- Volume 68, Issue 10, 2018
Volume 68, Issue 10, 2018
- Notification List
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- New Taxa
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- Actinobacteria
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Streptomyces caeni sp. nov., isolated from mangrove mud
More LessA novel aerobic actinomycete, designated as HA15955T, was isolated from a mangrove mud sample collected in Sanya, China. Scanning electron microscopy revealed that HA15955T produced straight to spiral spore chains with smooth cylindrical spores. 16S rRNA gene sequence similarity showed that strain HA15955T belonged to the genus Streptomyces , was most closely related to Streptomyces speibonae NRRL B-24240T (98.7 % similarity) and formed a distinct subclade. The low relatedness value of DNA–DNA hybridization showed that it formed a distinct genomic species. Based on phenotypic, genotypic and phylogenetic data, strain HA15955T should be classified as a novel species of the genus Streptomyces , for which the name Streptomyces caeni sp. nov. is proposed. The type strain is HA15955T (=CGMCC 4.7426T=DSM 105693T).
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Nonomuraea mangrovi sp. nov., an actinomycete isolated from mangrove soil
More LessA novel aerobic actinomycete, designated HA15826T, was isolated from a mangrove soil sample collected in Sanya, China. Scanning electron microscopy revealed that the isolate produced straight to slightly flexural spore chains with rough cylindrical spores. Chemotaxonomic tests showed that the cell wall contained meso-diaminopimelic acid and the major fatty acids were iso-C16 : 0, 10-methyl-C17 : 0, C17 : 1ω8c and C16 : 0. 16S rRNA gene sequence similarity analysis showed that strain HA15826T belonged to the genus Nonomuraea , being most closely related to Nonomuraea dietziae DSM 44320T (98.7 %), Nonomuraea candida HMC10T (98.4 %), Nonomuraea africana IFO 14745T (98.4 %), Nonomuraea roseola IFO 14685T (98.2 %) and Nonomuraea recticatena IFO 14525T (98.1 %). The DNA G+C content of the type strain is 73.2 %. DNA–DNA relatedness and comparative analyses of physiological, biochemical and chemotaxonomic data allowed genotypic and phenotypic differentiation of strain HA15826T from the closely related species. Thus, strain HA15826T should be classified as a novel species of the genus Nonomuraea , for which the name Nonomuraea mangrovi sp. nov. is proposed. The type strain is HA15826T (=CGMCC 4.7425T=DSM 105694T).
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Streptacidiphilus pinicola sp. nov., isolated from pine grove soil
A moderately acidophilic actinobacterial strain, designated MMS16-CNU450T, was isolated from pine grove soil, and its taxonomic position was analysed using a polyphasic approach. The isolate showed best growth at 30 °C, pH 6 and 0.5 % (w/v) NaCl. On the basis of 16S rRNA gene sequence similarity, the isolate was assigned to the genus Streptacidiphilus , and the closest species were Streptacidiphilus rugosus AM-16T (sequence similarity, 98.61 %), Streptacidiphilus melanogenes NBRC 103184T (98.53 %), Streptacidiphilus jiangxiensis NBRC 100920T (98.19 %) and Streptacidiphilus anmyonensis NBRC 103185T (98.05 %). The isolate formed a distinct cluster of its own within the Streptacidiphilus clade in the phylogenetic tree. Based on whole-genome comparison between the strain MMS16-CNU450T and the type strains of related species, the orthologous average nucleotide identity and in silico DNA–DNA hybridization values were in the range of 77.9–87.0 and 22.3–32.7 %, respectively. The DNA G+C content of the isolate was 68.6 mol%. The phylogenetic, phenotypic, chemotaxonomic and genomic data supported the affiliation of the strain to Streptacidiphilus , and the name Streptacidiphilus pinicola sp. nov. (type strain, MMS16-CNU450T=KCTC 49008T=JCM 32300T) is proposed accordingly.
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Acidipropionibacterium virtanenii sp. nov., isolated from malted barley
A Gram-stain-positive, catalase-positive and pleomorphic rod organism was isolated from malted barley in Finland, classified initially by partial 16S rRNA gene sequencing and originally deposited in the VTT Culture Collection as a strain of Propionibacterium acidipropionici (currently Acidipropionibacterium acidipropionici ). The subsequent comparison of the whole 16S rRNA gene with other representatives of the genus Acidipropionibacterium revealed that the strain belongs to a novel species, most closely related to Acidipropionibacterium microaerophilum and Acidipropionibacterium acidipropionici , with similarity values of 98.46 and 98.31 %, respectively. The whole genome sequencing using PacBio RS II platform allowed further comparison of the genome with all of the other DNA sequences available for the type strains of the Acidipropionibacterium species. Those comparisons revealed the highest similarity of strain JS278T to A. acidipropionici , which was confirmed by the average nucleotide identity analysis. The genome of strain JS278T is intermediate in size compared to the A. acidipropionici and Acidipropionibacterium jensenii at 3 432 872 bp, the G+C content is 68.4 mol%. The strain fermented a wide range of carbon sources, and produced propionic acid as the major fermentation product. Besides its poor ability to grow at 37 °C and positive catalase reaction, the observed phenotype was almost indistinguishable from those of A. acidipropionici and A. jensenii . Based on our findings, we conclude that the organism represents a novel member of the genus Acidipropionibacterium , for which we propose the name Acidipropionibacterium virtanenii sp. nov. The type strain is JS278T (=VTT E-113202T=DSM 106790T).
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Aestuariimicrobium soli sp. nov., isolated from farmland soil, and emended description of the genus Aestuariimicrobium
More LessA Gram-reaction-positive, catalase-positive, non-spore-forming and short rod- or oval-shaped bacterial strain, designated D6T, was isolated from farmland soil in Xuancheng, Anhui Province, China. Growth occurred at 4–37 °C (optimum, 30 °C), at pH 6.5–8.5 (optimum, 7.0) and with 0–7 % (w/v) NaCl (optimum, 0.5 % NaCl). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain D6T was most closely related to Aestuariimicrobium kwangyangense DSM 21549T (98.47 %), followed by Tessaracoccus rhinocerotis YIM 101269T (94.46 %). Strain D6T had a cell-wall peptidoglycan based on ll-diaminopimelic acid. MK-9(H4) was the predominant menaquinone. The major fatty acids of strain D6T were anteiso-C15 : 0, iso-C15 : 0 and summed feature 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The major polar lipids were a lipid, glycolipid and phospholipid. The DNA G+C content was 69.2 mol% and strain D6T showed low DNA–DNA relatedness to A. kwangyangense DSM 21549T (36.45±0.42 %). Based on these genotypic and phenotypic data, strain D6T represents a novel species in the genus Aestuariimicrobium , for which the name Aestuariimicrobium soli sp. nov. is proposed. The type strain is D6T (=KCTC 39995T=DSM 105824T). An emended description of the genus Aestuariimicrobium is presented.
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Streptomyces dengpaensis sp. nov., an actinomycete isolated from desert soil
Yamei Li, Yumei Li, Long wei Wang and Jie BaoA novel actinomycete, designated strain XZHG99T, was isolated from soil taken from colour desert, Dengpa District, Tibet Autonomous Region, China. Its taxonomic position was determined by a polyphasic approach. The strain showed morphological and chemotaxonomic features typical of the genus Streptomyces : branched substrate and aerial mycelia, straight spore chains and smooth spores; ll-diaminopimelic acid in the cell-wall peptidoglycan; MK-9(H8), MK-9(H2), MK-9(H6) and MK-9(H10) as menaquinones; diphosphatidylglycerol, phospatidylethanolamine, phosphatidylinositol, phosphotidylinositol mannoside and phosphatidylglycerol as prominent phospholipids; iso-C16 : 0, anteiso-C15 : 0 and C16 : 0 as major cellular fatty acids; and DNA G+C content of 69.9 mol%. 16S rRNA gene sequence analysis indicated that strain XZHG99T showed high similarity to Streptomyces albiflavescens m20T (98.42 %) and Streptomyces krungchingensis KC-035T (98.14 %) as well as formed a monophyletic clade with them in the phylogenetic tree. Based on comparison of phenotypic properties and the low level of DNA–DNA relatedness, strain XZHG99T can be distinguished from phylogenetically related Streptomyces species and is suggested to represent a novel species of the genus Streptomyces , for which the name Streptomyces dengpaensis sp. nov. is proposed. The type strain is XZHG99T (=CGMCC 4.7472T=KCTC 49090T).
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Streptomyces triticisoli sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.)
A novel actinomycete, designated strain NEAU-DSCPA1-4-4T, was isolated from rhizosphere soil of wheat and characterized using a polyphasic approach. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the organism should be assigned to the genus Streptomyces . The strain formed a monophyletic clade with its closest relatives, Streptomyces ghanaensis DSM 40746T (97.7 % 16S rRNA gene sequence similarity) and Streptomyces viridosporus DSM 40243T (97.6 %). Similarly, chemotaxonomic data, including major menaquinones, fatty acid compositions and polar lipid profile, also supported the placement of strain NEAU-DSCPA1-4-4T in the genus Streptomyces . However, DNA–DNA relatedness, physiological and biochemical data showed that strain NEAU-DSCPA1-4-4T could be distinguished from its closest relatives. Therefore, we propose that strain NEAU-DSCPA1-4-4T represents a novel species of the genus Streptomyces , for which the name Streptomyces triticisoli sp. nov. is proposed, with NEAU-DSCPA1-4-4T (=CCTCC AA 2017025T=DSM 105118T) as the type strain.
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Streptomyces venetus sp. nov., an actinomycete with a blue aerial mycelium
More LessA Gram-positive bacterium, designated CMU-AB225T, was isolated from rhizosphere soil of an oil palm (Elaeis guineensis). The strain exhibited a blue aerial spore mass and a light cream to moderate yellow substrate mycelium and formed chains of spiny spores. Whole-cell hydrolysates consisted of ll-diaminopimelic acid, glucose, ribose, mannose and galactose. The predominant menaquinones were MK-9(H6), MK-9(H8) and MK-9(H4). The polar lipids profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol, phosphatidylinositol-mannoside, four unidentified lipids, two unidentified aminolipids and an unidentified glycolipid. The major cellular fatty acids (>10 %) were iso-C16 : 0, C16 : 0, anteiso-C15 : 0 and iso-C15 : 0. The G+C content of genomic DNA was 69.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CMU-AB225T was a member of the genus Streptomyces and formed a distinct phyletic line which was most closely related to Streptomyces koyangensis JCM 14915T, Streptomyces misionensis JCM 4497T and Streptomyces aurantiogriseus JCM 4346T. Multilocus sequence analysis (MLSA) using five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) showed that the MLSA distances of strain CMU-AB225T to phylogenetically related species were greater than the 0.007 threshold. Moreover, the low values of DNA–DNA relatedness and phenotypic differences, especially a blue aerial mycelium, enabled strain CMU-AB225T to be distinguished from its closely related species. It is thus proposed that strain CMU-AB225T represents a novel species, namely Streptomyces venetus sp. nov. The type strain is CMU-AB225T (=JCM 31290T=TBRC 2001T).
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Jishengella zingiberis sp. nov., isolated from root tissue of Zingiber montanum
More LessA novel actinomycete, strain PLAI 1-1T, which formed spiny single spore directly on substrate mycelium was isolated from root tissue of Zingiber montanum. The isolate contained meso-diaminopimelic acid and 3-hydroxydiaminopimelic acid in the cell-wall peptidoglycan. The acyl type of the cell-wall muramic acid was glycolyl. The whole-cell sugars of strain PLAI 1-1T were glucose, arabinose, xylose, ribose and a trace amount of mannose. The membrane phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine and phosphatidylinositol. The major menaquinone was MK-9 (H4). The main cellular fatty acids were iso-C15 : 0 and C17 : 1ω8c. The G+C content of the genomic DNA was 70.6 mol%. 16S rRNA gene sequence analysis revealed that strain PLAI 1-1T was a member of the genus Jishengella and had the highest 16S rRNA gene sequence similarity to Jishengella endophytica DSM 45430T (99.2 %). Based on the data of physiological and biochemical tests, including the result of DNA–DNA hybridization, strain PLAI 1-1T represents a novel species of the genus Jishengella , for which the name Jishengella zingiberis sp. nov. is proposed. The type strain is PLAI 1-1T (=TBRC 7644T=NBRC 113144T).
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- Archaea
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Nitrosarchaeum koreense gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon member of the phylum Thaumarchaeota isolated from agricultural soil
More LessA mesophilic, chemolithoautotrophic, neutrophilic and aerobic ammonia-oxidizing archaeon, designated strain MY1T, was isolated from agricultural soil. Microscopic observation revealed short, rod-shaped cells with a diameter of 0.3–0.5 µm and length of 0.6–1.0 µm. The isolate had no flagella and pili, and possessed no genes associated with archaeal flagella synthesis. The major membrane lipids consisted mainly of the glycerol dibiphytanyl glycerol tetraether (GDGT) lipids GDGT-0 to GDGT-4 and crenarchaeol. The major intact polar lipids (IPLs) were determined as hexose plus phosphohexose IPL and dihexose IPL. Strain MY1T obtains energy by aerobically oxidizing ammonia and carbon by fixing CO2. An optimal growth was observed at 25 °C, at pH 7 and with 0.2–0.4 % (w/v) salinity that corresponds with its terrestrial habitat. The addition of α-keto acids was necessary to stimulate growth. The strain tolerated ammonium and nitrite concentrations up to 10 and 5 mM, respectively. The MY1T genome has a DNA G+C content of 32.7 mol%. Phylogenetic analysis based on the 16S rRNA gene showed that strain MY1T belongs to the family Nitrosopumilaceae of the phylum Thaumarchaeota , sharing the highest 16S rRNA gene sequence similarity (96.6–97.1 %) with marine isolates of the genus Nitrosopumilus . The average nucleotide identity was 78 % between strain MY1T and Nitrosopumilus maritimus SCM1T, indicating distant relatedness. Based on the phenotypic, phylogenetic and genomic analyses, it was concluded that strain MY1T belongs to the novel genus Nitrosarchaeum, under which the name Nitrosarchaeum koreense sp. nov. is proposed as the type species. The type strain is MY1T (=JCM 31640T=KCTC 4249T).
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Haloplanus rallus sp. nov., a halophilic archaeon isolated from crude solar salt
More LessA halophilic archaeon, strain MBLA0036T, was isolated from Sorae solar saltern near Incheon, Republic of Korea. Strain MBLA0036T had three 16S rRNA genes: rrnA, rrnB and rrnC. The 16S rRNA gene sequence similarities between strain MBLA0036T (based on the rrnA gene) and Haloplanus ruber R35T and Haloplanus litoreus GX21T were 98.0 and 97.3 %, respectively. The similarities of the RNA polymerase subunit B′ gene between strain MBLA0036T and H. ruber R35T and H. litoreus GX21T were 94.0 and 92.1 %, respectively. Cells of strain MBLA0036T were Gram-stain-negative, motile, red-pigmented, pleomorphic, flat and contained gas vesicles. Strain MBLA0036T grew at 15‒55 °C (optimum, 37 °C), in 10‒30 % (w/v) NaCl (15 %, w/v) with 0‒0.5 M MgSO4.7H2O (0.2 M) and at pH 6.0–9.0 (pH 7.0). The cells lysed in distilled water and the minimum NaCl concentration that prevented cell lysis was 5 % (w/v). Major polar lipids of strain MBLA0036T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a glycolipid that was chromatographically identical to sulfated mannosyl glucosyl diether. The major isoprenoid quinone was menaquinone-8. The genomic DNA G+C content was 65.5 mol%. DNA–DNA hybridization values between strain MBLA0036T and H. ruber JCM 17271T and H. litoreus JCM 17092T were 35±3 and 18±1 %, respectively. Therefore, strain MBLA0036T is described a novel species of the Haloplanus , for which we propose the name Haloplanus rallus sp. nov. The type strain is MBLA0036T (=KCTC 4239T=JCM 31425T).
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- Bacteroidetes
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Flavobacterium effusum sp. nov., isolated from a freshwater river
More LessA yellowish-orange-coloured bacterial strain, PSI-22T, was isolated from a freshwater river in Taiwan. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain PSI-22T belonged to the genus Flavobacterium and showed the highest identity with respect to Flavobacterium dispersum MVW-23T (98.0 %), Flavobacterium tistrianum GB 56.1T (97.1 %), Flavobacterium denitrificans ED5T (97.1 %) and Flavobacterium daemonense THG-DJ7T (97.0 %) and less than 97 % to other members of the genus. Cells of strain PSI-22T were Gram-negative, strictly aerobic, motile by gliding and rod-shaped. Optimal growth occurred at 30 °C, pH 6 and in the presence of 0.5 % NaCl. Strain PSI-22T contained iso-C15 : 0 and summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized aminophosphoglycolipid, two uncharacterized aminolipids, one uncharacterized phospholipid and one uncharacterized lipid. The major polyamine was homospermidine. The major isoprenoid quinone was MK-6 and the DNA G+C content of the genomic DNA was 41.4 mol%. The DNA–DNA hybridization value for strain PSI-22T with F. dispersum BCRC 80978T, F. tistrianum KCTC 42679T, F. denitrificans DSM 15936T and F. daemonense KACC 17651T was less than 30 %. On the basis of the phylogenetic inference and phenotypic data, strain PSI-22T should be classified as a novel species, for which the name Flavobacterium effusum sp. nov. is proposed. The type strain is PSI-22T (=BCRC 80973T=LMG 29553T=KCTC 52233T).
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Flavobacterium chryseum sp. nov. and Flavobacterium psychroterrae sp. nov., novel environmental bacteria isolated from Antarctica
More LessA group of rod-shaped, aerobic, Gram-stain-negative, gliding bacteria producing flexirubin-type pigment was isolated from environmental samples collected in Antarctica in 2009–2014. Phylogenetic analysis of the almost complete 16S rRNA gene sequences revealed two separated branches belonging to the genus Flavobacterium . Group I (n=8), represented by strain CCM 8826T, shared the highest sequence similarity to Flavobacterium collinsii 983-08T (98.8 %) and Flavobacterium saccharophilum DSM 1811T (98.4 %), and group II (n=4) represented by strain CCM 8827T shared the highest similarity to Flavobacterium aquidurense WB 1.1-56T (99.6 %). High genetic homogeneity of both groups, separation from each other and from phylogenetically close Flavobacterium species was verified by the rep-PCR fingerprinting method. DNA–DNA hybridization confirmed low genomic relatedness between strain CCM 8826T and F. collinsii 983-08T and F. saccharophilum DSM 1811T (18 and 28 %, respectively) and between strain CCM 8827T and F. aquidurense WB 1.1-56T (27 %). Chemotaxonomic analyses of strains CCM 8826T and CCM 8827T revealed the respiratory quinone to be MK-6, the major identified polar lipid was phosphatidylethanolamine and the predominant polyamine was sym-homospermidine. The common major fatty acids were C15 : 0 iso, C17 : 0 iso 3OH, C15 : 1 iso G, Summed Feature 3 (C16 : 1 ω7c/C16 : 1 ω6c), C15 : 0 iso 3OH and additionally, C15 : 0 anteiso among group II members. All analyses confirmed that strains of group I and II represent two novel species of the genus Flavobacterium , for which the names Flavobacterium chryseum sp. nov. (type strain CCM 8826T=P3160T=LMG 30615T) and Flavobacterium psychroterrae sp. nov. (type strain CCM 8827T=P3922T=LMG 30616T) are proposed.
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Pontibacter terrae sp. nov., isolated from soil
More LessA bacterial strain, designated 17SD1-15T, was isolated from soil. Cells of this strain were Gram-stain-negative and aerobic rods. The major fatty acids of strain 17SD1-15T were iso-C15 : 0 and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I). The polar lipids were phosphatidylethanolamine, one phospholipid and five unidentified lipids. The G+C content of the genomic DNA of strain 17SD1-15T was 49.0 mol%. The 16S rRNA gene sequence analysis showed that strain 17SD1-15T was phylogenetically related to Pontibacter saemangeumensis GCM0142T, Pontibacter korlensis X14-1T, Pontibacter yuliensis H9XT, Pontibacter diazotrophicus H4XT and Pontibacter humi SWU8T (98.3, 96.4, 96.4, 96.4 and 96.0 % sequence similarity, respectively). DNA–DNA relatedness between 17SD1-15T and the most closely related type strain of Pontibacter species was 42.9±0.8 %. The low level of DNA–DNA relatedness identified strain 17SD1-15T as a member of a novel species in the genus Pontibacter . The results of genotypic and phenotypic data, including chemotaxonomic traits, showed that strain 17SD1-15T could be distinguished from its phylogenetically related species. Therefore, strain 17SD1-15T represents a novel species within the genus Pontibacter , for which the name Pontibacter terrae sp. nov. is proposed, with the type strain 17SD1-15T (=KCTC 52915T=NBRC 113057T).
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Pontibacter silvestris sp. nov., isolated from the soil of a Populus euphratica forest and emended description of the genus Pontibacter
More LessStrain XAAS-R86T, a Gram-stain-negative, short rod-shaped, non-motile, aerobic bacterium, was isolated from a Populus euphratica forest near the city of Hotan, Xinjiang, PR China. The cells were found to be positive for catalase and oxidase activities. Growth occurred optimally at 28–30 °C, pH 7.0–7.5 and in the presence of 0.5–2.0 % NaCl (w/v). The results of phylogenetic analysis of the 16S rRNA gene indicated that XAAS-R86T represents a member of the genus Pontibacter within the family Hymenobacteraceae. Pontibacter akesuensis CCTCC AB 206086T is the most closely related species with a validly published name, based on 16S rRNA gene sequence identity (95.7 %). The DNA G+C content of the strain is 43.9 mol%. The main respiratory quinone is MK-7 and the major cellular fatty acids are summed feature 4 (iso-C17 : 1I and/or anteiso-C17 : 1B) and iso-C15 : 0 and its major polar lipids are phosphatidylethanolamine and two unidentified lipids. On the basis of the results of tests performed using a polyphasic approach, XAAS-R86T represents a novel species of the genus Pontibacter , for which the name Pontibacter silvestris sp. nov. is proposed, with the type strain XAAS-R86T (=CCTCC AB 2017165T=KCTC 62047T).
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Spirosoma pollinicola sp. nov., isolated from pollen of common hazel (Corylus avellana L.)
A Gram-negative bacterium, strain HA7T, was isolated from the microhabitat of common hazel (Corylus avellana L.) pollen. HA7T was found to be an aerobic, rod-shaped, catalase-positive, oxidase-negative bacterium with an optimum growth temperature of 25 °C and pH of 7. The nearly complete 16S rRNA gene sequence of HA7T strain showed the closest similarities to Spirosoma linguale DSM 74T (97.4 %) and Spirosoma fluviale DSM 29961T (97.43 %). The major fatty acids (>5 %) were C16 : 1ω5c, summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), iso-C15 : 0 and iso-C17 : 0 3-OH. The major polar lipids were an unidentified aminophospholipid and phosphatidylethanolamine. The major respiratory quinone detected was menaquinone MK-7 (95 %). The draft genome sequence included 8 794 837 bases, which contained 3665 predicted coding sequences and had a G+C content of 47.9 mol%. The genome-based comparison between HA7T and S. linguale DSM 74T and S. fluviale DSM 29961T with pairwise average nucleotide identity indicated a clear distinction, between 76.2–76.3 %. Moreover, the digital DNA–DNA relatedness of HA7T to these strains was 26.5 and 25.1 %. Based on the differential genotypic, phenotypic and chemotaxonomic properties to closely related type strains, strain HA7T ought to be assigned with the status of a new species, for which the name Spirosoma pollinicola sp. nov. is proposed. The type strain is HA7T (DSM 105799T=LMG 30282T).
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Winogradskyella aurantiaca sp. nov., isolated from seawater
More LessA Gram-stain-negative, non-flagellated, motile-by-gliding, orange-coloured bacterial strain, designated strain IMCC20180T, was isolated from seawater collected off the coast of the East Sea in the Republic of Korea. The 16S rRNA gene sequence analysis showed that strain IMCC20180T was most closely related to Winogradskyellaporiferorum UST030701-295T (95.7 % sequence similarity) and formed a robust phylogenetic clade with other Winogradskyella species, indicating that the strain was affiliated with the genus Winogradskyella . Growth of strain IMCC20180T was observed at 20–30 °C (optimum, 25 °C), pH 7.0–9.0 (pH 8.0) and with 1.0–3.5 % NaCl (3.0 %, w/v). The predominant isoprenoid quinone was MK-6. Major fatty acid constituents were iso-C15 : 1 G, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), iso-C15 : 0, iso-C17 : 0 3-OH and iso-C16 : 0 3-OH. The major polar lipids were phosphatidylethanolamine, four unknown aminolipids and five unknown lipids. The estimated genome size and the DNA G+C content of strain IMCC20180T were 3.1 Mb and 37.7 %, respectively. Based on 16S rRNA gene phylogeny, physiological and chemotaxonomic characterization, strain IMCC20180T represented a novel species in the genus Winogradskyella , for which the name Winogradskyella aurantiaca sp. nov. is proposed. The type strain is IMCC20180T (=KACC 18883T=KCTC 52240T=JCM 31383T).
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Flagellimonas aquimarina sp. nov., and transfer of Spongiibacterium flavum Yoon and Oh 2012 and S. pacificum Gao et al. 2015 to the genus Flagellimonas Bae et al. 2007 as Flagellimonas flava comb. nov. and F. pacifica comb. nov., respectively
More LessA Gram-stain-negative, non-spore-forming, rod-shaped, aerobic and diffusible yellow-coloured bacterial strain, designated strain ECD12T was isolated from a seaweed, Ecklonia cava. The isolate required sea salts for growth. Catalase-positive and oxidase-negative. A phylogenetic tree based on 16S rRNA gene sequences showed that strain ECD12T formed an evolutionary lineage within the radiation enclosing the members of genera Spongiibacterium and Flagellimonas sharing the highest similarity to Flagellimonas eckloniae DOKDO007T (96.8 % 16S rRNA gene sequence similarity) followed by Spongiibacterium pacificum SW169T (96.4 %) and Spongiibacterium flavum DSM 22638T (96.1 %). The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1 G. The new isolate contained MK-6 as the only isoprenoid quinone and phosphatidylethanolamine, two unidentified amino lipids and two unidentified lipids as the major polar lipids. The genomic DNA G+C content is 39 mol%. A number of phenotypic characteristics such as the production of diffusible pigment distinguished strain ECD12T from the related species. On the basis of the evidence presented in this study, a novel species, Flagellimonas aquimarina sp. nov., is proposed for strain ECD12T (=KCTC 52351T=JCM 32292T). Based on the sequence similarity, phylogenetic relationship and common morphological, physiological and chemical characters among the members of the genera Spongiibacterium and Flagellimonas , it is recommended that the two genera are combined into a single genus. Thus, transfer of S. flavum Yoon and Oh 2012 and S . pacificum Gao et al. 2015 to the genus Flagellimonas Bae et al. 2007 as Flagellimonas flava comb. nov. and Flagellimonas pacifica comb. nov., respectively, is also proposed.
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Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert
More LessA Gram-stain-negative, non-motile, aerobic, non-spore-forming, rod-shaped, bacterial strain, designated 5JN-11T, was isolated from Haloxylonammodendron stems in Kumtag desert, Xinjiang province, China. Strain 5JN-11T grew at salinities of 0–6 % (w/v; optimum 0–2 %), a pH of 7.0–9.0 (pH 7.0–8.0) and temperatures of 20–42 °C (28–30 °C). Based on 16S rRNA gene sequences, the strain was designated a member of the genus Sphingobacterium and the phylogenetic analysis showed that strain 5JN-11T shared the highest similarity to Sphingobacterium gobiense H7T, followed by Sphingobacterium chuzhouense DH-5T and Sphingobacterium arenae H-12T. The unfinished draft genome of strain 5JN-11T was 4.69 Mb. The G+C content of strain 5JN-11T was 42.8 mol%. The average nucleotide identity to S. gobiense H7T was 90.5 %. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. On the basis of phenotypic, genotypic and phylogenetic evidence, strain 5JN-11T represents a novel species in the genus Sphingobacterium , for which the name Sphingobacterium haloxyli sp. nov. is proposed. The type strain is 5JN-11T (=ACCC 60072T=KCTC 62457T).
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Flavipsychrobacter stenotrophus gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from a glacier
More LessA Gram-stain-negative strain, designated RB1R16T, was isolated from ice collected from the ice tongue surface of the Renlongba glacier in Tibet. Strain RB1R16T was catalase-negative, oxidase-negative and grew at 10–22 °C, pH 6.0–8.0 and in the presence of 0–0.5 % NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain RB1R16T belonged to Chitinophagaceae and formed an independent linkage. The highest level of 16S rRNA gene sequence similarities were found to Lacibacter cauensis CGMCC 1.7271T (90.3 %), Flavihumibacter cheonanensis WS16T (90.1 %) and Flavihumibacter solisilvae 3-3T (90.1 %). The major fatty acids were iso-C15 : 1 G, iso-C15 : 0, summed feature 4 (comprising iso-C17 : 1 I and/or anteiso-C17 : 1 B) and iso-C17 : 0 3OH. The polar lipids contained phosphatidylethanolamine, one unidentified aminolipid and four unidentified lipids. The quinone system contained menaquinone MK-7 as the only component. The DNA G+C content was 43.1 mol%. On the basis of a polyphasic approach, a novel species of a new genus Flavipsychrobacter stenotrophus gen. nov., sp. nov. within the family Chitinophagaceae is proposed, with RB1R16T (=CGMCC 1.16126T=NBRC 113112T) as the type strain.
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- Firmicutes and Related Organisms
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Lactobacillus porci sp. nov., isolated from small intestine of a swine
More LessA facultatively anaerobic, Gram-stain-positive, catalase-negative, rod-shaped lactic acid bacterium, designated SG816T, was isolated from small intestine of a swine. Optimal growth occurred at 37 °C and pH 7.0. Furthermore, growth occurred in NaCl up to 0.5 % (w/v) but not at levels of salinity higher than 1 %. Comparative 16S rRNA gene sequencing and the matrix-associated laser desorption/ionization–time-of-flight mass spectometry profiling showed that strain SG816T was closely related to Lactobacillus delbrueckii subsp. bulgaricus KCTC 3635T (95.9 %) and Lactobacillus delbrueckii subsp. indicus JCM 15610T (95.9 %), followed by other Lactobacillus delbrueckii subspecies (95.9–95.7 %) and Lactobacillus equicursoris DSM 19284T (95.6 %). A comparison of two housekeeping genes, RNA polymerase alpha subunit (rpoA) and phenylalanyl-tRNA synthase alpha subunit (pheS), revealed that strain SG816T formed a separate branch within the clade of the genus Lactobacillus . The DNA G+C content level of the strain SG816T was 51.5 mol%. The strain was homofermentative and produced d-lactic acid from glucose fermentation. The major cellular fatty acids (>10 %) of the isolate were C18 : 1ω9c and C16 : 0. The peptidoglycan type was A4α l-Lys-d-Asp. On the basis of distinct phenotypic and phylogenetic properties, strain SG816T represents a novel species of the genus Lactobacillus , for which the name Lactobacillus porci sp. nov. is proposed. The type strain is SG816T (=KCTC 21090T=NBRC 112917T).
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Paenibacillus xerothermodurans sp. nov., an extremely dry heat resistant spore forming bacterium isolated from the soil of Cape Canaveral, Florida
A Gram-stain-positive, motile, endospore-producing, facultative anaerobic bacterial strain, designated ATCC 27380T, was isolated from heat-stressed soil of Cape Canaveral, Florida, USA. Growth was observed at 20–42 °C (optimum, 37 °C), at pH 6.0–10.0 (optimum pH 7.0) and in the presence of 0.5–3 % NaCl (optimum 0.5 %). The cell wall contained meso-diaminopimelic acid as the diagnostic amino acid and the isoprenoid quinone was MK-7. The polar lipids present were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol and one unknown phospholipid. The main fatty acids were iso-C15 : 0 and anteiso-C15 : 0. Phylogenetic analysis based on 16S rRNA gene sequencing affiliated strain ATCC 27380T to the genus Paenibacillus , and showed the highest sequence similarity to Paenibacillus rigui JCM 16352T (97.0 %). The other closely related type strains exhibited 16S rRNA gene sequence similarity values below 95.9 %. The draft genome of ATCC 27380T had a size of 4,361,187 bases, with a G+C content of 51.0 %. The average nucleotide identity and in silico DNA–DNA hybridization values between strain ATCC 27380T and P. rigui JCM 16352T were 72.5% and 18.5 %, respectively, which were below the threshold suggested for species differentiation (96% and 70 %, respectively). The average amino acid identity between strain ATCC 27380T and P. rigui JCM 16352T was 68.72 %, which was above the suggested genus level demarcation of 65 %. Based on phenotypic, genotypic and chemotaxonomic data, strain ATCC 27380T represents a novel species in the genus Paenibacillus , for which the name Paenibacillus xerothermodurans sp. nov. (=DSM 520T=NRRL NRS-1629T=ATCC 27380T) is proposed.
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Petroclostridium xylanilyticum gen. nov., sp. nov., a xylan-degrading bacterium isolated from an oilfield, and reclassification of clostridial cluster III members into four novel genera in a new Hungateiclostridiaceae fam. nov.
A rod-shaped, Gram-stain-positive, obligately anaerobic, xylan-degrading bacterium, SK-Y3T, was isolated from oily-sludge of Shengli oilfield, China. Optimum growth occurred at 50 °C, at pH 7.5 and without addition of NaCl. The predominant cellular fatty acids of strain SK-Y3T were iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 0, and the main polar lipids were glycolipids (GL), lipids (L), phosphatidylglycerol (PG) and diphosphatidylglycerol (DPG); no respiratory quinones were detected. The genomic DNA G+C content was 37.2 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed that strain SK-Y3T belongs to clostridial cluster III, exhibiting 91–92% sequence similarity to the most closely related species, namely Clostridium clariflavum , Clostridium straminisolvens and Acetivibrio cellulolyticus . Based on distinct physiological and phylogenetic differences from the aforementioned described taxa, strain SK-Y3T (=DSM 103557T=ACCC 19952T) is proposed as the type strain of a novel species of a new genus, Petroclostridium xylanilyticum gen. nov., sp. nov. Furthermore, analysis through 16S rRNA gene, ribosomal protein and whole genome sequences indicated that clostridial cluster III members should be reclassified into four novel genera for which the names Hungateiclostridium gen. nov., Thermoclostridium gen. nov., Ruminiclostridium gen. nov. and Pseudoclostridium gen. nov. are proposed. In combination with the genera Anaerobacterium , Cellulosibacter , Ercella , Fastidiosipila , Mageeibacillus , Pseudobacteroides , Petroclostridium and Saccharofermentans , clostridial cluster III members formed a monophyletic clade within the order Clostridiales but that was clearly distinguished from other Ruminococcaceae members, which is proposed as a novel family, Hungateiclostridiaceae fam. nov.
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Lactobacilus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter
A rod-shaped, Gram-stain-positive, non-flagellated, facultatively anaerobic bacterium, designated SYF10-1aT, was isolated from Nuruk, a Korean traditional fermentation starter. It grew at 4–40 °C (optimum 37 °C), at pH 3.0–9.0 (optimum, pH 7.0) and with 0–5 % (w/v) NaCl. Phylogenetic analysis using 16S rRNA gene sequences revealed that strain SYF10-1aT belonged to the genus Lactobacillus and showed the highest sequence similarity of 98.7 % to Lactobacillus crustorum LMG 23699T. A comparison of two housekeeping genes, pheS and rpoA, supported the suggestion that strain SYF10-1aT fell within the radius of the genus Lactobacillus , but was clearly separated from its closest related species. The average nucleotide identity value and digital DNA–DNA hybridization value between strain SYF10-1aT and the most closely related species, L. crustorum LMG 23699T, were 80.5 and 33.3 %, respectively. The predominant cellular fatty acids were C16 : 0, C18 : 1ω9c, C18 : 1ω7c and summed feature 3 (including iso-C15 : 0 2-OH and/or C16 : 1ω7c). Polar lipids were diphosphatidylglycerol, phosphatidylglycerol, two unidentified aminolipids and two unidentified glycolipids. The cell-wall peptidoglycan was of the A4α type with an interpeptide bridge comprising l-Lys-d-Asp. The DNA G+C content was 34.2 mol%. On the basis of this taxonomic study, strain SYF10-1aT represents a novel species within the genus Lactobacillus , for which the name Lactobacillus nuruki sp. nov. is proposed. The type strain is SYF10-1aT (=KACC 18726T=NBRC 112011T).
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Listeria goaensis sp. nov.
Swapnil P. Doijad, Krupali V. Poharkar, Satyajit B. Kale, Savita Kerkar, Dewanand R. Kalorey, Nitin V. Kurkure, Deepak B. Rawool, Satya Veer Singh Malik, Rafed Yassin Ahmad, Martina Hudel, Sandeep P. Chaudhari, Birte Abt, Jörg Overmann, Markus Weigel, Torsten Hain, Sukhadeo B. Barbuddhe and Trinad ChakrabortyTwo Listeria -like isolates obtained from mangrove swamps in Goa, India were characterized using polyphasic combinations of phenotypic, chemotaxonomic and whole-genome sequence (WGS)-based approaches. The isolates presented as short, non-spore-forming, Gram-positive rods, that were non-motile, oxidase-negative, catalase-positive and exhibited α-haemolysis on 5 % sheep- and horse-blood agar plates. The 16S rRNA gene sequences exhibited 93.7–99.7 % nucleotide identity to other Listeria species and had less than 92 % nucleotide identity to species of closely related genera, indicating that the isolates are de facto members of the genus Listeria . Their overall fatty acid composition resembled that of other Listeria species, with quantitative differences in iso C15 : 0, anteiso C15 : 0, iso C16 : 0, C16 : 0, iso C17 : 0 and anteiso C17 : 0 fatty acid profiles. Phylogeny based on 406 core coding DNA sequences grouped these two isolates in a monophyletic clade within the genus Listeria . WGS-based average nucleotide identity and in silico DNA–DNA hybridization values were lower than the recommended cut-off values of 95 and 70 %, respectively, to the other Listeria species, indicating that they are founding members of a novel Listeria species. We suggest the name Listeria goaensis sp. nov. be created and the type strain is ILCC801T (=KCTC 33909;=DSM 29886;=MCC 3285).
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Catenibacillus scindens gen. nov., sp. nov., a C-deglycosylating human intestinal representative of the Lachnospiraceae
More LessAn anaerobic Gram-stain-positive, non-spore-forming and non-motile bacterium isolated from the human gut, designated CG19-1T, capable of cleaving aromatic C-glucosides was characterized using a polyphasic taxonomic approach. Major fermentation products of this asaccharolytic organism were acetate and butyrate when grown on a complex medium. Growth of strain CG19-1T was stimulated by glucose or pyruvate. Growth inhibition was observed in the presence of several phenolic acids including ferulic acid, which nevertheless was reduced to dihydroferulic acid. Strain CG19-1T contained peptidoglycan type A4β l-Orn–d-Asp. The major cellular fatty acids were C16 : 0 and C18 : 1ω9c. The genomic DNA G+C content was 47.1 mol%. Based on its 16S rRNA gene sequence, strain CG19-1T is a member of the Lachnospiraceae . However, sequence identity to other Lachnospiraceae species with validly published names is approximately 93.0 % with Frisingicoccus caecimuris being the most closely related species according to phylogenetic analysis. Based on these findings, it is proposed to create a novel genus, Catenibacillus, and a novel species, Catenibacillus scindens, with the type strain CG19-1T (=DSM 106146T=CCUG 71490T).
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- Other Bacteria
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Deinococcus irradiatisoli sp. nov., isolated from gamma ray-irradiated soil
Strain 17bor-2T, a gamma-resistant, pink-to-red-coloured, aerobic, catalase-positive, oxidase-negative and Gram-stain-negative bacterium, was isolated from gamma ray-irradiated soil. The isolate grew aerobically at 18–37 °C (optimum, 28–30 °C), pH 6.0–8.0 (pH 6.5–7.5) and in the presence of 0–1 % (w/v) NaCl (0 % NaCl). Phylogenetic analysis based on its 16S rRNA gene sequence indicated that strain 17bor-2T belonged to the genus Deinococcus with a highest sequence similarity of 96.4 % to Deinococcus alpinitundrae ME-04-04-52T. The major fatty acids of the strain were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and cyclo C17 : 0. The only respiratory quinone was MK-8. The major polar lipids of the strain were phosphoglycolipid, aminophospholipid and an unknown glycolipid. The DNA G+C content of strain 17bor-2T was 62.8 mol%. On the basis of its phenotypic, genotypic and chemotaxonomic characteristics, strain 17bor-2T should be classified as a novel species in the genus Deinococcus , for which the name Deinococcus irradiatisoli sp. nov. is proposed. The type strain is 17bor-2T (=KCTC 33907T=NBRC 113037T).
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- Proteobacteria
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Ottowia oryzae sp. nov., isolated from Andong sikhye, a Korean traditional rice beverage
More LessA Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped bacterial strain, designated KADR8-3T, isolated from Andong sikhye in Andong-si, Gyeongsangbuk-do, Republic of Korea, was characterized using a polyphasic approach. On the basis of morphological, genetic and chemotaxonomic characteristics, it was determined to belong to the genus Ottowia . The phylogenetic similarity based on the 16S rRNA gene sequences indicated the strain formed a clade with Ottowia beijingensis GCS-AN-3T, Ottowia thiooxydans DSM 14619T, Ottowia pentelensis RB3-7T and ‘ Ottowia shaoguanensis ’ J5-66T, showing the highest similarity to O. beijingensis GCS-AN-3T (96.3 %). The major fatty acids were C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and summed feature 8 (C18 : 1 ω6c and/or C18 : 1 ω7c). The predominant respiratory quinone was Q-8. The polar lipids present were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two unidentified aminolipids and two unidentified lipids. The genomic DNA G+C content was 66.80 mol%. These results supported that strain KADR8-3T was clearly distinguishable from its closely related species and represents a novel species of the genus Ottowia , for which the name Ottowia oryzae is proposed. The type strain is KADR8-3T (=KACC 19325T=NBRC 113109T).
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Simulacricoccus ruber gen. nov., sp. nov., a microaerotolerant, non-fruiting, myxospore-forming soil myxobacterium and emended description of the family Myxococcaceae
More LessA non-fruiting group of myxobacteria was previously speculated to exist in nature based on metagenomics data containing uncultured members of the order Myxococcales. Here, we describe a myxobacterial strain, designated MCy10636T, which was isolated from a German soil sample collected in 2013. It exhibits swarming characteristics but atypically produces myxospores in the absence of fruiting bodies. The novel strain stains Gram-negative and Congo-red-negative and is characterized mesophilic, neutrophilic, chemoheterotrophic and microaerotolerant. Branched-chain fatty acids are the predominant cellular fatty acids over the straight-chain type, and contain the major fatty acids iso-C17 : 0 2-OH, C16 : 1, iso-C17 : 0 and iso-C15 : 0. Based on blastn results, the 16S rRNA gene sequence reveals similarity (97 %) to Aggregicoccus edonensis MCy1366T, (97 %) Myxococcus macrosporus DSM 14697T, (96 %) Corallococcus coralloides DSM2259T and Corallococcus exiguus Cc e167T. Phylogenetic analysis showed a novel lineage of MCy10636T in the family Myxococcaceae , suborder Cystobacterineae. Based on polyphasic taxonomic characterization, we propose that this unusual, non-fruiting, myxospore-forming and microaerotolerant myxobacterial strain, MCy10636T, represents a novel genus and species, Simulacricoccus ruber gen. nov., sp. nov. (DSM 106554T=NCCB 100651T).
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Komagataeibacter cocois sp. nov., a novel cellulose-producing strain isolated from coconut milk
Phylogenetic analysis was performed on a cellulose-producing strain, designated WE7T, isolated from contaminated coconut milk. The analysis utilized nearly complete 16S rRNA gene sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, and allowed identification of the strain as belonging to the genus Komagataeibacter . DNA–DNA correlation or average nucleotide identity analysis was performed between WE7T and its closest phylogenetic neighbours, and the resulting values were below the species level (<70 % and <95 %), suggesting that the strain represents a novel species in genus Komagataeibacter. Strain WE7T was coupled with Komagataeibacter species more tightly than with Gluconacetobacter species in a 16S rRNA gene sequence phylogenetic tree. Strain WE7T can be differentiated from closely related Komagataeibacter and Gluconacetobacter entanii species by the ability to grow on the carbon sources d-mannitol, sodium d-gluconate and glycerol, the ability to form acid by d-fructose, sucrose, d-mannitol, d-galactose and ethanol, and the ability to grow without acetic acid. The major fatty acid of WE7T is C18 : 1ω9c (52.3 %). The DNA G+C content of WE7T is 63.2 mol%. The name Komagataeibacter cocois sp. nov. is proposed, with the type strain WE7T (=CGMCC 1.15338T=JCM 31140T).
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Agaribacter flavus sp. nov., isolated from red algae
More LessA Gram-stain-negative, non-motile, aerobic, curved-rod bacterium, designated as strain 2p52T, was isolated from the marine algae Gracilaria blodgettii collected off the coast of Lingshui county, in Hainan province, China. Strain 2p52T grew at 15–42 °C (optimally at 30–33 °C), at pH 6.0–10.0 (7.5–8.0) and in the presence of 1.0–8.0 % (w/v) NaCl (2.0–3.0 %). The most closely related species was Agaribacter marinus (96.5 % 16S rRNA gene sequence similarity). Phylogenetic analysis based on the sequence of the 16S rRNA gene revealed that strain 2p52T belonged to the genus Agaribacter . The novel strain contained phophatidylethanolamine and phosphatidylglycerol as the major polar lipids. The predominant isoprenoid quinine was Q-8, and the DNA G+C content was 43.2 mol%. The major cellular fatty acids were C16 : 1ω7c and/or iso-C15 : 0 2-OH, C16 : 0, and C18 : 1ω7c. The phenotypic and systematic comparative analyses indicated that the isolate is representative of a novel species of the genus Agaribacter , and the name Agaribacter flavus sp. nov. is proposed. The type strain is 2p52T (=KCTC 52473T=MCCC 1H00151T).
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Marinobacter fuscus sp. nov., a marine bacterium of Gammaproteobacteria isolated from surface seawater
A Gram-stain-negative bacterium, designated NH169-3T, was isolated from a surface seawater sample of the South China Sea and subjected to a taxonomic polyphasic investigation. Strain NH169-3T was strictly aerobic, non-motile, non-spore-forming and rod-shaped. The colony was 1.0–2.0 mm in diameter after the growth on marine agar at 30 °C for 72 h. The centre of the colony was smooth, circular, convex and brown with a transparent periphery. Strain NH169-3T was able to grow at temperatures between 4–40 °C (optimum, 37 °C), pH 5.5–9.0 (pH 7.5) and with 0–12.5 % (w/v) NaCl (3.0 %). Chemotaxonomic analysis showed that the sole respiratory quinone of strain NH169-3T was ubiquinone 9; major fatty acids were C16 : 0 and C18 : 1 ω9c, and major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and one unidentified glycolipid. The DNA G+C content was 52.7 mol%. The comparison of 16S rRNA gene sequences showed that strain NH169-3T was closely related to Marinobacter shengliensis SL013A34A2T with a similarity of 98.0 %. Three phylogenetic trees reconstructed with neighbour-joining, maximum-parsimony and maximum-likelihood methods using 16S rRNA gene sequences showed that strain NH169-3T was grouped into a separated branch with M. shengliensis SL013A34A2T in a clade of the genus Marinobacter and closely related to Marinobacter halophilus JCM 30472T, Marinobacter vinifirmus DSM 17747T and Marinobacter hydrocarbonoclasticus DSM 8798T. Analyses of both phenotypic and phylogenetic properties have suggested that strain NH169-3T was distinctive from species with validly published names in genus Marinobacter . Thus, strain NH169-3T (=MCCC 1K03455T=KCTC 62226T) is proposed as a novel species in genus Marinobacter with the name Marinobacter fuscus sp. nov.
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Thauera hydrothermalis sp. nov., a thermophilic bacterium isolated from hot spring
More LessA Gram-stain-negative, non-spore-forming, rod-shaped, motile bacterial strain, designated GD-2T, was isolated from a sediment sample collected from a hot spring in the Tibet Autonomous Region, China. Strain GD-2T grew at a temperature range of 37–55 °C (optimum, 45–50 °C), a pH range of 5.5–11.0 (pH 7.0–7.5) and a NaCl concentration range of 0–4.0 % (0 %). The phylogenetic analysis based on 16S rRNA gene sequencing showed that strain GD-2T represented a member of the genus Thauera within the family Zoogloeaceae . Strain GD-2T was closely related to Thauera linaloolentis 47LolT with the highest 16S rRNA gene sequence similarity of 95.5 %. The whole genomic average nucleotide identity value for GD-2T and 47LolT was 75.3 %. The predominant cellular fatty acids of the strain were C16 : 0, summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C10 : 0 3-OH and C12 : 0. The main polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, three unidentified phospholipids and two unidentified aminolipids. The major isoprenoid quinone was ubiquinone 8. Genome sequencing revealed that the genome size of GD-2T was 3 059 321 bp with a G+C content of 63.57 mol%. On the basis of phylogenetic, phenotypic and chemotaxonomic characteristics, strain GD-2T is considered to represent a novel species of the genus Thauera , for which the name Thauera hydrothermalis sp. nov. is proposed. The type strain is GD-2T (=NBRC 112472T=CGMCC 1.15527T).
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Primorskyibacter marinus sp. nov., isolated from coastal sediment
More LessA novel Gram-stain-negative, whitish-yellow, rod-shaped, non-pigmented, aerobic, oxidase-positive and catalase-positive bacterium, designated PX7T, was isolated from coastal sediment of Xiaoshi Island, Weihai, China (37° 31′ 36″ N, 122° 00′ 58″ E). Strain PX7T grew optimally at 30 °C, at pH 7.0–7.5 and in the presence of 3.0 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain PX7T formed a robust clade with members of the genus Primorskyibacter and was closely related to Primorskyibacter sedentarius , Primorskyibacter aestuariivivens and Primorskyibacter insulae with 96.5, 96.2 and 95.1 % sequence similarities, respectively. The sole respiratory quinone of strain PX7T was ubiquinone-10, and the dominant fatty acid was C18 : 1ω7c (80.2 %). The major polar lipids were phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, one unidentified aminolipid, one unidentified phospholipid and one unidentified lipid. The DNA G+C content of strain PX7T was 60.2 mol%. Based on the combination of phylogenetic analyses, phenotypic and chemotaxonomic data, strain PX7T is considered to represent a novel species within the genus Primorskyibacter in the family Rhodobacteraceae , for which the name Primorskyibacter marinus sp. nov. is proposed. The type strain of the new species is PX7T (=KCTC 42952T=MCCC 1H00196T).
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Acinetobacter wuhouensis sp. nov., isolated from hospital sewage
We recovered eight strains of the genus Acinetobacter from hospital sewage at West China Hospital in Chengdu, China. Based on the comparative analysis of the rpoB sequence, these strains formed a strongly supported and internally coherent cluster (intra-cluster identity of ≥98.0 %), which was clearly separated from all known Acinetobacter species (≤91.1 %). The eight strains also formed a tight and distinct cluster based on the genus-wide comparison of whole-cell mass fingerprints generated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. In addition, the combination of their ability to assimilate 2,3-butanediol and phenylacetate, but not 4-hydroxybenzoate, and the inability to grow at 37 °C could distinguish these eight strains from all known Acinetobacter species. Whole-genomic sequencing has been performed for two selected strains, WCHA60T and WCHA62. There were 96.65 % average nucleotide identity (ANI) and 72 % in silico DNA–DNA hybridization (isDDH) values between WCHA60T and WCHA62, suggesting that the two strains indeed belonged to the same species. In contrast, the ANI and isDDH values between the two strains and the known Acinetobacter species were <83 and <30 %, respectively; both of which were far below the cut-off to define a bacterial species. Therefore, the eight strains should be considered to represent a novel species of the genus Acinetobacter , for which the name Acinetobacter wuhouensis sp. nov. is proposed. The type strain is WCHA60T (=CCTCC AB 2016204T=GDMCC 1.1100T=KCTC 52505T).
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Dyella halodurans sp. nov., isolated from lower subtropical forest soil
More LessA Gram-stain-negative, aerobic, non-endospore-forming, motile by a polar flagellum, rod-shaped bacterium, designated strain DHOG02T, which produced yellow-pigmented colonies, was isolated from a soil sample collected from the lower subtropical forest of the Dinghushan Biosphere Reserve, Guangdong Province, PR China. Strain DHOG02T grew at 12–37 °C, pH 4–9 and 0–4 % (w/v) NaCl, with optima at 28 °C, pH 6–7 and 0.5 % (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene sequences showed that this strain formed a clade with Dyella lipolytica DHOB07T and Dyella jejuensis JP1T, with sequence similarities of 98.0 and 97.4 %, respectively. The result of the concatenated partial gyrB, lepA and recA gene sequence analysis confirmed that strain DHOG02T belongs to the genus Dyella, but is distinct from all currently known species of the genus. The G+C content of the genomic DNA was 62 mol%. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid and phospholipid. Ubiquinone-8 was the only respiratory quinone detected, and iso-C15 : 0, iso-C17 : 1 ω9c and summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) were the major fatty acids, all of which supported the affiliation of strain DHOG02T to the genus Dyella . On the basis of the evidence presented here, strain DHOG02T represents a novel species of the genus Dyella , for which the name Dyella halodurans sp. nov. is proposed. The type strain is DHOG02T (=NBRC 111474T=CGMCC 1.15435T).
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Motiliproteus coralliicola sp. nov., a bacterium isolated from coral
A Gram-stain-negative, non-spore-forming, aerobic, motile, ovoid or rod-shaped bacterium, designated strain C34T, was isolated from a Porites species coral on Weizhou Island, China. Optimal growth occurred in 4 % NaCl (w/v), at 30 °C and pH 8. The only detected respiratory quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, two unidentified ninhydrin-positive lipids, one ninhydrin-positive unidentified phospholipid and two unidentified polar lipids. The genome DNA G+C content was 56.7 mol%. The major cellular fatty acids were C16 : 1ω7c/iso-C15 : 0 2-OH, C16 : 0, C18 : 1ω7c/ω6c, C18 : 0 and iso-C11 : 0 3-OH. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain C34T forms a stable cluster with Motiliproteus sediminis CICC 10858T (with the highest sequence similarity of 95.7 %). Strain C34T was also physiologically and chemical taxonomically similar to M. sediminis CICC 10858T, although they could be distinguished by colony colour on 2216E agar, the flagellum position and the diphosphatidylglycerol content in the cellular polar lipid. Thus, strain C34T is suggested to represent a new species in the genus Motiliproteus , for which the name Motiliproteus coralliicola is proposed. The type strain is C34T (=MCCC 1K03462T=KCTC 62319T).
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Roseomonas globiformis sp. nov., an airborne bacteria isolated from an urban area of Beijing
A novel dark pink pigmented bacterium, designated strain CPCC 100847T (deposited with strain code 0113-15), was isolated from the urban air of Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain CPCC 100847T was related to members of the genus Roseomonas and had the highest 16S rRNA gene sequence similarity to Roseomonas aestuarii JC17T (97.5 %). A low level of DNA–DNA relatedness (18.7 %) with its closest type strain R. aestuarii JC17T (KCTC 22692T) proved that strain CPCC 100847T belonged to a unique genomic species. CPCC 100847T had many common characteristics of the genus Roseomonas , but also had a range of cultural, physiological and biochemical characteristics that separated it from related Roseomonas species. Cells were Gram-negative, cocci- to oval-shaped, non-motile, non-endospore-forming and strictly aerobic. The respiratory ubiquinone was Q-10. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified phospholipid. The major fatty acids (>5 %) were C18 : 1ω7c, anteiso-C15 : 0, C16 : 0, iso-C15 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). The combined genotypic and phenotypic data indicated that the isolate represents a novel species of the genus Roseomonas. The name proposed for this species is Roseomonas globiformis sp. nov., with CPCC 100847T (=KCTC 52094T) as the type strain. The DNA G+C composition is 65.2 mol%.
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Acuticoccus kandeliae sp. nov., isolated from rhizosphere soil of the mangrove plant Kandelia, and emended description of Acuticoccus yangtzensis
Qi Yin, Jinyou Liang, Lv Zhang, Ke Ma, Zhang-Li Hu, Yu Zhang and Ying XuA novel bacterial strain, J103T, was isolated from rhizosphere soil of the mangrove plant Kandelia in Mai Po Inner Deep Bay Ramsar Site, Hong Kong. The strain was aerobic, Gram-stain-negative, oval-shaped with folds in the middle, non-motile and non-spore-forming. It grew at temperatures of 20–30 °C (optimum, 25–30 °C), at pH 6.0–9.0 (optimum pH 6.0) and at NaCl concentrations of 0.5–5.0 % (w/v) (optimum 1.0–2.0 %). Strain J103T was able to reduce nitrate to nitrite, and hydrolyse urea, Tween 40 and Tween 60. The major polar lipids were aminolipid, glycolipid, phosphatidylcholine and phosphatidylglycerol. The major fatty acids were C18 : 1 ω7c and C19 : 0 cyclo ω8c. The respiratory quinone was Q-10. The DNA G+C content was 68.5 mol%. Sequence analysis of the 16S rRNA gene indicated that strain J103T belongs to the genus Acuticoccus , within the family Rhodobacteraceae . The closest phylogenetic neighbour was Acuticoccus yangtzensis JL1095T, showing 96.2 % 16S rRNA gene sequence similarity. The genome size of strain J103T was 6 478 100 bp. The average nucleotide identity and digital DNA–DNA hybridization values between strain J103T and Acuticoccus yangtzensis JL1095T were 75.44 and 16.43 %, respectively. Characterization based on phylogenetic, phenotypic, chemotaxonomic and genomic evidence demonstrated that strain J103T represents a novel species of the genus Acuticoccus , for which the name Acuticoccus kandeliae sp. nov. is proposed. The type strain is J103T (=DSM 104434T=MCCC 1K03288T).
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- Eukaryotic Micro-Organisms
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Penicillium tunisiense sp. nov., a novel species of Penicillium section Ramosa discovered from Tunisian orchard apples
Two similar Penicillium isolates could not be identified as previously described species in a survey of orchard apples from Tunisia for patulin-producing fungi. These isolates are described as novel species using multilocus DNA sequence analysis of partial β-tubulin, calmodulin and nuclear ribosomal internal transcribed spacer regions; and morphological, physiological and biochemical characteristics. The isolates were considered negative for patulin production since the IDH gene fragment was not detected and the compound detected at the same retention time of patulin (14.9 min) showed a different UV spectrum using U-HPLC/UV-DAD. In terms of phylogeny, the two isolates clustered with Penicillium section Ramosa and are closely related to Penicillium chroogomphum, Penicillium lenticrescens and Penicillium soppii. Furthermore, their macro- and micromorphological traits differed from these species. Hence, the isolates represent a novel species in Penicillium section Ramosa and the name Penicillium tunisiense sp. nov. is proposed, with the type strain MUM 17.62T (=ITEM 17445T).
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Drechmeria panacis sp. nov., an endophyte isolated from Panax notoginseng
More LessAn endophytic strain (designated as strain SYPF 8335T) was isolated from a root of Panax notoginseng in Wenshan district, Yunnan province of China. Strain SYPF 8335T grew very slowly and formed white colonies. Phylogenetic analysis of four loci indicated that strain SYPF 8335T was placed in the Drechmeria clade with Drechmeria campanulata as its closest phylogenetic neighbour. The nucleotide differences between strain SYPF 8335T and D. campanulata are 30 substitutions in the internal transcriber region region. A key morphological feature that differentiates the two fungi is that D. campanulata produces campanulate conidia. Combined with the morphology and molecular analyses, a new species named Drechmeria panacis sp. nov., is proposed.
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Sugiyamaella xiaguanensis f.a., sp. nov., a yeast species isolated from rotting wood
More LessThree strains representing a novel yeast species, Sugiyamaella xiaguanensis f.a., sp. nov. (type strain NYNU 161041T=CICC 33167T=CBS 14696T), were isolated from rotting wood samples collected in Henan and Yunnan Provinces, PR China. The novel species is able to assimilate cellobiose, salicin and d-xylose, which was typical of the species of the genus Sugiyamaella. Analysis of the D1/D2 domains of the large subunit rRNA gene and internal transcribed spacer regions of these strains showed that this species was related to Sugiyamaella lignohabitans and Sugiyamaella marionensis, its closest relatives. Su. xiaguanensis sp. nov. differed by 1.4 % nucleotide substitutions from Su. lignohabitans, and by 1.9 % nucleotide substitutions from Su. marionensis in the D1/D2 sequences. The ITS sequences of Su. xiaguanensis sp. nov. displayed more than 6.5 % nucleotide substitutions from the latter two species, showing that it is a genetically separate species.
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Pichia nanzhaoensis sp. nov. and Pichia paraexigua f.a., sp. nov., two yeast species isolated from rotting wood
More LessFour yeast strains were isolated from rotting wood samples collected in the Baotianman Nature Reserve in Henan Province, Central China. On the basis of sequence analysis of the D1/D2 domains of the large subunit rRNA gene and the internal transcribed spacer regions, they were suggested to be two novel species of the genus Pichia. Pichia nanzhaoensis sp. nov. produces one to four spherical ascospores per ascus, and is most closely related to Candida pseudolambica. Pichia paraexigua f.a., sp. nov. is a sister taxa to Pichia exigua, but the formation of ascospores was not observed on various sporulation media. P. nanzhaoensis sp. nov. can weakly assimilate inulin, whereas P. paraexigua sp. nov. can weakly assimilate d-glucosamine. The type strain of Pichia nanzhaoensis is NYNU 178136T (=CICC 33279T=CBS 15346T) and the type strain of Pichia paraexigua is NYNU 178135T (=CICC 33278T=CBS 15237T).
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Wickerhamiella dianesei f.a., sp. nov. and Wickerhamiella kurtzmanii f.a., sp. nov., two yeast species isolated from plants and insects
Six yeast strains representing two novel Wickerhamiella species were isolated from plants and insects collected in Costa Rica, Brazil, and French Guiana. They belong to a subclade containing Wickerhamiella domercqiae and Wickerhamiella bombiphila, and differ by approximately 12 % in the D1/D2 sequences of the large subunit rRNA gene from these species. The intergenic spacer (ITS) regions of the two novel species differ by around 19 and 27 %, respectively, from those of W. domercqiae. The novel species exhibit 5 % divergence in the D1/D2 sequences among them (around 4 % in the ITS). The names Wickerhamiella dianesei f.a., sp. nov. and Wickerhamiella kurtzmanii f.a., sp. nov. are proposed to accommodate these species, for which a sexual cycle has not been observed. Wickerhamiella dianesei was isolated from the stingless bee, Trigona fulviventris, collected in an Asteraceae flower in Costa Rica, and from leaves of Sabicea brasiliensis (Rubiaceae) and a flower of Byrsonima crassifolia (Malpighiaceae) in Brazil. Wickerhamiellsa kurtzmanii was isolated from a flower of Ipomoea batatoides (Convolvulaceae) in Costa Rica, the surface of a fruit of B. crassifolia in Brazil, and flowers in French Guiana. The type strains are Wickerhamiella dianesei UWOPS 00-107.1T (=CBS 14185=NRRL Y-63789; Mycobank number MB 827008) and Wickerhamiella kurtzmanii UWOPS 00-192.1T (=CBS 15383=NRRL Y-63979; MB 827011).
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- ICSP Matters
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Proposal to emend Rules 50a and 50b of the International Code of Nomenclature of Prokaryotes
More LessRules 50a and 50b of the International Code of Nomenclature of Prokaryotes respectively regulate the elevation of a subspecies to the rank of a species and the lowering of a species to the rank of subspecies. The Code does not indicate that the resulting new names must be considered new combinations, as the cases described in Rules 50a and 50b are not covered by Rule 34a. Based on the rules of the Code, new combination events are applicable only at the identical rank, and therefore new combination events and new species/subspecies events are mutually exclusive. In spite of this there have been at least 44 cases in which the new names were described as comb. nov. during elevation in rank from subspecies to species and at least 30 such cases during lowering in rank from species to subspecies. To prevent confusion in the future we propose adding notes to Rules 50a and 50b to clarify the issue.
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- Corrigendum
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Volumes and issues
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Volume 74 (2024)
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Volume 73 (2023)
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Volume 72 (2022 - 2023)
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Volume 71 (2020 - 2021)
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Volume 70 (2020)
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Volume 69 (2019)
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Volume 68 (2018)
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Volume 67 (2017)
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Volume 66 (2016)
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Volume 65 (2015)
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Volume 64 (2014)
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Volume 63 (2013)
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Volume 62 (2012)
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Volume 61 (2011)
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Volume 60 (2010)
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Volume 59 (2009)
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Volume 58 (2008)
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Volume 57 (2007)
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Volume 56 (2006)
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Volume 55 (2005)
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Volume 54 (2004)
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Volume 53 (2003)
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Volume 52 (2002)
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Volume 51 (2001)
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Volume 50 (2000)
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Volume 49 (1999)
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Volume 48 (1998)
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Volume 47 (1997)
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Volume 46 (1996)
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Volume 45 (1995)
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Volume 44 (1994)
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Volume 43 (1993)
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Volume 42 (1992)
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Volume 41 (1991)
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Volume 40 (1990)
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Volume 39 (1989)
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Volume 38 (1988)
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Volume 37 (1987)
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Volume 36 (1986)
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Volume 35 (1985)
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Volume 34 (1984)
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Volume 33 (1983)
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Volume 32 (1982)
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Volume 31 (1981)
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Volume 30 (1980)
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Volume 29 (1979)
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Volume 28 (1978)
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Volume 27 (1977)
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Volume 26 (1976)
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Volume 25 (1975)
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Volume 24 (1974)
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Volume 23 (1973)
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Volume 22 (1972)
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Volume 21 (1971)
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Volume 20 (1970)
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Volume 19 (1969)
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Volume 18 (1968)
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Volume 17 (1967)
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Volume 16 (1966)
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Volume 15 (1965)
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Volume 14 (1964)
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Volume 13 (1963)
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Volume 12 (1962)
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Volume 11 (1961)
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Volume 10 (1960)
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Volume 9 (1959)
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Volume 8 (1958)
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Volume 7 (1957)
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Volume 6 (1956)
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Volume 5 (1955)
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Volume 4 (1954)
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Volume 3 (1953)
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Volume 2 (1952)
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Volume 1 (1951)