- Volume 66, Issue 6, 2016
Volume 66, Issue 6, 2016
- New taxa
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- Proteobacteria
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Marinicella pacifica sp. nov., isolated from seawater
More LessA Gram-stain-negative, strictly aerobic, non-motile, non-gliding, oxidase-positive, catalase-positive, rod-shaped bacterium, designated strain sw153T, was isolated from surface seawater of the South Pacific Gyre (39° 19′ S 139° 48′ W) during Integrated Ocean Drilling Program Expedition 329. Growth occurred at 10–42 °C (optimum 28 °C), in the presence of 1–8 % (w/v) NaCl (optimum 2 %) and at pH 6.0–10.0 (optimum pH 7.5–8.5). The major fatty acids (>10 %) were iso-C15:0 and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). The major polar lipids comprised phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylcholine, phosphatidylglycerol, an unidentified polar lipid and an unidentified phospholipid. The major respiratory quinone was ubiquinone-8 (Q-8). The DNA G+C content of strain sw153T was 44.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences placed strain sw153T within the genus Marinicella , class Gammaproteobacteria. The most closely related species was Marinicella litoralis KMM 3900T (96.6 % 16S rRNA gene sequence similarity). Based on the polyphasic analyses in this study, strain sw153T is considered to represent a novel species of the genus Marinicella , for which the name Marinicella pacifica sp. nov. is proposed. The type strain is sw153T (=JCM 18208T=CGMCC 1.12181T).
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Crenalkalicoccus roseus gen. nov., sp. nov., a thermophilic bacterium isolated from alkaline hot springs
Two closely related thermophilic bacterial strains, designated YIM 78023T and YIM 78058, were isolated from samples collected from two alkaline hot springs in Tengchong county, Yunnan province, south-west China. The novel isolates were Gram-stain-negative, non-motile, aerobic ovoid- to coccoid-shaped and non-spore-forming. Strain YIM 78023T grew at 20–60 ºC and pH 6.0–9.0 with optimal growth observed at 40–50 ºC and pH 8.0, while strain YIM 78058 grew at 25–60 ºC and pH 6.0–10.0 with optimal growth at 45–50 ºC and pH 8.0. Phylogenetic analysis based on 16S rRNA gene sequences affiliated these two isolates within the family Acetobacteraceae with high sequence similarities to members of the genera Roseomonas and Belnapia (all sequence similarities <94.5 %). In addition to the above two genera, these strains also clustered with the genera Craurococcus and Paracraurococcus (having sequence similarities <93.3 %) in the phylogenetic tree, but with a distinct lineage within the family Acetobacteraceae . The major ubiquinone was Q-10 and the major fatty acids observed were C18:1 ω7c, summed feature 4 and C16:0. The genomic DNA G+C contents observed for strains YIM 78023T and YIM 78058 were 74.3 and 74.0 mol%, respectively. Morphological, phylogenetic and chemotaxonomic results suggest that strains YIM 78023T and YIM 78058 are representatives of a novel species of a new genus within the family Acetobacteraceae , for which the name Crenalkalicoccus roseus gen. nov., sp. nov. is proposed. The type strain of Crenalkalicoccus roseus is YIM 78023T (=JCM 19657T=KACC 17825T).
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Cupriavidus nantongensis sp. nov., a novel chlorpyrifos-degrading bacterium isolated from sludge
More LessA Gram-stain-negative, aerobic, coccoid to small rod-shaped bacterium, designated X1T, was isolated from sludge collected from the vicinity of a pesticide manufacturer in Nantong, Jiangsu Province, China. Based on 16S rRNA gene sequence analysis, strain X1T belonged to the genus Cupriavidus , and was most closely related to Cupriavidus taiwanensis LMG 19424T (99.1 % 16S rRNA gene sequence similarity) and Cupriavidus alkaliphilus LMG 26294T (98.9 %). Strain X1T showed 16S rRNA gene sequence similarities of 97.2–98.2 % with other species of the genus Cupriavidus . The major cellular fatty acids of strain X1T were C16 : 0, C16 : 1ω7c and/or iso-C15 : 0 2-OH (summed feature 3), C18 : 1ω7c and C17 : 0 cyclo, and the major respiratory quinone was ubiquinone Q-8. The major polar lipids of strain X1T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, aminophospholipid, phospholipid and hydroxyphosphatidylethanolamine. The DNA G+C content was 66.6 mol%. The DNA–DNA relatedness values of strain X1T with the five reference strains C. taiwanensis LMG 19424T, C. alkaliphilus LMG 26294T, Cupriavidus necator LMG 8453T, Cupriavidus gilardii LMG 5886T and ‘ Cupriavidus yeoncheonense ' KCTC 42053 were lower than 70 %. The results obtained from phylogenetic analysis, phenotypic characterization and DNA–DNA hybridization indicated that strain X1T should be proposed to represent a novel species of the genus Cupriavidus , for which the name Cupriavidus nantongensis sp. nov. is proposed. The type strain is X1T (=KCTC 42909T=LMG 29218T).
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Characterization of the N2O-producing soil bacterium Rhizobium azooxidifex sp. nov.
More LessIn the context of studying the bacterial community involved in nitrogen transformation processes in arable soils exposed to different extents of erosion and sedimentation in a long-term experiment (CarboZALF), a strain was isolated that reduced nitrate to nitrous oxide without formation of molecular nitrogen. The presence of the functional gene nirK, encoding the respiratory copper-containing nitrite reductase, and the absence of the nitrous oxide reductase gene nosZ indicated a truncated denitrification pathway and that this bacterium may contribute significantly to the formation of the important greenhouse gas N2O. Phylogenetic analysis based on the 16S rRNA gene sequence and the housekeeping genes recA and atpD demonstrated that the investigated soil isolate belongs to the genus Rhizobium . The closest phylogenetic neighbours were the type strains of Rhizobium. subbaraonis and Rhizobium. halophytocola . The close relationship with R. subbaraonis was reflected by similarity analysis of the recA and atpD genes and their amino acid positions. DNA–DNA hybridization studies revealed genetic differences at the species level, which were substantiated by analysis of the whole-cell fatty acid profile and several distinct physiological characteristics. Based on these results, it was concluded that the soil isolate represents a novel species of the genus Rhizobium, for which the name Rhizobium azooxidifex sp. nov. (type strain Po 20/26T=DSM 100211T=LMG 28788 T ) is proposed.
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Racemicystis crocea gen. nov., sp. nov., a soil myxobacterium in the family Polyangiaceae
More LessA novel bacterial strain designated MSr9521T was isolated in 2014 from a soil sample collected in 1986 from the Philippines. The novel bacterium shows myxobacterial characteristics that include pseudoplasmodial swarming, fruiting body formation and predatory ability to lyse microorganisms. The strain is chemoheterotrophic, mesophilic and aerobic. Major fatty acids are C18:1, C17:1 2-OH and iso-C15:0, and also contains trace amounts of omega-3/-6 polyunsaturated fatty acids. The G+C content of the genomic DNA is 70.4 mol%. The 16S rRNA gene sequence shows 95–96 % closest similarity to Sorangium cellulosum DSM 14627T, Polyangium fumosum Pl fu5T, Jahnella thaxteri Pl t4T and Byssovorax cruenta By c2T. The molecular phylogenetic analysis shows that the novel isolate forms a novel branch in the family Polyangiaceae , suborder Sorangiineae. Polyphasic taxonomic characterization suggests that the strain MSr9521T represents a novel species of a new genus in the family Polyangiaceae, for which the name Racemicystis crocea gen. nov., sp. nov. is proposed. The type strain of Racemicystis crocea is MSr9521T (=DSM 100773T=NCCB 100574T).
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Klebsiella alba is a later heterotypic synonym of Klebsiella quasipneumoniae subsp. similipneumoniae
More LessThe taxonomic position of Klebsiella alba was re-examined. The reconstructed phylogenetic tree based on multilocus sequence analysis showed that Klebsiella alba LMG 24441T (=KCTC 12878T) was closely related to Klebsiella quasipneumoniae subsp. similipneumoniae 07A044T, showing 99.5–100 % similarities for fusA, gapA, gyrA, leuS, pyrG, rpoB, rpoB2, atpD, gyrB and infB gene sequences and concatenated partial fusA, gapA, gyrA, leuS, pyrG, rpoB2, atpD, gyrB and infB gene sequences. High sequence similarities between Klebsiella alba LMG 24441T and Klebsiella quasipneumoniae subsp. similipneumoniae 07A044T indicated that they have the same taxonomic position. Klebsiella alba was reclassified as Klebsiella quasipneumoniae subsp. similipneumoniae and Klebsiella alba is a later heterotypic synonym of Klebsiella quasipneumoniae subsp. similipneumoniae .
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Methylovulum psychrotolerans sp. nov., a cold-adapted methanotroph from low-temperature terrestrial environments, and emended description of the genus Methylovulum
Two isolates of aerobic methanotrophic bacteria, strains Sph1T and Sph2, were obtained from cold methane seeps in a floodplain of the river Mukhrinskaya, Irtysh basin, West Siberia. Another morphologically and phenotypically similar methanotroph, strain OZ2, was isolated from a sediment of a subarctic freshwater lake, Archangelsk region, northern Russia. Cells of these three strains were Gram-stain-negative, light-pink-pigmented, non-motile, encapsulated, large cocci that contained an intracytoplasmic membrane system typical of type I methanotrophs. They possessed a particulate methane monooxygenase enzyme and utilized only methane and methanol. Strains Sph1T, Sph2 and OZ2 were able to grow at a pH range of 4.0–8.9 (optimum at pH 6.0–7.0) and at temperatures between 2 and 36 °C. Although their temperature optimum was at 20–25 °C, these methanotrophs grew well at lower temperatures, down to 4 °C. The major cellular fatty acids were C16 : 1ω5c, C16 : 1ω6c, C16 : 1ω7c, C16 : 1ω8c, C16 : 0 and C14 : 0; the DNA G+C content was 51.4–51.9 mol%. Strains Sph1T, Sph2 and OZ2 displayed nearly identical (99.1–99.7 % similarity) 16S rRNA gene sequences and belonged to the family Methylococcaceae of the class Gammaproteobacteria . The most closely related organism was Methylovulum miyakonense HT12T (96.0–96.5 % 16S rRNA gene sequence similarity and 90 % pmoA sequence similarity). The novel isolates, however, differed from Methylovulum miyakonense HT12T by cell morphology, pigmentation, absence of soluble methane monooxygenase, more active growth at low temperatures, growth over a broader pH range and higher DNA G+C content. On the basis of these differences, we propose a novel species, Methylovulum psychrotolerans sp. nov., to accommodate these methanotrophs. Strain Sph1T (=LMG 29227T=VKM B-3018T) is the type strain.
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- Eukaryotic micro-organisms
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Wickerhamomyces spegazzinii sp. nov., an ascomycetous yeast isolated from the fungus garden of Acromyrmex lundii nest (Hymenoptera: Formicidae)
More LessA novel ascomycetous yeast species in the genus Wickerhamomyces was isolated from the fungus garden of an attine ant nest, Acromyrmex lundii (Hymenoptera: Formicidae), from Santa Fe province, Argentina. Pairwise sequence alignment of D1/D2 sequences in the GenBank (http://www.ncbi.nlm.nih.gov) database revealed that the novel species is related most closely to Wickerhamomyces subpelliculosus, Wickerhamomyces linferdii, Wickerhamomyces anomalus, Wickerhamomyces siamensis and Wickerhamomyces ciferrii with 96% similarity to the first four. The species name Wickerhamomyces spegazzinii sp. nov. is proposed to accommodate this novel strain, which differs from the above species in melibiose, 5-keto-D-gluconate, succinate, and DL-lactate assimilation among others. The type strain is JLU025T (=CBS 12756T=CBMAI 1619T).
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- Evolution, Phylogeny and Biodiversity
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Taxonomic evaluation of species in the Streptomyces hirsutus clade using multi-locus sequence analysis and proposals to reclassify several species in this clade
More LessPrevious phylogenetic analysis of species of the genus Streptomyces based on 16S rRNA gene sequences resulted in a statistically well-supported clade (100 % bootstrap value) containing eight species that exhibited very similar gross morphology in producing open looped (Retinaculum–Apertum) to spiral (Spira) chains of spiny- to hairysurfaced, dark green spores on their aerial mycelium. The type strains of the species in this clade, specifically Streptomyces bambergiensis, Streptomyces cyanoalbus, Streptomyces emeiensis, Streptomyces hirsutus, Streptomyces prasinopilosus , , , , and Streptomyces prasinus , were subjected to multi-locus sequence analysis (MLSA) utilizing partial sequences of the housekeeping genes atpD, gyrB, recA, rpoB and trpB to clarify their taxonomic status. The type strains of several recently described species with similar gross morphology, including Streptomyces chlorus, Streptomyces herbaceus, Streptomyces incanus, Streptomyces pratens , , , and Streptomyces viridis , were also studied along with six unidentified green-spored Streptomyces strains from the ARS Culture Collection. The MLSAs suggest that three of the species under study ( S. bambergiensis, S. cyanoalbus , and S. emeiensis ) represent synonyms of other previously described species ( S. prasinus, S. hirsutus , and S. prasinopilosus , respectively). These relationships were confirmed through determination of in silico DNA–DNA hybridization estimates based on draft genome sequences. The five recently described species appear to be phylogenetically distinct but the unidentified strains from the ARS Culture Collection could be identified as representatives of S. hirsutus, S. prasinopilosus , or S. prasinus .
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- Letter to the Editor
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- Taxonomic Note
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Formation of names of genera of prokaryotes that end on -oides or -opsis. A proposal for addenda to Rule 65(2) and Appendix 9 of the International Code of Nomenclature of Prokaryotes
More LessIn view of the current confusion about the correct gender of genus names ending on –oides, and possible confusion in the future for genus names ending on –opsis, we propose non-retroactive addenda to Rule 65(2) and Appendix 9 of the International Code of Nomenclature of Prokaryotes so that new genera to be formed by adding the ending –oides to the stem of an existing genus name or another (Neo-) Latin word must be treated as neuter and genus names ending on –opsis are to be treated as feminine.
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- Erratum
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Erratum to Paraclostridium benzoelyticum gen. nov. sp. nov., isolated from marine sediment and reclassification of Clostridium bifermentans as Paraclostridium bifermentans comb. nov. Proposal of a new genus Paeniclostridium gen. nov. to accommodate Clostridium sordellii and Clostridium ghonii
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- Corrigendum
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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)