- Volume 66, Issue 2, 2016
Volume 66, Issue 2, 2016
- NEW TAXA
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- Proteobacteria
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Mesorhizobium calcicola sp. nov., Mesorhizobium waitakense sp. nov., Mesorhizobium sophorae sp. nov., Mesorhizobium newzealandense sp. nov. and Mesorhizobium kowhaii sp. nov. isolated from Sophora root nodules
More LessIn total, 31 strains of Gram-stain-negative, rod-shaped bacteria were isolated from Sophora root nodules and authenticated as rhizobia on this host. Based on 16S rRNA gene phylogeny, they were shown to belong to the genus Mesorhizobium, with the representative strains ICMP 19560T, ICMP 19523T, ICMP 19535T, ICMP 19545T and ICMP 19512T being related most closely to Mesorhizobium sangaii SCAU7T (99.9–99.6 % similarity), Mesorhizobium cantuariense ICMP 19515T (99.7–99.6 %) and Mesorhizobium ciceri UMP-CA7T (99.7–99.5 %). Additionally, the novel strains formed distinct groups based on housekeeping gene sequence analysis and were closely related to Mesorhizobium waimense ICMP 19557T (93.5–94.9, 92.5–95.6 and 94.2–96.0 %), M. cantuariense ICMP 19515T (93.1–97.7, 93.5–95.4 and 94.8–96.8 %) and M. ciceri UMP-CA7T (93.2–97.2, 94.6–96.8 and 95.5–97.3 %) for glnII, recA and rpoB, respectively. Chemotaxonomic data supported the assignment of the strains to the genus Mesorhizobium, and DNA–DNA hybridizations, matrix-assisted laser desorption/ionization time-of-flight MS analysis, enterobacterial repetitive intergenic consensus PCR, physiological and biochemical tests allowed the genotypic and phenotypic differentiation from their nearest neighbouring species. Therefore, these strains represent five novel species for which the names Mesorhizobium calcicola sp. nov. (type strain ICMP 19560T = LMG 28224T = HAMBI 3609T), Mesorhizobium waitakense sp. nov. (type strain ICMP 19523T = LMG 28227T = HAMBI 3605T), Mesorhizobium sophorae sp. nov. (type strain ICMP 19535T = LMG 28223T = HAMBI 3606T), Mesorhizobium newzealandense sp. nov. (type strain ICMP 19545T = LMG 28226T = HAMBI 3607T) and Mesorhizobium kowhaii sp. nov. (type strain ICMP 19512T = LMG 28222T = HAMBI 3603T) are proposed.
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Bacillus cavernae sp. nov. isolated from cave soil
More LessA Gram-stain-positive, spore-forming, motile, strictly aerobic, rod-shaped bacterium, designated strain L5T, was isolated from soil of Tenglong cave, China. 16S rRNA gene sequence analysis showed that strain L5T was related most closely to Bacillus asahii MA001T (96.5 %) (the highest 16S rRNA gene sequence similarity), Bacillus kribbensis BT080T (96.4 %) and Bacillus deserti ZLD-8T (96.2 %). The DNA G+C content of strain L5T was 45.6 mol%. The major menaquinone was MK-7. The major fatty acids were iso-C14 : 0, anteiso-C15 : 0 and iso-C16 : 0, and the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The diagnostic diamino acid in the cell-wall peptidoglycan was meso-diaminopimelic acid. In addition, strain L5T had different characteristics compared with the other Bacillus strains such as pink colony colour, low growth temperature and low nutrient requirement. The results indicate that strain L5T represents a novel species of the genus Bacillus, for which the name Bacillus cavernae sp. nov. is proposed. The type strain is L5T ( = KCTC 33637T = CCTCC AB 2015055T).
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Vogesella facilis sp. nov., isolated from a freshwater river, and emended description of the genus Vogesella
More LessA bacterial strain, designated TTM-24T, was isolated from a freshwater river in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain TTM-24T were Gram-stain-negative, facultatively anaerobic, poly-β-hydroxybutyrate-accumulating, motile by a single polar flagellum, rod-shaped, with rods surrounded by a thick capsule and forming white-coloured colonies. Growth occurred at 15–37 °C (optimum, 25 °C), at pH 6.0–8.0 (optimum, pH 7.0) and with 0–1 % NaCl (optimum, 0.5 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain TTM-24T belonged to the genus Vogesella and was most closely related to ‘Vogesella amnigena’ Npb-02 with sequence similarity of 97.1 %. Strain TTM-24T contained summed feature 3 (comprising C16 : 1 ω7c and/or C16 : 1 ω6c) and C16 : 0 as the major fatty acids. The major respiratory quinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The genomic DNA G+C content of strain TTM-24T was 67.4 mol%. The DNA–DNA hybridization value for strain TTM-24T with ‘V. amnigena’ Npb-02 was less than 45 %. On the basis of the phylogenetic inference and phenotypic data, strain TTM-24T should be classified as a novel species, for which the name Vogesella facilis sp. nov. is proposed. The type strain is TTM-24T ( = BCRC 80912T = KCTC 42742T = LMG 29003T).
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Deferrisoma palaeochoriense sp. nov., a thermophilic, iron(III)-reducing bacterium from a shallow-water hydrothermal vent in the Mediterranean Sea
More LessA novel thermophilic, anaerobic, mixotrophic bacterium, designated strain MAG-PB1T, was isolated from a shallow-water hydrothermal vent system in Palaeochori Bay off the coast of the island of Milos, Greece. The cells were Gram-negative, rugose, short rods, approximately 1.0 μm long and 0.5 μm wide. Strain MAG-PB1T grew at 30–70 °C (optimum 60 °C), 0–50 g NaCl l− 1 (optimum 15–20 g l− 1) and pH 5.5–8.0 (optimum pH 6.0). Generation time under optimal conditions was 2.5 h. Optimal growth occurred under chemolithoautotrophic conditions with H2 as the energy source and CO2 as the carbon source. Fe(III), Mn(IV), arsenate and selenate were used as electron acceptors. Peptone, tryptone, Casamino acids, sucrose, yeast extract, d-fructose, α-d-glucose and ( − )-d-arabinose also served as electron donors. No growth occurred in the presence of lactate or formate. The G+C content of the genomic DNA was 66.7 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Deferrisoma camini, the first species of a recently described genus in the Deltaproteobacteria. Based on the 16S rRNA gene phylogenetic analysis and on physiological, biochemical and structural characteristics, the strain was found to represent a novel species, for which the name Deferrisoma palaeochoriense sp. nov. is proposed. The type strain is MAG-PB1T ( = JCM 30394T = DSM 29363T).
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Marimicrobium arenosum gen. nov., sp. nov., a moderately halophilic bacterium isolated from sea sand
More LessA Gram-stain-negative, non-pigmented, non-spore-forming, non-motile, strictly aerobic bacterial strain, designated CAU 1038T, was isolated from a sea sand sample in Modo, Republic of Korea, and its taxonomic position was examined using a polyphasic approach. Cells of strain CAU 1038T grew optimally at 30 °C, pH 7.5 in 2 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CAU 1038T formed a distinct lineage within the class Gammaproteobacteria as a separate deep branch, with 95.2 % or lower sequence similarity to representatives of the genera Haliea, Halioglobus and Chromatocurvus, and 92.3 % or lower with Luminiphilus, Pseudohaliea and Congregibacter. The major cellular fatty acids of strain CAU 1038T were C16 : 0, C16 : 1ω7c and C18 : 1ω7c. The polar lipid pattern of the isolate consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified aminolipid and two unidentified lipids. The strain contained lipoquinone (Q-8) as the sole respiratory quinone. The G+C content of the genomic DNA was 65 mol%. On the basis of phenotypic and chemotaxonomic data, and phylogenetic inference, strain CAU 1038T represents a novel species of a new genus in the family Halieaceae, for which the name Marimicrobium arenosum gen. nov., sp. nov. is proposed. The type strain of the type species is CAU 1038T ( = KCTC 42300T = NBRC 110727T).
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Ahrensia marina sp. nov., a dimethylsulfoniopropionate-cleaving bacterium isolated from seawater, and emended descriptions of the genus Ahrensia and Ahrensia kielensis
More LessA Gram-stain-negative, strictly aerobic, light-beige, rod-shaped, motile bacterium with peritrichous flagella that cleaves dimethylsulfoniopropionate (DMSP), designated strain LZD062T, was isolated from bottom seawater of the East China Sea. The isolate required sea salts for growth and grew optimally at pH 8.0 and 28 °C and in the presence of 2 % (w/v) NaCl. The major fatty acid (>10 %) was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, one unidentified aminolipid and one unidentified glycolipid. Ubiquinone Q-10 was the only quinone detected. Phylogenetic analyses based on 16S rRNA and atpD gene sequences placed LZD062T within the genus Ahrensia of the family Phyllobacteriaceae in the class Alphaproteobacteria. The most closely related type strain was, in both cases, Ahrensia kielensis JCM 20689T ( = IAM 12618T = DSM 5890T), which gave sequence similarities of 97.7 % in the 16S rRNA gene and 90.4 % in the atpD gene. Genome relatedness between strain LZD062T and A. kielensis JCM 20689T was computed using both genome-to-genome distance analysis and average nucleotide identity, giving values of 22.10 ± 2.35 and 79.55 %, respectively. The genomic DNA G+C content calculated from the genome sequence was 50.1 mol%. On the basis of our polyphasic analyses, strain LZD062T is considered to represent a novel species of the genus Ahrensia, for which the name Ahrensia marina sp. nov. is proposed. The type strain is LZD062T ( = MCCC 1K00254T = JCM 30117T = DSM 28886T). Emended descriptions of the genus Ahrensia and Ahrensia kielensis are also proposed.
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Acinetobacter equi sp. nov., isolated from horse faeces
The taxonomic position of five strains isolated from horse faeces, and which shared identical 16S rRNA gene sequences, were studied. Cells of all isolates are Gram-stain-negative, obligately aerobic and have a rod-shaped appearance. The strains show highest 16S rRNA gene sequence similarities to Acinetobacter lwoffii (98.3 %), Acinetobacter haemolyticus (98.0 %), Acienetobacter johnsonii (97.9 %) and Acinetobacter brisouii (97.9 %). Whole-genome sequencing of strain 114T and phylogeny reconstruction based on a core set of 1061 Acinetobacter genes indicated that A. bouvetii CIP 107468T was the closest relative among species of the genus Acinetobacter for which whole genome sequences are available. The genomic DNA G+C content of strain 114T is 34.9 mol%, which is lower than any other value reported for the genus Acinetobacter. The predominant polyamine is 1,3-diaminopropane, which is typical for the genus Acinetobacter. The most abundant fatty acids are C16 : 1ω7c and/or iso-C15 : 0 2-OH (36 %) and C16 : 0 (28 %). The proportion of C18 : 1ω9c (7 %) is distinctively low compared to most species of the genus. The major ubiquinone of strain 114T is Q-9. Microscopic studies revealed the presence of pili and the absence of flagella. The capability of all five strains to utilize l-arabinose and gentisate as well as their lack of growth at temperatures of 41 °C and above provide sufficient criteria to distinguish the isolates from all species of the genus Acinetobacter with validly published names. Based on these combined data, the five isolates represent a novel species of the genus Acinetobacter, for which the name Acinetobacter equi sp. nov. is proposed. The type strain is 114T ( = DSM 27228T = CCUG 65204T).
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Aetherobacter fasciculatus gen. nov., sp. nov. and Aetherobacter rufus sp. nov., novel myxobacteria with promising biotechnological applications
More LessBacterial strains SBSr002T and SBSr003T were isolated in 2007 from dried soil samples containing decaying plant material. The organisms were recognized as myxobacteria by growth-stage characteristics, forming swarming colonies and fruiting bodies on agar and on filter paper. These strains were unusual for their ring-like or halo colony appearance in an agar. Both isolates were characterized as bacteriolytic, non-cellulolytic, mesophilic, aerobic and chemoheterotrophic and showed resistance to various antibiotics. GC-MS analysis of their cellular fatty acids revealed rather large quantities of docosahexaenoic acid, and they also both contained eicosapentaenoic acid, arachidonic acid and docosapentaenoic acid. Strain SBSr003T was previously identified as the producer organism of a novel class of potent antiviral metabolites that were called aetheramides. The G+C content of the genomic DNA was 68.0–68.9 mol%. Phylogenetic analysis revealed that both strains belong within the family Polyangiaceae, suborder Sorangiineae, order Myxococcales. Their 16S rRNA gene sequences showed the highest similarity (97–99 %) to sequences derived from clones of uncultured bacteria, 95–96 % similarity to Byssovorax cruenta and Sorangium cellulosum and 94 % similarity to Chondromyces apiculatus. The results of a polyphasic taxonomic characterization suggested that strains SBSr002T and SBSr003T represent two distinct species of a novel genus, Aetherobacter gen. nov., for which the names Aetherobacter fasciculatus sp. nov. (type strain SBSr002T = DSM 24601T = NCCB 100377T) and Aetherobacter rufus sp. nov. (type strain SBSr003T = DSM 24628T = NCCB 100378T) are proposed. The type species of Aetherobacter is Aetherobacter fasciculatus.
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Luteimonas notoginsengisoli sp. nov., isolated from rhizosphere
A Gram-staining-negative, yellow-pigmented strain, designated SYP-B804T, was isolated from the rhizosphere of Panax notoginseng. The strain was rod-shaped with a single polar flagellum. The optimum temperature and pH required for growth of the strain were 28–32 °C and pH 7–8, respectively. 16S rRNA gene sequence analysis indicated that strain SYP-B804T showed highest 16S rRNA gene sequence similarity with Luteimonas mephitis DSM 12574T (98.0 %). However, the DNA–DNA relatedness value between them (38.1 ± 0.6 %) was less than the threshold value for the delineation of genomic species. Ubiquinone-8 (Q-8) was the predominant quinone. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The major polar lipids of the strain were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genomic DNA was 71 %. On the basis of phenotypic, chemotaxonomic and molecular characteristics, strain SYP-B804T merits recognition as a representative of a novel species of the genus Luteimonas, for which the name Luteimonas notoginsengisoli sp. nov. is proposed, with SYP-B804T ( = KCTC 42211T = JCM 30329T) as the type strain.
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Acetobacter musti sp. nov., isolated from Bobal grape must
More LessAn acetic acid bacterium (strain Bo7T), obtained during a study of the microbial diversity of spontaneous fermentations of Bobal grape must, was subjected to a taxonomic study using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences allocated strain Bo7T to the genus Acetobacter, and revealed Acetobacter aceti and Acetobacter oeni to be nearest neighbours (99.57 % 16S rRNA gene sequence similarity between strain Bo7T and A. oeni CECT 5830T, and 98.76 % between strain Bo7T and A. aceti CECT 298T). Cells of strain Bo7T are Gram-negative, motile rods, catalase-positive and oxidase-negative. The DNA G+C content of strain Bo7T was 58.0 mol%. DNA–DNA hybridizations demonstrated that strain Bo7T belongs to a single novel genospecies that can be differentiated from its nearest phylogenetic neighbours by the following phenotypic characteristics: no production of 5-keto-d-gluconic acid from d-glucose, growth with glycerol but not with methanol or maltose as sole carbon sources, and growth on yeast extract with 30 % d-glucose. The major fatty acid was C18 : 1ω7c/C18 : 1ω6c (summed feature 8; approx. 56 %); other fatty acids in significant amounts (>5 %) were C16 : 0 2-OH (11 %), C16 : 0 (7 %), C14 : 0 2-OH (7 %) and C14 : 0 3-OH/iso-C16 : 1 I (summed feature 2; 6 %). The results obtained indicate that strain Bo7T represents a novel species of the genus Acetobacter, for which the name Acetobacter musti sp. nov. is proposed. The type strain is Bo7T ( = DSM 23824T = CECT 7722T).
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Aquitalea pelogenes sp. nov., isolated from mineral peloid
Strain P1297T was isolated in the frame of a project aimed on the psychrotolerant microbiota occurring in water sources. The strain initially identified as a tentative species of the genus Aeromonas was rod-shaped, Gram-stain-negative, facultatively anaerobic and oxidase-positive. Subsequently, 16S rRNA gene sequence analysis placed strain P1297T within the class Betaproteobacteria and showed Aquitalea magnusonii TRO-001DR8T as the closest phylogenetic relative with 99.28 % 16S rRNA gene sequence similarity. Digital DDH and average nucleotide identity (ANI) were determined to evaluate the genomic relationship between strain P1297T and Aquitalea magnusonii CCM 7607T. Digital DDH estimation (31.3 ± 2.46 %) as well as ANI (85.6001 %; reciprocal value 85.3277 %) proved the dissimilarity of strain P1297T. Further investigation using phenotyping, automated ribotyping, whole-cell protein profiling and PCR-fingerprinting methods showed a distinct taxonomic position of strain P1297T among hitherto described species of the genus Aquitalea. DNA–DNA hybridization experiments revealed low binding values between strain P1297T and Aquitalea magnusonii CCM 7607T (57 ± 3 %) and Aquitalea denitrificans CCM 7935T (41 ± 5 %). The DNA G+C content of strain P1297T was 60.3 mol%. The predominant fatty acids were C16 : 1ω7c/ iso-C15 : 0 2-OH (47.0 %), C16 : 0 (24.5 %) and C18 : 1ω7c (10.6 %), and the quinone system contained predominantly ubiquinone Q-8. The polar lipids detected were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unidentified phospholipids and one unidentified aminophospholipid. Obtained results of genotypic and chemotaxonomic methods clearly proved that strain P1297T represents a novel species of the genus Aquitalea, for which the name Aquitalea pelogenes sp. nov. is proposed. The type strain is P1297T ( = CCM 7557T = LMG 28989T = CCUG 67440T).
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Enterobacter bugandensis sp. nov., isolated from neonatal blood
A total of 17 Enterobacter-like isolates were obtained from blood during a septicaemia outbreak in a neonatal unit, Tanzania, that could not be assigned based on phenotypic test to any existing Enterobacter species. Eight representative outbreak isolates were investigated in detail. Fermentation characteristics, biochemical assays and fatty acid profiles for taxonomic analysis were determined and supplemented with information derived from whole genome sequences. Phenotypic and morphological tests revealed that these isolates were Gram-stain-negative, rod-shaped, highly motile and facultatively anaerobic. The fatty acid profile was similar to those of the type strains for all recognized Enterobacter species, with quantitative differences in C17 : 0, C18 : 1ω7c and C17 : 0 cyclo fatty acids. Whole genome sequencing was used to identify taxonomically relevant characteristics, i.e. for 16S rRNA gene sequence analysis, multi-locus sequence analysis (MLSA), in silico DNA–DNA hybridization (isDDH) and average nucleotide identity (ANI). Draft genomes were approximately 4.9 Mb in size with a G+C content of 56.0 mol%. The 16S rRNA gene sequence of these eight isolates showed >97 % similarity to all Enterobacter species, while MLSA clustered them closely with the type strains of Enterobacter xiangfangensis and Enterobacter hormaechei. These eight strains showed less than 70 % isDDH identity with the type strains of Enterobacter species. In addition, less than 95 % ANI to the type strains of Enterobacter species was observed. From these results, it is concluded that these isolates possess sufficient characteristics to differentiate them from all recognized Enterobacter species, and should therefore be considered as representing a novel species. The name Enterobacter bugandensis sp. nov. is proposed with EB-247T ( = DSM 29888T = NCCB 100573T) as the type strain.
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Erwinia endophytica sp. nov., isolated from potato (Solanum tuberosum L.) stems
We analysed, using a polyphasic taxonomic approach, two bacterial strains coded BSTT30T and BSTT40, isolated in the course of a study of endophytic bacteria occurring in the stems and roots of potatoes growing in soil from Salamanca, Spain. The 16S rRNA gene sequence was identical in both strains and had 98.4 % identity with respect to the closest relatives Erwinia tasmaniensis Et1/99T and Erwinia rhapontici ATCC29283T. Erwinia billingiae E63T and Erwinia toletana A37T were also closely related with 98.2 % sequence similarities, so the novel strains were classified within the genus Erwinia. The analysis of the housekeeping genes gpd, gyrB and rpoD confirmed the phylogenetic affiliation of strains BSTT30T and BSTT40 with similarities of lower than 90 % in all cases with respect to the closest relatives mentioned above. The respiratory quinone of strain BSTT30T was Q8. The major fatty acids were C16 : 0, C16 : 1ω7c/16 : 1ω6c in summed feature 3 and C18 : 1ω7c/18 : 2ω6,9c in summed feature 8. The novel strains were oxidase-negative and catalase-positive. Glucose was fermented without gas production. They were negative for arginine dihydrolase, urease and indole production. The strains could grow at 35 °C and at pH 10. DNA G+C content was 50.1 mol%. DNA–DNA hybridization results showed values of lower than 29 % relatedness with respect to the type strains of the four most closely related species. Therefore, the combined genotypic, phenotypic and chemotaxonomic data support the classification of strains BSTT30T and BSTT40 into a novel species of the genus Erwinia, for which the name Erwinia endophytica sp. nov. is proposed. The type strain is BSTT30T ( = LMG 28457T, CECT 8692T).
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Niveibacterium umoris gen. nov., sp. nov., isolated from wetland freshwater
More LessA taxonomic study was carried out on a novel bacterial strain, designated MIC2059T, which was isolated from Ungok Wetland of Gochang in Korea. Cells of the isolate were found to be Gram-stain-negative, rod-shaped and motile. Comparison of the 16S rRNA gene sequences indicated that the isolate belonged to the family Rhodocyclaceae, with Uliginosibacterium gangwonense as its closest relative, with a similarity of 94.8 %. It contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 0, summed feature 8 (comprising C18 : 1ω7c and/or C18 : 1ω6c) and C12 : 0 3-OH as the major fatty acids and Q8 as the respiratory ubiquinone. The polar lipid profile of strain MIC2059T revealed the presence of phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol as major polar lipids. In addition, phosphatidylserine, an unidentified aminophospholipid and unidentified lipids were present in small amounts. The DNA G+C content of the strain was 65.1 mol%. On the basis of the evidence presented, it is concluded that strain MIC2059T represents a novel species of a novel genus within the family Rhodocyclaceae, for which the name Niveibacterium umoris gen. nov., sp. nov. is proposed. The type strain is MIC2059T ( = KACC 17062T = JCM 18716T).
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Dissulfurimicrobium hydrothermale gen. nov., sp. nov., a thermophilic, autotrophic, sulfur-disproportionating deltaproteobacterium isolated from a hydrothermal pond
A thermophilic, anaerobic, chemolithoautotrophic bacterium (strain Sh68T) was isolated from a hydrothermal pond at Uzon Caldera, Kamchatka, Russia, using anoxic medium with elemental sulfur as the only energy source. Cells of strain Sh68T were Gram-stain-negative rods, 0.5–0.8 μm in diameter and 1.2–2.0 μm in length, motile by means of flagella. The temperature range for growth was 30–65 °C, with an optimum at 50–52 °C. The pH range for growth was 5.2–7.5, with optimum growth at pH 6.0–6.2. Growth of strain Sh68T was observed at NaCl concentrations ranging from 0 to 2.3 % (w/v). Strain Sh68T grew anaerobically with elemental sulfur as an energy source and bicarbonate/CO2 as a carbon source. Elemental sulfur was disproportionated to sulfide and sulfate. Growth was enhanced in the presence of poorly crystalline Fe(III) oxide (ferrihydrite) as a sulfide-scavenging agent. Strain Sh68T was also able to grow by disproportionation of thiosulfate and sulfite. Sulfate was not used as an electron acceptor either with H2 or with organic electron donors. Analysis of the 16S rRNA gene sequence revealed that the isolate belongs to the class Deltaproteobacteria and is related most closely to Dissulfuribacter thermophilus S69T (90.0 % similarity). On the basis of its physiological properties and results of phylogenetic analyses, strain Sh68T is considered to represent a novel species of a new genus, for which the name Dissulfurimicrobium hydrothermale gen. nov., sp. nov. is proposed. The type strain of Dissulfurimicrobium hydrothermale is Sh68T ( = JCM 19990T = VKM B-2854T). This is the first description of a sulfur-disproportionating thermophile from a terrestrial ecosystem.
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Ideonella paludis sp. nov., isolated from a marsh
More LessA bacterial strain, designated KBP-31T, was isolated from a water sample taken from the Banping Lake Wetland Park in Taiwan and characterized using a polyphasic taxonomic approach. Cells of strain KBP-31T were Gram-stain-negative, strictly aerobic, motile, light-yellow rods. Growth occurred at 10–37 °C (optimum 25 °C), at pH 6–8 (optimum pH 6) and with 0–1 % NaCl (w/v, optimum 0 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KBP-31T belonged to the genus Ideonella and was most closely related to Ideonella dechloratans ATCC 51718T with a sequence similarity of 98.2 %. Strain KBP-31T contained summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and C16 : 0 as the predominant fatty acids. The major hydroxyl fatty acid was C10 : 0 3-OH. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and two uncharacterized phospholipids. The DNA G+C content of the genomic DNA was 67.9 mol%. The DNA–DNA relatedness of strain KBP-31T with respect to recognized species of the genus Ideonella was less than 70 %. On the basis of the phylogenetic inference and phenotypic data, strain KBP-31T should be classified as a novel species, for which the name Ideonella paludis sp. nov. is proposed. The type strain is KBP-31T ( = BCRC 80524T = KCTC 32238T).
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Pseudorhodobacter psychrotolerans sp. nov., a psychrotolerant bacterium isolated from terrestrial soil, and emended description of the genus Pseudorhodobacter
More LessA Gram-stain-negative, facultatively aerobic, cream-coloured, ovoid-shaped, non-motile and psychrotolerant bacterial strain, PAMC 27389T, was isolated from terrestrial soil collected on King George Island, Antarctica. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain PAMC 27389T belongs to the genus Pseudorhodobacter, sharing highest similarities with the type strains of Pseudorhodobacter wandonensis (96.9 %), Pseudorhodobacter antarcticus (96.8 %), Pseudorhodobacter ferrugineus (96.5 %) and Pseudorhodobacter aquimaris (95.4 %). Average nucleotide identity values between strain PAMC 27389T and the type strains of P. wandonensis, P. antarcticus, P. ferrugineus and P. aquimaris were 70.8, 70.9, 71.0 and 70.5 %, respectively and the genome-to-genome distances were 18.4–19.1 %, indicating PAMC 27389T is clearly distinguished from the most closely related Pseudorhodobacter species. The genomic DNA G+C content was 60.1 mol%. Strain PAMC 27389T grew at 0–37 °C (optimally at 15–20 °C), at pH 5.5–9.0 (optimally at pH 6.5–7.0) and in the presence of 0.5–3.0 % (w/v) sea salt (optimally with 0.5 %). It lacked bacteriochlorophyll a. The major fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c) and C18 : 1ω7c 11-methyl. The major polar lipids were phosphatidylcholine, phosphatidylglycerol, an unidentified phospholipid, an unidentified aminolipid, an unidentified lipid and three unidentified aminophospholipids. The major respiratory quinone was Q-10. Based on the phenotypic, chemotaxonomic and genomic data presented, we propose the name Pseudorhodobacter psychrotolerans sp. nov. with the type strain PAMC 27389T ( = KCTC 42640T = JCM 30764T).
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Pontibacter ummariensis sp. nov., isolated from a hexachlorocyclohexane-contaminated soil
More LessA Gram-stain-negative, pinkish-red, rod-shaped bacterium designated strain NKM1T was isolated from soil samples contaminated with hexachlorocyclohexane isomers, collected from Ummari village, Lucknow, Uttar Pradesh, India. The strain was characterized by a polyphasic taxonomic approach. 16S rRNA gene sequence analysis showed that strain NKM1T clustered exclusively with members of the genus Pontibacter of the family Cytophagaceae, phylum Bacteroidetes. The 16S rRNA gene sequence similarity to type strains of the genus Pontibacter ranged from 96.7 to 93.8 %, with the highest sequence similarity found with Pontibacter odishensis JC130T (96.7 %). Cells of strain NKM1T were aerobic, non-flagellated and non-motile. Strain NKM1T was catalase- and oxidase-positive but negative for nitrate reduction and hydrolysis of gelatin. The major fatty acids in strain NKM1T were anteiso-C15 : 0, iso-C15 : 0, C16 : 0, C18 : 1ω9c and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The polar lipid profile of strain NKM1T showed the presence of phosphatidylethanolamine and unknown glycolipids as well as aminolipids. sym-Homospermidine was found to be the major polyamine and menaquinone 7 (MK-7) was the major respiratory quinone. The DNA G+C content of strain NKM1T was determined to be 58.6 mol%. Based on phenotypic, chemotaxonomic, physiological and biochemical evidence, it is proposed that isolate NKM1T represents a novel species that belongs to the genus Pontibacter, for which the name Pontibacter ummariensis sp. nov. is proposed. The type strain is NKM1T ( = DSM 100161T = KCTC 42944T = MCC 2777T).
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- Bacteroidetes
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Flavitalea soli sp. nov. isolated from soil
A Gram-stain-negative, rod-shaped, non-flagellated, mesophilic, yellow-pigmented, aerobic bacterium, designated strain KIS20-3T, was isolated from a soil sample of Baengnyeong Island in Onjin county, Republic of Korea. According to 16S rRNA gene sequence analysis, the isolate showed highest similarities with Flavitalea populi HY-50RT (94.5 %), Niastella populi THYL-44T (94.2 %) and Flavitalea gansuensis JCN-23T (93.7 %). The neighbour-joining tree based on 16S rRNA gene sequences showed that strain KIS20-3T formed a subcluster with members of the genus Flavitalea, and this subcluster was closely related to members of the genera Niastella, Segetibacter and Parasegetibacter within the family Chitinophagaceae. The major fatty acids of strain KIS20-3T were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G, and the predominant isoprenoid quinone was menaquinone 7. The polar lipid profile comprised large amounts of phosphatidylethanolamine and one unknown polar lipid, and moderate or small amounts of four unknown aminophospholipids, two unknown aminolipids, three unknown lipids and one unknown phospholipid. The G+C content of the DNA of strain KIS20-3T was 55.7 mol%. On the basis of the results of the polyphasic characterization presented in this study, it is concluded that strain KIS20-3T represents a novel species of the genus Flavitalea, for which the name Flavitalea soli sp. nov. is proposed. The type strain is KIS20-3T ( = KACC 17319T = JCM 19937T).
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Ichthyobacterium seriolicida gen. nov., sp. nov., a member of the phylum ‘Bacteroidetes’, isolated from yellowtail fish (Seriola quinqueradiata) affected by bacterial haemolytic jaundice, and proposal of a new family, Ichthyobacteriaceae fam. nov.
A novel Gram-stain-negative, rod-shaped (0.3 × 4–6 μm), non-flagellated, aerobic strain with gliding motility, designated JBKA-6T, was isolated in 1991 from a yellowtail fish, Seriola quinqueradiata, showing symptoms of bacterial haemolytic jaundice. 16S rRNA gene sequence analysis showed that strain JBKA-6T was related most closely to members of the family Flavobacteriaceae in the phylum ‘Bacteroidetes’. Furthermore, based on gyrB gene sequence analysis, JBKA-6T was classified into a single clade within the order Flavobacteriales, which was distinct from the known clades of the families Flavobacteriaceae, Blattabacteriaceae and Cryomorphaceae. The predominant isoprenoid quinone was identified as MK-6 (97.9 %), and the major cellular fatty acids (>10 %) were C14 : 0 and iso-C15 : 0. The main polar lipids were phosphatidylethanolamine, three unidentified phospholipids, two unidentified aminophospholipids and two unidentified polar lipids. The DNA G+C content of JBKA-6T, as derived from its whole genome, was 33.4 mol%. The distinct phylogenetic position and phenotypic traits of strain JBKA-6T distinguish it from all other described species of the phylum ‘Bacteroidetes’, and therefore it was concluded that strain JBKA-6T represents a new member of the phylum ‘Bacteroidetes’, and the name Ichthyobacterium seriolicida gen. nov., sp. nov. is proposed. The type strain of Ichthyobacterium seriolicida is JBKA-6T ( = ATCC BAA-2465T = JCM 18228T). We also propose that Icthyobacterium gen. nov. is the type genus of a novel family, Ichthyobacteriaceae fam. nov.
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Lacinutrix gracilariae sp. nov., isolated from the surface of a marine red alga Gracilaria sp.
More LessA Gram-stain-negative, aerobic, non-flagellated, rod-shaped bacterium, designated strain Lxc1T, was isolated from the surface of a marine red alga, Gracilaria sp., which was collected from the coastal regions in Jinjiang, Fujian Province, China. Colonies of the strain were orange–yellow, circular and smooth. The 16S rRNA gene of strain Lxc1T had maximum sequence similarity with Lacinutrix himadriensis E4-9aT (97.1 %), followed by Lacinutrix jangbogonensis PAMC 27137T, Lacinutrix copepodicola DJ3T, Lacinutrix algicola AKS293T and Lacinutrix mariniflava AKS 432T (similarities < 96.4 %). Phylogenetic analysis showed strain Lxc1T formed a tight cluster with L. himadriensis E4-9aT and L. copepodicola DJ3T, but represented a novel lineage belonging to the genus Lacinutrix. The predominant fatty acids were iso-C15 : 1 G (18.3 %), iso-C15 : 0 (16.7 %), iso-C17 : 0 3-OH (10.6 %) and iso-C15 : 0 3-OH (8.6 %). Menaquinone-6 (MK-6) was the only respiratory quinone present. The DNA G+C content of strain Lxc1T was 31.7 mol%. Combining the results above, it was ascertained that strain Lxc1T represented a novel species of the genus Lacinutrix, for which the name Lacinutrix gracilariae sp. nov. is proposed. The type strain is Lxc1T ( = MCCC 1A01567T = KCTC 42808T).
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Chryseobacterium frigidum sp. nov., isolated from high-Arctic tundra soil, and emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense
A yellow, Gram-reaction-negative, non-motile, aerobic bacterium, designated D07T, was isolated from a tundra soil near Ny-Ålesund, Svalbard archipelago, Norway (78° N). Growth occurred at 4–37 °C (optimum 28–30 °C) and at pH 6.0–9.0 (optimum pH 7.0–8.0). The strain produced flexirubin-type pigments. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D07T belonged to the genus Chryseobacterium in the family Flavobacteriaceae. The 16S rRNA gene sequence of this strain showed 93.83 and 93.31 % sequence similarity, respectively, to those of Chryseobacterium contaminans C26T and Chryseobacterium taklimakanense X-65T. Strain D07T contained anteiso-C15 : 0 (25.91 %), iso-C15 : 0 (16.05 %), iso-C16 : 0 3-OH (9.64 %), iso-C16 : 0 (9.42 %) and iso-C14 : 0 (7.36 %) as the predominant cellular fatty acids, MK-6 as the major respiratory quinone and phosphatidylethanolamine, five unknown aminolipids and three unknown lipids as the main polar lipids. The DNA G+C content was 49.3 mol%. On the basis of phenotypic, chemotaxonomic and phylogenetic data, strain D07T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium frigidum sp. nov. is proposed. The type strain is D07T ( = CCTCC AB 2011160T = KCTC 42897T). Emended descriptions of Chryseobacterium bernardetii and Chryseobacterium taklimakanense are also provided.
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Paenibacillus radicis sp. nov., an endophytic bacterium isolated from maize root
More LessA novel Gram-stain-positive, aerobic, endospore-forming, and rod-shaped strain designated 694T was isolated from surface-sterilized root tissue of a maize planted in the Fangshan District of Beijing, People's Republic of China. A polyphasic taxonomic study was performed on the new isolate. On the basis of 16S rRNA gene sequence similarity studies, this isolate belongs to the genus Paenibacillus. High levels of 16S rRNA gene sequence similarity were found between strain 694T and Paenibacillus xinjiangensis DSM 30034T (98.5 %) and Paenibacillus glycanilyticus (98.1 %), respectively. However, the DNA–DNA hybridization values between strain 694T and its close relatives P. xinjiangensis 16970T and Paenibacillus algorifonticola CGMCC 1.10223T were 30.0 % and 36.7 % respectively. The DNA G+C content of strain 694T was determined to be 46.9 mol%. The predominant respiratory quinone was identified as menaquinone-7 and the polar lipid profile was found to be composed of the major lipids diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were found to be anteiso-C15 : 0 (42.1 %), iso-C15 : 0 (18.4 %), iso-C16 : 0 (11.2 %) and C16 : 0 (12.1 %). The results of physiological and biochemical tests and minor differences in the fatty acid profiles allowed a clear phenotypic differentiation of strain 694T from the closely related species in the genus Paenibacillus. Strain 694T is concluded to represent a novel species within the genus Paenibacillus, for which the name Paenibacillus radicis sp. nov. is proposed, with the type strain 694T ( = CGMCC 1.15286T = DSM 100762T).
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Hymenobacter monticola sp. nov., isolated from mountain soil
More LessA Gram-reaction-negative, aerobic, non-motile, red-pigmented and rod-shaped bacterium, designated XF-6RT, was isolated from mountain soil in the Sichuan province of China. Phylogenetic trees based on 16S rRNA gene sequence analysis showed that XF-6RT belonged to the genus Hymenobacter. The greatest 16S rRNA gene sequence similarities of strain XF-6RT were with Hymenobacter soli PB17T (96.4 %) and Hymenobacter saemangeumensis GSR0100T (95.8 %). Summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0, C16 : 1ω5c and anteiso-C15 : 0 were the major fatty acids (>10 %). The only menaquinone was menaquinone-7. The major polar lipids were phosphatidylethanolamine, four aminolipids, four phosphoaminolipids and three lipids. The DNA G+C content was 62 mol%. On the basis of the polyphasic taxonomic analysis, strain XF-6RT is considered to represent a novel species of the genus Hymenobacter, for which the name Hymenobacter monticola sp. nov. is proposed. The type strain is XF-6RT ( = KCTC 42733T = CCTCC AB 2015206T).
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Confluentibacter lentus gen. nov., sp. nov., isolated from the junction between the ocean and a freshwater lake
More LessA Gram-stain-negative, non-flagellated, non-gliding, aerobic and rod-shaped bacterium, designated HJM-3T, was isolated from the place where the ocean and a freshwater lake meet at Hwajinpo on the East Sea, South Korea, and subjected to a polyphasic taxonomic study. The novel strain grew optimally at 30–35 °C, at pH 7.0–7.5 and in the presence of 1.0–2.0 % (w/v) NaCl. A neighbour-joining phylogenetic tree based on 16S rRNA gene sequences showed that strain HJM-3T clustered with the type strain of Yeosuana aromativorans and the proposed type strain of Mariniflexile ostreae. Strain HJM-3T exhibited the highest 16S rRNA gene sequence similarity values (each 95.1 %) to these representative strains of Y. aromativorans and M. ostreae, and sequence similarities of less than 94.9 % to the type strains of other recognized species. Strain HJM-3T contained menaquinone-6 as the predominant isoprenoid quinone, and iso-C15 : 0, iso-C15 : 1 G and iso-C17 : 0 3-OH as the major fatty acids. The major polar lipids detected in strain HJM-3T were phosphatidylethanolamine and one unidentified lipid. The DNA G+C content of strain HJM-3T was 34.7 mol%. The fatty acid and polar lipid profiles and DNA G+C content of strain HJM-3T could be distinguished from those of the phylogenetically related taxa. On the basis of the phylogenetic, chemotaxonomic and other phenotypic properties, strain HJM-3T is considered to represent a novel genus and species within the family Flavobacteriaceae, for which the name Confluentibacter lentus gen. nov., sp. nov., is proposed. The type strain is HJM-3T ( = KCTC 42777T = NBRC 111588T).
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Salinicola rhizosphaerae sp. nov., isolated from the rhizosphere of the mangrove Avicennia marina L.
More LessA Gram-stain-negative, motile, rod-shaped bacterium, designated MSSRFH1T, was isolated from the rhizosphere of the mangrove, Avicennia marina, in Pichavaram, Tamil Nadu, India. Phylogenetic analysis, based on the 16S rRNA gene sequence of MSSRFH1T, indicated that it clustered in the genus Salinicola and was most closely related to Salinicola peritrichatus JCM18795T (96.7 % similarity). The 16S rRNA gene sequence similarity was < 96.5 % with other strains of species of the genus Salinicola. The distinctiveness of strain MSSRFH1T was also shown by low similarities of its rpoD ( < 87 % similarity) and gyrB ( < 85 %) gene sequences with those of other members of the genus Salinicola. Strain MSSRFH1T could tolerate NaCl concentrations of up to 30 % (w/v). The main fatty acids of MSSRFH1T included C18 : 1ω7c, C16 : 0 and C19 : 0ω8c. The polar lipids present included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, an unidentified amino lipid and unidentified phospholipids. Comparison of BOX-PCR fingerprints indicated that MSSRFH1T showed a unique DNA profile and its genomic G+C content was 64 mol%. On the basis of the data presented, strain MSSRFH1T represents a novel species of the genus Salinicola, for which the name Salinicola rhizosphaerae sp. nov. is proposed. The type strain is MSSRFH1T ( = KCTC 32998T = NBRC 110222T).
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Mongoliibacter ruber gen. nov., sp. nov., a haloalkalitolerant bacterium of the family Cyclobacteriaceae isolated from a haloalkaline lake
A novel haloalkalitolerant, rod-shaped bacterium, designated strain YIM 4-4T, was isolated from the surface water of the Dugerno lake, a haloalkaline lake in Inner Mongolia. The taxonomy of strain YIM 4-4T was investigated by a polyphasic approach. Strain YIM 4-4T was Gram-stain-negative, strictly aerobic, non-motile and formed red colonies. Optimal growth conditions were 28 °C, pH 8.0–11.0 and 0.5–2 % NaCl. The major respiratory quinone was menaquinone-7 (MK-7). The polar lipid profile was composed predominantly of phosphatidylethanolamine, six unidentified polar lipids, one phospholipid and one aminolipid. The predominant cellular fatty acids (>5 %) were iso-C15 : 0, iso-C17 : 1I/anteiso-C17 : 1B, iso-C16 : 1G, iso-C17 : 0 3-OH, C16 : 1ω7c/C16 : 1ω6c and iso-C16 : 1. The genomic DNA G+C content was 43.0 mol%. 16S rRNA gene sequence analysis indicated that the members of the genera Cecembia, Fontibacter, Aquiflexum and Indibacter of the family Cyclobacteriaceae (phylum Bacteroidetes) were the most closely related, with 16S rRNA gene sequence similarities ranging from 93.6 to 94.2 %. Other members of the family Cyclobacteriaceae showed sequence similarities < 93.0 %. On the basis of phenotypic, chemotaxonomic and phylogenetic properties, strain YIM 4-4T represents a novel species of a new genus, for which the name Mongoliibacter ruber gen. nov., sp. nov. is proposed. The type strain is YIM 4-4T ( = CCTCC AB 2012966T = DSM 27929T).
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Fabivirga thermotolerans gen. nov., sp. nov., a novel marine bacterium isolated from culture broth of a marine cyanobacterium
More LessA Gram-stain-negative, red, non-spore-forming, strictly aerobic bacterium, designated strain A4T, was isolated from culture broth of a marine cyanobacterium. Cells were flexible rods with gliding motility. Phylogenetic analysis, based on 16S rRNA gene sequences, revealed that strain A4T formed a coherent cluster with members of the genera Roseivirga and Fabibacter, and represents a distinct lineage in the family Flammeovirgaceae. Thermotolerance and a distinctive cellular fatty acid profile could readily distinguish this isolate from any bacteria of the genera Roseivirga and Fabibacter with a validly published name. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, strain A4T is suggested to represent a novel species in a novel genus, for which the name Fabivirga thermotolerans gen. nov., sp. nov. is proposed. The type strain is A4T ( = KCTC 42507T = CGMCC 1.15111T).
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- Other bacteria
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Thermostilla marina gen. nov., sp. nov., a thermophilic, facultatively anaerobic planctomycete isolated from a shallow submarine hydrothermal vent
A novel thermophilic planctomycete (strain SVX8T) was isolated from a shallow submarine hydrothermal vent, Vulcano Island, Italy. The temperature range for growth was 30–68 °C, with an optimum at 55 °C. The pH range for growth was 5.0–9.0, with an optimum at pH 7.0–8.0. Growth was observed at NaCl concentrations ranging from 0.8 to 4.5 % (w/v) with an optimum at 2.5–3.5 % (w/v). The isolate grew anaerobically using a number of mono-, di- and polysaccharides as electron donors and nitrate or elemental sulfur as electron acceptors or by fermentation. Nitrate was reduced to nitrite; sulfur was reduced to sulfide. Strain SVX8T did not grow at atmospheric concentration of oxygen but grew microaerobically (up to 2 % oxygen in the gas phase). The G+C content of the DNA of strain SVX8T was 58.5 mol%. Based on phylogenetic position and phenotypic features, the new isolate is considered to represent a novel species belonging to a new genus in the order Planctomycetales, for which the name Thermostilla marina gen. nov., sp. nov. is proposed. The type strain of Thermostilla marina is SVX8T ( = JCM 19992T = VKM B-2881T). Strain SVX8T is the first thermophilic planctomycete isolated from a marine environment.
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Phyllonema aviceniicola gen. nov., sp. nov. and Foliisarcina bertiogensis gen. nov., sp. nov., epiphyllic cyanobacteria associated with Avicennia schaueriana leaves
Cyanobacteria dwelling on the salt-excreting leaves of the mangrove tree Avicennia schaueriana were isolated and characterized by ecological, morphological and genetic approaches. Leaves were collected in a mangrove with a history of oil contamination on the coastline of São Paulo state, Brazil, and isolation was achieved by smearing leaves on the surface of solid media or by submerging leaves in liquid media. Twenty-nine isolated strains were shown to belong to five cyanobacterial orders (thirteen to Synechococcales, seven to Nostocales, seven to Pleurocapsales, one to Chroococcales, and one to Oscillatoriales) according to morphological and 16S rRNA gene sequence evaluations. More detailed investigations pointed six Rivulariacean and four Xenococcacean strains as novel taxa. These strains were classified as Phyllonema gen. nov. (type species Phyllonema aviceniicola sp. nov. with type strain CENA341T) and Foliisarcina gen. nov. (type species Foliisarcina bertiogensis sp. nov. with type strain CENA333T), according to the International Code of Nomenclature for Algae, Fungi, and Plants. This investigation shows some of the unique cyanobacteria inhabiting the phyllosphere of Avicennia schaueriana can be retrieved by culturing techniques, improving current taxonomy and providing new insights into the evolution, ecology, and biogeography of this phylum.
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Paludisphaera borealis gen. nov., sp. nov., a hydrolytic planctomycete from northern wetlands, and proposal of Isosphaeraceae fam. nov.
Two isolates of aerobic, budding, pink-pigmented bacteria, designated strains PX4T and PT1, were isolated from a boreal Sphagnum peat bog and a forested tundra wetland. Cells of these strains were non-motile spheres that occurred singly or in short chains. Novel isolates were capable of growth at pH values between 3.5 and 6.5 (optimum at pH 5.0–5.5) and at temperatures between 6 and 30 °C (optimum at 15–25 °C). Most sugars and a number of polysaccharides including pectin, xylan, lichenin and Phytagel were used as growth substrates. The major fatty acids were C16 : 0, C18 : 1ω9 and C18 : 0; the major polar lipids were phosphocholine and trimethylornithine. The quinone was menaquinone-6, and the G+C content of the DNA was 66 mol%. Strains PX4T and PT1 were members of the order Planctomycetales and displayed 93–94 % 16S rRNA gene sequence similarity to Aquisphaera giovannonii, 91–92 % to species of the genus Singulisphaera and 90–91 % to Isosphaera pallida. The two novel strains, however, differed from members of these genera by cell morphology, substrate utilization pattern and a number of physiological characteristics. Based on these data, the novel isolates should be considered as representing a novel genus and species of planctomycetes, for which the name Paludisphaera borealis gen. nov., sp. nov., is proposed. The type strain is PX4T ( = DSM 28747T = VKM B-2904T). We also suggest the establishment of a novel family, Isosphaeraceae fam. nov., to accommodate stalk-free planctomycetes with spherical cells, which can be assembled in short chains, long filaments or shapeless aggregates. This family includes the genera Isosphaera, Aquisphaera, Singulisphaera and Paludisphaera.
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Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi
A novel obligately anaerobic bacterium, designated strain TC1T, was isolated from methanogenic granular sludge in a full-scale mesophilic upflow anaerobic sludge blanket reactor treating high-strength starch-based wastewater. Cells had a multicellular filamentous morphology, stained Gram-negative and were non-motile. The filaments were flexible, generally >100 μm long and 0.3–0.4 μm wide. Growth of the isolate was observed at 25–43 °C (optimum 37 °C) and pH 6.0–8.5 (optimum pH 7.0). Strain TC1T grew chemo-organotrophically on a range of carbohydrates under anaerobic conditions. Yeast extract was required for growth. The major fermentative end products of glucose, supplemented with yeast extract, were acetate, lactate, succinate, propionate, formate and hydrogen. Co-cultivation with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864T enhanced growth of the isolate. The DNA G+C content was determined experimentally to be 42.1 mol%. The major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and iso-C17 : 0 3-OH. Based on 16S rRNA gene sequence analysis, strain TC1T belonged to the class Anaerolineae in the phylum Chloroflexi, in which Ornatilinea apprima P3M-1T was its closest phylogenetic relative (88.3 % nucleotide identity). Phylogenomic analyses using 38 and 83 single-copy marker genes also supported the novelty of strain TC1T at least at the genus level. Based on phylogenetic, genomic and phenotypic characteristics, we propose that strain TC1T represents a novel species of a new genus, for which we suggest the name Flexilinea flocculi gen. nov., sp. nov. The type strain of Flexilinea flocculi is strain TC1T ( = JCM 30897T = CGMCC 1.5202T).
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Deinococcus actinosclerus sp. nov., a novel bacterium isolated from soil of a rocky hillside
Three Gram-stain-positive, catalase- and oxidase-positive coccus- or rod-shaped bacterial strains, designated BM2T, BM4 and BM5, were isolated from soil in South Korea. They showed strong resistance to gamma radiation with a D 10 value of 9 kGy but weak UVC resistance. The 16S rRNA sequences of strains BM2T, BM4 and BM5 represent a novel subline within the genus Deinococcus in the family Deinococcaceae. The 16S rRNA gene sequences of strains BM2T, BM4 and BM5 were indistinguishable and showed 98.1–87.3 % similarity with other species of the genus Deinococcus. Strain BM2T exhibited relatively high levels of DNA–DNA hybridization with BM4 (87 ± 0.8 %) and BM5 (92 ± 1.2 %). Meanwhile, it showed a low level of DNA–DNA hybridization ( < 30 %) with other closely related species of the genus Deinococcus. The strains showed the typical chemotaxonomic characteristics of the genus Deinococcus, with the presence of menaquinone 8 as the respiratory quinone; the major fatty acids were summed feature 3 (composed of C16 : 1ω7c/C16 : 1ω6c), C15 : 1ω6c and C16 : 0. The DNA G+C content of strain BM2T was 69.7 mol%. The polar lipid profile included major amounts of phosphatidylglycerol, phosphatidylcholine and an unknown aminolipid. On the basis of phenotypic and genotypic properties, and phylogenetic distinctiveness, strains BM2T, BM4 and BM5 should be classified in a novel species in the genus Deinococcus, for which the name Deinococcus actinosclerus sp. nov. is proposed. The type strain is BM2T ( = KEMB 5401-184T = JCM 30700T); reference strains are BM4 ( = JCM 30701) and BM5 ( = JCM 30702).
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Athalassotoga saccharophila gen. nov., sp. nov., isolated from an acidic terrestrial hot spring, and proposal of Mesoaciditogales ord. nov. and Mesoaciditogaceae fam. nov. in the phylum Thermotogae
A novel moderately thermophilic, weakly acidophilic, heterotrophic, anaerobic, short-rod bacterium having an outer sheath-like structure (toga) was isolated from a low-salt acidic terrestrial hot spring in Oku-Shiobara, Tochigi, Japan. The strain, designated NAS-01T, grew between 30 and 60 °C (optimum 55 °C), and at pH 4.5 and 7.5 (optimum pH 5.5 to 6.0) and could not grow in media with ≥ 1 % NaCl (optimum 0 % NaCl). It utilized Fe(III), thiosulfate or l-cystine as electron acceptor for growth, and yeast extract, peptone or a variety of sugars as carbon and energy sources. The major cellular fatty acid was C16 : 0, and no lipoquinone was detected. Strain NAS-01T contained phospholipids and glycolipids, but not aminolipids. The DNA G+C content was 41.1 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain was included in the phylum Thermotogae, and was closely related to Mesoaciditoga lauensis. The 16S rRNA gene sequence similarity between them was 90 %, and they were deeply branched off the rest of the known Thermotogae species. On the basis of the phylogenetic and ecophysiological properties, strain NAS-01T represents a novel species of a new genus in the phylum Thermotogae, for which we propose the name Athalassotoga saccharophila gen. nov., sp. nov. The type strain of the type species is NAS-01T ( = JCM 19762T = DSM 28954T). In addition, we propose a new order and family, Mesoaciditogales ord. nov. and Mesoaciditogaceae fam. nov., respectively, to accommodate the novel genus and the closely related genus Mesoaciditoga.
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- Eukaryotic micro-organisms
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Spencermartinsiella silvicola sp. nov., a yeast species isolated from rotting wood
More LessThree strains of a new xylanase-producing yeast species were isolated from rotting wood samples collected in the Atlantic Rain Forest of Brazil. The sequences of the internal transcribed spacer region and D1/D2 domains of the large subunit of the rRNA gene showed that this novel yeast species belongs to the genus Spencermartinsiella, and its closest relatives among recognized species are Spencermartinsiella europaea and Spencermartinsiella ligniputridi. A novel species, named Spencermartinsiella silvicola sp. nov., is proposed to accommodate these isolates. The type strain is UFMG-CM-Y274T ( = CBS 13490T). The MycoBank number is MB 813053. In addition, Candida cellulosicola is reassigned to the genus Spencermartinsiella as a new combination.
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Jaminaea phylloscopi sp. nov. (Microstromatales), a basidiomycetous yeast isolated from migratory birds in the Mediterranean basin
During a survey of yeasts vectored by migratory birds in the Mediterranean basin, isolations from the cloacae of members of the order Passeriformes collected in Ustica (Italy) were performed. Based on phylogenetic analysis of the D1/D2 domain of the 26S rRNA gene and the internal transcribed spacer ITS1-5.8S rRNA gene-ITS2 region, five yeast isolates clustered in a new lineage within the Microstromatales clade. The DNA sequences of these isolates differed from those of their closest relatives, Jaminaea angkorensis and Jaminaea lanaiensis, by 20 and 25 nt substitutions in the D1/D2 domain and 119 and 131 nt substitutions in the complete ITS region, respectively. In addition, the five isolates showed phenotypic characteristics not observed in their closest relatives, such as the ability to grow at 44 °C and at pH 2.5, which suggests a possible adaptation to the bird gastrointestinal tract. On the basis of the isolation source, phenotypic features and molecular strain typing carried out with randomly amplified polymorphic DNA (RAPD)-PCR and mini-satellite-primed (MSP)-PCR analysis, the five isolates were characterized as five distinct strains of a novel species formally described as Jaminaea phylloscopi sp. nov., with 551B6T ( = PYCC 6783T = CBS 14087T) as the type strain. The Mycobank accession number is MB811984.
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A unique species in Phytophthora clade 10, Phytophthora intercalaris sp. nov., recovered from stream and irrigation water in the eastern USA
More LessA novel species of the genus Phytophthora was recovered during surveys of stream and nursery irrigation water in Maryland, Massachusetts, North Carolina, Virginia and West Virginia in the USA. The novel species is heterothallic, and all examined isolates were A1 mating type. It produced rare ornamented oogonia and amphigynous antheridia when paired with A2 mating type testers of Phytophthora cinnamomi and Phytophthora cryptogea. Sporangia of this novel species were non-papillate and non-caducous. Thin-walled intercalary chlamydospores were abundant in hemp seed agar and carrot agar, while they were produced only rarely in aged cultures grown in clarified V8 juice agar. Phylogenetic analyses based on sequences of the internal transcribed spacer region and the β-tubulin and mitochondrial cytochrome-c oxidase 1 (cox1) genes indicated that the novel species is phylogenetically close to Phytophthora gallica in Phytophthora clade 10. The novel species has morphological and molecular features that are distinct from those of other species in Phytophthora clade 10. It is formally described here as Phytophthora intercalaris sp. nov. Description of this unique clade-10 species is important for understanding the phylogeny and evolution of Phytophthora clade 10.
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Cystofilobasidium intermedium sp. nov. and Cystofilobasidium alribaticum f.a. sp. nov., isolated from Mediterranean forest soils
Multiple isolates belonging to the basidiomycetous genus Cystofilobasidium were obtained from forest soils in Serra da Arrábida Natural Park in Portugal. Phylogenetic analyses employing concatenated sequences of the D1/D2 domain and ITS region support the recognition of two novel species: Cystofilobasidium alribaticum f.a., sp. nov. (type strain CBS 14164T = PYCC 6956T = DSM 101473T) and Cystofilobasidium intermedium sp. nov. (type strain CBS 14089T = PYCC 6856T = DSM 101474T). Whereas C. alribaticum f. a. sp. nov. does not form hyphae, even when different strains are crossed, C. intermedium sp. nov. is self-fertile and forms mycelium with teliospores that upon germination give rise to slender basidia. The most remarkable physiological trait of the two novel species is their ability to grow at 35 °C, a property not observed for remaining species of the genus.
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- EVOLUTION, PHYLOGENY AND BIODIVERSITY
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OrthoANI: An improved algorithm and software for calculating average nucleotide identity
More LessSpecies demarcation in Bacteria and Archaea is mainly based on overall genome relatedness, which serves a framework for modern microbiology. Current practice for obtaining these measures between two strains is shifting from experimentally determined similarity obtained by DNA–DNA hybridization (DDH) to genome-sequence-based similarity. Average nucleotide identity (ANI) is a simple algorithm that mimics DDH. Like DDH, ANI values between two genome sequences may be different from each other when reciprocal calculations are compared. We compared 63 690 pairs of genome sequences and found that the differences in reciprocal ANI values are significantly high, exceeding 1 % in some cases. To resolve this problem of not being symmetrical, a new algorithm, named OrthoANI, was developed to accommodate the concept of orthology for which both genome sequences were fragmented and only orthologous fragment pairs taken into consideration for calculating nucleotide identities. OrthoANI is highly correlated with ANI (using BLASTn) and the former showed approximately 0.1 % higher values than the latter. In conclusion, OrthoANI provides a more robust and faster means of calculating average nucleotide identity for taxonomic purposes. The standalone software tools are freely available at http://www.ezbiocloud.net/sw/oat.
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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)