- Volume 54, Issue 6, 2004
Volume 54, Issue 6, 2004
- New Taxa
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- Gram-Positive Bacteria
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Mycobacterium nebraskense sp. nov., a novel slowly growing scotochromogenic species
More LessThe characterization of a novel slowly growing, scotochromogenic Mycobacterium species is reported. This previously undescribed mycobacterial species was isolated from five different patients with symptomatic pulmonary infections. All isolates were acid-fast-positive and the mycolic acid profiles were unique and supported placement into the genus Mycobacterium. Phenotypic characteristics of each strain included optimal growth after 3 weeks at a temperature range of 30–35 °C, yellow pigmentation after incubation in the dark and production of a heat-stable catalase. The 16S rRNA gene and internal transcribed spacer 1 sequences were identical for all five strains, but distinct from all known mycobacterial species. Phylogenetic analysis based on the 16S rRNA gene sequence placed the novel species within the slowly growing mycobacteria group in close proximity to Mycobacterium malmoense, Mycobacterium avium, Mycobacterium kansasii and Mycobacterium scrofulaceum. These data support the conclusion that the related five described organisms represent a novel Mycobacterium species, for which the name Mycobacterium nebraskense sp. nov. is proposed, with the type strain UNMC-MY1349T (=ATCC BAA-837T=DSM 44803T).
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Streptomyces ferralitis sp. nov., a novel streptomycete isolated from a New-Caledonian ultramafic soil
More LessThe taxonomic position of an actinomycete isolated from an ultramafic soil in New Caledonia was determined using a polyphasic approach. The isolate, which was designated SFOp68T, was shown to have chemical and morphological properties typical of streptomycetes. An almost complete 16S rRNA gene sequence of the isolate was generated and compared with sequences of representative streptomycetes. The 16S rRNA data not only supported the classification of the strain in the genus Streptomyces, but also showed that it formed a distinct phyletic line that was most closely related to one composed of the type strain of Streptomyces rimosus. The two organisms can be readily separated using a diverse range of phenotypic properties. It is proposed that strain SFOp68T (=DSM 41836T=NCIMB 13954T) be classified in the genus Streptomyces as Streptomyces ferralitis sp. nov.
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Arthrobacter psychrophenolicus sp. nov., isolated from an alpine ice cave
More LessOn the basis of phenotypic, genotypic and chemotaxonomic characteristics, a novel species belonging to the genus Arthrobacter is described. A facultatively psychrophilic bacterium, strain AG31T, was isolated from an alpine ice cave. The aerobic, Gram-positive, non-spore-forming, non-motile strain exhibited a rod–coccus growth cycle and produced a yellow pigment. Good growth and phenol biodegradation occurred at a temperature range of 1–25 °C. Up to 10 mM phenol was utilized as a sole carbon source. Glucose was not assimilated. Analysis of the 16S rRNA gene revealed that strain AG31T represents a distinct lineage within the genus Arthrobacter, being most closely related to Arthrobacter sulfureus. The level of DNA–DNA relatedness to the type strain of A. sulfureus was 29·9 %. Anteiso-C15 : 0 was the predominant fatty acid (72 %). Strain AG31T exhibited A4α l-lys–l-Glu-type peptidoglycan and contained glucose as the only cell-wall sugar. MK-10 was the predominant menaquinone, and the polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. Strain AG31T (=DSM 15454T=LMG 21914T) is assigned as the type strain of a novel Arthrobacter species, Arthrobacter psychrophenolicus sp. nov.
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Streptomyces glauciniger sp. nov., a novel mesophilic streptomycete isolated from soil in south China
A polyphasic study was undertaken to establish the taxonomic status of a soil isolate. The organism, strain FXJ14T, was found to have chemical and morphological properties characteristic of streptomycetes. Phylogenetic analyses based on an almost complete 16S rRNA gene sequence of the strain and on the 120 nt variable γ-region of the 16S rRNA molecule showed that it formed a distinct phyletic line within the range of variation encompassed by the genus Streptomyces. The sharp separation of the organism from representatives of the genus Streptomyces was strengthened by the fact that its BOX-PCR and RFLP of 16S rDNA-ITS fingerprints differed from those of over 450 recognized Streptomyces species. The isolate also had a profile of phenotypic properties that readily distinguished it from the genotypically close type strains. It is evident from the combination of genotypic and phenotypic data that strain FXJ14T (=AS 4.1858T=JCM 12278T=LMG 22082T) should be classified as the type strain of a novel species of the genus Streptomyces, for which the name Streptomyces glauciniger sp. nov. is proposed.
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Saccharothrix xinjiangensis sp. nov., a pyrene-degrading actinomycete isolated from Tianchi Lake, Xinjiang, China
More LessA pyrene-degrading isolate, strain PYX-6T, was obtained from Tianchi Lake, Xinjiang Uygur Autonomous Region, China, and was identified by means of polyphasic taxonomy. On the basis of 16S rRNA gene sequence similarity, strain PYX-6T was closely related to members of the genus Saccharothrix. Its 16S rRNA gene sequence similarity to each of Saccharothrix syringae, Saccharothrix australiensis, Saccharothrix algeriensis and Saccharothrix coeruleofusca was 98 %. Chemotaxonomic and physiological properties of strain PYX-6T further supported its affiliation to the genus Saccharothrix. DNA–DNA hybridization results and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain PYX-6T from recognized Saccharothrix species. Therefore, strain PYX-6T represents a novel species, for which the name Saccharothrix xinjiangensis sp. nov. is proposed, with type strain PYX-6T (=AS 4.1731T=JCM 12329T).
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Brevibacterium celere sp. nov., isolated from degraded thallus of a brown alga
Two whitish yellow, Gram-positive, non-motile, aerobic bacteria were isolated from enrichment culture during degradation of the thallus of the brown alga Fucus evanescens. The bacteria studied were chemo-organotrophic, mesophilic and grew well on nutrient media containing up to 15 % (w/v) NaCl. The DNA G+C content was 61 mol%. The two isolates exhibited a conspecific DNA–DNA relatedness value of 98 %, indicating that they belong to the same species. A comparative analysis of 16S rRNA gene sequences revealed that strain KMM 3637T formed a distinct phyletic lineage in the genus Brevibacterium (family Brevibacteriaceae, class Actinobacteria) and showed the highest sequence similarity (about 97 %) to Brevibacterium casei. DNA–DNA hybridization experiments demonstrated 45 % binding with the DNA of B. casei DSM 20657T. Physiological and chemotaxonomic characteristics (meso-diaminopimelic acid in the peptidoglycan, major cellular fatty acids 15 : 0ai and 17 : 0ai) of the bacteria studied were consistent with the genomic and phylogenetic data. On the basis of the results of this study, a novel species, Brevibacterium celere sp. nov., is proposed. The type strain is KMM 3637T (=DSM 15453T=ATCC BAA-809T).
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Bacillus vietnamensis sp. nov., a moderately halotolerant, aerobic, endospore-forming bacterium isolated from Vietnamese fish sauce
Five strains of Gram-positive, endospore-forming, moderately halotolerant bacteria were studied taxonomically. Four were isolated from Vietnamese fish sauce and one from the Gulf of Mexico. Phylogenetic analysis based on 16S rRNA gene sequences showed that these strains clustered within the radiation of the genus Bacillus but separately from recognized Bacillus species. DNA G+C composition of the isolates ranged from 43 to 44 mol%. Strains 15-1T and NRRL B-14850 showed high levels of DNA–DNA relatedness (82–100 %) to each other and to the other strains isolated here; they displayed low levels of DNA–DNA relatedness (<29 %) to the type strains of selected recognized Bacillus species. They grew in 15 % NaCl and optimally in 1 % NaCl, which is characteristic of moderately halotolerant bacteria. The isolates grew at pH 6·5 to 10·0 but not at pH 6·0. Their cell walls contained meso-diaminopimelic acid. The major isoprenoid quinone was MK-7 and the principal cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. Based on these results, the strains tested were regarded as members of a novel Bacillus species for which the name Bacillus vietnamensis sp. nov. is proposed. The type strain is 15-1T (=JCM 11124T=NRIC 0531T=NRRL 23890T).
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Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov.
A polyphasic study was carried out to establish the taxonomic positions of six strains isolated from diverse soil samples and provisionally assigned to the genus Kitasatospora. The isolates were found to have chemical and morphological properties consistent with their classification as Kitasatospora strains. Direct 16S rRNA gene sequence data confirmed the taxonomic position of the strains following the generation of phylogenetic trees by using three tree-making algorithms. Five of the isolates were considered to merit species status using complementary genotypic and phenotypic data. These organisms were designated Kitasatospora arboriphila sp. nov. (HKI 0189T=2291-120T=DSM 44785T=NCIMB 13973T), Kitasatospora gansuensis sp. nov. (HKI 0314T=2050-015T=DSM 44786T=NCIMB 13974T), Kitasatospora nipponensis sp. nov. (HKI 0315T=2148-013T=DSM 44787T=NCIMB 13975T), Kitasatospora paranensis sp. nov. (HKI 0190T=2292-041T=DSM 44788T=NCIMB 13976T) and Kitasatospora terrestris sp. nov. (HKI 0186T=2293-012T=DSM 44789T=NCIMB 13977T). The remaining organism, isolate HKI 0316 (=2122-022=DSM 44790=NCIMB 13978), was considered to be a strain of Kitasatospora kifunensis on the basis of 16S rRNA gene sequence, DNA–DNA relatedness and phenotypic data.
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Nocardioides aestuarii sp. nov., isolated from tidal flat sediment
Hana Yi and Jongsik ChunA strictly aerobic, non-motile, rod-shaped actinomycete, designated strain JC2056T, was isolated from a sediment sample of getbol, the tidal flat of Korea. Results of 16S rRNA gene sequence analysis indicated that the isolate belonged to the genus Nocardioides, with the highest similarity being to Nocardioides luteus KCTC 9575T (95·7 %). The major menaquinone was MK-8(H4), and predominant cellular fatty acids were iso-16 : 0 and iso-16 : 1 H. The DNA G+C content was 70 mol%. Based on the morphological, physiological, biochemical and chemotaxonomical data presented in this study, strain JC2056T should be classified as a novel species, for which the name Nocardioides aestuarii sp. nov. is proposed; the type strain is JC2056T (=IMSNU 14029T=KCTC 9921T=JCM 12125T).
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Transfer of Bacillus halodenitrificans Denariaz et al. 1989 to the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.
More LessA Gram-variable, endospore-forming moderately halophilic rod, strain SF-121, was isolated from a marine solar saltern of the Yellow Sea in Korea. The result of 16S rRNA gene sequence analysis showed that strain SF-121 has highest sequence similarity (99·7 %) with the type strain of Bacillus halodenitrificans. Phylogenetic analyses based on 16S rRNA gene sequences revealed that B. halodenitrificans DSM 10037T and strain SF-121 are more closely related to the genus Virgibacillus than to the genus Bacillus. Strain SF-121 and B. halodenitrificans DSM 10037T exhibited 16S rRNA gene similarity levels of 95·3–97·5 % with the type strains of Virgibacillus species and 94·0 % with the type strain of Bacillus subtilis. DNA–DNA relatedness and phenotypic data indicated that B. halodenitrificans DSM 10037T and strain SF-121 are members of the same species. B. halodenitrificans DSM 10037T and strain SF-121 exhibited DNA–DNA relatedness values of 9–11 % with the type strains of Virgibacillus carmonensis and Virgibacillus marismortui. On the basis of the phenotypic, chemotaxonomic, phylogenetic and genetic data, B. halodenitrificans should be reclassified in the genus Virgibacillus as Virgibacillus halodenitrificans comb. nov.
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Mahella australiensis gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from an Australian oil well
A novel Gram-positive, anaerobic and moderately thermophilic bacterium, strain 50-1 BONT, was isolated from an Australian terrestrial oil reservoir. Cells were spore-forming straight rods, motile by peritrichous flagella. The optimum growth conditions were 50 °C, pH 7·5 and 0·1 % NaCl. Strain 50-1 BONT fermented arabinose, cellobiose, fructose, galactose, glucose, mannose, sucrose, xylose and yeast extract. Glucose was fermented mainly into lactate, formate, hydrogen and CO2. The major end product of pyruvate fermentation was acetate together with H2 and CO2. Thiosulfate, sulfate, elemental sulfur and nitrate were not used as terminal electron acceptors. The DNA G+C content was 55·5 mol%. The closest phylogenetic relative of strain 50-1 BONT was Thermoanaerobacterium thermosulfurigenes (16S rRNA gene sequence similarity of 85·7 %). As strain 50-1 BONT was physiologically and phylogenetically different from members of the order ‘Thermoanaerobacteriales’, it is proposed that strain 50-1 BONT (=DSM 15567T=CIP 107919T) be classified as the type strain of a novel species of a new genus, Mahella australiensis gen. nov., sp. nov.
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Enterococcus saccharominimus sp. nov., from dairy products
Four isolates, which were obtained from Belgian, Moroccan and Romanian dairy products, constituted a homogeneous but unidentified taxon after screening with whole-cell protein fingerprinting. Complete 16S rRNA gene sequence analysis classified representative strains in the genus Enterococcus. Highest sequence similarities of 98·6 and 98·0 % were obtained with the species Enterococcus sulfureus and Enterococcus saccharolyticus, respectively. Growth characteristics, biochemical features, tRNA intergenic length polymorphism analysis, DNA–DNA hybridization and DNA G+C contents of selected strains demonstrated that they represent a single, novel Enterococcus species. It differs phenotypically from other enterococci in characteristics commonly considered as typical of this genus: no growth in 6·5 % NaCl or 0·4 % sodium azide, and no acid production from a wide range of carbohydrates. The name Enterococcus saccharominimus sp. nov. is proposed for this novel species; the type strain (LMG 21727T=CCM 7220T) was isolated from contaminated pasteurized cow's milk.
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Jonesia quinghaiensis sp. nov., a new member of the suborder Micrococcineae
A coryneform strain isolated from soda lake mud in China corresponded in chemotaxonomic characteristics such as peptidoglycan type A4α l-lys–l-ser–d-Glu and major menaquinone MK-9, as well as in its DNA base composition (57 mol% G+C), to its phylogenetic neighbour Jonesia denitrificans. Differences in phenotypic characteristics and the phylogenetic distance (96·6 % 16S rRNA gene sequence similarity) from J. denitrificans justify the proposal of a second species of the genus Jonesia, Jonesia quinghaiensis sp. nov., with the type strain QH3A7T (=DSM 15701T=CGMCC 1.3459T).
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Corynebacterium ciconiae sp. nov., isolated from the trachea of black storks (Ciconia nigra)
Eight unidentified Gram-positive, rod-shaped organisms were recovered from the tracheas of apparently healthy black storks (Ciconia nigra) and subjected to a polyphasic taxonomic analysis. Based on cellular morphology and biochemical criteria the isolates were tentatively assigned to the genus Corynebacterium, although three of the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequencing studies demonstrated that all of the isolates were phylogenetically members of the genus Corynebacterium. Five strains were genotypically identified as representing Corynebacterium falsenii, whereas the remaining three strains represented a hitherto unknown subline, associated with a small subcluster of species that includes Corynebacterium mastitidis and its close relatives. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from black storks represent a novel species within the genus Corynebacterium, for which the Corynebacterium ciconiae sp. nov. is proposed. The type strain is CECT 5779T (=BS13T=CCUG 47525T).
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Geobacillus debilis sp. nov., a novel obligately thermophilic bacterium isolated from a cool soil environment, and reassignment of Bacillus pallidus to Geobacillus pallidus comb. nov.
More LessSeveral aerobic, motile, rod-shaped, thermophilic, spore-forming Geobacillus bacteria predominantly giving a Gram-positive staining reaction were isolated from a cool soil environment in Northern Ireland and taxonomically investigated. Two isolates, F10 and TfT, showed low 16S rRNA gene sequence similarity to recognized members of the genus Geobacillus. Phylogenetic tree investigation using neighbour-joining, maximum-likelihood and parsimony methods indicated that strains F10 and TfT represent a single novel species, for which the name Geobacillus debilis sp. nov. is proposed, with type strain TfT (=DSM 16016T=NCIMB 13995T) and which belongs to a subgroup of the genus Geobacillus comprising Geobacillus toebii and Geobacillus caldoxylosilyticus. However, G. debilis showed closest affinities to Bacillus pallidus, which we propose should become Geobacillus pallidus comb. nov.
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Reclassification of Staphylococcus pulvereri Zakrzewska-Czerwińska et al. 1995 as a later synonym of Staphylococcus vitulinus Webster et al. 1994
A polyphasic taxonomic approach was applied to strains of the species Staphylococcus vitulinus and Staphylococcus pulvereri in order to clarify their taxonomic relatedness. Four reference strains, representing both species, and seven strains isolated from human clinical material were characterized by biotyping, ribotyping and SDS-PAGE analysis of whole-cell proteins, and none of the screening approaches allowed the two taxa to be distinguished. DNA–DNA hybridization experiments between four selected representative strains, including the type strains, confirmed that Staphylococcus pulvereri is a later synonym of Staphylococcus vitulinus.
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Bacillus macyae sp. nov., an arsenate-respiring bacterium isolated from an Australian gold mine
More LessA strictly anaerobic arsenate-respiring bacterium isolated from a gold mine in Bendigo, Victoria, Australia, belonging to the genus Bacillus is described. Cells are Gram-positive, motile rods capable of respiring with arsenate and nitrate as terminal electron acceptors using a variety of substrates, including acetate as the electron donor. Reduction of arsenate to arsenite is catalysed by a membrane-bound arsenate reductase that displays activity over a broad pH range. Synthesis of the enzyme is regulated; maximal activity is obtained when the organism is grown with arsenate as the terminal electron acceptor and no activity is detectable when it is grown with nitrate. Mass of the catalytic subunit was determined to be approximately 87 kDa based on ingel activity stains. The closest phylogenetic relative, based on 16S rRNA gene sequence analysis, is Bacillus arseniciselenatis, but DNA–DNA hybridization experiments clearly show that strain JMM-4T represents a novel Bacillus species, for which the name Bacillus macyae sp. nov. is proposed. The type strain is JMM-4T (=DSM 16346T=JCM 12340T).
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Acetanaerobacterium elongatum gen. nov., sp. nov., from paper mill waste water
More LessTwo mesophilic anaerobic bacterial strains (Z7T and Z1) were isolated from waste water sludge of the Xinanzhang paper mill, Beijing, China. The strains were Gram-positive, non-spore-forming and motile. Cells were thin rods (0·2–0·4×4·0–8·0 μm). Growth of the strains was observed at 20–42 °C and pH 5·0–7·5. Both strains hydrolysed gelatin and aesculin and fermented several kinds of mono-, di- and oligosaccharides. The fermentation end products formed from glucose were acetate, ethanol, hydrogen and carbon dioxide. The predominant cellular fatty acids were the branched-chain fatty acids isoC15 : 0 (42·83 %) and isoC14 : 0 (32·11 %). The DNA G+C contents of strains Z7T and Z1 were 50·4 and 48·6 mol%, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolates represent a new phyletic sublineage within the Clostridium leptum rRNA cluster, with <91 % 16S rRNA gene sequence similarity to currently described species. On the basis of polyphasic evidence from this study, Acetanaerobacterium elongatum gen. nov., sp. nov., a novel genus and species, is proposed, with strain Z7T (=JCM 12359T=AS 1.5012T) as the type strain.
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Streptococcus equi subsp. ruminatorum subsp. nov., isolated from mastitis in small ruminants
Six isolates of an unknown Gram-positive, catalase-negative, chain-forming, coccus-shaped organism isolated from ovine and caprine mastitis were characterized by phenotypic and molecular taxonomic methods. On the basis of cellular morphology and the results of biochemical tests, the organism was tentatively identified as a streptococcal species. Comparative 16S rRNA gene sequencing studies confirmed that the organism is a member of the genus Streptococcus, with Streptococcus equi as its closest phylogenetic relative (98·8 % similarity). DNA–DNA pairing studies showed that the unidentified organism displayed more than 70 % relatedness to the type strains of S. equi subsp. equi and subsp. zooepidemicus. Despite the relatively high DNA–DNA reassociation values, biotyping and ribotyping allowed clear differentiation of the unknown bacterium from the two recognized subspecies of S. equi. On the basis of phenotypic and molecular genetic evidence, it is proposed that the unknown Streptococcus isolates from ovine and caprine mastitis be classified as a novel subspecies, Streptococcus equi subsp. ruminatorum subsp. nov. The type strain is CECT 5772T (=CCUG 47520T=Mt 167T).
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Nocardia xishanensis sp. nov., a novel actinomycete isolated from soil
More LessThe taxonomic position of a soil isolate, strain 276T, was established using a polyphasic approach. The organism showed a range of chemical and morphological properties consistent with its classification in the genus Nocardia. An almost complete 16S rRNA gene sequence determined for the strain was aligned with corresponding sequences of representatives of the genus Nocardia and related taxa using three tree-making algorithms. The organism formed a distinct phyletic line within the evolutionary radiation occupied by the genus Nocardia and was most closely related to the type strain of Nocardia abscessus. However, the two strains shared a low DNA–DNA relatedness value and were readily distinguished using a combination of phenotypic properties. The combined genotypic and phenotypic data show that strain 276T should be assigned to the genus Nocardia as a novel species. The name proposed for this new taxon is Nocardia xishanensis sp. nov. The type strain is 276T (=CGMCC 4.1860T=JCM 12160T).
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Mycobacterium pyrenivorans sp. nov., a novel polycyclic-aromatic-hydrocarbon-degrading species
More LessThe taxonomic position of a polycyclic-aromatic-hydrocarbon-degrading bacterium, strain 17A3T, isolated from contaminated soil was determined using a combination of phenotypic and genotypic properties. The isolate showed phenotypic properties that were diagnostic for species of the genus Mycobacterium. Comparative 16S rRNA gene sequence analysis assigned 17A3T to the 16S rRNA gene subgroup that contains Mycobacterium aurum, Mycobacterium austroafricanum, Mycobacterium vaccae and Mycobacterium vanbaalenii, but it could clearly be distinguished from these species using a combination of physiological, chemotaxonomic markers and internal rRNA gene spacer analyses. The data showed that strain 17A3T (=DSM 44605T=NRRL B-24244T) merits recognition as the type strain of a novel species of the genus Mycobacterium. The name Mycobacterium pyrenivorans sp. nov. is proposed for the species because of its ability to use pyrene as a sole source of carbon and energy.
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Emended description of the genus Glycomyces and description of Glycomyces algeriensis sp. nov., Glycomyces arizonensis sp. nov. and Glycomyces lechevalierae sp. nov.
More LessA polyphasic taxonomic evaluation of presumptive strains representative of the genus Glycomyces held within the Agricultural Research Service Culture Collection resulted in the discovery of three novel species. Analysis of the whole cell sugar content of these novel species, as well as of two species presently assigned to the genus, revealed that the whole cell sugar pattern was different from that reported in the formal description of the genus Glycomyces. The sugars present in all strains studied included ribose, xylose, mannose and galactose rather than xylose and arabinose as reported in the original description of the genus. Moreover, the menaquinone patterns observed for the novel species also deviated from the original genus description. The formal description of the genus Glycomyces is emended to reflect these new data. The novel species proposed and described are Glycomyces algeriensis sp. nov. (type strain NRRL B-16327T=DSM 44727T), Glycomyces arizonensis sp. nov. (type strain NRRL B-16153T=DSM 44726T) and Glycomyces lechevalierae sp. nov. (type strain NRRL B-16149T=DSM 44724T).
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Thermosinus carboxydivorans gen. nov., sp. nov., a new anaerobic, thermophilic, carbon-monoxide-oxidizing, hydrogenogenic bacterium from a hot pool of Yellowstone National Park
A new anaerobic, thermophilic, facultatively carboxydotrophic bacterium, strain Nor1T, was isolated from a hot spring at Norris Basin, Yellowstone National Park. Cells of strain Nor1T were curved motile rods with a length of 2·6–3 μm, a width of about 0·5 μm and lateral flagellation. The cell wall structure was of the Gram-negative type. Strain Nor1T was thermophilic (temperature range for growth was 40–68 °C, with an optimum at 60 °C) and neutrophilic (pH range for growth was 6·5–7·6, with an optimum at 6·8–7·0). It grew chemolithotrophically on CO (generation time, 1·15 h), producing equimolar quantities of H2 and CO2 according to the equation CO+H2O→CO2+H2. During growth on CO in the presence of ferric citrate or amorphous ferric iron oxide, strain Nor1T reduced ferric iron but produced H2 and CO2 at a ratio close to 1 : 1, and growth stimulation was slight. Growth on CO in the presence of sodium selenite was accompanied by precipitation of elemental selenium. Elemental sulfur, thiosulfate, sulfate and nitrate did not stimulate growth of strain Nor1T on CO and none of these chemicals was reduced. Strain Nor1T was able to grow on glucose, sucrose, lactose, arabinose, maltose, fructose, xylose and pyruvate, but not on cellobiose, galactose, peptone, yeast extract, lactate, acetate, formate, ethanol, methanol or sodium citrate. During glucose fermentation, acetate, H2 and CO2 were produced. Thiosulfate was found to enhance the growth rate and cell yield of strain Nor1T when it was grown on glucose, sucrose or lactose; in this case, acetate, H2S and CO2 were produced. In the presence of thiosulfate or ferric iron, strain Nor1T was also able to grow on yeast extract. Lactate, acetate, formate and H2 were not utilized either in the absence or in the presence of ferric iron, thiosulfate, sulfate, sulfite, elemental sulfur or nitrate. Growth was completely inhibited by penicillin, ampicillin, streptomycin, kanamycin and neomycin. The DNA G+C content of the strain was 51·7±1 mol%. Analysis of the 16S rRNA gene sequence revealed that strain Nor1T belongs to the Bacillus–Clostridium phylum of the Gram-positive bacteria. On the basis of the studied phenotypic and phylogenetic features, we propose that strain Nor1T be assigned to a new genus, Thermosinus gen. nov. The type species is Thermosinus carboxydivorans sp. nov. (type strain, Nor1T=DSM 14886T=VKM B-2281T).
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Classification of isolates from locations in Austria and Yellowstone National Park as Geobacillus tepidamans sp. nov.
Two moderately thermophilic, Gram-positive, spore-forming bacteria were isolated from different geographical locations and sources; strain GS5-97T from a beet sugar factory in Leopoldsdorf, Lower Austria, and strain YNP10 from a geothermally heated soil, Yellowstone National Park, USA. The sequences of their 16S rRNA genes were found to be 99·8 % identical, and DNA–DNA hybridization experiments revealed that strains GS5-97T and YNP10 share 89·9 mol% similarity to each other, but only 34·3 and 39·2 mol% similarity, respectively, to Geobacillus caldoxylosilyticus DSM 12041T, which is their closest related type strain. A polyphasic analysis showed that these two isolates were more similar to each other than to other characterized geobacilli. Their DNA G+C content was 43·2 and 42·4 mol%, respectively, and they were identical with respect to many phenotypic features (e.g. Topt 55 °C; pHopt 7·0). Both strains clearly displayed best growth when cultured aerobically. They differed slightly in their cellular fatty acid profiles and polar lipid pattern, and genotypically they could also be distinguished based on randomly amplified polymorphic DNA fingerprints and internal transcribed spacer analysis. Freeze-etching experiments revealed oblique surface layer (S-layer) lattices in both strains, and biochemical analyses of the purified S-layer proteins indicated the occurrence of glycosylation. Based on the properties of these organisms relative to those currently documented for the genus Geobacillus and for the various sister genera in the Bacillus radiation, a novel species is proposed, Geobacillus tepidamans sp. nov., with GS5-97T (=ATCC BAA-942T=DSM 16325T) as the type strain. Strain YNP10 has been deposited in the American Type Culture Collection as ATCC BAA-943.
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Arthrobacter gangotriensis sp. nov. and Arthrobacter kerguelensis sp. nov. from Antarctica
More LessTwo coryneform bacteria were isolated from a penguin rookery soil sample collected in Antarctica, near the Indian station Dakshin Gangotri (strain Lz1yT), and from sea water from Kerguelen island, Antarctica (strain KGN15T). They have morphological and chemotaxonomic properties (peptidoglycan A4α type; major menaquinones MK-8, MK-9 and MK-10; predominant fatty acids anteiso-C15 : 0 and anteiso-C17 : 0) that are characteristic of members of the genus Arthrobacter. The isolates shared 97·8 % 16S rRNA gene sequence similarity to each other and were most closely related to Arthrobacter sulfureus (about 98·5 % sequence similarity). DNA–DNA hybridization experiments revealed 50 % relatedness between the isolates, while the levels of DNA–DNA relatedness between strains Lz1yT and KGN15 T and their phylogenetic relative, A. sulfureus, were respectively 54 and 12 %. Based on the above data and distinct phenotypic differences between the isolates and A. sulfureus, two novel species are proposed, Arthrobacter gangotriensis sp. nov. (type strain Lz1yT=DSM 15796T=JCM 12166T) and Arthrobacter kerguelensis sp. nov. (type strain KGN15T=DSM 15797T=JCM 12165T).
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Alkalibacterium psychrotolerans sp. nov., a psychrotolerant obligate alkaliphile that reduces an indigo dye
More LessA psychrotolerant, obligately alkaliphilic bacterium, IDR2-2T, which is able to reduce indigo dye was isolated from a fermented polygonum indigo (Polygonum tinctorium Lour.) produced in Date, Hokkaido, using a traditional Japanese method. The isolate grew at pH 9–12 but not at pH 7–8. It was a Gram-positive, facultatively anaerobic, straight rod-shaped bacterium with peritrichous flagella. The isolate grew in 0–17 % (w/v) NaCl but not at NaCl concentrations higher than 18 % (w/v). Its major cellular fatty acids were C14 : 0, C16 : 0, C16 : 19c and C18 : 19c, and its DNA G+C content was 40·6 mol%. dl-lactic acid was the major end-product from d-glucose. No quinones could be detected. The peptidoglycan type was A4β, Orn–d-Glu. A phylogenetic analysis based on 16S rRNA gene sequence data indicated that strain IDR2-2T is a member of the genus Alkalibacterium. DNA–DNA hybridization revealed low relatedness (less than 25 %) between the isolate and two phylogenetically related strains, Alkalibacterium olivapovliticus and Marinilactibacillus psychrotolerans. On the basis of phenotypic characteristics, phylogenetic data and DNA–DNA relatedness data, the isolate merits classification as a novel species, for which the name Alkalibacterium psychrotolerans sp. nov. is proposed. The type strain is IDR2-2T (=JCM 12281T=NCIMB 13981T).
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Mycobacterium cosmeticum sp. nov., a novel rapidly growing species isolated from a cosmetic infection and from a nail salon
Four isolates of a rapidly growing Mycobacterium species had a mycolic acid pattern similar to that of Mycobacterium smegmatis, as determined by HPLC analyses. Three of the isolates were from footbath drains and a sink at a nail salon located in Atlanta, GA, USA; the fourth was obtained from a granulomatous subdermal lesion of a female patient in Venezuela who was undergoing mesotherapy. By random amplified polymorphic DNA electrophoresis and PFGE of large restriction fragments, the three isolates from the nail salon were shown to be the same strain but different from the strain from the patient in Venezuela. Polymorphisms in regions of the rpoB, hsp65 and 16S rRNA genes that were shown to be useful for species identification matched for the two strains but were different from those of other Mycobacterium species. The 16S rRNA gene sequence placed the strains in a taxonomic group along with Mycobacterium frederiksbergense, Mycobacterium hodleri, Mycobacterium diernhoferi and Mycobacterium neoaurum. The strains produced a pale-yellow pigment when grown in the dark at the optimal temperature of 35 °C. Biochemical testing showed that the strains were positive for iron uptake, nitrate reduction and utilization of d-mannitol, d-xylose, iso-myo-inositol, l-arabinose, citrate and d-trehalose. The strains were negative for d-sorbitol utilization and production of niacin and 3-day arylsulfatase, although arylsulfatase activity was observed after 14 days. The isolates grew on MacConkey agar without crystal violet but not on media containing 5 % (w/v) NaCl or at 45 °C. They were susceptible to ciprofloxacin, amikacin, tobramycin, cefoxitin, clarithromycin, doxycycline, sulfamethoxazole and imipenem. The name Mycobacterium cosmeticum sp. nov. is proposed for this novel species; two strains, LTA-388T (=ATCC BAA-878T=CIP 108170T) (the type strain) and 2003-11-06 (=ATCC BAA-879=CIP 108169) have been designated, respectively, for the strains of the patient in Venezuela and from the nail salon in Atlanta, GA, USA.
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- Unicellular Eukaryotes
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Phylum-specific environmental DNA analysis reveals remarkably high global biodiversity of Cercozoa (Protozoa)
More LessThis study presents the first 18S rRNA multi-library environmental PCR survey of a single protozoan phylum, Cercozoa Cavalier-Smith 1998, from a range of different habitats. Phylogenetic analysis reveals at least nine novel clades within the phylum, several possibly at the level of order or above. Further experiments are described to ascertain the true ecological and geographical distributions of some clades that might be inferred from the tree to be restricted in either or both ways. These results suggest that the diversity of cercozoan taxa may run into thousands of lineages, making it comparable in diversity to the largest better-characterized protozoan phyla, e.g. Ciliophora (ciliates and suctorians) and Foraminifera. New sequences of cultured Spongomonas, Metromonas and Metopion are also presented. In the light of these additions, and the increased taxon sampling from the environmental libraries, some revisions of cercozoan classification are made: the transfer of Spongomonadea from Reticulofilosa to Monadofilosa; the removal of Metopiida from Sarcomonadea; and the creation of the new order Metromonadida, currently containing the single genus Metromonas. Although Metromonas groups with weak to moderate support with Chlorarachnea, it is here placed in superclass Monadofilosa, to which it is morphologically more similar.
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Candida leandrae sp. nov., an asexual ascomycetous yeast species isolated from tropical plants
The novel yeast species Candida leandrae is described based on eight isolates from decaying fruits of Leandra reversa Cogn. (Melastomataceae) in an Atlantic rainforest site in Brazil, one from a Convolvulaceae flower in Costa Rica and one from a drosophilid in Hawai'i. The strains differed in their colony morphology, one being butyrous and smooth and the other being filamentous and rugose. Sequences of the D1/D2 domains of the large-subunit rRNA gene from both morphotypes were identical. C. leandrae belongs to the Kodamaea clade and is closely related to Candida restingae. The two species can be separated on the basis of growth at 37 °C and the assimilation of melezitose, negative in the novel species. The type culture of C. leandrae is strain UNESP 00-64RT (=CBS 9735T=NRRL Y-27757T).
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Expansion of the Candida tanzawaensis yeast clade: 16 novel Candida species from basidiocarp-feeding beetles
More LessA major clade of new yeast taxa from the digestive tract of basidiocarp-feeding beetles is recognized based on rRNA gene sequence analyses. Almost 30 % of 650 gut isolates formed a statistically well-supported clade that included Candida tanzawaensis. The yeasts in the clade were isolated from 11 families of beetles, of which Tenebrionidae and Erotylidae were most commonly sampled. Repeated isolation of certain yeasts from the same beetle species at different times and places indicated strong host associations. Sexual reproduction was never observed in the yeasts. Based on comparisons of small- and large-subunit rRNA gene sequences and morphological and physiological traits, the yeasts were placed in Candida ambrosiae and in 16 other undescribed taxa. In this report, the novel species in the genus Candida are described and their relationships with other taxa in the Saccharomycetes are discussed. The novel species and their type strains are as follows: Candida guaymorum (NRRL Y-27568T=CBS 9823T), Candida bokatorum (NRRL Y-27571T=CBS 9824T), Candida kunorum (NRRL Y-27580T=CBS 9825T), Candida terraborum (NRRL Y-27573T=CBS 9826T), Candida emberorum (NRRL Y-27606T=CBS 9827T), Candida wounanorum (NRRL Y-27574T=CBS 9828T), Candida yuchorum (NRRL Y-27569T=CBS 9829T), Candida chickasaworum (NRRL Y-27566T=CBS 9830T), Candida choctaworum (NRRL Y-27584T=CBS 9831T), Candida bolitotheri (NRRL Y-27587T=CBS 9832T), Candida atakaporum (NRRL Y-27570T=CBS 9833T), Candida panamericana (NRRL Y-27567T=CBS 9834T), Candida bribrorum (NRRL Y-27572T=CBS 9835T), Candida maxii (NRRL Y-27588T=CBS 9836T), Candida anneliseae (NRRL Y-27563T=CBS 9837T) and Candida taliae (NRRL Y-27589T=CBS 9838T).
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Kazachstania aerobia sp. nov., an ascomycetous yeast species from aerobically deteriorating corn silage
More LessIn an investigation of the yeast biota involved in silage deterioration, a considerable number of strains belonging to Saccharomyces and related genera were isolated from aerobically deteriorating corn silage in Tochigi, Japan. Analysis of sequences of the internal transcribed spacer and the large-subunit rRNA gene D1/D2 domain and electrophoretic karyotyping indicated that two of the strains, NS 14T and NS 26, represent a novel species with close phylogenetic relationships to Kazachstania servazzii and Kazachstania unispora. It is proposed that the novel species be named Kazachstania aerobia sp. nov., with NS 14T (=AS 2.2384T=CBS 9918T) as the type strain.
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- Evolution, Phylogeny And Biodiversity
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Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis
More LessObligatory intracellular parasites have undergone significant genome reduction by gene loss over time in the context of their obligate associations with the host. The flux, streamlining and elimination of genes in these genomes constitute a selective and ongoing process. Comparative analyses of five completely sequenced obligatory intracellular parasite genomes reveal that these genomes display marked similarities in patterns of protein length and frequency distribution, with substantial sharing of a ‘backbone genome’. From category distribution based on the database of cluster of orthologous groups of proteins (COG), it is clear that habitat is a major factor contributing to genome reduction. It is also observed that, in all five obligatory intracellular parasites, the reduction in number of genes/proteins is greater for proteins with lengths of 200–600 amino acids. These comparative analyses highlight that gene loss is function-dependent, but is independent of protein length. These comparisons enhance our knowledge of the forces that drive the extreme specialization of the bacteria and their association with the host.
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Diversity of bartonellae associated with small mammals inhabiting Free State province, South Africa
More LessThe prevalence and diversity of bartonellae infecting the blood of 10 small mammal species inhabiting nine Nature Reserves of the Free State province, South Africa, was assessed using phenotypic, genotypic and phylogenetic methods. Of 86 small mammals sampled, 38 animals belonging to five different species yielded putative bartonellae. Thirty-two isolates were confirmed as bartonellae and were characterized by comparison of partial citrate synthase gene (gltA) sequences. Phylogenetic reconstructions derived from alignment of these sequences with those available for other bartonellae indicated that the South African rodent-associated isolates formed two distinct clades within the radius of the genus Bartonella. One of these clades also included recognized Bartonella species associated with rodents native to Eurasia but not to the New World, whereas the second clade contained exclusively isolates associated with South African rodents. Comparison of gltA sequences delineated the isolates into a number of ecologically distinct populations and provided an indication that a combination of phylogenetics and the identification of sequence clusters in housekeeping protein-encoding genes could be developed as a key criterion in the classification of bartonellae. This study is the first to investigate wildlife-associated bartonellae in Africa, adding support to their ubiquity and broad diversity and to the paradigm that the phylogenetic positions of the Bartonella species encountered today have been influenced by the geographical distribution of their hosts.
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Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing
More LessThe current classification of non-pigmented and late-pigmenting rapidly growing mycobacteria (RGM) capable of producing disease in humans and animals consists primarily of three groups, the Mycobacterium fortuitum group, the Mycobacterium chelonae–abscessus group and the Mycobacterium smegmatis group. Since 1995, eight emerging species have been tentatively assigned to these groups on the basis of their phenotypic characters and 16S rRNA gene sequence, resulting in confusing taxonomy. In order to assess further taxonomic relationships among RGM, complete sequences of the 16S rRNA gene (1483–1489 bp), rpoB (3486–3495 bp) and recA (1041–1056 bp) and partial sequences of hsp65 (420 bp) and sodA (441 bp) were determined in 19 species of RGM. Phylogenetic trees based upon each gene sequence, those based on the combined dataset of the five gene sequences and one based on the combined dataset of the rpoB and recA gene sequences were then compared using the neighbour-joining, maximum-parsimony and maximum-likelihood methods after using the incongruence length difference test. Combined datasets of the five gene sequences comprising nearly 7000 bp and of the rpoB+recA gene sequences comprising nearly 4600 bp distinguished six phylogenetic groups, the M. chelonae–abscessus group, the Mycobacterium mucogenicum group, the M. fortuitum group, the Mycobacterium mageritense group, the Mycobacterium wolinskyi group and the M. smegmatis group, respectively comprising four, three, eight, one, one and two species. The two protein-encoding genes rpoB and recA improved meaningfully the bootstrap values at the nodes of the different groups. The species M. mucogenicum, M. mageritense and M. wolinskyi formed new groups separated from the M. chelonae–abscessus, M. fortuitum and M. smegmatis groups, respectively. The M. mucogenicum group was well delineated, in contrast to the M. mageritense and M. wolinskyi groups. For phylogenetic organizations derived from the hsp65 and sodA gene sequences, the bootstrap values at the nodes of a few clusters were <70 %. In contrast, phylogenetic organizations obtained from the 16S rRNA, rpoB and recA genes were globally similar to that inferred from combined datasets, indicating that the rpoB and recA genes appeared to be useful tools in addition to the 16S rRNA gene for the investigation of evolutionary relationships among RGM species. Moreover, rpoB gene sequence analysis yielded bootstrap values higher than those observed with recA and 16S rRNA genes. Also, molecular signatures in the rpoB and 16S rRNA genes of the M. mucogenicum group showed that it was a sister group of the M. chelonae–abscessus group. In this group, M. mucogenicum ATCC 49650T was clearly distinguished from M. mucogenicum ATCC 49649 with regard to analysis of the five gene sequences. This was in agreement with phenotypic and biochemical characteristics and suggested that these strains are representatives of two closely related, albeit distinct species.
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- Letters To The Editor
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- International Committee On Systematics Of Prokaryotes
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- Request For An Opinion
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Proposal to acknowledge Beijerinck as the original author of the species Pantoea agglomerans. Request for an Opinion
More LessThe name ‘Bacillus agglomerans’ was first published by Beijerinck in 1888. Ewing and Fife changed the name to Enterobacter agglomerans in 1972 as a new combination, acknowledging that Beijerinck had been the original author and making the new full name Enterobacter agglomerans ( Beijerinck 1888 ) Ewing and Fife 1972 . Beijerinck's name was omitted from the Approved Lists of Bacterial Names in 1980, which listed only Ewing and Fife as the authors. The current listings in the List of Bacterial Names with Standing in Nomenclature follow the Approved Lists and omit Beijerinck from the names for both Enterobacter agglomerans and Pantoea agglomerans. It is proposed that Beijerinck be acknowledged as the original author of this species by having his name reinstated in its full name, Pantoea agglomerans ( Beijerinck 1888 ) Gavini et al. 1989, and a Request for an Opinion is put forward to the Judicial Commission.
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Proposal to list ATCC 43642 as the type strain of Leptospira interrogans in the Approved Lists of Bacterial Names. Request for an Opinion
More LessATCC 23581T has been cited as the type strain of Leptospira interrogans since 1980. In 1986, the Centers for Disease Control informed the ATCC that this strain was Leptospira interrogans serovar budapest, not serovar icterohaemorrhagiae as deposited originally. An authentic culture of the Leptospira interrogans serovar icterohaemorrhagiae RGAT strain was then submitted and assigned ATCC 43642, which was designated as the type strain of Leptospira interrogans in an article by Yasuda et al. [ Yasuda et al. (1987) . Int J Syst Bacteriol 37, 407–415]. In this Request for an Opinion to the Judicial Commission, it is proposed that a correction be made in the Approved Lists of Bacterial Names to acknowledge ATCC 43642 as the type strain of Leptospira interrogans.
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- Errata
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 51 (2001)
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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)