- Volume 65, Issue Pt_2, 2015
Volume 65, Issue Pt_2, 2015
- New Taxa
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- Bacteroidetes
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Marivirga lumbricoides sp. nov., a marine bacterium isolated from the South China Sea
More LessA novel, aerobic, heterotrophic, orange-pigmented, Gram-staining-negative, rod-shaped, gliding bacterial strain, designated JLT2000T, was isolated from surface water of the South China Sea. The strain was oxidase- and catalase-positive. The major cellular fatty acids of strain JLT2000 T were C12 : 0, iso-C15 : 1 G, iso-C15 : 0, iso-C17 : 0 3-OH, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0 and C18 : 0. MK-7 was the major respiratory quinone and the major polar lipids were phosphatidylcholine and phosphatidylethanolamine. The genomic DNA G+C content of strain JLT2000T was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain JLT2000T formed a branch within the genus Marivirga , but was clearly separated from the two established species of this genus, Marivirga tractuosa and Marivirga sericea . The 16S rRNA gene sequence similarity of strain JLT2000T with the type strains of these two species was 95.8 % and 96.1 %, respectively. Strain JLT2000T had a shorter cell length and wider growth range in different temperatures and salinities than those of Marivirga tractuosa NBRC 15989T and Marivirga sericea NBRC 15983T. In addition, strain JLT2000T could utilize more carbon sources and hydrolyse more polymers than Marivirga tractuosa NBRC 15989T and Marivirga sericea NBRC 15983T. Based on this polyphasic analysis, strain JLT2000T represents a novel species of the genus Marivirga , for which the name Marivirga lumbricoides sp. nov. is proposed. The type strain is JLT2000T ( = JCM 18012T = CGMCC 1.10832T).
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Belliella kenyensis sp. nov., isolated from an alkaline lake
A red-pigmented, Gram-reaction-negative, aerobic bacterial strain, designated No.164T, was isolated from sediment sample from the alkaline Lake Elmenteita located in the Kenyan Rift Valley. Results of 16S rRNA gene sequence analysis indicated that the isolate represented a member of the genus Belliella , with the highest sequence similarity (97 %) to Belliella pelovolcani DSM 46698T. Optimal growth temperature was 30–35 °C, at pH 7.0–12.0 in the presence of 0–4 % (w/v) NaCl. Flexirubins were absent. The respiratory menaquinone (MK-7), predominant cellular fatty acids (iso-C15 : 0, anteiso-C15 : 0 and a mixture of C16 : 1ω7c and/or iso-C15 : 0 2-OH) and DNA G+C content (38.1 mol%) of strain No.164T were consistent with those of other members of the genus Belliella . The polar lipids consisted of phosphatidylethanolamine, eight unspecified lipids and one unspecified phospholipid. Several phenotypic characteristics can be used to differentiate this isolate from those of other species of the genus Belliella . The results of polyphasic analyses presented in this study indicated that this isolate should be classified as representing a novel species of the genus Belliella . The name Belliella kenyensis sp. nov. is therefore proposed; the type strain is strain No.164T ( = DSM 46651T = CECT 8551T).
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Lutibacter oricola sp. nov., a marine bacterium isolated from seawater
More LessA bacterial strain, UDC377T, was isolated from seawater samples collected at Seo-do on the coast of Dokdo island in the East Sea, and was subjected to taxonomic study using a polyphasic approach. Strain UDC377T was pale-yellow, Gram-staining-negative, non-motile, rod-shaped and aerobic. The strain grew optimally at 25–28 °C, in the presence of 2 % (w/v) NaCl and at pH 7.0–7.5. Strain UDC377T produced carotenoid pigments; however, it did not produce flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain UDC377T clustered with members of the genus Lutibacter and appeared most closely related to Lutibacter agarilyticus KYW566T (96.0 % 16S rRNA gene sequence similarity) followed by L. aestuarii MA-My1T (95.0 %), L. litoralis CL-TF09T (94.9 %), L. maritimus S7-2T (94.1 %) and L. flavus IMCC1507T (94.0 %). The DNA G+C content of strain UDC377T was 30.8 mol%. Strain UDC377T contained MK-6 as the predominant menaquinone, iso-C15 : 0 3-OH, iso-C15 : 0 and iso-C16 : 0 3-OH as the major fatty acids, and phosphatidylethanolamine, two unknown aminolipids and six unknown lipids as the major polar lipids. Based on phenotypic properties and phylogenetic data presented, strain UDC377T is considered to represent a novel species of the genus Lutibacter , for which the name Lutibacter oricola sp. nov. is proposed. The type strain is UDC377T ( = DSM 24956T = KCTC 23668T).
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Arachidicoccus rhizosphaerae gen. nov., sp. nov., a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil
Three novel bacterial strains, designated Vu-144T, Vu-7 and Vu-35, were isolated on minimal medium from rhizosphere soil of field-grown cowpea and subjected to a taxonomic study using a polyphasic approach. Cells of the strains were Gram-stain-negative, non-motile, non-spore-forming, coccoid rods, and formed non-pigmented colonies. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain Vu-144T was affiliated with an uncultivated lineage of the phylum Bacteroidetes . Its closest phylogenetic neighbour was the recently described species Niastella populi , a member of the family Chitinophagaceae , with just 90.7 % sequence similarity to the type strain. The only isoprenoid quinone detected was menaquinone 7 (MK-7). The fatty acid profiles showed large amounts of iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G and minor amounts of summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and other fatty acids, allowing the differentiation of the strains from other genera. The G+C content of the genomic DNA of the three strains ranged from 43.1 to 44.3 mol%. In addition to phosphatidylethanolamine, the major polar lipids were three unidentified aminophospholipids (APL1–APL3), two unidentified phospholipids (PL1, PL2) and three unidentified lipids (UL1–UL3). Biochemical test patterns also differed from those of Niastella populi and members of other genera. All three isolates showed plant-growth-promoting properties, e.g. the ability to produce indole-3-acetic acid and NH3 and to solubilize phosphate, utilized 1-aminocyclopropane 1-carboxylate (ACC) as a sole source of nitrogen and possessed the ACC deaminase enzyme. The novel isolates readily colonized roots and stimulated growth of tomato and cowpea under glasshouse conditions. Inoculated plants showed a 45–60 % increase in dry matter weight with respect to uninoculated controls. On the basis of the evidence from our polyphasic study, isolate Vu-144T represents a novel genus and species in the family Chitinophagaceae , for which the name Arachidicoccus rhizosphaerae gen. nov., sp. nov. is proposed. The type strain of Arachidicoccus rhizosphaerae is Vu-144T ( = KCTC 22378T = NCIMB 14473T).
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Arcticibacter eurypsychrophilus sp. nov., isolated from ice core
A Gram-stain-negative, rod-shaped, non-flagellated bacterium, strain MJ9-5T, was isolated from ice core of Muji Glacier. Colonies of strain MJ9-5T were pink, convex and round on R2A agar. Strain MJ9-5T grew between −1 to 25 °C with an optimum growth temperature of 10–15 °C. The strain tolerated 0–1.2 % (w/v) NaCl with an optimum of 1 %. The major cellular fatty acids of strain MJ9-5T were iso-C15 : 0, summed feature 3 (C16 : 1ω6c and/or C1 6 : 1ω7c). The G+C content of the genomic DNA was 38.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ9-5T was related to members of the genus Arcticibacter . On the basis of the phenotypic characteristics and phylogenetic analysis, a novel species of this genus, Arcticibacter eurypsychrophilus sp. nov., is proposed. The type strain is MJ9-5T ( = KCTC 42008T = JCM 19862T).
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Flaviramulus aquimarinus sp. nov., isolated from seawater
More LessA yellow-coloured, rod-shaped, non-motile, Gram-stain-negative and facultative anaerobic bacterium, designated KYW499T, was isolated from seawater collected at Suncheon Bay, Republic of Korea. The isolate required sea salts for growth. Flexirubin-type pigments were absent. Major cellular fatty acids (>10 % of total) were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C15 : 0 3-OH. The main polar lipids were phosphatidylethanolamine and two unidentified polar lipids. The predominant isoprenoid quinone was MK-6. The genomic DNA G+C content was 31.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain KYW499T belonged to the family Flavobacteriaceae , and was related to the genus Flaviramulus . Data from a polyphasic taxonomy study suggested that the isolate represents a novel species of the genus Flaviramulus , for which the name Flaviramulus aquimarinus sp. nov. is proposed. The type strain is KYW499T ( = KCTC 23924T = JCM 18274T).
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Dysgonomonas termitidis sp. nov., isolated from the gut of the subterranean termite Reticulitermes speratus
More LessA facultatively anaerobic, Gram-stain-negative, non-motile and rod-shaped bacterium, strain N-10T, was isolated from the gut of the termite Reticulitermes speratus. Strain N-10T was closely related to Dysgonomonas gadei JCM 16698T according to 16S rRNA gene sequence similarity analysis (98 %) and DNA–DNA relatedness value (≤61.3 %). The optimum growth temperature of strain N-10T was 30 °C, which was distinct from that (37 °C) of known species of the genus Dysgonomonas . Growth of strain N-10T was inhibited on medium containing 5 or 20 % bile, unlike other species of the genus Dysgonomonas . In addition, acid production in the API 20A system and enzymic reactions in the Rapid ID 32A system of strain N-10T differed from those of other species of the genus Dysgonomonas . Based on these characteristics, strain N-10T represents a novel species of the genus Dysgonomonas , for which the name Dysgonomonas termitidis sp. nov. is proposed. The type strain is N-10T ( = JCM 30204T = CCUG 66188T).
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Vitellibacter nionensis sp. nov., isolated from a shallow water hydrothermal vent
A novel, Gram-stain-negative, non-motile, rod-shaped yellow bacterium, designated VBW088T was isolated from a shallow water hydrothermal vent in Espalamaca in the Azores. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain VBW088T clustered with three type strains of species of the genus Vitellibacter and exhibited a sequence similarity of 97.3 % with Vitellibacter soesokkakensis RSSK-12T. However, strain VBW088T and V. soesokkakensis RSSK-12T exhibited low DNA–DNA relatedness (12.7±3.5 %). Strain VBW088T was positive for catalase and oxidase. Growth occurred at 10–37 °C, with the optimum at 30 °C, and at pH 6.0–8.0 (optimum pH 6.0) and in up to 5 % (w/v) NaCl with optimum growth at 1–2 % (w/v) NaCl. The major fatty acids (>10 %) were iso-C15 : 0 (33.5 %) and iso-C17 : 0 3-OH (32.0 %). The polar lipids detected in strain VBW088T consisted of phosphatidylethanolamine, one unidentified aminolipid and three unidentified phospholipids. The DNA G+C content of strain VBW088T was 36.7 mol%. On the basis of phylogenetic inference, DNA–DNA relatedness, chemotaxonomic analysis and physiological data, the isolate represents a novel species of the genus Vitellibacter , for which the name Vitellibacter nionensis sp. nov. is proposed, with the type strain as VBW088T ( = KCTC 32420T = MCC 2354T).
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Mucilaginibacter aquaedulcis sp. nov., isolated from fresh water
More LessAn aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain PGW1-R01T, was isolated from fresh water from the Yeongju in the Republic of Korea. The strain grew optimally at 30 °C and at pH 6-8 on R2A agar. The major cellular fatty acids were summed feature 3 [comprising C16 : 1ω7c and/or C16 : 1ω6c (50.2 %) and iso-C15 : 0 (24.8 %)]. The major respiratory quinone was MK-7. The G+C contents were 39.4 mol% and the predominant respiratory quinone was MK-7. Based on 16S rRNA gene phylogeny, the strain belongs to the genus Mucilaginibacter . The strain PGW1-R01T was closely related to ‘ Mucilaginibacter ginsenosidivorax’ (96.6 % sequence similarity), Mucilaginibacter lappiensis (96.4 %) and Mucilaginibacter flavus (96.4 %). On the basis of the evidence presented in this study, strain PGW1-R01T represents a novel species of the genus Mucilaginibacter , for which the name Mucilaginibacter http://dx.doi.org/10.1601/nm.11437 aquaedulcis sp. nov., is proposed. The type strain is PGW1-R01T( = KCTC 23942T = CECT 8102T).
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- Other Bacteria
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Deinococcus antarcticus sp. nov., isolated from soil
More LessA pink-pigmented, non-motile, coccoid bacterial strain, designated G3-6-20T, was isolated from a soil sample collected in the Grove Mountains, East Antarctica. This strain was resistant to UV irradiation (810 J m−2) and slightly more sensitive to desiccation as compared with Deinococcus radiodurans . Phylogenetic analyses based on the 16S rRNA gene sequence of the isolate indicated that the organism belongs to the genus Deinococcus . Highest sequence similarities were with Deinococcus ficus CC-FR2-10T (93.5 %), Deinococcus xinjiangensis X-82T (92.8 %), Deinococcus indicus Wt/1aT (92.5 %), Deinococcus daejeonensis MJ27T (92.3 %), Deinococcus wulumuqiensis R-12T (92.3 %), Deinococcus aquaticus PB314T (92.2 %) and Deinococcus radiodurans DSM 20539T (92.2 %). Major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), anteiso-C15 : 0 and C16 : 0. The G+C content of the genomic DNA of strain G3-6-20T was 63.1 mol%. Menaquinone 8 (MK-8) was the predominant respiratory quinone. Based on its phylogenetic position, and chemotaxonomic and phenotypic characteristics, strain G3-6-20T represents a novel species of the genus Deinococcus , for which the name Deinococcus antarcticus sp. nov. is proposed. The type strain is G3-6-20T ( = DSM 27864T = CCTCC AB 2013263T).
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Tepidisphaera mucosa gen. nov., sp. nov., a moderately thermophilic member of the class Phycisphaerae in the phylum Planctomycetes, and proposal of a new family, Tepidisphaeraceae fam. nov., and a new order, Tepidisphaerales ord. nov.
Three strains of facultatively aerobic, moderately thermophilic bacteria were isolated from terrestrial hot springs in Baikal Lake region and Kamchatka (Russia). Cells of the new isolates were cocci reproducing by binary fission. The temperature range for growth was between 20 and 56 °C and the pH range for growth from pH 4.5 to 8.5, with optimal growth at 47–50 °C and pH 7.0–7.5. The organisms were chemoheterotrophs preferring sugars and polysaccharides as growth substrates. 16S rRNA gene sequences of strains 2842, 2813 and 2918Kr were nearly identical (99.7–100 % similarity) and indicated that the strains belonged to the phylum Planctomycetes . The phylogenetically closest cultivated relatives were Algisphaera agarilytica 06SJR6-2T and Phycisphaera mikurensis FYK2301M01T with 16S rRNA gene sequence similarity values of 82.4 and 80.3 %, respectively. The novel strains differed from them by higher growth temperature, sensitivity to NaCl concentration above 3.0 % and by their cellular fatty acids profile. On the basis of phylogenetic and physiological data, strains 2842T, 2813 and 2918Kr represent a novel genus and species for which we propose the name Tepidisphaera mucosa sp. nov. The type strain is 2842T ( = VKM B-2832T = JCM 19875T). We also propose that Tepidisphaera gen. nov. is the type genus of a novel family, Tepidisphaeraceae fam. nov. and a novel order, Tepidisphaerales ord. nov.
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Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes
A new Gram-staining-positive, non-sporulating, mesophilic, amino acid-degrading anaerobic bacterium, designated strain OTA 102T, was isolated from an anaerobic sequencing batch reactor treating wastewater from cooking tuna. The cells were curved rods (0.6–2.5×0.5 µm) and occurred singly or in pairs. The strain was motile by means of one lateral flagellum. Strain OTA 102T grew at temperatures between 30 and 45 °C (optimum 40 °C), between pH 6.0 and 8.4 (optimum pH 7.2) and NaCl concentrations between 1 and 5 % (optimum 2 %, w/v). Strain OTA 102T required yeast extract for growth. Serine, threonine, glycine, cysteine, citrate, fumarate, α-ketoglutarate and pyruvate were fermented. When co-cultured with Methanobacterium formicicum as the hydrogen scavenger, strain OTA 102T oxidized alanine, valine, leucine, isoleucine, aspartate, tyrosine, methionine, histidine and asparagine. The genomic DNA G+C content of strain OTA 102T was 41.7 mol%. The main fatty acid was iso-C15 : 0. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain OTA 102T was related to Aminobacterium colombiense and Aminobacterium mobile (95.5 and 95.2 % similarity, respectively), of the phylum Synergistetes . On the basis of phylogenetic, genetic and physiological characteristics, strain OTA 102T is proposed to represent a novel species of the genus Aminobacterium , Aminobacterium thunnarium sp. nov. The type strain is OTA 102T ( = DSM 27500T = JCM 19320T).
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Halotia gen. nov., a phylogenetically and physiologically coherent cyanobacterial genus isolated from marine coastal environments
Nostoc is a common and well-studied genus of cyanobacteria and, according to molecular phylogeny, is a polyphyletic group. Therefore, revisions of this genus are urged in an attempt to clarify its taxonomy. Novel strains isolated from underexplored environments and assigned morphologically to the genus Nostoc are not genetically related to the ‘true Nostoc’ group. In this study, four strains isolated from biofilms collected in Antarctica and five strains originated from Brazilian mangroves were evaluated. Despite their morphological similarities to other morphotypes of Nostoc , these nine strains differed from other morphotypes in ecological, physiological and genetic aspects. Based on the phylogeny of the 16S rRNA gene, the Antarctic sequences were grouped together with the sequences of the Brazilian mangrove isolates and Nostoc sp. Mollenhauer 1 : 1-067 in a well-supported cluster (74 % bootstrap value, maximum-likelihood). This novel cluster was separated phylogenetically from the ‘true Nostoc’ clade and from the clades of the morphologically similar genera Mojavia and Desmonostoc. The 16S rRNA gene sequences generated in this study exhibited 96 % similarity to sequences from the nostocacean genera mentioned above. Physiologically, these nine strains showed the capacity to grow in a salinity range of 1–10 % NaCl, indicating their tolerance of saline conditions. These results provide support for the description of a new genus, named Halotia gen. nov., which is related morphologically to the genera Nostoc , Mojavia and Desmonostoc. Within this new genus, three novel species were recognized and described based on morphology and internal transcribed spacer secondary structures: Halotia branconii sp. nov., Halotia longispora sp. nov. and Halotia wernerae sp. nov., under the provisions of the International Code of Nomenclature for Algae, Fungi and Plants.
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- Evolution, Phylogeny and Biodiversity
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Three novel lineages of ‘Candidatus Liberibacter africanus’ associated with native rutaceous hosts of Trioza erytreae in South Africa
More LessGreening disease of citrus in South Africa is associated with ‘Candidatus Liberibacter africanus’ (Laf), a phloem-limited bacterium vectored by the sap-sucking insect Trioza erytreae (Triozidae). Despite the implementation of control strategies, this disease remains problematic, suggesting the existence of reservoir hosts to Laf. The current study aimed to identify such hosts. Samples from 234 trees of Clausena anisata, 289 trees of Vepris lanceolata and 231 trees of Zanthoxylum capense were collected throughout the natural distribution of these trees in South Africa. Total DNA was extracted from samples and tested for the presence of liberibacters by a generic Liberibacter TaqMan real-time PCR assay. Liberibacters present in positive samples were characterized by amplifying and sequencing rplJ, omp and 16S rRNA gene regions. The identity of tree host species from which liberibacter sequences were obtained was verified by sequencing host rbcL genes. Of the trees tested, 33 specimens of Clausena, 17 specimens of Vepris and 10 specimens of Zanthoxylum tested positive for liberibacter. None of the samples contained typical citrus-infecting Laf sequences. Phylogenetic analysis of 16S rRNA gene sequences indicated that the liberibacters obtained from Vepris and Clausena had 16S rRNA gene sequences identical to that of ‘Candidatus Liberibacter africanus subsp. capensis’ (LafC), whereas those from Zanthoxylum species grouped separately. Phylogenetic analysis of the rplJ and omp gene regions revealed unique clusters for liberibacters associated with each tree species. We propose the following names for these novel liberibacters: ‘Candidatus Liberibacter africanus subsp. clausenae’ (LafCl), ‘Candidatus Liberibacter africanus subsp. vepridis’ (LafV) and ‘Candidatus Liberibacter africanus subsp. zanthoxyli’ (LafZ). This study did not find any natural hosts of Laf associated with greening of citrus. While native citrus relatives were shown to be infected with Laf-related liberibacters, nucleotide sequence data suggest that these are not alternative sources of Laf to citrus orchards, per se.
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- Letter to Editor
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- Taxonomic Note
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Proposal for ‘Candidatus Mycoplasma haemomuris subsp. musculi’ in mice, and ‘Candidatus Mycoplasma haemomuris subsp. ratti’ in rats
More LessMycoplasma haemomuris is causative of infectious anaemia or splenomegaly in rodents. We examined the nucleotide sequences of the non-ribosomal genes, rnpB and dnaK, in strains of the species M. haemomuris detected in small field mice and black rats. rnpB nucleotide sequences in strains of the species M. haemomuris isolated from small field mice and black rats had only 89 % sequence similarity, suggesting their separation into two distinct subgroups. dnaK had a nucleotide sequence similarity of 84 % between the subgroups. These results support the classification of M. haemomuris into two genetically distinct subgroups. Here we propose the establishment of these subgroups as ‘Candidatus Mycoplasma haemomuris subsp. musculi’, detected in small field mice (Apodemus argenteus), and ‘Candidatus Mycoplasma haemomuris subsp. ratti’, detected in black rats (Rattus rattus).
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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)