type strain is V5/3MT (=LMG 29787T=RCAM 02728T). Three additional strains of the species are V5/5K, V5/5M and V5/13.
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Marimonas arenosa gen. nov., sp. nov., isolated from sea sand
More LessA Gram-stain-negative, non-motile, non-spore-forming, aerobic and short rod-shaped bacterial strain, CAU 1311T, was isolated from sea sand in the Republic of Korea. Strain CAU 1311T grew at temperatures from 20–37 °C, in the range of pH 6.5–10.0, and under various NaCl concentrations from 0–6 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence of CAU 1311T showed that it formed a distinct lineage within the family Rhodobacteraceae as a separate deep branch, with 96.2 % or lower sequence identity to representatives of the genera Marivita , Aestuariivita , Mameliella , Sulfitobacter and Maritimibacter . The major fatty acid was C18 : 1 ω7c and the predominant respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and an unidentified glycolipid. The DNA G+C content was 60.7 mol%. On the basis of genotypic, phenotypic and chemotaxanomic findings, strain CAU 1311T could be classified as representing a novel species of a new genus of the family Rhodobacteraceae , for which the name Marimonas arenosa gen. nov., sp. nov. is proposed. The type strain of the type species is CAU 1311T (=KCTC 52189T=NBRC 111988T).
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Microvirga soli sp. nov., an alphaproteobacterium isolated from soil
More LessAn aerobic, Gram-stain-negative, catalase-positive and oxidase-negative, non-motile, non-spore-forming, rod-shaped, pink-pigmented bacterium designated strain R491T was isolated from soil. Flexirubin-type pigments were absent. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain R491T formed a lineage within the family Methylobacteriaceae of the phylum Proteobacteria that was distinct from various species of the genus Microvirga , including Microvirgaaerilata 5420S-16T (97.83 % 16S rRNA gene sequence similarity), Microvirga zambiensis WSM3693T (97.76 %), Microvirga flocculans ATCC BAA-817T (97.41 %), and Microvirga lupini Lut6T, Microvirga subterranea DSM 14364T, Microvirga vignae BR3299T, and Microvirga guangxiensis 25BT (96.99 %). The major polar lipids of strain R491T were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c; 71.2 %), C16 : 0 (12.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 4.7 %), and C18 : 0 (4.2 %). The DNA G+C content of strain R491T was 61.8 mol%. DNA–DNA hybridization values between strain R491T and other members of the genus Microvirga ranged from 27 to 57 %. On the basis of phenotypic, genotypic and phylogenetic analyses, strain R491T represents a novel species of the genus Microvirga , for which the name Microvirga soli sp. nov. is proposed. The type strain is R491T (=KEMB 9005-408T=KACC 18969T=NBRC 112417T).
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Citrobacter europaeus sp. nov., isolated from water and human faecal samples
Strains 97/79T and A121, recovered respectively from human faeces and well water, were compared to currently known species of the genus Citrobacter using genotypic and phenotypic approaches. Multilocus sequence analysis based on housekeeping genes fusA, leuS, pyrG, rpoB and recN, showed that the two strains formed a distinct phylogenetic lineage within the genus Citrobacter . Average nucleotide identity (ANI) between strains 97/79T and A121 was 99.2 %, whereas ANI values of strain 97/79T with the type strains of closely related species of the genus Citrobacter , C. werkmanii , C. braakii , C. freundii , C. youngae and C. pasteurii , were all below 93.0 %. The ability to metabolize different compounds also discriminated strains 97/79T and A121 from other species of the genus Citrobacter . Based on these results, strains 97/79T and A121 represent a novel species of the genus Citrobacter , for which the name Citrobacter europaeus sp. nov. is proposed, with strain 97/79T (=CIP 106467T=DSM 103031T) as the type strain. The DNA G+C content of strain 97/79T is 52.0 %.
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- Evolution, Phylogeny and Biodiversity
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Multigenetic characterization of ‘Candidatus Xenohaliotis californiensis’
‘Candidatus Xenohaliotis californiensis’ (or Ca.Xc) is the aetiological agent of withering syndrome, a chronic wasting disease affecting most if not all North American species of abalone, and has been described as a Rickettsiales -like prokaryote. Genetic data regarding this species are limited to the 16S rRNA gene. The inability to grow it axenically has hindered its genetic and genomic characterization and, in consequence, a thorough analysis of its systematics. Here, we amplified and sequenced five genes (16S rRNA, 23S rRNA, ftsZ, virD4 and virB11) of Ca.Xc from infected abalone to analyse its phylogenetic position. Phylogenies from concatenated DNA and amino acid sequences with representative genera of most Rickettsiales unequivocally place Ca.Xc in the family Anaplasmataceae . Furthermore, the family has two reciprocally monophyletic lineages: one leading to ( Neorickettsia , Ca.Xc) and the other to (( Ehrlichia , Anaplasma ), Wolbachia )). A molecular-clock Bayesian reconstruction places Ca.Xc as the most basal lineage in Anaplasmataceae . These phylogenetic hypotheses shed light on patterns of host evolution and of ecological transitions. Specifically, Neorickettsia and Ca.Xc inhabit aquatic hosts whereas the remaining Anaplasmataceae are found in terrestrial hosts. Additionally, our evolutionary timeline places the directly transmitted marine Ca.Xc as the basal Anaplasmataceae , ancestral to both freshwater and terrestrial species with adaptations leading to more complex life cycles involving intermediate vectors or reservoir species; this supports the hypothesis of a marine origin for this bacterial family.
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- Letter to the Editor
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- ICSP Matters
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The consequences of Bacillus axarquiensis Ruiz-García et al. 2005, Bacillus malacitensis Ruiz-García et al. 2005 and Brevibacterium halotolerans Delaporte and Sasson 1967 (Approved Lists 1980) being treated as heterotypic synonyms
More LessIn a recent publication, data was presented supporting Bacillus axarquiensis Ruiz-García et al. 2005, Bacillus malacitensis Ruiz-García et al. 2005 and Brevibacterium halotolerans Delaporte and Sasson 1967 (Approved Lists 1980) being treated as heterotypic synonyms. The nomenclatural consequences proposed were that under these circumstances the correct name to be used is Bacillus axarquiensis Ruiz-García et al. 2005, but this is not consistent with the wording of the International Code of Nomenclature of Prokaryotes and it is, therefore, it is necessary to establish the correct name to be used.
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- Corrigendum
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Volumes and issues
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Volume 74 (2024)
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Volume 70 (2020)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)