- Volume 66, Issue 3, 2016
Volume 66, Issue 3, 2016
- NEW TAXA
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- Proteobacteria
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Azospirillum agricola sp. nov., a nitrogen-fixing species isolated from cultivated soil
More LessA polyphasic approach was used to characterize a novel nitrogen-fixing bacterial strain, designated CC-HIH038T, isolated from cultivated soil in Taiwan. Cells of strain CC-HIH038T were Gram-stain-negative, facultatively aerobic and spiral-shaped, with motility provided by a single polar flagellum. The 16S rRNA gene sequence analysis of strain CC-HIH038T showed highest sequence similarity to Azospirillum doebereinerae (98.0 %), Azospirillum thiophilum (97.5 %), Azospirillum rugosum (97.4 %) and Azospirillum zeae (97.2 %) and lower sequence similarity ( < 97.0 %) to all other species of the genus Azospirillum. According to DNA–DNA association, the relatedness values of strain CC-HIH038T with A. doebereinerae, A. thiophilum, A. rugosum and A. zeae were 51.8 %, 41.2 %, 56.5 % and 37.5 %, respectively. Strain CC-HIH038T was able to grow at 20–37 °C and pH 7.0–8.0. Strain CC-HIH038T gave positive amplification for dinitrogen reductase (nifH gene); the activity was recorded as 8.4 nmol ethylene h− 1. The predominant quinone system was ubiquinone Q-10 and the DNA G+C content was 68.8 mol%. The major fatty acids found in strain CC-HIH038T were C16 : 0, iso-C18 : 0, C16 : 0 3-OH, C14 : 0 3-OH/iso-C16 : 1 and C18 : 1ω7c/C18 : 1ω6c. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-HIH038T is considered to represent a novel species in the genus Azospirillum, for which the name Azospirillum agricola sp. nov. is proposed. The type strain is CC-HIH038T ( = BCRC 80909T = JCM 30827T).
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Ampullimonas aquatilis gen. nov., sp. nov. isolated from bottled mineral water
More LessTwo isolates, designated B15.09-116T and B15.09-124, were recovered from bottled mineral water in Portugal. Based on 16S rRNA gene sequence analysis, these strains were related most closely to species of the genus Derxia (belonging to the family Alcaligenaceae) with pairwise sequence similarities of 93.0–93.6 %. The isolates were not pigmented and formed Gram-stain-negative, short, motile rod-shaped cells. The organisms were strictly aerobic, oxidase-positive and catalase-negative. These organisms also fixed N2. The major polar lipids were phosphatidylglycerol and phosphatidylethanolamine. Ubiquinone 8 was the major respiratory quinone. The DNA G+C content of strain B15.09-116T was 49.8 mol%. Based on phylogenetic, physiological and biochemical characteristics the two strains are considered to represent a novel species of a new genus, for which the name Ampullimonas aquatilis gen. nov., sp. nov. is proposed. The type strain of Ampullimonas aquatilis is B15.09-116T ( = CECT 8581T = LMG 28208T).
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Xuhuaishuia manganoxidans gen. nov., sp. nov., a manganese-oxidizing bacterium isolated from deep-sea sediments from the Pacific Polymetallic Nodule Province
More LessA Gram-stain-negative, strictly aerobic, non-motile, rod-shaped, manganese-oxidizing bacterial strain, designated DY6-4T, was isolated from the surface sediment of the Pacific Clarion-Clipperton Fracture Zone. Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain DY6-4T formed a lineage within the family Rhodobacteraceae and was distinct from the most closely related genera Sulfitobacter, Aliiroseovarius and Loktanella (94.0–96.0 %, 93.4–96.0 % and 91.9–95.9 % 16S rRNA gene sequence similarity, repectively). Optimal growth occurred in the presence of 1 % (w/v) NaCl, at pH 7.0 and at 28 °C. Strain DY6-4T contained ubiquinone-10 (Q-10) as the major ubiquinone, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine and one unidentified aminolipid as the predominant polar lipids, C18 : 1ω7c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the main fatty acids (>10 % of the total). The DNA G+C content of strain DY6-4T was 66.6 mol%. On the basis of the polyphasic analyses, strain DY6-4T is considered to represent a novel species of a novel genus in the Roseobacter clade of the family Rhodobacteraceae, for which the name Xuhuaishuia manganoxidans gen. nov., sp. nov. is proposed. The type strain is DY6-4T ( = KCTC 42421T = MCCC 1K00502T).
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Arenimonas aestuarii sp. nov., isolated from estuary sediment
More LessA novel species of the genus Arenimonas, represented by strain S2-21T, was isolated from an estuary of Asan in South Korea. Cells of strain S2-21T were Gram-stain-negative, aerobic, non-motile rods that were oxidase- and catalase-positive. Growth of strain S2-21T was observed at 15–40 °C (optimum, 25–30 °C), at pH 7.0–8.0 (optimum, pH 7.0) and in the presence of 0–2.0 % (w/v) NaCl (optimum, 0 %). The major cellular fatty acids were iso-C15 : 0, C11 : 0 3-OH, iso-C16 : 0, summed feature 9 (comprising iso-C17 : 1ω9c and/or C16 : 0 10-methyl), anteiso-C17 : 0 and iso-C11 : 0. The only respiratory quinone detected was ubiquinone-8 (Q-8) and the major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanol and two unknown phospholipids. The G+C content of the genomic DNA was 62.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain S2-21T formed a tight phyletic lineage with Arenimonas donghaensis HO3-R19T within the genus Arenimonas. Strain S2-21T was related most closely to A. donghaensis HO3-R19T at 98.1 % 16S rRNA gene sequence similarity and the mean DNA–DNA relatedness value between strain S2-21T and the type strain of A. donghaensis was 23.6 ± 2.2 %. On the basis of phenotypic, chemotaxonomic and molecular features, strain S2-21T is considered to represent a novel species of the genus Arenimonas, for which the name Arenimonas aestuarii sp. nov. is proposed. The type strain is S2-21T ( = KACC 18504T = JCM 31129T).
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Novosphingobium piscinae sp. nov., isolated from a fish culture pond
More LessA bacterial strain designated SLH-16T was isolated from a fish culture pond in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain SLH-16T were Gram-stain-negative, aerobic, motile rods that were covered by large capsules and formed yellow colonies. Growth occurred at 20–40 °C (optimum, 37–40 °C), at pH 4.0–9.0 (optimum, pH 5.0–6.0) and with 0–0.5 % (w/v) NaCl (optimum, 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain SLH-16T belonged to the genus Novosphingobium and was related most closely to Novosphingobium taihuense T3-B9T with sequence similarity of 97.3 %. The major fatty acids (>10 %) of strain SLH-16T were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0. The major 2-hydroxy fatty acid was C14 : 0 2-OH. The polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, sphingoglycolipid, phosphatidylcholine and several uncharacterized lipids. The major polyamine was spermidine. The major isoprenoid quinone was Q-10. The DNA G+C content was 65.2 mol%. The DNA–DNA hybridization value for strain SLH-16T and the type strain of N. taihuense was less than 43.2 %. Phenotypic characteristics of the novel strain also differed from those of the closest related species of the genus Novosphingobium. On the basis of the genotypic, chemotaxonomic and phenotypic data, strain SLH-16T represents a novel species in the genus Novosphingobium, for which the name Novosphingobium piscinae sp. nov. is proposed. The type strain is SLH-16T ( = BCRC 80888T = LMG 28418T = KCTC 42194T).
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Marinobacterium profundum sp. nov., a marine bacterium from deep-sea sediment
A Gram-stain-negative, rod-shaped and motile strain, designated PAMC 27536T, was isolated from deep-sea sediment in the East Sea, Korea. Analysis of the 16S rRNA gene sequence of the strain showed an affiliation with the genus Marinobacterium. Phylogenetic analyses revealed that strain PAMC 27536T was related most closely to Marinobacterium rhizophilum CL-YJ9T with a 16S rRNA gene sequence similarity of 98.5 % and to other members of the genus Marinobacterium (94.0–91.7 %). Genomic relatedness analyses between strain PAMC 27536T and M. rhizophilum KCCM 42386T gave an average nucleotide identity of 85.6 % and an estimated DNA–DNA hybridization of 24.6 % using the genome-to-genome distance calculator, indicating that they represent genomically distinct species. Cells of strain PAMC 27536T grew optimally at 25–30 °C and pH 7.0–7.5 in the presence of 3 % (w/v) sea salts. The major cellular fatty acids were C16 : 1ω6c and/or C16 : 1ω7c, C18 : 1ω6c and/or C18 : 1ω7c, and C16 : 0. The major isoprenoid quinone was Q-8. The genomic DNA G+C content was 56.1–57.2 mol%. Based on the phylogenetic, chemotaxonomic, genomic and phenotypic data presented, a novel species with the name Marinobacterium profundum sp. nov. is proposed, with PAMC 27536T ( = KCCM 43095T = JCM 30410T) as the type strain.
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Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees
A survey to obtain potential antagonists of pome fruit tree diseases yielded two yellow epiphytic bacterial isolates morphologically similar to Pantoea agglomerans, but showing no biocontrol activity. Whole-cell MALDI-TOF mass spectrometry and analysis of 16S rRNA gene and gyrB sequences suggested the possibility of a novel species with a phylogenetic position in either the genus Pantoea or the genus Erwinia. Multi-locus sequence analysis (MLSA) placed the two strains in the genus Erwinia and supported their classification as a novel species. The strains showed general phenotypic characteristics typical of this genus and results of DNA–DNA hybridizations confirmed that they represent a single novel species. Both strains showed a DNA G+C content, as determined by HPLC, of 54.5 mol% and could be discriminated from phylogenetically related species of the genus Erwinia by their ability to utilize potassium gluconate, potassium 2-ketogluconate, maltose, melibiose and raffinose. Whole-genome sequencing of strain EM595T revealed the presence of a chromosomal carotenoid biosynthesis gene cluster similar to those found in species of the genera Cronobacter and Pantoea that explains the pigmentation of the strain, which is atypical for the genus Erwinia. Additional strains belonging to the same species were recovered from different plant hosts in three different continents, revealing the cosmopolitan nature of this epiphyte. The name Erwinia gerundensis sp. nov. is proposed, with EM595T ( = LMG 28990T = CCOS 903T) as the designated type strain.
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Marinagarivorans algicola gen. nov., sp. nov., isolated from marine algae
More LessTwo novel agar-degrading, Gram-stain-negative, motile, heterotrophic, facultatively anaerobic and pale yellow-pigmented bacterial strains, designated Z1T and JL1, were isolated from marine algae Gelidium amansii (Lamouroux) and Gracilaria verrucosa, respectively. Growth of the isolates was optimal at 28–30 °C, pH 7.0–7.5 and with 2–3 % (w/v) NaCl. Both strains contained Q-8 as the sole respiratory quinone. The major cellular fatty acids in strain Z1T were C18 : 1ω7c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH). The predominant polar lipids in strain Z1T were phosphatidylethanolamine, phosphatidylglycerol and an aminolipid. The genomic DNA G+C content of both strains was 45.1 mol%. Strains Z1T and JL1 were closely related, with 99.9 % 16S rRNA gene sequence similarity. The average nucleotide identity (ANI) value between strains Z1T and JL1 was 99.3 %. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains Z1T and JL1 form a distinct phyletic line within the class Gammaproteobacteria, with less than 92.3 % similarity to their closest relatives. Based on data from the current polyphasic study, the isolates are proposed to belong to a novel species of a new genus designated Marinagarivorans algicola gen. nov., sp. nov. The type strain of the type species is Z1T ( = ATCC BAA-2617T = CICC 10859T).
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- Bacteroidetes
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Mucilaginibacter roseus sp. nov., isolated from a freshwater river
More LessA bacterial strain, designated TTM-1T, was isolated from a water sample taken from the Caohu River in Taiwan and characterized in a taxonomic study using a polyphasic approach. Cells of strain TTM-1T were Gram-stain-negative, aerobic, non-motile, rod-shaped and covered by large capsules, and formed pink-coloured colonies. Growth occurred at 10–37 °C (optimum 30–37 °C), at pH 6–8 (optimum pH 6–7) and with 0–2 % NaCl (optimum 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TTM-1T belonged to the genus Mucilaginibacter and was most closely related to Mucilaginibacter defluvii A5T with a 16S rRNA gene sequence similarity of 97.3 %. The predominant fatty acids of strain TTM-1T were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c; 37.1 %) and iso-C15 : 0 (30.7 %). The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized aminophospholipids and phospholipids. The major isoprenoid quinone was MK-7. The DNA G+C content of the genomic DNA was 45.1 mol%. The DNA–DNA relatedness of strain TTM-1T with respect to recognized species of the genus Mucilaginibacter was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain TTM-1T represents a novel species of the genus Mucilaginibacter, for which the name Mucilaginibacter roseus sp. nov. is proposed. The type strain is TTM-1T ( = LMG 28454T = KCTC 42273T).
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Anseongella ginsenosidimutans gen. nov., sp. nov., isolated from soil cultivating ginseng
More LessA Gram-stain-negative, rod-shaped, non-spore-forming, oxidase and catalase-positive, strictly aerobic bacterium, designated strain Gsoil 524T, was isolated from the soil of a ginseng field and subjected to polyphasic taxonomic analysis. Phylogenetic analysis, based on the 16S rRNA gene sequence, placed Gsoil 524T in a distinct lineage in the family Sphingobacteriaceae, sharing 87.2–88.0 % sequence similarity with members of the closely related genera Pedobacter, Mucilaginibacter and Solitalea. Strain Gsoil 524T contained MK-7 as the predominant quinone, and iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 1ω5c as the major fatty acids. Strain Gsoil 524T could be distinguished from the other members of the family Sphingobacteriaceae by a number of chemotaxonomic and phenotypic characteristics. The major polar lipids in strain Gsoil 524T were phosphatidylethanolamine and two unidentified polar lipids. Compared with the standard and reference strains unidentified sphingolipid was also found. Based on this polyphasic taxonomic analysis, strain Gsoil 524T represents a novel species within a novel genus, for which the name Anseongella ginsenosidimutans gen. nov., sp. nov. is proposed. The type strain of Anseongella ginsenosidimutans is Gsoil 524T ( = KACC 14636T = KCTC 22261T = LMG 24494T).
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Gaetbulibacter aquiaggeris sp. nov., a member of the Flavobacteriaceae isolated from seawater
More LessA Gram-stain-negative, non-flagellated, non-gliding and rod-shaped bacterial strain, designated KEM-8T, was isolated from seawater in the Korean peninsula. Strain KEM-8T was found to grow optimally at pH 7.0–8.0, at 30 °C and in the presence of 2–3 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain KEM-8T falls within the clade comprising species of the genus Gaetbulibacter, clustering with the type strains of Gaetbulibacter marinus and Gaetbulibacter lutimaris with which it exhibits 98.4 and 97.2 % 16S rRNA gene sequence similarity, respectively. Sequence similarities to Gaetbulibacter saemankumensis SMK-12T and Gaetbulibacter aestuarii KCTC 23303T were 95.4 and 95.2 %, respectively. Strain KEM-8T was found to contain MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH and iso-C15 : 1 G as the major fatty acids. The major polar lipids were identified as phosphatidylethanolamine and an unidentified lipid. The DNA G+C content of strain KEM-8T was 36.0 mol% and mean DNA–DNA relatedness values with G. marinus KCTC 23046T and G. lutimaris D1-y4T were 27.6 ± 0.9 and 10.3 ± 1.4 %, respectively. Differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain KEM-8T is distinguishable from species of the genus Gaetbulibacter with validly published names. On the basis of the data presented, strain KEM-8T represents a novel species of the genus Gaetbulibacter, for which the name Gaetbulibacter aquiaggeris sp. nov. is proposed. The type strain is KEM-8T ( = KCTC 42198T = NBRC 110553T).
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Tenacibaculum ascidiaceicola sp. nov., isolated from the golden sea squirt Halocynthia aurantium
More LessA Gram-stain-negative, non-flagellated, non-spore-forming bacterial strain motile by gliding, designated RSS1-6T, was isolated from a golden sea squirt Halocynthia aurantium and its taxonomic position was investigated by using a polyphasic approach. Strain RSS1-6T grew optimally at 30–37 °C and in the presence of 1.0–4.0 % (w/v) NaCl. Phylogenetic trees based on 16S rRNA gene sequences showed that strain RSS1-6T fell within the clade comprising species of the genus Tenacibaculum, clustering with the type strains of Tenacibaculum discolor, Tenacibaculum litoreum and Tenacibaculum gallaicum with which it exhibited 16S rRNA gene sequence similarity values of 98.5–99.5 %. Strain RSS1-6T contained MK-6 as the predominant menaquinone and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the major fatty acids. The major polar lipids of strain RSS1-6T were phosphatidylethanolamine, two unidentified lipids, one unidentified aminophospholipid and one unidentified glycolipid. The DNA G+C content was 32.5 mol% and the mean DNA–DNA relatedness values with the type strains of T. discolor, T. litoreum and T. gallaicum were 17.3–25.2 %. The differential phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that strain RSS1-6T is separated from other recognized species of the genus Tenacibaculum. On the basis of the data presented, strain RSS1-6T is considered to represent a novel species of the genus Tenacibaculum, for which the name Tenacibaculum ascidiaceicola sp. nov. is proposed. The type strain is RSS1-6T ( = KCTC 42702T = NBRC 111225T).
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Membranicola marinus gen. nov., sp. nov., a new member of the family Saprospiraceae isolated from a biofilter in a recirculating aquaculture system
More LessA Gram-staining-negative bacterial strain (termed CZ-AZ5T) was isolated from a biological filter in a marine recirculating aquaculture system in Tianjin, China. Its taxonomic status was determined using a polyphasic approach. CZ-AZ5T cells were non-spore-forming, non-motile rods, 0.6–0.7 μm wide and 3.0–3.7 μm long. CZ-AZ5T was strictly heterotrophic, aerobic, oxidase-negative and catalase-positive. Growth occurred in the temperature range 20–40 °C (optimal: 30 °C), pH range 6.0–8.5 (optimal: pH 7.5) and salinity range 0–5 % (w/v) NaCl (optimal: 1 %). In phylogenetic analyses based on 16S rRNA gene sequences, CZ-AZ5T was assigned to the family Saprospiraceae (phylum Bacteroidetes) and was clustered with the genera Saprospira and Aureispira within this family. It showed highest sequence similarity to ‘Candidatus Haliscomenobacter calcifugiens’ (86.2 %), followed by Saprospira grandis ATCC 23119T (85.7 %) and Lewinella persica T-3T (85.6 %). DNA G+C content was 40.1 mol%, the major menaquinone was MK-7, and the major cellular fatty acids (>10 %) were C16 : 1ω7c and iso-C15 : 0. Our phenotypic, chemotaxonomic and phylogenetic observations, taken together, led us to conclude that strain CZ-AZ5T represents a novel species and genus of the family Saprospiraceae, for which the name Membranicola marinus gen. nov., sp. nov. is proposed. The type strain is CZ-AZ5T ( = CGMCC 1.13179T = JCM 18886T).
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Pseudofulvibacter marinus sp. nov., isolated from seawater
A novel Gram-stain-negative, rod-shaped, non-spore-forming, non-flagellated, strictly aerobic strain, designated RZW2-1T, was isolated from coastal seawater of the Yellow Sea in China (35.475° N 119.613° E). The organism grew optimally at 24 °C, at pH 7.0 and in the presence of 3.0 % (w/v) NaCl. The strain requires seawater or artificial seawater for growth and NaCl alone does not support growth. Strain RZW2-1T contained MK-6 as the only respiratory quinone and iso-C15 : 0, iso-C15 : 1 G and 10-methyl C16 : 0 and/or iso-C17 : 1ω9c as the dominant fatty acids. The polar lipids of strain RZW2-1T were four unidentified phospholipids (PL1–PL4), two unknown lipids (L1, L2) and one unidentified aminolipid (AL1). The DNA G+C content of strain RZW2-1T was 32 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was most closely related to the type strain of the only described species of genus Pseudofulvibacter, Pseudofulvibacter geojedonensis YCS-9T, with 95.1 % 16S rRNA gene sequence similarity. On the basis of polyphasic analyses, strain RZW2-1T represents a novel species of the genus Pseudofulvibacter, for which the name Pseudofulvibacter marinus sp. nov. is proposed. The type strain is RZW2-1T ( = JCM 30826T = MCCC 1K00695T).
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Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees
More LessHoney bees and bumble bees harbour a small, defined set of gut bacterial associates. Strains matching sequences from 16S rRNA gene surveys of bee gut microbiotas were isolated from two honey bee species from East Asia. These isolates were mesophlic, non-pigmented, catalase-positive and oxidase-negative. The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, C16 : 0 and C16 : 0 3-OH. The DNA G+C content was 29–31 mol%. They had ∼87 % 16S rRNA gene sequence identity to the closest relatives described. Phylogenetic reconstruction using 20 protein-coding genes showed that these bee-derived strains formed a highly supported monophyletic clade, sister to the clade containing species of the genera Chryseobacterium and Elizabethkingia within the family Flavobacteriaceae of the phylum Bacteroidetes. On the basis of phenotypic and genotypic characteristics, we propose placing these strains in a novel genus and species: Apibacter adventoris gen. nov., sp. nov. The type strain of Apibacter adventoris is wkB301T ( = NRRL B-65307T = NCIMB 14986T).
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Leeuwenhoekiella nanhaiensis sp. nov., isolated from deep-sea water
More LessA novel heterotrophic, aerobic, Gram-stain-negative, rod-shaped and yellow bacterium, designated strain G18T, was isolated from a water sample collected from the deep South China Sea. Strain G18T grew at 4–40 °C (optimum 28–32 °C), at pH 6.0–8.0 (optimum pH 6.5–7.5) and with 0–12 % (w/v) NaCl (optimum 3–4 %). The organism was mesophilic and piezotolerant, its optimal growth pressure was 0.1 MPa, which was lower than that at the depth from which it was isolated. Its optimal growth temperature was higher than that at the depth of its isolation. The predominant cellular fatty acids were C15 : 0iso, C17 : 0iso 3-OH and C15 : 1iso. The major polar lipids were composed of phosphatidylethanolamine, one unknown aminolipid and one unknown polar lipid. The major respiratory quinone was menaquinone 6. The G+C content of the genomic DNA was 35 mol%. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain G18T clustered with species of the genus Leeuwenhoekiella with validly published names within the family Flavobacteriaceae with 95.9–98.2 % sequence similarity. DNA–DNA reassociation values ranged from 9 to 42 %. Differential phenotypic properties, together with the phylogenetic distinctiveness, suggest that strain G18T differs from species of the genus Leeuwenhoekiella with validly published names. On the basis of the polyphasic evidence, strain G18T represents a novel species, isolated from deep-sea, of the genus Leeuwenhoekiella for which the name Leeuwenhoekiella nanhaiensis sp. nov. is proposed. The type strain is G18T ( = CCTCC AB 2015204T = KCTC 42729T).
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Flavobacterium lutivivi sp. nov., isolated from activated sludge
More LessA Gram-stain-negative, strictly aerobic, yellow, rod-shaped bacterium, designated strain HQQT, was isolated from a municipal wastewater treatment plant in Hebei Province, PR China. Comparative 16S rRNA gene sequence analyses showed that strain HQQT is a member of the genus Flavobacterium and is closely related to ‘Flavobacterium shanxiense’ CCTCC AB 2014079T (94.8 %) and Flavobacterium macrobrachii DSM 22219T (94.7 %). Phylogenetic analysis showed that strain HQQT clustered with Flavobacterium fontis JCM 18212T and Flavobacterium squillarum KCTC 23915T. The polar lipid profile of strain HQQT revealed the presence of phosphatidylethanolamine, six unknown aminolipids, one unknown glycolipid and one unknown lipid and the only isoprenoid quinone was MK-6. The dominant fatty acids of strain HQQT were iso-C15 : 0, C15 : 0 and C16 : 1ω7c. The DNA G+C content of strain HQQT is 32 mol%. On the basis of the phylogenetic and phenotypic data, strain HQQT represents a novel species of the genus Flavobacterium, for which the name Flavobacterium lutivivi sp. nov. is proposed. The type strain is HQQT ( = CGMCC 1.15347T = KCTC 42935T).
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Bacteroides caecicola sp. nov. and Bacteroides gallinaceum sp. nov., isolated from the caecum of an Indonesian chicken
Six strains of anaerobic bacteria, C13EG70T, C13EG118, C13EG186T, C13GAMG5, C13GAMG28 and C13GAMG40, were isolated from the caecum of a healthy chicken bred in Bogor, Indonesia. Phylogenetic analysis showed the isolates were separated into two groups. Group I (C13EG70T and C13EG118) showed nearly identical 16S rRNA gene sequences (99.9 % sequence similarity). Group II (C13EG186T, C13GAMG5, C13GAMG28 and C13GAMG40) showed nearly identical 16S rRNA gene sequences (>99.4 % sequence similarity). The isolates showed low 16S rRNA gene sequence similarities to recognized species of the genus Bacteroides. High gene sequence similarities were found between type strains (C13EG70T and C13EG186T) and Bacteroides salanitronis JCM 13657T (87.9, 91.5 %, respectively). Physiological, biochemical and genotypic characteristics demonstrated that these strains could be separated from the type strain of B. salanitronis. It is concluded that Group I and Group II represent novel species. Two novel species of the genus Bacteroides are proposed as Bacteroides caecicola sp. nov. (type strain C13EG70T = LIPI12-4-Ck732T = JSAT12-4-Ck732T = InaCC B449T = NBRC 110958T) and Bacteroides gallinaceum sp. nov. (type strain C13EG186T = LIPI12-4-Ck844T = JSAT12-4-Ck884T = InaCC B451T = NBRC 110963T).
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Description of Proteiniphilum saccharofermentans sp. nov., Petrimonas mucosa sp. nov. and Fermentimonas caenicola gen. nov., sp. nov., isolated from mesophilic laboratory-scale biogas reactors, and emended description of the genus Proteiniphilum
More LessThree novel, facultatively anaerobic bacteria of the family Porphyromonadaceae (phylum Bacteroidetes) were isolated from mesophilic laboratory-scale biogas reactors. The strains were Gram-negative rods. Optimal growth occurred between 35 and 45 °C and at pH 7.1–7.8. The main fermentation products were acetic and propionic acids. The predominant fatty acid in all strains was anteiso-C15 : 0, and the only respiratory quinone detected was menaquinone MK-8. 16S rRNA gene sequence comparison indicated that strains M3/6T and ING2-E5BT were most closely related to the type strain of Proteiniphilum acetatigenes, with sequence similarities of 97.3 and 94.5 %. Strain ING2-E5AT showed the closest affiliation to the type strain of Petrimonas sulfuriphila, with 97 % sequence identity. DNA–DNA hybridization of strain M3/6T and ING2-E5AT with the most closely related type strains showed 43.3–45.6 and 23.8–25.7 % relatedness, respectively, which supports the conclusion that both isolates represent novel species. Phylogenetic analysis and comparison of cellular fatty acid patterns indicated that strain ING2-E5BT cannot be classified as a member of any previously described genus. Therefore, because of the physiological, genotypic and chemotaxonomic differences, it is proposed to designate novel species within the genera Proteiniphilum and Petrimonas, Proteiniphilum saccharofermentans sp. nov. (type strain M3/6T = DSM 28694T = CECT 8610T = LMG 28299T) and Petrimonas mucosa sp. nov. (type strain ING2-E5AT = DSM 28695T = CECT 8611T), and a novel species of a new genus, Fermentimonas caenicola gen. nov., sp. nov. (type strain of Fermentimonas caenicola is ING2-E5BT = DSM 28696T = CECT 8609T = LMG 28429T). In addition, an emended description of the genus Proteiniphilum is provided.
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Hymenobacter paludis sp. nov., isolated from a marsh
More LessA bacterial strain, designated KBP-30T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized taxonomically using a polyphasic approach. Cells of strain KBP-30T were Gram-stain-negative, aerobic, motile by gliding rods that were covered by large capsules and formed red colonies. Growth occurred at 10–37 °C (optimum 20 °C), at pH 6–8 (optimum pH 6) and with 0–1 % NaCl (optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-30T belonged to the genus Hymenobacter and was most closely related to Hymenobacter ocellatus Myx 2105T with a sequence similarity of 97.7 %; 16S rRNA gene sequence similarities were less than 95.1 % with other members of the genus. Strain KBP-30T contained iso-C15 : 0, summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B), anteiso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) as the predominant fatty acids. The major isoprenoid quinone was MK-7. The polar lipid profile consisted of phosphatidylethanolamine, three unidentified aminophospholipids, an unidentified aminolipid, an unidentified glycolipid and eight unidentified lipids. The major polyamine was homospermidine. The DNA G+C content of the genomic DNA was 60.3 mol%. The DNA–DNA relatedness of strain KBP-30T with respect to Hymenobacter ocellatus Myx 2105T was less than 42 %. On the basis of the phylogenetic inference and phenotypic data, strain KBP-30T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter paludis sp. nov. is proposed. The type strain is KBP-30T ( = LMG 27293T = KCTC 32237T).
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- Other Bacteria
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Multigene characterization of a new ‘Candidatus Phytoplasma rubi’-related strain associated with blackberry witches’ broom
A new phytoplasma was identified in naturally infected blackberry plants exhibiting witches’ broom symptoms in Portugal. The 16S rRNA gene sequence revealed that it is related to ‘Candidatus Phytoplasma rubi’ (16SrV-E ribosomal subgroup) and RFLP analysis revealed a unique profile following MseI endonuclease digestion of R16F2n/R2 amplicons that distinguished it from the strains belonging to previously established 16SrV phytoplasma subgroups. The in silico restriction analyses confirmed that the phytoplasma strain from blackberry is different from all the other strains reported in group 16SrV. Phylogeny of the 16S rRNA gene sequences, sequence analyses of 16S–23S, tuf, rplV-rpsC, rplF-rplR, rplO-SecY-map and uvrB-degV genetic loci, as well as the variability of unique oligonucleotide sequences defined for ‘Candidatus Phytoplasma rubi’ confirmed the uniqueness of this phytoplasma strain from Portugal for which a novel ribosomal subgroup, 16SrV-I, is proposed. The representative of this new subgroup was named blackPort phytoplasma (Portuguese blackberry phytoplasma).
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Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov. prevail in diverse enzootic transmission cycles
Two species of the genus Borrelia, Borrelia bissettiae sp. nov. and Borrelia californiensis sp. nov., were first described by Postic and co-workers on the basis of genetic analyses of several loci. Multilocus sequence analysis of eight housekeeping loci confirmed that these two Borrelia genomospecies are distinct members of the Borrelia burgdorferi sensu lato complex. B. bissettiae sp. nov. was initially described in transmission cycles involving Neotoma fuscipes wood rats and Ixodes pacificus ticks in California, and Neotoma mexicana and Ixodes spinipalpis in Colorado. The preferred host of B. californiensis sp. nov. appears to be the California kangaroo rat, Dipodomys californicus; Ixodes jellisoni, I. spinipalipis and I. pacificus ticks are naturally infected with it. Thus, the ecological associations of the two genomospecies and their genetic distance from all other known Borrelia genomospecies species justify their description as separate genomospecies: B. bissettiae sp. nov. (type strain DN127T = DSM 17990T = CIP 109136T) and B. californiensis (type strain CA446T = DSM 17989T = ATCC BAA-2689T).
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Reclassification of Anaerobaculum mobile, Anaerobaculum thermoterrenum, Anaerobaculum hydrogeniformans as Acetomicrobium mobile comb. nov., Acetomicrobium thermoterrenum comb. nov. and Acetomicrobium hydrogeniformans comb. nov., respectively, and emendation of the genus Acetomicrobium
More LessTaking into account their 16S rRNA gene sequences, it appears that Acetomicrobium flavidum and the three species of the genus Anaerobaculum described so far belong to the same phylogenetic clade with high levels (>95 %) of similarity. In this respect, these three Anaerobaculum species should be reclassified within the genus Acetomicrobium, which has priority over the genus Anaerobaculum, which was validated since the genus Acetomicrobium. The DNA G+C content of Acetomicrobium flavidum is 47.1 mol%, which is of the same order as that of the three Anaerobaculum species. All these bacteria have in common iso-C15 : 0 as their main fatty acid. Based on further phylogenetic, genetic and chemotaxonomic studies, we propose that Anaerobaculum mobile ( = DSM 13181T = JCM 12221T), Anaerobaculum thermoterrenum ( = DSM 13490T = ACM 5076T) and Anaerobaculum hydrogeniformans ( = DSM 22491T = ATCC BAA-1850T) be reclassified as Acetomicrobium mobile comb. nov., Acetomicrobium thermoterrenum comb. nov. and Acetomicrobium hydrogeniformans comb. nov., respectively. The four bacterial species belong to the phylum Synergistetes.
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- Eukaryotic micro-organisms
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Trichosporon heliocopridis sp. nov., a urease-negative basidiomycetous yeast associated with dung beetles (Heliocopris bucephalus Fabricius)
Ninety-six yeast isolates associated with dung beetles (Heliocopris bucephalus Fabricius) were examined based on a culture-dependent method. A comparison of the colony morphology and PCR-fingerprints obtained by (GTG)5 microsatellite-primed PCR indicated that 84 of these isolates belonged to one group. Five strains (DD1-1T, DD2-33, DD4-11, DD5-15 and DD6-1) were selected as the representatives of this main group, where each of the five selected strains had been derived from a different dung beetle collected in northern Thailand. A comparison of the D1/D2 domain sequence of the large subunit rRNA gene (LSU D1/D2) and the internal transcribed spacer (ITS) sequences revealed that these five strains were the same and were related to the genus Trichosporon. Phylogenetic analysis based on the LSU D1/D2 plus ITS sequences placed this group within the Trichosporon brassicae clade, but it was clearly separated from any known species. In addition, physiological tests showed that this group had the unusual property of the inability to hydrolyse urea, which was distinctly different from the related taxon. Therefore a novel yeast species named Trichosporon heliocopridis sp. nov. (ex-type strain DD1-1T = TISTR 5946T = JCM 30786T = CBS 14168T) is proposed. The MycoBank number is MB812098.
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Starmerella orientalis f.a., sp. nov., an ascomycetous yeast species isolated from flowers
Four strains of a novel ascomycetous yeast species were isolated from flowers in Iran and China. Phylogenetic analysis of the sequences of the ITS region (including 5.8S rRNA gene) and the LSU rRNA gene D1/D2 domains indicated that these strains belong to the Starmerella clade and show divergence from previously described species in this clade. Growth reactions on carbon and nitrogen sources were similar to those observed in related species of the Starmerella clade. Sexual reproduction was not observed after mating tests on different sporulation media. Based on physiological characteristics and phylogeny of rRNA gene sequences, the novel species is most closely related to Candida (iter. nom. Starmerella) powellii and Candida (iter. nom. Starmerella) floricola. It is therefore assigned to the genus Starmerella and described as Starmerella orientalis f.a., sp. nov. The type strain is SAM09T ( = IBRC-M 30204T = CBS 14142T). The MycoBank accession number is MB 814379.
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Prototheca miyajii sp. nov., isolated from a patient with systemic protothecosis
More LessSpecies of the genus Prototheca are achlorophyllous algae and ubiquitous in nature, and so far, six species have been listed in this genus: Prototheca wickerhamii, Prototheca zopfii, Prototheca blaschkeae, Prototheca cutis, Prototheca stagnora and Prototheca ulmea. A strain of the genus Prototheca, IFM 53848T, was isolated in Japan from a patient with systemic protothecosis and had been designated P. wickerhamii. Our previous study, by using PCR analysis, revealed that its SSU rRNA gene (rDNA) was distinctively larger than that of P. wickerhamii and other species of the genus Prototheca. In this study, molecular analysis showed that the exceptionally large SSU rDNA of IFM 53848T contains four group I introns. The morphology of IFM 53848T was indistinguishable from those of P. wickerhamii or P. cutis, and phylogenetic analyses, based on the sequences of the SSU rDNA exons and the D1/D2 region of the large subunit rDNA, indicated that IFM 53848T was closely related to P. cutis. On the other hand, unlike P. cutis, IFM 53848T failed to assimilate fructose or lysine and grew well at higher temperatures of up to 42 °C. In addition, the nucleotide sequence of the ribosomal internal transcribed spacer and the matrix assisted laser desorption ionization time-of-flight mass spectrometry profile of IFM 53848T were clearly distinct from those of P. cutis. The results strongly suggest that IFM 53848T represents a novel species, and so the seventh member of the genus Prototheca, which we have named Prototheca miyajii sp. nov. The unique characteristics of the strain may provide useful insights into the systematic taxonomy of the genus Prototheca.
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- EVOLUTION, PHYLOGENY AND BIODIVERSITY
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Complete genome sequence and cell structure of Limnochorda pilosa, a Gram-negative spore-former within the phylum Firmicutes
More LessLimnochorda pilosa is a pleomorphic facultative anaerobe and the sole species in the class Limnochordia, which has tentatively been placed in the phylum Firmicutes. In the present study, the complete genome sequence of L. pilosa HC45T was obtained and analysed. The genome size was 3.82 Mbp and the DNA G+C content was 69.73 %. Phylogenetic analyses based on the 30S-50S ribosomal proteins and 23S rRNA gene consistently indicated that L. pilosa is phylogenetically isolated from the other members of the phylum Firmicutes. Ultrastructural observation revealed that L. pilosa possesses a Gram-negative-type cell wall and the capacity to form endospores. Accordingly, the L. pilosa genome has characteristics that are specific to Gram-negative bacteria and contains many genes that are involved in sporulation. On the other hand, several sporulation genes were absent from the L. pilosa genome although they have been regarded as essential for the endospore-forming system of members of the phylum Firmicutes. The gyrB gene of L. pilosa possesses an intein sequence. The genome has a high percentage of GTG start codons and lacks several conserved genes related to cell division.
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)